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Changes between Initial Version and Version 1 of Ticket #17846

Timestamp:: May 29, 2025, 10:54:59 AM (5 months ago)
Author:: Eric Pettersen
Comment:: Reported by Guillermo Montoya

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #17846
- 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 #17846 – Description

-              initial
+              v1
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+    "name" : "givens_elimination.cpython-311-darwin.so"
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+    "name" : "_bglu_dense.cpython-311-darwin.so"
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+    "name" : "_qhull.cpython-311-darwin.so"
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+    "name" : "_voronoi.cpython-311-darwin.so"
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+    "name" : "_distance_wrap.cpython-311-darwin.so"
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+    "name" : "libsf_error_state.dylib"
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+    "name" : "_ufuncs_cxx.cpython-311-darwin.so"
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+    "name" : "_gufuncs.cpython-311-darwin.so"
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+    "name" : "_specfun.cpython-311-darwin.so"
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+    "name" : "_comb.cpython-311-darwin.so"
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+    "name" : "_ellip_harm_2.cpython-311-darwin.so"
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+    "name" : "_distance_pybind.cpython-311-darwin.so"
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+[deleted to fit within ticket limits]
 ],
   "sharedCache" : {
 …
 > hide #8 models
+> show #8 models
+> show #9/M atoms
+> show #9/N atoms
+> hide #!9 models
+> show #!9 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> hide #!9 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #10
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #10 atoms
+> show #10 cartoons
+> cartoon style nucleic xsection oval width 1.6 thickness 1.6
+> color #10/L light gray
+> color #10/K dim gray
+> color #10/J dark red
+> color #10/I rebecca purple
+> color #10/B forest green
+> color #10/C,D,E,F,G,H khaki
+> color #10/A steel blue
+> color #10/A:232-350 dark turquoise
+> show #10/K atoms
+> style stick
+Changed 131055 atom styles
+> show #10 & nucleic atoms
+> select #10
+atoms, 24925 bonds, 3 pseudobonds, 2803 residues, 2 models selected
+> nucleotides sel ladder
+> select clear
+> show #!4 models
+> volume #4 level 0.06
+> show #10/M,N,O atoms
+> select clear
+> select #10/K:4
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #10/K:3
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #10/K:2
+atoms, 47 bonds, 3 residues, 1 model selected
+> select add #10/K:1
+atoms, 56 bonds, 4 residues, 1 model selected
+> hide sel cartoons
+> nucleotides sel atoms
+> style nucleic & sel stick
+Changed 54 atom styles
+> select clear
+> color zone #4 near #10 distance 10
+> transparency 50
+> volume #4 level 0.05
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #10/L light gray
+> color #10/K dim gray
+> color #10/J dark red
+> color #10/I rebecca purple
+> color #10/B forest green
+> color #10/C,D,E,F,G,H khaki
+> color #10/A steel blue
+> color #10/A:232-350 dark turquoise
+> color zone #4 near #10 distance 10
+> hide #!10 models
+> hide #!4 models
+> show #!10 models
+> select #10/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select #10/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select clear
+> color zone #4 near #10 distance 10
+> show #!4 models
+> hide #!10 models
+> color zone #4 near #10 distance 5
+> volume #4 level 0.09
+> lighting soft
+> lighting full
+> lighting soft
+> color zone #4 near #10 distance 4
+> color zone #4 near #10 distance 3
+> volume #4 level 0.07
+> surface zone #4 nearAtoms #10 distance 2.5
+> surface zone #4 nearAtoms #10 distance 3
+> select add #4
+models selected
+> ui tool show "Color Actions"
+> color sel navajo white
+> set bgColor white
+> lighting simple
+> transparency sel 50
+> show #!10 models
+> volume #4 level 0.05
+> volume #4 level 0.09
+> volume #4 level 0.08
+> color #10 byhetero
+> select clear
+> select #10/K:1@N9
+atom, 1 residue, 1 model selected
+> select up
+atoms, 9 bonds, 1 residue, 1 model selected
+> select add #10/K:2@OP2
+atoms, 9 bonds, 2 residues, 1 model selected
+> select up
+atoms, 31 bonds, 2 residues, 1 model selected
+> select down
+atoms, 9 bonds, 2 residues, 1 model selected
+> select add #10/K:2@OP1
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #10/K:2@O2
+atoms, 17 bonds, 2 residues, 1 model selected
+> select add #10/K:2@O4
+atoms, 20 bonds, 2 residues, 1 model selected
+> select add #10/K:2@C5
+atoms, 21 bonds, 2 residues, 1 model selected
+> select add #10/K:2@C7
+atoms, 24 bonds, 2 residues, 1 model selected
+> select add #10/K:3@N6
+atoms, 25 bonds, 3 residues, 1 model selected
+> select up
+atoms, 27 bonds, 3 residues, 1 model selected
+> select up
+atoms, 55 bonds, 3 residues, 1 model selected
+> hide #!4 models
+> select subtract #10/K:3@OP1
+atoms, 53 bonds, 3 residues, 1 model selected
+> select subtract #10/K:3@P
+atoms, 51 bonds, 3 residues, 1 model selected
+> select subtract #10/K:3@OP2
+atoms, 51 bonds, 3 residues, 1 model selected
+> select add #10/K:4@P
+atoms, 51 bonds, 4 residues, 1 model selected
+> select add #10/K:4@OP1
+atoms, 52 bonds, 4 residues, 1 model selected
+> select add #10/K:4@OP2
+atoms, 54 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@O3'
+atoms, 53 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C4'
+atoms, 50 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@O4'
+atoms, 48 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C3'
+atoms, 48 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C2'
+atoms, 47 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C1'
+atoms, 46 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C5'
+atoms, 46 bonds, 4 residues, 1 model selected
+> hide sel atoms
+> show #10/K:3 atoms
+> hide sel atoms
+> select #10/K:3@C5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #10/K:3@C4'
+atom, 1 residue, 1 model selected
+> select add #10/K:3@O3'
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C2'
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@O4'
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select #10/K:3@C3'
+atom, 1 residue, 1 model selected
+> select add #10/K:3@C1'
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C8
+atoms, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select down
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N3
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C4
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C5
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N7
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C6
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N6
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N1
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C2
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select #10/K:3@N9
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> select #10/K:2@C5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> volume #4 level 0.07
+> show #10/A:305,304,280,328
+> volume #4 level 0.09
+> select #10/K:4@O5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> color #10/M red
+> color #10/O blue
+> color #10/O dark blue
+> color #10/O blue
+> volume #4 level 0.07
+> show #10/K:2 atoms
+> volume #4 level 0.06
+> show #10/K:1-2 atoms
+> show #!5 models
+> hide #!5 models
+> show #!2 models
+> hide #!2 models
+> hide #!4 models
+> hide #!10 models
+> show #!10 models
+> select #10/K:1@O5'
+atom, 1 residue, 1 model selected
+> select add #10/K:1@C5'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C4'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@O4'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C1'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@N9
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C2'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C3'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@O3'
+atoms, 1 residue, 1 model selected
+> select add #10/K:2@P
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@OP2
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@OP1
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@O5'
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@C5'
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> show #!4 models
+> hide #!4 models
+> ui tool show Distances
+> select #10/O:1@O
+atom, 1 residue, 1 model selected
+> select #10/K:3@OP2
+atom, 1 residue, 1 model selected
+> select add #10/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #10/K:3@OP2 #10/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/K DA 3 OP2
+and /O HOH 1 O: 2.479Å
+> select #10/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #10/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #10/A:304@ND1 #10/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 304 ND1
+and /M MG 1 MG: 2.377Å
+> select #10/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #10/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #10/A:328@NE2 #10/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 328 NE2
+and /M MG 1 MG: 2.352Å
+> select #10/M:1@MG
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP1
+atoms, 2 residues, 1 model selected
+> distance #10/M:1@MG #10/K:3@OP1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/M MG 1 MG and
+/K DA 3 OP1: 3.166Å
+> select #10/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #10/A:280@NH2 #10/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH2
+and /K DA 3 OP2: 2.389Å
+> select #10/A:280@NH1
+atom, 1 residue, 1 model selected
+> select add #10/K:3@O5'
+atoms, 2 residues, 1 model selected
+> distance #10/A:280@NH1 #10/K:3@O5'
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH1
+and /K DA 3 O5': 2.765Å
+> select #10/A:238
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #10/A:319
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #10/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #10/A:305@ND1 #10/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
+and /K DA 3 OP2: 3.592Å
+> select #10/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> select #10/A:309@N
+atom, 1 residue, 1 model selected
+> select add #10/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #10/A:309@N #10/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A LEU 309 N
+and /O HOH 1 O: 3.104Å
+> select #10/A:309@N
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> view
+> select #10/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP1
+atoms, 2 residues, 1 model selected
+> distance #10/A:305@ND1 #10/K:3@OP1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
+and /K DA 3 OP1: 3.734Å
+> delete sel
+> ~distance #10/A:305@ND1 #10/K:3@OP1
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 155221 atom styles
+> hide #12 atoms
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> hide #!11 models
+> show #!11 models
+> close #11
+> show #12 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> show #12/K:2-3 atoms
+> hide #12/K:1-3 cartoons
+> select clear
+> select #12/K:2@OP1
+atom, 1 residue, 1 model selected
+> select add #12/K:2@OP2
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@P
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:3@C5'
+atoms, 2 residues, 1 model selected
+> select add #12/K:3@C4'
+atoms, 2 residues, 1 model selected
+> select add #12/K:3@C3'
+atoms, 2 residues, 1 model selected
+> select add #12/K:4
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@O4'
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C2'
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C1'
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N9
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C8
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C4
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C5
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N7
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C6
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N6
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N1
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C2
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N3
+atoms, 3 bonds, 3 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select #12/K:3@O3'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> select #12/K:2@O5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show #12/M,O atoms
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select clear
+> show #12/A:304-305,328,280
+> select #12/A:319
+atoms, 7 bonds, 1 residue, 1 model selected
+> select ~sel & ##selected
+atoms, 24918 bonds, 3 pseudobonds, 2802 residues, 2 models selected
+> show #12/A:304-305,328,280,319
+> color #12 byhetero
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> select add #12/M:1@MG
+atoms, 2 residues, 1 model selected
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select clear
+> select #12/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/A:305@ND1 #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 305 ND1
+and /K DA 3 OP2: 3.159Å
+> select #12/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/A:280@NH2 #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH2
+and /K DA 3 OP2: 2.389Å
+> select #12/A:280@NH1
+atom, 1 residue, 1 model selected
+> select add #12/K:3@O5'
+atoms, 2 residues, 1 model selected
+> distance #12/A:280@NH1 #12/K:3@O5'
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH1
+and /K DA 3 O5': 2.765Å
+> view
+> select #12/K:3@OP1
+atom, 1 residue, 1 model selected
+> select add #12/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP1 #12/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP1
+and /M MG 1 MG: 3.166Å
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> select add #12/A:304@ND1
+atoms, 2 residues, 1 model selected
+> distance #12/M:1@MG #12/A:304@ND1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/M MG 1 MG and
+/A HIS 304 ND1: 2.377Å
+> select #12/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #12/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #12/A:328@NE2 #12/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 328 NE2
+and /M MG 1 MG: 2.352Å
+> select clear
+> color sel maroon
+> color sel teal
+> color sel cornflower blue
+> color sel dark salmon
+> color sel dark khaki
+> color sel peru
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> color sel indigo
+> color sel red
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select #12/K:3@OP2
+atom, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP2 #12/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP2
+and /O HOH 1 O: 2.479Å
+> color sel indigo
+> select clear
+> color sel dark blue
+[Repeated 1 time(s)]
+> select clear
+> select #12/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 7 bonds, 2 residues, 1 model selected
+Exactly two atoms must be selected!
+> select clear
+> select #12/A LEU 309 N
+Expected a keyword
+> select #12/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> select #12/A:309@N
+atom, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #12/A:309@N #12/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A LEU 309 N
+and /O HOH 1 O: 3.104Å
+> distance style decimalPlaces 2
+[Repeated 2 time(s)]
+> distance style decimalPlaces 1
+[Repeated 2 time(s)]
+> select subtract #12/O:1@O
+atom, 1 residue, 1 model selected
+> select ~sel & ##selected
+atoms, 24925 bonds, 11 pseudobonds, 2803 residues, 3 models selected
+> hide #12/A:309 atoms
+> show #12/A:309 cartoons
+> select clear
+> show #!4 models
+> volume #4 level 0.07
+> volume #4 level 0.08
+> select #12/K:2@N3
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> select down
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> surface dust #4 size 7.25
+[Repeated 1 time(s)]
+> surface dust #4 1
+Expected a keyword
+> surface dust #4 size 1
+> show (sel-residues & sidechain) target ab
+> hide sel atoms
+> select clear
+> select #12/K:3@O5'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> show #12/K:2 atoms
+> select #12/K:2@C2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide #!4 models
+> select subtract #12/K:2@O3'
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> volume #4 level 0.06
+> volume #4 level 0.08
+> volume #4 level 0.09
+> volume #4 level 0.08
+> view matrix models
+> #12,0.95038,0.072866,-0.30245,40.949,-0.29386,-0.10887,-0.94963,361.72,-0.10212,0.99138,-0.082056,19.143
+> show #!10 models
+> hide #!10 models
+> mmaker #12 to #10
+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 halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#10) with
+halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#12), sequence alignment
+score = 1753
+RMSD between 340 pruned atom pairs is 0.001 angstroms; (across all 340 pairs:
+.001)
+> ui tool show "Side View"
+> hide #11.1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3 transparentBackground true
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!4 models
+> select #2/E:804@O1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #2/E:731@CG
+atoms, 4 bonds, 2 residues, 1 model selected
+> select up
+atoms, 14 bonds, 2 residues, 1 model selected
+> select up
+atoms, 15 bonds, 3 residues, 1 model selected
+> select up
+atoms, 16 bonds, 4 residues, 1 model selected
+> select add #12/A:319@OD1
+atoms, 16 bonds, 5 residues, 2 models selected
+> select up
+atoms, 35 bonds, 5 residues, 2 models selected
+> select add #2/E:31@O
+atoms, 35 bonds, 6 residues, 2 models selected
+> select add #2/E:298@O
+atoms, 35 bonds, 7 residues, 2 models selected
+> select subtract #2/E:298@O
+atoms, 35 bonds, 6 residues, 2 models selected
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> select add #12
+atoms, 24953 bonds, 11 pseudobonds, 2808 residues, 4 models selected
+> select subtract #12
+atoms, 28 bonds, 5 residues, 1 model selected
+> hide sel atoms
+> select #2/E:701@CB
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #12/A:319@OD1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/E:298@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> color sel dark blue
+> select clear
+> show #!4 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!12 models
+> hide #!4 models
+> show #!2 models
+> select #2/E:904@ZN
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> hide #!2 models
+> show #!12 models
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel silver
+> color sel metallic
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color sel dark gray
+> color sel dim gray
+> select clear
+> color sel red
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> color sel dim gray
+> select clear
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> color sel red
+> color #12/M red
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!4 models
+> color sel tan
+> color sel dim gray
+[Repeated 1 time(s)]
+> show #!4 models
+> select clear
+> hide #!2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> hide #!4 models
+> show #!2 models
+> hide #!11 models
+> color #2 yellow
+> sle #2/E
+Unknown command: sle #2/E
+> select #2/E
+atoms, 1075 bonds, 4 pseudobonds, 190 residues, 2 models selected
+> select clear
+> ui tool show "Show Sequence Viewer"
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> hide #!2 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #13
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #13 atoms
+> show #13 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #13/DA light gray
+> color #13/EA dim gray
+> color #13/FA dark red
+> color #13/Ca rebecca purple
+> color #13/Ba forest green
+> color #13/Da,Db,Dc,Dd,De,Df khaki
+> color #13/Aa steel blue
+> color #13/Aa:232-350 dark turquoise
+> hide #!12 models
+> show #!12 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> color #13/L light gray
+> color #13/K dim gray
+> color #13/J dark red
+> color #13/I rebecca purple
+> color #13/B forest green
+> color #13/C,D,E,F,G,H khaki
+> color #13/A steel blue
+> color #13/A:232-350 dark turquoise
+> color #13 byhetero
+> hide #!12 models
+> color #13/M red
+> show #13/K:2 atoms
+> style stick
+Changed 179387 atom styles
+> select #13/K:3
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #13/K:4
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #13/K:2
+atoms, 47 bonds, 3 residues, 1 model selected
+> hide sel cartoons
+> show #13/K:3 atoms
+> select subtract #13/K:3@O5'
+atoms, 45 bonds, 3 residues, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 44 bonds, 3 residues, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 43 bonds, 3 residues, 1 model selected
+> select subtract #13/K:2@O3'
+atoms, 42 bonds, 3 residues, 1 model selected
+> select subtract #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> select add #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> select subtract #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> select add #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> hide sel atoms
+> select #13/K:2@O3'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> show sel atoms
+> select #13/K:4@O5'
+atom, 1 residue, 1 model selected
+> select add #13/K:4@OP1
+atoms, 1 residue, 1 model selected
+> select add #13/K:3@O3'
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 27 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@O5'
+atoms, 25 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@P
+atoms, 23 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 23 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 23 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select up
+atoms, 24 bonds, 3 residues, 1 model selected
+> select up
+atoms, 49 bonds, 3 residues, 1 model selected
+> select down
+atoms, 24 bonds, 3 residues, 1 model selected
+> select #13/K:2@N1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select subtract #13/K:2@O3'
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #13/A:304-305,328,280
+> show #13/M,O
+> select #13/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!4 models
+> show #!12 models
+> hide #!12 models
+> select #13/K:1
+atoms, 9 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select #13/K:1@O5'
+atom, 1 residue, 1 model selected
+> select add #13/K:1@C5'
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select Mg
+atoms, 6 residues, 6 models selected
+> select Zn
+atoms, 5 residues, 2 models selected
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> select add #2
+atoms, 4317 bonds, 16 pseudobonds, 856 residues, 3 models selected
+> select subtract #2
+atom, 1 residue, 1 model selected
+> hide #!4 models
+> select add #5
+atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> select add #5
+atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> hide #!5 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select Zn
+atoms, 5 residues, 2 models selected
+> select add #5
+atoms, 4 bonds, 1 pseudobond, 6 residues, 3 models selected
+> select subtract #5
+atoms, 4 residues, 1 model selected
+> show sel atoms
+> show #!2 models
+> select water
+Expected an objects specifier or a keyword
+> ui tool show "Check Waters"
+> hbonds #13/O interModel false reveal true restrict any name "water H-bonds"
+The following atoms were skipped as donors/acceptors due to missing heavy-atom
+bond partners: halfcleaved_HNH_center_main_model_temp2.pdb #13/K DG 1 N9
+hydrogen bonds found
+> show #4 models
+> select #13/O
+atom, 1 residue, 1 model selected
+> display #13/O : view #13/O @ select add #13/K:3@N7
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 23 bonds, 2 residues, 1 model selected
+> hide #!2 models
+> hide #!4 models
+> select subtract #13/K:3@O5'
+atoms, 21 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 20 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 19 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select #13/K:3@O5'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@P
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@O5'
+atoms, 19 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select subtract #13/K:2@O3'
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 9 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #13/A:308@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> hide sel cartoons
+> select #13/A:309@N
+atom, 1 residue, 1 model selected
+> show #13/O atoms
+> show #!11 models
+> hide #!11 models
+> close #11
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> hide sel
+> select #13/O:1@O
+atom, 1 residue, 1 model selected
+> select add #13/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #13/O:1@O #13/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/O HOH 1 O and
+/K DA 3 OP2: 2.5Å
+> select #13/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> show sel atoms
+> select #13/A:309@N
+atom, 1 residue, 1 model selected
+> select add #13/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #13/A:309@N #13/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LEU 309 N
+and /O HOH 1 O: 3.1Å
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> hide #11.1 models
+> select #13/M:2@MG
+atom, 1 residue, 1 model selected
+> select add #13/K:2@O3'
+atoms, 2 residues, 1 model selected
+> distance #13/M:2@MG #13/K:2@O3'
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/M MG 2 MG and
+/K DT 2 O3': 2.9Å
+> select #13/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #13/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #13/A:304@ND1 #13/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 304 ND1
+and /M MG 2 MG: 2.6Å
+> select #13/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #13/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #13/A:328@NE2 #13/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 328 NE2
+and /M MG 2 MG: 2.0Å
+> select clear
+> select #13/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #13/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #13/A:305@ND1 #13/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 305 ND1
+and /K DA 3 OP2: 3.2Å
+> select #13/K:3@O5'
+atom, 1 residue, 1 model selected
+> select add #13/A:280@NH1
+atoms, 2 residues, 1 model selected
+> distance #13/K:3@O5' #13/A:280@NH1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 O5'
+and /A ARG 280 NH1: 2.8Å
+> select #13/K:3@OP2
+atom, 1 residue, 1 model selected
+> select add #13/A:280@NH2
+atoms, 2 residues, 1 model selected
+> distance #13/K:3@OP2 #13/A:280@NH2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 OP2
+and /A ARG 280 NH2: 2.4Å
+> select add #11
+pseudobonds, 2 models selected
+> color sel dim gray
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> unsel
+Unknown command: unsel
+> select
+atoms, 183813 bonds, 57 pseudobonds, 19979 residues, 49 models selected
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> show #!2 models
+> hide #!4 models
+> hide #!11 models
+> select #2/E:31@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
+> 1210 supersample 3
+> lighting soft
+> show #!4 models
+> hide #!2 models
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> show #!2 models
+> hide #!4 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
+> 1210 supersample 3
+> hide #!2 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> volume #4 level 0.09
+> volume #4 level 0.1
+> volume #4 level 0.95
+> volume #4 level 0.095
+> volume #4 level 0.09
+> volume #4 level 0.08
+> volume #4 level 0.09
+> select #13/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> show #13/L atoms
+> select clear
+> show #13/L,J atoms
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Mon Mar 24 00:43:04 2025 ———
+opened ChimeraX session
+> volume #4 level 0.08
+> hide #13/J,L atoms
+> hide #13/K:6-46 atoms
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_zoom_out.tif" width 1984 height
+> 1210 supersample 3
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> volume #4 level 0.06
+> show #13/A:83,85 atoms
+> show #13/K:39-40 atoms
+> show #13/L:6-7 atoms
+> select clear
+> show #13/L,J #13/K:7-46 atoms
+> color #13/L light gray
+> color #13/K dim gray
+> color #13/J dark red
+> color #13/I rebecca purple
+> color #13/B forest green
+> color #13/C,D,E,F,G,H khaki
+> color #13/A steel blue
+> color #13/A:232-350 dark turquoise
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoom_out.tif" width 1984 height
+> 1210 supersample 3
+> color #13/A. byhet
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #13/A byhetero
+> ui tool show "Side View"
+> hide #13/K:7-46 #13/L cartoons
+> hide #13/K:7-46 #13/L atoms
+> show #13/K:39-40 #13/L:6-7 atoms
+> ui tool show Distances
+> show #!11 models
+Exactly two atoms must be selected!
