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Changes between Initial Version and Version 1 of Ticket #17280

Timestamp:: Apr 3, 2025, 10:44:20 AM (7 months ago)
Author:: Eric Pettersen
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #17280
- Property Component Unassigned → Window Toolkit
- Property Owner set to Tom Goddard
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

Ticket #17280 – Description

-              initial
+              v1
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+    "uuid" : "c4b2ad90-cc7d-3780-bee9-9f1dbc2aa560",
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+    "name" : "_sha512.cpython-311-darwin.so"
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+    "name" : "_random.cpython-311-darwin.so"
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+    "name" : "_bz2.cpython-311-darwin.so"
+  },
+  {
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+    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
+    "name" : "zlib.cpython-311-darwin.so"
+  },
+  {
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+    "size" : 16384,
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+    "name" : "_datetime.cpython-311-darwin.so"
+  },
+  {
+    "source" : "P",
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+    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
+    "name" : "math.cpython-311-darwin.so"
+  },
+  {
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+    "base" : 4318150656,
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+    "name" : "Python",
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+    "name" : "ChimeraX",
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+    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
+    "name" : "libsystem_kernel.dylib"
+  },
+  {
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+    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
+    "name" : "libsystem_pthread.dylib"
+  },
+  {
+    "source" : "P",
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+    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
+    "name" : "libsystem_c.dylib"
+  },
+  {
+    "source" : "P",
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+    "name" : "libsystem_platform.dylib"
+  },
+  {
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+    "name" : "SkyLight"
+  },
+  {
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+    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
+    "name" : "libdispatch.dylib"
+  },
+  {
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+    "name" : "CoreFoundation",
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+  {
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+    "name" : "HIToolbox"
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+  {
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+    "uuid" : "37bbc384-0755-31c7-a808-0ed49e44dd8e",
+    "path" : "\/usr\/lib\/dyld",
+    "name" : "dyld"
+  },
+  {
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+    "source" : "A",
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+    "uuid" : "00000000-0000-0000-0000-000000000000"
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+  {
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+    "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
+    "name" : "Foundation",
+    "CFBundleVersion" : "2503.1"
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+[deleted to fit within ticket limits]
 ],
   "sharedCache" : {
 …
 > color sel gold
+> select #3/A:555-912
+atoms, 2695 bonds, 3 pseudobonds, 329 residues, 2 models selected
+> color sel sienna
+> select clear
+> select #3/B:352-554
+atoms, 1356 bonds, 1 pseudobond, 166 residues, 2 models selected
+> color sel sandy brown
+> color sel khaki
+> select #3/B:555-912
+atoms, 2695 bonds, 3 pseudobonds, 329 residues, 2 models selected
+> color sel sandy brown
+> select clear
+> cartoon style #3.1,3-4#!3 modeHelix tube sides 20
+> select clear
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb
+Chain information for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb #4
+---
+Chain | Description
+A B | No description available
+G | No description available
+Computing secondary structure
+> color sel light grey
+> color #4l light grey
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #4 light grey
+> select clear
+> cartoon style #4#3.1,3-4#!3 modeHelix tube sides 20
+> select clear
+> nucleotides ladder
+> view p1
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting full
+> lighting simple
+> lighting soft
+> lighting full
+> lighting soft
+> lighting full
+> lighting soft
+> undo
+> color #4 #929292ff
+> color #4 darkgrey
+> color #4 silver
+> color #4 darkgrey
+> color #4 whitesmoke
+> color #4 #cbccccff
+> color #4 darkgrey
+> color #4 silver
+> select clear
+> save /Users/justinvanriper/Desktop/image15.png supersample 3
+> select #4/A,B
+atoms, 14894 bonds, 1824 residues, 1 model selected
+> hide sel cartoons
+> hide sel atoms
+> select #3/A,B
+atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
+> hide sel cartoons
+> hide sel atoms
+Drag select of 1 atoms
+> hide sel atoms
+> roll y 1 90
+> roll x 1 50
+> select ~sel & ##selected
+atoms, 16851 bonds, 1 pseudobond, 1906 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 16851 bonds, 1 pseudobond, 1906 residues, 2 models selected
+> roll y -1 90
+> roll x 1 90
+> roll y -1 90
+> select clear
+> save /Users/justinvanriper/Desktop/image16.png supersample 3
+> select #4/G
+atoms, 1957 bonds, 82 residues, 1 model selected
+> select #4/G:1-7,75-82
+atoms, 358 bonds, 15 residues, 1 model selected
+> color sel forest green
+> view name p01
+> select #4/G:10-25
+atoms, 388 bonds, 16 residues, 1 model selected
+> color sel dodger blue
+> select clear
+> select #4/G:27-43
+atoms, 403 bonds, 17 residues, 1 model selected
+> color sel dark orchid
+> selct clear
+Unknown command: selct clear
+> select #4/G:45-55
+atoms, 257 bonds, 11 residues, 1 model selected
+> color sel crimson
+> select #4/G:58-74
+atoms, 402 bonds, 17 residues, 1 model selected
+> color sel gold
+> select clear
+> select #4/G:8,9,26,44,56,57
+atoms, 140 bonds, 6 residues, 1 model selected
+> color sel oldlace linen
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color sel old lace
+> select clear
+> save /Users/justinvanriper/Desktop/image17.png supersample 3
+> select #4/G:26-57
+atoms, 757 bonds, 32 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select ~sel & ##selected
+atoms, 16094 bonds, 1 pseudobond, 1878 residues, 2 models selected
+> select up
+atoms, 16094 bonds, 1 pseudobond, 1880 residues, 2 models selected
+> select #4/G:10-57
+atoms, 1146 bonds, 48 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select #4/G:8-57
+atoms, 1194 bonds, 50 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select #4/G:10-82
+atoms, 1739 bonds, 73 residues, 1 model selected
+> select #4/G:1-57
+atoms, 1364 bonds, 57 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select #4/G:1-57,77-82
+atoms, 1505 bonds, 63 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select clear
+> view p01
+> view name p02
+> save /Users/justinvanriper/Desktop/image18.png supersample 3
+> roll y -1 90
+> view name p03
+> save /Users/justinvanriper/Desktop/image19.png supersample 3
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_4/SLFN14_session_alignment_RNA.cxs
+> show cartoons
+> view p01
+> select #4/G:
+Expected an objects specifier or a keyword
+> select #4/G
+atoms, 1957 bonds, 82 residues, 1 model selected
+> show sel atoms
+> select clear
+> view p1
+> roll x 1 90
+> select #3/A,B:352-912
+atoms, 8104 bonds, 8 pseudobonds, 990 residues, 2 models selected
+> hide sel cartoons
+> select #3,4/A,B:352-912
+atoms, 17224 bonds, 8 pseudobonds, 2112 residues, 3 models selected
+> show sel cartoons
+> hide sel atoms
+> hide sel cartoons
+> select #4/G
+atoms, 1957 bonds, 82 residues, 1 model selected
+> color sel old lace
+> select #4/A,B
+atoms, 14894 bonds, 1824 residues, 1 model selected
+> color sel old lace
+> select clear
+> select #3,4/A,B:218,219,220,223
+atoms, 136 bonds, 16 residues, 2 models selected
+> show sel atoms
+> style sel sphere
+Changed 144 atom styles
+> select ::name="MG"
+atoms, 5 residues, 2 models selected
+> show sel atoms
+> select clear
+> select #3,4/A,B:206,211,213
+atoms, 96 bonds, 12 residues, 2 models selected
+> show sel atoms
+> color sel byhetero target a
+> select clear
+> select #3/A,B:206,211,213
+atoms, 48 bonds, 6 residues, 1 model selected
+> select #3/A,B:218,219,220,223
+atoms, 68 bonds, 8 residues, 1 model selected
+> color sel white
+> color sel old lace
+> select #4/A,B:218,219,220,223
+atoms, 68 bonds, 8 residues, 1 model selected
+> color sel cyan
+> select clear
+> lighting simple
+> lighting soft
+> lighting full
+> lighting soft
+> view name p11
+> select #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+> select #3/A,B
+atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
+> color sel old lace
+> select #4/A
+atoms, 7447 bonds, 912 residues, 1 model selected
+> color sel cornflower blue target c
+> color sel light blue target c
+> select #4/B
+atoms, 7447 bonds, 912 residues, 1 model selected
+> color sel cornflower blue target c
+> select clear
+> save /Users/justinvanriper/Desktop/image20.png supersample 3
+> select #4 Mg
+Expected a keyword
+> select ::name="MG"
+atoms, 5 residues, 2 models selected
+> color sel byhetero
+> select #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+> select #3/A,B
+atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
+> color sel old lace
+> select clear
+> save /Users/justinvanriper/Desktop/image21.png supersample 3
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_4/SLFN14_session_DiseaseMut_alignment_RNA.cxs
+> select #4
+atoms, 16851 bonds, 1 pseudobond, 1910 residues, 2 models selected
+> hide #!4 models
+> coulombic #!3
+Using Amber 20 recommended default charges and atom types for standard
+residues
+Coulombic values for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb_A SES surface #3.3: minimum, -18.85, mean
+.28, maximum 15.66
+Coulombic values for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb_B SES surface #3.4: minimum, -21.91, mean
+.09, maximum 16.30
+Coulombic values for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb_C SES surface #3.5: minimum, -17.13, mean
+-7.14, maximum 0.91
+Coulombic values for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb_D SES surface #3.6: minimum, -17.77, mean
+-8.59, maximum -1.01
+To also show corresponding color key, enter the above coulombic command and
+add key true
+> select #3/C,D
+atoms, 280 bonds, 12 residues, 1 model selected
+> hide sel surfaces
+> select clear
+> hide #!3 surfaces
+> select ~sel & ##selected
+Nothing selected
+> select #3/A,B:1-351
+atoms, 5358 bonds, 2 pseudobonds, 653 residues, 2 models selected
+> show sel surfaces
+> select clear
+> select #3/A,B
+atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
+> hide sel atoms
+> select clear
+> view name p21
+> view p21
+> show #!4 models
+> hide #!4 models
+> select ~sel & ##selected
+Nothing selected
+> view name p21
+> save /Users/justinvanriper/Desktop/image22.png supersample 3
+> hide #!3 models
+> show #!4 models
+> coulombic #!4
+Using Amber 20 recommended default charges and atom types for standard
+residues
+Coulombic values for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb_A SES surface #4.2:
+minimum, -20.28, mean 0.14, maximum 20.52
