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Opened 5 years ago
Last modified 5 years ago
#3545 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description I am trying to hide the chain traces (pseudobonds) using setattr #1 model autochain false for each model and it's not working. I get Assigning autochain attribute to 4 items Not creating attribute 'autochain'; use 'create true' to override Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\Nitrogenase CO > reduction\Chimera\FinalAlignNearco.cxs" format session registering illegal selector name "5A" Log from Thu Jul 23 14:57:09 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\Nitrogenase CO > reduction\Chimera\FinalAlignNearco.cxs" format session registering illegal selector name "5A" Log from Thu Jul 23 14:54:36 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:/Users/dharr/Box/ChimeraX Movie/Final_with_figure.cxs" registering illegal selector name "5A" Log from Thu Jul 23 12:48:24 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\ChimeraX Movie\Final figure image.cxs" format > session registering illegal selector name "5A" Log from Wed Jul 22 14:12:03 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\ChimeraX Movie\Alignments.cxs" format session registering illegal selector name "5A" Log from Thu Jul 16 21:53:22 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\ChimeraX Movie\Alignments.cxs" format session registering illegal selector name "5A" Frozen name "trash" not restored: nothing is selected by specifier Frozen name "trashbonds" not restored: nothing is selected by specifier Frozen name "junk" not restored: nothing is selected by specifier Log from Thu Jul 16 16:41:32 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\ChimeraX Movie\All 3 N2ase > colored_labeled_master_view.cxs" format session Log from Thu Jul 16 10:00:20 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\ChimeraX Movie\All 3 N2ase > aligned_colored_labeled.cxs" format session Log from Fri Jul 10 09:45:41 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open "C:\Users\dharr\Box\ChimeraX Movie\All 3 N2ase > aligned_colored_labeled.cxs" format session Log from Thu Jul 9 13:23:53 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3u7q 3u7q title: A. vinelandii nitrogenase MoFe protein at atomic resolution [more info...] Chain information for 3u7q #1 --- Chain | Description A C | Nitrogenase molybdenum-iron protein α chain B D | Nitrogenase molybdenum-iron protein β chain Non-standard residues in 3u7q #1 --- 1CL — Fe(8)-S(7) cluster, oxidized CA — calcium ion CLF — Fe(8)-S(7) cluster HCA — 3-hydroxy-3-carboxy-adipic acid ICS — iron-sulfur-molybdenum cluster with interstitial carbon IMD — imidazole MG — magnesium ion > open 5n6y 5n6y title: Azotobacter vinelandii vanadium nitrogenase [more info...] Chain information for 5n6y #2 --- Chain | Description A D | Nitrogenase vanadium-iron protein α chain B E | Nitrogenase vanadium-iron protein β chain C F | Nitrogenase vanadium-iron protein δ chain Non-standard residues in 5n6y #2 --- 8P8 — C Fe7 S8 V CLF — Fe(8)-S(7) cluster CO3 — carbonate ion HCA — 3-hydroxy-3-carboxy-adipic acid MG — magnesium ion > hide water Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select water Expected an objects specifier or a keyword > cartoon > show cartoons > hide > ~ribbon > ribbon > ~sphere Unknown command: ~sphere > open "C:/Users/dharr/Box/ChimeraX Movie/FeN2ase Model Swiss Model > VN2ase.pdb" FeN2ase Model Swiss Model VN2ase.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for FeN2ase Model Swiss Model VN2ase.pdb #3 --- Chain | Description A D | No description available B E | No description available C F | No description available Non-standard residues in FeN2ase Model Swiss Model VN2ase.pdb #3 --- MG — (MG) Drag select of 29255 atoms, 56 pseudobonds, 2327 residues, 140 bonds > style sel sphere Changed 37486 atom styles > style sel sphere Changed 37486 atom styles > show sel cartoons > hide sel cartoons > show sel cartoons > undo > undo > undo > undo > undo > style sel stick Changed 37486 atom styles > style sel stick Changed 37486 atom styles > hide sel atoms > stick Unknown command: stick > show stick Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ribbons > ribbon > cartoon > hide cartoons > cartoon Drag select of 596 atoms, 49 pseudobonds, 2170 residues, 538 bonds > hide sel atoms > show sel cartoons > hide sel cartoons > show sel cartoons > select clear > select :1cl 30 atoms, 44 bonds, 1 model selected > style sel stick Changed 30 atom styles > show sel atoms > color byelement > select clf Expected an objects specifier or a keyword > select :clf 60 atoms, 96 bonds, 2 models selected > show sel atoms > style sel stick Changed 60 atom styles > select :1cl 30 atoms, 44 bonds, 1 model selected > delete atoms sel > delete bonds sel > select :clf :hca :ics 152 atoms, 208 bonds, 2 models selected > help show > show atoms > show atoms :clf :hca :ics Expected ',' or a keyword > show :clf :hca :ics atoms > select clear > select up Nothing selected > select :clf :hca :ics 152 atoms, 208 bonds, 2 models selected > style sel stick Changed 152 atom styles > select clear > hide #1 ribbons > select Mo 2 atoms, 1 model selected > color magenta > color Mo magenta > select clear Drag select of 94 atoms, 134 bonds > select clear Drag select of Drag select of 94 atoms, 134 bonds > name frozen Mocos sel > name frozen Mocos sel > show #1 cartoons > select clear > hide #3 cartoons > hide #2 cartoons > select co3 Expected an objects specifier or a keyword > show :co3 > show :8p8 > select clear Drag select of 100 atoms, 8 pseudobonds, 136 bonds > name frozen Vcos sel > hide vcos Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel vcos Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select Mocos 94 atoms, 134 bonds, 1 model selected > select vcos Expected an objects specifier or a keyword > select Mocos 94 atoms, 134 bonds, 1 model selected > select Vcos 100 atoms, 136 bonds, 8 pseudobonds, 2 models selected > help user-defined selectors No help found for 'user-defined selectors' > help selectors No help found for 'selectors' > select clear > select #1 18668 atoms, 16490 bonds, 37 pseudobonds, 2 models selected > hide > help hide > select clear > hide #1 > hide #1 cartoons > hide #1 stick Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1 atoms > show #1 atoms > show #1 cartoons > hide #1 atoms > show Mocos > hide Mocos > hide Vcos > show Vcos > show Mocos > show #2 cartoons > show #3 cartoons > color Mocos dodger blue > color Mocos by element Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color Mocos byelement > color Mo magenta > help script No help found for 'script' > mmaker #2 to #1 bring #3 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > hide Mocos > show Mocos > hide Vcos > show Vcos > hide #2 atoms > show #2 atoms > hide #2 atoms > show Vcos > hide #2 atoms Vcos Expected ',' or a keyword > hide #2 atoms, Vcos Missing or invalid "what" argument: Should be one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' > hide #2 cartoon, Vcos Missing or invalid "what" argument: Should be one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' > hide #2 atoms > hide Vcos > show vcos Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show Vcos > hide #2 cartoons > hide Vcos > show #2 cartoons > show Vcos > help wait > open "C:/Users/dharr/Box/ChimeraX Movie/Script.txt" Unrecognized file suffix '.txt' > open Script 'Script' has no suffix > open Script.txt Unrecognized file suffix '.txt' > pwd Current working directory is: C:\ProgramData\ChimeraX > help cd > cd C:\Users\dharr\Box\ChimeraX Movie Expected a keyword > cd "C:/Users/dharr/Box/ChimeraX Movie" Current working directory is: C:\Users\dharr\Box\ChimeraX Movie > open Script.txt Unrecognized file suffix '.txt' > open Script 'Script' has no suffix > open Script format txt Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf', 'segger', 'session', 'situs', 'smiles', 'spider', 'stl', 'stockholm', 'storm', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch', 'xplor', or 'xtc' > help movie > open Script.cxc > hide #2 cartoons > hide Vcos > hide #3 cartoons > wait 2 > hide #1 cartoons > hide Mocos > wait 10 > show #2 cartoons > show Vcos > wait 2 > hide #2 cartoons > hide Vcos > wait 5 > show #3 cartoons executed Script.cxc > open Script.cxc > hide #2 cartoons > hide Vcos > hide #3 cartoons > wait 2 > hide #1 cartoons > hide Mocos > wait 10 > show #2 cartoons > show Vcos > wait 2 > hide #2 cartoons > hide Vcos > wait 5 > show #3 cartoons executed Script.cxc > open Script.cxc > hide #2 cartoons > hide Vcos > hide #3 cartoons > wait 2 > hide #1 cartoons > hide Mocos > wait 10 > show #2 cartoons > show Vcos > wait 2 > hide #2 cartoons > hide Vcos > wait 5 > show #3 cartoons executed Script.cxc > open Script.cxc > hide #2 cartoons > hide Vcos > hide #3 cartoons > wait 2 > hide #1 cartoons > hide Mocos > wait 10 > show #2 cartoons > show Vcos > wait 2 > hide #2 cartoons > hide Vcos > wait 5 > show #3 cartoons executed Script.cxc > open Script.cxc > hide #2 cartoons > hide Vcos > hide #3 cartoons > wait 2 > hide #1 cartoons > hide Mocos > wait 10 > show #2 cartoons > show Vcos > wait 2 > hide #2 cartoons > hide Vcos > wait 5 > show #3 cartoons executed Script.cxc > open Script.cxc > hide #2 cartoons > hide Vcos > hide #3 cartoons > wait 2 > hide #1 cartoons > hide Mocos > wait 10 > show #2 cartoons > show Vcos > wait 2 > hide #2 cartoons > hide Vcos > wait 5 > show #3 cartoons executed Script.cxc > open Script.cxc > show #1 cartoons > show Mocos > show #2 cartoons > show Vcos > show #3 cartoons > color #3 purple executed Script.cxc > undo > help wait > open Script.cxc > show #1 cartoons > show Mocos > wait 500 > show #2 cartoons > show Vcos > show #3 cartoons > color #3 purple executed Script.cxc > open Script.cxc > show #1 cartoons > show Mocos > wait 500 > show #2 cartoons > show Vcos > show #3 cartoons > color #3 purple executed Script.cxc > open Script.cxc > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > wait 500 > color #3 red > wait 500 > color #3 purple executed Script.cxc > open Script.cxc > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > wait 500 > color #3 red > wait 500 > color #3 purple executed Script.cxc > roll y 3 > roll y 3 120 > roll y 3 120 > roll y 3 600 > roll y 3 > roll y 3 > roll y 3 > roll y 3 > roll y 3 > roll y 3 > roll y 3 > roll y 3 > roll y 3 > stop > roll y 3 120 > roll y 3 120 > wait > roll y 4 > roll y 1 > stop > roll y 1 > stop > roll y > stop > roll y 360 > roll y 1 360 > roll y 1 720 > roll x 1 360 > roll x 1 360 > wait > roll y 1 360 > roll x 1 360 > roll y 1 360 > roll x 1 360 > roll y 1 360 > color #3 red > wait 240 > color #3 purple > open Script.cxc > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > wait 500 > color #3 red > wait 500 > color #3 purple executed Script.cxc > open Script.cxc > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > wait 500 > color #3 red > wait 500 > color #3 purple executed Script.cxc > open Script.cxc > color #3 pink > wait 50 > color #3 red > wait 50 > color #3 purple > wait 5 > color #3 blue executed Script.cxc > hide #3 cartoons > show #1 cartoons > show Mocos > color #1 cartoon blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 bymodel blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1 dodger blue > color cartoon blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 bymodel > help 2dlabels > view > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase aligned.cxs" > select #1/a 4420 atoms, 3931 bonds, 1 pseudobond, 2 models selected > color #1/a dodger blue > color #1/c dodger blue > color #1/b cyan > color #1/d cyan > color Mocos byelement > select clear > color #1/a cartoon dodger blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color cartoon #1/a dodger blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > help 2dlabel > hide #2 > hide #1 > hide #2 cartoons > hide Mocos > hide #2 cartoons > hide #2 ribbons > hide cartoons #2 Expected ',' or a keyword > hide #2 cartoons > hide #1 cartoons > show #2 cartoons > show Vcos > ui tool show "Color Actions" > hide #2 cartoons > hide Vcos > show #1 cartoons > show Mocos > select /b/d 25674 atoms, 23796 bonds, 33 pseudobonds, 5 models selected > color dodger blue > select /a/c 18894 atoms, 17589 bonds, 18 pseudobonds, 5 models selected > color cyan > select clear > select /b/d 25674 atoms, 23796 bonds, 33 pseudobonds, 5 models selected > color dodger blue > color /a/c cyan > color Mocos byelement > select clear > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase aligned.cxs" > hide #1 cartoons > hide Mocos > show #2 cartoons > show #1 cartoons > hide #1 cartoons > color #2/a green > show Vcos > color Vcos byelement > color chartreuse > undo > color #2/a chartreuse > color #2/a pale green > color #2/b dark sea green > color #2/b medium sea green > color #2/b sea green > color #2/a light green > select up Nothing selected > select up Nothing selected > select up Nothing selected > select up Nothing selected > color #2/b dark sea green > color #2/a light green > color #2/a medium spring green > color #2/a light green > color #2/b medium sea green > color #2/c light green > color dark sea green > undo > color #2/c dark sea green > color #2/c light green > color #2/a dark sea green > color #2/a medium sea green > color #2/b forest green > color #2/d forest green > color #2/c medium sea green > color #2/e forest green > color #2/d medium sea green > color #2/f light green > color Vcos byelement > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase aligned.cxs" > hide #2 cartoons > hide Vcos > show #3 cartoons > color #3/a/e light salmon > color #3/a/d light salmon > color #3/a/d tomato > color #3/a/d salmon > color #3/c/f pink > color #3/c/f light salmon > color #3/c/f light salmon > color #3/b/e tomato > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase aligned_colored.cxs" > show #2 cartoons > show #1 cartoons > show Mocos > show Vcos > hide #3 > hide #3 cartoons > hide #2 cartoons > hide #1 cartoons > hide mocos Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide Mocos > hide Vcos > color #1 cartoon red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1/a red > show #1 cartoons > help pair No help found for 'pair' > help ss No help found for 'ss' > help 2dlabels > 2dlabels text "MoFe protein" color cyan size 24 font arial bold true > 2dlabels 4.1 size 42 Expected 'all' or a 2d label name or a label models specifier or a keyword > 2dlabels #4.1 size 42 > ui mousemode right "move label" > 2dlabels #4.1 xpos 0.377 ypos 0.865 > 2dlabels #4.1 xpos 0.381 ypos 0.878 > 2dlabels #4.1 size 50 > 2dlabels #4.1 xpos 0.363 ypos 0.881 > 2dlabels #4.1 xpos 0.358 ypos 0.873 > 2dlabels text "α2β2 heterotetramer" size 30 color cyan font arial bold true > 2dlabels #4.2 xpos 0.366 ypos 0.809 > 2dlabels text "α2 color cyan β2 color dodger blue heterotetramer" size 30 > color cyan font arial bold true > close #4.3 > select up Nothing selected > select up Nothing selected > select up Nothing selected > 2dlabels text "PDB: 3U7Q" color cyan font arial size 20 bold true > 2dlabels #4.3 xpos 0.556 ypos 0.081 > 2dlabels text β color dodger blue size 30 font arial bold true > 2dlabels #4.4 xpos 0.336 ypos 0.742 > 2dlabels text β color dodger blue size 30 font arial bold true > 2dlabels #4.5 xpos 0.530 ypos 0.271 > 2dlabels #4.5 xpos 0.502 ypos 0.081 > 2dlabels #4.3 xpos 0.626 ypos 0.115 > 2dlabels #4.5 xpos 0.561 ypos 0.077 > 2dlabels text α color dodger blue size 30 font arial bold true > close #4.6 > 2dlabels text α color dodger blue size 30 font arial bold true > close #4.6 > 2dlabels text α color cyan size 30 font arial bold true > 2dlabels #4.6 xpos 0.178 ypos 0.205 > 2dlabels text α color cyan size 30 font arial bold true > 2dlabels #4.7 xpos 0.643 ypos 0.720 > show #2 cartoons > show Vcos > hide Vcos > show Vcos > show #3 cartoons > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > select #3/E 3581 atoms, 3656 bonds, 1 model selected > select #3/A 3795 atoms, 3889 bonds, 1 model selected > select #3/B 3581 atoms, 3656 bonds, 1 model selected > select #3/C 917 atoms, 937 bonds, 1 model selected > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > hide Vcos > hide #2 cartoons > hide #3 cartoons > 2dlabels #4.5 xpos 0.566 ypos 0.093 > 2dlabels #4.3 xpos 0.637 ypos 0.126 > 2dlabels #4.4 xpos 0.334 ypos 0.735 > 2dlabels #4.7 xpos 0.641 ypos 0.715 > 2dlabels #4.3 xpos 0.638 ypos 0.126 > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" > 2dlabels #4.6 xpos 0.189 ypos 0.202 > 2dlabels #4.5 xpos 0.574 ypos 0.103 > 2dlabels #4.7 xpos 0.637 ypos 0.714 > 2dlabels #4.4 xpos 0.335 ypos 0.735 > 2dlabels #4.7 xpos 0.637 ypos 0.716 > hide 4.1 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #4.1 > hide #4.2 > hide #4.3 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > hide Mocos > hide #1 cartoons > show #2 cartoons > show Vcos > 2dlabels text "VFe protein" color medium sea green size 50 font arial bold > true > 2dlabels #4.8 xpos 0.393 ypos 0.883 > 2dlabels text α2β2 color medium sea green size 30 font arial bold true > close #4.9 > 2dlabels text "α2β2 heterohexamer" color medium sea green size 30 font arial > bold true > 2dlabels #4.9 xpos 0.385 ypos 0.821 > 2dlabels text α color medium sea green size 30 font arial bold true > 2dlabels #4.10 xpos 0.345 ypos 0.100 > 2dlabels text α color medium sea green size 30 font arial bold true > 2dlabels #4.11 xpos 0.605 ypos 0.752 > 2dlabels text β color forest green size 30 font arial bold true > 2dlabels #4.12 xpos 0.370 ypos 0.762 > 2dlabels text β color forest green size 30 font arial bold true > 2dlabels #4.13 xpos 0.589 ypos 0.106 > 2dlabels text δ color light green size 30 font arial bold true > 2dlabels #4.14 xpos 0.760 ypos 0.808 > 2dlabels text δ color light green size 30 font arial bold true > 2dlabels #4.15 xpos 0.164 ypos 0.125 > 2dlabels text "PDB: 5N6Y" color medium sea green size 20 font arial bold > true > 2dlabels #4.16 xpos 0.644 ypos 0.140 > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" > hide #4.8,4.9.4.10,4.11,4.12 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > hide #4.14 > hide #4.15 > hide #4.16 > hide Vcos > hide #2 cartoons > show #3 cartoons > select clear > select up Nothing selected > select up Nothing selected > select up Nothing selected > 2dlabels text "FeFe protein" color salmon size 50 font arial bold true > 2dlabels #4.17 xpos 0.352 ypos 0.870 > 2dlabels #4.1 xpos 0.356 ypos 0.875 > 2dlabels #4.1 xpos 0.352 ypos 0.871 > hide #4.1 models > 2dlabels text δ color light salmon size 50 font arial bold true > 2dlabels #4.18 xpos 0.753 ypos 0.799 > close #4.18 > 2dlabels text δ color light salmon size 30 font arial bold true > 2dlabels #4.18 xpos 0.758 ypos 0.784 > 2dlabels text δ color light salmon size 30 font arial bold true > 2dlabels #4.19 xpos 0.167 ypos 0.106 > 2dlabels text α color salmon size 30 font arial bold true > 2dlabels #4.20 xpos 0.585 ypos 0.760 > 2dlabels text α color salmon size 30 font arial bold true > 2dlabels #4.21 xpos 0.342 ypos 0.099 > 2dlabels text β color tomato size 30 font arial bold true > 2dlabels #4.22 xpos 0.587 ypos 0.113 > 2dlabels text β color tomato size 30 font arial bold true > 2dlabels #4.23 xpos 0.377 ypos 0.757 > 2dlabels text α2β2 color light salmon size 30 font arial bold true > close #4.24 > 2dlabels text "α2β2 heterohexamer" color light salmon size 30 font arial > bold true > close #4.24 > 2dlabels text "α2β2 heterohexamer" color salmon size 30 font arial bold true > 2dlabels #4.24 xpos 0.356 ypos 0.823 > 2dlabels text "Homology model to PDB: 5N6Y generated with SWISS-MODEL" color > salmon size 20 font arial bold true > 2dlabels #4.13 xpos 0.586 ypos 0.076 > undo > hide #4.1 target m > 2dlabels #4.13 xpos 0.587 ypos 0.113 > hide #4.13 target m > 2dlabels #4.13 xpos 0.587 ypos 0.114 > 2dlabels #4.13 xpos 0.572 ypos 0.082 > 2dlabels #4.22 xpos 0.556 ypos 0.089 > hide #4.13 models > 2dlabels #4.15 xpos 0.164 ypos 0.116 > 2dlabels #4.15 xpos 0.141 ypos 0.101 > 2dlabels #4.19 xpos 0.172 ypos 0.095 > 2dlabels #4.15 xpos 0.158 ypos 0.106 > hide #4.15 models > 2dlabels #4.10 xpos 0.344 ypos 0.120 > 2dlabels #4.10 xpos 0.337 ypos 0.131 > 2dlabels #4.21 xpos 0.348 ypos 0.117 > 2dlabels #4.10 xpos 0.336 ypos 0.122 > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.22 models > hide #4.23 models > hide #4.24 models > hide #4.25 models > hide #4.20 models > hide #4.21 models > hide #4.10 models > show #4.17 models > show #4.18 models > show #4.19 models > show #4.21 models > show #4.20 models > show #4.22 models > show #4.23 models > show #4.24 models > show #4.25 models > 2dlabels #4.25 xpos 0.250 ypos 0.050 > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" > hide #!1 models > hide #!2 models > hide #3 models > hide #!4 models > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.20 models > hide #4.21 models > hide #4.22 models > hide #4.23 models > hide #4.24 models > hide #4.25 models > open Script.cxc > show #1 cartoons > show Mocos > wait 20 > show #4.1 > show #4.2 > show #4.3 > wait 20 > show #4.6 > wait 10 > show #4.7 > wait 10 > show #4.4 > wait 10 > show #4.5 > wait 10 executed Script.cxc > show #!1 models > show #!2 models > show #3 models > hide #!1 models > hide #!2 models > hide #3 models > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > open Script.cxc > show #1 cartoons > show Mocos > wait 20 > show #4.1 > show #4.2 > show #4.3 > wait 20 > show #4.6 > wait 10 > show #4.7 > wait 10 > show #4.4 > wait 10 > show #4.5 > wait 10 executed Script.cxc > show #1 cartoons > show #1 > show #!1 models > style #!1 stick Changed 18668 atom styles > style #!1 stick Changed 18668 atom styles > hide #!1 atoms > show Mocos > hide Mocos > hide #1 cartoons > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > open Script.cxc > show #1 cartoons > show Mocos > wait 20 > show #4.1 > show #4.2 > show #4.3 > wait 20 > show #4.6 > wait 10 > show #4.7 > wait 10 > show #4.4 > wait 10 > show #4.5 > wait 10 executed Script.cxc > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 20 > show #4.1 > show #4.2 > show #4.3 > wait 20 > show #4.6 > wait 10 > show #4.7 > wait 10 > show #4.4 > wait 10 > show #4.5 > wait 10 executed Script.cxc > hide #1 cartoons > hide Mocos > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 executed Script.cxc > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #1 cartoons > hide Mocos > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 executed Script.cxc > hide #4.7 models > hide #4.6 models > hide #4.1 models > hide #4.2 models > hide #!4 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > show #4.5 models > hide #4.5 models > hide #!4 models > show #!4 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 executed Script.cxc > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 executed Script.cxc > help roll > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait executed Script.cxc > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait executed Script.cxc > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #1 cartoons > hide Mocos > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.5 > show #4.7 executed Script.cxc > show #4.6 models > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 executed Script.cxc > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 executed Script.cxc > 2dlabels text α/U2207Aβ/U2207A > 2dlabels #4.26 xpos 0.792 ypos 0.480 > close #4.26 > 2dlabels text α/U2082β/U2082 > close #4.26 > 2dlabels text α/U208xβ/U2082 > close #4.26 > 2dlabels text α/U+2082β/U2082 > close #4.26 > 2dlabels text "α\\\U+2082β/U2082" > 2dlabels text hello⁺ > hide #4.26 models > close #4.26 > close #4.27 > 2dlabels text 'α\U+2082 Invalid "text" argument: incomplete quoted text > 2dlabels text α₂ > close #4.26 > 2dlabels text α₂ > 2dlabels #4.26 xpos 0.830 ypos 0.530 > 2dlabels text α2 > close #4.27 > close #4.26 > 2dlabels text "α\\\U+2082βȈ2" > 2dlabels text α₂ β\u+2082 Expected a keyword > 2dlabels text "α\\\U+2082 β₂" > close #4.26 > close #4.27 > 2dlabels text "α\\\U+2082 β₂" > 2dlabels text α₂ β\U+2082 Expected a keyword > 2dlabels text "α\\\U+2082β₂" > close #4.26 > close #4.27 > 2dlabels text "α\\\U+2082β₂" > 2dlabels text "α\\\U+2082 β\\\U+2082 heterotetramer" > close #4.26 > 2dlabels text α₂ > close #4.26 > close #4.27 > 2dlabels text α₂ color cyan size 30 bold true font arial > 2dlabels #4.26 xpos 0.366 ypos 0.811 > 2dlabels text β₂ color cyan size 30 bold true font arial > 2dlabels #4.27 xpos 0.398 ypos 0.810 > 2dlabels text heterotetramer color cyan size 30 bold true font arial > 2dlabels #4.28 xpos 0.436 ypos 0.809 > close #4.2 > select #4.26 1 model selected > select #4.27 1 model selected > select #4.28 1 model selected > select #4.27 1 model selected > select #4.28 1 model selected > select #4.27 1 model selected > select clear > select clear > select clear Drag select of Drag select of Drag select of > select #4.26 1 model selected > ui tool show "Model Panel" > view #4.28 clip false > view #4.28 clip false > view #4.28 clip false > undo > undo > undo > help model panel modeller comparative targets [block true or false] [multichain true or false] [customScript name of a file to open/read] [distRestraints name of a file to open/read] [executableLocation name of a file to open/read] [fast true or false] [hetPreserve true or false] [hydrogens true or false] [licenseKey a password] [numModels an integer] [showGui true or false] [tempPath name of a folder to open/read] [thoroughOpt true or false] [waterPreserve true or false] — Use Modeller to generate comparative model targets: some [alignment-id:]sequence-name-or-number modeller scores structures [block true or false] [licenseKey a password] [refresh true or false] — Fetch scores for models from Modeller web site > help deactivate No help found for 'deactivate' > deactivate Unknown command: deactivate > lock Unknown command: lock > help lock No help found for 'lock' > hide #4.28 models > hide #4.27 models > hide #4.26 models > ~select #4.26 Nothing selected > show #4.26 models > show #4.27 models > show #4.28 models > hide #4.28 models > hide #4.27 models > hide #4.26 models > hide #4.1 models > show #4.8 models > show #4.24 models > show #4.9 models > hide #4.24 models > select up Nothing selected > select up Nothing selected > 2dlabels text α₂ color medium sea green size 30 bold true font arial > 2dlabels #4.2 xpos 0.385 ypos 0.822 > 2dlabels text β₂ color medium sea green size 30 bold true font arial > 2dlabels #4.29 xpos 0.417 ypos 0.822 > 2dlabels text heterohexamer color medium sea green size 30 bold true font > arial > 2dlabels #4.30 xpos 0.455 ypos 0.822 > close #4.9 > hide #4.8 models > show #4.17 models > hide #4.29 models > hide #4.30 models > show #4.29 models > hide #4.29 models > show #4.30 models > hide #4.2 models > show #4.2 models > hide #4.2 models > close #4.2 > show #4.29 models > select up Nothing selected > 2dlabels text α₂ color salmon size 30 bold true font arial > 2dlabels #4.2 xpos 0.385 ypos 0.821 > hide #4.2 models > show #4.2 models > 2dlabels text β₂ color salmon size 30 bold true font arial > 2dlabels #4.9 xpos 0.417 ypos 0.822 > 2dlabels text heterohexamer color salmon size 30 bold true font arial > 2dlabels #4.31 xpos 0.455 ypos 0.822 > 2dlabels #4.1 xpos 0.352 ypos 0.870 > hide #4.1 models > hide #4.2 models > show #4.2 models > hide #4.3 models > show #4.3 models > 2dlabels #4.1 xpos 0.354 ypos 0.870 > 2dlabels #4.1 xpos 0.370 ypos 0.874 > 2dlabels #4.17 xpos 0.381 ypos 0.865 > 2dlabels #4.1 xpos 0.379 ypos 0.864 > hide #4.2 models > hide #4.9 models > close #4.29 > close #4.30 > hide #4.17 models > hide #4.31 models > show #4.28 models > show #4.26 models > show #4.27 models > 2dlabels #4.1 xpos 0.357 ypos 0.863 > hide #!4 models > hide #4.1 models > hide #4.3 models > show #!4 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #4.26 models > hide #4.27 models > hide #4.28 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 200 > show #4.1 > show #4.2 > show #4.3 > wait 200 > show #4.6 > wait 100 > show #4.7 > wait 100 > show #4.4 > wait 100 > show #4.5 > wait 100 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 executed Script.cxc > help roll > cofr Center of rotation: -4.05 -4.4166 21.151 center of view > cofr centerOfView > roll x 1 360 > cofr frontCenter > roll x 1 360 > roll y 1 360 > roll x 1 360 > roll y 1 360 > roll x 1 360 > hide #4.2 models > hide #4.1 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #1 cartoons > hide Mocos > open Script.cxc > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.3 > wait 100 > show #4.26 > show #4.6 > wait 50 > show #4.7 > wait 50 > show #4.4 > wait 50 > show #4.5 > wait 50 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 executed Script.cxc > hide #4.1 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #4.26 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.3 > wait 100 > show #4.26 > show #4.6 > wait 50 > show #4.7 > wait 50 > show #4.4 > wait 50 > show #4.5 > wait 50 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 executed Script.cxc > hide #4.1 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #4.26 models > hide Mocos > hide #1 cartoons > open Script.cxc > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.3 > wait 100 > show #4.26 > show #4.27 > show #4.28 > wait 100 > show #4.6 > wait 50 > show #4.7 > wait 50 > show #4.4 > wait 50 > show #4.5 > wait 50 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 executed Script.cxc > roll x 1 360 > roll y 1 360 > 2dlabels #4.4 xpos 0.340 ypos 0.737 > open Script.cxc > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.3 > wait 100 > show #4.26 > show #4.27 > show #4.28 > wait 100 > show #4.6 > wait 50 > show #4.7 > wait 50 > show #4.4 > wait 50 > show #4.5 > wait 50 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 > wait 200 > hide Mocos > hide #1 cartoons > hide #4.1 > hide #4.3 > hide #4.26 > hide #4.27 > hide #4.28 > hide #4.6 > hide #4.4 > hide #4.5 > hide #4.7 executed Script.cxc > help movie > open Script.cxc > movie record > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.3 > wait 100 > show #4.26 > show #4.27 > show #4.28 > wait 100 > show #4.6 > wait 50 > show #4.7 > wait 50 > show #4.4 > wait 50 > show #4.5 > wait 50 > hide #4.4 > hide #4.5 > hide #4.6 > hide #4.7 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.6 > show #4.7 > wait 200 > hide Mocos > hide #1 cartoons > hide #4.1 > hide #4.3 > hide #4.26 > hide #4.27 > hide #4.28 > hide #4.6 > hide #4.4 > hide #4.5 > hide #4.7 > movie encode C:\Users\dharr/Desktop/movietest.mp4 Movie saved to C:\Users\dharr/Desktop/movietest.mp4 executed Script.cxc > show Mocos > 2dlabels text P-cluster size 20 color cyan bold true font arial > 2dlabels #4.29 xpos 0.206 ypos 0.569 > 2dlabels text P-cluster size 20 color cyan bold true font arial > 2dlabels #4.30 xpos 0.694 ypos 0.363 > 2dlabels text 'FeMoco with R-homocitrate size 20 color cyan bold true font > arial Invalid "text" argument: incomplete quoted text > 2dlabels text "FeMoco with R-homocitrate" size 20 color cyan bold true font > arial > 2dlabels #4.32 xpos 0.672 ypos 0.534 > 2dlabels text "FeMoco with R-homocitrate" size 20 color cyan bold true font > arial > 2dlabels #4.33 xpos 0.046 ypos 0.361 > select Mo 2 atoms, 1 model selected > color Mo magenta > select clear > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" opened ChimeraX session > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.5 models > hide #4.4 models > hide #4.6 models > hide #4.7 models > hide #4.8 models > hide #4.10 models > hide #4.9 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.14 models > hide #4.15 models > hide #4.16 models > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.20 models > hide #4.21 models > hide #4.22 models > hide #4.23 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #4.28 models > hide #4.27 models > hide #4.29 models > hide #4.30 models > hide #4.31 models > hide #4.32 models > hide #4.33 models > 2dlabels text P-cluster size 20 color medium sea green font arial bold true > hide Mocos > show Vcos > show #!2 models > 2dlabels #4.34 xpos 0.678 ypos 0.338 > show Vcos > 2dlabels text P-cluster size 20 color medium sea green font arial bold true > 2dlabels #4.35 xpos 0.207 ypos 0.555 > 2dlabels text "FeVco with R-homocitrate" size 20 color medium sea green font > arial bold true > 2dlabels #4.36 xpos 0.672 ypos 0.510 > 2dlabels text "FeVco with R-homocitrate" size 20 color medium sea green font > arial bold true > 2dlabels #4.37 xpos 0.062 ypos 0.372 > 2dlabels #4.36 xpos 0.670 ypos 0.510 > 2dlabels #4.36 xpos 0.674 ypos 0.521 > 2dlabels #4.34 xpos 0.682 ypos 0.335 > 2dlabels #4.33 xpos 0.047 ypos 0.371 > hide #4.33 models > hide #4.34 models > hide #4.35 models > hide #4.36 models > hide #4.37 models > show #3 models > hide #3 cartoons > hide Vcos > help movie > open Script.cxc > movie record > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.2 > wait 100 > show #4.24 > show #4.25 > show #4.26 > wait 100 > show #4.5 > wait 50 > show #4.6 > wait 50 > show #4.3 > wait 50 > show #4.4 > wait 50 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.4 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.4 > wait 200 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 100 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 100 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 100 > show #2 cartoons > show Vcos > wait 100 > show #4.7 > show #4.14 > wait 100 > show #4.27 > show #4.28 > show #4.29 > wait 100 > show #4.18 > wait 50 > show #4.19 > wait 50 > show #4.20 > wait 50 > show #4.21 > wait 50 > show #4.16 > wait 50 > show #4.17 > wait 50 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 200 > hide #2 cartoons > hide #4.7 > hide #4.14 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > wait 100 > show #4.34 > show #4.35 > show #4.36 > show #4.37 > wait 100 > hide Vcos > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > wait 100 > show #3 cartoons > wait 100 > show #4.15 > show #4.23 > wait 100 > show #4.27 > show #4.28 > show #4.29 > wait 100 > show #4.18 > wait 50 > show #4.19 > wait 50 > show #4.20 > wait 50 > show #4.21 > wait 50 > show #4.16 > wait 50 > show #4.17 > wait 50 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 100 > hide #3 cartoons > hide #4.15 > hide #4.23 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > move #3 x 160;move #1 x -160;show #1 cartoon;show Mocos;show #2 cartoon;show > Vcos;show #3 cartoon;wait 100 Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 16588 atoms > show #1 cartoons > show #2 cartoons > show #3 cartoons > help move > move x 160 #3 Expected an integer >= 1 or a keyword > help move > move x 160 models #3 > move x -160 models #1 > move x 160 models #1 > move x -160 models #3 > hide models #1 Expected ',' or a keyword > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > open Script.cxc > movie record Already recording a movie > stop > movie stop > open Script.cxc > movie record > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.2 > wait 100 > show #4.24 > show #4.25 > show #4.26 > wait 100 > show #4.5 > wait 50 > show #4.6 > wait 50 > show #4.3 > wait 50 > show #4.4 > wait 50 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.4 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.4 > wait 200 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 100 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 100 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 100 > show #2 cartoons > show Vcos > wait 100 > show #4.7 > show #4.14 > wait 100 > show #4.27 > show #4.28 > show #4.29 > wait 100 > show #4.18 > wait 50 > show #4.19 > wait 50 > show #4.20 > wait 50 > show #4.21 > wait 50 > show #4.16 > wait 50 > show #4.17 > wait 50 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 200 > hide #2 cartoons > hide #4.7 > hide #4.14 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > wait 100 > show #4.34 > show #4.35 > show #4.36 > show #4.37 > wait 100 > hide Vcos > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > wait 100 > show #3 cartoons > wait 100 > show #4.15 > show #4.23 > wait 100 > show #4.27 > show #4.28 > show #4.29 > wait 100 > show #4.18 > wait 50 > show #4.19 > wait 50 > show #4.20 > wait 50 > show #4.21 > wait 50 > show #4.16 > wait 50 > show #4.17 > wait 50 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 100 > hide #3 cartoons > hide #4.15 > hide #4.23 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > move x 160 models #3 > move x -160 models #1 > show #1 cartoons > show Mocos > show #2 cartoons > show Vcos > show #3 cartoons > wait 100 > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode C:\Users\dharr/Desktop/testmovie.mp4 Movie saved to C:\Users\dharr/Desktop/testmovie.mp4 executed Script.cxc > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > hide Mocos > hide Vcos > hide #2 cartoons > hide #3 cartoons > show Mocos > show #4.1 models > show #4.2 models > 2dlabels #4.1 xpos 0.331 ypos 0.844 > show #4.24 models > show #4.25 models > show #4.26 models > show #4.3 models > show #4.4 models > show #4.5 models > show #4.6 models > 2dlabels #4.5 xpos 0.210 ypos 0.165 > 2dlabels #4.4 xpos 0.585 ypos 0.120 > 2dlabels #4.6 xpos 0.638 ypos 0.732 > 2dlabels #4.3 xpos 0.336 ypos 0.761 > 2dlabels #4.1 xpos 0.349 ypos 0.858 > 2dlabels #4.2 xpos 0.641 ypos 0.154 > 2dlabels #4.5 xpos 0.216 ypos 0.157 > 2dlabels #4.3 xpos 0.340 ypos 0.764 > 2dlabels #4.6 xpos 0.628 ypos 0.752 > 2dlabels #4.1 xpos 0.353 ypos 0.858 > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #2 cartoons > hide #1 cartoons > hide Mocos > show #2 cartoons > show Vcos > show #4.7 models > show #4.8 models > show #4.9 models > show #4.10 models > show #4.11 models > show #4.12 models > show #4.13 models > show #4.14 models > 2dlabels #4.12 xpos 0.760 ypos 0.796 > 2dlabels #4.9 xpos 0.599 ypos 0.779 > 2dlabels #4.11 xpos 0.591 ypos 0.124 > 2dlabels #4.8 xpos 0.344 ypos 0.121 > 2dlabels #4.13 xpos 0.157 ypos 0.100 > 2dlabels #4.2 xpos 0.643 ypos 0.154 > 2dlabels #4.14 xpos 0.654 ypos 0.156 > 2dlabels #4.2 xpos 0.643 ypos 0.145 > 2dlabels #4.10 xpos 0.354 ypos 0.788 > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" > 2dlabels text α₂ color medium sea green size 30 bold true font arial > 2dlabels #4.38 xpos 0.395 ypos 0.841 > 2dlabels text β₂ color medium sea green size 30 bold true font arial > 2dlabels #4.39 xpos 0.428 ypos 0.841 > 2dlabels text δ₂ color medium sea green size 30 bold true font arial > 2dlabels #4.40 xpos 0.460 ypos 0.839 > 2dlabels #4.1 xpos 0.353 ypos 0.863 > 2dlabels #4.1 xpos 0.354 ypos 0.859 > 2dlabels #4.7 xpos 0.388 ypos 0.883 > hide #4.1 models > 2dlabels text heterohexamer color medium sea green size 30 bold true font > arial > 2dlabels #4.41 xpos 0.496 ypos 0.838 > 2dlabels #4.1 xpos 0.351 ypos 0.859 > 2dlabels #4.22 xpos 0.354 ypos 0.823 > 2dlabels #4.22 xpos 0.354 ypos 0.823 > hide #4.22 models > 2dlabels #4.1 xpos 0.353 ypos 0.862 > 2dlabels #4.1 xpos 0.357 ypos 0.867 > 2dlabels #4.22 xpos 0.354 ypos 0.816 > 2dlabels #4.1 xpos 0.357 ypos 0.870 > 2dlabels #4.1 xpos 0.358 ypos 0.873 > 2dlabels #4.15 xpos 0.379 ypos 0.869 > 2dlabels #4.22 xpos 0.364 ypos 0.794 > 2dlabels #4.25 xpos 0.399 ypos 0.784 > 2dlabels #4.27 xpos 0.374 ypos 0.792 > 2dlabels #4.38 xpos 0.377 ypos 0.841 > 2dlabels #4.28 xpos 0.417 ypos 0.804 > 2dlabels #4.15 xpos 0.377 ypos 0.869 > 2dlabels #4.39 xpos 0.409 ypos 0.842 > 2dlabels #4.26 xpos 0.435 ypos 0.799 > 2dlabels #4.29 xpos 0.456 ypos 0.806 > 2dlabels #4.15 xpos 0.375 ypos 0.879 > 2dlabels #4.40 xpos 0.442 ypos 0.841 > 2dlabels #4.41 xpos 0.481 ypos 0.838 > 2dlabels #4.21 xpos 0.366 ypos 0.739 > 2dlabels #4.22 xpos 0.056 ypos 0.874 > 2dlabels #4.24 xpos 0.362 ypos 0.816 > 2dlabels #4.27 xpos 0.377 ypos 0.841 > 2dlabels #4.25 xpos 0.391 ypos 0.778 > 2dlabels #4.28 xpos 0.410 ypos 0.842 > 2dlabels #4.29 xpos 0.481 ypos 0.838 > select up Nothing selected > 2dlabels text δ₂ color salmon size 30 bold true font arial > 2dlabels #4.42 xpos 0.442 ypos 0.841 > hide #4.1 models > hide #4.2 models > hide #4.7 models > hide #4.8 models > hide #4.11 models > hide #4.10 models > hide #4.9 models > hide #4.12 models > hide #4.13 models > hide #4.14 models > hide #4.15 models > hide #4.21 models > hide #4.24 models > hide #4.22 models > hide #4.25 models > hide #4.26 models > hide #4.27 models > hide #4.28 models > hide #4.29 models > hide #4.42 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #2 cartoons > hide Vcos > show Mocos > show #1 cartoons > show #4.1 models > show #4.2 models > show #4.3 models > show #4.4 models > show #4.5 models > show #4.6 models > show #4.24 models > show #4.25 models > show #4.26 models > 2dlabels #4.25 xpos 0.394 ypos 0.816 > 2dlabels #4.26 xpos 0.434 ypos 0.815 > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" > hide #1 cartoons > hide Mocos > hide #4.2 models > hide #4.1 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > show #2 cartoons > show Vcos > show #4.7 models > show #4.8 models > show #4.9 models > show #4.10 models > show #4.11 models > show #4.12 models > show #4.13 models > show #4.14 models > show #4.34 models > hide #4.34 models > show #4.38 models > show #4.39 models > show #4.40 models > show #4.41 models > 2dlabels #4.29 xpos 0.483 ypos 0.810 > 2dlabels #4.41 xpos 0.481 ypos 0.837 > 2dlabels #4.1 xpos 0.358 ypos 0.913 > 2dlabels #4.1 xpos 0.358 ypos 0.924 > 2dlabels #4.7 xpos 0.389 ypos 0.889 > hide #4.29 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.14 models > show #1 cartoons > show #4.24 models > show #4.25 models > show #4.26 models > 2dlabels #4.1 xpos 0.349 ypos 0.873 > hide #4.1 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #1 cartoons > hide #2 cartoons > hide Vcos > show #3 cartoons > show #4.15 models > show #4.16 models > show #4.17 models > show #4.18 models > show #4.19 models > show #4.20 models > show #4.21 models > show #4.22 models > hide #4.22 models > show #4.27 models > show #4.28 models > show #4.29 models > show #4.42 models > 2dlabels #4.29 xpos 0.481 ypos 0.839 > 2dlabels #4.15 xpos 0.389 ypos 0.891 > 2dlabels #4.20 xpos 0.587 ypos 0.126 > 2dlabels #4.17 xpos 0.158 ypos 0.093 > hide #4.19 models > show #4.19 models > 2dlabels #4.18 xpos 0.595 ypos 0.779 > hide #4.21 models > show #4.21 models > 2dlabels #4.21 xpos 0.350 ypos 0.783 > show #4.23 models > 2dlabels #4.23 xpos 0.286 ypos 0.076 > hide #4.15 models > hide #4.16 models > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.20 models > hide #4.21 models > hide #4.23 models > hide #4.27 models > hide #4.28 models > hide #4.29 models > hide #4.42 models > hide #3 cartoons > show #1 cartoons > show Mocos > show #2 cartoons > show Vcos > show #3 cartoons > view > move x -160 models #2 > move x 160 models #2 > move x -80 models #2 > move x 80 models #2 > move x -100 models #2 > move x 100 models #2 > color #1 cartoon cyan Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > coloar #1 cyan Unknown command: coloar #1 cyan > color #1 cyan > color #1 cyan > color Mocos byelement > ui tool show "Color Actions" > 2dlabels text "Alignment of all three" color dark slate blue size 30 bold > true font arial > close #4.43 > 2dlabels text "Alignment of all three" color dark slate blue size 50 bold > true font arial > 2dlabels #4.32 xpos 0.695 ypos 0.530 > 2dlabels #4.36 xpos 0.674 ypos 0.527 > 2dlabels #4.43 xpos 0.264 ypos 0.894 > hide #4.36 models > hide #4.32 models > hide #4.43 models > hide #3 cartoons > hide #2 cartoons > hide Vcos > hide #1 cartoons > hide Mocos > open Script.cxc > movie record > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.2 > wait 100 > show #4.24 > show #4.25 > show #4.26 > wait 100 > show #4.5 > wait 50 > show #4.6 > wait 50 > show #4.3 > wait 50 > show #4.4 > wait 50 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.4 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.4 > wait 200 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 100 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 100 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 100 > show #2 cartoons > show Vcos > wait 100 > show #4.7 > show #4.14 > wait 100 > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 100 > show #4.8 > wait 50 > show #4.9 > wait 50 > show #4.10 > wait 50 > show #4.11 > wait 50 > show #4.12 > wait 50 > show #4.13 > wait 50 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 200 > hide #2 cartoons > hide #4.7 > hide #4.14 > hide #4.38 > hide #4.38 > hide #4.40 > hide #4.41 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 100 > show #4.34 > show #4.35 > show #4.36 > show #4.37 > wait 100 > hide Vcos > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > wait 100 > show #3 cartoons > wait 100 > show #4.15 > show #4.23 > wait 100 > show #4.27 > show #4.28 > show #4.29 > show #4.42 > wait 100 > show #4.18 > wait 50 > show #4.19 > wait 50 > show #4.20 > wait 50 > show #4.21 > wait 50 > show #4.16 > wait 50 > show #4.17 > wait 50 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 100 > hide #3 cartoons > hide #4.15 > hide #4.23 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.42 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > show #1 cartoons > show Mocos > color #1 cyan > color Mocos byelement > wait 50 > hide #1 cartoons > hide Mocos > wait 50 > show #2 cartoons > show Vcos > color #1 medium sea green > color Vcos byelement > wait 50 > hide #2 cartoons > hide Vcos > wait 50 > show #3 cartoons > color #3 salmon > wait 50 > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > show #1 cartoons > show Mocos > show #2 cartoons > show Vcos > show #3 cartoons > show #4.43 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode C:\Users\dharr/Desktop/testmovie.mp4 Movie saved to C:\Users\dharr/Desktop/testmovie.mp4 executed Script.cxc > show #1 cartoons > hide #1 cartoons > show #1 cartoons > color #1 cyan > color Mocos by element Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > hide #2 cartoons > hide Vcos > hide #3 cartoons > show #4.1 models > show #4.2 models > show #4.3 models > show #4.4 models > show #4.5 models > show #4.6 models > select #1/A,C 8809 atoms, 7862 bonds, 2 pseudobonds, 2 models selected > color dodger blue > color #1/A,C dodger blue > color #1/A,C cyan > color #1/B,D dodger blue > select clear > color Mocos byelement > hide #2 cartoons > hide #1 cartoons > hide Mocos > show #2 cartoons > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > show #4.7 models > show #4.8 models > show #4.9 models > show #4.10 models > show #4.11 models > show #4.12 models > show #4.13 models > show Vcos > hide #2 cartoons > hide Vcos > show #3 cartoons > hide #4.13 models > hide #4.12 models > hide #4.11 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.39 models > hide #4.43 models > show #4.42 models > show #4.29 models > show #4.28 models > show #4.27 models > show #4.23 models > show #4.22 models > show #4.21 models > show #4.20 models > hide #4.22 models > show #4.19 models > show #4.18 models > show #4.17 models > show #4.16 models > show #4.15 models > color #3/A,D salmon > color #3/B,E tomato > color #3/C,F light salmon > hide #4.15 models > hide #4.16 models > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.20 models > hide #4.21 models > hide #4.27 models > hide #4.28 models > hide #4.29 models > hide #4.23 models > hide #4.42 models > hide #3 cartoons > open Script.cxc > movie record > show #1 cartoons > show Mocos > wait 100 > show #4.1 > show #4.2 > wait 100 > show #4.24 > show #4.25 > show #4.26 > wait 100 > show #4.5 > wait 50 > show #4.6 > wait 50 > show #4.3 > wait 50 > show #4.4 > wait 50 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.4 > wait 200 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 100 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 100 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 100 > show #2 cartoons > show Vcos > wait 100 > show #4.7 > show #4.14 > wait 100 > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 100 > show #4.8 > wait 50 > show #4.9 > wait 50 > show #4.10 > wait 50 > show #4.11 > wait 50 > show #4.12 > wait 50 > show #4.13 > wait 50 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 200 > hide #2 cartoons > hide #4.7 > hide #4.14 > hide #4.38 > hide #4.39 > hide #4.40 > hide #4.41 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 100 > show #4.34 > show #4.35 > show #4.36 > show #4.37 > wait 100 > hide Vcos > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > wait 100 > show #3 cartoons > wait 100 > show #4.15 > show #4.23 > wait 100 > show #4.27 > show #4.28 > show #4.29 > show #4.42 > wait 100 > show #4.18 > wait 50 > show #4.19 > wait 50 > show #4.20 > wait 50 > show #4.21 > wait 50 > show #4.16 > wait 50 > show #4.17 > wait 50 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 100 > hide #3 cartoons > hide #4.15 > hide #4.23 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.42 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > show #1 cartoons > show Mocos > wait 50 > color #1 cyan > color Mocos byelement > wait 50 > hide #1 cartoons > hide Mocos > wait 50 > show #2 cartoons > show Vcos > wait 50 > color #1 medium sea green > color Vcos byelement > wait 50 > hide #2 cartoons > hide Vcos > wait 50 > show #3 cartoons > wait 50 > color #3 salmon > wait 50 > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > show #1 cartoons > show Mocos > show #2 cartoons > show Vcos > show #3 cartoons > show #4.43 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode C:\Users\dharr/Desktop/testmovie(1).mp4 Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-00807.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-00812.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-00851.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-00943.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-01010.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-01104.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-01339.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-01758.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-01865.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-01882.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02007.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02096.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02274.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02402.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02562.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02662.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02755.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-02904.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03097.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03227.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03464.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03511.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03528.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03557.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03754.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03796.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03818.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03841.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03878.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03918.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03958.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-03998.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04016.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04043.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04080.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04122.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04150.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04178.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04230.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04278.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04298.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04388.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04426.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04474.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04514.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04548.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04588.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04638.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04671.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04703.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04747.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04809.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04827.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04847.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04915.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04939.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-04982.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-05081.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-05125.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-05140.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-05169.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-05199.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-05202.ppm Error removing file C:\Users\dharr\AppData\Local\Temp\chimovie_MpT4-05579.ppm Movie saved to C:\Users\dharr/Desktop/testmovie(1).mp4 executed Script.cxc > show #1 cartoons > color #1 cyan > hide #1 cartoons > hide #3 cartoons > color Mocos byelement > hide Mocos > hide #2 cartoons > hide Vcos > show #1 cartoons > color #1/C,D dodger blue > color #1/B,D dodger blue > color Mocos byelement > close #3 cartoon Expected a keyword > hide #3 cartoons > hide #1 cartoons > show #3 cartoons > color #3/A,D salmon > color #3/B,E tomato > color #3/C,F light salmon > hide #4.43 models > hide #3 cartoons > open Script.cxc > movie record > show #1 cartoons > show Mocos > wait 50 > show #4.1 > show #4.2 > wait 50 > show #4.24 > show #4.25 > show #4.26 > wait 50 > show #4.5 > wait 25 > show #4.6 > wait 25 > show #4.3 > wait 25 > show #4.4 > wait 25 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.4 > wait 50 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 > show #2 cartoons > show Vcos > wait 50 > show #4.7 > show #4.14 > wait 50 > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > show #4.8 > wait 25 > show #4.9 > wait 25 > show #4.10 > wait 25 > show #4.11 > wait 25 > show #4.12 > wait 25 > show #4.13 > wait 25 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > hide #2 cartoons > hide #4.7 > hide #4.14 > hide #4.38 > hide #4.39 > hide #4.40 > hide #4.41 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 50 > show #4.34 > show #4.35 > show #4.36 > show #4.37 > wait 50 > hide Vcos > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > wait 50 > show #3 cartoons > wait 50 > show #4.15 > show #4.23 > wait 50 > show #4.27 > show #4.28 > show #4.29 > show #4.42 > wait 50 > show #4.18 > wait 25 > show #4.19 > wait 25 > show #4.20 > wait 25 > show #4.21 > wait 25 > show #4.16 > wait 25 > show #4.17 > wait 25 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 50 > hide #3 cartoons > hide #4.15 > hide #4.23 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.42 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > show #1 cartoons > show Mocos > wait 25 > color #1 cyan > color Mocos byelement > wait 25 > hide #1 cartoons > hide Mocos > wait 25 > show #2 cartoons > show Vcos > wait 25 > color #2 medium sea green > color Vcos byelement > wait 25 > hide #2 cartoons > hide Vcos > wait 25 > show #3 cartoons > wait 25 > color #3 salmon > wait 25 > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 25 > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 25 > show #1 cartoons > show Mocos > show #2 cartoons > show Vcos > show #3 cartoons > show #4.43 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode C:\Users\dharr/Desktop/testmovie(1).mp4 Movie saved to C:\Users\dharr/Desktop/testmovie(1).mp4 executed Script.cxc > show #4.1 models > show #4.2 models > show #4.3 models > show #4.4 models > show #4.6 models > show #4.5 models > show #4.8 models > show #4.9 models > show #4.10 models > show #4.11 models > show #4.12 models > show #4.13 models > hide #3 cartoons > hide #2 cartoons > hide #1 cartoons > show #2 cartoons > hide #2 cartoons > show #1 cartoons > show #4.7 models > show #4.38 models > show #4.39 models > show #4.40 models > show #4.41 models > show #2 cartoons > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.13 models > hide #4.12 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #4.43 models > color #1/B,D dodger blue > color Mocos byelement > hide #1 cartoons > hide Mocos > colr #2/A,D medium sea green Unknown command: colr #2/A,D medium sea green > color #2/A,D medium sea green > color #2/B,E forest green > color #2/C,F light green > color Vcos byelement > hide #2 cartoons > hide Vcos > show #3 cartoons > color #3/B,E tomato > color #3/C,F light salmon > hide #3 cartoons > open Script.cxc > movie record > show #1 cartoons > show Mocos > wait 50 > show #4.1 > show #4.2 > wait 50 > show #4.24 > show #4.25 > show #4.26 > wait 50 > show #4.5 > wait 25 > show #4.6 > wait 25 > show #4.3 > wait 25 > show #4.4 > wait 25 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.4 > wait 50 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 > show #2 cartoons > show Vcos > wait 50 > show #4.7 > show #4.14 > wait 50 > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > show #4.8 > wait 25 > show #4.9 > wait 25 > show #4.10 > wait 25 > show #4.11 > wait 25 > show #4.12 > wait 25 > show #4.13 > wait 25 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > hide #2 cartoons > hide #4.7 > hide #4.14 > hide #4.38 > hide #4.39 > hide #4.40 > hide #4.41 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > wait 50 > show #4.34 > show #4.35 > show #4.36 > show #4.37 > wait 50 > hide Vcos > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > wait 50 > show #3 cartoons > wait 50 > show #4.15 > show #4.23 > wait 50 > show #4.27 > show #4.28 > show #4.29 > show #4.42 > wait 50 > show #4.18 > wait 25 > show #4.19 > wait 25 > show #4.20 > wait 25 > show #4.21 > wait 25 > show #4.16 > wait 25 > show #4.17 > wait 25 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.18 > show #4.19 > show #4.20 > show #4.21 > show #4.16 > show #4.17 > wait 50 > hide #3 cartoons > hide #4.15 > hide #4.23 > hide #4.27 > hide #4.28 > hide #4.29 > hide #4.42 > hide #4.18 > hide #4.19 > hide #4.20 > hide #4.21 > hide #4.16 > hide #4.17 > show #1 cartoons > show Mocos > wait 25 > color #1 cyan > color Mocos byelement > wait 25 > hide #1 cartoons > hide Mocos > wait 25 > show #2 cartoons > show Vcos > wait 25 > color #2 medium sea green > color Vcos byelement > wait 25 > hide #2 cartoons > hide Vcos > wait 25 > show #3 cartoons > wait 25 > color #3 salmon > wait 25 > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 25 > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 25 > show #1 cartoons > show Mocos > show #2 cartoons > show Vcos > show #3 cartoons > show #4.43 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode C:\Users\dharr/Desktop/testmovie(1).mp4 Movie saved to C:\Users\dharr/Desktop/testmovie(1).mp4 executed Script.cxc > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > aligned_colored_labeled.cxs" opened ChimeraX session > hide #!4 models > hide #2 cartoons > hide Vcos > hide #3 cartoons > open Crossfade_test.cxc No such file/path: Crossfade_test.cxc > open Script(1).cxc No such file/path: Script(1).cxc > open Script1.cxc No such file/path: Script1.cxc > cd "C:/Users/dharr/Box/ChimeraX Movie" Current working directory is: C:\Users\dharr\Box\ChimeraX Movie > open Script(1).cxc No such file/path: Script(1).cxc > open Sccript.cxc > movie record > crossfade > hide #1 cartoons > wait 30 > crossfade > show #1 cartoons > wait 30 > crossfade > color #1 cartoon dodger blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color cartoon #1 dodger blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 dodger blue > color cartoon #1 dodger blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > redo > open Sccript.cxc > movie record Already recording a movie > movie stop > open Sccript.cxc > movie record > crossfade > hide #1 cartoons > wait 30 > crossfade > show #1 cartoons > wait 30 > crossfade > color #1/B,D dodger blue > movie encode C:\Users\dharr/Desktop/crossfade_script_test Unrecognized movie file suffix crossfade_script_test, use *.ogv, *.mov, *.mp4, *.avi, *.wmv, *.webm > movie stop > help making movies No help found for 'making movies' > help movie making > view :8P8 > view :hca > view :hca > view > view > view all > view #1/A > view all > zoom :8P8 Expected a number or a keyword > help zoom > view :8p8 > zoom 1 > zoom 2 > help zoom > help frames No help found for 'frames' > help frame No help found for 'frame' > zoom :8p8 Expected a number or a keyword > zoom -1 > zoom 1 > view > view all > view #1 > help zoom > zoom -1 frames 2 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py", line 258, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2805, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\zoom.py", line 46, in zoom ff = math.pow(factor, 1/frames) ValueError: math domain error ValueError: math domain error File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\zoom.py", line 46, in zoom ff = math.pow(factor, 1/frames) See log for complete Python traceback. > zoom -1 frames 2 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\cmd_line\tool.py", line 258, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2805, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\zoom.py", line 46, in zoom ff = math.pow(factor, 1/frames) ValueError: math domain error ValueError: math domain error File "C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\std_commands\zoom.py", line 46, in zoom ff = math.pow(factor, 1/frames) See log for complete Python traceback. > zoom 1 frames 2 > zoom 2 frames 2 > zoom 2 frames 2 > zoom 2 frames 2 > view all > zoom .2 > zoom .002 > view all > view #1 :8p8 No objects specified. > view :8p8 > move z 20 > move z 360 > move z -360 > help view > view :8p8 clip false > view :8p8 clip false > view :8p8 clip true > view :8p8 clip false > view :8p8 clip false > view :8p8 clip false > view #1/A > select #1/A :70 7 atoms, 6 bonds, 1 model selected > help turn > center #1/A :8p8 Unknown command: center #1/A :8p8 > center #1/A :70 Unknown command: center #1/A :70 > view #1 > view #1/A :70 > view #1/A :70 clipping false Expected an integer >= 1 or a keyword > help view > view #1/A :70 clip false > view #1/A :70 clip true > clip false Expected a keyword > view #1/A :70 clip false > view #1 > view #1/A > view #1/A :8P8 No objects specified. > view #1/A :HCA > view #1/A :ICS clip false > select Mo 2 atoms, 1 model selected > color Mo magenta > view all > view #1 > crossfade > view #1/A :ics > view #1 > cel #1/A :70 Unknown command: cel #1/A :70 > select #1/A :70 7 atoms, 6 bonds, 1 model selected > show atoms > show sel atoms > show atoms #1/A :70 Expected ',' or a keyword > show #1/A :70 atoms > view name V70 > viewl #1 Unknown command: viewl #1 > view #1 > view V70 > show #1 atoms > hide #1 cartoons > show #1 atoms > hide #1 cartoons > color #1 by element Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > show #1 atoms > hide #1 cartoons > color #1/A by element Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1/A byelement > select ::name="HOH" 4851 atoms, 2 models selected > delete atoms sel > delete bonds sel > hide #1 atoms > show #1 cartoons > show Mocos > show #!4 models > hide #1 cartoons > show #1 cartoons > color Mocos byelement > show Vcos > color Vcos byelement > view #1 > move y 20 > move y -40 > move y 20 > move y -10 > undo > view #1 > move y -10 > ui mousemode right "move label" > 2dlabels #4.32 xpos 0.707 ypos 0.454 > 2dlabels #4.36 xpos 0.707 ypos 0.453 > 