+> hide #!4 models
+> show #13/K:39-41 #13/L:6-7 atoms
+> select #13/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #13/K:40@N2
+atoms, 2 residues, 1 model selected
+> distance #13/A:83@OD1 #13/K:40@N2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
+and /K DG 40 N2: 3.013Å
+> distance style color black
+[Repeated 2 time(s)]
+> ui tool show "Color Actions"
+> distance style color dimgrey
+[Repeated 2 time(s)]
+> select #13/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #13/K:41@O2
+atoms, 2 residues, 1 model selected
+> distance #13/A:85@NZ #13/K:41@O2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
+and /K DC 41 O2: 3.020Å
+> select #13/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #13/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #13/A:85@NZ #13/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
+and /L DG 6 N2: 3.258Å
+> select #13/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #13/A:85@NZ
+atoms, 2 residues, 1 model selected
+> distance #13/A:83@OD1 #13/A:85@NZ
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
+and LYS 85 NZ: 2.939Å
+> select add #11
+atoms, 12 pseudobonds, 2 residues, 3 models selected
+> color sel dim gray
+> select clear
+> select add #13/A:85
+atoms, 9 bonds, 1 residue, 1 model selected
+> select add #13/A:83
+atoms, 15 bonds, 2 residues, 1 model selected
+> color sel steel blue
+> color sel byhetero
+> color sel dim gray
+> select clear
+> show #!4 models
+> volume #4 level 0.08
+> volume #4 level 0.07
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
+> 1210 supersample 3
+> hide #!4 models
+> hide #13/K:39 atoms
+> show #!4 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
+> 1210 supersample 3
+> show #11.1 models
+> distance style decimalPlaces 1
+[Repeated 2 time(s)]
+> hide #11.1 models
+> view #13/L
+> volume #4 level 0.06
+> show #13/k,l cartoons
+> show #13/k:7-46 #13/l atoms
+> hide #!4 models
+> select #13/A:178
+atoms, 12 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #13/A:193
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show #!4 models
+> hide #!11 models
+> hide #13/A:83,85 atoms
+> select clear
+> surface dust #4 size 7.25
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
+> 1984 height 1210 supersample 3
+> show #13/A:191 atoms
+> select #13/A:193@OD1
+atom, 1 residue, 1 model selected
+> select add #13/L:9@N2
+atoms, 2 residues, 1 model selected
+> distance #13/A:193@OD1 #13/L:9@N2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASN 193 OD1
+and /L DG 9 N2: 2.6Å
+> show #!11 models
+> select #13/K:39
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> hide #!4 models
+> select #13/K:39@OP1
+atom, 1 residue, 1 model selected
+> select add #13/A:191@OG
+atoms, 2 residues, 1 model selected
+> distance #13/K:39@OP1 #13/A:191@OG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DC 39 OP1
+and /A SER 191 OG: 2.9Å
+> show sel cartoons
+> show #!4 models
+> color sel dim gray
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
+> 1984 height 1210 supersample 3
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!13 models
+> show #!13 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> volume #4 level 0.09
+> volume #4 level 0.05
+> volume #4 level 0.06
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
+> 1984 height 1210 supersample 3
+> hide #!4 models
+> show #!4 models
+> hide #!11 models
+> select #13/K:4
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #13/K:3
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #13/K:2
+atoms, 47 bonds, 3 residues, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> select down
+atoms, 47 bonds, 3 residues, 1 model selected
+> hide #!4 models
+> select add #13/K:1
+atoms, 56 bonds, 4 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #13/K:3@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> select down
+atoms, 23 bonds, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #13/K:2@O3'
+atoms, 23 bonds, 2 residues, 1 model selected
+> select up
+atoms, 45 bonds, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> select #13/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #13/A:295
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #13/I:140
+atoms, 10 bonds, 2 residues, 1 model selected
+> show sel atoms
+> show #!4 models
+> hide #!4 models
+> select #13/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> select add #13/K:7
+atoms, 45 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> show #!4 models
+> volume #4 level 0.09
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 24 bonds, 1 residue, 1 model selected
+> hide #!4 models
+> select subtract #13/K:6@O3'
+atoms, 23 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> hide #!4 models
+> select #13/K:7@OP1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> select #13/K:6@O3'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> hide #!4 models
+> select #13/I:50
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #13/I:51
+atoms, 16 bonds, 2 residues, 1 model selected
+> show sel atoms
+> show #!4 models
+> volume #4 level 0.06
+> volume #4 level 0.08
+> select #13/I:51@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 9 bonds, 2 residues, 1 model selected
+> select up
+atoms, 17 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> volume #4 level 0.1
+> color #13/i byhetero
+> select clear
+> select #13/K:7
+atoms, 21 bonds, 1 residue, 1 model selected
+> volume #4 level 0.07
+> select clear
+> volume #4 level 0.09
+> show #!2 models
+> hide #!2 models
+> hide #!4 models
+> select #13/A:295@SG
+atom, 1 residue, 1 model selected
+> select add #13/I:140@SG
+atoms, 2 residues, 1 model selected
+> distance #13/A:295@SG #13/I:140@SG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A CYS 295 SG
+and /I CYS 140 SG: 3.9Å
+> show #!11 models
+> color sel dim gray
+> select clear
+> hide #13/A:230-350 atoms
+> hide #13/o atoms
+> select #13/A:295
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> show #!4 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/cas8_cas6_cys_pair_0p09.tif" width
+> 1984 height 1210 supersample 3
+> hide #!4 models
+> show #11.1 models
+> hide #11.1 models
+> show #!2 models
+> select #2/E:706@CG
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/E:706@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+[Repeated 1 time(s)]
+> select clear
+> select #2/E:706@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/E:707@CD1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+[Repeated 1 time(s)]
+> select clear
+> select #13/I:140@SG
+atom, 1 residue, 1 model selected
+> select add #13/A:295@SG
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 10 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> show #13/A:305,304,280,328
+> select #2/E:718
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #13/A:319
+atoms, 14 bonds, 2 residues, 2 models selected
+> show sel atoms
+> show #13/O
+> select clear
+> hide #!11 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj_2.tif" width 1984
+> height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Mon Mar 24 13:31:18 2025 ———
+opened ChimeraX session
+> hide #!2 models
+> ui tool show "Side View"
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!13 models
+> close #12
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #12 atoms
+> show #12 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/M red
+> color #12/o blue
+> select clear
+> select #12/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> style stick
+Changed 179387 atom styles
+> select clear
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> select #12/K:7
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide #12/K cartoons
+> show #12/k atoms
+> select clear
+> volume #4 level 0.06
+> hide #!4 models
+> select #12/A:295
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #12/I:50
+atoms, 13 bonds, 2 residues, 1 model selected
+> select add #12/I:140
+atoms, 18 bonds, 3 residues, 1 model selected
+> show sel atoms
+> show #!4 models
+> hide #!4 models
+> select #12/A:290
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show #!4 models
+> volume #4 level 0.08
+> hide #!4 models
+> select #12/A:296
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #12/I:51
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> show #!4 models
+> volume #4 level 0.07
+> volume #4 level 0.09
+> volume #4 level 0.05
+> surface dust #4 size 7.25
+> color #12/K:1-4 red
+> show #12/m,o atoms
+> select clear
+> close #13
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Tue Mar 25 00:19:58 2025 ———
+opened ChimeraX session
+> close #12
+> hide #!4 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp.pdb #12
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 155168 atom styles
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> cartoon style nucleic xsection oval width 1 thickness 1
+> show #12 cartoons
+> hide #12 atoms
+> hide #12/k:1-6 cartoons
+> show #12/k:1-6 atoms
+> show #12/m,o atoms
+> color #12/m red
+> color #12/o blue
+> select clear
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_center_sharp3Å.mrc"
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.00305, step 2, values float32
+> volume #13 step 1
+> volume #13 level 0.01
+> volume #13 level 0.02
+> transparency #13.1 50
+> color zone #13 near #12 distance 5
+> select subtract #11
+Nothing selected
+> hide #!12 models
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 near #12/m,o dis
+> 1
+Repeated keyword argument "near"
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 #12/m,o dis 1
+Expected a keyword
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3.5
+> color zone #13 near #12/ dis 3.5
+Expected a keyword
+> color zone #13 near #12 distance 3.5
+> color zone #13 near #12 distance 3
+> color zone #13 near #12 distance 1
+> color zone #13 near #12 distance 1.5
+> color zone #13 near #12 distance 2
+> color zone #13 near #12 distance 2.4
+> color zone #13 near #12 distance 2.5
+> color zone #13 near #12 distance 3
+> color zone #13 near #12 distance 4
+> color zone #13 near #12 distance 4.5
+> color zone #13 near #12 distance 5
+> lighting soft
+> hide #!13 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_in_sharp3Å.mrc"
+Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+> volume #14 step 1
+> volume #14 level 0.02
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
+Chain information for halfcleaved_HNH_inwards_refined.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> color #15/L light gray
+> color #15/K dim gray
+> color #15/J dark red
+> color #15/I rebecca purple
+> color #15/B forest green
+> color #15/C,D,E,F,G,H khaki
+> color #15/A steel blue
+> color #15/A:232-350 dark turquoise
+> hide #15 atoms
+> show #!14 models
+> color zone #14 near #15 distance 5
+> hide #!15 models
+> show #!15 models
+> hide #!14 models
+> show #!14 models
+> show cartoons #15
+Expected ',' or a keyword
+> show #15 cartoons
+> hide #!14 models
+> combine #15
+> delete #15/b,c,d,e,f,g,h,j,k,l
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> delete #15/b,c,d,e,f,g,h,j,k,l,i
+> delete #15/a:1-230
+> delete #15/a:1-231
+> show #!14 models
+> transparency #14.1 50
+> fitmap #15 inMap #14
+Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
+halfcleaved_HNH_in_sharp3Å.mrc (#14) using 897 atoms
+average map value = 0.1033, steps = 48
+shifted from previous position = 0.103
+rotated from previous position = 0.723 degrees
+atoms outside contour = 296, contour level = 0.02
+Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
+halfcleaved_HNH_in_sharp3Å.mrc (#14) coordinates:
+Matrix rotation and translation
+.99995867 0.00821061 0.00390412 -2.00149362
+-0.00817612 0.99992812 -0.00876986 2.45517496
+-0.00397584 0.00873757 0.99995392 -1.09279831
+Axis 0.69359957 0.31218363 -0.64920029
+Axis point 0.00000000 120.00927253 275.85141597
+Rotation angle (degrees) 0.72313237
+Shift along axis 0.08767530
+> hide #!14 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_refined.pdb"
+Chain information for postcleavage_HNH_inwards_refined.pdb #17
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_3p93Å.mrc"
+Opened postcleavage_HNH_inwards_3p93Å.mrc as #18, grid size 420,420,420,
+pixel 0.725, shown at level 0.0417, step 2, values float32
+> close #18
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_in_sharp_4p5.mrc"
+Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+> volume #18 step 1
+> hide #!15 models
+> show #!15 models
+> hide #!17 models
+> transparency #18.1 50
+> lighting simple
+> fitmap #15 inMap #18
+Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
+post_HNH_in_sharp_4p5.mrc (#18) using 897 atoms
+average map value = 0.1722, steps = 88
+shifted from previous position = 5.79
+rotated from previous position = 18.5 degrees
+atoms outside contour = 305, contour level = 0.025678
+Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
+post_HNH_in_sharp_4p5.mrc (#18) coordinates:
+Matrix rotation and translation
+.98515450 -0.14232903 -0.09598467 36.22127193
+.16215106 0.95508370 0.24803662 -52.49007293
+.05637058 -0.25991841 0.96398381 44.34612442
+Axis -0.83066353 -0.24914793 0.49791908
+Axis point 0.00000000 129.04516803 229.89711725
+Rotation angle (degrees) 17.80344657
+Shift along axis 5.07088499
+> hide #17 atoms
+> show #17 cartoons
+> show #!17 models
+> hide #!17 models
+> hide #!15 models
+> show #!15 models
+> show #!16 models
+> hide #!16 models
+> hide #!15 models
+> show #!16 models
+> hide #!16 models
+> show #!17 models
+> select add #18
+models selected
+> ui tool show "Color Actions"
+> color sel navajo white
+> lighting simple
+> lighting soft
+> lighting simple
+> color #17/DA light gray
+> color #17/EA dim gray
+> color #17/FA dark red
+> color #17/Ca rebecca purple
+> color #17/Ba forest green
+> color #17/Da,Db,Dc,Dd,De,Df khaki
+> color #17/Aa steel blue
+> color #17/Aa:232-350 dark turquoise
+> color #17/L light gray
+> color #17/K dim gray
+> color #17/J dark red
+> color #17/I rebecca purple
+> color #17/B forest green
+> color #17/C,D,E,F,G,H khaki
+> color #17/A steel blue
+> color #17/A:232-350 dark turquoise
+> select subtract #18
+Nothing selected
+> hide #!18 models
+> show #!18 models
+> hide #!17 models
+> hide #!18 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
+shown at level 0.00149, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #20
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #20 atoms
+> show #20 cartoons
+> volume #19 step 1
+> volume #19 level 0.07
+> volume #19 level 0.05
+> volume #19 level 0.02
+> volume #19 level 0.01
+> combine #19
+No structures specified
+> combine #20
+> hide #!20 models
+> delete #21/a,b,c,d,e,f,g,h,k,l
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2726 atoms
+average map value = 0.1694, steps = 2000
+shifted from previous position = 0.186
+rotated from previous position = 0.199 degrees
+atoms outside contour = 1261, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999396 0.00180060 0.00297193 -0.76393106
+-0.00180072 0.99999838 0.00003869 0.16921571
+-0.00297185 -0.00004404 0.99999558 0.56555929
+Axis -0.01190446 0.85519891 -0.51816321
+Axis point 165.64366772 0.00000000 257.94336417
+Rotation angle (degrees) 0.19910813
+Shift along axis -0.13924475
+> select #21/J:51
+atoms, 25 bonds, 1 residue, 1 model selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #21,0.99951,0.00060373,-0.031401,4.2416,-0.0016237,0.99947,-0.032468,6.0991,0.031365,0.032503,0.99898,-9.4868
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2726 atoms
+average map value = 0.1688, steps = 2000
+shifted from previous position = 1.36
+rotated from previous position = 2.61 degrees
+atoms outside contour = 1266, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999350 0.00327561 0.00150351 -0.76518814
+-0.00327402 0.99999408 -0.00105700 0.62813683
+-0.00150696 0.00105207 0.99999831 -0.07731006
+Axis 0.28081232 0.40083125 -0.87205433
+Axis point 178.64402650 242.89942515 0.00000000
+Rotation angle (degrees) 0.21516256
+Shift along axis 0.10432118
+> delete #21/i:119-133
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1781, steps = 2000
+shifted from previous position = 0.132
+rotated from previous position = 0.117 degrees
+atoms outside contour = 1140, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999500 0.00239001 0.00207238 -0.60674616
+-0.00239146 0.99999689 0.00070090 0.14244066
+-0.00207070 -0.00070585 0.99999761 0.40363617
+Axis -0.21704908 0.63924101 -0.73774021
+Axis point 79.27931343 260.84792943 -0.00000000
+Rotation angle (degrees) 0.18567412
+Shift along axis -0.07503103
+> show #21/j atoms
+> style stick
+Changed 229983 atom styles
+> select clear
+> select #21/J:44
+atoms, 21 bonds, 1 residue, 1 model selected
+> view matrix models
+> #21,0.99372,-0.10871,0.026365,13.992,0.10722,0.99284,0.052567,-20.988,-0.031891,-0.04941,0.99827,11.548
+> select up
+atoms, 1444 bonds, 60 residues, 1 model selected
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1752, steps = 2000
+shifted from previous position = 4.3
+rotated from previous position = 7.23 degrees
+atoms outside contour = 1149, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99998549 0.00368109 0.00393188 -1.30544186
+-0.00367497 0.99999203 -0.00156309 0.73010434
+-0.00393760 0.00154862 0.99999105 0.48740849
+Axis 0.27751762 0.70184056 -0.65605168
+Axis point 94.79211019 0.00000000 320.39166369
+Rotation angle (degrees) 0.32121992
+Shift along axis -0.16963143
+> view matrix models
+> #21,0.95316,-0.16312,0.2547,-4.7007,0.14,0.98441,0.10651,-33.244,-0.2681,-0.065869,0.96114,54.875
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1731, steps = 2000
+shifted from previous position = 0.932
+rotated from previous position = 18.4 degrees
+atoms outside contour = 1177, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99994904 -0.00778267 -0.00643051 1.98761314
+.00779564 0.99996762 0.00199459 -1.51674316
+.00641478 -0.00204462 0.99997733 -0.91523181
+Axis -0.19616124 -0.62382235 0.75654904
+Axis point 206.49736911 250.60632995 0.00000000
+Rotation angle (degrees) 0.58990690
+Shift along axis -0.13613214
+> view matrix models
+> #21,0.99995,-0.0077827,-0.0064305,3.3447,0.0077956,0.99997,0.0019946,-2.7803,0.0064148,-0.0020446,0.99998,0.39857
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1778, steps = 2000
+shifted from previous position = 1.77
+rotated from previous position = 0.414 degrees
+atoms outside contour = 1144, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999337 -0.00330202 -0.00153324 0.70289684
+.00330074 0.99999420 -0.00083994 -0.52418630
+.00153600 0.00083487 0.99999847 -0.38974171
+Axis 0.22416395 -0.41079927 0.88373892
+Axis point 155.63582398 210.62363526 0.00000000
+Rotation angle (degrees) 0.21403999
+Shift along axis 0.02846957
+> delete #21/j:1-41
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02377, steps = 68
+shifted from previous position = 0.607
+rotated from previous position = 0.441 degrees
+atoms outside contour = 1066, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99996474 -0.00055599 -0.00837886 1.69415235
+.00053058 0.99999525 -0.00303455 0.64823116
+.00838051 0.00303000 0.99996029 -1.81624530
+Axis 0.33963693 -0.93858608 0.06085174
+Axis point 216.66154710 0.00000000 207.10057130
+Rotation angle (degrees) 0.51154276
+Shift along axis -0.14354572
+> view matrix models
+> #21,0.95152,0.063441,0.30097,-58.133,0.017073,0.9661,-0.25762,48.854,-0.30711,0.25027,0.91818,-0.5168
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.01942, steps = 92
+shifted from previous position = 1.42
+rotated from previous position = 9.42 degrees
+atoms outside contour = 1173, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.97435965 -0.00668895 0.22489671 -33.93326133
+.03560741 0.99154562 -0.12477740 17.25587377
+-0.22216072 0.12958605 0.96636022 5.49530082
+Axis 0.49286534 0.86623732 0.08195521
+Axis point 2.77043250 0.00000000 148.29261146
+Rotation angle (degrees) 14.95412576
+Shift along axis -1.32647815
+> view matrix models
+> #21,0.90553,-0.2837,0.31547,16.944,0.29673,0.95494,0.0070231,-29.813,-0.30325,0.08725,0.94891,27.343
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.01933, steps = 104
+shifted from previous position = 2.05
+rotated from previous position = 9.43 degrees
+atoms outside contour = 1170, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.94411256 -0.12450182 0.30520610 -21.00938346
+.14744888 0.98763632 -0.05322902 -8.92619050
+-0.29480552 0.09525648 0.95079751 24.92749364
+Axis 0.21988344 0.88852194 0.40271582
+Axis point 74.52306659 0.00000000 80.67313058
+Rotation angle (degrees) 19.73351564
+Shift along axis -2.51203568
+> view matrix models
+> #21,0.94411,-0.1245,0.30521,-17.873,0.14745,0.98764,-0.053229,-5.6643,-0.29481,0.095256,0.9508,23.681
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.01942, steps = 156
+shifted from previous position = 3.04
+rotated from previous position = 8.27 degrees
+atoms outside contour = 1166, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.97438343 -0.01578899 0.22433822 -31.97489437
+.04417306 0.99153739 -0.12207515 15.64761333
+-0.22051229 0.12885771 0.96683505 5.34685589
+Axis 0.48795736 0.86504446 0.11660060
+Axis point 3.97780903 0.00000000 139.84528015
+Rotation angle (degrees) 14.89958612
+Shift along axis -1.44305704
+> view matrix models
+> #21,0.97881,0.079073,-0.18889,14.498,-0.093393,0.99329,-0.068145,23.787,0.18223,0.084342,0.97963,-36.826
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02378, steps = 112
+shifted from previous position = 4.26
+rotated from previous position = 12.1 degrees
+atoms outside contour = 1061, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99995850 -0.00058011 -0.00909169 1.82468704
+.00055786 0.99999684 -0.00244989 0.54145676
+.00909308 0.00244471 0.99995567 -1.79847577
+Axis 0.25943577 -0.96387493 0.06031750
+Axis point 197.73964432 0.00000000 204.27550886
+Rotation angle (degrees) 0.54048814
+Shift along axis -0.15698708
+> select clear
+> select #21/J:50
+atoms, 21 bonds, 1 residue, 1 model selected
+> view matrix models
+> #21,0.96924,-0.18193,0.16576,13.795,0.16697,0.98085,0.10023,-33.405,-0.18082,-0.069465,0.98106,39.844
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02378, steps = 120
+shifted from previous position = 0.698
+rotated from previous position = 15.5 degrees
+atoms outside contour = 1064, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99996372 -0.00034050 -0.00851103 1.66866582
+.00031330 0.99999484 -0.00319750 0.69973282
+.00851207 0.00319472 0.99995867 -1.87660250
+Axis 0.35130930 -0.93556970 0.03593210
+Axis point 220.86482619 0.00000000 200.72582758
+Rotation angle (degrees) 0.52126798
+Shift along axis -0.13586127
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> view matrix models
+> #21,0.94284,-0.16526,0.28937,-7.4067,0.16063,0.98621,0.039865,-23.627,-0.29196,0.0088937,0.95639,41.501
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02377, steps = 140
+shifted from previous position = 0.641
+rotated from previous position = 19.9 degrees
+atoms outside contour = 1065, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99996409 -0.00060556 -0.00845233 1.72034129
+.00057980 0.99999518 -0.00304995 0.64758353
+.00845413 0.00304494 0.99995963 -1.83001040
+Axis 0.33840585 -0.93869583 0.06581501
+Axis point 216.32111144 0.00000000 208.46719481
+Rotation angle (degrees) 0.51597228
+Shift along axis -0.14615257
+> hide #!20 models
+> delete #21/i:107-118
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1617 atoms
+average map value = 0.025, steps = 44
+shifted from previous position = 0.0515
+rotated from previous position = 0.51 degrees
+atoms outside contour = 976, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99991658 -0.00665991 -0.01106673 3.46514203
+.00669212 0.99997347 0.00287541 -1.15618478
+.01104728 -0.00294923 0.99993463 -0.94027532
+Axis -0.21995713 -0.83509609 0.50421561
+Axis point 74.57354161 0.00000000 307.17000003
+Rotation angle (degrees) 0.75864102
+Shift along axis -0.27075880
+> view matrix models
+> #21,0.9761,-0.050009,0.2115,-22.223,0.037779,0.99739,0.061477,-14.46,-0.21402,-0.052017,0.97544,41.647
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1617 atoms
+average map value = 0.025, steps = 112
+shifted from previous position = 0.714
+rotated from previous position = 13.5 degrees
+atoms outside contour = 978, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99991534 -0.00691325 -0.01102344 3.51324748
+.00694686 0.99997133 0.00301354 -1.20471924
+.01100229 -0.00308986 0.99993470 -0.89660439
+Axis -0.22833637 -0.82401113 0.51852498
+Axis point 70.41448246 0.00000000 312.48223472
+Rotation angle (degrees) 0.76577763
+Shift along axis -0.27441187
+> hide #!21 models
+> hide #!19 models
+> show #!19 models
+> show #!18 models
+> hide #!18 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!19 models
+> show #!18 models
+> hide #!18 models
+> hide #!17 models
+> show #!16 models
+> hide #!16 models
+> show #!14 models
+> select add #14
+atoms, 21 bonds, 1 residue, 3 models selected
+> transparency sel 0
+> select clear
+> show #!13 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!4 models
+> lighting soft
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> hide #!13 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Wed Mar 26 12:19:53 2025 ———
+opened ChimeraX session
+> show #!13 models
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color #13 navajo white
+> show #!12 models
+> transparency #13.1 50
+> lighting simple
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> view
+> lighting soft
+> lighting simple
+> hide #12/l,k cartoons
+> show #12/k:39-40
+> show #12/l:6-7
+> show #12/l:6-8
+> hide #12/l:6 atoms
+> show #12/a:83,85 atoms
+> color #12/a:83,85 byhetero
+> ui tool show "Side View"
+> show #12/l:6-7
+> hide #12/l:8 atoms
+> hide #12/k:39 atoms
+> show #12/k:41 atoms
+> hide #!13 models
+> show #11 models
+> ui tool show Distances
+> select #12/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #12/A:83@OD1
+atoms, 2 residues, 1 model selected
+> distance #12/A:85@NZ #12/A:83@OD1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
+and ASP 83 OD1: 2.939Å
+> select #12/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #12/K:41@O2
+atoms, 2 residues, 1 model selected
+> distance #12/A:85@NZ #12/K:41@O2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
+and /K DC 41 O2: 3.020Å
+> select #12/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #12/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #12/A:85@NZ #12/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
+and /L DG 6 N2: 3.258Å
+> select #12/K:40@N2
+atom, 1 residue, 1 model selected
+> select add #12/A:83@OD1
+atoms, 2 residues, 1 model selected
+> distance #12/K:40@N2 #12/A:83@OD1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DG 40 N2 and
+/A ASP 83 OD1: 3.013Å
+> select add #11
+atoms, 4 pseudobonds, 2 residues, 3 models selected
+> color sel dim gray
+> select clear
+> show #!13 models
+> hide #11.1 models
+> lighting soft
+> lighting full
+> lighting simple
+> color #12/a byhetero
+> surface zone #13 nearAtoms #12/a,k,l
+> surface zone #13 nearAtoms #12/a,k,l distance 10
+> surface zone #13 nearAtoms #12/a,k,l distance 5
+> surface zone #13 nearAtoms #12/a,k,l distance 10
+> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 10
+> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 5
+> hide #12/b,c cartoons
+> hide #12/b,c,d cartoons
+> lighting soft
+> lighting simple
+> lighting full
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp.tif" width 1984 height
+> 1210 supersample 3
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #12 cartoons
+> show #12/j,k,l atoms
+> select #12
+atoms, 24865 bonds, 7 pseudobonds, 2801 residues, 3 models selected
+> nucleotides sel ladder
+> select clear
+> hide #12 cartoons
+> show #12 cartoons
+> surface zone #13 nearAtoms #12 distance 10
+> surface dust #13 size 7.25
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out.tif" width 1984
+> height 1210 supersample 3
+> hide #!13 models
+> hide #!12 models
+> show #!12 models
+> show #!13 models
+> hide #12/l,k,j cartoons
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 tube/slab shape ellipsoid
+> nucleotides #!12 tube/slab shape box
+> nucleotides #!12 slab
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> lighting soft
+> lighting simple
+> hide #12/a:83,85 atoms
+> hide #!13 models
+> select #12/A:178
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #12/A:193
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #12/A:192
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #12/A:191
+atoms, 17 bonds, 3 residues, 1 model selected
+> select add #12/A:178
+atoms, 29 bonds, 4 residues, 1 model selected
+> show sel atoms
+> show #!13 models
+> hide #!13 models
+> select #12/A:191@OG
+atom, 1 residue, 1 model selected
+> select add #12/K:39@OP1
+atoms, 2 residues, 1 model selected
+> distance #12/A:191@OG #12/K:39@OP1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A SER 191 OG
+and /K DC 39 OP1: 2.884Å
+> select #12/A:193@OD1
+atom, 1 residue, 1 model selected
+> select add #12/L:9@N2
+atoms, 2 residues, 1 model selected
+> distance #12/A:193@OD1 #12/L:9@N2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ASN 193 OD1
+and /L DG 9 N2: 2.565Å
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> select #12/A:205
+atoms, 8 bonds, 1 residue, 1 model selected
+> show #12/a:205 atoms
+> show #!13 models
+> hide #12/a:205 atoms
+> color zone #13 near #12 distance 10
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> volume #!13 style image
+> volume #!13 style surface
+> transparency #13.1 0
+> transparency #13.1 50
+> color #12 white
+[Repeated 1 time(s)]
+> color #12 black
+> color #12 gray
+> color #12 dim gray
+> color #12 light gray
+> color #12 dim gray
+> color #12 red
+> orange
+Unknown command: orange
+> color #12 orange
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #13 navajo white
+> transparency #13.1 50
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #13 navajo white
+> transparency #13 50
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12 rosy brown
+> color #12 orange
+> color #12 sienna
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 sienna
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 sienna
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> select clear
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 sienna
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 peru
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 khaki
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 violet
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 alice blue
+> transparency #13 50
+> select #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> color sel violet
+> select subtract #12
+Nothing selected
+> select add #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> select subtract #12
+Nothing selected
+> select add #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> select subtract #12
+Nothing selected
+> select add #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> color sel lemon chiffon
+> color sel light coral
+> color sel burly wood
+> color sel pale green
+> color sel gray
+> select clear
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/o blue
+> color zone #13 near #12/o distance 1
+> surface dust #13 size 7.25
+> surface dust #13 size 0
+> transparency #13 50
+> color zone #13 near #12
+> color zone #13 near #12 distance 10
+> transparency #13 50
+> surface dust #13 size 7.25
+> color #12 byhetero
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/a byhetero
+> hide #12/a:192 atoms
+> select add #11
+pseudobonds, 2 models selected
+> color sel white
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel yellow
+> color sel dark orange
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel orange red
+> select clear
+> hide #12/j atoms
+> hide #12/c,d,e,f,g,h,i cartoons
+> color #12 red
+> color #12 blue
+> color #12 green
+> color #12 cyan
+> select clear
+> color #12/a byhetero
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel dark red
+> color sel red
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding_shar_colormap.tif"
+> width 1984 height 1210 supersample 3
+> hide #12 atoms
+> show #12/k:39,40 atoms
+> show #12/l:7-8 atoms
+> select #13
+models selected
+> select clear
+> show #12/a:83,85 atoms
+> show #12/k:40-41 atoms
+> show #12/l:6 atoms
+> hide #12/k:39 #12/l:8 atoms
+> select clear
+> hide #12 cartoons
+> show #12/a:32-86 cartoons
+> lighting soft
+> lighting simple
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_colormap.tif" width 1984
+> height 1210 supersample 3
+> view
+> show #12 cartoons
+> select clear
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> hide #!11 models
+> hide #!13 models
+> lighting soft
+> lighting simple
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> show #!13 models
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+[Repeated 1 time(s)]
+> lighting soft
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out_colormap.tif"
+> width 1984 height 1210 supersample 3
+> color #12/m,o turquoise
+> color zone #13 near #12 distance 10
+> surface dust #13 size 0
+> color zone #13 near #12 distance 10
+> color #12/o blue
+> color zone #13 near #12 distance 1
+> color zone #13 near #12 distance 10
+> color #12/o blue
+> color zone #13 near #12/o distance 1
+> color blue zon #13 nea #12/o
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select #13 & zon 5 #12
+Expected a keyword
+> zone #13 within 5 of #12
+Expected a keyword
+> select zone #13 nea #12 dis 5
+Missing or invalid "range" argument: Expected a number
+> zone #13 nea #12 dis 5
+Expected a keyword
+> zone #13 nea #12 dis 5
+Expected a keyword
+> color zone #13 near #12 distance 5
+> split map #13
+Expected a structures specifier or a keyword
+> volume copy #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy as #22, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!22 models
+> show #!22 models
+> color #22 nea #12 dis 5
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color zone #22 near #12 distance 5
+> split map #22 nea #12
+Expected a structures specifier or a keyword
+> color zone #13 near #12 distance 5 split map
+Expected a keyword
+> split map zon #22 nea #12 dis 5
+Expected a structures specifier or a keyword
+> ui tool show "Color Zone"
+> volume splitbyzone #22
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 0 as #23.1, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 1 as #23.2, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 2 as #23.3, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 3 as #23.4, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 4 as #23.5, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 5 as #23.6, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 6 as #23.7, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 7 as #23.8, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 8 as #23.9, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 9 as #23.10, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 10 as #23.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> show #!22 models
+> hide #!22 models
+> hide #!23 models
+> show #!23 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.2 models
+> show #!23.2 models
+> hide #!23.2 models
+> show #!23.2 models
+> hide #!23.2 models
+> show #!23.2 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> hide #!23.3 models
+> show #!23.3 models
+> hide #!12 models
+> hide #!23.11 models
+> show #!23.11 models
+> hide #!23.11 models
+> show #!23.11 models
+> hide #!23.10 models
+> show #!23.10 models
+> hide #!23.10 models
+> show #!23.10 models
+> select add #23.10
+models selected
+> color sel turquoise
+> select subtract #23.10
+Nothing selected
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.8 models
+> show #!23.8 models
+> hide #!23.8 models
+> show #!23.8 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23 models
+> show #!23 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> hide #!23.2 models
+> hide #!23.3 models
+> hide #!23.4 models
+> hide #!23.5 models
+> hide #!23.6 models
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.8 models
+> show #!23.8 models
+> hide #!23.8 models
+> show #!23.8 models
+> show #!23.6 models
+> show #!23.5 models
+> show #!23.4 models
+> show #!23.3 models
+> show #!23.2 models
+> show #!23.1 models
+> show #!22 models
+> show #!21 models
+> show #!20 models
+> show #!19 models
+> show #!18 models
+> hide #!18 models
+> hide #!19 models
+> hide #!20 models
+> hide #!21 models
+> hide #!22 models
+> close #22
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> close #23
+> color zone #13 near #12
+> show #!13 models
+> color zone #13 near #12 distance 4
+> color zone #13 near #12 distance 4.25
+> color zone #13 near #12 distance 5
+> volume splitbyzone #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 10 as #22.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> hide #!22 models
+> show #!22 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> view
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.8 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> select add #22.10
+models selected
+> color sel turquoise
+> select subtract #22.10
+Nothing selected
+> select #22.10
+models selected
+> color sel dark turquoise
+> select clear
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> show #!22.3 models
+> lighting soft
+> lighting simple
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> volume #22.1-11 hide
+> volume #22.2 show
+> show #!22.3 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.9 models
+> show #!22.7 models
+> hide #!22.7 models
+> show #!22.8 models
+> show #!22.7 models
+> show #!22.10 models
+> show #!22.11 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> transparency #22 50
+> show #!13 models
+> hide #!13 models
+> show #!12 models
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide #12/k:1-3 atoms
+> hide #12/k:1-3 cartoons
+> show #12/a:280,304-305,319,328 atoms
+> color #12/a byhetero
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> color #22.10 #ff2600ff models
+> select add #22.10
+atoms, 8 bonds, 1 residue, 3 models selected
+> color sel dark turquoise
+> select clear
+> select add #22.10
+models selected
+> transparency sel 50
+> select clear
+> show #12/o,m atoms
+> color #12/m red
+> select clear
+> volume #22 hide
+> select #12/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> select #12/A:309@N
+atom, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #12/A:309@N #12/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LEU 309 N
+and /O HOH 1 O: 3.004Å
+> distance #12/A:309@N #12/O:1@O
+Distance already exists; modify distance properties with 'distance style'
+> show #!11 models
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> show #12/k:1-3 atoms
+> select #12/K:2@O3'
+atom, 1 residue, 1 model selected
+> select add #12/K:2@C3'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C2'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O5'
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> show sel atoms
+> select subtract #12/K:2@O3'
+atoms, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select down
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select #12/K:2@O3'
+atom, 1 residue, 1 model selected
+> color sel dim gray
+> select clear
+> hide #12.1 models
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/O:1@O #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/O HOH 1 O and
+/K DA 3 OP2: 2.868Å
+> select #12/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/A:280@NH2 #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ARG 280 NH2
+and /K DA 3 OP2: 2.709Å
+> select #12/K:3@OP1
+atom, 1 residue, 1 model selected
+> select add #12/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP1 #12/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP1 and
+/M MG 2 MG: 2.496Å
+> select #12/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #12/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #12/A:328@NE2 #12/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A HIS 328 NE2
+and /M MG 2 MG: 1.829Å
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> select add #12/A:304@ND1
+atoms, 2 residues, 1 model selected
+> distance #12/M:2@MG #12/A:304@ND1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/M MG 2 MG and
+/A HIS 304 ND1: 2.331Å
+> select #12/A:305@ND1
+atom, 1 residue, 1 model selected
+> select #12/K:3@OP2
+atom, 1 residue, 1 model selected
+Exactly two atoms must be selected!