+Coulombic values for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb_B SES surface #4.3:
+minimum, -22.66, mean 0.14, maximum 17.42
+Coulombic values for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb_G SES surface #4.4:
+minimum, -49.29, mean -22.91, maximum -5.91
+To also show corresponding color key, enter the above coulombic command and
+add key true
+> hide #!4 surfaces
+> select #4/A,B:1-351
+atoms, 5772 bonds, 702 residues, 1 model selected
+> show sel surfaces
+> hide sel atoms
+> select clear
+> save /Users/justinvanriper/Desktop/image23.png supersample 3
+Unsupported scale factor (0.000000) detected on Display0
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_4/tRNA_ElectrostaticMap_SLFN14_Fig4.cxs
+> hide #!4 models
+> show #!1 models
+> close
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v2.cxs
+Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.15,
+step 1, values float32
+opened ChimeraX session
+> show #!2 models
+> view p21
+Expected an objects specifier or a view name or a keyword
+> view name p1
+> select clear
+> hide #!2 models
+> select #4/U:77@P
+atom, 1 residue, 1 model selected
+Drag select of 6 atoms, 5 bonds
+> select clear
+Drag select of 8 atoms, 6 bonds
+> show sel atoms
+> select clear
+> select #3/D:7
+atoms, 21 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #4/U:77
+atoms, 21 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> show #!2 models
+> hide #!4 models
+> select clear
+Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc , 52 atoms, 45 bonds
+> volume zone #1 nearAtoms sel range 5 minimalBounds false
+> volume zone #2 nearAtoms sel range 5 minimalBounds false
+> volume zone #2 nearAtoms sel range 2minimalBounds false
+Invalid "range" argument: Expected a number
+> volume zone #2 nearAtoms sel range 2 minimalBounds false
+> volume zone #2 nearAtoms sel range 20 minimalBounds false
+> volume #2 level 0.06773
+> volume #2 style mesh
+> volume #2 level 0.3939
+> volume #2 style surface
+> show #!4 models
+> hide #!1 models
+> hide #!4 models
+> show #!4 models
+> hide #!3 models
+> hide #!2 models
+> select #4/B:1002@MN
+atom, 1 residue, 1 model selected
+> select add #4/B:1003@MN
+atoms, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> select #4/U:66,65
+Nothing selected
+> select #4/U:77,78
+atoms, 43 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select #4/U:77,78,76
+atoms, 43 bonds, 2 residues, 1 model selected
+> show sel atoms
+> show sel cartoons
+> show sel atoms
+> hide sel cartoons
+> select #4/U:77,78,76
+atoms, 43 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select #4/U:77,78,76,75
+atoms, 43 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select #4/U:77,78,76,75,78
+atoms, 43 bonds, 2 residues, 1 model selected
+> show sel cartoons
+> show sel atoms
+> hide sel cartoons
+> select clear
+> select #4/U
+atoms, 91 bonds, 4 residues, 1 model selected
+> show sel atoms
+> select #4/T
+atoms, 1249 bonds, 6 pseudobonds, 56 residues, 3 models selected
+> show sel atoms
+> hide sel atoms
+> select #4/T:76
+atoms, 21 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #4/U:77
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #4/U:78-90
+atoms, 69 bonds, 3 residues, 1 model selected
+> hide sel atoms
+> show #!3 models
+> select clear
+> select #4/T:76
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!2 models
+> select clear
+Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc , 104 atoms, 90 bonds
+> volume zone #2 nearAtoms sel range 20 minimalBounds false
+> volume zone #2 nearAtoms sel range 200 minimalBounds false
+> volume #2 level 0.0284
+> volume #2 level 0.1858
+> hide #!4 models
+> volume #2 level 0.1334
+> select #3/C:7-5
+Nothing selected
+> select #3/D:7-5
+Nothing selected
+> select #3/D:5-7
+atoms, 65 bonds, 3 residues, 1 model selected
+> show sel atoms
+> color sel byhetero target a
+> color sel orange
+> color sel byhetero
+> select clear
+Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc
+> select #2
+models selected
+> select #2
+models selected
+Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc
+> select #2
+models selected
+> select #2
+models selected
+> select clear
+> select #2
+models selected
+> select #2
+models selected
+> select #2
+models selected
+> select #2
+models selected
+> select #2
+models selected
+> select #2
+models selected
+> select clear
+> volume #2 level 0.2908
+> volume #2 level 0.1184
+> volume #2 level 0.3695
+> open
+> "/Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM
+> Maps/State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+> sharpened-highres.mrc"
+Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc as #5, grid size 300,300,300, pixel 0.832, shown at
+level 0.0049, step 2, values float32
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited-
+> coot-15_real_space_refined_015.pdb
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb #6
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+> hide #!5 models
+> align #6 #3
+Missing required "to_atoms" argument
+> matchMaker #6 #3
+Unknown command: matchMaker #6 #3
+> matchMaker #6 to #3
+Unknown command: matchMaker #6 to #3
+> matchmaker #6 to #3
+Computing secondary structure
+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 real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
+chain B (#3) with real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb, chain B (#6), sequence alignment score =
+.2
+RMSD between 823 pruned atom pairs is 0.000 angstroms; (across all 823 pairs:
+.000)
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!5 models
+> fitMap #5 #2
+Unknown command: fitMap #5 #2
+> fitMap #5 to #2
+Unknown command: fitMap #5 to #2
+> fitMap #5 inMap #2
+Unknown command: fitMap #5 inMap #2
+> fitmap #5 inMap #2
+Fit map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc in map
+cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc using 33671 points
+correlation = 0.2174, correlation about mean = 0.04112, overlap = 237.1
+steps = 80, shift = 0.594, angle = 1.18 degrees
+Position of
+State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#5) relative to
+cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.49093697 -0.86901817 -0.06154935 180.57446509
+.85839817 0.49458163 -0.13616756 -28.14054668
+.14877326 0.01401584 0.98877201 -18.53097395
+Axis 0.08598408 -0.12041542 0.98899285
+Axis point 115.25822066 140.21594117 0.00000000
+Rotation angle (degrees) 60.84687762
+Shift along axis 0.58808435
+> ui mousemode right rotate
+> ui mousemode right "rotate selected models"
+> select add #5
+models selected
+> view matrix models
+> #5,0.86956,0.28743,0.40156,-77.867,-0.36997,0.91778,0.14421,37.739,-0.32709,-0.27397,0.90441,92.416
+> view matrix models
+> #5,0.93675,0.31834,-0.14547,-14.538,-0.31142,0.94778,0.068705,36.682,0.15974,-0.019057,0.98697,-15.975
+> view matrix models
+> #5,0.9119,0.36696,0.18378,-63.838,-0.39413,0.90789,0.14284,42.361,-0.11444,-0.20269,0.97253,46.091
+> view matrix models
+> #5,0.83191,0.18763,0.52222,-76.207,-0.3153,0.93425,0.16662,25.403,-0.45662,-0.30327,0.83638,122.4
+> view matrix models
+> #5,0.80642,0.251,0.53543,-83.467,-0.30673,0.95167,0.015837,42.909,-0.50558,-0.177,0.84443,110.24
+> view matrix models
+> #5,0.58595,0.6547,0.47753,-102.55,-0.73093,0.68143,-0.037369,141.33,-0.34987,-0.32714,0.87782,106.29
+> view matrix models
+> #5,0.55983,0.70952,0.42799,-99.825,-0.77263,0.63361,-0.039764,153.52,-0.29939,-0.30842,0.90291,93.808
+> view matrix models
+> #5,0.56832,0.70324,0.42716,-99.932,-0.7727,0.63456,-0.016629,150.18,-0.28275,-0.32061,0.90402,93.202
+> volume #5 level 0.07792
+> volume #5 step 1
+> transparency #6 50
+> transparency #5 50
+> hide #!2 models
+> select add #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 6 models selected
+> show sel cartoons
+> view matrix models
+> #3,0.72097,0.44589,-0.53046,47.646,-0.54116,0.84042,-0.029076,86.505,0.43284,0.30802,0.84721,-86.27,#5,0.59849,0.71718,0.35702,-96.718,-0.76798,0.64047,0.00080783,146.6,-0.22808,-0.27467,0.9341,76.454
+> view matrix models
+> #3,0.71289,0.45635,-0.53247,47.56,-0.54968,0.83513,-0.020195,86.962,0.43547,0.30709,0.84621,-86.325,#5,0.58873,0.72613,0.35515,-96.319,-0.77632,0.63033,-0.0018491,149.32,-0.2252,-0.27462,0.93481,75.977
+> view matrix models
+> #3,0.71287,0.45638,-0.53248,47.56,-0.5497,0.83512,-0.020173,86.963,0.43548,0.30709,0.8462,-86.325,#5,0.58871,0.72615,0.35514,-96.318,-0.77634,0.63031,-0.0018557,149.33,-0.2252,-0.27462,0.93481,75.976
+> select subtract #3
+models selected
+> view matrix models
+> #5,0.64532,0.75454,-0.11929,-46.01,-0.73531,0.65587,0.17073,118.84,0.20706,-0.022467,0.97807,-15.117
+> ui mousemode right "translate selected models"
+> view matrix models
+> #5,0.64532,0.75454,-0.11929,-33.098,-0.73531,0.65587,0.17073,117.84,0.20706,-0.022467,0.97807,-17.108
+> view matrix models
+> #5,0.64532,0.75454,-0.11929,-31.521,-0.73531,0.65587,0.17073,112.2,0.20706,-0.022467,0.97807,-17.91
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #5,0.6506,0.75522,-0.079794,-37.34,-0.75574,0.65419,0.029836,133.07,0.074734,0.040893,0.99636,-11.503
+> ui mousemode right "translate selected models"
+> view matrix models
+> #5,0.6506,0.75522,-0.079794,-37.908,-0.75574,0.65419,0.029836,135.06,0.074734,0.040893,0.99636,-14.225
+> fitmap #3 inMap #5
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map
+State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#5) using 13446 atoms
+average map value = 0.3504, steps = 116
+shifted from previous position = 2.36
+rotated from previous position = 9.54 degrees
+atoms outside contour = 2689, contour level = 0.077924
+Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) relative to
+State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#5) coordinates:
+Matrix rotation and translation
+.85608006 -0.45325355 -0.24837099 110.20658380
+.30092060 0.82781164 -0.47347089 41.63304292
+.42020676 0.33058905 0.84506637 -85.76061070
+Axis 0.62364205 -0.51855984 0.58494982
+Axis point 0.00000000 250.94986784 -6.64552907
+Rotation angle (degrees) 40.13933325
+Shift along axis -3.02541784
+> select clear
+> ui mousemode right zoom
+> transparency #5 90
+> hide #!3 cartoons
+> volume #5 level 0.5427
+> volume #5 level 0.2616
+> volume #5 level 0.1192
+> select #3/D:
+Expected an objects specifier or a keyword
+> select #3/D:5
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> matchmaker #2 #3
+Missing required "to" argument
+> matchmaker #2 to #3
+No molecules/chains to match specified
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> matchmaker #4 to #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 real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
+chain A (#3) with 9ere.pdb, chain B (#4), sequence alignment score = 2189.5
+RMSD between 442 pruned atom pairs is 1.346 angstroms; (across all 799 pairs:
+.355)
+> select clear
+> hide #!4 models
+> volume #5 level 0.1491
+> show #!3 cartoons
+> hide #!3 cartoons
+> show #!3 cartoons
+> hide #!3 cartoons
+> ui mousemode right select
+Drag select of 72 atoms, 67 bonds, 5
+State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc
+> select clear
+> show #!3 cartoons
+> select backbone
+atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected
+> show sel & #!3 atoms
+> select clear
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> color sel medium violet red
+> hide sel atoms
+> show sel atoms
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> color sel byhetero