2dlabels #4.31 xpos 0.721 ypos 0.280 > 2dlabels #4.34 xpos 0.721 ypos 0.280 > 2dlabels #4.33 xpos 0.014 ypos 0.303 > 2dlabels #4.37 xpos 0.014 ypos 0.303 > 2dlabels #4.30 xpos 0.197 ypos 0.505 > 2dlabels #4.35 xpos 0.197 ypos 0.505 > 2dlabels #4.23 xpos 0.290 ypos 0.034 > 2dlabels #4.6 xpos 0.628 ypos 0.714 > 2dlabels #4.9 xpos 0.628 ypos 0.713 > 2dlabels #4.18 xpos 0.628 ypos 0.713 > 2dlabels #4.3 xpos 0.377 ypos 0.709 > 2dlabels #4.21 xpos 0.377 ypos 0.709 > 2dlabels #4.10 xpos 0.377 ypos 0.707 > 2dlabels #4.13 xpos 0.157 ypos 0.097 > 2dlabels #4.23 xpos 0.294 ypos 0.012 > 2dlabels #4.11 xpos 0.604 ypos 0.065 > 2dlabels #4.4 xpos 0.604 ypos 0.065 > 2dlabels #4.20 xpos 0.604 ypos 0.065 > 2dlabels #4.8 xpos 0.352 ypos 0.064 > 2dlabels #4.19 xpos 0.352 ypos 0.064 > 2dlabels #4.5 xpos 0.352 ypos 0.063 > show #2 cartoons > show #3 cartoons > 2dlabels #4.12 xpos 0.784 ypos 0.788 > 2dlabels #4.16 xpos 0.783 ypos 0.788 > 2dlabels #4.4 xpos 0.617 ypos 0.061 > 2dlabels #4.11 xpos 0.617 ypos 0.060 > 2dlabels #4.20 xpos 0.618 ypos 0.060 > 2dlabels #4.13 xpos 0.147 ypos 0.044 > 2dlabels #4.17 xpos 0.147 ypos 0.044 > 2dlabels #4.14 xpos 0.686 ypos 0.088 > 2dlabels #4.2 xpos 0.686 ypos 0.089 > hide #4.22 models > help 2dlabels > help 2dlabels > 2dlabels 4.16 text γ Expected 'all' or a 2d label name or a label models specifier or a keyword > 2dlabels #4.16 text γ > 2dlabels #4.17 text γ > 2dlabels #4.12 text γ > 2dlabels #4.13 text γ > 2dlabels #4.40 text γ⠈ > 2dlabels #4.26 xpos 0.275 ypos 0.800 > 2dlabels #4.40 xpos 0.468 ypos 0.756 > 2dlabels #4.40 text γ₈ > 2dlabels #4.40 text γ₂ > 2dlabels #4.42 text γ₂ > 2dlabels #4.40 xpos 0.140 ypos 0.837 > 2dlabels #4.26 xpos 0.481 ypos 0.775 > 2dlabels #4.29 xpos 0.481 ypos 0.776 > 2dlabels #4.41 xpos 0.480 ypos 0.776 > 2dlabels #4.42 xpos 0.445 ypos 0.782 > show #4.22 models > view name master > 2dlabels #4.24 xpos 0.037 ypos 0.723 > view master > view master > 2dlabels #4.13 xpos 0.141 ypos 0.043 > 2dlabels #4.13 xpos 0.138 ypos 0.043 > 2dlabels #4.17 xpos 0.138 ypos 0.043 > 2dlabels #4.2 xpos 0.691 ypos 0.081 > 2dlabels #4.14 xpos 0.691 ypos 0.081 > 2dlabels #4.25 xpos 0.346 ypos 0.785 > 2dlabels #4.28 xpos 0.466 ypos 0.777 > move #4.28 x -2 Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z" or two atoms > move #4.28 x -2 Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z" or two atoms > move #4.28 x 7 Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z" or two atoms > move #4.28 x Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z" or two atoms > move #1 x 120 Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 16066 atoms > help move > select #4.28 1 model selected > move x -2 > move x -2 #4.28 Expected an integer >= 1 or a keyword > view master > help 2dlabel > 2dlabels #4.42 xpos 0.441 ypos 0.777 > 2dlabels #4.28 xpos 0.409 ypos 0.776 > 2dlabels #4.27 xpos 0.287 ypos 0.811 > 2dlabels #4.27 xpos 0.374 ypos 0.777 > 2dlabels #4.40 xpos 0.441 ypos 0.777 > 2dlabels #4.39 xpos 0.409 ypos 0.776 > 2dlabels #4.38 xpos 0.374 ypos 0.777 > 2dlabels #4.25 xpos 0.408 ypos 0.775 > 2dlabels #4.25 xpos 0.439 ypos 0.777 > 2dlabels #4.24 xpos 0.408 ypos 0.775 > 2dlabels #4.1 xpos 0.388 ypos 0.834 > 2dlabels #4.1 xpos 0.389 ypos 0.828 > 2dlabels #4.7 xpos 0.402 ypos 0.828 > 2dlabels #4.15 xpos 0.378 ypos 0.828 > 2dlabels #4.43 xpos 0.262 ypos 0.832 > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > colored_labeled_master_view.cxs" > select #4 44 models selected > ~select #4 Nothing selected > hide #!4 models > view V70 > crossfade > view master > view V70 > hide #1 cartoons > hide #3 cartoons > hide #2 cartoons > color Mo magenta Drag select of 30 atoms, 48 bonds Drag select of 30 atoms, 48 bonds > name frozen P sel "P" is reserved and cannot be redefined > name frozen Pclust sel > name frozen Pclust sel > hide Pclust > view V70 > crossfade > view master > view V70 > hide #1 cartoons > hide #3 cartoons > hide #2 cartoons > crossfade > view master > view V70 > hide #1 cartoons > hide #3 cartoons > hide #2 cartoons > view master > view master > crossfade > view master > view V70 > hide #1 cartoons > hide #3 cartoons > hide #2 cartoons > view master > crossfade > view master > view V70 > hide #1 cartoons > hide #3 cartoons > hide #2 cartoons > view master > show #1 cartoons > crossfade > view #1/A > view V70 > hide #1 cartoons > open Sccript.cxc > crossfade > view master > crossfade > show #1 cartoons > crossfade > view #1/A > crossfade > view V70 > crossfade > hide cartoons #1 Expected ',' or a keyword > open Sccript.cxc > crossfade > view master > crossfade > show #1 cartoons > crossfade > view #1/A > crossfade > view V70 > crossfade > hide cartoons #1 Expected ',' or a keyword > view master > open Sccript.cxc > crossfade > view master > wait 10 > crossfade > show #1 cartoons > wait 10 > crossfade > view #1/A > wait 10 > crossfade > view V70 > wait 10 > crossfade > hide cartoons #1 Expected ',' or a keyword > open Sccript.cxc > crossfade > view master > wait 100 > crossfade > show #1 cartoons > wait 100 > crossfade > view #1/A > wait 100 > crossfade > view V70 > wait 100 > crossfade > hide #1 cartoons executed Sccript.cxc > master view Unknown command: master view > view master > show #1 cartoons > select V70 Expected an objects specifier or a keyword > select #1/A :70 7 atoms, 6 bonds, 1 model selected > show #!4 models > view master > hide #!4 models > select #1/C :70 7 atoms, 6 bonds, 1 model selected > view > view master > view #1/C :70 > view #1/C :70 clip falsh Invalid "clip" argument: Expected true or false (or 1 or 0) > view #1/C :70 clip false > show #1/C :70 atoms > color #1/C :70 byelement > view name V70 > view master > clear sel Unknown command: clear sel > select clear > view V70 > hide #1/C :70 atoms > view master > open Sccript.cxc > crossfade > view master > wait 100 > crossfade > show #1 cartoons > wait 100 > crossfade > view #1/C > wait 100 > crossfade > view V70 > wait 100 > crossfade > hide #1 cartoons executed Sccript.cxc > view master > show #1 cartoons > view :ics > view master > view #1/C :ics > view #1/C :ics clip false > clip true Expected a keyword > hide #1 cartoons > show #1/C :70 > view name FeMoco No visible atoms or bonds selected > select clear > view name FeMoco > view master > view FeMoco > view master > show #1 cartoons > view #1/C > ui mousemode right clip > ui mousemode right clip > ui mousemode right "clip rotate" > ui mousemode right clip > ui mousemode right clip > ui mousemode right "move label" > ui mousemode right select > select #1/D:171 9 atoms, 8 bonds, 1 model selected > select clear > view mnaster Expected an objects specifier or a view name or a keyword > view master > show #!4 models > show Mocos > show Vcos > show Pclust > hide Pclust > show Pclust > how Vcos Unknown command: how Vcos > hide #!4 models > help crossfade > crossfade > hide #1 cartoons > show #1 cartoons > crossfade > hide #1 cartoons > wait 30 > crossfade > hide #1 cartoons > show #1 cartoons > crossfade > hide #1 cartoons > show #1 cartoons > crossfade > hide #1 cartoons > show #1 cartoons > crossfade > hide #1 cartoons > wait 30 > show #1 cartoons > crossfade > hide #1 cartoons > wait 30 > show #1 cartoons > crossfade > hide #1 cartoons > wait 30 > crossfade > show #1 cartoons > crossfade 100 > hide #1 cartoons > wait 30 > crossfade 100 > show #1 cartoons > crossfade 100 > hide #1 cartoons > wait 30 > crossfade 100 > show #1 cartoons > crossfade 100 > hide #1 cartoons > wait 100 > crossfade 100 > show #1 cartoons > crossfade 100 > hide #1 cartoons > wait 100 > crossfade 100 > show #1 cartoons > hide #1 cartoons > hide Mocos > hide Vcos > hide #1/C :70 atoms > open Sccript.cxc > crossfade > show #1 cartoons > show Mocos > wait 50 > show #4.1 > show #4.2 > wait 50 > show #4.24 > show #4.25 > show #4.26 > wait 50 > show #4.5 > wait 25 > show #4.6 > wait 25 > show #4.3 > wait 25 > show #4.4 > wait 25 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 executed Sccript.cxc > hide #!4 models > show #!4 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.14 models > hide #4.15 models > hide #4.16 models > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.20 models > hide #4.21 models > hide #4.22 models > hide #4.23 models > hide #4.27 models > hide #4.28 models > hide #4.29 models > hide #4.34 models > hide #4.35 models > hide #4.37 models > hide #4.36 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #4.42 models > hide #4.43 models > open Sccript.cxc > crossfade > show #1 cartoons > show Mocos > wait 50 > show #4.1 > show #4.2 > wait 50 > show #4.24 > show #4.25 > show #4.26 > wait 50 > show #4.5 > wait 25 > show #4.6 > wait 25 > show #4.3 > wait 25 > show #4.4 > wait 25 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 executed Sccript.cxc > open Sccript.cxc > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > show #4.5 > wait 25 > crossfade > show #4.6 > wait 25 > crossfade > show #4.3 > wait 25 > crossfade > show #4.4 > wait 25 > crossfade > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > crossfade > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 > movie encode C:\Users\dharr\Box\ChimeraX Movie\Movie iterations Expected ',' or a keyword > open Sccript.cxc > movie record Already recording a movie > movie stop > open Sccript.cxc > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > show #4.5 > wait 25 > crossfade > show #4.6 > wait 25 > crossfade > show #4.3 > wait 25 > crossfade > show #4.4 > wait 25 > crossfade > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > crossfade > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 > movie encode C:\Users\dharr\Box\ChimeraX Movie\Movie iterations\test1.mp4 Expected ',' or a keyword > movie stop > help movie > output browse Unknown command: output browse > output browse Unknown command: movie output browse > movie encode output Missing "output" keyword's argument > open Sccript.cxc > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > show #4.5 > wait 25 > crossfade > show #4.6 > wait 25 > crossfade > show #4.3 > wait 25 > crossfade > show #4.4 > wait 25 > crossfade > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > crossfade > hide Mocos > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test1" Unrecognized movie file suffix test1, use *.ogv, *.mov, *.mp4, *.avi, *.wmv, *.webm > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test1.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test1.mp4 > show #1 cartoons > show Mocos Drag select of 61 residues > select clear > ui mousemode right select > ui mousemode right select > ui mousemode right rotate > view master > hide Pclust > show Pclust > hide Vcos > select :clf 60 atoms, 96 bonds, 2 models selected > show Vcos > select clear > select #1 :clf 30 atoms, 48 bonds, 1 model selected > name frozen MPclust sel > select clear > show Vcos > select #2 :clf 30 atoms, 48 bonds, 1 model selected > name frozen VPclust sel > view master > hide Vcos > select clear > view master > show #4.1 models > show #4.2 models > show #4.4 models > show #4.3 models > show #4.5 models > show #4.6 models > show #4.9 models > show #4.7 models > show #4.8 models > show #4.10 models > show #4.11 models > show #4.12 models > show #4.13 models > show #4.14 models > show #4.15 models > show #4.16 models > show #4.17 models > show #4.18 models > show #4.19 models > show #4.20 models > show #4.21 models > show #4.22 models > show #4.23 models > show #4.24 models > show #4.25 models > show #4.26 models > show #4.27 models > show #4.28 models > show #4.29 models > show #4.30 models > show #4.31 models > show #4.32 models > show #4.33 models > show #4.34 models > show #4.35 models > show #4.36 models > show #4.37 models > show #4.38 models > show #4.39 models > show #4.42 models > show #4.43 models > show #4.40 models > show #4.41 models > view master > show #2 cartoons > show #3 cartoons > ui mousemode right "move label" > view master > 2dlabels #4.24 xpos 0.407 ypos 0.775 > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.14 models > hide #4.15 models > hide #4.16 models > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.20 models > hide #4.21 models > hide #4.22 models > hide #4.23 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #4.27 models > hide #4.28 models > hide #4.29 models > hide #4.30 models > hide #4.31 models > hide #4.33 models > hide #4.34 models > hide #4.35 models > hide #4.32 models > hide #4.36 models > hide #4.37 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #4.42 models > hide #4.43 models > hide #!4 models > hide #2 cartoons > hide #3 cartoons > hide #1/A,C > hide #1/A,C cartoons > show #1/A,C > hide #1/B,D > show #1/A,C cartoons > hide #1/B,D cartoons > hide atoms > show #1 cartoons > show Mocos > view master > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 25 > crossfade > hide #1/A,C cartoons > show #1/B,D > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 25 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 25 > hide atoms > show #1 cartoons > view master > hide #4.3 models > hide #4.4 models > select up Nothing selected > select up Nothing selected > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 25 > hide #4.3 models > hide #4.4 models > hide #1 cartoons > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > hide atoms > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > wait 50 > crossfade > hide #1 cartoons > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > wait 50 > 2dlabels text '(in α subunit) font arial color cyan bold true size 20 Invalid "text" argument: incomplete quoted text > 2dlabels text "(in α subunit)" font arial color cyan bold true size 20 > 2dlabels #4.44 xpos 0.773 ypos 0.418 > 2dlabels text "(in α subunit)" font arial color cyan bold true size 20 > 2dlabels #4.45 xpos 0.082 ypos 0.263 > 2dlabels text "(bridges α-β subunits)" font arial color cyan bold true size > 20 > 2dlabels #4.46 xpos 0.053 ypos 0.468 > 2dlabels #4.30 xpos 0.128 ypos 0.510 > 2dlabels text "(bridges α-β subunits)" font arial color cyan bold true size > 20 > 2dlabels #4.47 xpos 0.726 ypos 0.246 > 2dlabels #4.31 xpos 0.795 ypos 0.294 > 2dlabels #4.47 xpos 0.724 ypos 0.257 > 2dlabels #4.31 xpos 0.794 ypos 0.295 > show #4.34 models > show #4.35 models > show #4.36 models > show #4.37 models > 2dlabels #4.34 xpos 0.794 ypos 0.294 > 2dlabels #4.35 xpos 0.128 ypos 0.510 > 2dlabels text "(bridges α-β subunits)" font arial color medium sea green > bold true size 20 > 2dlabels text "(bridges α-β subunits)" font arial color medium sea green > bold true size 20 > 2dlabels #4.48 xpos 0.724 ypos 0.257 > 2dlabels #4.49 xpos 0.053 ypos 0.468 > select up Nothing selected > select up Nothing selected > 2dlabels text "(in α subunit)" font arial color medium sea green bold true > size 20 > 2dlabels text "(in α subunit)" font arial color medium sea green bold true > size 20 > 2dlabels #4.50 xpos 0.773 ypos 0.418 > 2dlabels #4.51 xpos 0.082 ypos 0.263 > hide Mocos > hide #!4 models > hide #4.30 models > hide #4.31 models > hide #4.32 models > hide #4.33 models > hide #4.34 models > hide #4.35 models > hide #4.36 models > hide #4.37 models > show #4.43 models > hide #4.44 models > hide #4.43 models > hide #4.45 models > hide #4.46 models > hide #4.47 models > hide #4.48 models > hide #4.49 models > hide #4.50 models > hide #4.51 models > open MScript.cxc > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test2.mp4 executed MScript.cxc > help roll > cofr #1 > roll y 1 360 > stop > view master > roll x 1 360 > hide #4.44 models > hide #4.45 models > hide #4.46 models > hide #4.47 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #4.6 models > hide #4.5 models > hide #4.4 models > hide #4.3 models > hide #4.2 models > hide #4.1 models > hide #!4 models > hide Mocos > hide #1 cartoons > open MScript.cxc > view master > cofr #1 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test3.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test3.mp4 executed MScript.cxc > open MScript.cxc > view master > cofr #1 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > movie stop > hide #1 cartoons > hide Mocos > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #!4 models > open Mscript.cxc > view master > cofr #1 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test4.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test4.mp4 executed Mscript.cxc > movie stop No movie being recorded. > movie stop No movie being recorded. > open MScript.cxc > view master > cofr #1 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > movie stop > movie stop Not currently recording > hide #4.1 models > hide #!4 models > hide #4.2 models > hide #4.6 models > hide #4.5 models > hide #4.4 models > hide #4.3 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide Mocos > hide #1 cartoons > open MScript.cxc > view master > cofr #1 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test5.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test5.mp4 executed MScript.cxc > hide #1 cartoons > movie stop No movie being recorded. > show #4.7 models > show #4.8 models > show #4.9 models > show #4.10 models > show #4.11 models > show #4.12 models > show #4.13 models > show #4.14 models > show #4.15 models > show #4.16 models > show #4.17 models > show #4.18 models > show #4.19 models > show #4.21 models > show #4.20 models > show #4.22 models > show #4.23 models > show #4.27 models > show #4.28 models > show #4.29 models > show #4.31 models > show #4.32 models > show #4.30 models > show #4.33 models > show #4.34 models > show #4.36 models > show #4.35 models > show #4.37 models > show #4.38 models > show #4.39 models > show #4.40 models > show #4.41 models > show #4.42 models > show #4.43 models > show #4.45 models > show #4.44 models > show #4.46 models > show #4.47 models > show #4.48 models > show #4.49 models > show #4.50 models > show #4.51 models > show Vcos > show #1 cartoons > show #2 cartoons > show #3 cartoons > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > colored_labeled_master_view.cxs" > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.14 models > hide #4.15 models > hide #4.16 models > hide #4.17 models > hide #4.18 models > hide #4.19 models > hide #4.21 models > hide #4.20 models > hide #4.22 models > hide #4.23 models > hide #4.24 models > hide #4.25 models > hide #4.27 models > hide #4.26 models > hide #4.29 models > hide #4.28 models > hide #4.31 models > hide #4.30 models > hide #4.32 models > hide #4.33 models > hide #4.34 models > hide #4.35 models > hide #4.36 models > hide #4.37 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #4.42 models > hide #4.43 models > hide #4.44 models > hide #4.45 models > hide #4.46 models > hide #4.47 models > hide #4.48 models > hide #4.49 models > hide #4.50 models > hide #4.51 models > hide Mocos > hide Vcos > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > colored_labeled_master_view.cxs" > open MScript.cxc > view master > cofr #1 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test6.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test6.mp4 executed MScript.cxc > view master > hide #1 cartoons > hide Mocos > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > open VScript.cxc > view master > cofr #1 > movie record > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,D cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,C cartoons > show #2/B,D cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,D cartoons > show #2/C,F cartoons > hide 4.10;hide 4.11;show #4.12;show 4.13;wait 50 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #2 cartoons > color #2/A,D medium sea green > color #2/B,E forest green > color #3/C,E light green > color #3/C,E light salmon > color #2/C,E light green > color #2/C,F light green > hide #2 cartoons > hide #4.7 models > hide #4.10 models > hide #4.11 models > hide #4.14 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #!4 models > open VScript.cxc > view master > cofr #1 > movie record Already recording a movie > movie stop > movie stop Not currently recording > movie stop Not currently recording > movie stop Not currently recording > movie stop Not currently recording > movie encode "C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/throwaway" Unrecognized movie file suffix throwaway, use *.ogv, *.mov, *.mp4, *.avi, *.wmv, *.webm > movie encode "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/throwaway.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/throwaway.mp4 > open VScript.cxc > view master > cofr #1 > movie record > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,D cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,D cartoons > show #2/B,E cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,E cartoons > show #2/C,F cartoons > hide #4.10 > hide #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #2 cartoons > hide #4.12 > hide #4.13 > wait 50 > crossfade > show Vcos > show #4.34 > show #4.35 > show #4.36 > show #4.37 > show #4.48 > show #4.49 > show #4.50 > show #4.51 > wait 50 > crossfade > show #2 cartoons > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > hide #4.48 > hide #4.49 > hide #4.50 > hide #4.51 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/throwaway2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/throwaway2.mp4 executed VScript.cxc > hide #2 cartoons > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.13 models > hide #4.14 models > hide #4.12 models > color Vcos byelement > hide Vcos > open VScript.cxc > view master > cofr #1 > movie record > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,D cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,D cartoons > show #2/B,E cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,E cartoons > show #2/C,F cartoons > hide #4.10 > hide #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #2 cartoons > hide #4.12 > hide #4.13 > wait 50 > crossfade > show Vcos > show #4.34 > show #4.35 > show #4.36 > show #4.37 > show #4.48 > show #4.49 > show #4.50 > show #4.51 > wait 50 > crossfade > show #2 cartoons > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > hide #4.48 > hide #4.49 > hide #4.50 > hide #4.51 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/testV1.