+> select add #12/A:305@ND1
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP2 #12/A:305@ND1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP2 and
+/A HIS 305 ND1: 2.858Å
+> select clear
+> volume #22 show
+> color #12/k byhetero
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel orange red
+> select clear
+> hide #12/a cartoons
+> show #12/a cartoons
+> select #12/K:6
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #12/K:7
+atoms, 32 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #22.8
+models selected
+> select clear
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> color zone #22.8 near #12/a distance 5
+> color #12/a:232-350 dark turquoise
+> color zone #22.8 near #12/a distance 5
+> transparency
+> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
+> 0
+> transparency
+> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
+> 50
+> combine #12
+> hide #!12 models
+> hide #!22 models
+> hide #!23 models
+> show #!23 models
+> select #23/K:2@O3'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select clear
+> close #23
+> show #12 models
+> show #12 cartoons
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #12/K:3
+atoms, 11 bonds, 2 residues, 1 model selected
+> color darkred turqoise
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color sel darkred turqoise
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select clear
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #12/K:3
+atoms, 11 bonds, 2 residues, 1 model selected
+> color sel dark turquoise
+> select clear
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> color sel darkred turqoise
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select clear
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> color sel dark turquoise
+> select clear
+> close #22
+> color zone #13 near #12 distance 5
+> volume splitbyzone #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 10 as #22.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 11 as #22.12, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 12 as #22.13, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 13 as #22.14, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> close #22
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #12/K:3
+atoms, 11 bonds, 2 residues, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select up
+atoms, 24865 bonds, 2801 residues, 1 model selected
+> select down
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 11 bonds, 2 residues, 1 model selected
+> select down
+atoms, 11 bonds, 2 residues, 1 model selected
+> select down
+atoms, 11 bonds, 2 residues, 1 model selected
+> select clear
+> select add #12/K:3
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #12/K:2
+atoms, 11 bonds, 2 residues, 1 model selected
+> color sel dark turquoise
+[Repeated 1 time(s)]
+> select clear
+> color zone #13 near #12 distance 5
+> hide #!12 models
+> show #!13 models
+> volume splitbyzone #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!22.6 models
+> show #!22.6 models
+> transparency
+> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 50
+> show #12 models
+> color #12/a byhetero
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide #12/k:1-6 cartoons
+> show #12/k:1-3 atoms
+> volume #22 hide
+> select subtract #12/K:2@O3'
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #12/K:2@O3'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #12/K:3@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #12/K:2@O3'
+atoms, 3 bonds, 2 residues, 1 model selected
+> color sel dim gray
+> color sel byhetero
+> select clear
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select clear
+> volume #22 show
+> transparency #22 90
+> transparency #22 80
+> transparency #22 75
+> hide #12/a cartoons
+> show #12/a cartoons
+> lighting soft
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_colormap.tif" width 1729
+> height 1210 supersample 3
+> view
+> view #22
+> hide #12 atoms
+> transparency #22 10
+> transparency #22 25
+> transparency #22 40
+> transparency #22 50
+> transparency #22 60
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_zoom_out_colormap.tif"
+> width 1729 height 1210 supersample 3
+> show #12/k:6 atoms
+> show #12/k:6-7 atoms
+> hide #12/k cartoons
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22 models
+> show #!13 models
+> transparency #13.1 0
+> transparency #13.1 50
+> hide #!13 models
+> select #12/I:140
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #12/A:295
+atoms, 10 bonds, 2 residues, 1 model selected
+> show sel atoms
+> color sel byhetero
+> select clear
+> show #!13 models
+> hide #12.1 models
+> color #12 cyan
+> transparency #13 90
+> transparency #13 75
+> color #12 dim gray
+> color #12 khaki
+> select #12
+atoms, 24865 bonds, 16 pseudobonds, 2801 residues, 3 models selected
+> color sel light salmon
+> color sel dark goldenrod
+> color sel olive
+> color sel green
+> color sel olive
+> color sel misty rose
+> color sel lavender blush
+> color sel snow
+> color sel dark green
+> color sel white
+> color sel light yellow
+> color sel ghost white
+> color sel mint cream
+> color sel white smoke
+> color sel papaya whip
+> color sel moccasin
+> color sel navajo white
+> select clear
+> color #12 byhetero
+> select #12/K:6@C5'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> color sel pale goldenrod
+> color #12 pale goldenrod
+> color #12/a,i byhetero
+> select clear
+> color #12 ivory
+> color #12 orange red
+> color #12 chocolate
+> select clear
+> color #12 goldenrod
+> select clear
+> color #12/a,i byhetero
+> select clear
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!12 models
+> hide #!11 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 253112 atom styles
+> close #23
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 253112 atom styles
+> color #23/j red
+> colse #23
+Unknown command: colse #23
+> close #23
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stu
+Expected a keyword
+> style stick
+Changed 253111 atom styles
+> select #23/J:61@P
+atom, 1 residue, 1 model selected
+> select add #23/J:60@O3'
+atoms, 2 residues, 1 model selected
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> close #23
+> show #!22 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> transparency
+> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 0
+> view
+> lighting soft
+> hide #!22.2 models
+> hide #!22.6 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.4 models
+> hide #!22.5 models
+> show #!22.2 models
+> hide #!22.3 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!12 models
+> show #12 cartoons
+> show #12/j,k,l atoms
+> hide #12/j,k,l cartoons
+> hide #12 cartoons
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.7 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.7 models
+> hide #12/k,l atoms
+> show #!22.3 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.4 models
+> hide #!22.2 models
+> hide #!12 models
+> show #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.4 models
+> hide #!22.3 models
+> hide #!22.7 models
+> show #!22.7 models
+> show #!22.3 models
+> show #!22.4 models
+> hide #!22.8 models
+> show #!22.9 models
+> show #!22.5 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!22.6 models
+> volume #22 copy
+Expected a keyword
+> volume copy #22
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 copy as #23, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 copy as #24, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 copy as #25, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 copy as #26, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 copy as #27, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 copy as #29, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 copy as #30, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 copy as #32, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+> close #23-27-29,30,32
+Expected a models specifier or a keyword
+> close #23-27,29,30,32
+> select add #31
+models selected
+> select add #28
+models selected
+> ui mousemode right "rotate selected models"
+Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy , 31
+halfcleaved_HNH_center_sharp3Å.mrc 8 copy
+> select clear
+> select add #28
+models selected
+> select add #31
+models selected
+> view matrix models
+> #28,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558,#31,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> show #!22.9 models
+> show #!22.6 models
+Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy
+> view matrix models #28,1,0,0,-26.099,0,1,0,28.092,0,0,1,69.137
+> undo
+> view matrix models #28,1,0,0,-27.45,0,1,0,25.948,0,0,1,59.885
+> undo
+> view matrix models
+> #28,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812,#31,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812
+> view matrix models
+> #28,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175,#31,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07,#31,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68,#31,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27,#31,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56,#31,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3,#31,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3
+> hide #!28 models
+> hide #!22.6 models
+> select clear
+> show #!28 models
+> volume copy #28,31
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+> select add #24
+models selected
+> select add #23
+models selected
+> hide #!23 models
+> view matrix models
+> #23,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77,#24,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77
+> view matrix models
+> #23,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97,#24,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97
+> view matrix models
+> #23,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07,#24,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07
+> view matrix models
+> #23,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16,#24,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16
+> view matrix models
+> #23,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3,#24,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3
+> view matrix models
+> #23,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159,#24,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159
+> view matrix models
+> #23,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62,#24,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62
+> show #!31 models
+> show #!22.3 models
+> hide #!22.3 models
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59,#24,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55,#24,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41,#24,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41
+> view
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68,#24,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68
+> show #!22.3 models
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71,#24,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21,#24,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137,#24,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137
+> hide #!22.3 models
+> select clear
+> show #!23 models
+> show #!28 models
+> show #!22.6 models
+> hide #!28 models
+> hide #!23 models
+> hide #!22.6 models
+> show #!22.3 models
+> show #!28 models
+> hide #!28 models
+> show #!23 models
+> show #!22.4 models
+> show #!22.6 models
+> show #!28 models
+> hide #!28 models
+> hide #!23 models
+> hide #!22.3 models
+> hide #!22.4 models
+> show #!22.2 models
+> show #!28 models
+> show #!23 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Thu Mar 27 17:05:34 2025 ———
+opened ChimeraX session
+> hide #!22.6 models
+> hide #!22.2 models
+> show #!22.6 models
+> hide #!22.6 models
+> hide #!23 models
+> hide #!28 models
+> show #!28 models
+> select add #28
+models selected
+> select add #31
+models selected
+> ui mousemode right "rotate selected models"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> view matrix models
+> #28,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74,#31,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74
+> show #!23 models
+> show #!22.6 models
+> hide #!28 models
+> hide #!23 models
+> hide #!22.6 models
+> select clear
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #25
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> volume #22 hide
+> volume #24-25 hide
+> volume #31 hide
+> style stick
+Changed 253111 atom styles
+> show #25 cartoons
+> hide #25
+> show #25 & nucleic
+> color #25/L light gray
+> color #25/K dim gray
+> color #25/J dark red
+> color #25/I rebecca purple
+> color #25/B forest green
+> color #25/C,D,E,F,G,H khaki
+> color #25/A steel blue
+> color #25/A:232-350 dark turquoise
+> hide #25 & nucleic cartoons
+> show #25
+> hide #25
+> show #25 & nucleic
+> show #25/j
+> open 3i4h
+Summary of feedback from opening 3i4h fetched from pdb
+---
+note | Fetching compressed mmCIF 3i4h from http://files.rcsb.org/download/3i4h.cif
+i4h title:
+Crystal structure of Cas6 in Pyrococcus furiosus [more info...]
+Chain information for 3i4h #26
+---
+Chain | Description | UniProt
+X | endoribonuclease | Q8U1S4_PYRFU 8-270
+> hide #!22 models
+> hide #!26 models
+> show #!26 models
+> hide #!25 models
+> show #!25 models
+> select #26/X:34
+atoms, 3 bonds, 1 residue, 1 model selected
+> view matrix models #26,1,0,0,11.063,0,1,0,112.94,0,0,1,76.569
+Drag select of 48 residues
+> view matrix models #26,1,0,0,25.302,0,1,0,250.11,0,0,1,200.98
+> view matrix models #26,1,0,0,73.305,0,1,0,249.54,0,0,1,132.47
+> view matrix models
+> #26,0.6118,0.31311,-0.72641,89.838,-0.77626,0.41421,-0.47524,242.91,0.15208,0.85463,0.49646,158
+> view matrix models
+> #26,0.20919,0.21723,-0.95344,137.17,-0.96272,0.21674,-0.16184,238.54,0.17149,0.95175,0.25447,203.29
+> view matrix models
+> #26,-0.18257,0.38275,-0.90563,144.87,-0.7876,0.49443,0.36774,240.71,0.58852,0.78041,0.21118,199.4
+> view matrix models
+> #26,0.24049,0.042201,-0.96973,126.99,-0.49179,0.86663,-0.084247,255.09,0.83685,0.49716,0.22917,198.15
+> view matrix models
+> #26,0.24049,0.042201,-0.96973,115.81,-0.49179,0.86663,-0.084247,256.61,0.83685,0.49716,0.22917,201.79
+> select #26 & name="tyr"
+Expected a keyword
+> select ::name="TYR"
+atoms, 15721 bonds, 1261 residues, 36 models selected
+> select #26::name="tyr"
+atoms, 193 bonds, 16 residues, 1 model selected
+> select #26::name="tyr" #26::name=lys
+atoms, 373 bonds, 38 residues, 1 model selected
+> select #26::name="tyr" #26::name=lys,his
+atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
+> select #26::name="tyr" #26::name=lys
+atoms, 373 bonds, 38 residues, 1 model selected
+> select #26::name=lys
+atoms, 178 bonds, 22 residues, 1 model selected
+> select #26::name=his
+atoms, 82 bonds, 8 residues, 1 model selected
+> view matrix models
+> #26,-0.89794,0.08841,0.43115,111.17,0.14503,0.98434,0.10021,254.49,-0.41554,0.15251,-0.8967,209.66
+> select #26::name="his,lys"
+Nothing selected
+> select #26::name=his,lys
+atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
+> select #26::name=his::name=lys
+atoms, 260 bonds, 30 residues, 1 model selected
+> select #26::name=his::name=lys::name=tyr
+atoms, 455 bonds, 46 residues, 1 model selected
+> show sel
+> select clear
+> mmaker #26 to #25/i
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain I (#25)
+with 3i4h, chain X (#26), sequence alignment score = 33.6
+RMSD between 6 pruned atom pairs is 1.546 angstroms; (across all 156 pairs:
+.266)
+> hide #!26 models
+> hide #!25 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 279140 atom styles
+> hide #27
+> show #27 cartoons
+> show #27/j,k,l
+> hide #27/j,k,l cartoons
+> color #27/L light gray
+> color #27/K dim gray
+> color #27/J dark red
+> color #27/I rebecca purple
+> color #27/B forest green
+> color #27/C,D,E,F,G,H khaki
+> color #27/A steel blue
+> color #27/A:232-350 dark turquoise
+> color #27/O blue
+> color #27/M red
+> volume #13 show
+> color zone #13 near #27 distance 10
+> color zone #13 near #27 distance 6
+> color zone #13 near #27 distance 4
+> color zone #13 near #27 distance 8
+> transparency #13 50
+> volume #13 hide
+> hide #27 models
+> close #27
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 279111 atom styles
+> hide #27
+> show #27 cartoons
+> show #27 & nucleic
+> color #27/L light gray
+> color #27/K dim gray
+> color #27/J dark red
+> color #27/I rebecca purple
+> color #27/B forest green
+> color #27/C,D,E,F,G,H khaki
+> color #27/A steel blue
+> color #27/A:232-350 dark turquoise
+> color #27/O blue
+> color #27/M red
+> hide #27& nucleic
+> hide #27& nucleic cartoons
+> hide #27& nucleic
+> show #27 & nucleic
+> select clear
+> select P
+atoms, 1108 residues, 15 models selected
+> color sel byhetero
+> select clear
+> hide #!27 models
+> open 3pkm
+Summary of feedback from opening 3pkm fetched from pdb
+---
+note | Fetching compressed mmCIF 3pkm from http://files.rcsb.org/download/3pkm.cif
+pkm title:
+Crystal structure of Cas6 with its substrate RNA [more info...]
+Chain information for 3pkm #29
+---
+Chain | Description | UniProt
+A X | CRISPR-associated endoribonuclease Cas6 | CAS6_PYRFU 8-270
+G | 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
+R | 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
+pkm mmCIF Assemblies
+---
+| author_defined_assembly
+| author_defined_assembly
+Drag select of 237 residues, 3 pseudobonds, 27 shapes
+> hide sel cartoons
+> select #29/A:106
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+Drag select of 71 atoms, 71 bonds, 27 shapes
+> hide sel
+Drag select of 13 atoms
+> hide sel
+> close #29
+> show #27 models
+> view
+> close #27
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style sty
+Expected a keyword
+> style stick
+Changed 279111 atom styles
+> hide #27
+> color #27/L light gray
+> color #27/K dim gray
+> color #27/J dark red
+> color #27/I rebecca purple
+> color #27/B forest green
+> color #27/C,D,E,F,G,H khaki
+> color #27/A steel blue
+> color #27/A:232-350 dark turquoise
+> color #27/O blue
+> color #27/M red
+> show #27 cartoons
+> show #27/j,k,l,m,o
+> hide #27 & nucleic cartoons
+> select P
+atoms, 1108 residues, 15 models selected
+> select #27::P
+Nothing selected
+> select #27::name=P
+Nothing selected
+> select #27 & P
+atoms, 111 residues, 1 model selected
+> color sel byhetero
+> select clear
+> hide #27 models
+> open /Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Phenix/eLBOW_54/elbow.001.pdb
+> view
+> close #29
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Mon Mar 31 18:07:43 2025 ———
+opened ChimeraX session
+> open /Users/zxc755/Downloads/J620_abinitio_map.mrc
+Opened J620_abinitio_map.mrc as #29, grid size 128,128,128, pixel 2.38, shown
+at level 0.218, step 1, values float32
+> hide #!29 models
+> show #!29 models
+> view
+> lighting soft
+> lighting simple
+> lighting soft
+> ui tool show "Color Actions"
+> select add #29
+models selected
+> color sel dark khaki
+[Repeated 1 time(s)]
+> color sel navajo white
+> select clear
+> lighting soft
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/half_abinitio.tif" width 1984 height
+> 1210 supersample 3 transparentBackground true
+> open /Users/zxc755/Downloads/half_hetref_J623_map.mrc
+Opened half_hetref_J623_map.mrc as #30, grid size 128,128,128, pixel 2.38,
+shown at level 0.227, step 1, values float32
+> select add #30
+models selected
+> color sel navajo white
+> hide #!29 models
+> select clear
+> volume #30 level 0.5
+> volume #30 level 0.3
+> volume #30 level 0.35
+> volume #30 level 0.33
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/half_hetref.tif" width 1984 height 1210
+> supersample 3
+> hide #!30 models
+Unsupported scale factor (0.000000) detected on Display0
+[Repeated 7 time(s)]
+> show #!31 models
+> hide #!31 models
+> show #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> hide #!29 models
+> show #!13 models
+> hide #!30 models
+> show #!30 models
+> hide #!30 models
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H salmon
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/O blue
+> color #12/M red
+> color zone #13 near #12 distance 10
+> show #!22.1 models
+> hide #!22 models
+> hide #!22.1 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> color #22.2 salmon
+> show #!22.2 models
+> hide #!22.2 models
+> hide #!13 models
+> show #!22.2 models
+> show #!22.1 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.1 models
+> show #!22.3 models
+> hide #!22.2 models
+> show #!22.2 models
+> surface dust #22.2-9 size 10
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.2 models
+> show #!22.4 models
+> hide #!22.3 models
+> show #!22.5 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.3 models
+> show #!22.7 models
+> hide #!22.7 models
+> surface dust #22.5 size 10
+> surface dust #22.4 size 10
+> surface dust #22.6 size 10
+> surface dust #22.7 size 10
+> surface dust #22.8 size 10
+> surface dust #22.9 size 10
+> show #!22.6 models
+> hide #!22.3 models
+> surface dust #22.6 size 10
+> hide #!22.4 models
+> hide #!22.5 models
+> show #!22.7 models
+> hide #!22.6 models
+> show #!22.8 models
+> show #!22.9 models
+> surface dust #22.7 size 10
+> surface dust #22.8 size 10
+> surface dust #22.9 size 10
+> show #!22.10 models
+> hide #!22.10 models
+> view
+> hide #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> show #!22.6 models
+> show #!22.9 models
+> hide #!22.9 models
+> hide #!22.6 models
+> show #!22.5 models
+> show #!22.4 models
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.2 models
+> hide #!22.4 models
+> hide #!22.3 models
+> show #!22.3 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.10 models
+> view
+[Repeated 1 time(s)]
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> volume #22 hide
+> show #12
+> hide #12
+> show #12 cartoons
+> show #12 & nucleic
+> volume #22 hide mod
+Expected a keyword
+> volume #22 hide model
+Expected a keyword
+> hide #22 models
+> show #22
+> hide #!22.1 models
+> hide #22 models
+> show #!13 models
+> hide #!13 models
+> show #22 models
+> hide #!22.1 models
+> transparency #22 70
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+> show #12/A:83,85
+> color #12/A byhetero
+> hide #12 & nucleic cartoons
+> ui tool show "Side View"
+> hide #!22.10 models
+> hide #!22.9 models
+> hide #!22.6 models
+> hide #!22.5 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.2 models
+> hide #12/c,d,e,f,g,h,i cartoons
+> show #!22.9 models
+> hide #!22.9 models
+> hide #12/c,d,e,f,g,h,i,j cartoons
+> hide #12/j
+> color #12/l wheat
+> color #22.7 wheat
+> show #!22.2 models
+> hide #!22.2 models
+> show #!21 models
+> hide #!21 models
+> show #!11 models
+> select add #11
+pseudobonds, 2 models selected
+> color sel black
+> color sel slate gray
+> color sel gray
+> color sel dim gray
+> select subtract #11
+Nothing selected
+> hide #!11 models
+> show #!11 models
+> show #!22.5 models
+> show #!22.2 models
+> show #!22.6 models
+> show #!22.9 models
+> show #!22.10 models
+> hide #!12 models
+> transparency #22 0
+> lighting soft
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> color #22.7 gold
+> color #22.7 khaki
+> color #22.7 dark khaki
+> color #22.7 olive
+> color #22.7 dark khaki
+> view
+> color #22.7 goldenrod
+> color #22.7 orange
+> color #22.7 dark orange
+> color #22.7 dark khaki
+> show #!12 models
+> transparency #22 70
+> graphics silhouettes true
+> lighting flat
+[Repeated 2 time(s)]
+> lighting soft
+> lighting flat
+> lighting soft
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> transparency #22 80
+> transparency #22 99
+> transparency #22 90
+> transparency #12/l:1-6 50
+> select add #11
+pseudobonds, 2 models selected
+> color sel crimson
+> color sel brown
+> color sel saddle brown
+> color sel indian red
+> color sel yellow
+> color sel gold
+[Repeated 1 time(s)]
+> color sel orange
+> color sel dark orange
+> color sel goldenrod
+> color sel salmon
+> color sel dark khaki
+> color sel peru
+> color sel dark goldenrod
+> select subtract #11
+Nothing selected
+> view
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> hide #!22.5 models
+> hide #!22.6 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22 models
+> show #!22 models
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+> volume #22.8 level 0.03
+> volume #22.8 level 0.02
+> volume #22 level 0.07
+> volume #22 level 0.05
+> hide #!22 models
+> show #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
+> 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
+> 1210 supersample 4
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
+[Repeated 1 time(s)]
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
+> 1210 supersample 3
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #12/a:83,85
+> volume #22 level 0.02
+> show #!22.5 models
+> show #!22.9 models
+> show #12/j
+> hide #12/a,b
+> hide #12/a,b cartoons
+> hide #!22.5 models
+> hide #!22.4 models
+> hide #!22.3 models
+> hide #!12 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #!32 models
+> show #!32 models
+> style ato
+Expected a keyword
+> style stick
+Changed 303224 atom styles
+> cki #32
+Unknown command: cki #32
+> close #32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 303277 atom styles
+> close #32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 303198 atom styles
+> hide #32
+> show #32 cartoons
+Computing secondary structure
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #32/L dark khaki
+> color #32/K dim gray
+> color #32/J dark red
+> color #32/I rebecca purple
+> color #32/B forest green
+> color #32/C,D,E,F,G,H salmon
+> color #32/A steel blue
+> color #32/A:232-350 dark turquoise
+> color #32/O blue
+> color #32/M red
+> hide #32 & nucleic cartoons
+> show #32 & nucleic
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> hide #!22.7 models
+> show #!22.7 models
+> show #!32 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> color #22.7 khaki
+> color #22.7 dark khaki
+> hide #!12 models
+> color #32/l khaki
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!32 models
+> show #!12 models
+> show #12/m,o
+> hide #!22.8 models
+> hide #!22.9 models
+> hide #!22.7 models
+> show #!22.5 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #12/a cartoons
+> hide #12/j
+> show #!22.4 models
+> show #12/a:304,305
+> hide #!22 models
+> select #12/A:280
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #12/A:319
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #12/A:280
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> select #12/K:2@C2'
+atom, 1 residue, 1 model selected
+> select add #12/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C3'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select clear
+> select #12/K:3@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 3 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #12/K:2@O3'
+atoms, 3 bonds, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> select #12/A:328
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> show #!22 models
+> hide #!22 models
+> hide #!12 models
+> show #!12 models
+> show #!22 models
+> hide #!22 models
+> hide #!12 models
+> show #!22 models
+> show #!12 models
+> transparency #22 90
+> transparency #22 95
+> hide #!22 models
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows true intensity 0.5
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows false
+> lighting flat
+[Repeated 1 time(s)]
+> graphics silhouettes false
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting flat
+> graphics silhouettes false
+> show #!22 models
+> graphics silhouettes true
+> view
+> view orient
+[Repeated 1 time(s)]
+> show #12/a
+> volume #22 level 0.05
+> volume #22 level 0.09
+> volume #22 level 0.02
+> hide #12/a
+> hide #!12 models
+> show #!22.2 models
+> show #!22.3 models
+> hide #!22.4 models
+> hide #!22.5 models
+> hide #!22.2 models
+> show #!12 models
+> hide #12/a cartoons
+> show #12/b cartoons
+> hide #12/k,l
+> show #12/b
+> hide #12/b
+> hide #12/b cartoons
+> hide #!22.3 models
+> show #!22.2 models
+> show #12/c,d,e,f,g,h
+> show #12/c,d,e,f,g,h cartoons
+> hide #12/c,d,e,f,g,h
+> hide #!22.2 models
+> hide #12/c,d,e,f,g,h cartoons
+> show #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> show #12/j,k,l
+> hide #!12 models
+> show #!32 models
+> hide #!32 models
+> show #!12 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!22.2 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> hide #!22 models
+> hide #!32 models
+> show #!32 models
+> show #32/m,o
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> select #32/l
+atoms, 280 bonds, 1 pseudobond, 12 residues, 2 models selected
+> color sel khaki
+> color sel burly wood
+> color sel rosy brown
+> color sel midnight blue
+> color sel purple
+> color sel rebecca purple
+> color sel cornflower blue
+> color sel dodger blue
+> color sel peru
+> color sel dark goldenrod
+> color sel dark orange
+> color sel orange
+> color sel dark orange
+> color sel orange
+> color sel dark orange
+> select clear
+> show #!22.1 models
+> select add #22.7
+models selected
+> select subtract #22.7
+Nothing selected
+> select add #22.7
+models selected
+> color sel dark orange
+> select clear
+> hide #!22.1 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!13 models
+> hide #!13 models
+> hide #!11 models
+> show #!13 models
+> graphics silhouettes false
+> lighting simple
+> lighting soft
+> color zone #13 near #32 distance 10
+> hide #!13 models
+> show #!22.1 models
+> hide #!22 models
+> select #32/K:40@N1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> color sel indigo
+> color sel peru
+> color sel maroon
+> color sel hot pink
+> show #!22 models
+> view
+> select clear
+> hide #32/c,d,e,f,g,h,j, car
+> hide #32/c,d,e,f,g,h,j cartoons
+> hide #!22 models
+> show #!22 models
+> hide #!22.1 models
+> hide #!22.2 models
+> hide #!22.6 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #32/m,o
+> show #32/a:83,85
+> color #32/a byhetero
+> show #!11 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Wed Apr 23 13:09:57 2025 ———
+opened ChimeraX session
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #!11 models
+> show #!11 models
+> ui tool show Distances
+> hide #!22 models
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /L DG 6 N2: 3.258Å
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.03
+[Repeated 2 time(s)]
+> distance style radius 0.02
+[Repeated 2 time(s)]
+> distance style radius 0.01
+[Repeated 2 time(s)]
+> distance style radius 0.02
+[Repeated 2 time(s)]
+> distance style radius 0.03
+[Repeated 2 time(s)]
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> distance style decimalPlaces 2
+[Repeated 2 time(s)]
+> distance style decimalPlaces 1
+[Repeated 2 time(s)]
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/K:41@O2