+> select clear
+> volume #5 level 0.1379
+> hide sel cartoons
+> hide sel atoms
+> select clear
+> select #5
+models selected
+> select #3/C:1@C1'
+atom, 1 residue, 1 model selected
+> hide sel cartoons
+> select clear
+> select #3/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> hide sel cartoons
+> hide sel atoms
+> select clear
+> ui mousemode right zoom
+> volume #5 level 0.1267
+> volume #5 level 0.1342
+> volume #5 level 0.1491
+> volume #5 level 0.1229
+> volume #5 level 0.1941
+> volume #5 level 0.2429
+> volume #5 level 0.1267
+> show #!4 models
+> volume #5 level 0.09292
+> volume #5 level 0.2541
+> size stickRadius 0.3 sidechain
+Expected a keyword
+> stickRadius 0.3 sidechain
+Unknown command: stickRadius 0.3 sidechain
+> size stickRadius 0.2
+Changed 99913 bond radii
+> size stickRadius 0.1
+Changed 99913 bond radii
+> size stickRadius 0.15
+Changed 99913 bond radii
+> hide #!4 models
+> select #3/A:251
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #3/A:248
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:251-252
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #3/A:251-254
+atoms, 30 bonds, 4 residues, 1 model selected
+> select #3/A:251-255
+atoms, 37 bonds, 5 residues, 1 model selected
+> select #3/A:251-256
+atoms, 41 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> hide sel atoms
+> hide sel cartoons
+> ui mousemode right select
+> select clear
+> hide #!3 cartoons
+> select backbone
+atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected
+> hide sel & #!3 atoms
+> select clear
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> select #3/D backbone
+Expected a keyword
+> select #3/D,
+Expected an objects specifier or a keyword
+> select backbone & sel
+atoms, 90 bonds, 7 residues, 1 model selected
+> select backbone & sel
+atoms, 90 bonds, 7 residues, 1 model selected
+> show sel atoms
+> select clear
+> view name p11
+> select clear
+> volume #5 level 0.2316
+> view p11
+> select backbone
+atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected
+> show sel & #!3 atoms
+> show sel & #!3 cartoons
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> hide sel cartoons
+> show sel cartoons
+> hide sel atoms
+> show sel atoms
+> hide sel cartoons
+> select clear
+> hide #!5 models
+> show #!4 models
+> show #!3-4 cartoons
+> select #4/U
+atoms, 91 bonds, 4 residues, 1 model selected
+> hide sel cartoons
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> hide sel cartoons
+> select #4/T
+atoms, 1249 bonds, 6 pseudobonds, 56 residues, 3 models selected
+> hide sel cartoons
+> select #3/D:1-6
+atoms, 134 bonds, 6 residues, 1 model selected
+> hide sel atoms
+> select clear
+> select #3/C:1@C1'
+atom, 1 residue, 1 model selected
+> select #3/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select #4/B:254
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #4/B:251
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel cartoons
+> hide sel atoms
+> show sel atoms
+> select clear
+> view p11
+> select #4/B:136
+atoms, 5 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel atoms
+> hide sel atoms
+> select #4/B:134
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #4/B:135
+atoms, 10 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel cartoons
+> hide sel atoms
+> show sel atoms
+> select clear
+> hide #!3-4 cartoons
+> view p1
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!6 models
+> hide #!6 models
+> show #!5 models
+> volume #5 level 0.2277
+> view p11
+> select clear
+> ui mousemode right zoom
+> select #3/A
+atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
+> show sel cartoons
+> ;ect c;ear
+Incomplete command: sequence
+> select clear
+> select #3/A:140
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:135140
+Nothing selected
+> select #3/A:135-140
+atoms, 40 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> hide sel atoms
+> select clear
+> volume #5 level 0.1143
+> size stickRadius 0.1
+Changed 99913 bond radii
+> size stickRadius 0.15
+Changed 99913 bond radii
+> size stickRadius 0.2
+Changed 99913 bond radii
+> size stickRadius 0.17
+Changed 99913 bond radii
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v3.cxs
+> ui tool show "Side View"
+> volume #5 level 0.1964
+> volume #5 level 0.1377
+> volume #5 level 0.1416
+> volume #5 level 0.1534
+> select #3/D:5-7
+atoms, 65 bonds, 3 residues, 1 model selected
+> show sel atoms
+> select ~sel & ##selected
+atoms, 13677 bonds, 20 pseudobonds, 1657 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 65 bonds, 3 residues, 1 model selected
+> select #3/D:4-7
+atoms, 90 bonds, 4 residues, 1 model selected
+> show sel atoms
+> select clear
+> volume #5 level 0.1456
+> volume #5 level 0.1495
+> volume #5 level 0.1143
+> hide #!5 models
+> ui mousemode right select
+> select clear
+> select #3/A:383
+atoms, 6 bonds, 1 residue, 1 model selected
+> select clear
+> show #!3 atoms
+> hide #!3 atoms
+> undo
+> select clear
+> select #3/c
+atoms, 124 bonds, 5 residues, 1 model selected
+> show sel surfaces
+> hide sel surfaces
+> hide sel cartoons
+> hide sel atoms
+> select clear
+> select #3/A
+atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
+> show sel cartoons
+> select clear
+> hide #!3 models
+> show #!3 models
+> hide #!3 atoms
+> select #3/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select clear
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> show sel atoms
+> select clear
+> show #!6 models
+> hide #!6 models
+> show #!5 models
+> select ::name="MG"
+atoms, 16 residues, 6 models selected
+> show sel & #!3 atoms
+> select clear
+> volume #5 level 0.1338
+> volume #5 level 0.1808
+> volume #5 level 0.1064
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> select clearviewname p0402
+Expected an objects specifier or a keyword
+> viewname p0402
+Unknown command: viewname p0402
+> view name p0402
+> volume #5 level 0.1338
+> lighting flat
+> lighting full
+> lighting soft
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting flat
+> lighting full
+> lighting soft
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> view p0402
+> select #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+> color sel cornflower blue
+> select #3/A
+atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
+> color sel cornflowerblue bloue
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color sel cornflower blue
+> cor sel byHetero target a
+Unknown command: cor sel byHetero target a
+> color sel byhetero target a
+> select clear
+> volume #2 level 0.3969
+> volume mask #1 atomSpec sel distance 5 softEdge 2 modelId #4
+Expected a keyword
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> volume mask #5 atomSpec sel distance 5 softEdge 2 modelId #4
+Expected a keyword
+> volume mask #5 atomSpec sel distance 5 softEdge 2
+Expected a keyword
+> volume zone #5 nearAtoms sel range 6 minimalBounds false
+> volume zone #5 nearAtoms sel range 2
+> hide #!5 models
+> show #!5 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> volume zone #5 nearAtoms sel range 2
+> select #3/D & select #3/A:206,211,213,
+Expected a keyword
+> select #3/D, #3/A:206,211,213,
+Expected an objects specifier or a keyword
+> select #3/D, #3/A:206,211,213
+Expected an objects specifier or a keyword
+> select #3/D #3/A:206,211,213
+atoms, 180 bonds, 10 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 2
+> select #3/D #3/A:206,211,213,133
+atoms, 190 bonds, 11 residues, 1 model selected
+> select #3/D #3/A:206,211,213,133.24,249
+Expected a keyword
+> select #3/D #3/A:206,211,213,133,248,249
+atoms, 205 bonds, 13 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 2
+> volume zone #5 nearAtoms sel range 4
+> volume zone #5 nearAtoms sel range 6
+> volume zone #5 nearAtoms sel range 8
+> select #3/D #3/A:200-249
+atoms, 571 bonds, 57 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 8
+> select #3/D #3/A:140-249
+atoms, 881 bonds, 1 pseudobond, 94 residues, 2 models selected
+> volume zone #5 nearAtoms sel range 8
+> select clear
+> ui tool show "Side View"
+> volume #5 level 0.1495
+> save /Users/justinvanriper/Desktop/image24.png supersample 3
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v4.cxs
+> view p1
+> view p0402
+> save /Users/justinvanriper/Desktop/image25.png supersample 3
+> view p0401
+Expected an objects specifier or a view name or a keyword
+> view name p0401
+> select #3/B:133,206,211,213,249,248
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> color sel light blue
+> color sel byhetero
+> select #3/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> show sel atoms
+> color sel hot pink
+> color sel byhetero
+> select #3/C, #3/B:133
+Expected an objects specifier or a keyword
+> select #3/C #3/B:133
+atoms, 134 bonds, 6 residues, 1 model selected
+> select #3/C #3/B:133-250
+atoms, 936 bonds, 1 pseudobond, 103 residues, 2 models selected
+> show sel cartoons
+> select#3/B:133-250
+Unknown command: select#3/B:133-250
+> select #3/B:133-250
+atoms, 812 bonds, 1 pseudobond, 98 residues, 2 models selected
+> volume zone #5 nearAtoms sel range 8
+> select #3/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 8
+> select #3/B:133-250
+atoms, 812 bonds, 1 pseudobond, 98 residues, 2 models selected
+> color sel light blue
+> color sel byhetero
+> select clear
+> select #3/B:133-250 #3/C
+atoms, 936 bonds, 1 pseudobond, 103 residues, 2 models selected
+> volume zone #5 nearAtoms sel range 8
+> select #3/B
+atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
+> color sel light blue
+> color sel byhetero
+> select #3/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> show sel cartoons
+> hide sel cartoons
+> show sel atoms
+Drag select of 5
+State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc
+> select clear
+Drag select of 1 atoms, 5
+State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc
+> select #5
+models selected
+> select #5
+models selected
+> select clear
+> save /Users/justinvanriper/Desktop/image26.png supersample 3
+> view name p0404
+> view p0404
+> view p0401
+> close
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited-
+> coot-15_real_space_refined_015.pdb
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+> select #1/A
+atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 7024 bonds, 10 pseudobonds, 837 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 7024 bonds, 10 pseudobonds, 837 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
+> select #1/A:1-351
+atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected
+> color sel cornflower blue
+> select #1/B:1-351
+atoms, 2692 bonds, 1 pseudobond, 328 residues, 2 models selected
+> color sel light blue
+> select #1/B:352-555
+atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
+> color sel khaki
+> select #1/A:352-555
+atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
+> color sel gold
+> select #1/A:556-912
+atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
+> color sel sienna
+> select #1/B:556-912
+atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
+> color sel sandy brown
+> select clear
+> split #1
+Split real_space_refined_036_edited-coot-15_real_space_refined_015.pdb (#1)
+into 4 models
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb A #1.1
+---
+Chain | Description
+A | No description available
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb B #1.2
+---
+Chain | Description
+B | No description available
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb C #1.3