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/testV1.mp4 executed VScript.cxc > crossfade > hide Vcos > hide #2/B,E cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > hide #2 cartoons > hide #!4 models > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.12 models > hide #4.11 models > hide #4.13 models > hide #4.14 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > open VScript.cxc > view master > cofr #1 > movie record > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,E cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,D cartoons > show #2/B,E cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,E cartoons > show #2/C,F cartoons > hide #4.10 > hide #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #2 cartoons > hide #4.12 > hide #4.13 > wait 50 > crossfade > show Vcos > show #4.34 > show #4.35 > show #4.36 > show #4.37 > show #4.48 > show #4.49 > show #4.50 > show #4.51 > wait 50 > crossfade > show #2 cartoons > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > hide #4.48 > hide #4.49 > hide #4.50 > hide #4.51 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/testV2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/testV2.mp4 executed VScript.cxc > hide #2 cartoons > show #3 cartoons > color #3/a,d salmon > color #3/b,e tomato > color #3/c,f light salmon > hide Vcos > hide #4.7 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.14 models > hide #!4 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #3 cartoons > open FScript.cxc > view master > cofr #1 > movie record > crossfade > show #3 cartoons > wait 50 > crossfade > show #4.15 > show #4.23 > wait 50 > crossfade > show #4.27 > show #4.28 > show #4.42 > show #4.29 > wait 50 > crossfade > hide #3/B,E cartoons > hide #3/C,F cartoons > show #4.18 > show #4.19 > wait 50 > crossfade > hide #3/A,D cartoons > show #3/B,E cartoons > hide #4.18 > hide #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #3/B,E cartoons > show #3/C,F cartoons > hide #4.20 > hide #4.21 > show #4.16 > show #4.17 > wait 50 > crossfade > hide #4.16 > hide #4.17 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/testF2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/testF2.mp4 executed FScript.cxc > hide #3 cartoons > hide #4.23 models > hide #4.27 models > hide #4.28 models > hide #4.29 models > hide #4.42 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.15 models > open FScript.cxc > view master > cofr #1 > movie record > crossfade > show #3 cartoons > wait 50 > crossfade > show #4.15 > show #4.23 > wait 50 > crossfade > show #4.27 > show #4.28 > show #4.42 > show #4.29 > wait 50 > crossfade > hide #3/B,E cartoons > hide #3/C,F cartoons > show #4.18 > show #4.19 > wait 50 > crossfade > hide #3/A,D cartoons > show #3/B,E cartoons > hide #4.18 > hide #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #3/B,E cartoons > show #3/C,F cartoons > hide #4.20 > hide #4.21 > show #4.16 > show #4.17 > wait 50 > crossfade > show #3 cartoons > hide #4.16 > hide #4.17 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.16 > show #4.17 > show #4.18 > show #4.19 > show #4.20 > show #4.21 > wait 50 > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/testF3.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/testF3.mp4 executed FScript.cxc > show #4.1 models > show #4.2 models > show #4.3 models > hide #4.2 models > show #4.2 models > show #4.4 models > show #4.5 models > show #4.6 models > show #4.7 models > show #4.8 models > show #4.9 models > show #4.10 models > show #4.11 models > show #4.12 models > show #4.13 models > show #4.14 models > show #4.22 models > show #4.24 models > show #4.25 models > show #4.26 models > show #4.30 models > show #4.31 models > show #4.33 models > show #4.32 models > show #4.34 models > show #4.35 models > show #4.36 models > show #4.37 models > show #4.39 models > show #4.38 models > show #4.40 models > show #4.41 models > show #4.43 models > show #4.44 models > show #4.45 models > show #4.46 models > show #4.47 models > show #4.48 models > show #4.49 models > show #4.50 models > show #4.51 models > 2dlabels #4.43 xpos 0.268 ypos 0.914 > 2dlabels #4.1 xpos 0.377 ypos 0.909 > 2dlabels #4.7 xpos 0.399 ypos 0.908 > 2dlabels #4.15 xpos 0.385 ypos 0.908 > 2dlabels #4.26 xpos 0.480 ypos 0.863 > 2dlabels #4.29 xpos 0.480 ypos 0.863 > 2dlabels #4.41 xpos 0.480 ypos 0.863 > 2dlabels #4.25 xpos 0.443 ypos 0.864 > 2dlabels #4.24 xpos 0.407 ypos 0.864 > 2dlabels #4.40 xpos 0.444 ypos 0.865 > 2dlabels #4.42 xpos 0.445 ypos 0.865 > 2dlabels #4.28 xpos 0.409 ypos 0.864 > 2dlabels #4.39 xpos 0.409 ypos 0.864 > 2dlabels #4.27 xpos 0.370 ypos 0.865 > 2dlabels #4.27 xpos 0.369 ypos 0.865 > 2dlabels #4.38 xpos 0.369 ypos 0.865 > 2dlabels #4.12 xpos 0.870 ypos 0.896 > 2dlabels #4.16 xpos 0.859 ypos 0.861 > 2dlabels #4.6 xpos 0.711 ypos 0.831 > 2dlabels #4.9 xpos 0.619 ypos 0.822 > 2dlabels #4.6 xpos 0.646 ypos 0.836 > 2dlabels #4.18 xpos 0.657 ypos 0.818 > 2dlabels #4.3 xpos 0.360 ypos 0.811 > 2dlabels #4.10 xpos 0.390 ypos 0.809 > 2dlabels #4.21 xpos 0.380 ypos 0.820 > show #1 cartoons > show #1 cartoons > show #2 cartoons > ui mousemode right "translate selected models" > hide #2 cartoons > hide #1 cartoons > hide #3 cartoons > show #1 cartoons > show #3 cartoons > hide #3 cartoons > ui mousemode right "move label" > 2dlabels #4.6 xpos 0.637 ypos 0.817 > 2dlabels #4.9 xpos 0.637 ypos 0.816 > 2dlabels #4.18 xpos 0.637 ypos 0.816 > 2dlabels #4.3 xpos 0.372 ypos 0.785 > 2dlabels #4.21 xpos 0.373 ypos 0.785 > 2dlabels #4.10 xpos 0.372 ypos 0.785 > 2dlabels #4.5 xpos 0.357 ypos 0.220 > 2dlabels #4.8 xpos 0.357 ypos 0.221 > 2dlabels #4.19 xpos 0.357 ypos 0.221 > 2dlabels #4.4 xpos 0.608 ypos 0.225 > 2dlabels #4.11 xpos 0.608 ypos 0.226 > 2dlabels #4.20 xpos 0.609 ypos 0.226 > hide #1 cartoons > show Mocos > show Vcos > 2dlabels #4.32 xpos 0.701 ypos 0.582 > 2dlabels #4.44 xpos 0.772 ypos 0.546 > 2dlabels #4.36 xpos 0.701 ypos 0.583 > 2dlabels #4.50 xpos 0.772 ypos 0.546 > 2dlabels #4.31 xpos 0.785 ypos 0.445 > 2dlabels #4.47 xpos 0.716 ypos 0.408 > 2dlabels #4.34 xpos 0.785 ypos 0.444 > 2dlabels #4.48 xpos 0.716 ypos 0.408 > 2dlabels #4.30 xpos 0.133 ypos 0.606 > 2dlabels #4.35 xpos 0.133 ypos 0.607 > 2dlabels #4.46 xpos 0.058 ypos 0.571 > 2dlabels #4.49 xpos 0.058 ypos 0.571 > 2dlabels #4.33 xpos 0.020 ypos 0.466 > 2dlabels #4.37 xpos 0.020 ypos 0.466 > 2dlabels #4.45 xpos 0.096 ypos 0.423 > 2dlabels #4.51 xpos 0.096 ypos 0.423 > show #3 cartoons > show #2 cartoons > 2dlabels #4.13 xpos 0.188 ypos 0.165 > 2dlabels #4.17 xpos 0.187 ypos 0.164 > 2dlabels #4.16 xpos 0.798 ypos 0.840 > 2dlabels #4.12 xpos 0.798 ypos 0.841 > 2dlabels #4.2 xpos 0.689 ypos 0.178 > show cartoons #1 Expected ',' or a keyword > show #1 cartoons > 2dlabels #4.4 xpos 0.613 ypos 0.219 > 2dlabels #4.11 xpos 0.613 ypos 0.218 > 2dlabels #4.20 xpos 0.613 ypos 0.218 > 2dlabels #4.2 xpos 0.681 ypos 0.246 > 2dlabels #4.14 xpos 0.682 ypos 0.246 > 2dlabels #4.23 xpos 0.304 ypos 0.162 > view name master > view master > hide cartoons > show cartoons > hide 2dlabels Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #4 > move x 120 #1 Expected an integer >= 1 or a keyword > move #1 x 120 Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 16066 atoms > move x 120 > move x -120 > move x 120 models #3 > move x-120 model #1 Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z" or two atoms > move x -120 models #1 > views Unknown command: views > view > move x 10 models #3 > move x -10 models #1 > roll x 1 360 > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > move x 120 > view master > roll x 360 1 > roll x 1 360 > roll x 1 360 > roll y 1 360 > move x 130 models #3 > move x -130 models #1 > view > view three Expected an objects specifier or a view name or a keyword > view row Expected an objects specifier or a view name or a keyword > view name three > view master > show #!4 models > show #4.1 models > show #4.2 models > show #4.3 models > show #4.4 models > show #4.5 models > show #4.6 models > show #4.7 models > show #4.8 models > show #4.9 models > show #4 > open AScript.cxc > movie record > crossfade > hide #4 > hide cartoons > hide Mocos > hide Vcos > wait 50 > move x 130 models #3 > move x -130 models #1 > view three > crossfade > show cartoons > show Mocos > show Vcos > wait 50 > crossfade > color #1 cyan > color #2 medium sea green > color #3 salmon > wait 50 > roll x 1 360 > wait > crossfade > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > crossfade > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/testA.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/testA.mp4 executed AScript.cxc > view master > show 2dlabels Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #4 > color Vcos byelement > color Mocos byelement > open AScript.cxc > movie record > crossfade > hide #4 > hide cartoons > hide Mocos > hide Vcos > wait 50 > move x 130 models #3 > move x -130 models #1 > view three > crossfade > show cartoons > show Mocos > show Vcos > wait 50 > crossfade > color #1 cyan > color #2 medium sea green > color #3 salmon > color Mocos byelement > color Vcos byelement > wait 50 > roll x 1 360 > wait > crossfade > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > crossfade > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > crossfade > view master > show #4.43 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/testA2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/testA2.mp4 executed AScript.cxc > hide all > hide cartoons > hide #4 > show #1 cartoons > color #1/b,d dodger blue > show Mocos > color Mocos byelement > hide #1 cartoons > show hide Mocos Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide Mocos > show #1 cartoons > hide #1 cartoons > show #2 cartoons > show Vcos > color #2/b,e forest green > color #2/c,f light green > color Vcos byelement > hide #2 cartoons > hide Vcos > show #3 cartoons > color #3/b,e tomato > color #3/c,f light salmon > view master > show #1 cartoons > show #2 cartoons > show #4 > show Vcos > show Mocos > open Script.cxc > view master > cofr #1 > hide all > hide cartoons > hide #4 > wait 50 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,E cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,D cartoons > show #2/B,E cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,E cartoons > show #2/C,F cartoons > hide #4.10 > hide #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #2 cartoons > hide #4.12 > hide #4.13 > wait 50 > crossfade > show Vcos > show #4.34 > show #4.35 > show #4.36 > show #4.37 > show #4.48 > show #4.49 > show #4.50 > show #4.51 > wait 50 > crossfade > show #2 cartoons > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > hide #4.48 > hide #4.49 > hide #4.50 > hide #4.51 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > show #3 cartoons > wait 50 > crossfade > show #4.15 > show #4.23 > wait 50 > crossfade > show #4.27 > show #4.28 > show #4.42 > show #4.29 > wait 50 > crossfade > hide #3/B,E cartoons > hide #3/C,F cartoons > show #4.18 > show #4.19 > wait 50 > crossfade > hide #3/A,D cartoons > show #3/B,E cartoons > hide #4.18 > hide #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #3/B,E cartoons > show #3/C,F cartoons > hide #4.20 > hide #4.21 > show #4.16 > show #4.17 > wait 50 > crossfade > show #3 cartoons > hide #4.16 > hide #4.17 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.16 > show #4.17 > show #4.18 > show #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #4 > hide cartoons > hide Mocos > hide Vcos > wait 50 > move x 130 models #3 > move x -130 models #1 > view three > crossfade > show cartoons > show Mocos > show Vcos > wait 50 > crossfade > color #1 cyan > color #2 medium sea green > color #3 salmon > color Mocos byelement > color Vcos byelement > wait 50 > roll x 1 360 > wait > crossfade > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > crossfade > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > crossfade > view master > show #4.43 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test_final1.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test_final1.mp4 executed Script.cxc > view master > color #1/b,d dodger blue > color #2/b,e forest green > color #2/c,f light green > color #3/b,e tomato > color #3/c,f light salmon > color Vcos byelement > color Mocos byelement > hide all > hide cartoons > hide #4 > open Script.cxc > view master > cofr #1 > hide all > hide cartoons > hide #4 > wait 50 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > crossfade > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > hide Mocos > hide #2 cartoons > wait 50 > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,E cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,D cartoons > show #2/B,E cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,E cartoons > show #2/C,F cartoons > hide #4.10 > hide #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #2 cartoons > hide #4.12 > hide #4.13 > wait 50 > crossfade > show Vcos > show #4.34 > show #4.35 > show #4.36 > show #4.37 > show #4.48 > show #4.49 > show #4.50 > show #4.51 > wait 50 > crossfade > show #2 cartoons > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > hide #4.48 > hide #4.49 > hide #4.50 > hide #4.51 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > hide Vcos > hide #2 cartoons > wait 50 > crossfade > show #3 cartoons > wait 50 > crossfade > show #4.15 > show #4.23 > wait 50 > crossfade > show #4.27 > show #4.28 > show #4.42 > show #4.29 > wait 50 > crossfade > hide #3/B,E cartoons > hide #3/C,F cartoons > show #4.18 > show #4.19 > wait 50 > crossfade > hide #3/A,D cartoons > show #3/B,E cartoons > hide #4.18 > hide #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #3/B,E cartoons > show #3/C,F cartoons > hide #4.20 > hide #4.21 > show #4.16 > show #4.17 > wait 50 > crossfade > show #3 cartoons > hide #4.16 > hide #4.17 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.16 > show #4.17 > show #4.18 > show #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #4 > hide cartoons > hide Mocos > hide Vcos > wait 50 > move x 130 models #3 > move x -130 models #1 > view three > crossfade > show cartoons > show Mocos > show Vcos > wait 50 > crossfade > color #1 cyan > color #2 medium sea green > color #3 salmon > color Mocos byelement > color Vcos byelement > wait 50 > roll x 1 360 > wait > crossfade > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > crossfade > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > crossfade > view master > show #4.43 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test_final2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test_final2.mp4 executed Script.cxc > view master > hide all > hide cartoons > hide #4 > open Script.cxc > view master > cofr #1 > hide all > hide cartoons > hide #4 > wait 50 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > crossfade > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > hide Mocos > hide #1 cartoons > wait 50 > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,E cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,D cartoons > show #2/B,E cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,E cartoons > show #2/C,F cartoons > hide #4.10 > hide #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #2 cartoons > hide #4.12 > hide #4.13 > wait 50 > crossfade > show Vcos > show #4.34 > show #4.35 > show #4.36 > show #4.37 > show #4.48 > show #4.49 > show #4.50 > show #4.51 > wait 50 > crossfade > show #2 cartoons > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > hide #4.48 > hide #4.49 > hide #4.50 > hide #4.51 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #4.7 > hide #4.38 > hide #4.39 > hide #4.40 > hide #4.41 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > hide Vcos > hide #2 cartoons > wait 50 > crossfade > show #3 cartoons > wait 50 > crossfade > show #4.15 > show #4.23 > wait 50 > crossfade > show #4.27 > show #4.28 > show #4.42 > show #4.29 > wait 50 > crossfade > hide #3/B,E cartoons > hide #3/C,F cartoons > show #4.18 > show #4.19 > wait 50 > crossfade > hide #3/A,D cartoons > show #3/B,E cartoons > hide #4.18 > hide #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #3/B,E cartoons > show #3/C,F cartoons > hide #4.20 > hide #4.21 > show #4.16 > show #4.17 > wait 50 > crossfade > show #3 cartoons > hide #4.16 > hide #4.17 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.16 > show #4.17 > show #4.18 > show #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #4 > hide cartoons > hide Mocos > hide Vcos > wait 50 > move x 130 models #3 > move x -130 models #1 > view three > crossfade > show cartoons > show Mocos > show Vcos > wait 50 > crossfade > color #1 cyan > color #2 medium sea green > color #3 salmon > color Mocos byelement > color Vcos byelement > wait 50 > roll x 1 360 > wait > crossfade > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > crossfade > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > crossfade > view master > show #4.43 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test_final3.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test_final3.mp4 executed Script.cxc > color #1/b,d dodger blue > color #2/b,e forest green > color #2/c,f light green > hide #1 cartoons > hide #3 cartoons > color Mocos byelement > color Vcos by element Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color Vcos byelement > hide Vcos > hide Mocos > hide #2 cartoons > show #3 cartoons > color #3/b,e tomato > color #3/c,f light salmon > hide #3 cartoons > show #1 cartoons > hide #1 cartoons > show #2 cartoons > hide #2 cartoons > hide #4 > open Script.cxc > view master > cofr #1 > hide all > hide cartoons > hide #4 > wait 50 > movie record > crossfade > show #1 cartoons > show Mocos > wait 50 > crossfade > show #4.1 > show #4.2 > wait 50 > crossfade > show #4.24 > show #4.25 > show #4.26 > wait 50 > crossfade > hide Mocos > hide #1/B,D cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1/A,C cartoons > show #1/B,D cartoons > hide #4.5 > hide #4.6 > show #4.3 > show #4.4 > wait 50 > crossfade > hide #1 cartoons > hide #4.5 > hide #4.6 > hide #4.3 > hide #4.4 > wait 50 > crossfade > show Mocos > show #4.30 > show #4.31 > show #4.32 > show #4.33 > show #4.44 > show #4.45 > show #4.46 > show #4.47 > wait 50 > crossfade > show #1 cartoons > hide #4.30 > hide #4.31 > hide #4.32 > hide #4.33 > hide #4.44 > hide #4.45 > hide #4.46 > hide #4.47 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.4 > show #4.5 > show #4.3 > show #4.6 > wait 50 > crossfade > hide #4.1 > hide #4.2 > hide #4.24 > hide #4.25 > hide #4.26 > hide #4.4 > hide #4.5 > hide #4.3 > hide #4.6 > hide Mocos > hide #1 cartoons > wait 50 > crossfade > show #2 cartoons > show Vcos > wait 50 > crossfade > show #4.7 > show #4.14 > wait 50 > crossfade > show #4.38 > show #4.39 > show #4.40 > show #4.41 > wait 50 > crossfade > hide Vcos > hide #2/B,E cartoons > hide #2/C,F cartoons > show #4.8 > show #4.9 > wait 50 > crossfade > hide #2/A,D cartoons > show #2/B,E cartoons > hide #4.8 > hide #4.9 > show #4.10 > show #4.11 > wait 50 > crossfade > hide #2/B,E cartoons > show #2/C,F cartoons > hide #4.10 > hide #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #2 cartoons > hide #4.12 > hide #4.13 > wait 50 > crossfade > show Vcos > show #4.34 > show #4.35 > show #4.36 > show #4.37 > show #4.48 > show #4.49 > show #4.50 > show #4.51 > wait 50 > crossfade > show #2 cartoons > hide #4.34 > hide #4.35 > hide #4.36 > hide #4.37 > hide #4.48 > hide #4.49 > hide #4.50 > hide #4.51 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.8 > show #4.9 > show #4.10 > show #4.11 > show #4.12 > show #4.13 > wait 50 > crossfade > hide #4.7 > hide #4.38 > hide #4.39 > hide #4.40 > hide #4.41 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > hide #4.12 > hide #4.13 > hide #4.14 > hide Vcos > hide #2 cartoons > wait 50 > crossfade > show #3 cartoons > wait 50 > crossfade > show #4.15 > show #4.23 > wait 50 > crossfade > show #4.27 > show #4.28 > show #4.42 > show #4.29 > wait 50 > crossfade > hide #3/B,E cartoons > hide #3/C,F cartoons > show #4.18 > show #4.19 > wait 50 > crossfade > hide #3/A,D cartoons > show #3/B,E cartoons > hide #4.18 > hide #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #3/B,E cartoons > show #3/C,F cartoons > hide #4.20 > hide #4.21 > show #4.16 > show #4.17 > wait 50 > crossfade > show #3 cartoons > hide #4.16 > hide #4.17 > wait 50 > crossfade > roll x 1 360 > wait > crossfade > roll y 1 360 > wait > crossfade > show #4.16 > show #4.17 > show #4.18 > show #4.19 > show #4.20 > show #4.21 > wait 50 > crossfade > hide #4 > hide cartoons > hide Mocos > hide Vcos > wait 50 > move x 130 models #3 > move x -130 models #1 > view three > crossfade > show cartoons > show Mocos > show Vcos > wait 50 > crossfade > color #1 cyan > color #2 medium sea green > color #3 salmon > color Mocos byelement > color Vcos byelement > wait 50 > roll x 1 360 > wait > crossfade > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > wait 50 > crossfade > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > wait 50 > crossfade > view master > show #4.43 > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Movie > iterations/test_final4.