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/K:41@O2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /K DC 41 O2: 3.0Å
+> select #32/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #32/A:85@NZ
+atoms, 2 residues, 1 model selected
+> distance #32/A:83@OD1 #32/A:85@NZ
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
+OD1 and LYS 85 NZ: 2.9Å
+> select #32/K:40@N2
+atom, 1 residue, 1 model selected
+> select #32/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:83@OD1 #32/K:40@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
+OD1 and /K DG 40 N2: 3.0Å
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel peru
+> color sel light salmon
+> color sel olive
+> color sel teal
+> select clear
+> close sel
+> delete sel
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> close #32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 303202 atom styles
+> color #32/L dark orange
+> color #32/K dim gray
+> color #32/J dark red
+> color #32/I rebecca purple
+> color #32/B forest green
+> color #32/C,D,E,F,G,H salmon
+> color #32/A steel blue
+> color #32/A:232-350 dark turquoise
+> color #32/O blue
+> color #32/M red
+> color #32/k:40 hot pink
+> hide #32
+> show #32/k,l
+> show #32/a,b cartoons
+Computing secondary structure
+> color #32/a byhetero
+> show #32/a:83-85
+> select #32/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:83@OD1 #32/K:40@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
+OD1 and /K DG 40 N2: 3.0Å
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/A:83@OD1
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/A:83@OD1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and ASP 83 OD1: 2.7Å
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /L DG 6 N2: 3.1Å
+> select #32/K:41@O2
+atom, 1 residue, 1 model selected
+> select add #32/A:85@NZ
+atoms, 2 residues, 1 model selected
+> distance #32/K:41@O2 #32/A:85@NZ
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DC
+O2 and /A LYS 85 NZ: 2.9Å
+> select add #11
+atoms, 17 pseudobonds, 2 residues, 3 models selected
+> color sel dark khaki
+> color sel teal
+> select clear
+> select #32/A:85
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel steel blue
+> color sel byhetero
+> select clear
+> select #32/K:41@O2
+atom, 1 residue, 1 model selected
+> color sel dim gray
+> select clear
+> select #32/L:7@C2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 20 bonds, 1 residue, 1 model selected
+> color sel hot pink
+> select clear
+> show #!22 models
+> hide #!22 models
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> show #11.1 models
+> hide #11.1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_nomap.tif" width 1984 height
+> 1210 supersample 3
+> show #!22 models
+> hide #!22 models
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
+> close #1-10
+> close #14-21
+> close #23-31
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
+> show #32 cartoons
+> hide #32/a
+> cartoon style nucleic xsection oval width 1 thickness 1
+> show #!22 models
+> show #!22.2 models
+> show #!22.6 models
+> show #!22.9 models
+> show #32/j
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout.tif" width 1984 height
+> 1210 supersample 3
+> hide #32/j,k,l cartoons
+> select clear
+> hide #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout_nomap.tif" width 1984
+> height 1210 supersample 3
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
+Chain information for halfcleaved_HNH_inwards_refined.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #1-2
+> hide #32/k:1-6
+> show #1-2 cartoons
+Computing secondary structure
+[Repeated 1 time(s)]
+> color #1,2/L dark orange
+> color #1,2/K dim gray
+> color #1,2/J dark red
+> color #1,2/I rebecca purple
+> color #1,2/B forest green
+> color #1,2/C,D,E,F,G,H salmon
+> color #1,2/A steel blue
+> color #1,2/A:232-350 dark turquoise
+> color #1,2/O blue
+> color #1,2/M red
+> cartoon style nucleic xsection oval width 1 thickness 1
+> hide #1-2 & nucleic cartoons
+> color #32/k dim gray
+> color #32/l dark orange
+> select clear
+> mmaker #1/a:150-200 to #32/a:150-200
+Computing secondary structure
+[Repeated 1 time(s)]  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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with halfcleaved_HNH_inwards_refined.pdb, chain A (#1), sequence alignment
+score = 253.2
+RMSD between 51 pruned atom pairs is 0.259 angstroms; (across all 51 pairs:
+.259)
+> mmaker #2/a:150-200 to #32/a:150-200
+Computing secondary structure
+[Repeated 1 time(s)]  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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with halfcleaved_HNH_outwards_refined.pdb, chain A (#2), sequence alignment
+score = 241.2
+RMSD between 51 pruned atom pairs is 0.283 angstroms; (across all 51 pairs:
+.283)
+> combine #1
+> combine #2
+> combine #32
+> morph #2 #32 #1 #5 #4
+Computed 201 frame morph #6
+> coordset #6 1,201
+> hide #!3 models
+> hide #!6 models
+> show #!6 models
+> show #6 & nucleic cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> nucleotides #!6 ladder
+> show #6 & nucleic
+> hide #!6 models
+> close #1-5
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
+Chain information for halfcleaved_HNH_inwards_refined.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #3
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> combine #32
+> hide #1-4
+> show #1-4 cartoons
+Computing secondary structure
+[Repeated 2 time(s)]
+> color #1-4/L dark orange
+> color #1-4/K dim gray
+> color #1-4/J dark red
+> color #1-4/I rebecca purple
+> color #1-4/B forest green
+> color #1-4/C,D,E,F,G,H salmon
+> color #1-4/A steel blue
+> color #1-4/A:232-350 dark turquoise
+> color #1-4/O blue
+> color #1-4/M red
+> hide #!4 models
+> hide #!3 models
+> hide #!2 models
+> hide #!1 models
+> morph #1 #3 #4 #32 #2
+Computed 201 frame morph #5
+> coordset #5 1,201
+> close #5
+> morph #1 #32 #2 #4 #3
+Computed 201 frame morph #5
+> coordset #5 1,201
+> hide #5/k:1-6
+> hide #5/k:1-6 cartoons
+> show #5 & nucleic
+> style stick
+Changed 192721 atom styles
+> nucleotides #!5 ladder
+> cartoon style nucleic xsection oval width 1 thickness 1
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> movie record
+> movie encode /Users/zxc755/Desktop/movie1.mp4 framerate 25.0
+Movie saved to /Users/zxc755/Desktop/movie1.mp4
+> hide #!5 models
+> show #!32 models
+> show #!22 models
+> show #32/k
+> hide #!22 models
+> select #32/K:2@O5'
+atom, 1 residue, 1 model selected
+> select add #32/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C2'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C3'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select #32/K:2@C5'
+atom, 1 residue, 1 model selected
+> hide sel
+> show #32/m,o
+> select clear
+> show #32/a:280,305,304
+> select #32/K:3@P
+atom, 1 residue, 1 model selected
+> select add #32/K:2@O3'
+atoms, 2 residues, 1 model selected
+> select add #32/K:3@OP1
+atoms, 2 residues, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> select add #32/K:3@O5'
+atoms, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> hide #32.1 models
+> select #32/A:328
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> select #32/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #32/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #32/A:304@ND1 #32/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
+ND1 and /M MG 2 MG: 2.3Å
+> select #32/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #32/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #32/A:328@NE2 #32/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
+NE2 and /M MG 2 MG: 1.8Å
+> hide #11.1 models
+> select #32/O:1@O
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #32/O:1@O #32/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/O HOH
+O and /K DA 3 OP2: 2.9Å
+> select #32/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #32/A:280@NH2 #32/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ARG
+NH2 and /K DA 3 OP2: 2.7Å
+> select #32/A:308
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #32/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel
+> hide sel cartoons
+> select #32/A:309@N
+atom, 1 residue, 1 model selected
+> select add #32/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #32/A:309@N #32/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LEU
+N and /O HOH 1 O: 3.0Å
+> select #32/A:309@CA
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> hide sel
+> select #32/M:2@MG
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/M:2@MG #32/K:3@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/M MG 2
+MG and /K DA 3 OP1: 2.5Å
+> color #11 teal
+> select clear
+> select #32/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance sel
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
+ND1 and /K DA 3 OP2: 2.9Å
+> color #11 teal
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 3
+[Repeated 2 time(s)]
+> distance style dashes 2
+[Repeated 2 time(s)]
+> distance style dashes 1
+[Repeated 2 time(s)]
+> distance style dashes 2
+[Repeated 2 time(s)]
+> distance style dashes 3
+[Repeated 2 time(s)]
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style dashes 6
+[Repeated 2 time(s)]
+> distance style dashes 7
+[Repeated 2 time(s)]
+> distance style dashes 8
+[Repeated 2 time(s)]
+> distance style dashes 7
+[Repeated 2 time(s)]
+> distance style dashes 8
+[Repeated 2 time(s)]
+> distance style dashes 7
+[Repeated 2 time(s)]
+> distance style dashes 6
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> select clear
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #32/a:319
+> show #!22 models
+> hide #!22 models
+> select #32/A:320
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #32/A:320
+atoms, 7 bonds, 1 residue, 1 model selected
+> select clear
+> ~distance #12/A:85@NZ #12/A:83@OD1
+> ~distance #12/K:3@OP2 #12/A:305@ND1
+> ~distance #12/M:2@MG #12/A:304@ND1
+> ~distance #12/K:40@N2 #12/A:83@OD1
+> ~distance #12/A:85@NZ #12/K:41@O2
+> ~distance #12/A:193@OD1 #12/L:9@N2
+> ~distance #12/A:280@NH2 #12/K:3@OP2
+> ~distance #12/A:85@NZ #12/L:6@N2
+> ~distance #12/A:191@OG #12/K:39@OP1
+> ~distance #12/A:328@NE2 #12/M:2@MG
+> ~distance #12/A:309@N #12/O:1@O
+> ~distance #12/K:3@OP1 #12/M:2@MG
+> ~distance #12/O:1@O #12/K:3@OP2
+> select #32/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 24845 bonds, 12 pseudobonds, 2799 residues, 3 models selected
+> select clear
+> select #32/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> ~distance sel
+> select #32/K:3@O5'
+atom, 1 residue, 1 model selected
+> select add #32/A:305@ND1
+atoms, 2 residues, 1 model selected
+> distance sel
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DA 3
+O5' and /A HIS 305 ND1: 2.9Å
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> color #11 teal
+> select clear
+> hide #32 cartoons
+> hide #32/j
+> show #32/a cartoons
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_nomap.tif" width 1984
+> height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs"
+> show #32 cartoons
+> hide #32/k:1-6 cartoons
+> select #32/J:48
+atoms, 25 bonds, 1 residue, 1 model selected
+> show #32/j
+> show #32/k:6 cartoons
+> select clear
+> hide #!11 models
+> hide #32/a
+> hide #32/m,o
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_zoomout_nomap.tif" width
+> 1984 height 1210 supersample 3
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> surface dust #13 size 10
+> hide #!32 models
+> lighting soft
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> view
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting soft
+> lighting flat
+> lighting soft
+> set bgColor gray
+> set bgColor white
+> view #13
+> show #!32 models
+> hide #!13 models
+> hide #!32 models
+> show #!12 models
+> color #12/L dark orange
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H salmon
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/O dark turquoise
+> color #12/M dark turquoise
+> color #12/k:1-3 dark turquoise
+> hide #!12 models
+> show #!13 models
+> color zone #13 near #12 distance 10
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> volume #13 level 0.05
+> volume #13 change image level 0.0001303,0 level 0.002946,0.8 level 1.983,1
+> volume #13 level 0.09
+> volume #13 level 0.06
+> volume #13 level 0.05
+> volume #13 level 0.03
+> turn x 90
+[Repeated 3 time(s)]
+> hide #!13 models
+> show #!32 models
+> hide #!32 models
+> show #!22 models
+> lighting soft
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting soft
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> show #!32 models
+> graphics silhouettes true
+> lighting flat
+> hide #!32 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript
+> save "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"
+——— End of log from Fri Apr 25 19:29:02 2025 ———
+opened ChimeraX session
+> hide #!32 models
+> show #!32 models
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #!32 models
+> show #!1 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> show #!32 models
+> hide #1,2,32 cartoons
+> hide #1,2,32
+> show #1,2,32/a
+> show #1,2,32/a cartoons
+> hide #1,2,32
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_fullTS_sharp.mrc"
+Opened halfcleaved_HNH_center_fullTS_sharp.mrc as #7, grid size 420,420,420,
+pixel 0.725, shown at level 0.00325, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_sharp.mrc"
+Opened halfcleaved_HNH_center_main_map_sharp.mrc as #8, grid size 420,420,420,
+pixel 0.725, shown at level 0.00305, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_in_sharp.mrc"
+Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725,
+shown at level 0.00277, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_out_sharp.mrc"
+Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+> close #7,8
+> hide #!2 models
+> hide #!1 models
+> color zone #9 near #2 distance 10
+> color zone #10 near #1 distance 10
+> ui tool show "Color Zone"
+> volume splitbyzone #9
+Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+> volume splitbyzone #10
+Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+> hide #!7.1 models
+> show #!7.1 models
+> hide #!7.1 models
+> hide #!7.4 models
+> hide #!7.5 models
+> hide #!7.6 models
+> hide #!7.7 models
+> hide #!7.8 models
+> hide #!7.9 models
+> hide #!8.1 models
+> hide #!8.4 models
+> hide #!8.5 models
+> hide #!8.6 models
+> hide #!8.7 models
+> hide #!8.8 models
+> hide #!8.9 models
+> hide #!8 models
+> show #!2 models
+> transparency #7,8 90
+> volume dus #7,8 siz 10
+Expected a density maps specifier or a keyword
+> surface dust #7.2 size 7.25
+> surface dust #7.3 size 7.25
+> surface dust #8 size 10
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> hide #!7 models
+> show #!7 models
+> volume #7.2 level 0.002
+> volume #7 level 0.002
+> volume #8 level 0.002
+> hide #!2 models
+> hide #!7 models
+> show #!8 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!32 models
+> show #!7 models
+> show #!2 models
+> hide #!1 models
+> hide #!8 models
+> surface dust #7 size 10
+> show #!1 models
+> hide #!2 models
+> show #!8 models
+> hide #!7 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out.tif" width
+> 1984 height 1210 supersample 3 transparentBackground true
+> show #!2 models
+> hide #!1 models
+> show #!7 models
+> hide #!8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in.tif" width
+> 1984 height 1210 supersample 3
+> hide #!2 models
+> hide #!7 models
+> show #!22 models
+> show #!32 models
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.6 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent.tif" width
+> 1984 height 1210 supersample 3
+> hide #!32 models
+> hide #!22.5 models
+> show #!22.5 models
+> hide #!22 models
+> show #!7 models
+> show #!8 models
+> hide #!7 models
+> show #!7 models
+> hide #!8 models
+> show #!7.4 models
+> show #!7.5 models
+> show #!7.6 models
+> show #!7.7 models
+> show #!7.8 models
+> show #!7.9 models
+> hide #!7.9 models
+> show #!7.9 models
+> hide #!7.4 models
+> hide #!7.5 models
+> hide #!7.6 models
+> hide #!7.7 models
+> hide #!7.8 models
+> hide #!7.9 models
+> show #!2 models
+> show #!1 models
+> show #!8 models
+> hide #!7 models
+> hide #!2 models
+> hide #!1 models
+> hide #!8 models
+> show #!22 models
+> show #!32 models
+> hide #!32 models
+> hide #!22 models
+> show #!7 models
+> show #!8 models
+> hide #!7 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out_2.tif" width
+> 1984 height 1210 supersample 3
+> hide #!8 models
+> show #!7 models
+> show #!2 models
+> hide #!1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in_2.tif" width
+> 1984 height 1210 supersample 3
+> hide #!2 models
+> hide #!7 models
+> show #!22 models
+> show #!32 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent_2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!32 models
+> hide #!22 models
+> show #!22 models
+> show #!32 models
+> hide #!32 models
+> hide #!22 models
+> show #!1 models
+> show #!2 models
+> hide #!2 models
+> hide #!1 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_center_refined.pdb"
+Chain information for apo_HNH_center_refined.pdb #14
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_inwards_refined.pdb"
+Chain information for apo_HNH_inwards_refined.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+F G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ILE a 6 ALA a 9 1 4
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 SER a 30 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 THR a 44 1
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 VAL a 93 1
+messages similar to the above omitted
+Chain information for apo_HNH_outwards_refined.pdb #16
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_cent_sharp.mrc"
+Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_in_sharp.mrc"
+Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_out_sharp.mrc"
+Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+> hide #!19 models
+> hide #!18 models
+> hide #!17 models
+> color ##14/L dark orange;col ##14/K dim gray;col ##14/J dark red;col ##14/I
+> rebecca purple;col ##14/B forest green;col ##14/C,D,E,F,G,H salmon;col
+> ##14/A steel blue;col ##14/A:232-350 dark turquoise; col ##14/O blue; col
+> ##14/M red
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #14/L dark orange
+> color #14/K dim gray
+> color #14/J dark red
+> color #14/I rebecca purple
+> color #14/B forest green
+> color #14/C,D,E,F,G,H salmon
+> color #14/A steel blue
+> color #14/A:232-350 dark turquoise
+> color #14/O blue
+> color #14/M red
+> color #15/L dark orange
+> color #15/K dim gray
+> color #15/J dark red
+> color #15/I rebecca purple
+> color #15/B forest green
+> color #15/C,D,E,F,G,H salmon
+> color #15/A steel blue
+> color #15/A:232-350 dark turquoise
+> color #15/O blue
+> color #15/M red
+> color #16/L dark orange
+> color #16/K dim gray
+> color #16/J dark red
+> color #16/I rebecca purple
+> color #16/B forest green
+> color #16/C,D,E,F,G,H salmon
+> color #16/A steel blue
+> color #16/A:232-350 dark turquoise
+> color #16/O blue
+> color #16/M red
+> color zone #17 near #14 distance 10
+> color zone #18 near #15 distance 10
+> color zone #19 near #16 distance 10
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> hide #!15 models
+> hide #!14 models
+> show #!17 models
+> show #!18 models
+> show #!19 models
+> hide #!19 models
+> hide #!18 models
+> hide #!17 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #20
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_refined.pdb"
+Chain information for postcleavage_HNH_inwards_refined.pdb #21
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_outwards.pdb"
+Chain information for postcleavage_HNH_outwards.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_in_sharp.mrc"
+Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_out_sharp.mrc"
+Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+> hide #!20 models
+> hide #!21 models
+> hide #!23 models
+> color #20/L dark orange
+> color #20/K dim gray
+> color #20/J dark red
+> color #20/I rebecca purple
+> color #20/B forest green
+> color #20/C,D,E,F,G,H salmon
+> color #20/A steel blue
+> color #20/A:232-350 dark turquoise
+> color #20/O blue
+> color #20/M red
+> color #21/L dark orange
+> color #21/K dim gray
+> color #21/J dark red
+> color #21/I rebecca purple
+> color #21/B forest green
+> color #21/C,D,E,F,G,H salmon
+> color #21/A steel blue
+> color #21/A:232-350 dark turquoise
+> color #21/O blue
+> color #21/M red
+> color #23/L dark orange
+> color #23/K dim gray
+> color #23/J dark red
+> color #23/I rebecca purple
+> color #23/B forest green
+> color #23/C,D,E,F,G,H salmon
+> color #23/A steel blue
+> color #23/A:232-350 dark turquoise
+> color #23/O blue
+> color #23/M red
+> color zone #24 near #20 distance 10
+> color zone #25 near #21 distance 10
+> color zone #26 near #23 distance 10
+> hide #!26 models
+> hide #!25 models
+> hide #!24 models
+> show #!17 models
+> hide #!17 models
+> volume splitbyzone #17
+Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 6 as #27.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+> hide #!27.1 models
+> hide #!27.4 models
+> hide #!27.5 models
+> hide #!27.6 models
+> hide #!27.7 models
+> volume splitbyzone #18
+Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 6 as #28.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+> hide #!28.1 models
+> hide #!28.4 models
+> hide #!28.5 models
+> hide #!28.6 models
+> hide #!28.7 models
+> volume splitbyzone #19
+Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 6 as #29.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+> hide #!29.1 models
+> hide #!29.4 models
+> show #!29.4 models
+> hide #!29.4 models
+> hide #!29.5 models
+> hide #!29.6 models
+> hide #!29.7 models
+> hide #!27 models
+> hide #!28 models
+> hide #!29 models
+> volume splitbyzone #24
+Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 8 as #30.9, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+> volume splitbyzone #25
+Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 8 as #31.9, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+> volume splitbyzone #26
+Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 8 as #33.9, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+> hide #!30.1 models
+> hide #!30.4 models
+> hide #!30.5 models
+> hide #!30.6 models
+> hide #!30.7 models
+> hide #!30.8 models
+> hide #!30.9 models
+> hide #!31.1 models
+> hide #!31.4 models
+> hide #!31.5 models
+> hide #!31.6 models
+> hide #!31.7 models
+> hide #!31.8 models
+> hide #!31.9 models
+> hide #!33.1 models
+> hide #!33.4 models
+> hide #!33.5 models
+> hide #!33.6 models
+> hide #!33.7 models
+> hide #!33.8 models
+> hide #!33.9 models
+> show #!32 models
+> hide #!32 models
+> show #!22 models
+> hide #!22 models
+> show #!29 models
+> show #!28 models
+> show #!27 models
+> transparency 90
+> surface dust siz 10
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #27-31 #33 size 10
+> hide #!33 models
+> hide #!31 models
+> hide #!30 models
+> hide #!29 models
+> hide #!28 models
+Must specify one map, got 10
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 53530 points
+correlation = 0, correlation about mean = 0, overlap = 0
+steps = 24, shift = 0, angle = 0 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.00000000 0.00000000 0.00000000 0.00000000
+.00000000 1.00000000 0.00000000 0.00000000
+.00000000 0.00000000 1.00000000 0.00000000
+Axis 0.00000000 0.00000000 1.00000000
+Axis point 0.00000000 0.00000000 0.00000000
+Rotation angle (degrees) 0.00000000
+Shift along axis 0.00000000
+> hide #!27.2 models
+> show #!27.2 models
+> hide #!27.2 models
+> show #!27.2 models
+> show #!22 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!27.2 models
+> show #!27.2 models
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 53530 points
+correlation = 0, correlation about mean = 0, overlap = 0
+steps = 24, shift = 0, angle = 0 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.00000000 0.00000000 0.00000000 0.00000000
+.00000000 1.00000000 0.00000000 0.00000000
+.00000000 0.00000000 1.00000000 0.00000000
+Axis 0.00000000 0.00000000 1.00000000
+Axis point 0.00000000 0.00000000 0.00000000
+Rotation angle (degrees) 0.00000000
+Shift along axis 0.00000000
+> select #27.2
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #27.2,-0.90481,-0.32416,-0.27613,332.21,0.31284,-0.94596,0.085389,229.16,-0.28888,-0.0091226,0.95732,44.701
+> view matrix models
+> #27.2,-0.97923,-0.19279,0.06285,325.19,0.18122,-0.97109,-0.15536,293.34,0.090985,-0.14075,0.98586,0.54729
+> undo
+[Repeated 2 time(s)]
+> close #27-31
+> close #33
+> color #14-16/a steel blue
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> show #!15 models
+> hide #!15 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> color #20,21,23/a steel blue
+> color zone #17 near #14 distance 10
+> color zone #18 near #15 distance 10
+> color zone #19 near #16 distance 10
+> color #24 nea #20 dis 10
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color zone #24 near #20 distance 10
+> color zone #25 near #21 distance 10
+> color zone #26 near #23 distance 10
+> volume splitbyzone #17
+Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+> volume splitbyzone #18
+Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+> volume splitbyzone #19
+Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+> volume splitbyzone #24
+Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+> volume splitbyzone #25
+Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+> volume splitbyzone #26
+Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+> hide #!33 models
+> hide #!33.1 models
+> hide #!33.3 models
+> show #!33 models
+> hide #!33.4 models
+> hide #!33.5 models
+> hide #!33.6 models
+> hide #!33.7 models
+> hide #!33.8 models
+> hide #!31.8 models
+> hide #!31.7 models
+> hide #!31.6 models
+> hide #!31.5 models
+> hide #!31.4 models
+> hide #!31.3 models
+> hide #!31.1 models
+> hide #!30.8 models
+> hide #!30.7 models
+> hide #!30.6 models
+> hide #!30.5 models
+> hide #!30.4 models
+> hide #!30.3 models
+> hide #!30.1 models
+> hide #!29.6 models
+> hide #!29.5 models
+> hide #!29.4 models
+> hide #!29.3 models
+> hide #!29.1 models
+> hide #!28.6 models
+> hide #!28.5 models
+> hide #!28.4 models
+> hide #!28.3 models
+> hide #!28.1 models
+> hide #!27.6 models
+> hide #!27.5 models
+> hide #!27.4 models
+> hide #!27.3 models
+> hide #!27.1 models
+> hide #!22 models
+> transparency #27-31,33 90
+> show #!22 models
+> hide #!28 models
+> hide #!29 models
+> hide #!30 models
+> hide #!31 models
+> hide #!33 models
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 82885 points
+correlation = 0, correlation about mean = 0, overlap = 0
+steps = 24, shift = 0, angle = 0 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.00000000 0.00000000 0.00000000 0.00000000
+.00000000 1.00000000 0.00000000 0.00000000
+.00000000 0.00000000 1.00000000 0.00000000
+Axis 0.00000000 0.00000000 1.00000000
+Axis point 0.00000000 0.00000000 0.00000000
+Rotation angle (degrees) 0.00000000
+Shift along axis 0.00000000
+> select #27.2
+models selected
+> select add #27
+models selected
+> view matrix models
+> #27,-0.9851,0.028378,0.1696,261.6,0.012815,-0.97143,0.23698,244.5,0.17148,0.23562,0.9566,-52.331
+Drag select of 27.2 apo_HNH_cent_sharp.mrc 1
+> view matrix models
+> #27.2,1,4.8572e-17,6.1062e-16,-14.27,8.32e-32,1,4.1633e-16,-23.71,3.8858e-16,1.6653e-16,1,-1.3138
+> view matrix models
+> #27.2,1,4.8572e-17,6.1062e-16,10.218,8.32e-32,1,4.1633e-16,-19.262,3.8858e-16,1.6653e-16,1,-23.993
+> color #27.2 red
+> view matrix models
+> #27.2,1,0.0011286,0.00024256,-17.671,-0.0011282,1,-0.001653,-23.156,-0.00024442,0.0016527,1,0.99344
+> view matrix models
+> #27.2,0.98647,0.15904,0.039716,-44.71,-0.15822,0.86043,0.48439,-45.115,0.042865,-0.48412,0.87395,80.037
+> surface dust #27-31,33 size 10
+> hide #!27 models
+> select add #27
+models selected
+> select subtract #27
+Nothing selected
+> hide #!22 models
+> show #!22 models
+> show #!30 models
+> select add #30
+models selected
+> color #30.2 green
+> view matrix models
+> #30,0.99278,0.11969,0.0075487,-17.819,-0.11662,0.97821,-0.17177,45.003,-0.027942,0.16965,0.98511,-26.609
+> select subtract #30
+Nothing selected
+> hide #!30 models
+> hide #!22 models
+> show #!2 models
+> hide #!2 models
+> show #!7 models
+> show #!28 models
+> color #28.2 red
+> color #29.2 red
+> color #31.2 green
+> color #33.2 green
+> select add #28
+models selected
+> view matrix models
+> #28,-0.93864,-0.18774,0.28933,282.81,0.11817,-0.96316,-0.24158,292.86,0.32402,-0.19257,0.92624,-7.1144
+> view matrix models
+> #28,-0.93864,-0.18774,0.28933,281.83,0.11817,-0.96316,-0.24158,308.33,0.32402,-0.19257,0.92624,-20.3
+> view matrix models
+> #28,-0.94765,-0.24867,0.20033,309.6,0.18207,-0.93615,-0.30078,306.85,0.26233,-0.24856,0.93242,-0.83323
+> view matrix models
+> #28,-0.95707,-0.19669,0.2129,302.83,0.13597,-0.95335,-0.26952,311.55,0.25597,-0.229,0.93917,-4.0077
+> view matrix models
+> #28,-0.95956,-0.22645,0.1672,313.45,0.18549,-0.95546,-0.22952,299.35,0.21173,-0.18923,0.95883,-5.8084
+> view matrix models
+> #28,-0.95956,-0.22645,0.1672,313,0.18549,-0.95546,-0.22952,299.82,0.21173,-0.18923,0.95883,-5.8642
+> view matrix models
+> #28,-0.94956,-0.28011,0.14095,322.64,0.23523,-0.93354,-0.2705,294.86,0.20736,-0.2237,0.95235,0.5275
+> select subtract #28
+Nothing selected
+> hide #!28 models
+> show #!31 models
+> select add #31
+models selected
+> view matrix models
+> #31,0.95745,0.28853,-0.0061963,-39.992,-0.2858,0.94498,-0.15916,77.745,-0.040066,0.15415,0.98723,-22.047
+> view matrix models
+> #31,0.98495,0.16362,0.055651,-31.707,-0.14812,0.9651,-0.21598,59.788,-0.089048,0.20449,0.97481,-20.953
+> view matrix models
+> #31,0.98502,0.15503,0.075475,-31.759,-0.13914,0.9732,-0.18309,50.935,-0.10184,0.16984,0.98019,-13.582
+> view matrix models
+> #31,0.98251,0.17881,0.052001,-31.724,-0.16394,0.96301,-0.21385,60.765,-0.088316,0.20159,0.97548,-20.561
+> view matrix models
+> #31,0.98782,0.1293,0.086525,-28.788,-0.10934,0.97261,-0.20513,49.258,-0.11068,0.19317,0.9749,-15.438
+> select subtract #31
+Nothing selected
+> hide #!31 models
+> hide #!7 models
+> show #!8 models
+> show #!29 models
+> select add #29
+models selected
+> view matrix models
+> #29,-0.96301,-0.11026,0.24587,268.61,0.020435,-0.93971,-0.34137,320.74,0.26869,-0.32372,0.9072,1.2682
+> view matrix models
+> #29,-0.92586,-0.36935,0.079794,337.56,0.33423,-0.89898,-0.28307,279.15,0.17629,-0.23541,0.95577,1.8338
+> view matrix models
+> #29,-0.9501,-0.28304,0.13113,324.32,0.24497,-0.93725,-0.24809,292.2,0.19312,-0.20359,0.95982,-2.6028
+> view matrix models
+> #29,-0.94885,-0.296,0.10988,328.51,0.25817,-0.9277,-0.26968,291.73,0.18176,-0.22752,0.95666,1.6234
+> view matrix models