+---
+Chain | Description
+C | No description available
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb D #1.4
+---
+Chain | Description
+D | No description available
+> hide #!1.1 models
+> show #!1.1 models
+> hide #!1.1 models
+> show #!1.1 models
+> hide #!1.2 models
+> show #!1.2 models
+> align #1.1 toAtoms #1.2
+Unequal number of atoms to pair, 6584 and 6609
+> align #1.1 #1.2
+Missing required "to_atoms" argument
+> matchmaker #1.1 #1.2
+Missing required "to" argument
+> matchmaker #1.1 to #1.2
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker real_space_refined_036_edited-coot-15_real_space_refined_015.pdb B,
+chain B (#1.2) with real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb A, chain A (#1.1), sequence alignment score
+= 4058.4
+RMSD between 795 pruned atom pairs is 0.752 angstroms; (across all 820 pairs:
+.884)
+> select clear
+> color byhetero target a
+> select clear
+> select #1.2/B:1002@MG
+atom, 1 residue, 1 model selected
+> hide #1.3 models
+> hide #1.4 models
+> show #1.3 models
+> hide #1.3 models
+> show #1.4 models
+> hide #1.4 models
+> select clear
+> hide #!1.1-2 atoms
+> select ::name="MG"::name="ZN"
+atoms, 5 residues, 2 models selected
+> show sel atoms
+> select clear
+> select #1/A,B: 133,206,211,213,248,249
+atoms, 98 bonds, 12 residues, 2 models selected
+> show sel atoms
+> select clear
+> select #1/A,B: 284,282,318,219
+atoms, 56 bonds, 8 residues, 2 models selected
+> show sel atoms
+> select clear
+> select cleartransparency #1.2 50
+Expected an objects specifier or a keyword
+> transparency #1.2 50
+> transparency #1.2 50 target c
+> transparency #1.2 50 target c,a
+Invalid "target" argument: Character ',' is not an allowed target, must be one
+of acrsbmpfl
+> transparency #1.2 50 target c a
+Expected a keyword
+> transparency #1.2 50 target a
+> select #1.2
+atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
+> color sel old lace
+> select clear
+> hide #!1 models
+> open
+> "/Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM
+> Maps/State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+> sharpened-highres.mrc"
+> "/Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM
+> Maps/State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
+> sharpened-highres.mrc"
+Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc as #2.1, grid size 300,300,300, pixel 0.832, shown at
+level 0.0049, step 2, values float32
+Opened
+State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
+sharpened-highres.mrc as #2.2, grid size 300,300,300, pixel 0.832, shown at
+level 0.00701, step 2, values float32
+> select clear
+> volume #2.1 step 1
+> volume #2.2 step 1
+> volume #2.1 level 0.0284
+> volume #2.2 level 0.03203
+> surface dust #2.1 size 8.32
+> surface dust #2.2 size 8.32
+> surface dust #2.1 size 8.32
+> surface dust #2.2 size 8.32
+> surface dust #2.1 size 8.32
+> surface dust #2.2 size 8.32
+> lighting flat
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> close #1
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited-
+> coot-15_real_space_refined_015.pdb
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+> color #2.2 darkgrey models
+> hide #!2 models
+> hide #!2.1-2 target m
+> show #!2.2 target m
+> hide #!1 target m
+> show #!2.1 target m
+> hide #!2.2 target m
+> show #!1 target m
+> hide #!2.1 target m
+> show #!2.2 target m
+> hide #!1 target m
+> show #!1 target m
+> hide #!2.2 target m
+> show #!2.1 target m
+> hide #!1 target m
+> show #!2.2 target m
+> hide #!2.1 target m
+> show #!1 target m
+> hide #!2.2 target m
+> select #1/A:1-351
+atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected
+> color sel cornflower blue
+> select #1/B:1-351
+atoms, 2692 bonds, 1 pseudobond, 328 residues, 2 models selected
+> color sel light blue
+> select #1/B:352-555
+atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
+> color sel khaki
+> select #1/A:352-555
+atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
+> color sel gold
+> select #1/A:556-912
+atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
+> color sel sienna
+> select #1/B:556-912
+atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
+> color sel sandy brown
+> select clear
+> show #!2.1 models
+> color zone #2.1 near #1 distance 4.99
+> select clear
+> hide #!2 models
+> show #!2 models
+> select #1/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> color sel hot pink
+> select #1/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> color sel medium violet red
+> color zone #2.1 near sel & #1 distance 4.99
+> hide #!2 models
+> hide #!2.1 models
+> show #!2.2 models
+> hide #!2.2 models
+> show #!2.1 models
+> select clear
+> color zone #2.1 near #1 distance 4.99
+> select clear
+> hide #!2.1 models
+> show #!2.1 models
+> show #!2.2 models
+> hide #!1 models
+> color #2.2 #ebebebff models
+> color #2.2 white models
+> color #2.2 #ebebebff models
+> color #2.2 white models
+> volume #2.1 level 0.04701
+> hide #!2.2 models
+> volume #2.1 level 0.05631
+> show #!2.2 models
+> volume #2.2 level 0.06777
+> ui tool show "Side View"
+> view name p1
+> roll y 1 90
+> roll y -1 90
+> roll y -1 45
+> roll y 1 45
+> save /Users/justinvanriper/Desktop/image27.png supersample 3
+> roll x 1 90
+> save /Users/justinvanriper/Desktop/image28.png supersample 3
+> view name p2
+> roll x 1 180
+> save /Users/justinvanriper/Desktop/image29.png supersample 3
+> roll x 1 90
+> roll y -1 90
+> save /Users/justinvanriper/Desktop/image30.png supersample 3
+> roll y 1 135
+> save /Users/justinvanriper/Desktop/image31.png supersample 3
+> hide #!2 models
+> show #!1 models
+> hide atoms
+> hide cartoons
+> select #1/A:284,282,318,319
+atoms, 26 bonds, 4 residues, 1 model selected
+> show sel atoms
+> color sel pink
+> color sel light pink
+> color sel magenta
+> ui tool show "Color Actions"
+> color sel orchid
+> color sel pale violet red
+> color sel hot pink
+> color sel thistle
+> color sel violet
+> color sel plum
+> color sel violet
+> color sel light pink
+> color sel violet
+> color sel byhetero
+> select clear
+Drag select of 28 atoms, 26 bonds
+> color sel #d6b8ddff
+> color sel #f4b8fbff
+> color sel #ecb1f1ff
+> select clear
+> color #1 byhetero
+> select clear
+> select ::name="ZN"
+atoms, 2 residues, 1 model selected
+> show sel atoms
+> select backbone
+atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
+> hide sel atoms
+> undo
+> select clear
+> select /A:318@N
+atom, 1 residue, 1 model selected
+> select add /A:319@O
+atoms, 5 bonds, 2 residues, 1 model selected
+> select add /A:318@O
+atoms, 5 bonds, 2 residues, 1 model selected
+> select subtract /A:318@O
+atoms, 5 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select /A:319@N
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select /A:318@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select /A:318@C
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select /A:319@C
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> hide atoms
+> undo
+> select /A:284@O
+atom, 1 residue, 1 model selected
+> select add /A:284@C
+atoms, 1 residue, 1 model selected
+> select add /A:284@CA
+atoms, 1 residue, 1 model selected
+> select subtract /A:284@CA
+atoms, 1 residue, 1 model selected
+> select add /A:284@CA
+atoms, 1 bond, 1 residue, 1 model selected
+> select subtract /A:284@CA
+atoms, 1 residue, 1 model selected
+> select add /A:284@N
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select /A:282@O
+atom, 1 residue, 1 model selected
+> select add /A:282@C
+atoms, 1 residue, 1 model selected
+> select add /A:282@N
+atoms, 1 residue, 1 model selected
+> select add /A:282@CA
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> undo
+> select subtract /A:282@CA
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> color #1.1 black models
+> color #1.1 #212121ff models
+> color #1.1 #424242ff models
+> select clear
+Drag select of 3 atoms, 2 bonds, 1 pseudobonds
+> ~hbonds
+> select clear
+> hide cartoons
+> hide atoms
+> undo
+> select clear
+> select main
+atoms, 13462 bonds, 13 pseudobonds, 1643 residues, 3 models selected
+> select clear
+> delete sel
+> hide pseudobonds
+> select /A:1001@ZN
+atom, 1 residue, 1 model selected
+> show pseudobonds sel
+Expected ',' or a keyword
+> show sel pseudobonds
+> metalBonds
+Unknown command: metalBonds
+> metalBonds #1
+Unknown command: metalBonds #1
+> hbonds sel reveal true
+hydrogen bonds found
+> ~hbonds
+> hide sel pbonds
+> select clear
+> save /Users/justinvanriper/Desktop/image32.png supersample 3
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb
+Chain information for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb #3
+---
+Chain | Description
+A B | No description available
+G | No description available
+Computing secondary structure
+> matchmaker #3 to #1
+Computing secondary structure
+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 real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
+chain A (#1) with Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb, chain A (#3),
+sequence alignment score = 3942.6
+RMSD between 766 pruned atom pairs is 1.001 angstroms; (across all 820 pairs:
+.544)
+> select clear
+> hide #!1 models
+> select #3/C:1@ZN
+atom, 1 residue, 1 model selected
+> show pbonds
+> select clear
+===== Log before crash end =====
+Log:
+UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v4.cxs
+Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.397,
+step 1, values float32
+Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc as #5, grid size 300,300,300, pixel 0.832, shown at
+level 0.149, step 1, values float32
+Log from Wed Apr 2 14:23:23 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v2.cxs
+Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.15,
+step 1, values float32
+Log from Sun Mar 30 16:27:42 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/justinvanriper/Library/CloudStorage/OneDrive-
+> BaylorCollegeofMedicine/Pillon
+> Lab/SLFN14/SLFN14_Figure5_Drafts/Figure5_draft_images/SLFN_Family_Alignments_Figures.cxs"
+> format session
+Log from Thu Aug 1 13:17:53 2024 Startup Messages
+---
+note | available bundle cache has not been initialized yet
+UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+How to cite UCSF ChimeraX
+> open /Users/justinvanriper/Desktop/all_aligned_SLFN.cif
+Summary of feedback from opening
+/Users/justinvanriper/Desktop/all_aligned_SLFN.cif
+---
+warnings | Missing entity information. Treating each chain as a separate entity.
+Missing or incomplete sequence information. Inferred polymer connectivity.
+Unknown polymer entity '1' on line 13552
+Unable to infer polymer connectivity due to unspecified label_seq_id for
+residue "GLY" on line 13558
+Missing or incomplete sequence information. Inferred polymer connectivity.
+Unknown polymer entity '1' on line 23886
+Unknown polymer entity '2' on line 28036
+Missing or incomplete sequence information. Inferred polymer connectivity.
+Missing entity information. Treating each chain as a separate entity.
+Missing or incomplete sequence information. Inferred polymer connectivity.
+Unknown polymer entity '1' on line 51632
+Missing or incomplete sequence information. Inferred polymer connectivity.
+Missing entity information. Treating each chain as a separate entity.
+Missing or incomplete sequence information. Inferred polymer connectivity.
+atoms have alternate locations. Control/examine alternate locations with
+Altloc Explorer [start tool...] or the altlocs command.