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Movie iterations/test_final4.mp4 executed Script.cxc > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > help chain pairing No help found for 'chain pairing' > help pairing No help found for 'pairing' > help ss No help found for 'ss' > help matchmaker > save "C:/Users/dharr/Box/ChimeraX Movie/All 3 N2ase > colored_labeled_master_view.cxs" opened ChimeraX session > move x 130 models #3 > move x -130 models #1 > view > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" > hide #4.2 models > show #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.6 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > hide #4.12 models > hide #4.13 models > hide #4.16 models > hide #4.17 models > hide #4.18 models > hide #4.20 models > hide #4.19 models > hide #4.21 models > hide #4.22 models > hide #4.23 models > hide #4.24 models > hide #4.25 models > hide #4.26 models > hide #4.27 models > hide #4.28 models > hide #4.29 models > hide #4.30 models > hide #4.31 models > hide #4.32 models > hide #4.33 models > hide #4.34 models > hide #4.35 models > hide #4.36 models > hide #4.37 models > hide #4.38 models > hide #4.39 models > hide #4.40 models > hide #4.41 models > hide #4.42 models > hide #4.43 models > hide #4.44 models > hide #4.45 models > hide #4.46 models > hide #4.48 models > hide #4.47 models > hide #4.49 models > hide #4.50 models > hide #4.51 models > show #4.23 models > ui mousemode right "move label" > 2dlabels #4.1 xpos 0.047 ypos 0.671 > 2dlabels #4.7 xpos 0.390 ypos 0.702 > 2dlabels #4.1 xpos 0.044 ypos 0.705 > 2dlabels #4.15 xpos 0.710 ypos 0.703 > help 2dlabels > ui tool show "Color Actions" > color #1 light sky blue > color #1 lightblue pale turquoise Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1 pale turquoise > color #1 powder blue > color #1 sky blue > color #2 light green > color #3 pale violet red > color #3 plum > color Mocos byelement > color Vcos byelement > help 2dlabels > 2dlabels #4.1 size 20 color sky blue > 2dlabels #4.1 size 30 color sky blue > 2dlabels #4.1 xpos 0.088 ypos 0.684 > 2dlabels #4.2 size 30 color sky blue > 2dlabels #4.2 xpos 0.122 ypos 0.258 > 2dlabels #4.2 size 20 color sky blue > 2dlabels #4.2 xpos 0.103 ypos 0.275 > 2dlabels #4.2 xpos 0.107 ypos 0.280 > 2dlabels #4.2 xpos 0.173 ypos 0.272 > 2dlabels #4.14 size 20 color light green > 2dlabels #4.14 xpos 0.518 ypos 0.273 > 2dlabels #4.7 size 30 color light green > 2dlabels #4.7 xpos 0.250 ypos 0.684 > 2dlabels #4.7 xpos 0.109 ypos 0.684 > move x 130 #4.7 Expected an integer >= 1 or a keyword > move x 130 models #4.7 > move x -130 models #4.7 > move x -13 models #4.7 > move x 13 models #4.7 > move x 1 models #4.7 > move x -1 models #4.7 > move x -10 models #4.7 > move x 10 models #4.7 > move x -2 models #4.7 > move x 2 models #4.7 > 2dlabels #4.1 xpos 0.090 ypos 0.684 > 2dlabels #4.1 xpos 0.090 ypos 0.682 > 2dlabels #4.7 xpos 0.430 ypos 0.684 > 2dlabels #4.15 size 30 color plum > 2dlabels #4.15 xpos 0.749 ypos 0.684 > 2dlabels #4.23 test 'Homology model to PDB: 5N6Y' size 20 color plum Expected a keyword > 2dlabels #4.23 text "Homology model to PDB: 5N6Y" size 20 color plum > 2dlabels #4.23 xpos 0.742 ypos 0.273 > 2dlabels #4.23 text "Homology model to PDB: 5N6Y" size 10 color plum > 2dlabels #4.23 text "Homology model to PDB: 5N6Y" size 15 color plum > 2dlabels #4.23 xpos 0.767 ypos 0.272 > select up Nothing selected > 2dlabels #4.14 size `5 color light green Invalid "size" argument: Expected an integer > 2dlabels #4.14 size 15 color light green > 2dlabels #4.2 size 15 color sky blue > 2dlabels #4.2 xpos 0.170 ypos 0.285 > 2dlabels #4.14 xpos 0.517 ypos 0.278 > 2dlabels #4.2 xpos 0.170 ypos 0.276 > 2dlabels #4.23 xpos 0.766 ypos 0.275 > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" > view master > view name master > 2dlabels text "MoFe protein" font arial bold true size 15 color sky blue > 2dlabels #4.52 xpos 0.186 ypos 0.064 > 2dlabels #4.52 size 20 text "MoFe protein (PDB:3U7Q)" > 2dlabels #4.52 xpos 0.065 ypos 0.031 > 2dlabels labels text 'VFe protein (PDB:5N6Y) font arial bold true color > light green size 20 Invalid "labels" argument: Expected 'all' or a 2d label name or a label models specifier > 2dlabels labels text 'VFe protein (PDB:5N6Y)' font arial bold true color > light green size 20 Invalid "labels" argument: Expected 'all' or a 2d label name or a label models specifier > 2dlabels text "VFe protein (PDB:5N6Y)" font arial bold true color light > green size 20 > 2dlabels #4.53 xpos 0.382 ypos 0.035 > 2dlabels text "FeFe protein (Homology model to PDB:5N6Y)" font arial bold > true color plum size 20 > 2dlabels #4.54 xpos 0.600 ypos 0.036 > 2dlabels #4.53 xpos 0.355 ypos 0.034 > 2dlabels #4.53 xpos 0.356 ypos 0.035 > 2dlabels #4.52 xpos 0.065 ypos 0.034 > hide $4 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #4 > hide cartoons #2 Expected ',' or a keyword > hide #2 cartoons > hide Vcos > hide #3 cartoons > move x 130 models #1 > ui mousemode right "translate selected models" > view name center > show #2 cartoons > show Vcos > hide #2 cartoons > hide Vcos > crossfade > show #2 cartoons > show Vcos > move x -130 models #3 > crossfade > show #3 > crossfade > show #3 cartoons > hide #3 atoms > ui tool show "Color Actions" > 2dlabels text Alignment font arial bold true size 40 color burly wood > show #!4 models > undo > redo > view center > show #3 cartoons > move x -130 models #3 > ui mousemode right "move label" > 2dlabels #4.55 xpos 0.427 ypos 0.859 > view master > view center > move x -130 models #3 > view name center > mmaker #2/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 Matchmaker 3u7q, chain B (#1) with 5n6y, chain B (#2), sequence alignment score = 966.3 Matchmaker 3u7q, chain C (#1) with 5n6y, chain D (#2), sequence alignment score = 1014.6 Matchmaker 3u7q, chain D (#1) with 5n6y, chain E (#2), sequence alignment score = 957.8 RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) > mmaker #3/A,B,D,E to #1/A,B,C,D pair ss Parameters --- Chain pairing | ss 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 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 Matchmaker 3u7q, chain B (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain B (#3), sequence alignment score = 918.6 Matchmaker 3u7q, chain C (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 Matchmaker 3u7q, chain D (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain E (#3), sequence alignment score = 899.3 RMSD between 461 pruned atom pairs is 1.310 angstroms; (across all 1769 pairs: 37.860) > view name center > view name center > 2dlabels #4.26 xpos 0.473 ypos 0.863 > 2dlabels #4.26 xpos 0.465 ypos 0.866 > 2dlabels #4.26 xpos 0.456 ypos 0.870 > 2dlabels #4.26 xpos 0.468 ypos 0.916 > ui mousemode right label > ui mousemode right "move label" > 2dlabels #4.29 xpos 0.239 ypos 0.923 > show #4.54 models > show #4.52 models > show #4.53 models > show #4.51 models > hide #4.51 models > show #4.15 models > show #4.7 models > show #4.1 models > hide #!4 models > show #!4 models > 2dlabels #4.41 xpos 0.658 ypos 0.913 > ui mousemode right label > ui mousemode right "move label" > 2dlabels #4.55 xpos 0.424 ypos 0.899 > roll x 1 360 > roll y 1 360 > cd C:\Users\dharr\Box\ChimeraX Movie\Alignment Expected a keyword > cd C:\Users\dharr\Box\'ChimeraX Movie'\Alignment Expected a keyword > cd C:\Users\dharr\Box\ChimeraX Movie\Alignment Expected a keyword > pwd Current working directory is: C:\ProgramData\ChimeraX > cd "C:/Users/dharr/Box/ChimeraX Movie/Alignment" Current working directory is: C:\Users\dharr\Box\ChimeraX Movie\Alignment > hide #4.26 models > hide #4.29 models > hide #4.41 models > view name center > hide #4.52 models > show #4.52 models > open Script.cxc > movie record > wait 25 > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 25 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 25 > crossfade > show #3 cartoons > show #4.23 > wait 25 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.23 > wait 25 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 25 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 25 > crossfade > show #3 cartoons > show #4.54 > wait 25 > roll y 1 360 > wait > roll x 1 360 > wait > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test1.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test1.mp4 executed Script.cxc > select #1/A :70 7 atoms, 6 bonds, 1 model selected > view #1/A :70 > view #1/A :70 clip false > help rotate No help found for 'rotate' > help roll > view center > show #1/A :70 atoms > color #1/A :70 red > view center > view #1/A > roll x 180 > stop > help roll > help rotate No help found for 'rotate' > help roll > roll y 1 10 > roll y 1 10 > roll y 1 10 > roll y 1 10 > roll y 1 10 > view #1/A > roll -y 180 > stop > view #1/A > view center > view #1/A > roll -y 1 180 > view center > roll -y 1 100 > roll x 1 10 > roll x 1 10 > roll -x 1 10 > roll -x 1 10 > roll -x 1 30 > roll x 1 30 > roll x 1 20 > roll -x 1 20 > roll -x 1 20 > clip true Expected a keyword > help clip > clip > clip off > view #1/A :ics > clip off > view center > roll -y 1 100 > roll -x 1 40 > view center > roll -y 1 100 > roll -x 1 60 > view center > roll -y 1 120 > roll -x 1 100 > view center > view center > view #1/A > view center > crossfade > view #1/A > view #1/A :70 > help crossfade > view center > crossfade 100 > view #1/A > view #1/A :70 > view center > view center > view #1/A > color Mo magenta > view #1/A > view center > view #1/A > roll x 1 100 > roll -x 1 100 > roll -x 1 100 > roll -x 1 20 > roll y 1 10 > roll -y 1 10 > roll x 1 10 > roll x 1 10 > roll x 1 10 > roll x 1 10 > roll x 1 10 > roll -x 1 10 > roll -x 1 10 > roll -x 1 10 > roll -x 1 10 > roll -x 1 10 > roll -x 1 10 > roll -x 1 10 > roll x 1 10 > roll x 1 10 > roll z 1 10 > roll -z 1 100 > roll -z 1 100 > view #1/A > view center > view #1/A > roll x 1 100 > roll -x 1 100 > roll -x 1 100 > roll -x 1 100 > view center > view #1/A > roll -x 1 120 > roll -z 1 120 > view center > crossfade > view #1/A > wait 25 > roll -x 1 120 > wait 25 > roll -z 1 120 > view center > view #1/A > roll -x 1 120 > roll -z 1 120 > view center > view #1/A > roll -x 1 100 > roll -z 1 120 > view center > view #1/A > roll -x 1 80 > roll -z 1 120 > view center > view #1/A > roll -x 1 120 > roll -z 1 120 > help roll > view center > view #1/A > roll -x 1 120 > roll -z 1 150 > roll y 20 > stop > roll -x 1 120 > roll -z 1 150 > roll y 1 20 > view center > view #1/A > roll -x 1 120 > roll -z 1 150 > roll y 1 20 > view center > view #1/A > view center > view #1/A > roll -x 1 120 > wait > roll -z 1 120 > view center > hide cartoons #1 Expected ',' or a keyword > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > show #1/A :70 atoms > show #1/A :70 > view center > roll -x 1 120 > wait > roll -z 1 120 > view center > view #1/A > roll -x 1 120 > wait > roll -z 1 120 > view #1/A :70 > view #1/A :70 clip false > roll x 1 10 > roll -x 1 10 > roll -x 1 10 > roll -z 1 10 > view center > view #1/A > roll -x 1 130 > wait > roll -z 1 130 > view #1/A :70 > roll -x 1 130 > wait > roll -z 1 130 > wait > view #1/A :70 clip false > view center > view #1/A > roll -x 1 130 > wait > roll -z 1 130 > wait > view #1/A :70 clip false > roll -x 1 130 > wait > roll -z 1 120 > wait > view #1/A :70 clip false > view center > view #1/A > roll -x 1 130 > wait > roll -z 1 120 > wait > view #1/A :70 clip false > view center > show #1 cartoons > show #1/A :70 cartoons > hide #1/A :70 atoms > color #1/A :70 sky blue > select clear > hide #1 cartoons > roll -x 1 130 > wait > roll -z 1 120 > wait > view #1/A :ics > view center > view #1/A > roll -x 1 130 > wait > roll -z 1 120 > wait > view #1/A :ics > view center > show #1 cartoons > crossfade 20 > hide #1 cartoons > show #1 cartoons > crossfade 100 > hide #1 cartoons > hide pclust Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide Pclust > show Pclust > show #1 cartoons > show #2 cartoons > show #3 cartoons > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > view #1/A :ics > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > wait wait requires a frame count argument unless motion is in progress > view center > view #1/A > show #1 cartoons > show #2 cartoons > show #3 cartoons > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > view #1/A :ics > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > wait wait requires a frame count argument unless motion is in progress > view master > show #1 cartoons > show #2 cartoons > show #3 cartoons > show Pclust > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > movie record > wait 25 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 25 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 25 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 25 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.23 > wait 25 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 25 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 25 > crossfade > show #3 cartoons > show #4.54 > wait 25 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > view #1/A > wait 25 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > view #1/A :ics > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > wait wait requires a frame count argument unless motion is in progress > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test2.mp4 executed Script.cxc > view center > view #1/A > roll -x 1 130 > roll -z 1 130 > view #1/A :ics > show #1 cartoons > help zoom > zoom .2 > zoome -.2 Unknown command: zoome -.2 > view center > view #1/A > roll -x 1 130 > roll -z 1 130 > show #1 cartoons > show #2 cartoons > show #3 cartoons > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > view #1/A :ics Drag select of 65 atoms, 87 bonds, 4 pseudobonds > name frozen Noco sel > name frozen Noco sel > hide Noco > show Noco > select clear Drag select of 65 atoms, 87 bonds, 4 pseudobonds > name frozen Noco sel > name frozen Noco sel > hide Noco > show Noco > clip false Expected a keyword > ui tool show "Side View" > hide Noco > show Noco > select clear Drag select of 66 atoms, 87 bonds, 4 pseudobonds > name frozen Noco sel > name frozen Noco sel > hide Noco > show Noco > view center > select clear > view master > show #1 cartoons > show #2 cartoons > show #3 cartoons > view center > hide #4 > view #1/A > roll -x 1 130 > roll -z 1 130 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Nocos;hide Pclust Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Noco > hide Pclust > view #1/A :ics > show #1/A :70 atoms > view name Mco > view Mco > hide #1/A :70 > show #1 cartoons > show #2 cartoons > show #3 cartoons > clip false Expected a keyword > help clip > clip off > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons Drag select of 67 atoms, 87 bonds, 4 pseudobonds > name frozen Yesco sel > name frozen Yesco sel > select sel :< 5 772 atoms, 764 bonds, 7 pseudobonds, 5 models selected > select sel :< 5 3700 atoms, 3793 bonds, 15 pseudobonds, 5 models selected > select ~sel 45738 atoms, 46861 bonds, 45 pseudobonds, 61 models selected > hide (#3#!1-2 & sel) target a > show #1 cartoons > show #2 cartoons > show #3 cartoons > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > view Mco Drag select of 67 atoms, 87 bonds, 4 pseudobonds > show #1 cartoons > show #2 cartoons > show #3 cartoons > clip off > select sel :< 5 772 atoms, 764 bonds, 7 pseudobonds, 5 models selected > name frozen 5A sel registering illegal selector name "5A" > name frozen Nearco sel > name frozen Nearco sel > select ~sel 48666 atoms, 49890 bonds, 53 pseudobonds, 61 models selected > hide (#3#!1-2 & sel) target a > cartoon hide (#3#!1-2 & sel) > select Nearco 772 atoms, 764 bonds, 7 pseudobonds, 5 models selected > help show > show atoms > show sel atoms > hide sel cartoons > hide Nearco > show Nearco > view name Nearco > select clear > hide Nearco > show Mocos > show Vcos > view master > show #1 cartoons > show #2 cartoons > show #3 cartoons > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > movie record > wait 25 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 25 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 25 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 25 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hidr #4.15;hide #4.23;wait 25 Unknown command: hidr #4.15;hide #4.23;wait 25 > stop record Expected fewer arguments > record stop Unknown command: record stop > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/throwaway.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/throwaway.mp4 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > movie record > wait 25 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 25 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 25 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 25 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hidr #4.15;hide #4.23;wait 25 Unknown command: hidr #4.15;hide #4.23;wait 25 > movie record output browse Expected a keyword > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/throwaway2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/throwaway2.mp4 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > movie record > wait 25 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 25 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 25 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 25 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 25 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 25 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 25 > crossfade > show #3 cartoons > show #4.54 > wait 25 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > view #1/A > wait 25 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > wait wait requires a frame count argument unless motion is in progress > view #1/A :ics > view Mco > roll x 1 360 > wait > roll y 1 360 > wait > crossfade > view Nearco > wait 25 > crossfade 100 > show Nearco > wait 25 > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test.mp4 executed Script.cxc > view Nearco > view Mco > view Nearco > view name Nearco > view Mco > view Nearco > select Nearco 772 atoms, 764 bonds, 7 pseudobonds, 5 models selected > select clear > view name Masterco > view Mco > view Masterco > hide Nearco > view Nearco > show Nearco > view Masterco > roll x 1 360 > roll y 160 > stop > roll y 1 360 Drag select of 772 atoms, 7 pseudobonds, 764 bonds > show (#3#!1-2 & sel-residues & sidechain) target ab > style sel stick Changed 772 atom styles > undo > hide sel cartoons > show sel atoms > hide sel atoms > show sel atoms > hide (#3#!1-2 & sel) target a > show (#3#!1-2 & sel-residues & sidechain) target ab > show (#!1-3 & sel) target ab > hide backbone > select clear > hide bonds > view Masterco > select Yesco 67 atoms, 87 bonds, 4 pseudobonds, 3 models selected > view Mco > clip off > select sel @< 5 427 atoms, 388 bonds, 7 pseudobonds, 5 models selected > show #1 cartoons > show #2 cartoons > show #3 cartoons > show atoms > hide cartoons > select ~sel 49011 atoms, 50266 bonds, 53 pseudobonds, 61 models selected > hide (#3#!1-2 & sel) target a > select clear > ui tool show "Show Sequence Viewer" > sequence chain #1/A #1/C Alignment identifier is 1 > sequence chain #2/A #2/D Alignment identifier is 2 > sequence chain #3/A #3/D Alignment identifier is 3 > show sel target ab > hide backbone > hide backbone > show atoms > hide atoms > show Mco Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show Yesco > show atoms > hide atoms > show MOco Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show Moco Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show Yesco Drag select of Drag select of 67 atoms, 87 bonds, 4 pseudobonds > select sel @< 5 427 atoms, 388 bonds, 7 pseudobonds, 5 models selected > select sel @< 5 1702 atoms, 1627 bonds, 7 pseudobonds, 5 models selected > show atoms > select ~sel 47736 atoms, 49027 bonds, 53 pseudobonds, 61 models selected > hide (#3#!1-2 & sel) target a Drag select of 1702 atoms, 7 pseudobonds, 1627 bonds Drag select of Drag select of 73 atoms, 63 bonds > select clear Drag select of 1702 atoms, 7 pseudobonds, 1627 bonds > hide backbone > select clear Drag select of 890 atoms, 7 pseudobonds, 720 bonds > name frozen Nearco sel > name frozen Nearco sel > select clear > color red > color sel red > color sel red > color sel red > select clear > color sel green > color sel green > color sel green > color sel red > color sel red > color sel red > color sel red > color sel red > color sel red > select clear > show sel atoms > hide backbone > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > color sel red > color sel red > color sel red > color