+> #29,-0.95084,-0.25098,0.18144,313.28,0.21054,-0.95351,-0.21564,295.36,0.22712,-0.16684,0.95947,-11.512
+> view matrix models
+> #29,-0.94437,-0.26912,0.18906,314.35,0.22158,-0.94541,-0.23894,296.14,0.24304,-0.18376,0.95245,-10.94
+> hide #!29 models
+> select subtract #29
+Nothing selected
+> show #!33 models
+> select add #33
+models selected
+> view matrix models
+> #33,0.95382,0.29041,-0.076702,-29.712,-0.30037,0.92263,-0.24193,98.778,0.0005105,0.25379,0.96726,-42.939
+> view matrix models
+> #33,0.96865,0.24664,-0.029782,-31.412,-0.24842,0.96286,-0.10577,62.659,0.0025886,0.10985,0.99394,-24.767
+> view matrix models
+> #33,0.9728,0.17623,-0.15036,-2.5415,-0.20302,0.96116,-0.18696,65.208,0.11158,0.2124,0.97079,-60.099
+> view matrix models
+> #33,0.98074,0.15825,0.11447,-37.799,-0.13348,0.97094,-0.19866,54.576,-0.14258,0.17955,0.97336,-11.971
+> view matrix models
+> #33,0.98222,0.15787,0.10163,-34.87,-0.13329,0.96753,-0.21473,54.252,-0.13223,0.19737,0.97137,-14.291
+> view matrix models
+> #33,0.98222,0.15787,0.10163,-35.019,-0.13329,0.96753,-0.21473,54.238,-0.13223,0.19737,0.97137,-13.879
+> fitmap #33.2 inMap #8.4
+Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 3 using
+points
+correlation = 0.2302, correlation about mean = 0.1069, overlap = 657.4
+steps = 364, shift = 12.6, angle = 27.8 degrees
+Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
+halfcleaved_HNH_out_sharp.mrc 3 (#8.4) coordinates:
+Matrix rotation and translation
+.88487665 -0.11856540 -0.45048370 86.96048472
+.12698700 0.99183644 -0.01160897 -10.81407486
+.44818257 -0.04693306 0.89270917 -57.31875206
+Axis -0.03789003 -0.96394524 0.26338929
+Axis point 159.50208814 0.00000000 151.60629729
+Rotation angle (degrees) 27.78400581
+Shift along axis -7.96790445
+> fitmap #33.2 inMap #8.2
+Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
+points
+correlation = 0.7507, correlation about mean = 0.6577, overlap = 3498
+steps = 300, shift = 13.1, angle = 25.8 degrees
+Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
+halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
+Matrix rotation and translation
+.99883251 0.02105205 -0.04347916 3.28381267
+-0.01860045 0.99825524 0.05604021 -3.01589348
+.04458306 -0.05516605 0.99748136 2.36658331
+Axis -0.75501980 -0.59788649 -0.26921525
+Axis point 0.00000000 33.34610426 68.86626768
+Rotation angle (degrees) 4.22334809
+Shift along axis -1.31330194
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!33 models
+> show #!29 models
+> fitmap #29.2 inMap #8.2
+Fit map apo_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
+points
+correlation = 0.6154, correlation about mean = 0.4909, overlap = 1988
+steps = 108, shift = 0.371, angle = 3.89 degrees
+Position of apo_HNH_out_sharp.mrc 1 (#29.2) relative to
+halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
+Matrix rotation and translation
+.99774720 -0.00616969 0.06680170 -7.75363432
+.00547813 0.99992955 0.01053061 -2.15873626
+-0.06686197 -0.01014094 0.99771070 11.37852778
+Axis -0.15227290 0.98460707 0.08580135
+Axis point 165.97569556 0.00000000 121.59503582
+Rotation angle (degrees) 3.89203832
+Shift along axis 0.03145444
+> select subtract #33
+Nothing selected
+> hide #!29 models
+> hide #!8 models
+> show #!7 models
+> show #!28 models
+> fitmap #28.2 inMap #7.2
+Fit map apo_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
+points
+correlation = 0.6568, correlation about mean = 0.5566, overlap = 1483
+steps = 100, shift = 1.93, angle = 2.75 degrees
+Position of apo_HNH_in_sharp.mrc 1 (#28.2) relative to
+halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
+Matrix rotation and translation
+.99894275 -0.01608144 0.04306693 -3.27929226
+.01666443 0.99977384 -0.01321212 -2.52037376
+-0.04284472 0.01391584 0.99898482 4.13599960
+Axis 0.28299722 0.89622541 0.34160298
+Axis point 109.08725783 0.00000000 67.16502763
+Rotation angle (degrees) 2.74722295
+Shift along axis -1.77398382
+> hide #!28 models
+> show #!31 models
+> fitmap #31.2 inMap #7.2
+Fit map post_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
+points
+correlation = 0.5948, correlation about mean = 0.441, overlap = 2814
+steps = 152, shift = 1.12, angle = 4.52 degrees
+Position of post_HNH_in_sharp.mrc 1 (#31.2) relative to
+halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
+Matrix rotation and translation
+.99726035 0.04676217 -0.05731570 1.19747961
+-0.04518981 0.99857380 0.02842974 4.02672915
+.05856339 -0.02576177 0.99795123 -4.59092844
+Axis -0.34397877 -0.73553868 -0.58366211
+Axis point 85.75257186 0.00000000 12.62773521
+Rotation angle (degrees) 4.51795970
+Shift along axis -0.69417165
+> hide #!31 models
+> show #!22 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!7 models
+> show #!30 models
+> fitmap #30.2 inMap #22.4
+Fit map post_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 86342 points
+correlation = 0.7861, correlation about mean = 0.6973, overlap = 3404
+steps = 84, shift = 0.298, angle = 2.98 degrees
+Position of post_HNH_cent_sharp.mrc 1 (#30.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.99880892 0.03024374 0.03828920 -9.33094617
+-0.03093378 0.99936719 0.01755928 3.13913491
+-0.03773391 -0.01872279 0.99911241 9.35512683
+Axis -0.34850229 0.73022926 -0.58763201
+Axis point 242.75204382 0.00000000 250.82225024
+Rotation angle (degrees) 2.98383902
+Shift along axis 0.04677237
+> hide #!30 models
+> show #!27 models
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 82885 points
+correlation = 0.608, correlation about mean = 0.4719, overlap = 1708
+steps = 124, shift = 1.2, angle = 3.81 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.97832698 0.19020262 0.08184916 -54.13025495
+-0.20662179 0.87084737 0.44601826 -34.04774174
+.01355572 -0.45326352 0.89127348 78.28203288
+Axis -0.91268658 0.06931143 -0.40273953
+Axis point 0.00000000 156.71923356 124.12929737
+Rotation angle (degrees) 29.51532960
+Shift along axis 15.51679105
+> show #!14 models
+> style stick
+Changed 332211 atom styles
+> hide #14
+> show #14/a cartoons
+Computing secondary structure
+> color #14/a red
+> fitmap #14/a inMap #27.2
+Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
+(#27.2) using 2728 atoms
+average map value = 0.0141, steps = 2000
+shifted from previous position = 21.7
+rotated from previous position = 19 degrees
+atoms outside contour = 2485, contour level = 0.0019908
+Position of apo_HNH_center_refined.pdb (#14) relative to
+apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
+Matrix rotation and translation
+.87515076 -0.42346707 0.23406577 55.94220375
+.48348878 0.74666401 -0.45687137 70.79007602
+.01870149 0.51299950 0.85818516 -55.77887122
+Axis 0.72097898 0.16009669 0.67420944
+Axis point 0.00000000 146.26043027 68.91682292
+Rotation angle (degrees) 42.26858727
+Shift along axis 14.05976817
+> select #14/A:169
+atoms, 7 bonds, 1 residue, 1 model selected
+> view matrix models
+> #14,-0.60187,-0.59648,-0.531,396.65,0.776,-0.27978,-0.56529,167.42,0.18862,-0.75229,0.63126,115.81
+> fitmap #14/a inMap #27.2
+Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
+(#27.2) using 2728 atoms
+average map value = 0.04066, steps = 124
+shifted from previous position = 2.25
+rotated from previous position = 10.1 degrees
+atoms outside contour = 1852, contour level = 0.0019908
+Position of apo_HNH_center_refined.pdb (#14) relative to
+apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
+Matrix rotation and translation
+-0.82083116 -0.46116689 -0.33698869 392.52408221
+.45571980 -0.17311548 -0.87312688 269.72015669
+.34431924 -0.87026214 0.35226145 171.58912907
+Axis 0.00250785 -0.59643049 0.80266081
+Axis point 145.87352872 275.32026651 0.00000000
+Rotation angle (degrees) 145.16922813
+Shift along axis -22.15706392
+> view matrix models
+> #14,-0.91976,-0.13361,0.36905,259.57,0.12723,-0.991,-0.041693,295.14,0.3713,0.0086066,0.92847,-56.6
+> view matrix models
+> #14,-0.94601,-0.32105,-0.044503,348.25,0.30157,-0.82153,-0.48389,302.66,0.1188,-0.47119,0.874,58.735
+> fitmap #14/a inMap #27.2
+Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
+(#27.2) using 2728 atoms
+average map value = 0.1677, steps = 128
+shifted from previous position = 5.27
+rotated from previous position = 18.3 degrees
+atoms outside contour = 544, contour level = 0.0019908
+Position of apo_HNH_center_refined.pdb (#14) relative to
+apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
+Matrix rotation and translation
+-0.98941113 -0.04220312 0.13886890 304.43360331
+-0.05300114 -0.78565708 -0.61638777 392.25034981
+.13511682 -0.61722111 0.77510102 112.81565364
+Axis -0.07270707 0.32735899 -0.94209860
+Axis point 148.46002111 215.26270714 0.00000000
+Rotation angle (degrees) 179.67164584
+Shift along axis -0.01126639
+> select clear
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> hide #!27 models
+> show #!30 models
+> show #!20 models
+> hide #20
+> show #20/a
+> color #20/a green
+> hide #20
+> show #20/a cartoons
+Computing secondary structure
+> fitmap #20/a inMap #30.2
+Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
+post_HNH_cent_sharp.mrc 1 (#30.2) using 2728 atoms
+average map value = 0.2822, steps = 108
+shifted from previous position = 5.73
+rotated from previous position = 12.7 degrees
+atoms outside contour = 221, contour level = 0.0032808
+Position of postcleavage_HNH_center_refined.pdb (#20) relative to
+post_HNH_cent_sharp.mrc 1 (#30.2) coordinates:
+Matrix rotation and translation
+.99338756 0.11381514 0.01507534 -17.65419683
+-0.10945975 0.97851549 -0.17471692 44.27616892
+-0.03463688 0.17191148 0.98450329 -25.68733743
+Axis 0.83464546 0.11970190 -0.53762293
+Axis point 0.00000000 156.57774257 231.16518944
+Rotation angle (degrees) 11.98467665
+Shift along axis 4.37504802
+> show #!32 models
+> show #!14 models
+> show #!17 models
+> hide #!17 models
+> show #!27 models
+> hide #!20 models
+> hide #!22 models
+> hide #!27 models
+> hide #!30 models
+> hide #!32 models
+> hide #!14 models
+> show #!15 models
+> hide #15-6
+> hide #15
+> hide #15,16
+> show #15,16/a cartoons
+Computing secondary structure
+[Repeated 1 time(s)]
+> color #15,16/a red
+> show #!28 models
+> select #15/A:341
+atoms, 15 bonds, 1 residue, 1 model selected
+> view matrix models
+> #15,-0.93405,-0.34831,-0.078927,345.57,0.30616,-0.66712,-0.67913,293.42,0.1839,-0.65851,0.72976,90.717
+> fitmap #15/a nea #28.2
+Expected a keyword
+> fitmap #15/a inMap #28.2
+Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
+(#28.2) using 2728 atoms
+average map value = 0.02958, steps = 260
+shifted from previous position = 11.6
+rotated from previous position = 23.4 degrees
+atoms outside contour = 2054, contour level = 0.0017272
+Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
+(#28.2) coordinates:
+Matrix rotation and translation
+-0.79630665 -0.43561221 -0.41968766 386.18629814
+.58540743 -0.38030007 -0.71600978 230.23651908
+.15229535 -0.81585162 0.55784610 144.52477351
+Axis -0.08500291 -0.48697238 0.86927120
+Axis point 158.93131778 227.39289934 0.00000000
+Rotation angle (degrees) 144.03543017
+Shift along axis -19.31456020
+> view matrix models
+> #15,-0.94602,-0.14843,-0.28813,357.26,0.24355,-0.9121,-0.32979,304.65,-0.21385,-0.38217,0.89901,84.308
+> fitmap #15/a inMap #28.2
+Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
+(#28.2) using 2728 atoms
+average map value = 0.1223, steps = 184
+shifted from previous position = 7.42
+rotated from previous position = 24 degrees
+atoms outside contour = 707, contour level = 0.0017272
+Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
+(#28.2) coordinates:
+Matrix rotation and translation
+-0.96127242 -0.26981301 0.05618076 335.20428011
+.25014099 -0.93972629 -0.23311799 292.00968965
+.11569280 -0.21003679 0.97082425 10.38879106
+Axis 0.04406009 -0.11360351 0.99254871
+Axis point 147.82603778 169.13090853 0.00000000
+Rotation angle (degrees) 164.81546446
+Shift along axis -8.09281367
+> select clear
+> hide #!15 models
+> hide #!28 models
+> show #!31 models
+> show #!15 models
+> hide #!15 models
+> show #!21 models
+> show #!20 models
+> hide #!20 models
+> show #!23 models
+> hide #!23 models
+> hide #21,23
+> show #21,23/a cartoons
+Computing secondary structure
+[Repeated 1 time(s)]
+> color #21,23/a green
+> fitmap #21/a inMap #31.2
+Fit molecule postcleavage_HNH_inwards_refined.pdb (#21) to map
+post_HNH_in_sharp.mrc 1 (#31.2) using 2703 atoms
+average map value = 0.2685, steps = 112
+shifted from previous position = 5.5
+rotated from previous position = 13.7 degrees
+atoms outside contour = 520, contour level = 0.025678
+Position of postcleavage_HNH_inwards_refined.pdb (#21) relative to
+post_HNH_in_sharp.mrc 1 (#31.2) coordinates:
+Matrix rotation and translation
+.98616651 0.13380918 0.09783004 -31.07144516
+-0.11332146 0.97498229 -0.19122706 47.65695927
+-0.12097049 0.17749548 0.97665833 -11.51991642
+Axis 0.74507872 0.44213088 -0.49937760
+Axis point 0.00000000 84.76781023 229.63504986
+Rotation angle (degrees) 14.32599614
+Shift along axis 3.67272934
+> hide #!31 models
+> show #!33 models
+> show #!23 models
+> hide #!21 models
+> fitmap #23/a inMap #33.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
+(#33.2) using 2728 atoms
+average map value = 0.2713, steps = 180
+shifted from previous position = 7.21
+rotated from previous position = 13.7 degrees
+atoms outside contour = 230, contour level = 0.003418
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
+Matrix rotation and translation
+.98012633 0.16191619 0.11461028 -37.06976884
+-0.13594647 0.96898777 -0.20635229 53.55638420
+-0.14446774 0.18667045 0.97174236 -10.17466150
+Axis 0.70553647 0.46508503 -0.53470946
+Axis point 0.00000000 78.56032267 238.27779114
+Rotation angle (degrees) 16.17234589
+Shift along axis 4.19468674
+> show #!20 models
+> hide #!23 models
+> hide #!33 models
+> show #!30 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> hide #!30 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> show #!23 models
+> hide #!23 models
+> hide #!21 models
+> show #!14 models
+> show #!32 models
+> hide #!32 models
+> hide #!20 models
+> hide #!14 models
+> show #!15 models
+> show #!21 models
+> show #!2 models
+> hide #!2 models
+> hide #!15 models
+> hide #!21 models
+> show #!16 models
+> show #!23 models
+> show #!1 models
+> show #!29 models
+> select #16/A:287
+atoms, 4 bonds, 1 residue, 1 model selected
+> view matrix models
+> #16,0.62757,-0.044878,-0.77726,162.91,0.38861,0.88314,0.26278,-73.948,0.67464,-0.46696,0.57167,26.566
+> view matrix models
+> #16,-0.40419,-0.68046,-0.61123,393.44,0.90481,-0.39532,-0.15824,86.915,-0.13395,-0.617,0.77548,143.78
+> view matrix models
+> #16,-0.39826,-0.68007,-0.61555,393.45,0.90771,-0.38883,-0.1577,112.35,-0.1321,-0.62154,0.77216,126.84
+> fitmap #23/a inMap #29.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
+(#29.2) using 2728 atoms
+average map value = 0.1546, steps = 40
+shifted from previous position = 0.0804
+rotated from previous position = 0.183 degrees
+atoms outside contour = 645, contour level = 0.0021375
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+.98502518 0.17240574 0.00128825 -22.90899269
+-0.16981904 0.97148276 -0.16547731 53.93769403
+-0.02978076 0.16278055 0.98621276 -24.79677780
+Axis 0.69074579 0.06537784 -0.72013610
+Axis point 285.26360326 179.92837540 0.00000000
+Rotation angle (degrees) 13.74559352
+Shift along axis 5.55909429
+> view matrix models
+> #16,-0.89523,-0.41361,-0.16578,367.07,0.41729,-0.64769,-0.63747,283.05,0.15628,-0.63986,0.75243,90.762
+> fitmap #23/a inMap #29.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
+(#29.2) using 2728 atoms
+average map value = 0.1546, steps = 40
+shifted from previous position = 0.0116
+rotated from previous position = 0.0128 degrees
+atoms outside contour = 644, contour level = 0.0021375
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+.98500387 0.17252839 0.00115057 -22.91842576
+-0.16996614 0.97147812 -0.16535350 53.95165575
+-0.02964593 0.16267828 0.98623369 -24.80251774
+Axis 0.69024031 0.06480160 -0.72067265
+Axis point 285.13190470 179.83196787 0.00000000
+Rotation angle (degrees) 13.74619735
+Shift along axis 5.55142851
+> hide #!29 models
+> show #!29 models
+> view matrix models
+> #16,-0.88458,-0.38657,-0.26093,381.82,0.46041,-0.81307,-0.35627,265.27,-0.074434,-0.43529,0.89721,76.738
+> fitmap #23/a inMap #29.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
+(#29.2) using 2728 atoms
+average map value = 0.1546, steps = 28
+shifted from previous position = 0.0105
+rotated from previous position = 0.016 degrees
+atoms outside contour = 645, contour level = 0.0021375
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+.98502926 0.17238229 0.00130491 -22.90911466
+-0.16979162 0.97147864 -0.16552961 53.94066736
+-0.02980207 0.16282995 0.98620396 -24.80004337
+Axis 0.69090730 0.06545276 -0.71997434
+Axis point 285.31689662 179.95179673 0.00000000
+Rotation angle (degrees) 13.74665869
+Shift along axis 5.55788562
+> fitmap #16/A inMap #29.2
+Fit molecule apo_HNH_outwards_refined.pdb (#16) to map apo_HNH_out_sharp.mrc 1
+(#29.2) using 2684 atoms
+average map value = 0.1709, steps = 164
+shifted from previous position = 5.87
+rotated from previous position = 25 degrees
+atoms outside contour = 433, contour level = 0.0021375
+Position of apo_HNH_outwards_refined.pdb (#16) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+-0.96402236 -0.25980162 0.05624954 334.31569824
+.23888339 -0.93953169 -0.24538732 293.59018493
+.11660025 -0.22312178 0.96779185 12.48674161
+Axis 0.04428161 -0.12002525 0.99178278
+Axis point 148.03200436 169.10595691 0.00000000
+Rotation angle (degrees) 165.43913121
+Shift along axis -8.05006265
+Must specify one map, got 0
+> fitmap #23/a inMap #33.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
+(#33.2) using 2728 atoms
+average map value = 0.2714, steps = 60
+shifted from previous position = 0.085
+rotated from previous position = 0.177 degrees
+atoms outside contour = 229, contour level = 0.003418
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
+Matrix rotation and translation
+.98009236 0.16199252 0.11479281 -37.09053836
+-0.13597963 0.96897219 -0.20640359 53.56869743
+-0.14466688 0.18668509 0.97170992 -10.14527457
+Axis 0.70529698 0.46553397 -0.53463472
+Axis point 0.00000000 78.41673669 238.26776560
+Rotation angle (degrees) 16.18077713
+Shift along axis 4.20221993
+> show #!33 models
+> show #!8 models
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!33 models
+> hide #!29 models
+> hide #!8 models
+> color #1/a steel blue
+> color #8.3 steel blue
+> show #!8 models
+> hide #!8.3 models
+> show #!8.3 models
+> hide #!8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap.tif"
+> width 1984 height 1210 supersample 3
+> show #!8 models
+> show #!29 models
+> show #!33 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!33 models
+> hide #!29 models
+> hide #!23 models
+> hide #!16 models
+> hide #!8 models
+> hide #!1 models
+> show #!32 models
+> color #32/a steel blue
+> show #!22 models
+> color #22.4 steel blue
+> color #22.5 steel blue
+> show #!30 models
+> show #!29 models
+> hide #!29 models
+> show #!27 models
+> show #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!20 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!30 models
+> hide #!27 models
+> hide #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap.tif"
+> width 1984 height 1210 supersample 3
+> hide #!32 models
+> hide #!20 models
+> hide #!14 models
+> show #!2 models
+> color #2/a steel blue
+> show #!16 models
+> hide #!16 models
+> show #!15 models
+> show #!21 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
+> width 1984 height 1210 supersample 3
+> show #!31 models
+> show #!28 models
+> volume step 1
+> volume #31.2 level 0.03
+> volume #31.2 level 0.07
+> show #!7 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!2 models
+> hide #!7 models
+> hide #!31 models
+> hide #!28 models
+> hide #!21 models
+> hide #!15 models
+> show #!14 models
+> show #!32 models
+> show #!20 models
+> show #!30 models
+> show #!27 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!20 models
+> hide #!22 models
+> hide #!27 models
+> hide #!30 models
+> hide #!32 models
+> hide #!14 models
+> show #!16 models
+> show #!1 models
+> show #!23 models
+> show #!29 models
+> show #!33 models
+> show #!8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!8 models
+> hide #!16 models
+> hide #!23 models
+> hide #!29 models
+> hide #!33 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/chimerax_session.cxs"
+> show #!32 models
+> hide #!1 models
+> show #!22 models
+> transparency #22 100
+> transparency #22 90
+> hide #!22 models
+> hide #!32 models
+> show #!2 models
+> show #!7 models
+> color #7.3 steel blue
+> show #!15 models
+> show #!31 models
+> show #!28 models
+> show #!21 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
+> width 1984 height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!31 models
+> hide #!28 models
+> hide #!7 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
+> width 1984 height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/chimerax_session.cxs"
+——— End of log from Thu May 1 15:38:06 2025 ———
+opened ChimeraX session
+> hide #!2 models
+> hide #!15 models
+> hide #!21 models
+> show #!32 models
+> select #32/a:283
+atoms, 8 bonds, 1 residue, 1 model selected
+> select ::name="ASN"
+atoms, 13797 bonds, 1945 residues, 14 models selected
+> select clear
+> show #!16 models
+> hide #!16 models
+> show #!14 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!20 models
+> color #14/a salmon
+> ui tool show "Color Actions"
+> color #20/a orchid
+> color #20/a aquamarine
+> color #20/a sea green
+> color #20/a pale green
+> color #15/a salmon
+> color #16/a salmon
+> color #21/a pale green
+> color #23/a pale green
+> color #30.2 #31.2 #33.2 pale green
+> color #27.2 #28.2 #29.2 salmon
+> show #!27 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> color #27.2 #28.2 #29.2 #14-16/a salmon
+> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
+> show #!22 models
+> color #27.2 #28.2 #29.2 #14-16/a hot pink
+> color #30.2 #31.2 #33.2 #20-21/a #23/a forest green
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> color #27.2 #28.2 #29.2 #14-16/a plum
+> color #30.2 #31.2 #33.2 #20-21/a #23/a dark sea green
+> color #27.2 #28.2 #29.2 #14-16/a vermilion
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #27.2 #28.2 #29.2 #14-16/a dark orange
+> color #30.2 #31.2 #33.2 #20-21/a #23/a bluish green
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #27.2 #28.2 #29.2 #14-16/a warm beige
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #27.2 #28.2 #29.2 #14-16/a beige
+> color #30.2 #31.2 #33.2 #20-21/a #23/a sof gra
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #30.2 #31.2 #33.2 #20-21/a #23/a dim gray
+> color #30.2 #31.2 #33.2 #20-21/a #23/a light gray
+> color #30.2 #31.2 #33.2 #20-21/a #23/a gray
+> color #27.2 #28.2 #29.2 #14-16/a plum
+> transparency 70
+> transparency 100
+> transparency 80
+> color #27.2 #28.2 #29.2 #14-16/a dark gray
+> color #30.2 #31.2 #33.2 #20-21/a #23/a medium sea green
+> color #27.2 #28.2 #29.2 #14-16/a plum
+> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
+> color #30.2 #31.2 #33.2 #20-21/a #23/a dark gray
+> color #27.2 #28.2 #29.2 #14-16/a orange
+> color #30.2 #31.2 #33.2 #20-21/a #23/a teal
+> color #30.2 #31.2 #33.2 #20-21/a #23/a cyan
+> color #30.2 #31.2 #33.2 #20-21/a #23/a turquoise
+> color #27.2 #28.2 #29.2 #14-16/a chocolate
+> color #27.2 #28.2 #29.2 #14-16/a coral
+> color #30.2 #31.2 #33.2 #20-21/a #23/a olive
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!14 models
+> hide #!20 models
+> hide #!22 models
+> hide #!27 models
+> hide #!30 models
+> hide #!32 models
+> show #!15 models
+> show #!2 models
+> show #!21 models
+> show #!7 models
+> show #!28 models
+> show #!31 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!31 models
+> hide #!28 models
+> hide #!21 models
+> hide #!15 models
+> hide #!7 models
+> hide #!2 models
+> show #!1 models
+> show #!8 models
+> show #!16 models
+> show #!26 models
+> hide #!26 models
+> show #!29 models
+> show #!33 models
+> show #!23 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!8 models
+> hide #!16 models
+> hide #!23 models
+> hide #!29 models
+> hide #!33 models
+> hide #!1 models
+> show #!22 models
+> show #!22.3 models
+> show #!22.2 models
+> show #!22.6 models
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> transparency 100
+> show #!22.1 models
+> hide #!22.1 models
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.4 models
+> hide #!22.5 models
+> hide #!22.6 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.9 models
+> show #!22.4 models
+> show #!22.5 models
+> hide #!22.5 models
+> show #!22.5 models
+> hide #!22.5 models
+> show #!22.5 models
+> show #!22.3 models
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> transparency 80
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.3 models
+> hide #!22.4 models
+> show #!22.3 models
+> hide #!22.3 models
+> hide #!22.2 models
+> show #!22.6 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> show #!22.7 models
+> show #!22.8 models
+> hide #!22.9 models
+> show #!22.2 models
+> show #!22.5 models
+> show #!22.4 models
+> show #!22.3 models
+> show #!22.9 models
+> transparency #22.2 100
+> transparency #22 100
+> show #!32 models
+> show #32 cartoons
+> hide #32 cartoons
+> hide #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> hide #!22.6 models
+> hide #!22.3 models
+> hide #!22.2 models
+> show #!22.2 models
+> show #!22.3 models
+> hide #!22.3 models
+> hide #!22.2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas8.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.3 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
+> width 1984 height 1210 supersample 3
+> hide #!22.3 models
+> show #!22.6 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas6.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.6 models
+> show #!22.3 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.3 models
+> show #!22.2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.2 models
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.7 models
+> show #!22.2 models
+> show #32/c cartoons
+> color #32/c green
+> color zone #22.2 near #32 distance 10
+> volume splitbyzone #22.2
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 0 as #34.1, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 1 as #34.2, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 2 as #34.3, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 3 as #34.4, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 4 as #34.5, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 5 as #34.6, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 6 as #34.7, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 7 as #34.8, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 8 as #34.9, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 9 as #34.10, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 10 as #34.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 11 as #34.12, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 12 as #34.13, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> hide #!22 models
+> hide #!34.1 models
+> hide #!34.2 models
+> hide #!34.4 models
+> show #!34.4 models
+> hide #!34.4 models
+> hide #!34.5 models
+> hide #!34.6 models
+> hide #!34.8 models
+> hide #!34.7 models
+> hide #!34.9 models
+> hide #!34.10 models
+> hide #!34.11 models
+> hide #!34.12 models
+> hide #!34.13 models
+> transparency 100
+> surface dust siz 10
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> dus siz 10
+Unknown command: dus siz 10
+> surface dust #34.3 size 7.25
+> hide #!32 models
+> show #!22 models
+> show #!22.8 models
+> hide #!22.9 models
+> hide #!22.8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> show #!22.2 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.6 models
+> hide #!22.5 models
+> hide #!22.4 models
+> hide #!22.3 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x_2.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.3 models
+> show #!22.6 models
+> transparency 0
+> lighting soft
+> lighting simple
+> lighting soft
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> show (#22.2-9#34.3#!22,34 & sidechain) target ab
+> ui tool show "Side View"
+> turn x 90
+[Repeated 3 time(s)]
+> view
+> turn x -90
+> turn x 90
+> show #!17 models
+> hide #!17 models
+> show #!18 models
+> hide #!18 models
+> show #!26 models
+> hide #!26 models
+> show #!26 models
+> hide #!26 models
+> show #!26 models
+> hide #!26 models
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> view
+> turn x 90
+[Repeated 3 time(s)]
+> turn x -90
+> turn x 90
+> turn x -90
+> turn x 90
+> turn x -90
+> turn x 90
+> turn x -90
+> turn x 90
+> turn x -90
+[Repeated 1 time(s)]
+> turn x 90
+[Repeated 1 time(s)]
+> turn x -90
+> hide #!34.3 models
+> hide #!34 models
+> hide #!22 models
+> show #!22 models
+> show #!1 models
+> show #!2 models
+> hide #!22 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!1 models
+> show #!32 models
+> hide #32/b cartoons
+> hide #32/c cartoons
+> show #32/a cartoons
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> hide #!2 models
+> show #!32 models
+> show #!1 models
+> hide #!32 models
+> show #!32 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!2 models
+> show #!1 models
+> hide #!32 models
+> show #!2 models
+> hide #!2 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> select ~sel & ##selected
+Nothing selected
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #!1 models
+> show #!33 models
+> hide #!33 models
+> hide #!32 models
+> show #!25 models
+> view
+> surface dust siz 10
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #25 size 10
+> volume level 0.05
+> volume level 0.06
+> hide #!25 models
+> show #!24 models
+> hide #!24 models
+> show #!26 models
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> graphics silhouettes true
+> graphics silhouettes false
+> transparency 0
+> hide #!26 models
+> show #!22 models
+> volume #22 show
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.5 models
+> show #!22.5 models
+> hide #!22.6 models
+> show #!22.6 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> lighting soft
+> lighting simple
+> lighting soft
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> transparency 0
+> volume level 0.05
+> hide #!22.1 models
+> transparency 90
+> transparency 10
+> transparency 1
+> transparency 0
+> lighting simple
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting full
+> lighting simple
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.4 models
+> hide #!22.5 models
+> hide #!22.6 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!32 models
+> hide #32 cartoons
+> show #32/j,k,l
+> hide #32/k:1-3