+Chain information for all_aligned_SLFN.cif
+---
+Chain | Description
+.1/A 1.1/B | No description available
+.2/A | No description available
+.3/A 1.3/C | No description available
+.4/A 1.4/B | No description available
+.5/A | No description available
+.6/A | No description available
+.2/B | No description available
+.3/B 1.3/D | No description available
+.5/B | No description available
+.1/C | No description available
+.2/C | No description available
+.1/D | No description available
+.2/D | No description available
+> hide #!1 models
+> hide #!1.1 models
+> show #!1.1 models
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> hide #1.6 models
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> show cartoons
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> show sel cartoons
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/C
+atoms, 121 bonds, 5 residues, 1 model selected
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/C
+atoms, 121 bonds, 5 residues, 1 model selected
+> show sel cartoons
+> nucleotides sel ladder
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> color sel light pink
+> select #1.1/B,D
+atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/C
+atoms, 121 bonds, 5 residues, 1 model selected
+> show sel cartoons
+> nucleotides sel ladder
+> set bgColor white
+> hide #1.1.1 models
+> show #1.1.1 models
+> hide #1.1.1 models
+> save /Users/justinvanriper/Desktop/SLFFN14_alignments_all.cxs
+> select #1.1/A
+atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/A:180-316
+atoms, 1150 bonds, 137 residues, 1 model selected
+> show sel cartoons
+> select #1.1/C
+atoms, 121 bonds, 5 residues, 1 model selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> show sel cartoons, show sel atoms, nucleotides sel ladder
+Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
+'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
+> show sel cartoons
+> show sel atoms
+> nucleotides sel ladder
+> hide atoms
+> select #1.1/A
+atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
+> show sel cartoons
+> select #1.1/C,D
+atoms, 238 bonds, 10 residues, 1 model selected
+> show sel cartoons
+> show sel atoms
+> nucloetides ladder
+Unknown command: nucloetides ladder
+> nucloetides sel ladder
+Unknown command: nucloetides sel ladder
+> nucleotides sel ladder
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> color sel blue violet
+> color sel byhetero
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> color sel blue violet
+> color sel byhetero
+> ui tool show "Color Actions"
+> color sel cornflower blue target c
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> color sel blue violet target a
+> color sel byhetero
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> select #1.1/C
+atoms, 121 bonds, 5 residues, 1 model selected
+> hide sel catoons; hide sel atoms
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> hide sel catoons
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> hide sel cartoons
+> hide sel atoms
+> ui mousemode right select
+Drag select of 455 residues
+> hide sel cartoons
+Drag select of 40 residues
+> hide sel cartoons
+> ui tool show "Side View"
+> lighting simple
+> lighting soft
+> lighting full
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting simple
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> size stickRadius 0.4
+Changed 58414 bond radii
+> size stickRadius 0.3
+Changed 58414 bond radii
+> size stickRadius 0.35
+Changed 58414 bond radii
+> select clear
+> select ::name="MG"
+atoms, 6 residues, 3 models selected
+> show sel & #!1.1 atoms
+> color (#!1.1 & sel) byelement
+> select clear
+> select #1.1/B:1002@MG
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> view name p1
+> show #!1.2 models
+> select #1.2/A
+atoms, 2639 bonds, 3 pseudobonds, 329 residues, 2 models selected
+> select #1.2/A:134,205,210,212,247,248
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select ~sel & ##selected
+atoms, 10425 bonds, 16 pseudobonds, 1300 residues, 2 models selected
+> hide cartoons
+Drag select of 40 atoms, 39 bonds, 10 shapes
+> hide atoms
+> select #1.2/A:134,205,210,212,247,248
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select #1.2/A:134,205,210,212,247,248
+atoms, 49 bonds, 6 residues, 1 model selected
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+Drag select of 12 atoms, 11 bonds
+> color #1.2 #ffcc99ff
+> color #1.2 #ccccccff
+> select #1.2/A:134,205,210,212,247,248
+atoms, 49 bonds, 6 residues, 1 model selected
+> color sel light grey
+> select #1.2/A:134,205,210,212,247,248
+atoms, 49 bonds, 6 residues, 1 model selected
+> color sel light grey
+> color sel byhetero
+> select ::name="MG"
+atoms, 6 residues, 3 models selected
+> show sel & #!1.1 atoms
+> size stickRadius 0.2
+Changed 58414 bond radii
+> show #!1.3 models
+> select #1.3/A
+atoms, 4221 bonds, 2 pseudobonds, 513 residues, 2 models selected
+> show sel cartoons
+> hide sel cartoons
+> select #1.3/A:129,200,205,207
+atoms, 34 bonds, 4 residues, 1 model selected
+> show sel atoms
+> select #1.3/A:129,200,205,207
+atoms, 34 bonds, 4 residues, 1 model selected
+> color sel light grey
+> color sel byhetero
+> select #1.4/A:135,209,214,216,251,252
+atoms, 49 bonds, 6 residues, 1 model selected
+> color sel light grey
+> color sel byhetero
+> select #1.4/A:135,209,214,216,251,252
+atoms, 49 bonds, 6 residues, 1 model selected
+> show sel atoms
+> color sel light grey
+> color sel byhetero
+> show #!1.4 models
+> show #!1.5 models
+> select ::name="MG"
+atoms, 6 residues, 3 models selected
+> select ::name="MG"
+atoms, 6 residues, 3 models selected
+> show sel atoms
+Drag select of 4 atoms
+> hide sel atoms
+> select #1.5/A:120,191,196,233
+atoms, 33 bonds, 4 residues, 1 model selected
+> show sel atoms
+> color sel light grey
+> color sel byhetero
+> select #1.5/B:120,191,196,233
+atoms, 33 bonds, 4 residues, 1 model selected
+> show sel atoms
+> color sel light grey
+> color sel byhetero
+Drag select of 37 atoms, 33 bonds
+> hide sel atoms
+> show #1.6 models
+> close #1.6
+> hide #!1.3 models
+> hide #!1.4 models
+> show #!1.4 models
+> hide #!1.5 models
+> hide #!1.2 models
+> view name p2
+> hide #!1.4 models
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> hide #!1.5 models
+> hide #!1.4 models
+> hide #!1.3 models
+> hide #!1.2 models
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> hide #!1.5 models
+> show #!1.5 models
+Drag select of 239 atoms, 214 bonds
+> hide sel target a
+> show (sel-residues & sidechain) target ab
+> select ::name="MG"
+atoms, 6 residues, 3 models selected
+> show sel atoms
+> select clear
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 1 pseudobond, 6 residues, 2 models selected
+> color sel blue violoet
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 1 pseudobond, 6 residues, 2 models selected
+> color sel blue violet
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> view p1
+> select #1.1/A
+atoms, 6769 bonds, 7 pseudobonds, 828 residues, 3 models selected
+> show sel cartoons
+> select #1.1/A
+atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
+> show sel cartoons
+> select #1.1/C
+atoms, 121 bonds, 5 residues, 1 model selected
+> show sel cartoons
+> select #1.1/A
+atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
+> show sel cartoons
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> show sel cartoons
+> select #1.1/C
+atoms, 121 bonds, 5 residues, 1 model selected
+> hide sel cartoons
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> show atoms
+> show sel atoms
+Drag select of 205 residues
+> hide sel cartoons
+> hide sel atoms
+> select clear
+[Repeated 1 time(s)]Drag select of 273 residues
+> hide sel cartoons
+Drag select of 3 residues
+> hide sel cartoons
+Drag select of 4 residues
+> hide sel cartoons
+Drag select of 6 residues
+> hide sel cartoons
+Drag select of 4 residues
+> hide sel cartoons
+> view p1
+> cartoon style sel modeHelix tube sides 20
+Drag select of 38 atoms, 356 residues, 30 bonds, 10 shapes
+> select clear
+> show #!1.2 models
+> hide #!1.2 models
+> view p1
+> show #!1.2 models
+> show #!1.3 models
+> hide #!1.3 models
+> hide #!1.2 models
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel light gray target c
+> select clear
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> color sel blue violoet
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel cornflower blue target a
+> select clear
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> color sel blue
+> ui tool show "Color Actions"
+> color sel blue target a
+> select ~sel & ##selected
+atoms, 13727 bonds, 12 pseudobonds, 1660 residues, 2 models selected
+> select down
+atoms, 13727 bonds, 12 pseudobonds, 1660 residues, 2 models selected
+> select clear
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> color sel cornflower blue
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> color sel light pink
+> select #1.1/A:1002@MG
+atom, 1 residue, 1 model selected
+> color sel byelement
+> select #1.1/A:133,206,211,213,248,249
+atoms, 49 bonds, 6 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel orange target a
+> color sel orange red target a
+> color sel magenta target a
+> color sel deep pink target a
+[Repeated 1 time(s)]
+> size stickRadius 0.4
+Changed 57471 bond radii
+> size stickRadius 0.3
+Changed 57471 bond radii
+> size stickRadius 0.34
+Changed 57471 bond radii
+> ui tool show "Color Actions"
+> color sel dark violet target a
+> color sel medium violet red target a
+> color sel violet target a
+> color sel medium violet red target a
+> color sel rebecca purple target a
+> color sel deep pink target a
+> color sel magenta target a
+> color sel deep pink target a
+[Repeated 1 time(s)]
+> color sel medium violet red target a
+[Repeated 2 time(s)]
+> color sel dark violet target a
+> color sel orange red target a
+> color sel red target a
+> color sel orange red target a
+> color sel crimson target a
+[Repeated 1 time(s)]
+> color sel orange red target a
+> color sel crimson target a
+> color sel red target a
+> color sel crimson target a
+> color sel byhetero target a
+> color sel dark orange target a
+> color sel byhetero target a
+> color sel green target a
+> color sel forest green target a
+[Repeated 1 time(s)]
+> color sel dark orange target a
+> color sel byhetero target a
+> select clear
+> view name p1
+> save /Users/justinvanriper/Desktop/image2.png supersample 3
+> select #1.1/B:1002@MG
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> save /Users/justinvanriper/Desktop/image3.png supersample 3
+> show #!1.2 models
+> hide #!1.1 models
+> show #!1.1 models
+> select up
+atoms, 6769 bonds, 828 residues, 1 model selected
+> select #1.1/A
+atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
+> hide sel cartoons
+> undo
+> select clear
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting full
+[Repeated 1 time(s)]
+> lighting soft
+> lighting simple
+> lighting flat
+> lighting full
+> lighting soft
+> lighting simple
+[Repeated 1 time(s)]
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> save /Users/justinvanriper/Desktop/image4.png supersample 3
+> select #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> hide sel cartoons
+Drag select of 40 atoms, 39 bonds, 10 shapes
+> hide sel atoms
+> view p2
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> size stickRadius 0.2
+Changed 57471 bond radii
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.5 models
+> select pbonds
+pseudobonds, 8 models selected
+> hide pbonds
+> select clear
+> select #1.4/B:1002@MG
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+[Repeated 1 time(s)]
+> show #!1.3 models
+> hide #!1.4 models
+> show #!1.2 models
+> show #!1.4 models
+> show #!1.5 models
+> hide #!1.2 models
+> show #!1.2 models
+> hide #!1.2 models
+> show #!1.2 models
+> hide #!1.4 models
+> hide #!1.3 models
+> hide #!1.5 models
+> hide #!1.2 models
+> show #!1.2 models
+> hide #!1.2 models
+> show #!1.2 models
+> hide #!1.2 models
+> show #!1.2 models
+> show cartoons
+> hide #!1.2 models
+> show #!1.3 models
+> select #1.3/A:242
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #1.3/A:243
+atoms, 15 bonds, 2 residues, 1 model selected
+> show sel atoms
+> color sel light grey
+> color sel byhetero
+> hide cartoons
+> hide pbonds
+> hide sel target a
+> show (sel-residues & sidechain) target ab
+> hide pbonds
+> view name final
+> hide #!1.3 models
+> show #!1.4 models
+> hide #!1.4 models
+> show #!1.5 models
+> show cartoons
+> select #1.5/B:198
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #1.5/B:232