sel green > color sel green > color sel green > select clear > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > color sel green > show sel atoms > hide backbone Drag select of Drag select of 890 atoms, 7 pseudobonds, 720 bonds > show backbone > show sel backbone Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > clear sel Yesco Unknown command: clear sel Yesco > clear sel Unknown command: clear sel > select clear Yesco Expected fewer arguments > select clear > color sel green > color sel green > color sel green > select clear > color sel red > color sel red > color sel red > color sel red > select clear > color sel red > color sel red > color sel red > color sel red > color sel red > color sel red > color sel red > color sel red > color sel green > color sel green > color sel green > color sel red > color sel red > color sel red Drag select of 106 atoms, 76 bonds > hide sel target a Drag select of 11 atoms, 6 bonds > hide sel atoms Drag select of 46 atoms, 28 bonds > hide sel atoms Drag select of 13 atoms, 8 bonds > hide sel atoms Drag select of 10 atoms, 7 bonds > hide sel atoms Drag select of 7 atoms, 1 bonds > hide sel atoms Drag select of 9 atoms, 6 bonds > hide sel atoms Drag select of 13 atoms, 8 bonds > hide sel atoms Drag select of 2 atoms, 1 bonds > hide sel atoms Drag select of 30 atoms, 18 bonds > hide sel atoms Drag select of 47 atoms, 41 bonds > hide sel atoms Drag select of 3 atoms > hide sel atoms Drag select of 10 atoms, 8 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 2 atoms > hide sel atoms Drag select of 29 atoms, 29 bonds > hide sel atoms Drag select of 40 atoms, 33 bonds > hide sel atoms Drag select of 15 atoms, 9 bonds > hide sel atoms Drag select of 8 atoms, 8 bonds Drag select of 23 atoms, 25 bonds > hide sel atoms Drag select of 8 atoms, 4 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 15 atoms, 9 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 4 atoms, 2 bonds > hide sel atoms Drag select of 5 atoms, 3 bonds > hide sel atoms Drag select of 14 atoms, 8 bonds > hide sel atoms Drag select of 2 atoms > hide sel atoms Drag select of 11 atoms, 6 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms > ui tool show "Side View" Drag select of 37 atoms, 21 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 8 atoms, 5 bonds > hide sel atoms Drag select of 3 atoms > hide sel atoms > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" Drag select of Drag select of 12 atoms, 12 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 5 atoms, 2 bonds > hide sel atoms Drag select of 8 atoms, 5 bonds > hide sel atoms Drag select of 30 atoms, 24 bonds > hide sel atoms > select clear > select clear Drag select of 306 atoms, 7 pseudobonds, 287 bonds > name frozen Nearcocolor sel > name frozen Nearcocolor sel > select clear Drag select of > select clear Drag select of 12 atoms, 9 bonds Drag select of Drag select of 12 atoms, 9 bonds Drag select of 21 atoms, 18 bonds Drag select of 2 atoms, 1 bonds Drag select of 26 atoms, 25 bonds Drag select of 15 atoms, 13 bonds Drag select of 17 atoms, 17 bonds Drag select of 16 atoms, 17 bonds > select clear > select backbone 24778 atoms, 24762 bonds, 3 models selected > undo > select green Expected an objects specifier or a keyword > hide Yesco Drag select of Drag select of Drag select of Drag select of 12 atoms, 9 bonds Drag select of 21 atoms, 18 bonds Drag select of 9 atoms, 6 bonds Drag select of 15 atoms, 12 bonds Drag select of Drag select of 18 atoms, 18 bonds Drag select of Drag select of Drag select of 6 atoms, 3 bonds Drag select of 6 atoms, 3 bonds Drag select of 18 atoms, 18 bonds Drag select of 21 atoms, 21 bonds > name frozen NearcocolorG sel > name frozen NearcocolorG sel > hide NearcocolorG Drag select of 113 atoms, 92 bonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > select clear Drag select of 113 atoms, 92 bonds > help 3dlabels No help found for '3dlabels' > help labels No help found for 'labels' > help label > show NearcocolorG > show Yesco > select clear Drag select of 2 atoms Drag select of 6 atoms, 3 bonds > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > undo > undo > show NearcocolorG > show (sel-residues & sidechain) target ab > select clear Drag select of 309 atoms, 7 pseudobonds, 290 bonds > show (#3#!1-2 & sel-residues & sidechain) target ab > select clear Drag select of Drag select of Drag select of 358 atoms, 20 pseudobonds, 339 bonds > hide backbone > show backbone > show (#3#!1-2 & sel-residues & sidechain) target ab > select clear > hide > hide sel > hide sel > hide sel > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" > color #2 sky blue > color NearcocolorG green > color NearcocolorR red > color Yesco byelement > hide Yesco Drag select of 18 atoms, 15 bonds Drag select of Drag select of 9 atoms, 6 bonds Drag select of 1 atoms Drag select of 15 atoms, 12 bonds Drag select of 25 atoms, 21 bonds Drag select of 19 atoms, 21 bonds Drag select of 25 atoms, 25 bonds > select clear Drag select of 18 atoms, 15 bonds Drag select of 21 atoms, 21 bonds Drag select of 15 atoms, 12 bonds Drag select of 9 atoms, 6 bonds Drag select of 9 atoms, 6 bonds Drag select of 24 atoms, 21 bonds Drag select of 12 atoms, 9 bonds Drag select of Drag select of Drag select of Drag select of 24 atoms, 24 bonds Drag select of 18 atoms, 20 bonds Drag select of > name frozen NearcocolorG sel > name frozen NearcocolorG sel > color NearcocolorG green > hide sel > show Nearcocolor G Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show NearcocolorG > name frozen NearcocolorG sel > name frozen NearcocolorG sel > name frozen NearcocolorG sel > hide sel Drag select of 138 atoms, 117 bonds, 3 pseudobonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > color NearcocolorR red > show NearcocolorG > show Yesco > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" No visible atoms or bonds selected > select delete Expected an objects specifier or a keyword > name frozen trash sel > name frozen trash sel > hide trash > color Mo magentsa Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color Mo magenta > hide Nearco > show Nearco > hide Nearco > show NearcocolorG > show Nearcocolor ribbons > show NearcocolorR > hide trash Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show trash Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show Yesco > name frozen trashbonds sel > name frozen trashbonds sel > select clear > select trashbonds 12 pseudobonds, 3 models selected > hide trashbonds > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" > hide #4 Drag select of Drag select of 358 atoms, 8 pseudobonds, 339 bonds > view name Nearco > name frozen Nearco sel > name frozen Nearco sel > hide Nearco > show Nearco > hide trashbonds Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select clear No visible atoms or bonds selected No visible atoms or bonds selected > name frozen junk sel > name frozen junk sel > color junk purple > hide junk > show junk > hide junk > hide Nearco > show Nearco No visible atoms or bonds selected > hide sel > hide sel > hide Nearco > show Nearco > color #1 cartoon sky blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 sky blue > color #2 light green > color #3 plum > color Mocos byelement > color Vcos byelement > color Mo magenta > color NearcocolorG green > color NearcocolorR red > ui tool show "Show Sequence Viewer" > sequence chain #1/A #1/C Alignment identifier is 1 > sequence chain #2/A #2/D Alignment identifier is 2 > sequence chain #3/A #3/D Alignment identifier is 3 > show (sel-residues & sidechain) target ab > show (sel-residues & sidechain) target ab > show (sel-residues & sidechain) target ab > show (sel-residues & sidechain) target ab > select clear > hide Yesco > hide NearcocolorR Drag select of 157 atoms, 135 bonds, 4 pseudobonds > ui tool show "Color Actions" > color sel green > name frozen NearcocolorG sel > name frozen NearcocolorG sel > select clear > show NearcocolorR > show Yesco > select clear No visible atoms selected > select clear > select clear > ui mousemode right label > label #1/A:231 > ui mousemode right "move label" > 2dlabels #4.26 xpos 0.468 ypos 0.916 Drag select of Drag select of > label height 1 Height must be a number Height must be a number > undo > undo > undo > select clear Height must be a number Pixels must be an integer Height must be a number > label #1-3 text test > undo > ~label sel residues No visible atoms selected Drag select of 362 atoms, 24 pseudobonds, 339 bonds Height must be a number > ~label (#!1-3 & sel) residues > select clear > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" Height must be a number Height must be a number > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" opened ChimeraX session > close #4.44 > close #4.3 > close #4.4 > close #4.5 > close #4.6 > close #4.8 > close #4.9 > close #4.10 > close #4.11 > close #4.12 > close #4.13 > close #4.16 > close #4.17 > close #4.19 > close #4.18 > close #4.20 > close #4.21 > close #4.22 > close #4.24 > close #4.25 > close #4.26 > close #4.27 > close #4.28 > close #4.29 > close #4.30 > close #4.31 > close #4.32 > close #4.33 > close #4.34 > close #4.35 > close #4.36 > close #4.37 > close #4.38 > close #4.39 > close #4.40 > close #4.41 > close #4.42 > close #4.43 > close #4.45 > close #4.46 > close #4.47 > close #4.48 > close #4.49 > close #4.50 > close #4.51 > select ~sel 49438 atoms, 50654 bonds, 77 pseudobonds, 22 models selected > select clear > view master Drag select of 1 atoms > show #1 cartoons > show #2 cartoons > show #3 cartoons Drag select of 360 atoms, 6191 residues, 7 pseudobonds, 340 bonds > hide #3.2 models > close #3.2 > close #2.3 > close #1.3 > select clear > view master > show #1 cartoons > hide #1 atoms > color #1 sky blue > show Mocos > color Mocos byelement > color #2 light green > hide #2 atoms > show Vcos > color Vcos byelement > hide #3 atoms > color #3 plum > open Script.cxc No such file/path: Script.cxc > cd "C:/Users/dharr/Box/ChimeraX Movie/Alignment" Current working directory is: C:\Users\dharr\Box\ChimeraX Movie\Alignment > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > movie record > wait 25 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 25 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 25 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 25 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 25 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 25 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 25 > crossfade > show #3 cartoons > show #4.54 > wait 25 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > view #1/A > wait 25 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.53 > hide #4.54 > hide #4.55 > wait 100 > view #1/A :ics > view Mco > wait 25 > roll x 1 360 > wait > roll y 1 360 > wait > crossfade > view Masterco > wait 25 > crossfade 100 > show Nearco > wait 25 > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test3.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test3.mp4 executed Script.cxc > view Masterco > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > help crossfade > view center > show #1 cartoons > hide #1 atoms > hide #2 atoms > hide #3 atoms > show #3 cartoons > show #2 cartoons > show Mocos > show Vcos > viewhide #4.52 Unknown command: viewhide #4.52 > hide #4.52 > view #1/A > view center > hide #1/B,C,D > hide #2/B,C,D,E,F > hide #3/B,C,D,E,F > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > view Moco Expected an objects specifier or a view name or a keyword > view Mco > view #1/A > roll -x 1 130 > roll -z 1 130 > view #1/A > view center > view #1/A > roll -x 1 130 > roll -z 1 130 > view center > view #1/A > roll -x 1 130 > roll -z 1 130 > crossfade > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > crossfade > view Mco > crossfade > show Nearco > crossfade > show Nearco clip false Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > clip off > view name Mco > hide Nearco > show Nearco > hide Moco Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide Mco Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide Mocos > hide Vcos Drag select of 291 atoms, 252 bonds, 13 pseudobonds > name frozen Nearco sel > name frozen Nearco sel > show Mocos > show Vcos > hide Pclust > select clear > crossfade > show NearcocolorG > show NearcocolorR > crossfade > show NearcocolorG > show NearcocolorR > hide Vcos > hide Mocos Drag select of Drag select of 295 atoms, 252 bonds, 17 pseudobonds > name frozen Nearco sel > name frozen Nearco sel > show Mocos > hide Mocos > show Yesco > select clear > crossfade > color NearcocolorG green > color NearcocolorR red > view Masterco > view Nearco > show Nearco > view name Masterco > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > movie record > wait 25 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 25 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 25 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 25 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 25 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 25 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 25 > crossfade > show #3 cartoons > show #4.54 > wait 25 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > crossfade > view #1/A > wait 25 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.52 > hide #4.53 > hide #4.54 > hide #4.55 > hide #1.2 > hide #2.2 > hide #3.1 > wait 100 > view #1/A :ics > crossfade > view Mco > wait 25 > roll x 1 360 > wait > roll y 1 360 > wait > crossfade > view Masterco > wait 25 > crossfade 100 > show Nearco > wait 25 > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test4.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test4.mp4 executed Script.cxc > view master > show #1 cartoons > show #2 cartoons > show #3 cartoons > show #4.1 models > show #4.2 models > show #4.7 models > show #4.14 models > show #4.15 models > show #4.23 models > view master > ui mousemode right "move label" > 2dlabels #4.1 xpos 0.088 ypos 0.650 > 2dlabels #4.2 xpos 0.174 ypos 0.305 > 2dlabels #4.14 xpos 0.515 ypos 0.301 > 2dlabels #4.7 xpos 0.429 ypos 0.651 > 2dlabels #4.15 xpos 0.738 ypos 0.647 > 2dlabels #4.23 xpos 0.764 ypos 0.302 > view center > show #4.52 models > show #4.53 models > show #4.54 models > 2dlabels #4.52 xpos 0.016 ypos 0.031 > 2dlabels #4.53 xpos 0.293 ypos 0.031 > 2dlabels #4.54 xpos 0.544 ypos 0.031 > hide Nocos Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > hide #!4 models > crossfade > view #1/A > wait 50 > crossfade > view #1/A > wait 50 > crossfade > view #1/A > wait 50 > crossfade > view #1/A > wait 50 > view center > view center > show Noco Drag select of 67 atoms, 87 bonds, 4 pseudobonds > name frozen Noco sel > name frozen Noco sel > hide Noco > view center > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.52 > hide #4.53 > hide #4.54 > hide #4.55 > hide #1.2 > hide #2.2 > hide #3.1 > wait 100 > hide #1 atoms > hide #2 atoms > hide #3 atoms > show Yesco > crossfade > view #1/A :ics > view Mco > view Masterco > crossfade 100 > show Nearco > hide #1.2 > hide #2.2 > hide #3.1 > wait 50 > hide #1.2 > hide #2.2 > hide #3.1 > view name Masterco > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color #3 plum > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 50 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 50 > crossfade > show #3 cartoons > show #4.54 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.52 > hide #4.53 > hide #4.54 > hide #4.55 > hide #1.2 > hide #2.2 > hide #3.1 > wait 100 > crossfade > view #1/A :ics > view Masterco > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > crossfade 100 > show Nearco > hide #1.2 > hide #2.2 > hide #3.1 > wait 50 > crossfade 100 > color NearcocolorG green > color NearcocolorR red > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test5.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test5.mp4 executed Script.cxc > hide #1.1 > hide #1.2 > hide #3.1 > show #1.1 > hide #1.1 Drag select of 3 atoms Drag select of 14 atoms, 2 bonds > select clear Drag select of 6 atoms > hide sel Drag select of 10 atoms > hide sel Drag select of 4 atoms > hide sel > view Masterco > hide #3.1 > hide #2.2 > hide #1.2 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color #3 plum > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 50 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 50 > crossfade > show #3 cartoons > show #4.54 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.52 > hide #4.53 > hide #4.54 > hide #4.55 > hide #1.2 > hide #2.2 > hide #3.1 > wait 100 > crossfade > view #1/A :ics > view Masterco > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait > hide #1.2 > hide #2.2 > hide #3.1 > crossfade 100 > show Nearco > wait 125 > crossfade 100 > color NearcocolorG green > color NearcocolorR red > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test6.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test6.mp4 executed Script.cxc > roll y 1 360 > wait 50 > roll y 1 360 > wait 50 > hide NearcocolorG > roll y 1 360 > wait 410 > show NearcocolorG > roll y 1 360 > wait 410 > hide NearcocolorG > hide #2.2 models > hide #1.2 models > hide #3.1 models > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color #3 plum > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 50 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 50 > crossfade > show #3 cartoons > show #4.54 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.52 > hide #4.53 > hide #4.54 > hide #4.55 > hide #1.2 > hide #2.2 > hide #3.1 > wait 100 > crossfade > view #1/A :ics > view Masterco > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > hide #1.2 > hide #2.2 > hide #3.1 > crossfade 100 > show Nearco > wait 125 > crossfade 100 > color NearcocolorG green > color NearcocolorR red > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test7.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test7.mp4 executed Script.cxc > hide #1.2 > hide #2.2 > hide #3.1 > crossfade 100 > show Nearco > wait 125 > crossfade 100 > color NearcocolorG green > color NearcocolorR red > crossfade 100 > color NearcocolorG green > color NearcocolorR red > color #1 sky blue > color #2 light green > color #3 plum > crossfade 100 > color NearcocolorG green > color NearcocolorR red > hide Nearco > show Nearco > hide nearco Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide Nearco > show Nearco > hide #1.2 > hide #2.2 > hide #3.1 > hide @CA pseudobonds > hide Nearco > show Nearco > hide Nearco > show Nearco > hide @pseudobonds > hide Nearco > show Nearco > hide @CA pseudobonds > show Nearco > hide @CA pseudobonds > hide Nearco > show Nearco > close #1.2 > close #2.2 > close #3.1 > hide Nearco > show Nearco > hide #1.2 models > hide #2.2 models > hide #3.1 models > hide Nearco > show Nearco > hide Nearco > show Nearco > wait 1 > hide @CA pseudobonds > hide Nearco > show Nearco > wait .1;hide @CA pseudobonds Expected an integer >= 1 or a keyword > show Nearco > wait 1 > hide @CA pseudobonds > hide Nearco > show Nearco > wait 1 > hide @CA pseudobonds > hide Nearco > color Mocos byelement > color Vcos byelement > show NearcocolorG > show NearcocolorR > hide @CA pseudobonds > view Masterco > ui tool show "Show Sequence Viewer" > sequence chain #1/A #1/C Alignment identifier is 1 > label sel text "Ile - 231" > label sel text "Arg - 96 (V,Fe - Lys)" > view Masterco > label sel text Gly-356 > label sel text Ile-231 > label sel text Arg-96(V,Fe-Lys) > label sel text Gly-69(V-Leu,Fe-His) > label sel text I-231 > label sel text R-96(V-L,Fe-H) > label sel text G-69(V-L,Fe-H) > label sel text R-96(V,Fe-K) > label sel text V-70 > label sel text Y-229(V,Fe-F) > label sel text H-442 > label sel text R-277 > label sel text S-278 > label sel text C-275 > label sel text H-195 > label sel text L-358(V-P,Fe-S) > label sel text R-359(Fe-K) > label sel text I-355(V-T,Fe-P) > label sel text F-381 > label sel text Q-191 > label sel text E-380(V,Fe-K) > view Masterco > label sel text M-441(V-G,Fe-A) > select clear > select #1/A:6496@FE2 1 atom, 1 model selected > label sel atoms text Fe2 > select #1/A:6496@FE7 1 atom, 1 model selected > label sel atoms text Fe7 > select #1/A:6496@FE6 1 atom, 1 model selected > label sel atoms text Fe6 > select #1/A:6496@FE3 1 atom, 1 model selected > label sel atoms text Fe3 > view Masterco > label sel text A-65(V,Fe-C) > view Masterco > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" > hide labels Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide labels residues Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide label Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #3.1 > hide #3.1 labels Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #3.1 > hide #1.3 models > show #1.3 models > hide #1.3 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 50 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 50 > crossfade > show #3 cartoons > show #4.54 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.52 > hide #4.53 > hide #4.54 > hide #4.55 > hide #1.2 > hide #2.2 > hide #3.1 > wait 100 > crossfade > view #1/A :ics > view Masterco > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 100 > show Nearco > wait 1 > hide @CA pseudobonds > wait 125 > crossfade 100 > color NearcocolorG green > color NearcocolorR red > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test8.