+> transparency 90
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> volume #22 level 0.03
+> volume #22 level 0.02
+> volume #22 level 0.01
+> volume #22 level 0.005
+> volume #22 level 0.001
+> volume #22 level 0.0001
+> volume #22 level 0.02
+> hide #32
+> hide #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> show #!22.6 models
+> hide #!22.6 models
+> show #!22.5 models
+> show #!22.4 models
+> show #32/a
+> hide #32
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.3 models
+> show #32/b
+> hide #!22.3 models
+> show #!22.2 models
+> hide #32
+> show #32/c
+> color #32/c salmon
+> show #32/c-h
+> hide #32
+> hide #!22.2 models
+> show #!22.6 models
+> hide #!22.6 models
+> show #!22.6 models
+> show #32/i
+> hide #!22.6 models
+> show #!22.6 models
+> show #32/d,b
+> show #32/j:41-60
+> show #32/j:41-65
+> hide #32
+> hide #!22.6 models
+> show #!22.2 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> show #!22.10 models
+> hide #!22.10 models
+> hide #!22 models
+> hide #!32 models
+> show #!32 models
+> show #32 cartoons
+> hide #32/k:1-3 cartoons
+> show #32/a:304
+> show #32/a:305
+> show #32/m,o
+> graphics silhouettes false
+> graphics silhouettes true
+> select ~sel & ##selected
+Nothing selected
+> show #32/a:328,319
+> show #32/a:328,319,280
+> show #32/k
+> select #32/A:281
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> show #!11 models
+> show #32/a:83-85
+> show #32/l
+> color #32/k:40 #32/l:6 hot pink
+> color #32/k:40 #32/l:7 hot pink
+> color #32/l:7 orange
+> color #32/l:6 orange
+> color #32/l:7 hot pink
+> hide #32 & nucleic cartoons
+> show #32/j
+> show #!22 models
+> show #!22.10 models
+> hide #!22 models
+> hide #!32 models
+> show #!8 models
+> show #!8.4 models
+> show #!8.5 models
+> show #!8.6 models
+> show #!8.7 models
+> show #!8.8 models
+> show #!8.9 models
+> hide #!8.9 models
+> show #!8.9 models
+> show #!1 models
+> show #1 cartoons
+> hide #!8 models
+> select #1/I:140
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel
+> show #1/a:295
+> show #!8 models
+> show #1/a:319,304,305,328,280
+> color #1/a:319,304,305,328,280 byhetero
+> show #!2 models
+> hide #!1 models
+> hide #!8 models
+> show #!7 models
+> color #2/a:319,304,305,328,280 byhetero
+> show #2/a:319,304,305,328,280
+> show #2/a:295
+> volume #7 level 0.02
+> show #!7.4 models
+> show #!7.5 models
+> show #!7.6 models
+> show #!7.7 models
+> show #!7.8 models
+> show #!7.9 models
+> show #!7.1 models
+> hide #!7.1 models
+> volume #7 level 0.01
+> volume #7 level 0.02
+> hide #!7 models
+> show #!9 models
+> volume #9 level 0.02
+> volume #9 level 0.01
+> volume #9 level 0.002
+> show #2 cartoons
+> surface dust siz 5
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #9 size 5
+> hide #!2 models
+> show #!2 models
+> hide #!9 models
+Drag select of 3 atoms, 57 residues, 2 bonds
+> show sel
+> hide #!2 models
+> show #!1 models
+Drag select of 2 atoms, 16 residues
+> show sel
+> hide #!1 models
+> show #!12 models
+> hide #!12 models
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!9 models
+> hide #!9 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> show #2/i
+> color #2/i,a byhetero
+> hide #!2 models
+> show #!1 models
+> show #!10 models
+> hide #!10 models
+> show #!8 models
+> hide #!7 models
+> hide sel
+> select clear
+> show #1-2/j
+> hide #1-2 & nucleic cartoons
+> select clear
+> show #!2 models
+> hide #!1 models
+> show #!7 models
+> hide #!8 models
+> hide #1-2
+> show #1-2 cartoons
+> show #!1 models
+> show #!3 models
+> hide #!7 models
+> show #!8 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!2 models
+> hide #!8 models
+> hide #!1 models
+> show #!19 models
+> hide #!19 models
+> show #!10 models
+> hide #!10 models
+> show #!32 models
+> select #32/A:193
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:192
+atoms, 12 bonds, 2 residues, 1 model selected
+> show sel
+> select clear
+> hide #32/k 1-33
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> hide #32/k:1-33
+> select #32/K:34@P
+atom, 1 residue, 1 model selected
+> select add #32/K:34@OP1
+atoms, 1 residue, 1 model selected
+> select add #32/K:34@OP2
+atoms, 1 residue, 1 model selected
+> select add #32/K:34@O5'
+atoms, 1 residue, 1 model selected
+> select add #32/K:34@C5'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select #32/a:220-243
+atoms, 197 bonds, 24 residues, 1 model selected
+> show #32/k
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/chimerax_session.cxs"
+——— End of log from Mon May 12 14:04:47 2025 ———
+opened ChimeraX session
+> hide #!11 models
+> hide #!32 models
+> show #!16 models
+> hide #16 cartoons
+> show #16/j
+> show #!29 models
+> hide #!29 models
+> show #!29 models
+> show #!28 models
+> hide #!28 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> select #29.2
+models selected
+> hide #!29.2 models
+> show #!29.2 models
+> hide #!29.2 models
+> show #!29.6 models
+> volume #29 level 0.02
+> hide #!29.6 models
+> show #!27 models
+> hide #!27 models
+> show #!26 models
+> hide #!26 models
+> show #!19 models
+> hide #!16 models
+> hide #!19 models
+> show #!29.6 models
+> show #!16 models
+> show #!15 models
+> hide #!15 models
+> show #!14 models
+> show #!15 models
+> hide #!15 models
+> hide #!14 models
+> combine #16
+> hide #!16 models
+> hide #!35 models
+> show #!35 models
+> fitmap #35/j inMap #29.6
+Fit molecule copy of apo_HNH_outwards_refined.pdb (#35) to map
+apo_HNH_out_sharp.mrc 5 (#29.6) using 1288 atoms
+average map value = 0.3487, steps = 184
+shifted from previous position = 2.25
+rotated from previous position = 3.92 degrees
+atoms outside contour = 340, contour level = 0.02
+Position of copy of apo_HNH_outwards_refined.pdb (#35) relative to
+apo_HNH_out_sharp.mrc 5 (#29.6) coordinates:
+Matrix rotation and translation
+-0.94445333 -0.26862857 0.18933201 314.24147225
+.22085794 -0.94540525 -0.23964699 296.35999000
+.24337151 -0.18451992 0.95221989 -10.86743333
+Axis 0.11124727 -0.10905253 0.98779127
+Axis point 138.91057616 167.65489171 0.00000000
+Rotation angle (degrees) 165.65451579
+Shift along axis -8.09505614
+> volume #29 level 0.002
+> volume #29 level 0.0002
+> volume #29 level 0.002
+> hide #!35 models
+> hide #!29 models
+> show #!30 models
+> hide #!30.2 models
+> show #!30.8 models
+> show #!30.7 models
+> show #!30.6 models
+> hide #!30.6 models
+> show #!30.5 models
+> show #!1 models
+> show #!3 models
+> hide #!3 models
+> hide #1 cartoons
+> show #1/j-l
+> hide #!1 models
+> show #!20 models
+> hide #20 cartoons
+> show #20/j-l
+> fitmap #20/j inMap #30.8
+Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
+post_HNH_cent_sharp.mrc 7 (#30.8) using 1288 atoms
+average map value = 0.3259, steps = 228
+shifted from previous position = 2.32
+rotated from previous position = 3 degrees
+atoms outside contour = 457, contour level = 0.05
+Position of postcleavage_HNH_center_refined.pdb (#20) relative to
+post_HNH_cent_sharp.mrc 7 (#30.8) coordinates:
+Matrix rotation and translation
+.99292341 0.11846591 0.00830222 -17.69757193
+-0.11532901 0.97858172 -0.17051988 44.51738269
+-0.02832520 0.16835570 0.98531926 -26.31185417
+Axis 0.81987504 0.08861632 -0.56564306
+Axis point 0.00000000 162.56775146 238.40498938
+Rotation angle (degrees) 11.92686357
+Shift along axis 4.31828685
+> volume #30 level 0.002
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_post.tif"
+> width 1984 height 1210 supersample 3
+> hide #!30 models
+> hide #!20 models
+> show #!35 models
+> show #!19 models
+> hide #!19 models
+> show #!29 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_apo.tif"
+> width 1984 height 1210 supersample 3
+> hide #!29 models
+> hide #!35 models
+> show #!30 models
+> show #!20 models
+> select #20/l:1
+atoms, 19 bonds, 1 residue, 1 model selected
+> select clear
+> hide #!30 models
+> show #20 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #20/L dark orange
+> color #20/K dim gray
+> color #20/J dark red
+> color #20/I rebecca purple
+> color #20/B forest green
+> color #20/C,D,E,F,G,H salmon
+> color #20/A steel blue
+> color #20/A:232-350 dark turquoise
+> color #20/O blue
+> color #20/M red
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/post_full_cartoon.tif" width 1984
+> height 1210 supersample 3
+> hide #!20 models
+> show #!16 models
+> show #16 cartoons
+> color #16/L dark orange
+> color #16/K dim gray
+> color #16/J dark red
+> color #16/I rebecca purple
+> color #16/B forest green
+> color #16/C,D,E,F,G,H salmon
+> color #16/A steel blue
+> color #16/A:232-350 dark turquoise
+> color #16/O blue
+> color #16/M red
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/apo_full_cartoon.tif" width 1984 height
+> 1210 supersample 3
+> hide #!16 models
+> show #!32 models
+> color #32/L dark orange
+> color #32/K dim gray
+> color #32/J dark red
+> color #32/I rebecca purple
+> color #32/B forest green
+> color #32/C,D,E,F,G,H salmon
+> color #32/A steel blue
+> color #32/A:232-350 dark turquoise
+> color #32/O blue
+> color #32/M red
+> show #32/m,o
+> show #32 cartoons
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/half_full_cartoon.tif" width 1984
+> height 1210 supersample 3
+> hide #!32 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> lighting simple
+> graphics silhouettes false
+> ui tool show "Surface Color"
+> color sample #13.1 map #13 palette #ff0000:#ffffff:#0000ff
+Map values for surface "surface": minimum 0.04997, mean 0.05, maximum 0.05003
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #36, grid size
+,420,420, pixel 0.725, shown at level 0.0319, step 2, values float32
+> hide #!13 models
+> hide #!36 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/fsc_and_halfmaps/halfcleaved_HNH_center/J635_005_volume_map_half_A.mrc"
+Opened J635_005_volume_map_half_A.mrc as #37, grid size 420,420,420, pixel
+.725, shown at level 0.138, step 2, values float32
+> color sample #13.1 map #37 palette
+> 0.04997,#ff0000:0.05,#ffffff:0.05003,#0000ff
+Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
+.4275
+> show #!13 models
+> hide #!37 models
+> key red-white-blue :0.05 :0.05 :0.05 showTool true
+> ui mousemode right "color key"
+> color sample #13.1 map #37 palette 2,#ff0000:2.5,#ffffff:3,#0000ff
+Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
+.4275
+> color sample #13.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
+Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
+.4275
+> show #!37 models
+> hide #!37 models
+> show #!37 models
+> hide #!37 models
+> hide #38 models
+> show #38 models
+> hide #!13 models
+> show #!36 models
+> color sample #36.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> key red-white-blue :2.1 :2.3 :2.8 showTool true
+> key red-white-blue :2.1 :2.5 :3.0 showTool true
+[Repeated 1 time(s)]
+> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color single #36.1
+> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color single #36.1
+> color sample #36.1 map #37 palette 2.5,#ff0000:3,#ffffff:3.5,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3,#ffffff:3.5,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:3.5,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> key red-white-blue :3.0 :3.5 :4.0 showTool true
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 2,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color single #36.1
+> key red-white-blue :2.0 :3.5 :4.0 showTool true
+> color sample #36.1 map #37 palette 2,#0433ff:2.5,#ffffff:3,#ff2600
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> hide #38 models
+> hide #!36 models
+> ui mousemode right translate
+Unsupported scale factor (0.000000) detected on Display0
+[Repeated 9 time(s)]
+> show #!32 models
+> show #!22 models
+> color #32/a byhetero
+> hide #!32 models
+> show #!13 models
+> show #!32 models
+> hide #!22 models
+> hide #!13 models
+> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range 2
+> newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+Unknown or unsupported skia image format
+> transparency #39 90
+> close #39
+> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range
+> 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #39 90
+> hide #32/k cartoons
+> volume zone #13 nearAtoms #32/o range 2 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> volume #40 level 0.02
+> close #40
+> volume zone #13 nearAtoms #32/o range 0.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> volume #40 level 0.02
+> close #40
+> volume zone #13 nearAtoms #32/o range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> volume #40 level 0.02
+> transparency #40 90
+> color #40 blue
+> color #39 turquoise
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> color #32/k:3 byhetero
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> close #39
+> hide #!40 models
+> show #!40 models
+> select #32/A:280@CG
+atom, 1 residue, 1 model selected
+> select add #32/A:305@ND1
+atoms, 2 residues, 1 model selected
+> select add #32/A:319@CG
+atoms, 3 residues, 1 model selected
+> select add #32/A:304@ND1
+atoms, 4 residues, 1 model selected
+> select add #32/M:2@MG
+atoms, 1 bond, 5 residues, 1 model selected
+> select add #32/K:2@O5'
+atoms, 1 bond, 6 residues, 1 model selected
+> select add #32/K:3@P
+atoms, 1 bond, 7 residues, 1 model selected
+> select up
+atoms, 1 bond, 8 residues, 1 model selected
+> select up
+atoms, 60 bonds, 8 residues, 1 model selected
+> volume zone nea sel range 1.5 newmap tru
+Missing or invalid "volumes" argument: invalid density maps specifier
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> select clear
+> transparency #39 90
+> volume #39 level 0.03
+> volume #39 level 0.02
+> volume #39 level 0.002
+> surface dust #40 size 7.25
+> surface dust #39 size 7.25
+> surface dust siz 0
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #39-40 size 0
+> volume #39 level 0.09
+> show #!11 models
+> volume #39 level 0.04054
+> hide #!39 models
+> hide #!40 models
+> select #32/A:280,304,305,319,328
+atoms, 48 bonds, 5 residues, 1 model selected
+> select #32/A:280,304,305,319,328 #32/k:1-3
+atoms, 60 bonds, 2 pseudobonds, 7 residues, 2 models selected
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #41, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> close #41
+> show #!39 models
+> show #!40 models
+> volume #39 level 0.04
+> volume #39 level 0.05
+> volume #49 level .03
+No volumes specified
+> volume #39 level .03
+> volume #39 level .04
+> volume #40 level .04
+> volume #40 level .03
+> volume #40 level .025
+> volume #40 level .021
+> volume #40 level .02
+> volume #40 level .01
+> volume #40 level .02
+> select clear
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> save "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/cat_pocket_with_nucleotide.tif"
+> width 1938 height 1210 supersample 3
+> save cat_pocket_with_nucleotide_test.tif supersample 3
+> save "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs" includeMaps
+> true
+> close #1-10,12,14-31,33-38
+> save HNH_cat_session.cxs includeMaps true
+——— End of log from Wed May 14 12:43:12 2025 ———
+opened ChimeraX session
+> hide #!39 models
+> select add /M:2@MG
+atom, 1 residue, 1 model selected
+> select add /A:304@ND1
+atoms, 2 residues, 1 model selected
+> select add /A:304@CE1
+atoms, 2 residues, 1 model selected
+> select add /A:304@NE2
+atoms, 2 residues, 1 model selected
+> select add /A:304@CD2
+atoms, 2 residues, 1 model selected
+> select add /A:304@CG
+atoms, 2 residues, 1 model selected
+> select add /A:304@CB
+atoms, 2 residues, 1 model selected
+> select add /A:328@CD2
+atoms, 3 residues, 1 model selected
+> select add /A:328@NE2
+atoms, 3 residues, 1 model selected
+> select add /A:328@CE1
+atoms, 3 residues, 1 model selected
+> select add /A:328@ND1
+atoms, 3 residues, 1 model selected
+> select add /A:328@CG
+atoms, 3 residues, 1 model selected
+> select add /A:328@CB
+atoms, 3 residues, 1 model selected
+> select add /A:319@ND2
+atoms, 4 residues, 1 model selected
+> select add /A:319@OD1
+atoms, 4 residues, 1 model selected
+> select add /A:319@CB
+atoms, 4 residues, 1 model selected
+> select add /A:305@CB
+atoms, 5 residues, 1 model selected
+> select add /A:305@CG
+atoms, 5 residues, 1 model selected
+> select add /A:305@CD2
+atoms, 5 residues, 1 model selected
+> select add /A:305@NE2
+atoms, 5 residues, 1 model selected
+> select add /A:305@CE1
+atoms, 5 residues, 1 model selected
+> select add /A:305@ND1
+atoms, 5 residues, 1 model selected
+> select add /K:3@OP2
+atoms, 6 residues, 1 model selected
+> select add /K:3@P
+atoms, 6 residues, 1 model selected
+> select add /K:3@O5'
+atoms, 6 residues, 1 model selected
+> select add /K:3@OP1
+atoms, 6 residues, 1 model selected
+> select subtract /K:3@P
+atoms, 6 residues, 1 model selected
+> select add /K:3@P
+atoms, 6 residues, 1 model selected
+> select add /K:2@O3'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C3'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C4'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C5'
+atoms, 7 residues, 1 model selected
+> select add /K:2@O5'
+atoms, 7 residues, 1 model selected
+> select add /K:2@O4'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C2'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C1'
+atoms, 7 residues, 1 model selected
+> select add /A:280@NH2
+atoms, 8 residues, 1 model selected
+> select add /A:280@NH1
+atoms, 8 residues, 1 model selected
+> select add /A:280@CZ
+atoms, 8 residues, 1 model selected
+> select add /A:280@NE
+atoms, 8 residues, 1 model selected
+> select add /A:280@CD
+atoms, 8 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #1, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #1 90
+> select add /A:280@CG
+atoms, 8 residues, 1 model selected
+> select add /A:280@CB
+atoms, 8 residues, 1 model selected
+> close #1
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #1, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #1 90
+> select clear
+> volume #1 level 0.02
+> show (#1,40#!11,32 & sidechain) target ab
+> ui tool show "Side View"
+> hide #32
+> show #32/a:280,304,305,319
+> show #32/a:280,304,305,319,328 #32/o,m
+> show #32/a:280,304,305,319,328 #32/o,m #32/k:1-3
+> hide #32 cartoons
+> show #32/a cartoons
+> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH
+Expected name of a folder to open/read; a name of 'browse' will bring up a
+file browser or a keyword
+> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/
+Expected name of a folder to open/read; a name of 'browse' will bring up a
+file browser or a keyword
+> cd "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> save cat_pocket_with_nucleotide_2.tif supersample 3
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_out_sharp.mrc"
+Opened halfcleaved_HNH_out_sharp.mrc as #3, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+> hide #!1 models
+> hide #!2 models
+> hide #!3 models
+> hide #!32 models
+> hide #!40 models
+> show #!3 models
+> show #!2 models
+> style stick
+Changed 48201 atom styles
+> hide #2
+> show #2 cartoons
+Computing secondary structure
+> transparency #3 90
+> color #2/L dark orange
+> color #2/K dim gray
+> color #2/J dark red
+> color #2/I rebecca purple
+> color #2/B forest green
+> color #2/C,D,E,F,G,H salmon
+> color #2/A steel blue
+> color #2/A:232-350 dark turquoise
+> color #2/O blue
+> color #2/M red
+> show #2/a:319,280,304,305
+> color #2/a byhetero
+> volume #3 level 0.005
+> volume #3 level 0.05
+> volume #3 level 0.09
+> show #2/a:328
+> hide #2 cartoons
+> show #2/a cartoons
+> hide #!3 models
+> hide #!2 models
+> show #!32 models
+> select #32/A:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel
+> select #32/A:333
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel
+> show #!13 models
+> volume #13 level 0.02
+> hide #!11 models
+> hide #!13 models
+> hide #!32 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #4
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+> hide #!5 models
+> style stick
+Changed 71932 atom styles
+> hide #4
+> show #4/a cartoons
+Computing secondary structure
+> show #4/m
+> color #4/L dark orange
+> color #4/K dim gray
+> color #4/J dark red
+> color #4/I rebecca purple
+> color #4/B forest green
+> color #4/C,D,E,F,G,H salmon
+> color #4/A steel blue
+> color #4/A:232-350 dark turquoise
+> color #4/O blue
+> color #4/M red
+> color #4/a byhetero
+> show #4/a:280,319,304,305
+> show #4/a:280,319,304,305,328
+> select #4/a280,319,304,305,328 #4/m
+atom, 1 residue, 1 model selected
+> select #4/a:280,319,304,305,328 #4/m
+atoms, 48 bonds, 6 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 1.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #6, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #6 90
+> volume #6 level 0.02
+> hide #!6 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> volume #6 level 0.09
+> volume zone #5 nearAtoms sel range 1 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> hide #!6 models
+> transparency #7 90
+> hide #!7 models
+> show #!6 models
+> volume #6 level 0.12
+> volume #6 level 0.1
+> volume #6 level 0.08
+> volume #6 level 0.06
+> select clear
+> show #!32 models
+> hide #!32 models
+> combine #4
+> hide #!4 models
+> hide #!6 models
+> show #!32 models
+> mmaker #8/a:220-350 to #32/a:220-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of postcleavage_HNH_center_refined.pdb, chain A (#8), sequence
+alignment score = 600
+RMSD between 122 pruned atom pairs is 0.599 angstroms; (across all 123 pairs:
+.646)
+> color #8/a salmon
+> hide #!32 models
+> hide #!8 models
+> show #!6 models
+> show #!4 models
+> show #!5 models
+> hide #!5 models
+> hide #!6 models
+> select add #4/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #4/A:304@ND1
+atoms, 2 residues, 1 model selected
+> select add #4/A:280@CZ
+atoms, 3 residues, 1 model selected
+> select add #4/A:305@CE1
+atoms, 4 residues, 1 model selected
+> select add #4/A:319@CG
+atoms, 5 residues, 1 model selected
+> select add #4/A:332
+atoms, 6 bonds, 6 residues, 1 model selected
+> select up
+atoms, 54 bonds, 6 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 1.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> close #9
+> select add #4/M:1@MG
+atoms, 54 bonds, 7 residues, 1 model selected
+> select up
+atoms, 415 bonds, 50 residues, 1 model selected
+> select down
+atoms, 54 bonds, 7 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 1.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #9 90
+> volume #9 level 0.06
+> select clear
+> hide #!9 models
+> select #4/A:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> show #!9 models
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> color #9 #ffcc99ff models
+> color #9 #ffd479ff models
+> color #9 white
+> transparency #9 90
+> ui tool show "Color Actions"
+> color #9 lavender
+> color #9 violet
+> color #9 navy
+> color #9 navajowhite
+> color #9 blanchedalmond
+> save cat_pocket_empty.tif supersample 3
+> hide #!9 models
+> show #!8 models
+> hide #!4 models
+> show #!32 models
+> color #8 salmon
+> select #32/K:2@C3'
+atom, 1 residue, 1 model selected
+> select add #32/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select #32/K:2@C4'
+atom, 1 residue, 1 model selected
+> select add #32/K:2@C3'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@O5'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C2'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select #32/K:2@O3'
+atom, 1 residue, 1 model selected
+> color sel byhetero
+> select clear
+> select #32/O:1@O
+atom, 1 residue, 1 model selected
+> hide sel
+> hide #!8 models
+> show #!8 models
+> select #8/A:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> select add #8/A:332@CG2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 2 models selected
+> select up
+atoms, 12 bonds, 2 residues, 2 models selected
+> hide sel
+> select clear
+> combine #8
+> hide #!8 models
+> mmaker #10/a to #32/a
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
+sequence alignment score = 1678.6
+RMSD between 328 pruned atom pairs is 0.795 angstroms; (across all 340 pairs:
+.913)
+> mmaker #10/a:232-350 to #32/a:232-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
+sequence alignment score = 542.1
+RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
+.605)
+> save cat_half_post_superimpose.tif supersample 3
+> hide #!10 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> close #10
+> show #!4 models
+> hide #!4 models
+> hide #!32 models
+> show #!4 models
+> close #4
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #4
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #10, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+> color #4/L dark orange
+> color #4/K dim gray
+> color #4/J dark red
+> color #4/I rebecca purple
+> color #4/B forest green
+> color #4/C,D,E,F,G,H salmon
+> color #4/A steel blue
+> color #4/A:232-350 dark turquoise
+> color #4/O blue
+> color #4/M red
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!10 models
+> hide #!4 models
+> show #!4 models
+> style stick
+Changed 95663 atom styles
+> hide #4
+> show #4/a cartoons
+Computing secondary structure
+> show #4/a:319,280,304,305 #4/m
+> show #4/a:319,280,304,305,328 #4/m
+> color #4/a byhetero
+> combine #4
+> hide #!4 models
+> mmaker #12/a:232-350 to #32/a:232-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of postcleavage_HNH_center_refined.pdb, chain A (#12), sequence
+alignment score = 542.1
+RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
+.605)
+> color #12 salmon
+> show #!32 models
+> select #32/A:333@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel
+> save cat_half_post_superimpose_2.tif supersample 3
+> hide #!32 models
+> hide #!12 models
+> show #!12 models
+> show #!4 models
+> hide #!12 models
+> show #!8 models
+> hide #!8 models
+> show #!6 models
+> hide #!6 models
+> show #!7 models
+> hide #!7 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> show #!9 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> ui tool show Distances
+> show #!11 models
+> select #4/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #4/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #4/A:304@ND1 #4/M:1@MG
+Distance between postcleavage_HNH_center_refined.pdb #4/A HIS 304 ND1 and /M
+MG 1 MG: 3.141Å
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style radius 0.09
+[Repeated 2 time(s)]
+> distance style radius 0.08
+[Repeated 2 time(s)]
+> distance style radius 0.07
+[Repeated 2 time(s)]
+> distance style radius 0.06
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> color #11 teal
+> select clear
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!9 models
+> save cat_pocket_empty_2.tif supersample 3
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting simple
+> lighting soft
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting full
+> graphics silhouettes false
+> lighting full
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #!4 models
+> hide #!9 models
+> show #!32 models
+> show #32/a:232
+> show #!10 models
+> hide #!10 models
+> show #11.1 models
+> hide #11.1 models
+> hide #!32 models
+> show #!32 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!8 models
+> combine #32
+> hide #!32 models
+> hide #!14 models
+> show #!14 models
+> morph#8 #14
+Unknown command: morph#8 #14
+> morph #8 #14
+Computed 51 frame morph #15
+> coordset #15 1,51
+> show #!32 models
+> hide #!32 models
+> close #15
+> show #!12 models
+> hide #!12 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> close #14
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_with_TS_for_morph.pdb #14
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> color #14/L dark orange
+> color #14/K dim gray
+> color #14/J dark red
+> color #14/I rebecca purple
+> color #14/B forest green
+> color #14/C,D,E,F,G,H salmon
+> color #14/A steel blue
+> color #14/A:232-350 dark turquoise
+> color #14/O blue
+> color #14/M red
+> style stick
+Changed 142917 atom styles
+> hide #14
+> show #14/a cartoons
+Computing secondary structure
+> show #14/k:1-3
+> show #!32 models
+> mmaker #14/A:232-350 to #32/A:232-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
+alignment score = 542.1
+RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
+.605)
+> show #14/a:280,304,305,317,328
+> show #14/a:280,304,305,319,328
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel
+> select clear
+> morph #14 #32
+Computed 51 frame morph #15
+> coordset #15 1,51
+> show #15/k:1-3
+> show #15/k
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
+Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #16
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+k | No description available
+> style stick
+Changed 190521 atom styles
+> hide #16
+> close #15
+> show #16/a cartoons
+> hide #!16 models
+> show #!16 models
+> show #16/a
+> view
+> hide #!16 models
+> show #!16 models
+> show #!14 models
+> hide #!14 models
+> hide #!16 models
+> show #!16 models
+> close #16
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
+Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+k | No description available
+> style stick
+Changed 167030 atom styles
+> hide #16
+> hide #15
+> show #15/a cartoons
+> hide #!15 models
+> show #!15 models
+> show #15
+> show #15/A cartoons
+Computing secondary structure
+> hide #15
+> show #15/Kk
+> show #15
+> select #15/k:2@C4'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 12 bonds, 2 residues, 1 model selected
+> hide #15
+> show sel
+> select clear
+> color #15/L dark orange
+> color #15/K dim gray
+> color #15/J dark red
+> color #15/I rebecca purple
+> color #15/B forest green
+> color #15/C,D,E,F,G,H salmon
+> color #15/A steel blue
+> color #15/A:232-350 dark turquoise
+> color #15/O blue
+> color #15/M red
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> select #15/k:2@O5'
+atom, 1 residue, 1 model selected
+> select add #15/k:2@C5'
+atoms, 1 residue, 1 model selected
+> delete sel
+> morph #14 #15
+models have different number of chains, 12 (Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
+(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
+> morph #14/A,Kk #15/A,Kk
+models have different number of chains, 12 (Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
+(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
+> close #14
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_with_TS_for_morph.pdb #14
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #!14 models
+> color #14/L dark orange
+> color #14/K dim gray
+> color #14/J dark red
+> color #14/I rebecca purple
+> color #14/B forest green
+> color #14/C,D,E,F,G,H salmon
+> color #14/A steel blue
+> color #14/A:232-350 dark turquoise
+> color #14/O blue
+> color #14/M red
+> show #!14 models
+> hide #!14 models
+> style #14 stick
+Changed 23523 atom styles
+> hide #14
+> show #14/A cartoons
+Computing secondary structure