+atoms, 16 bonds, 2 residues, 1 model selected
+> show (sel-residues & sidechain) target ab
+> color sel light grey
+> color sel byhetero
+> hide cartoons
+> hide pbonds
+> hide #!1.5 models
+> save /Users/justinvanriper/Desktop/image1.png supersample 3
+> show #!1.2 models
+> save /Users/justinvanriper/Desktop/image2.png supersample 3
+> hide #!1.2 models
+> show #!1.3 models
+> save /Users/justinvanriper/Desktop/image3.png supersample 3
+> hide #!1.3 models
+> show #!1.4 models
+> save /Users/justinvanriper/Desktop/image4.png supersample 3
+> hide #!1.4 models
+> show #!1.5 models
+> save /Users/justinvanriper/Desktop/image5.png supersample 3
+> hide #!1.5 models
+> show cartoons
+> view p1
+> view p2
+> view p3
+Expected an objects specifier or a view name or a keyword
+> view p1
+> select #1.1/B,C
+atoms, 6890 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+Drag select of 180 residues
+Drag select of 389 residues
+> hide sel cartoons
+Drag select of 90 residues
+> hide sel cartoons
+Drag select of 7 residues
+> hide sel cartoons
+Drag select of 8 residues
+> hide sel cartoons
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> show sel atoms
+> select clear
+> save /Users/justinvanriper/Desktop/image6.png supersample 3
+> show #1.1.1 models
+> select #1.1/A
+atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
+> show cartoons
+> select #1.1/B,C
+atoms, 6890 bonds, 6 pseudobonds, 833 residues, 2 models selected
+> hide sel cartoons
+> hide #1.1.1 models
+> show #1.1.1 models
+> select #1.1/A:349
+atoms, 7 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1.1/A #1.1/B
+Alignment identifier is 1
+> select #1.1/A-B:381-383
+atoms, 46 bonds, 6 residues, 1 model selected
+> select #1.1/A-B:381-402
+atoms, 386 bonds, 44 residues, 1 model selected
+> select #1.1/A-B:334-335
+atoms, 26 bonds, 4 residues, 1 model selected
+> select #1.1/A-B:334-405
+atoms, 706 bonds, 2 pseudobonds, 82 residues, 2 models selected
+> select #1.1/A-B:334-337
+atoms, 54 bonds, 8 residues, 1 model selected
+> select #1.1/A-B:334-384
+atoms, 328 bonds, 2 pseudobonds, 40 residues, 2 models selected
+> select clear
+[Repeated 1 time(s)]
+> select #1.1/A:349
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1.1/A-B:381-384
+atoms, 68 bonds, 8 residues, 1 model selected
+> select #1.1/A-B:381-403
+atoms, 404 bonds, 46 residues, 1 model selected
+Drag select of 145 residues
+> hide sel cartoons
+Drag select of 178 residues
+> hide sel cartoons
+> view p1
+Drag select of 173 residues
+> hide sel cartoons
+Drag select of 49 residues
+> hide sel cartoons
+> view p1
+> save /Users/justinvanriper/Desktop/image7.png supersample 3
+> size stickRadius 0.3
+Changed 57471 bond radii
+> size stickRadius 0.35
+Changed 57471 bond radii
+> size stickRadius 0.34
+Changed 57471 bond radii
+> size stickRadius 0.4
+Changed 57471 bond radii
+> size stickRadius 0.3
+Changed 57471 bond radii
+> size stickRadius 0.35
+Changed 57471 bond radii
+> save /Users/justinvanriper/Desktop/image8.png supersample 3
+> view final
+> hide cartoons
+> hide pbonds
+> select #1.1/D
+atoms, 117 bonds, 5 residues, 1 model selected
+> hide sel atoms
+> size stickRadius 0.2
+Changed 57471 bond radii
+> show #!1.3 models
+> hide #!1.3 models
+> show #!1.4 models
+> hide #!1.4 models
+> show #!1.5 models
+> save /Users/justinvanriper/Desktop/image9.png supersample 3
+> select #1.1/A:211@CD
+atom, 1 residue, 1 model selected
+> view ginal
+Expected an objects specifier or a view name or a keyword
+> view final
+> color sel byhetero
+> select add #1.5/B:198@CA
+atom, 3 bonds, 1 residue, 1 model selected
+> select add #1.5/B:198@CG2
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #1.5/B:198@CG1
+atoms, 3 bonds, 1 residue, 1 model selected
+> color sel byhetero
+> view final
+> select clear
+> show #!1.4 models
+> hide #!1.5 models
+> select #1.4/A:1002@MG
+atom, 1 residue, 1 model selected
+> color sel light grey
+> select clear
+[Repeated 1 time(s)]
+> view final
+> save /Users/justinvanriper/Desktop/image1.png supersample 3
+> hide #!1.4 models
+> show #!1.2 models
+> select ::name="MG"
+atoms, 6 residues, 3 models selected
+> show sel & #!1.1 atoms
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> select ::name="MG"
+atoms, 6 residues, 3 models selected
+> hide sel atoms
+> show sel atoms
+> hide #!1.5 models
+> hide #!1.4 models
+> hide #!1.3 models
+> hide #!1.2 models
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> hide #!1 models
+> show #!1 models
+> hide #!1.1 models
+> hide #1.1.1 models
+> show #!1.1 models
+> show #1.1.1 models
+> select #1.4/A
+atoms, 6809 bonds, 4 pseudobonds, 829 residues, 3 models selected
+> select #1.4/A:1002
+atom, 1 residue, 1 model selected
+> show sel atoms
+> hide #!1.4 models
+> show #!1.4 models
+> hide #!1.4 models
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.5 models
+> show #!1.4 models
+> show #!1.5 models
+> show #!1.3 models
+> show #!1.2 models
+> view final
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> select add #1.4
+atoms, 13618 bonds, 7 pseudobonds, 1658 residues, 3 models selected
+> select subtract #1.4
+Nothing selected
+> select clear
+> select #1.1/A:1002@MG
+atom, 1 residue, 1 model selected
+> show #1.1/A cartoons
+Drag select of 477 residues
+> hide sel cartoons
+Drag select of 64 residues
+> hide sel cartoons
+Drag select of 4 residues
+Drag select of 1 residues
+> hide sel cartoons
+> save /Users/justinvanriper/Desktop/SLFN_Family_Alignments_Figures.cxs
+——— End of log from Thu Aug 1 13:17:53 2024 ———
+opened ChimeraX session
+> hide #!1 models
+> show #!1 models
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> view matrix models #1.1,1,0,0,0.028681,0,1,0,-1.0855,0,0,1,0.26887
+> view matrix models #1.1,1,0,0,5.6932,0,1,0,-8.7173,0,0,1,5.9219
+> undo
+[Repeated 6 time(s)]
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> ui mousemode right select
+> select #1.1/B:1002@MG
+atom, 1 residue, 1 model selected
+> select #1.4/B:1002@MG
+atom, 1 residue, 1 model selected
+> select add #1.1/B:1002@MG
+atoms, 2 residues, 2 models selected
+Drag select of 2 atoms
+> hide sel atoms
+> open
+> /Users/justinvanriper/Downloads/cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+> sharpened-highres.mrc
+Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.0049,
+step 2, values float32
+> volume #2 step 1
+> surface dust #2 size 8.32
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> hide #!1.3 models
+> select add #1.3
+atoms, 14642 bonds, 9 pseudobonds, 1776 residues, 5 models selected
+> select add #1.4
+atoms, 28260 bonds, 16 pseudobonds, 3433 residues, 7 models selected
+> select subtract #1.4
+atoms, 14642 bonds, 9 pseudobonds, 1775 residues, 4 models selected
+> select subtract #1.3
+atom, 1 residue, 1 model selected
+> select add #1.1
+atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
+> select subtract #1.1
+Nothing selected
+> select add #1
+atoms, 57471 bonds, 51 pseudobonds, 7310 residues, 15 models selected
+> show #!1.3 models
+> hide #!2 models
+> show #!2 models
+> fitmap #1 to #2
+Expected a keyword
+> fitmap #1 #2
+Missing required "in_map" argument
+> fitmap #1 inMap #2
+Fit molecules all_aligned_SLFN.cif (#1.1), all_aligned_SLFN.cif (#1.2),
+all_aligned_SLFN.cif (#1.3), all_aligned_SLFN.cif (#1.4), all_aligned_SLFN.cif
+(#1.5) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 56626 atoms
+average map value = 0.03678, steps = 108
+shifted from previous position = 1.51
+rotated from previous position = 2.3 degrees
+atoms outside contour = 43242, contour level = 0.0049001
+Position of all_aligned_SLFN.cif (#1.1) relative to
+cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.99978234 0.01984455 -0.00643950 -2.55579678
+-0.01961186 0.99921634 0.03438151 -2.62383682
+.00711674 -0.03424774 0.99938803 3.12635629
+Axis -0.85449739 -0.16878777 -0.49126867
+Axis point 0.00000000 105.62417749 73.36727950
+Rotation angle (degrees) 2.30148392
+Shift along axis 1.09091235
+Position of all_aligned_SLFN.cif (#1.2) relative to
+cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.99978234 0.01984455 -0.00643950 -2.55579678
+-0.01961186 0.99921634 0.03438151 -2.62383682
+.00711674 -0.03424774 0.99938803 3.12635629
+Axis -0.85449739 -0.16878777 -0.49126867
+Axis point 0.00000000 105.62417749 73.36727950
+Rotation angle (degrees) 2.30148392
+Shift along axis 1.09091235
+Position of all_aligned_SLFN.cif (#1.3) relative to
+cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.99978234 0.01984455 -0.00643950 -2.55579678
+-0.01961186 0.99921634 0.03438151 -2.62383682
+.00711674 -0.03424774 0.99938803 3.12635629
+Axis -0.85449739 -0.16878777 -0.49126867
+Axis point 0.00000000 105.62417749 73.36727950
+Rotation angle (degrees) 2.30148392
+Shift along axis 1.09091235
+Position of all_aligned_SLFN.cif (#1.4) relative to
+cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.99978234 0.01984455 -0.00643950 -2.55579678
+-0.01961186 0.99921634 0.03438151 -2.62383682
+.00711674 -0.03424774 0.99938803 3.12635629
+Axis -0.85449739 -0.16878777 -0.49126867
+Axis point 0.00000000 105.62417749 73.36727950
+Rotation angle (degrees) 2.30148392
+Shift along axis 1.09091235
+Position of all_aligned_SLFN.cif (#1.5) relative to
+cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
+highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.99978234 0.01984455 -0.00643950 -2.55579678
+-0.01961186 0.99921634 0.03438151 -2.62383682
+.00711674 -0.03424774 0.99938803 3.12635629
+Axis -0.85449739 -0.16878777 -0.49126867
+Axis point 0.00000000 105.62417749 73.36727950
+Rotation angle (degrees) 2.30148392
+Shift along axis 1.09091235
+> hide #!2 models
+> show #!1.3 models
+> hide #!2 models
+> open
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited-
+> coot-15_real_space_refined_015.pdb
+Chain information for real_space_refined_036_edited-
+coot-15_real_space_refined_015.pdb #3
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+> matchmaker #3 #1
+Missing required "to" argument
+> matchmaker #3 to #1
+Specify a single 'to' model only
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> show #!2 models
+> ui mousemode right rotate
+> select add #2
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.99515,0.098138,0.0064363,-12.459,-0.09771,0.99402,-0.048809,19.329,-0.011188,0.047943,0.99879,-4.4154
+> view matrix models
+> #2,0.47802,0.46441,-0.74553,103.42,-0.7247,0.68812,-0.036009,134.97,0.49629,0.5575,0.6655,-89.337
+> view matrix models
+> #2,0.69209,0.72031,-0.04649,-45.074,-0.71049,0.69118,0.13222,111.25,0.12737,-0.058477,0.99013,-7.5108
+> view matrix models
+> #2,0.64049,0.73429,-0.22493,-17.447,-0.72548,0.67459,0.13642,114.67,0.25191,0.075804,0.96478,-36.733
+> view matrix models
+> #2,0.50071,0.84809,-0.1733,-20.624,-0.83512,0.52596,0.16105,143.9,0.22773,0.064085,0.97161,-33.096
+> view matrix models
+> #2,0.55426,0.83134,0.040907,-52.732,-0.83234,0.55369,0.025237,157.49,-0.0016697,-0.048037,0.99884,6.3529
+> view matrix models
+> #2,0.54925,0.83515,0.029066,-51.059,-0.83387,0.54548,0.084295,151.14,0.054544,-0.070537,0.99602,2.4296
+> view matrix models
+> #2,0.47841,0.8769,0.046701,-49.588,-0.87704,0.47447,0.075363,166.59,0.043927,-0.077012,0.99606,4.5714
+> view matrix models
+> #2,0.48897,0.86406,0.1196,-58.658,-0.8723,0.48419,0.068276,165.69,0.0010878,-0.13771,0.99047,18.267
+> fitmap map #3 inMap #2
+Missing or invalid "atomsOrMap" argument: invalid objects specifier
+> fitmap #3 inMap #2
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 76
+shifted from previous position = 3.29
+rotated from previous position = 3.6 degrees
+atoms outside contour = 713, contour level = 0.0049001
+Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.00000000 0.00006645 -0.00003656 -0.00279354
+-0.00006644 0.99999999 0.00017232 -0.01425049
+.00003658 -0.00017231 0.99999999 0.00900773
+Axis -0.91526123 -0.19423949 -0.35294178
+Axis point 0.00000000 56.66272325 80.28668892
+Rotation angle (degrees) 0.01078700
+Shift along axis 0.00214563
+> volume #2 level 0.1498
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
+> ui mousemode right translate
+> volume #2 level 0.3454
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> hide #!1 models
+> show #!2 models
+> volume #2 level 0.2911
+> volume #2 level 0.0284
+> volume #2 style mesh
+> ui mousemode right select
+> select clear
+> volume #2 level 0.1008
+> volume #2 style surface
+> volume #2 level 0.07544
+> select clear
+> hide #!2 models
+> select #3/A:206,211,213
+atoms, 24 bonds, 3 residues, 1 model selected
+Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
+models, 0 maps.