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test8.mp4 executed Script.cxc > save "C:/Users/dharr/Box/ChimeraX Movie/Alignments.cxs" opened ChimeraX session > hide #!4 models > setattr #1 model autochain false Assigning autochain attribute to 4 items Not creating attribute 'autochain'; use 'create true' to override > setattr #2 model autochain false Assigning autochain attribute to 3 items Not creating attribute 'autochain'; use 'create true' to override > setattr #3 model autochain false Assigning autochain attribute to 2 items Not creating attribute 'autochain'; use 'create true' to override > set bgColor white > hide #1.2 models > hide #2.2 models > hide #3.1 models > hide #2.1 models > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > show #1.3 models > color labels black Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1.3 black > color #1.3 model black Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1.3 labels black Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color black #1.3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1.3 black > color #1.3 > color #1.3 black > color #1.3 model black Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1.3 models black Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > help labels No help found for 'labels' > help label > label color black > ui mousemode right "move label" > 2dlabels #4.10 xpos 0.439 ypos 0.885 > 2dlabels #4.10 xpos 0.449 ypos 0.884 > 2dlabels #4.10 xpos 0.470 ypos 0.863 > color Mo magenta > ui tool show "Show Sequence Viewer" > sequence chain #3/A #3/D Alignment identifier is 2 > show (sel-residues & sidechain) target ab > hide nearco Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide Nearco > hide Yesco > show NearcocolorR Drag select of 99 atoms, 85 bonds, 2 pseudobonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > show Yesco > show NearcocolorG > hide #1.2 models > hide #1.1 models > hide #2.2 models > hide #3.1 models > help label > 2dlabels #4.5 xpos 0.733 ypos 0.654 > 2dlabels #4.3 xpos 0.426 ypos 0.650 > 2dlabels #4.3 xpos 0.423 ypos 0.642 > 2dlabels #4.3 xpos 0.412 ypos 0.643 > 2dlabels #4.3 xpos 0.454 ypos 0.694 > color NearcocolorR red > select clear > 2dlabels #4.5 xpos 0.729 ypos 0.657 > help arrow No help found for 'arrow' > help arrows No help found for 'arrows' > help 2dlabels > 2dlabels arrow No 2D arrows in session > show (sel-residues & sidechain) target ab > hide Yesco > hide NearcocolorG Drag select of 102 atoms, 87 bonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > color NearcocolorR red > show Yesco > show NearcocolorG > select clear > ui tool show "Color Actions" > color V magenta > color V cyan > ui tool show "Color Actions" > color V violet > save C:\Users\dharr\Desktop\image1.png supersample 3 > save "C:/Users/dharr/Box/ChimeraX Movie/Final figure image.cxs" > label sel text G-356 > save "C:/Users/dharr/Box/ChimeraX Movie/Final figure image.cxs" > help image No help found for 'image' > help images No help found for 'images' > lighting simple > lighting soft > lighting full > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes true > graphics silhouettes false > help 2dlabels > 2dlabels text homocitrate color black > show #!4 models > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #4.4 models > hide #4.5 models > hide #4.7 models > hide #4.6 models > hide #4.8 models > hide #4.9 models > hide #4.10 models > hide #4.11 models > show #4.11 models > 2dlabels #4.11 xpos 0.696 ypos 0.534 > 2dlabels #4.11 xpos 0.717 ypos 0.574 > 2dlabels #4.11 xpos 0.717 ypos 0.571 > 2dlabels #4.1 bold false > 2dlabels #4.1 bold true > 2dlabels #4.11 bold true > 2dlabels #4.11 bold false > close #4.11 > select #1/A :HCA 14 atoms, 13 bonds, 1 model selected > label sel text homocitrate > hide #4.1 models > hide #!4 models > select clear > save "C:/Users/dharr/Box/ChimeraX Movie/Final figure image.cxs" > save C:\Users\dharr\Desktop\image2.png supersample 3 > save "C:/Users/dharr/Box/ChimeraX Movie/Final figure image.cxs" opened ChimeraX session > show #!4 models > hide #!4 models > view name Cofinal > background black Unknown command: background black > color background black Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > help background No help found for 'background' > set bgColor black > labels color white Unknown command: labels color white > help labels No help found for 'labels' > help label > label color white > hide #1.3 > cdr browse Unknown command: cdr browse > open Script.cxc No such file/path: Script.cxc > help directory No help found for 'directory' > help save > cd "C:/Users/dharr/Box/ChimeraX Movie/Alignment" Current working directory is: C:\Users\dharr\Box\ChimeraX Movie\Alignment > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.7 > show #4.14 > wait 50 > crossfade > show #3 cartoons > show #4.23 > show #4.15 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.7 > hide #4.14 > hide #3 cartoons > hide #4.15 > hide #4.23 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.52 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.53 > show #4.55 > wait 50 > crossfade > show #3 cartoons > show #4.54 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.52 > hide #4.53 > hide #4.54 > hide #4.55 > hide #1.2 > hide #2.2 > hide #3.1 > wait 100 > crossfade > view #1/A :ics > view Masterco > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 100 > show Nearco > wait 1 > hide @CA pseudobonds > wait 125 > crossfade 100 > color NearcocolorG green > color NearcocolorR red > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Align_test9.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Align_test9.mp4 executed Script.cxc > save "C:/Users/dharr/Box/ChimeraX Movie/Final_with_figure.cxs" opened ChimeraX session > hide #!4 models > hide Yesco > hide NearcocolorG Drag select of 138 atoms, 3 pseudobonds, 117 bonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > color NearcocolorR red > select clear > hide @CA pseudobonds > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > color Mo magenta > color V pink > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > wait 100 > crossfade > view #1/A :ics > view Cofinal > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 50 > show Nearco > wait 1 > hide @CA pseudobonds > wait 100 > crossfade 50 > color NearcocolorG green > color NearcocolorR red > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade > show #1.3 > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Video_final1" Unrecognized movie file suffix Video_final1, use *.ogv, *.avi, *.mp4, *.wmv, *.webm, *.mov > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Video_final1.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Video_final1.mp4 > view master > hide #1.3 > show #1 cartoons > show #2 cartoons > show #3 cartoons > show #4.1 models > show #4.2 models > show #4.3 models > show #4.4 models > show #4.5 models > show #4.6 models > show #4.7 models > show #4.8 models > show #4.9 models > show #4.10 models > view master > ui mousemode right "move label" > 2dlabels #4.3 xpos 0.422 ypos 0.656 > 2dlabels #4.5 xpos 0.732 ypos 0.654 > view center > 2dlabels #4.10 text 'Alignment of all three Invalid "text" argument: incomplete quoted text > 2dlabels #4.10 text "Alignment of all three" > 2dlabels #4.10 xpos 0.322 ypos 0.854 > help 2dlabel > ui tool show "Color Actions" > 2dlabels text "Alignment of α subunit" font arial size 40 bold true color > burly wood > 2dlabels #4.11 xpos 0.322 ypos 0.854 > hide #!4 models > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > wait 50 > show #1 cartoons > show #2 cartoons > show #3 cartoons > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > mmaker #3/A to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > wait 100 > 2dlabels #4.10 text "Global alignment of all three" > hide #4.10 models > show #4.10 models > view center > show #2 cartoons > 2dlabels #4.10 xpos 0.280 ypos 0.853 > view Cofinal > hide #2 cartoons > show #1.3 models > ui tool show "Show Sequence Viewer" > sequence chain #2/A #2/D Alignment identifier is 1 > sequence chain #3/A #3/D Alignment identifier is 2 > show (sel-residues & sidechain) target ab > show (sel-residues & sidechain) target ab > hide Yesco > hide NearcocolorG > hide #!4 models > hide #1.3 models Drag select of 95 atoms, 79 bonds, 2 pseudobonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > name frozen NearcocolorR sel > color NearcocolorR red > select clear > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color Mo magenta > color V pink > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > show #4.11 > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > wait 100 > crossfade > view #1/A :ics > view Cofinal > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 50 > show Nearco > show NearcocolorG > show NearcocolorR > wait 1 > hide @CA pseudobonds > wait 100 > crossfade 50 > color NearcocolorG green > color NearcocolorR red > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade > show #1.3 > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Video_final2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Video_final2.mp4 executed Script.cxc > hide all > show Nearco > show NearcocolorR > show NearcocolorG > show Yesco > show Nearco > show (sel-residues & sidechain) target ab > select clear > hide Yesco > hide NearcocolorG > hide #1.3 Drag select of 102 atoms, 86 bonds, 2 pseudobonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > name frozen NearcocolorR sel > name frozen NearcocolorR sel > hide NearcocolorR > show NearcocolorR > color NearcocolorR red > show NearcocolorG > show Yesco > show #1.3 > show #3/D > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > select clear > view Masterco > view Cofinal > view Masterco > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > view Cofinal > hide #3 cartoons > hide #3 > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > show #3 > show Nearco > hide #3 > show Nearco > show #3 > hide #3 > show Nearco > hide Yesco > hide NearcocolorG > hide #1.3 Drag select of 139 atoms, 117 bonds, 3 pseudobonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > color NearcocolorR red > show Yesco > show NearcocolorG > show #1.3 > setattr #1 model autochain false Assigning autochain attribute to 4 items Not creating attribute 'autochain'; use 'create true' to override > setattr #1 model autochain create false Expected a keyword > setattr #1 autochain create false Unknown attribute target: 'autochain' > setattr #1 model autochain false Assigning autochain attribute to 4 items Not creating attribute 'autochain'; use 'create true' to override > setattr #2 autochain create false Unknown attribute target: 'autochain' > setattr #2 model chain trace create false Assigning chain attribute to 3 items Not creating attribute 'chain'; use 'create true' to override > setattr #1.2 create false Missing or invalid "attrValue" argument: Expected an integer, a number, true or false, or a text string > setattr #1.2 model create false Assigning create attribute to 1 item Not creating attribute 'create'; use 'create true' to override > setattr #1 model pseudobonds create false Expected a keyword > setattr #1 model pseudobonds false Assigning pseudobonds attribute to 4 items Not creating attribute 'pseudobonds'; use 'create true' to override > setattr #1 model autochain Missing or invalid "attrValue" argument: Expected an integer, a number, true or false, or a text string > setattr #1 model autochain true Assigning autochain attribute to 4 items Not creating attribute 'autochain'; use 'create true' to override > setattr #1 model autochain false Assigning autochain attribute to 4 items Not creating attribute 'autochain'; use 'create true' to override > setattr #2 model autochain false Assigning autochain attribute to 3 items Not creating attribute 'autochain'; use 'create true' to override > setattr #3 model autochain false Assigning autochain attribute to 2 items Not creating attribute 'autochain'; use 'create true' to override > hide NearcocolorR > hide NearcocolorG > show NearcocolorR > show NearcocolorG > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color Mo magenta > color V pink > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide 4.10;hide Pclust;hide Noco;wait 50 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/throwaway.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/throwaway.mp4 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color Mo magenta > color V pink > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide 4.10;hide Pclust;hide Noco;wait 50 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > movie encode output "C:/Users/dharr/Box/ChimeraX Movie/Alignment/throwaway2" Unrecognized movie file suffix throwaway2, use *.ogv, *.avi, *.mp4, *.wmv, *.webm, *.mov > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/throwaway2.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/throwaway2.mp4 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color Mo magenta > color V pink > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide #4.10 > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > show #4.11 > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3/D to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > wait 100 > crossfade > view #1/A :ics > view Cofinal > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 50 > show Nearco > show NearcocolorG > show NearcocolorR > wait 1 > hide @CA pseudobonds > wait 100 > crossfade 50 > color NearcocolorG green > color NearcocolorR red > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade > show #1.3 > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Video_final3.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/Video_final3.mp4 executed Script.cxc > show NearcocolorG > show NearcocolorR > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > mmaker #3/D to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain D (#3), sequence alignment score = 987.1 RMSD between 373 pruned atom pairs is 0.975 angstroms; (across all 451 pairs: 3.034) > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color Mo magenta > color V pink > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide #4.10 > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > show #4.11 > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > wait 100 > crossfade > view #1/A :ics > view Cofinal > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 50 > show Nearco > show NearcocolorG > show NearcocolorR > wait 1 > hide @CA pseudobonds > wait 100 > crossfade 50 > color NearcocolorG green > color NearcocolorR red > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade > show #1.3 > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/Video_final4mp4" Unrecognized movie file suffix Video_final4mp4, use *.ogv, *.avi, *.mp4, *.wmv, *.webm, *.mov > show NearcocolorR > show NearcocolorG > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > view center > show #1 cartoons > show #2 cartoons > show #3 cartoons > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide #4.10 > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > hide #1.3 > movie stop > roll -z 1 130 > wait > crossfade > show #4.11 > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > wait 100 > hide Yesco > hide #1.2 models > hide #2.2 models > hide #3.1 models Drag select of 13 atoms, 11 bonds Drag select of 8 atoms, 5 bonds Drag select of 13 atoms, 10 bonds Drag select of 26 atoms, 26 bonds Drag select of 21 atoms, 15 bonds Drag select of 26 atoms, 26 bonds Drag select of 21 atoms, 16 bonds Drag select of 20 atoms, 17 bonds Drag select of 12 atoms, 9 bonds Drag select of 18 atoms, 15 bonds Drag select of 21 atoms, 19 bonds > name frozen NearcocolorR sel > name frozen NearcocolorR sel > name frozen NearcocolorR sel > name frozen NearcocolorR sel > color NearcocolorR red > hide NearcocolorR Drag select of 156 atoms, 135 bonds > name frozen NearcocolorG sel > name frozen NearcocolorG sel > name frozen NearcocolorG sel > name frozen NearcocolorG sel > select clear > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/throwaway3.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/throwaway3.mp4 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color Mo magenta > color V pink > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide #4.10 > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > show #4.11 > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > wait 100 > crossfade > view #1/A :ics > view Cofinal > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 50 > show Nearco > show NearcocolorG > show NearcocolorR > wait 1 > hide @CA pseudobonds > wait 100 > crossfade 50 > color NearcocolorG green > color NearcocolorR red > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade > show #1.3 > movie stop > show NearcolorR Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show NearcocolorR > hide NearcocolorR > mmaker #3/a to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > undo > undo > view centetr Expected an objects specifier or a view name or a keyword > view center > show #1 cartoons > show #2 cartoons > show #3 cartoons > hide #1.3 > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide #4.10 > hide Pclust > hide Noco > wait 50 > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > wait 100 > crossfade > view #1/A :ics > view Cofinal > wait 50 > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > view Cofinal > view Cofinal > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > show #1.3 > hide #1.3 models > show #1.3 models > movie stop Not currently recording > show #1.3 > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > show #1.3 lables Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #1.3 labels Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1.3 > show #1.3 > view Cofinal > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > view name Cofinal > movie encode output "C:/Users/dharr/Box/ChimeraX > Movie/Alignment/throwaway4.mp4" Movie saved to C:/Users/dharr/Box/ChimeraX Movie/Alignment/throwaway4.mp4 > open Script.cxc > view master > hide #1 cartoons > hide Mocos > hide #2 cartoons > hide Vcos > hide #3 cartoons > hide #4 > hide #1 atoms > hide #2 atoms > hide #3 atoms > color #1 sky blue > color Mocos byelement > color #2 light green > color Vcos byelement > color Mo magenta > color V pink > color #3 plum > hide #1.3 > select clear > movie record > wait 50 > crossfade > show #1 cartoons > show Mocos > show #4.1 > show #4.2 > wait 50 > crossfade > show #2 cartoons > show Vcos > show #4.3 > show #4.4 > wait 50 > crossfade > show #3 cartoons > show #4.5 > show #4.6 > wait 50 > crossfade > hide #1 cartoons > hide Mocos > hide #4.1 > hide #4.2 > hide #2 cartoons > hide Vcos > hide #4.3 > hide #4.4 > hide #3 cartoons > hide #4.5 > hide #4.6 > wait 50 > view center > crossfade > show #1 cartoons > show Mocos > show #4.7 > wait 50 > crossfade > show #2 cartoons > show Vcos > show # 4.8 > show #4.10 > wait 50 > crossfade > show #3 cartoons > show #4.9 > wait 50 > roll y 1 360 > wait > roll x 1 360 > wait > crossfade > hide #1/B,C,D cartoons > hide #2/B,C,D,E,F cartoons > hide #3/B,C,D,E,F cartoons > hide #4.10 > hide Pclust > hide Noco > wait 50 > crossfade > view #1/A > wait 50 > roll -x 1 130 > wait > roll -z 1 130 > wait > crossfade > show #4.11 > crossfade > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with 5n6y, chain A (#2), sequence alignment score = 1047.6 RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > wait 50 > crossfade > mmaker #3/A to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3u7q, chain A (#1) with FeN2ase Model Swiss Model VN2ase.pdb, chain A (#3), sequence alignment score = 984.1 RMSD between 378 pruned atom pairs is 0.973 angstroms; (across all 451 pairs: 3.031) > wait 50 > crossfade 100 > hide #1 cartoons > hide #2 cartoons > hide #3 cartoons > hide Pclust > hide Noco > hide #4.7 > hide #4.8 > hide #4.9 > hide #4.10 > hide #4.11 > wait 100 > crossfade > view #1/A :ics > view Cofinal > wait 50 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade 50 > show Nearco > show NearcocolorG > show NearcocolorR > wait 1 > hide @CA pseudobonds > wait 100 > crossfade 50 > color NearcocolorG green > color NearcocolorR red > wait 100 > roll x 1 360 > wait > roll y 1 360 > wait 410 > crossfade > show #1.3 > movie encode output "C:/Users/dharr/Box/Nitrogenase CO > reduction/Chimera/Video_final_draft.mp4" Movie saved to C:/Users/dharr/Box/Nitrogenase CO reduction/Chimera/Video_final_draft.mp4 executed Script.cxc > save "C:/Users/dharr/Box/ChimeraX Movie/FinalVideo.cxs" > close #4 > set bgColor white > color #1.3 black > label color black > save "C:/Users/dharr/Box/Nitrogenase CO > reduction/Chimera/FinalAlignNearco.cxs" opened ChimeraX session > close #1.2 > close #2.2 > close #3.1 > save "C:/Users/dharr/Box/Nitrogenase CO > reduction/Chimera/FinalAlignNearco.cxs" opened ChimeraX session > setattr #1 model autochain false Assigning autochain attribute to 4 items Not creating attribute 'autochain'; use 'create true' to override OpenGL version: 3.3.0 NVIDIA 451.67 OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: XPS 8930 OS: Microsoft Windows 10 Home (Build 18362) Memory: 16,977,567,744 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: FinalAlignNearco.cxs
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