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> mmaker #14/A:232-350 to #15/A:232-250
+Computing secondary structure
+[Repeated 1 time(s)]  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 halfcleaved_HNH_center_main_model_for_cat_morph.pdb, chain A (#15)
+with postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
+alignment score = 94.9
+RMSD between 19 pruned atom pairs is 0.653 angstroms; (across all 19 pairs:
+.653)
+> show #14,15/A:280
+> show #14,15/A:280,319,304,305,329
+> show #14,15/A:280,319,304,305,328
+> hide #14-15/A:329
+> show #14/Kk:1-3
+> morph #14 #15
+models have different number of chains, 12 (Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
+(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
+> close #15
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
+Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+k | No description available
+> close #15
+> hide #!14 models
+> show #!32 models
+> hide #!32 models
+> show #!14 models
+> hide #!14 models
+> show #!32 models
+> hide #32
+> show #32/b cartoons
+> hide #32/b cartoons
+> show #32/k,l
+> show #32/a:83,85
+> color #32/k:40 #32/l:7 hot pink
+> select add #32/A:85@CE
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 15 bonds, 2 residues, 1 model selected
+> volume zone #13 nearAtoms rang 1 new tru
+Invalid "nearAtoms" argument: invalid atoms specifier
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #15, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #15 90
+> hide #32/a:200-350 cartoons
+> hide #32/k:1-38
+> hide #32/l:9-12
+> select #32/L:7@N3
+atom, 1 residue, 1 model selected
+> select add #32/K:40@O6
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #16, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> select up
+atoms, 2 bonds, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #17, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency 16-17 90
+Missing or invalid "percent" argument: Expected a number
+> transparency #16-17 90
+> hide #11.1 models
+> hide #32/a:1-20
+> hide #32/a:1-20 cartoons
+> hide #32/a:87-200 cartoons
+Drag select of 163 atoms, 183 bonds
+> select up
+atoms, 185 bonds, 10 residues, 1 model selected
+> select up
+atoms, 225 bonds, 10 residues, 1 model selected
+Drag select of 133 atoms, 152 bonds
+> select up
+atoms, 154 bonds, 8 residues, 1 model selected
+> select up
+atoms, 179 bonds, 8 residues, 1 model selected
+> hide sel
+> select #15
+models selected
+> color sel steel blue
+> select #16
+models selected
+> color sel hot pink
+> select clear
+> select #17
+models selected
+> color zone sel near #32
+> transparency sel 90
+> select clear
+> select #32/L:5@C4'
+atom, 1 residue, 1 model selected
+> select add #32/K:42@C4
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> hide sel
+Drag select of 8 residues
+> select #32/A:47
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:48
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #32/A:46
+atoms, 18 bonds, 3 residues, 1 model selected
+> select add #32/A:49
+atoms, 25 bonds, 4 residues, 1 model selected
+> show sel
+> select clear
+> show #32/b:95
+> select #32/K:39@C4
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> hide sel
+> volume zone #13 nearAtoms #32 range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> color zone #18 near #32 distance 10
+> volume #18 level 0.01
+> hide #!32 models
+> hide #!17 models
+> hide #!16 models
+> hide #!15 models
+> show #!15 models
+> show #!16 models
+> show #!17 models
+> show #!32 models
+> volume #18 level 0.0001
+> lighting soft
+> lighting flat
+> close #18
+> select #32/A:47@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel
+> show #32/b:90-100 cartoons
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 10 bonds, 1 residue, 1 model selected
+> color byhetero
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select add #32/A:49@CD
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 13 bonds, 2 residues, 1 model selected
+> hide sel
+> show #32/a:32
+> show #32/a:42
+> select clear
+[Repeated 1 time(s)]
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel
+> select clear
+> show #32/a:82
+> show #32/K:42
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!15 models
+> show #!15 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> select add #32/K:41@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select #32/K:41@C1'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> select add #32/K:42@P
+atoms, 44 bonds, 3 residues, 1 model selected
+> select add #32/K:42@OP1
+atoms, 44 bonds, 3 residues, 1 model selected
+> select add #32/K:42@OP2
+atoms, 44 bonds, 3 residues, 1 model selected
+> select add #32/K:42@O5'
+atoms, 44 bonds, 3 residues, 1 model selected
+> select up
+atoms, 66 bonds, 3 residues, 1 model selected
+> select down
+atoms, 44 bonds, 3 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> hide #!18 models
+> show #!17 models
+> hide #!17 models
+> show #!18 models
+> hide #!18 models
+> show #!17 models
+> show #!18 models
+> hide #!17 models
+> transparency #18 90
+> hide #!18 models
+> select #32/K:42@C4
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@OP2
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@OP1
+atoms, 19 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@P
+atoms, 18 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@O5'
+atoms, 17 bonds, 1 residue, 1 model selected
+> hide sel
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 24 bonds, 1 residue, 1 model selected
+> color sel orange
+> color sel dark orange
+> select #32/K:41@C4
+atom, 1 residue, 1 model selected
+> select up
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #32/K:42@P
+atoms, 20 bonds, 2 residues, 1 model selected
+> select up
+atoms, 42 bonds, 2 residues, 1 model selected
+> color sel dim gray
+> hide #!16 models
+> select add #32/K:40@C6
+atom, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> color sel hot pink
+> select clear
+> show #!16 models
+> show #!18 models
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select down
+bond, 1 model selected
+> select #32/B:95@CB
+atom, 1 residue, 1 model selected
+> select add #32/B:95@CG
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@ND1
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@CE1
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@NE2
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@CD2
+atoms, 1 residue, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #19, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> color zone #19 near #32
+> hide #!19 models
+> show #!19 models
+> select ~sel & ##selected
+atoms, 24839 bonds, 13 pseudobonds, 2799 residues, 3 models selected
+> color #19 forest green
+> transparency #19 90
+> select clear
+> select add #32/A:82@OD1
+atom, 1 residue, 1 model selected
+> select add #32/A:82@ND2
+atoms, 1 residue, 1 model selected
+> select add #32/A:82@CG
+atoms, 1 residue, 1 model selected
+> select add #32/A:82@CB
+atoms, 1 residue, 1 model selected
+> select add #32/A:42@NZ
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CE
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CD
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CG
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CB
+atoms, 2 residues, 1 model selected
+> select add #32/A:46@OG1
+atoms, 3 residues, 1 model selected
+> select add #32/A:46@CB
+atoms, 3 residues, 1 model selected
+> select add #32/A:46@CG2
+atoms, 3 residues, 1 model selected
+> hide #!15 models
+> select add #32/A:85@NZ
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CE
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CD
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CG
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CB
+atoms, 4 residues, 1 model selected
+> select add #32/A:83@CB
+atoms, 5 residues, 1 model selected
+> select add #32/A:83@CG
+atoms, 5 residues, 1 model selected
+> select add #32/A:83@OD2
+atoms, 5 residues, 1 model selected
+> select add #32/A:83@OD1
+atoms, 5 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> color #20 steel blue
+> transparency #20 90
+> select #18
+models selected
+> color zone sel near #32
+> color #32/:l dar ora
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #32/:L dark ora
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #32/:L ora
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> hide #!18 models
+> select #32/L:6@OP2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 24 bonds, 1 residue, 1 model selected
+> color sel orange
+> color sel dark orange
+> color #32/L dark orange
+> color #32/L:7 hot pink
+> show #!18 models
+> select #18
+models selected
+> color zone sel near #32
+> transparency sel 90
+> select clear
+> ui tool show Distances
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> hide #!18 models
+> hide #!19 models
+> hide #!20 models
+> show #!17 models
+> hide #!17 models
+> select #32/A:82@ND2
+atom, 1 residue, 1 model selected
+> select add #32/K:42@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/A:82@ND2 #32/K:42@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASN
+ND2 and /K DT 42 OP1: 2.690Å
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> select #32/A:42@NZ
+atom, 1 residue, 1 model selected
+> select add #32/K:41@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/A:42@NZ #32/K:41@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /K DC 41 OP1: 2.885Å
+> select #32/A:46@OG1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/A:46@OG1 #32/K:40@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A THR
+OG1 and /K DG 40 OP1: 2.817Å
+> select #32/B:95@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/B:95@ND1 #32/K:40@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/B HIS
+ND1 and /K DG 40 OP1: 2.646Å
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> distance style radius 50
+[Repeated 2 time(s)]
+> distance style radius 0.01
+[Repeated 4 time(s)]
+> distance style radius 0.02
+[Repeated 2 time(s)]
+> distance style radius 0.03
+[Repeated 2 time(s)]
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> color #11 teal
+> select clear
+> show #!20 models
+> show #!19 models
+> show #!18 models
+> show #!16 models
+> select #32/A:47
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:48
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #32/A:49
+atoms, 19 bonds, 3 residues, 1 model selected
+> select add #32/A:50
+atoms, 22 bonds, 4 residues, 1 model selected
+> select add #32/A:51
+atoms, 29 bonds, 5 residues, 1 model selected
+> select add #32/A:52
+atoms, 36 bonds, 6 residues, 1 model selected
+> select add #32/A:53
+atoms, 39 bonds, 7 residues, 1 model selected
+> select add #32/A:54
+atoms, 43 bonds, 8 residues, 1 model selected
+> select subtract #32/A:47
+atoms, 36 bonds, 7 residues, 1 model selected
+> hide sel cartoons
+> select #32/A:78
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:77
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #32/A:76
+atoms, 22 bonds, 3 residues, 1 model selected
+> select add #32/A:75
+atoms, 30 bonds, 4 residues, 1 model selected
+> select add #32/A:74
+atoms, 45 bonds, 5 residues, 1 model selected
+> select add #32/A:73
+atoms, 48 bonds, 6 residues, 1 model selected
+> select add #32/A:55
+atoms, 60 bonds, 7 residues, 1 model selected
+> select add #32/A:56
+atoms, 67 bonds, 8 residues, 1 model selected
+> select add #32/A:57
+atoms, 74 bonds, 9 residues, 1 model selected
+> select add #32/A:58
+atoms, 81 bonds, 10 residues, 1 model selected
+> select add #32/A:59
+atoms, 86 bonds, 11 residues, 1 model selected
+> select add #32/A:60
+atoms, 91 bonds, 12 residues, 1 model selected
+> select add #32/A:61
+atoms, 98 bonds, 13 residues, 1 model selected
+> select add #32/A:62
+atoms, 105 bonds, 14 residues, 1 model selected
+> select add #32/A:63
+atoms, 112 bonds, 15 residues, 1 model selected
+> select add #32/A:64
+atoms, 117 bonds, 16 residues, 1 model selected
+> select add #32/A:65
+atoms, 120 bonds, 17 residues, 1 model selected
+> select add #32/A:66
+atoms, 132 bonds, 18 residues, 1 model selected
+> select add #32/A:67
+atoms, 139 bonds, 19 residues, 1 model selected
+> select add #32/A:68
+atoms, 146 bonds, 20 residues, 1 model selected
+> select add #32/A:69
+atoms, 152 bonds, 21 residues, 1 model selected
+> select add #32/A:70
+atoms, 156 bonds, 22 residues, 1 model selected
+> select add #32/A:71
+atoms, 163 bonds, 23 residues, 1 model selected
+> select add #32/A:72
+atoms, 167 bonds, 24 residues, 1 model selected
+> hide sel cartoons
+> select #32/A:21
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:22
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #32/A:23
+atoms, 27 bonds, 3 residues, 1 model selected
+> select add #32/A:25
+atoms, 35 bonds, 4 residues, 1 model selected
+> select add #32/A:24
+atoms, 42 bonds, 5 residues, 1 model selected
+> select add #32/A:26
+atoms, 45 bonds, 6 residues, 1 model selected
+> select add #32/A:27
+atoms, 52 bonds, 7 residues, 1 model selected
+> select add #32/A:29
+atoms, 60 bonds, 8 residues, 1 model selected
+> select add #32/A:28
+atoms, 71 bonds, 9 residues, 1 model selected
+> hide sel cartoons
+> select add #32/A:30
+atoms, 76 bonds, 10 residues, 1 model selected
+> select add #32/A:31
+atoms, 83 bonds, 11 residues, 1 model selected
+> select add #32/A:32
+atoms, 90 bonds, 12 residues, 1 model selected
+> select add #32/A:33
+atoms, 98 bonds, 13 residues, 1 model selected
+> select add #32/A:34
+atoms, 105 bonds, 14 residues, 1 model selected
+> select add #32/A:35
+atoms, 115 bonds, 15 residues, 1 model selected
+> select subtract #32/A:35
+atoms, 105 bonds, 14 residues, 1 model selected
+> select add #32/A:35
+atoms, 115 bonds, 15 residues, 1 model selected
+> select add #32/A:36
+atoms, 122 bonds, 16 residues, 1 model selected
+> select add #32/A:37
+atoms, 126 bonds, 17 residues, 1 model selected
+> select add #32/A:38
+atoms, 132 bonds, 18 residues, 1 model selected
+> select add #32/A:39
+atoms, 142 bonds, 19 residues, 1 model selected
+> hide sel cartoons
+> select #32/A:47
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:41
+atoms, 11 bonds, 2 residues, 1 model selected
+> select add #32/A:40
+atoms, 17 bonds, 3 residues, 1 model selected
+> select add #32/A:79
+atoms, 24 bonds, 4 residues, 1 model selected
+> select add #32/A:80
+atoms, 30 bonds, 5 residues, 1 model selected
+> select add #32/A:81
+atoms, 36 bonds, 6 residues, 1 model selected
+> select add #32/A:86
+atoms, 48 bonds, 7 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #32/B:94
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #32/B:90
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #32/B:91
+atoms, 20 bonds, 3 residues, 1 model selected
+> select add #32/B:92
+atoms, 27 bonds, 4 residues, 1 model selected
+> select add #32/B:93
+atoms, 34 bonds, 5 residues, 1 model selected
+> select add #32/B:97
+atoms, 41 bonds, 6 residues, 1 model selected
+> select add #32/B:98
+atoms, 48 bonds, 7 residues, 1 model selected
+> select add #32/B:99
+atoms, 56 bonds, 8 residues, 1 model selected
+> select add #32/B:100
+atoms, 60 bonds, 9 residues, 1 model selected
+> hide sel cartoons
+> turn y 45
+> turn y -45
+[Repeated 1 time(s)]
+> turn y 45
+> turn y 10
+> turn y -10
+> turn y -20
+[Repeated 2 time(s)]
+> turn y 40
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/PAM
+> save PAM_with_map.tif supersample 3
+> turn y -40
+> save PAM_with_map_rotate_40degree.tif supersample 3
+> turn y 40
+> close #1-10
+> show #!12 models
+> hide #!12 models
+> close #12
+> show #!14 models
+> hide #!14 models
+> close #14
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> close #39-40
+> save PAM_session.cxs includeMaps true
+> select /A:85
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add /A:84
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add /A:83
+atoms, 19 bonds, 3 residues, 1 model selected
+> select hid car
+Expected an objects specifier or a keyword
+> hide sel cartoons
+> show sel
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> select /A:84@CB
+atom, 1 residue, 1 model selected
+> hide sel
+> select clear
+> turn y 180
+[Repeated 14 time(s)]
+> save PAM_with_map_front.tif supersample 3
+> turn y 180
+> save PAM_with_map_back.tif supersample 3
+> hide #!18 models
+> hide #!19 models
+> hide #!20 models
+> hide #!16 models
+> hide #32
+> show #32 cartoons
+> hide #32 & nucleic cartoons
+> show #32 & nucle
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> show #32 & nucleic
+> color #32/L dark orange
+> color #32/K dim gray
+> color #32/J dark red
+> color #32/I rebecca purple
+> color #32/B forest green
+> color #32/C,D,E,F,G,H salmon
+> color #32/A steel blue
+> color #32/A:232-350 dark turquoise
+> color #32/O blue
+> color #32/M red
+> select /K:3@P
+atom, 1 residue, 1 model selected
+> select add /K:2@O3'
+atoms, 2 residues, 1 model selected
+> select add /K:3@OP1
+atoms, 2 residues, 1 model selected
+> select add /K:3@OP2
+atoms, 2 residues, 1 model selected
+> select add /K:3@O5'
+atoms, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> color #32/a byhetero
+> select clear
+> show #32/a:319,328,280,304,305
+> select /A:280@CB
+atom, 1 residue, 1 model selected
+> select add /A:280@CG
+atoms, 1 residue, 1 model selected
+> select add /A:280@CD
+atoms, 1 residue, 1 model selected
+> select add /A:280@NE
+atoms, 1 residue, 1 model selected
+> select add /A:280@CZ
+atoms, 1 residue, 1 model selected
+> select add /A:280@NH1
+atoms, 1 residue, 1 model selected
+> select add /A:280@NH2
+atoms, 1 residue, 1 model selected
+> select add /A:305@CE1
+atoms, 2 residues, 1 model selected
+> select add /A:305@NE2
+atoms, 2 residues, 1 model selected
+> select add /A:305@CD2
+atoms, 2 residues, 1 model selected
+> select add /A:305@CG
+atoms, 2 residues, 1 model selected
+> select add /A:305@ND1
+atoms, 2 residues, 1 model selected
+> select add /A:305@CB
+atoms, 2 residues, 1 model selected
+> select add /A:319@ND2
+atoms, 3 residues, 1 model selected
+> select add /A:319@OD1
+atoms, 3 residues, 1 model selected
+> select add /A:319@CG
+atoms, 3 residues, 1 model selected
+> select add /A:319@CB
+atoms, 3 residues, 1 model selected
+> select add /A:304@ND1
+atoms, 4 residues, 1 model selected
+> select add /A:304@CE1
+atoms, 4 residues, 1 model selected
+> select add /A:304@NE2
+atoms, 4 residues, 1 model selected
+> select add /A:304@CD2
+atoms, 4 residues, 1 model selected
+> select add /A:304@CG
+atoms, 4 residues, 1 model selected
+> select add /A:304@CB
+atoms, 4 residues, 1 model selected
+> select add /A:328@NE2
+atoms, 5 residues, 1 model selected
+> select add /A:328@CD2
+atoms, 5 residues, 1 model selected
+> select add /A:328@CG
+atoms, 5 residues, 1 model selected
+> select add /A:328@ND1
+atoms, 5 residues, 1 model selected
+> select add /A:328@CE1
+atoms, 5 residues, 1 model selected
+> select add /A:328@CB
+atoms, 5 residues, 1 model selected
+> show #32/m,o
+> select add /M:2@MG
+atoms, 6 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #1, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #1 90
+> select /K:3@P
+atom, 1 residue, 1 model selected
+> select add /K:3@OP2
+atoms, 1 residue, 1 model selected
+> select add /K:3@OP1
+atoms, 1 residue, 1 model selected
+> select add /K:3@O5'
+atoms, 1 residue, 1 model selected
+> select add /K:2@O3'
+atoms, 2 residues, 1 model selected
+> select add /K:2@C3'
+atoms, 2 residues, 1 model selected
+> select add /K:2@C2'
+atoms, 2 residues, 1 model selected
+> select add /K:2@C1'
+atoms, 2 residues, 1 model selected
+> select add /K:2@O4'
+atoms, 2 residues, 1 model selected
+> select add /K:2@C4'
+atoms, 2 residues, 1 model selected
+> select add /K:2@C5'
+atoms, 2 residues, 1 model selected
+> select add /K:2@O5'
+atoms, 2 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #2, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #2 90
+> select /O:1@O
+atom, 1 residue, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #3, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #3 90
+> color #1 turquoise
+> color #2 dim gray
+> color #3 blue
+> select clear
+> hide #32/b-l cartoons
+> hide #32/j-l
+> show #32/k:1-3
+> hide #32/a:1-232 cartoons
+> show #32/a:225-232 cartoons
+> select /A:232
+atoms, 12 bonds, 1 residue, 1 model selected
+> select /A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add /A:230
+atoms, 16 bonds, 2 residues, 1 model selected
+> select add /A:229
+atoms, 23 bonds, 3 residues, 1 model selected
+> select add /A:228
+atoms, 30 bonds, 4 residues, 1 model selected
+> select add /A:226
+atoms, 38 bonds, 5 residues, 1 model selected
+> select add /A:227
+atoms, 42 bonds, 6 residues, 1 model selected
+> select add /A:225
+atoms, 46 bonds, 7 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> hide #32/a:324-350 cartoons
+> hide #32/a:282-301 cartoons
+> show #32/a:300-320 cartoons
+> show #32/a:300-330 cartoons
+> select add /A:301
+atoms, 12 bonds, 1 residue, 1 model selected
+> select add /A:300
+atoms, 15 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select /A:278
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide #32/a:252-278 cartoons
+> hide #32/a:232-251 cartoons
+> hide #32/a:310-318 cartoons
+> select /A:306
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add /A:307
+atoms, 13 bonds, 2 residues, 1 model selected
+> show sel
+> hide sel
+> select clear
+> graphics silhouettes false
+> lighting soft
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting soft
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting soft
+> lighting full
+> lighting flat
+> graphics silhouettes false
+> lighting soft
+> lighting full
+[Repeated 1 time(s)]
+> lighting soft
+> lighting full
+> lighting shadows false
+> lighting soft
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting simple
+> lighting shadows true
+> lighting shadows false
+> lighting soft
+> lighting full
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> 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
+> lighting full
+> lighting flat
+> lighting simple
+> graphics silhouettes false
+> lighting soft
+> lighting flat
+> hide cd "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH"
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> select /A:307
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add /A:306
+atoms, 13 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #4
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+> hide #!4 models
+> show #!4 models
+> hide #!5 models
+> hide #!4 models
+> style #4 stick
+Changed 23513 atom styles
+> hide #4
+> show #4/a:279-330 cartoons
+Computing secondary structure
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> combine #4
+> hide #!4 models
+> mmaker #6/a:232-350 to #32/a:232-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of postcleavage_HNH_center_refined.pdb, chain A (#6), sequence
+alignment score = 542.1
+RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
+.605)
+> show #6/A:280,319,328,304,305
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!6 models
+> save half_HNH_minimal_with_map.tif supersample 3
+> show #!6 models
+> hide #!2 models
+> hide #!1 models
+> hide #!3 models
+> hide #32/k,m,o
+> hide #4,6/a:282-301
+> hide #4,6/a:282-301 cartoons
+> select #6/A:307
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #6/A:306
+atoms, 13 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select #6/A:318
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #6/A:317
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #6/A:316
+atoms, 20 bonds, 3 residues, 1 model selected
+> select add #6/A:315
+atoms, 27 bonds, 4 residues, 1 model selected
+> select add #6/A:314
+atoms, 31 bonds, 5 residues, 1 model selected
+> select add #6/A:313
+atoms, 34 bonds, 6 residues, 1 model selected
+> select add #6/A:312
+atoms, 37 bonds, 7 residues, 1 model selected
+> select add #6/A:311
+atoms, 45 bonds, 8 residues, 1 model selected
+> select add #6/A:310
+atoms, 50 bonds, 9 residues, 1 model selected
+> hide sel cartoons
+Drag select of 4 residues
+> hide sel cartoons
+> save minimal_HNH_superimposition.tif supersample 3
+> color #4,6 salmon
+> save minimal_HNH_superimposition.tif supersample 3
+> hide #!6 models
+> hide #!32 models
+> show #!4 models
+> show #4/a:280,319,328,304,305
+> color #4/a byhetero
+> select clear
+> select #4/A:305@CE1
+atom, 1 residue, 1 model selected
+> select add #4/A:305@ND1
+atoms, 1 residue, 1 model selected
+> select add #4/A:305@CG
+atoms, 1 residue, 1 model selected
+> select add #4/A:305@CD2
+atoms, 1 residue, 1 model selected
+> select add #4/A:305@NE2
+atoms, 1 residue, 1 model selected
+> select add #4/A:305@CB
+atoms, 1 residue, 1 model selected
+> select add #4/A:319@ND2
+atoms, 2 residues, 1 model selected
+> select add #4/A:319@OD1
+atoms, 2 residues, 1 model selected
+> select add #4/A:319@CB
+atoms, 2 residues, 1 model selected
+> select add #4/A:280@NE
+atoms, 3 residues, 1 model selected
+> select add #4/A:280@CZ
+atoms, 3 residues, 1 model selected
+> select add #4/A:280@NH1
+atoms, 3 residues, 1 model selected
+> select add #4/A:280@NH2
+atoms, 3 residues, 1 model selected
+> select add #4/A:280@CD
+atoms, 3 residues, 1 model selected
+> select add #4/A:280@CG
+atoms, 3 residues, 1 model selected
+> select add #4/A:280@CB
+atoms, 3 residues, 1 model selected
+> select add #4/A:304@ND1
+atoms, 4 residues, 1 model selected
+> select add #4/A:304@CE1
+atoms, 4 residues, 1 model selected
+> select add #4/A:304@NE2
+atoms, 4 residues, 1 model selected
+> select add #4/A:304@CD2
+atoms, 4 residues, 1 model selected
+> select add #4/A:304@CG
+atoms, 4 residues, 1 model selected
+> select add #4/A:304@CB
+atoms, 4 residues, 1 model selected
+> select add #4/A:328@NE2
+atoms, 5 residues, 1 model selected
+> select add #4/A:328@CD2
+atoms, 5 residues, 1 model selected
+> select add #4/A:328@CG
+atoms, 5 residues, 1 model selected
+> select add #4/A:328@CB
+atoms, 5 residues, 1 model selected
+> select add #4/A:328@ND1
+atoms, 5 residues, 1 model selected
+> select add #4/A:328@CE1
+atoms, 5 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 1 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> close #7
+> volume zone #5 nearAtoms sel range 1.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #7 90
+> volume #7 level 0.02
+> volume #7 level 0.06
+> volume #7 level 0.04
+> volume #7 level 0.09
+> color #7 salmon
+> color #7 charcoal
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #7 coal
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #7 dim gray
+> color #7 light slate gray
+> volume #7 level .03
+> select clear
+> save post_HNH_minimal_with_map.tif supersample 3
+> hide #!11 models
+> hide #!7 models
+> hide #!4 models
+> show #!32 models
+> show #!3 models
+> show #!2 models
+> show #!1 models
+> show #32/m,o
+> select clear
+> show #32/k:1-3
+> select clear
+> save HNH_cat_session.cxs includeMaps true
+> show #32 cartoons
+> select #32/a:1-100
+atoms, 777 bonds, 1 pseudobond, 98 residues, 2 models selected
+> select #32/a:1-90
+atoms, 706 bonds, 1 pseudobond, 88 residues, 2 models selected
+> select #32/a:1-80
+atoms, 619 bonds, 78 residues, 1 model selected
+> select #32/a:1-40
+atoms, 313 bonds, 38 residues, 1 model selected
+> select #32/a:1-30
+atoms, 231 bonds, 28 residues, 1 model selected
+> select #32/a:1-35
+atoms, 275 bonds, 33 residues, 1 model selected
+> select #32/a:80-150
+atoms, 593 bonds, 1 pseudobond, 71 residues, 2 models selected
+> select #32/a:80-135
+atoms, 461 bonds, 1 pseudobond, 56 residues, 2 models selected
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/apo_HNH_center_refined-
+> coot-0.pdb"
+Chain information for apo_HNH_center_refined-coot-0.pdb #8
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_cent_sharp.mrc"
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+> hide #!1 models
+> hide #!2 models
+> hide #!3 models
+> hide #!32 models
+> style stick
+Changed 94148 atom styles
+> hide #8
+> show #8 cartoons
+Computing secondary structure
+> transparency #9 90
+> color #8/L dark orange
+> color #8/K dim gray
+> color #8/J dark red
+> color #8/I rebecca purple
+> color #8/B forest green
+> color #8/C,D,E,F,G,H salmon
+> color #8/A steel blue
+> color #8/A:232-350 dark turquoise
+> color #8/O blue
+> color #8/M red
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> volume zone #9 nearAtoms #8/A range 3 newMap true
+Opened apo_HNH_cent_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> show #!9 models
+> hide #!9 models
+> hide #!10 models
+> show #!10 models
+> transparency #10 90
+> volume #10 level 0.02
+> hide #!10 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> show #!10 models
+> hide #!9 models
+> hide #8 cartoons
+> show #8/a cartoons
+> surface dust #10 size 5
+> combine #8
+> hide #!8 models
+> fitmap #12/A:232-350 inMap #9
+Fit molecule copy of apo_HNH_center_refined-coot-0.pdb (#12) to map
+apo_HNH_cent_sharp.mrc (#9) using 897 atoms
+average map value = 0.1137, steps = 76
+shifted from previous position = 1.81
+rotated from previous position = 3.94 degrees
+atoms outside contour = 144, contour level = 0.0019908
+Position of copy of apo_HNH_center_refined-coot-0.pdb (#12) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.99849050 0.04622093 0.02967081 -7.99164150
+-0.04495289 0.99810294 -0.04206845 14.50694265
+-0.03155897 0.04067116 0.99867407 0.51270662
+Axis 0.60172121 0.44529167 -0.66305876
+Axis point 301.29448148 199.80947793 0.00000000
+Rotation angle (degrees) 3.94233491
+Shift along axis 1.31112589
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_HNH_fit.pdb" models #12
+> fitmap #12/A:80-135 inMap #9
+Fit molecule copy of apo_HNH_center_refined-coot-0.pdb (#12) to map
+apo_HNH_cent_sharp.mrc (#9) using 456 atoms
+average map value = 0.05565, steps = 96
+shifted from previous position = 6.74
+rotated from previous position = 5.58 degrees
+atoms outside contour = 120, contour level = 0.0019908
+Position of copy of apo_HNH_center_refined-coot-0.pdb (#12) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.99481363 0.04551028 0.09096513 -18.50883752
+-0.04872161 0.99825385 0.03339856 1.51076745
+-0.08928631 -0.03765731 0.99529387 16.74468113
+Axis -0.32980050 0.83662351 -0.43737025
+Axis point 176.51077727 0.00000000 213.37405101
+Rotation angle (degrees) 6.18421935
+Shift along axis 0.04454214
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_N-ter_fit.pdb"
+> hide #!12 models
+> show #!8 models
+> fitmap #8/A:80-135 inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 456 atoms
+average map value = 0.05868, steps = 176
+shifted from previous position = 2.5
+rotated from previous position = 13.2 degrees
+atoms outside contour = 119, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.97387880 0.10270175 -0.20251527 8.86888724
+-0.10753121 0.99411722 -0.01296093 14.32149660
+.19999281 0.03439909 0.97919333 -23.07565390
+Axis 0.10373066 -0.88159654 -0.46046443