+> volume zone #2 nearAtoms sel range 5
+> show #!2 models
+> volume zone #2 nearAtoms sel range 1
+> volume zone #2 nearAtoms sel range 2
+> volume zone #2 nearAtoms sel range 3
+> volume zone #2 nearAtoms sel range 2
+> select sidechain #3/A:206,211,213
+Expected a keyword
+> select #3/A:206,211,213 sidechain
+Expected a keyword
+> select sidechain & #3/A:206,211,213
+atoms, 15 bonds, 3 residues, 1 model selected
+> select up
+atoms, 24 bonds, 3 residues, 1 model selected
+> select up
+atoms, 144 bonds, 16 residues, 1 model selected
+> select down
+atoms, 24 bonds, 3 residues, 1 model selected
+> select down
+atoms, 15 bonds, 3 residues, 1 model selected
+> select sidechain & #3/A:206,211,213
+atoms, 15 bonds, 3 residues, 1 model selected
+> volume zone #2 nearAtoms sel range 2
+> show #!1 models
+> hide #!3 models
+> show #!3 models
+> hide #!1 models
+> select up
+atoms, 24 bonds, 3 residues, 1 model selected
+> select down
+atoms, 15 bonds, 3 residues, 1 model selected
+> transparency #2 50
+Drag select of 1 residues
+> volume #2 level 0.1008
+> surface dust #2 size 8.32
+[Repeated 1 time(s)]
+> volume zone #2 nearAtoms sel range 2
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> select clear
+> volume show
+> volume hide
+> volume show
+[Repeated 1 time(s)]
+> select down
+Nothing selected
+> select #2
+models selected
+> select #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+> volume zone #2 nearAtoms sel range 2
+> select clear
+> volume #2 level 0.01393
+> volume #2 level 0.0284
+> fitmap #3 inMap #2
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 40
+shifted from previous position = 0.0107
+rotated from previous position = 0.0149 degrees
+atoms outside contour = 1486, contour level = 0.0284
+Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.00000000 0.00004132 -0.00004587 -0.00356102
+-0.00004132 1.00000000 -0.00008578 0.01324767
+.00004587 0.00008579 1.00000000 -0.01510254
+Axis 0.81167482 -0.43401395 -0.39091671
+Axis point 0.00000000 188.52719661 140.57808315
+Rotation angle (degrees) 0.00605547
+Shift along axis -0.00273622
+> show #!1 models
+> hide #!1 models
+> hide #!1.1 models
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> hide #!2 models
+> show #!2 models
+> fitmap #3 inMap #2
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 40
+shifted from previous position = 0.0104
+rotated from previous position = 0.0113 degrees
+atoms outside contour = 1489, contour level = 0.0284
+Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.00000000 0.00006037 -0.00004170 -0.00151559
+-0.00006036 1.00000000 0.00011091 -0.00511879
+.00004171 -0.00011091 1.00000000 0.00183937
+Axis -0.83401456 -0.31360939 -0.45394809
+Axis point 0.00000000 24.90828027 40.40123494
+Rotation angle (degrees) 0.00761946
+Shift along axis 0.00203434
+> hide #!2 models
+> show #!1 models
+> show #!1.1 models
+> align #1.1 #3
+Missing required "to_atoms" argument
+> matchmaker maker #1.1 #3
+Missing or invalid "matchAtoms" argument: invalid atoms specifier
+> matchMaker #1.1 #3
+Unknown command: matchMaker #1.1 #3
+> matchMaker #1.1 to #3
+Unknown command: matchMaker #1.1 to #3
+> matchmaker #1.1 to #3
+Computing secondary structure
+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 real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
+chain A (#3) with all_aligned_SLFN.cif, chain A (#1.1), sequence alignment
+score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> hide #!3 models
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> show #!2 models
+> hide #!2 models
+> undo
+[Repeated 9 time(s)]
+> redo
+> show #!1 models
+> show #!1.1 models
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> hide #!2 models
+> select #3/A,B:351-912
+atoms, 8104 bonds, 8 pseudobonds, 990 residues, 2 models selected
+> hide sel cartoons
+> select clear
+> select #3/B
+atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
+> hide sel cartoons
+> select clear
+[Repeated 13 time(s)]
+> ui mousemode right "rotate selected models"
+> ui mousemode right rotate
+> ui mousemode right select
+> select clear
+[Repeated 2 time(s)]
+> select #3/C,D
+atoms, 280 bonds, 12 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select clear
+[Repeated 1 time(s)]
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
+> select clear
+[Repeated 1 time(s)]
+> select add #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+Drag select of 19 atoms, 19 bonds
+Drag select of 29 atoms, 4 pseudobonds, 26 bonds
+Drag select of 15 atoms, 10 bonds
+Drag select of 24 atoms, 21 bonds
+Drag select of 1 atoms, 1 bonds
+Drag select of 2 atoms, 3 bonds
+Drag select of 12 atoms, 12 bonds
+> hide sel atoms
+Drag select of 34 atoms, 20 bonds
+> hide sel atoms
+Drag select of 2 atoms
+> hide sel atoms
+> select #3/A:78@CB
+atom, 1 residue, 1 model selected
+> hide #!1.1 models
+Drag select of 10 atoms, 29 residues, 8 bonds
+> hide sel atoms
+> select clear
+Drag select of 6 atoms, 9 residues, 4 bonds
+> hide sel atoms
+Drag select of 17 atoms, 25 residues, 4 pseudobonds, 13 bonds
+> hide sel cartoons
+> show sel cartoons
+> hide sel atoms
+> select clear
+> show #!1.1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> select #1.1/A:248
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:248
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #3/A:214
+atoms, 10 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/A:136@CA
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/A:136@CG2
+atom, 1 residue, 1 model selected
+> select #3/A:136
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/A:133
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #3/A:212
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide #3.1 models
+> hide #3.2 models
+> cartoon style sel modeHelix tube sides 20
+> select #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+> color sel cornflower blue
+> select clear
+> select #3/A:133,2016,211,213,249,248
+atoms, 41 bonds, 5 residues, 1 model selected
+> color sel orange
+> color sel byhetero
+> select clear
+> color sel backbone cornflower blue
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color red backbone & /A:133,206,211,213,248,249
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color red backbone & #3/A:133,206,211,213,248,249
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select #3/A:133,206,211,213,248,249 & color backbone red
+Expected a keyword
+> select #3/A:133,206,211,213,248,249 & color red backbone
+Expected a keyword
+> select #3/A:133,2016,211,213,249,248
+atoms, 41 bonds, 5 residues, 1 model selected
+> select #3/A:133,206,211,213,249,248
+atoms, 49 bonds, 6 residues, 1 model selected
+> color sel orange
+> color sel byhetero
+> ui tool show "Color Actions"
+> color sel cornflower blue target cspf
+> select clear
+> view p1
+> view p2
+> view p1
+> hide #!1.1 models
+> select #3/A:1003@MG
+atom, 1 residue, 1 model selected
+> select add #3/A:1002@MG
+atoms, 2 residues, 1 model selected
+> color sel byelement
+> select clear
+> select #3/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> select #3/C,D
+atoms, 280 bonds, 12 residues, 1 model selected
+> show sel cartoons
+> select clear
+> select #3/C:2
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #3/C:1
+atoms, 24 bonds, 1 residue, 1 model selected
+> select add #3/C:2
+atoms, 45 bonds, 2 residues, 1 model selected
+> select add #3/C:3
+atoms, 70 bonds, 3 residues, 1 model selected
+> select add #3/C:4
+atoms, 95 bonds, 4 residues, 1 model selected
+> select add #3/C:5
+atoms, 120 bonds, 5 residues, 1 model selected
+> hide sel cartoons
+> select #3/C
+atoms, 124 bonds, 5 residues, 1 model selected
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> color sel pale violet red
+> select clear
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> show sel atoms
+> nucleotides sel ladder
+> show sel cartoons
+[Repeated 1 time(s)]
+> show sel atoms
+> show sel cartoons
+> hide sel atoms
+> show sel atoms
+> hide sel cartoons
+> show sel cartoons
+> select clear
+> show #3.2 models
+> hide #3.2 models
+> show #3.2 models
+> color #3.2 black models
+> hide #3.2 models
+> show #3.2 models
+> color #3.1 #6495ed00 models
+> color #3.1 cornflowerblue models
+> view name p11
+> vire p2
+Unknown command: vire p2
+> view p2
+> show #!1.1 models
+> show #!1.2 models
+> hide #!1.1 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> show #!2 models
+> hide #!3 models
+> hide #!2 models
+> show #!3 models
+> show #!1.1 models
+> hide cartoons
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> hide sel atoms
+Drag select of 239 atoms, 201 bonds, 5 pseudobonds
+> select backbone
+atoms, 34691 bonds, 62 pseudobonds, 8643 residues, 17 models selected
+> hide sel atoms
+> ui mousemode right "translate selected models"
+> view matrix models
+> #1.1,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.2,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.3,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.4,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.5,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#3,0.48893,0.86408,0.11967,-58.776,-0.87232,0.48413,0.068366,165.51,0.0011374,-0.13782,0.99046,18.726
+> select add #1
+atoms, 64183 bonds, 59 pseudobonds, 8965 residues, 13 models selected
+> select subtract #1.1
+atoms, 50407 bonds, 47 pseudobonds, 7299 residues, 11 models selected
+> select add #1
+atoms, 64183 bonds, 59 pseudobonds, 8965 residues, 13 models selected
+> select subtract #1
+atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
+> view matrix models
+> #3,0.48893,0.86408,0.11967,-58.637,-0.87232,0.48413,0.068366,166.23,0.0011374,-0.13782,0.99046,16.797
+> view matrix models
+> #3,0.48893,0.86408,0.11967,-59.011,-0.87232,0.48413,0.068366,166.4,0.0011374,-0.13782,0.99046,16.755
+> view matrix models
+> #3,0.48893,0.86408,0.11967,-58.793,-0.87232,0.48413,0.068366,166.88,0.0011374,-0.13782,0.99046,16.902
+> view matrix models
+> #3,0.48893,0.86408,0.11967,-58.625,-0.87232,0.48413,0.068366,167.25,0.0011374,-0.13782,0.99046,17.017
+> view matrix models
+> #3,0.48893,0.86408,0.11967,-58.535,-0.87232,0.48413,0.068366,167.41,0.0011374,-0.13782,0.99046,17.156
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #3,0.49063,0.86171,0.12936,-59.282,-0.87134,0.48635,0.065052,167.29,-0.006858,-0.14463,0.98946,19.083
+> view matrix models
+> #3,0.47006,0.87172,0.13835,-59.22,-0.88263,0.46475,0.070539,171.05,-0.002808,-0.15527,0.98787,20.262
+> view matrix models
+> #3,0.46863,0.87844,0.093401,-55.878,-0.88303,0.46275,0.07824,170.67,0.025508,-0.11914,0.99255,11.659
+> select #3,#1.1
+Expected an objects specifier or a keyword
+> select #3,1.1
+atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected
+> show sel cartoons
+> hide #!1.1 models
+> show #!1.1 models
+> select #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+> show sel cartoons
+> matchmaker maker #3 to #1.1
+Missing or invalid "matchAtoms" argument: invalid atoms specifier
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> select clear
+> hide cartoons
+> view p2
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #3.2 models
+> hide #!2 models
+> ui mousemode right select
+Drag select of 32 atoms, 24 bonds
+> select clear
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!3 cartoons
+> save
+> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
+> surface dust #2 size 8.32
+> ui mousemode right "translate selected models"
+> hide #!1.1 models
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> hide #!3 models
+> show #3.1 models
+> hide #!3 models
+> show #!3 models
+> select add #2
+models selected
+> view matrix models
+> #2,0.48897,0.86406,0.1196,-57.839,-0.8723,0.48419,0.068276,166.16,0.0010878,-0.13771,0.99047,18.386
+> view matrix models
+> #2,0.48897,0.86406,0.1196,-58.089,-0.8723,0.48419,0.068276,166.55,0.0010878,-0.13771,0.99047,18.727
+> view matrix models
+> #2,0.48897,0.86406,0.1196,-58.642,-0.8723,0.48419,0.068276,166.16,0.0010878,-0.13771,0.99047,18.62
+> view matrix models
+> #2,0.48897,0.86406,0.1196,-59.549,-0.8723,0.48419,0.068276,165.88,0.0010878,-0.13771,0.99047,17.459
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.40736,0.90161,0.14548,-57.285,-0.91324,0.40081,0.073143,180.79,0.0076376,-0.16265,0.98665,20.234
+> view matrix models
+> #2,0.46634,0.86424,0.18872,-65.594,-0.88348,0.4658,0.050027,171.92,-0.044671,-0.19006,0.98076,30.986
+> view matrix models
+> #2,0.51985,0.7748,0.35978,-83.124,-0.83128,0.55583,0.0041312,160.02,-0.19678,-0.30123,0.93303,70.093
+> view matrix models
+> #2,0.52461,0.80745,0.26985,-76.253,-0.83481,0.55006,-0.022946,164.66,-0.16696,-0.21324,0.96263,51.58
+> view matrix models
+> #2,0.4793,0.85608,0.19337,-66.804,-0.86923,0.49349,-0.030249,176.97,-0.12132,-0.15358,0.98066,36.09
+> view matrix models
+> #2,0.46412,0.86465,0.1923,-65.825,-0.87821,0.47749,-0.027378,179.73,-0.11549,-0.15617,0.98095,35.643
+> view matrix models
+> #2,0.47314,0.8608,0.1875,-65.864,-0.87645,0.4815,0.0011274,175.35,-0.089308,-0.16486,0.98226,33.265
+> view matrix models
+> #2,0.56676,0.809,0.1559,-67.127,-0.82184,0.56846,0.037859,152.93,-0.057996,-0.14958,0.98705,26.809
+> view matrix models
+> #2,0.50028,0.84503,0.18877,-67.476,-0.86237,0.50583,0.021132,167.98,-0.077631,-0.17337,0.98179,32.916
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.50028,0.84503,0.18877,-65.329,-0.86237,0.50583,0.021132,165.99,-0.077631,-0.17337,0.98179,32.636
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.52798,0.82687,0.1937,-67.181,-0.84696,0.52943,0.048615,157.58,-0.062353,-0.18973,0.97985,33.003
+> view matrix models
+> #2,0.50792,0.84968,0.14163,-60.82,-0.86131,0.49859,0.097719,156.93,0.012414,-0.17162,0.98508,20.672
+> view matrix models
+> #2,0.48388,0.86251,0.14809,-60.224,-0.87513,0.47635,0.085094,163.06,0.0028543,-0.17077,0.98531,21.74
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.48388,0.86251,0.14809,-61.455,-0.87513,0.47635,0.085094,162.01,0.0028543,-0.17077,0.98531,23.993
+> view matrix models
+> #2,0.48388,0.86251,0.14809,-60.934,-0.87513,0.47635,0.085094,162.77,0.0028543,-0.17077,0.98531,22.016
+> view matrix models
+> #2,0.48388,0.86251,0.14809,-60.859,-0.87513,0.47635,0.085094,164.04,0.0028543,-0.17077,0.98531,20.478
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.48083,0.86314,0.15424,-61.343,-0.87561,0.48191,0.032763,170.12,-0.046053,-0.15081,0.98749,23.86
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.48083,0.86314,0.15424,-61.207,-0.87561,0.48191,0.032763,169.77,-0.046053,-0.15081,0.98749,25.375
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.47873,0.86361,0.15807,-61.493,-0.87457,0.4849,-0.00055203,173.54,-0.077125,-0.13798,0.98743,27.692
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.47873,0.86361,0.15807,-61.593,-0.87457,0.4849,-0.00055203,174.46,-0.077125,-0.13798,0.98743,27.789
+> select subtract #2
+Nothing selected
+> fitmap #2 #3 moveModel false moveMap true
+Expected a keyword
+> fitmap #3 #2 moveWholeMolecules false
+Missing required "in_map" argument
+> fitmap #2 #3 moveWholeMolecules false
+Missing required "in_map" argument
+Must specify one map, got 0
+> fitmap #3 inMap #2 moveWholeMolecules false
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 80
+shifted from previous position = 1.68
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1486, contour level = 0.0284
+> show #!1 models
+> show #!1.1 models
+> show #!1.2 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> show cartoons
+> hide #!1.1 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> hide #!2 models
+> hide #!3 models
+> show #!1.3 models
+> show #!1.4 models
+> show #!1.5 models
+> show #!2 models
+> hide #!2 models
+> hide #!1 models
+> show #!1 models
+> hide #!1.2 models
+> hide #!1.3 models
+> hide #!1.4 models
+> hide #!1.5 models
+> show #!1.1 models
+> fitmap #3 inMap #2 moveWholeMolecules false
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3504, steps = 28
+shifted from previous position = 0.0115
+rotated from previous position = 0.0206 degrees
+atoms outside contour = 1483, contour level = 0.0284
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> fitmap #3 inMap #2 moveWholeMolecules false
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 96
+shifted from previous position = 1.92
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1489, contour level = 0.0284
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> fitmap #3 moveWholeMolecules false inMap #2
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 96
+shifted from previous position = 1.92
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1489, contour level = 0.0284
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> fitmap #3 inMap #2
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 96
+shifted from previous position = 1.92
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1489, contour level = 0.0284
+Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) coordinates:
+Matrix rotation and translation
+.97266502 -0.18741863 -0.13710221 45.36695106
+.15853109 0.96736060 -0.19769010 7.37317493
+.16967808 0.17055129 0.97062949 -43.56203686
+Axis 0.62297837 -0.51900056 0.58526607
+Axis point 0.00000000 250.60204610 -6.86010354
+Rotation angle (degrees) 17.19046649
+Shift along axis -1.05943510
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> fitmap #3 moveWholeMolecules false inMap #2
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 96
+shifted from previous position = 1.92
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1489, contour level = 0.0284
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> align #2 toAtoms #3
+Unequal number of atoms to pair, 0 and 13446
+> fitmap #3 inMap #2 moveWholeMolecules false moveWholeMolecules false
+Repeated keyword argument "moveWholeMolecules"
+> fitmap #3 inMap #2 moveWholeMolecules false
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 96
+shifted from previous position = 1.92
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1489, contour level = 0.0284
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> show #!1.1 models
+> hide #!1.5 models
+> fitmap #3 inMap #2 moveWholeMolecules false
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 96
+shifted from previous position = 1.92
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1489, contour level = 0.0284
+> hide #!1.5 models
+> hide #!3 target m
+> show #!3 target m
+> hide #!2 target m
+> show #!2 models
+> show #!1.1 models
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> select add #2
+models selected
+> select subtract #2
+Nothing selected
+> matchmaker #3 to #1.1
+Computing secondary structure
+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 all_aligned_SLFN.cif, chain A (#1.1) with
+real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
+(#3), sequence alignment score = 3964.3
+RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
+.728)
+> fitmap #3 inMap #2 moveWholeMolecules false
+Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
+(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc (#2) using 13446 atoms
+average map value = 0.3505, steps = 96
+shifted from previous position = 1.92
+rotated from previous position = 5.74 degrees
+atoms outside contour = 1489, contour level = 0.0284
+> hide #!1 models
+> view p2
+> show #!3 cartoons
+> select add #3
+atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
+> hide sel cartoons
+> hide #!2 models
+> select clear
+> ui mousemode right select
+Drag select of 32 atoms, 24 bonds
+> volume zone #2 nearAtoms sel range 4
+> show #!2 models
+> volume zone #2 nearAtoms sel range 3
+> surface dust #2 size 8.32
+> volume zone #2 nearAtoms sel range 2
+> volume #2 level 0.04919
+> volume #2 level 0.1858
+> volume #2 level 0.2631
+> volume zone #2 nearAtoms sel range 1
+> volume #2 level 0.3284
+> volume zone #2 nearAtoms sel range 5
+> volume #2 level 0.8037
+> volume zone #2 nearAtoms sel range 2
+> volume #2 level 0.2571
+> transparency #2 10
+> transparency #2 90
+> select clear
+> volume #2 level 0.2363
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> show sel cartoons
+> select clear
+> select #3/D:6
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #3/D:1
+atoms, 21 bonds, 1 residue, 1 model selected
+> select add #3/D:2
+atoms, 42 bonds, 2 residues, 1 model selected
+> select add #3/D:3
+atoms, 63 bonds, 3 residues, 1 model selected
+> select add #3/D:4
+atoms, 87 bonds, 4 residues, 1 model selected
+> select add #3/D:5
+atoms, 108 bonds, 5 residues, 1 model selected
+> select add #3/D:7
+atoms, 129 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> select #3/D:6
+atoms, 21 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> undo
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> select #3/D
+atoms, 156 bonds, 7 residues, 1 model selected
+> show sel atoms
+> select #3/D:6
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+Drag select of 40 atoms, 39 bonds, 10 shapes
+> hide sel atoms
+> select #3/D:7@P
+atom, 1 residue, 1 model selected
+> select subtract #3/D:7@P
+Nothing selected
+> select #3/D:7@P
+atom, 1 residue, 1 model selected
+> view p2
+> show sel atoms
+> nucleotides sel ladder
+[Repeated 2 time(s)]
+> nucleotides sel fill
+> style nucleic & sel stick
+Changed 20 atom styles
+> color sel byelement
+> select clear
+> view p2
+Drag select of 15 atoms, 16 bonds, 2 shapes
+> hide sel atoms
+> select #3/D:7@C5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> view p2
+Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc , 36 atoms, 27 bonds
+> volume zone #2 nearAtoms sel range 2
+> volume #2 level 0.2245
+> select clear
+> volume #2 level 0.2839
+> view p2
+> volume #2 level 0.1591
+> volume zone #2 nearAtoms sel range 3
+no atoms specified for zone
+Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc , 35 atoms, 27 bonds
+> volume zone #2 nearAtoms sel range 3
+> volume #2 level 0.1027
+> volume zone #2 nearAtoms sel range 4
+> volume #2 level 0.3076
+> volume zone #2 nearAtoms sel range 1
+> volume #2 level 0.5631
+> volume zone #2 nearAtoms sel range 2
+> volume #2 level 0.3403
+> volume zone #2 nearAtoms sel range 2.5
+> volume #2 level 0.2898
+> volume zone #2 nearAtoms sel range 2
+> view p2
+> select clear
+> volume #2 level 0.1413
+> select clear
+> view p2
+> view p22
+Expected an objects specifier or a view name or a keyword
+> view name p22
+> view p2
+[Repeated 1 time(s)]
+> view p22
+Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
+sharpened-highres.mrc , 36 atoms, 27 bonds
+[deleted to fit within ticket limits]
 > volume zone #2 nearAtoms sel range 2.3