+Axis point 120.86155715 0.00000000 28.75781651
+Rotation angle (degrees) 13.19604193
+Shift along axis -1.08028845
+> fitmap #8/A inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 2728 atoms
+average map value = 0.05474, steps = 136
+shifted from previous position = 1.91
+rotated from previous position = 11.7 degrees
+atoms outside contour = 1271, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.96863084 -0.03548685 -0.24595725 34.61064363
+-0.01015117 0.98327484 -0.18184486 22.60765338
+.24829668 0.17863729 0.95207010 -47.86311464
+Axis 0.58876206 -0.80724652 0.04137982
+Axis point 214.60251744 0.00000000 112.99623949
+Rotation angle (degrees) 17.82650237
+Shift along axis 0.14691702
+> show #!9 models
+> hide #!9 models
+> fitmap #8/A inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms
+average map value = 0.04338, steps = 68
+shifted from previous position = 0.747
+rotated from previous position = 1.19 degrees
+atoms outside contour = 1886, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.96913985 -0.02068010 -0.24564259 32.81429654
+-0.02062424 0.98617920 -0.16439353 21.97080178
+.24564729 0.16438651 0.95531905 -46.25105779
+Axis 0.55616727 -0.83107037 0.00009450
+Axis point 207.83659879 0.00000000 107.50533490
+Rotation angle (degrees) 17.19211508
+Shift along axis -0.01341541
+> select clear
+> select #8/A:231
+atoms, 8 bonds, 1 residue, 1 model selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #8,0.98518,0.053245,-0.16304,14.087,-0.04686,0.99799,0.042762,-2.3863,0.16499,-0.034489,0.98569,-19.98
+> fitmap #8/A inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms
+average map value = 0.1094, steps = 112
+shifted from previous position = 5.82
+rotated from previous position = 10.7 degrees
+atoms outside contour = 1095, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.99997652 -0.00466439 0.00502091 0.20988985
+.00473618 0.99988534 -0.01438311 1.27122337
+-0.00495325 0.01440656 0.99988395 -0.80414690
+Axis 0.90290151 0.31280943 0.29482049
+Axis point 0.00000000 63.62884067 80.26210486
+Rotation angle (degrees) 0.91349740
+Shift along axis 0.35008153
+> fitmap #8/A:80-135 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 456 atoms
+average map value = 0.05864, steps = 96
+shifted from previous position = 1.63
+rotated from previous position = 12.7 degrees
+atoms outside contour = 227, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.97694589 0.10504409 -0.18585603 6.38549743
+-0.10761365 0.99418567 -0.00376302 13.31326798
+.18438012 0.02367691 0.98256978 -20.25353573
+Axis 0.06413527 -0.86535176 -0.49704425
+Axis point 114.59977050 0.00000000 20.50228547
+Rotation angle (degrees) 12.35231087
+Shift along axis -1.04422077
+> fitmap #8/A:1-135 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 1057 atoms
+average map value = 0.07052, steps = 108
+shifted from previous position = 2.65
+rotated from previous position = 10.5 degrees
+atoms outside contour = 524, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.99946033 0.02326146 -0.02319395 -0.64828860
+-0.02335695 0.99971976 -0.00385462 3.15728544
+.02309779 0.00439427 0.99972355 -2.67969831
+Axis 0.12457993 -0.69912699 -0.70406057
+Axis point 122.81669961 28.56907646 0.00000000
+Rotation angle (degrees) 1.89722763
+Shift along axis -0.40143729
+> fitmap #8/A:232-350 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 897 atoms
+average map value = 0.1135, steps = 88
+shifted from previous position = 3.95
+rotated from previous position = 3.77 degrees
+atoms outside contour = 263, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.99894847 0.03136930 0.03343540 -6.87861474
+-0.03015042 0.99888397 -0.03635608 10.87881307
+-0.03453855 0.03530975 0.99877941 1.73316127
+Axis 0.61586393 0.58413756 -0.52867281
+Axis point 0.00000000 -57.34675321 281.67474684
+Rotation angle (degrees) 3.33553382
+Shift along axis 1.20215737
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_HNH_fit.pdb" models #8
+> hide #!10 models
+Drag select of 129 residues
+> show #!10 models
+> fitmap sel inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 1033 atoms
+average map value = 0.06563, steps = 304
+shifted from previous position = 5.04
+rotated from previous position = 19.6 degrees
+atoms outside contour = 527, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.97550451 -0.21809449 0.02873560 32.60163060
+.20802092 0.95705305 0.20193255 -41.53482359
+-0.07154187 -0.19100851 0.97897779 42.51583633
+Axis -0.66798838 0.17046879 0.72438382
+Axis point 228.05641713 129.81114836 0.00000000
+Rotation angle (degrees) 17.10493668
+Shift along axis 1.93988222
+> hide #!10 models
+Drag select of 92 residues
+> show #!10 models
+> fitmap #8/a inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms
+average map value = 0.1094, steps = 152
+shifted from previous position = 8.19
+rotated from previous position = 17.4 degrees
+atoms outside contour = 1095, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.99997611 -0.00472570 0.00504416 0.21355520
+.00479823 0.99988385 -0.01446572 1.27948594
+-0.00497521 0.01448958 0.99988264 -0.80934348
+Axis 0.90243179 0.31226729 0.29682657
+Axis point 0.00000000 63.71907535 80.33882755
+Rotation angle (degrees) 0.91923153
+Shift along axis 0.35202596
+> fitmap sel inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 751 atoms
+average map value = 0.04893, steps = 116
+shifted from previous position = 0.796
+rotated from previous position = 3.08 degrees
+atoms outside contour = 429, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.99892100 0.03260019 -0.03307674 -0.59088395
+-0.03287494 0.99942906 -0.00779691 4.45668233
+.03280367 0.00887590 0.99942240 -4.33104269
+Axis 0.17667979 -0.69812691 -0.69383217
+Axis point 136.11302865 -0.00000000 -21.17869303
+Rotation angle (degrees) 2.70443076
+Shift along axis -0.21071038
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_N-ter_fit.pdb" models #8
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!10 models
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.04893, steps = 64
+shifted from previous position = 0.00612
+rotated from previous position = 0.0147 degrees
+atoms outside contour = 222, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.99891180 0.03266370 -0.03329126 -0.57577626
+-0.03294448 0.99942580 -0.00792044 4.48398773
+.03301344 0.00900858 0.99941431 -4.37110048
+Axis 0.17857319 -0.69940507 -0.69205792
+Axis point 136.52172827 0.00000000 -20.61037254
+Rotation angle (degrees) 2.71688308
+Shift along axis -0.21388724
+Drag select of 2 residues, 9 apo_HNH_cent_sharp.mrc
+> hide #!9 models
+Drag select of 92 residues
+> show #!9 models
+> view matrix models
+> #8,0.99891,0.032664,-0.033291,-3.0428,-0.032944,0.99943,-0.0079204,1.8123,0.033013,0.0090086,0.99941,-4.4427
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.04941, steps = 112
+shifted from previous position = 1.87
+rotated from previous position = 13.6 degrees
+atoms outside contour = 241, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.99824896 -0.04930729 -0.03267722 10.31067123
+.05510661 0.97598361 0.21075875 -27.44944198
+.02150049 -0.21219043 0.97699179 35.29516095
+Axis -0.96343154 -0.12341082 0.23784331
+Axis point 0.00000000 148.42617946 146.07203449
+Rotation angle (degrees) 12.67975067
+Shift along axis 1.84865039
+> view matrix models
+> #8,0.99825,-0.049307,-0.032677,9.4603,0.055107,0.97598,0.21076,-22.821,0.0215,-0.21219,0.97699,34.178
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.0484, steps = 320
+shifted from previous position = 4.25
+rotated from previous position = 13 degrees
+atoms outside contour = 234, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.97609557 0.09991348 -0.19301485 8.78155338
+-0.06675455 0.98296459 0.17124380 -9.35267581
+.20683633 -0.15426570 0.96613706 4.94968795
+Axis -0.60072274 -0.73791918 -0.30758327
+Axis point -16.25369823 0.00000000 47.83281120
+Rotation angle (degrees) 15.71970747
+Shift along axis 0.10379886
+> view matrix models
+> #8,0.94061,-0.031443,-0.33802,47.216,-0.0044741,0.99447,-0.10496,14.912,0.33945,0.10024,0.93527,-47.508
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.04895, steps = 140
+shifted from previous position = 4.05
+rotated from previous position = 13.8 degrees
+atoms outside contour = 235, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.98211439 0.09352479 -0.16341495 5.31498086
+-0.09144608 0.99560485 0.02021373 8.63776478
+.16458720 -0.00490854 0.98635032 -14.18520647
+Axis -0.06656667 -0.86911010 -0.49011888
+Axis point 90.73511369 0.00000000 22.22348540
+Rotation angle (degrees) 10.87692740
+Shift along axis -0.90853175
+> view matrix models
+> #8,0.98211,0.093525,-0.16341,-3.653,-0.091446,0.9956,0.020214,15.181,0.16459,-0.0049085,0.98635,-17.989
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.04278, steps = 204
+shifted from previous position = 11.5
+rotated from previous position = 49.1 degrees
+atoms outside contour = 286, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.51617442 0.50434421 -0.69224337 52.94424808
+-0.36241786 0.86093017 0.35700496 22.73796343
+.77602659 0.06660453 0.62717348 -56.46806541
+Axis -0.16790288 -0.84892009 -0.50114200
+Axis point 81.93964639 0.00000000 19.23832231
+Rotation angle (degrees) 59.85838174
+Shift along axis 0.10631310
+> view matrix models
+> #8,0.75563,0.53552,0.37715,-102.7,-0.65339,0.65658,0.37681,98.385,-0.045843,-0.53116,0.84603,110.59
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.02767, steps = 144
+shifted from previous position = 7.5
+rotated from previous position = 13 degrees
+atoms outside contour = 399, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.84445830 0.49866537 0.19550710 -85.59391132
+-0.52302025 0.68898866 0.50174140 57.10323282
+.11549889 -0.52595387 0.84263428 92.00315528
+Axis -0.70809886 0.05512697 -0.70395811
+Axis point 0.00000000 175.17228734 -5.33803959
+Rotation angle (degrees) 46.52479336
+Shift along axis -1.00948880
+> view matrix models
+> #8,0.22325,-0.12434,0.9668,1.3433,-0.96716,-0.1519,0.2038,273.03,0.12152,-0.98054,-0.15417,271.04
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.02054, steps = 72
+shifted from previous position = 0.557
+rotated from previous position = 6.62 degrees
+atoms outside contour = 451, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.32093819 -0.07334501 0.94425589 -15.53284174
+-0.93429007 -0.18794079 0.30295267 264.15586909
+.15524413 -0.97943798 -0.12884289 264.10267667
+Axis -0.73936752 0.45490792 -0.49638136
+Axis point 0.00000000 230.80804800 33.94290972
+Rotation angle (degrees) 119.86266478
+Shift along axis 0.55543077
+> view matrix models
+> #8,0.51797,0.29889,0.80148,-77.363,-0.84718,0.3088,0.43234,159.71,-0.11827,-0.90294,0.41316,217.23
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.03756, steps = 156
+shifted from previous position = 8.79
+rotated from previous position = 28.4 degrees
+atoms outside contour = 345, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.82035985 0.09006159 0.56471110 -54.91363732
+-0.57114524 0.17797173 0.80132339 101.29105575
+-0.02833415 -0.97990559 0.19743911 248.32489572
+Axis -0.89491213 0.29795349 -0.33219874
+Axis point 0.00000000 193.91338679 71.34026782
+Rotation angle (degrees) 84.38258802
+Shift along axis -3.17031318
+> fitmap #8/a:1-232 inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 1843 atoms
+average map value = 0.07444, steps = 132
+shifted from previous position = 5.34
+rotated from previous position = 8.06 degrees
+atoms outside contour = 740, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.85556495 0.03689190 0.51637932 -43.24932520
+-0.51768413 0.06757577 0.85289897 100.05195461
+-0.00342966 -0.99703184 0.07691381 261.90564432
+Axis -0.92496541 0.25990449 -0.27728802
+Axis point 0.00000000 184.53788363 82.42044866
+Rotation angle (degrees) 89.99843794
+Shift along axis -6.61521397
+> fitmap #8/a:1-232 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms
+average map value = 0.04496, steps = 204
+shifted from previous position = 3.49
+rotated from previous position = 15.1 degrees
+atoms outside contour = 1324, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.85917065 0.12276216 0.49674464 -53.18821240
+-0.50867642 0.31010579 0.80317040 65.81149160
+-0.05544446 -0.94274272 0.32888002 229.17603074
+Axis -0.90136454 0.28507929 -0.32599351
+Axis point 0.00000000 186.58673918 75.48977018
+Rotation angle (degrees) 75.57702649
+Shift along axis -8.00643664
+> view matrix models
+> #8,0.85917,0.12276,0.49674,-64.07,-0.50868,0.31011,0.80317,70.614,-0.055444,-0.94274,0.32888,227.33
+> fitmap #8/a:1-232 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms
+average map value = 0.03523, steps = 100
+shifted from previous position = 1.41
+rotated from previous position = 6.44 degrees
+atoms outside contour = 1400, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.80480185 0.18549600 0.56381310 -75.67146644
+-0.59351183 0.26133077 0.76121609 93.91370671
+-0.00613918 -0.94725786 0.32041356 222.16366887
+Axis -0.87065314 0.29045262 -0.39698914
+Axis point 0.00000000 190.88011217 63.74735928
+Rotation angle (degrees) 78.85614004
+Shift along axis 4.96451775
+> view matrix models
+> #8,0.95413,0.18283,0.2371,-44.561,-0.29249,0.73836,0.60767,1.8038,-0.063966,-0.64915,0.75797,133.99
+> fitmap #8/a:1-232 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms
+average map value = 0.04793, steps = 112
+shifted from previous position = 1.31
+rotated from previous position = 8.5 degrees
+atoms outside contour = 1301, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.93571186 0.27776002 0.21746882 -53.80939596
+-0.35134002 0.78914218 0.50380035 13.01747719
+-0.03167822 -0.54781747 0.83599791 104.83057724
+Axis -0.84096032 0.19923852 -0.50308027
+Axis point 0.00000000 173.44882492 44.82069031
+Rotation angle (degrees) 38.70040585
+Shift along axis -4.89304496
+> view matrix models
+> #8,-0.34192,-0.82356,0.4526,255.51,0.043806,-0.49507,-0.86775,319.8,0.93871,-0.27688,0.20535,9.9731
+> fitmap #8/a:1-232 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms
+average map value = 0.01904, steps = 240
+shifted from previous position = 15.2
+rotated from previous position = 14.3 degrees
+atoms outside contour = 1658, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+-0.25816560 -0.79737188 0.54548016 216.97863355
+.22288946 -0.59854746 -0.76945515 298.39643581
+.94003766 -0.07706507 0.33225015 -41.78946055
+Axis 0.53482557 -0.30476959 0.78808445
+Axis point 53.68514190 192.65985646 0.00000000
+Rotation angle (degrees) 139.66131452
+Shift along axis -7.83006181
+> hide #!8 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!9 models
+> show #!8 models
+> view matrix models
+> #8,0.99221,0.12413,0.010984,-16.454,-0.11883,0.91586,0.38351,-21.706,0.037546,-0.38183,0.92347,54.561
+> fitmap #8/a:1-232 inMap #10
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms
+average map value = 0.1142, steps = 192
+shifted from previous position = 7.86
+rotated from previous position = 24.2 degrees
+atoms outside contour = 781, contour level = 0.02
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc zone (#10) coordinates:
+Matrix rotation and translation
+.99991970 -0.01233620 -0.00289962 2.01037916
+.01231916 0.99990715 -0.00582431 -0.62951411
+.00297120 0.00578812 0.99997883 -0.74339140
+Axis 0.41653941 -0.21058730 0.88439126
+Axis point 46.90450042 152.10806215 0.00000000
+Rotation angle (degrees) 0.79868134
+Shift along axis 0.31252097
+> fitmap sel inMap #9
+Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
+apo_HNH_cent_sharp.mrc (#9) using 751 atoms
+average map value = 0.04894, steps = 72
+shifted from previous position = 1.03
+rotated from previous position = 3.1 degrees
+atoms outside contour = 222, contour level = 0.0019908
+Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+.99892404 0.03249695 -0.03308647 -0.57194403
+-0.03277317 0.99943206 -0.00784060 4.44583961
+.03281289 0.00891651 0.99942174 -4.34188516
+Axis 0.17778779 -0.69917177 -0.69249573
+Axis point 136.25073516 0.00000000 -20.62446803
+Rotation angle (degrees) 2.70116337
+Shift along axis -0.20335325
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/apo_HNH_center_refined-
+> coot-0.pdb"
+Chain information for apo_HNH_center_refined-coot-0.pdb #14
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+> style stick
+Changed 140210 atom styles
+> hide #!8 models
+> hide #14
+> show #14/A cartoons
+Computing secondary structure
+> hide #14/a:1-231 cartoons
+> hide #!10 models
+> select up
+atoms, 1283 bonds, 157 residues, 1 model selected
+> select up
+atoms, 2786 bonds, 340 residues, 1 model selected
+> select down
+atoms, 1283 bonds, 157 residues, 1 model selected
+> select down
+atoms, 92 residues, 1 model selected
+> show #14/A cartoons
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> volume zone #9 nearAtoms #14/a range 2.5 newMap true
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #21 90
+> surface dust #21
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_inwards_refined.pdb"
+Chain information for apo_HNH_inwards_refined.pdb #22
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+F G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_in_sharp.mrc"
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+> hide #!23 models
+> hide #!21 models
+> hide #!14 models
+> hide #22
+> show #22/a cartoons
+Computing secondary structure
+> volume zone #23 nearAtoms #22/a range 2.5 newMap true
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #24 90
+> hide #!24 models
+> hide #!22 models
+> show #!21 models
+> show #!14 models
+> hide #!14 models
+> hide #!21 models
+> show #!22 models
+> show #!24 models
+> hide #!24 models
+> hide #!22 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ILE a 6 ALA a 9 1 4
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 SER a 30 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 THR a 44 1
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 VAL a 93 1
+messages similar to the above omitted
+Chain information for apo_HNH_outwards_refined.pdb #25
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_out_sharp.mrc"
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+> hide #!26 models
+> style stick
+Changed 185894 atom styles
+> hide #25
+> show #25/a cartoons
+Computing secondary structure
+> volume zone #26 nearAtoms #25/a range 2.5 newMap true
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #27 90
+> show #!24 models
+> show #!21 models
+> hide #!21 models
+> hide #!24 models
+> hide #!27 models
+> show #!22 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> morph #14,22,25
+Computed 101 frame morph #28
+> coordset #28 1,101
+> close #28
+> morph #22,14,25
+Computed 101 frame morph #28
+> coordset #28 1,101
+> close #28
+> show #!27 models
+> volume zone #26 nearAtoms #25/a range 1 newMap true
+Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> hide #!27 models
+> close #28
+> volume zone #26 nearAtoms #25/a range 1.5 newMap true
+Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> close #28
+> volume zone #26 nearAtoms #25/a range 2 newMap true
+Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> hide #!28 models
+> show #!27 models
+> close #28
+> show #!1 models
+> hide #!1 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> hide #!6 models
+> select ~sel & ##selected
+atoms, 22901 bonds, 1 pseudobond, 2652 residues, 2 models selected
+> show #!7 models
+> hide #!7 models
+> show #!12 models
+> hide #!12 models
+> show #!15 models
+> hide #!15 models
+> show #!16 models
+> show #!17 models
+> show #!15 models
+> show #!18 models
+> show #!19 models
+> show #!20 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!22 models
+> hide #!22 models
+> close #1-3,6,7,12,15-20
+> hide #!27 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #4
+> show #4/a cartoons
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> select clear
+> show #!8 models
+> hide #!8 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_refined.pdb"
+Chain information for postcleavage_HNH_inwards_refined.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_in_sharp.mrc"
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+> hide #!1 models
+> hide #!2 models
+> hide #!4 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_outwards.pdb"
+Chain information for postcleavage_HNH_outwards.pdb #3
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_out_sharp.mrc"
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+> hide #!3 models
+> hide #!6 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
+Chain information for halfcleaved_HNH_inwards_refined.pdb #7
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_in_sharp.mrc"
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+> hide #!7 models
+> hide #!12 models
+> show #!7 models
+> hide #!7 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_out_sharp.mrc"
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+> hide #!16 models
+> hide #!15 models
+> style stick
+Changed 234593 atom styles
+> show #!1 models
+> hide #!1 models
+> volume zone #2 nearAtoms #1/a range 2.5 newMap true
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> show #!1 models
+> hide #1
+> show #1 cartoons
+Computing secondary structure
+> select vol
+Expected an objects specifier or a keyword
+> transparency 90
+> hide #1 cartoons
+> show #1/a cartoons
+> hide #!1 models
+> hide #!17 models
+> show #!3 models
+> show #!6 models
+> hide #!6 models
+> hide #3
+> show #3/a cartoons
+Computing secondary structure
+> show #!6 models
+> hide #!6 models
+> volume zone #6 nearAtoms #3/a range 2.5 newMap true
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> hide #!18 models
+> hide #!3 models
+> show #!4 models
+> show #!5 models
+> hide #!5 models
+> volume zone #5 nearAtoms #4/a range 2.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at step 1, values float32
+> hide #!19 models
+> hide #!4 models
+> volume zone #13 nearAtoms #32/a range 2.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> show #!32 models
+> hide #32 cartoons
+> show #32/a cartoons
+> transparency 90
+> hide #!20 models
+> hide #!32 models
+> show #!7 models
+> volume zone #12 nearAtoms #7/a range 2.5 newMap true
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at step 1, values float32
+> hide #7
+> show #7/a cartoons
+Computing secondary structure
+> transparency 90
+> hide #!28 models
+> hide #!7 models
+> hide #15
+> show #15/a cartoons
+Computing secondary structure
+> volume zone #16 nearAtoms #15/a range 2.5 newMap true
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at step 1, values float32
+> hide #!29 models
+> show #!27 models
+> hide #!27 models
+> show #!21 models
+> hide #!21 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> show #!21 models
+> hide #!21 models
+> hide #!14 models
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/cas8_movement
+> save cas8_movement.cxs includeMaps true
+——— End of log from Sat May 17 13:40:51 2025 ———
+opened ChimeraX session
+> rename #1 postcleavage_HNH_inwards.pdb
+> rename #4 postcleavage_HNH_center.pdb
+> show #!2 models
+> hide #!2 models
+> show #!1 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> show #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> hide #!6 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> rename #7 halfcleaved_HNH_inwards.pdb
+> rename #32 halfcleaved_HNH_center_main_model.pdb
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!29 models
+> show #!28 models
+> hide #!28 models
+> hide #!29 models
+> show #!29 models
+> hide #!29 models
+> hide #!4 models
+> hide #!3 models
+> hide #!1 models
+> show #!5 models
+> hide #!5 models
+> rename #8 apo_HNH_center.pdb
+> show #!10 models
+> show #!8 models
+> hide #!8 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!1 models
+> show #!12 models
+> hide #!12 models
+> show #!17 models
+> rename #22 apo_HNH_inwards.pdb
+> show #!22 models
+> hide #!22 models
+> show #!23 models
+> hide #!23 models
+> show #!28 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> show #!28 models
+> rename #15 halfcleaved_HNH_outwards.pdb
+> rename #14 apo_HNH_center.pdb
+> show #!14 models
+> show #!8 models
+> hide #!8 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> hide #!14 models
+> hide #!17 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> rename #20 "halfcleaved_HNH_center.mrc zone"
+> show #!13 models
+> hide #!13 models
+> rename #13 halfcleaved_HNH_center_sharp.mrc
+> show #!13 models
+> hide #!13 models
+> show #!12 models
+> hide #!12 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> show #!22 models
+> show #!24 models
+> show #!3 models
+> show #!18 models
+> show #!4 models
+> show #!19 models
+> show #!15 models
+> show #!29 models
+> show #!32 models
+> show #!20 models
+> show #!27 models
+> show #!25 models
+> show #!14 models
+> show #!21 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> close #8,10
+> hide #!29 models
+> show #!29 models
+> hide #!29 models
+> show #!29 models
+> transparency 90
+> hide #!32 models
+> hide #!29 models
+> hide #!28 models
+> hide #!27 models
+> hide #!25 models
+> hide #!24 models
+> hide #!22 models
+> hide #!21 models
+> hide #!20 models
+> hide #!19 models
+> hide #!18 models
+> hide #!17 models
+> hide #!15 models
+> hide #!14 models
+> hide #!7 models
+> hide #!4 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!1 models
+> show #!3 models
+> show #!18 models
+> hide #!18 models
+> hide #!3 models
+> show #!1 models
+> show #!17 models
+> hide #!17 models
+> hide #!1 models
+> show #!4 models
+> show #!19 models
+> hide #!19 models
+> hide #!4 models
+> show #!7 models
+> show #!28 models
+> hide #!7 models
+> hide #!28 models
+> show #!15 models
+> show #!29 models
+> hide #!15 models
+> hide #!29 models
+> show #!32 models
+> show #!20 models
+> hide #32
+> hide #!32 models
+> hide #!20 models
+> show #!22 models
+> show #!24 models
+> hide #!22 models
+> hide #!24 models
+> show #!25 models
+> show #!27 models
+> hide #!25 models
+> hide #!27 models
+> show #!21 models
+> show #!14 models
+> hide #!21 models
+> hide #!14 models
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/cas8_movement
+> save cas8_movment.cxs includeMaps true
+——— End of log from Wed May 28 12:25:00 2025 ———
+opened ChimeraX session
+> show #!1 models
+> show #!3 models
+> show #!4 models
+> show #!2 models
+> show #!5 models
+> show #!6 models
+> hide #!6 models
+> hide #!5 models
+> hide #!4 models
+> hide #!3 models
+> hide #!2 models
+> show #!3 models
+> show #!4 models
+> graphics silhouettes true
+> graphics silhouettes width 1
+> lighting multiShadow 600
+> ui tool show Toolbar
+> volume zone #2 nearAtoms #1/A range 2 newMap true
+Opened post_HNH_in_sharp.mrc zone as #8, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> volume zone #2 nearAtoms #2/A range 2 newMap true
+no atoms specified for zone
+> volume zone #2 nearAtoms #3/A range 2 newMap true
+Opened post_HNH_in_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> volume morph #8,10
+Opened morph as #30, grid size 420,420,420, pixel 0.725, shown at step 1,
+values float32
+> hide #!1 models
+> close session
+> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+opened ChimeraX session
+> show #!22 models
+> show #!25 models
+> show #!14 models
+> graphics silhouettes true
+> graphics silhouettes width 1
+> lighting multiShadow 600
+> hide #!25 models
+> hide #!22 models
+> show #!22 models
+> show #!25 models
+> hide #!25 models
+> hide #!22 models
+> show #!4 models
+> ui tool show Matchmaker
+> matchmaker #14/A to #4/A pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker postcleavage_HNH_center.pdb, chain A (#4) with apo_HNH_center.pdb,
+chain A (#14), sequence alignment score = 1511.2
+RMSD between 184 pruned atom pairs is 1.025 angstroms; (across all 340 pairs:
+.799)
+> show #!25 models
+> matchmaker #25/A to #4/A pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker postcleavage_HNH_center.pdb, chain A (#4) with
+apo_HNH_outwards_refined.pdb, chain A (#25), sequence alignment score = 1630.9
+RMSD between 194 pruned atom pairs is 1.023 angstroms; (across all 336 pairs:
+.486)
+> hide #!14 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> dssp
+> hide #!4 models
+> show #!4 models
+> hide #!25 models
+> show #!25 models
+> close session
+> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+opened ChimeraX session
+> show #!1 models
+> show #!3 models
+> show #!4 models
+> graphics silhouettes true
+> graphics silhouettes width 1
+> lighting multiShadow 600
+> hide #!3 models
+> hide #!1 models
+> show #!1 models
+> show #!3 models
+> dssp
+> hide #!3 models
+> hide #!1 models
+> show #!3 models
+> show #!1 models
+> morph #3:A,4:A,1:A frames 40
+Require at least 2 structures for morph
+> morph #3,4 frames 40
+Computed 41 frame morph #8
+> coordset #8 1,41
+> morph #3/A,4/A frames 40
+Require at least 2 structures for morph
+> morph #3,4,1 frames 40
+Computed 81 frame morph #10
+> coordset #10 1,81
+> hide #!1 models
+> close #8
+> select #10/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #10/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> show sel cartoons
+> select #10/A:1-210
+atoms, 1695 bonds, 208 residues, 1 model selected
+> hide sel cartoons
+> hide #!10 models
+> show #!3 models
+> show #!4 models
+> show #!1 models
+> move 30 #1
+Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
+or two atoms
+> move x 30 #1
+Expected an integer >= 1 or a keyword
+> move x 30 models #1
+> move x 30 models #13
+> move x 30 models #3
+> move x -30 models #3
+> close session
+> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+opened ChimeraX session
+> show #!22 models
+> show #!25 models
+> show #!14 models
+> graphics silhouettes true
+> graphics silhouettes width 1
+> lighting multiShadow 600
+> hide #!25 models
+> hide #!22 models
+> show #!25 models
+> hide #!25 models
+> show #!4 models
+> matchmaker #4 to #14 chain A
+Expected a keyword
+> matchmaker #4/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with postcleavage_HNH_center.pdb,
+chain A (#4), sequence alignment score = 1511.2
+RMSD between 184 pruned atom pairs is 1.025 angstroms; (across all 340 pairs:
+.799)
+> hide #!4 models
+> show #!4 models
+> show #!5 models
+> show #!9 models
+> matrixcopy #4 to #5
+Unknown command: matrixcopy #4 to #5
+> copy #4 to #5 transform true
+Unknown command: copy #4 to #5 transform true
+> hide #!9 models
+> show #!9 models
+> fitmap #4 to #9 move true
+Expected a keyword
+> fitmap #4 inMap #9 moveWholeMolecules true
+Fit molecule postcleavage_HNH_center.pdb (#4) to map apo_HNH_cent_sharp.mrc
+(#9) using 23513 atoms
+average map value = 0.2887, steps = 96
+shifted from previous position = 1.39
+rotated from previous position = 1.86 degrees
+atoms outside contour = 2792, contour level = 0.0019908
+Position of postcleavage_HNH_center.pdb (#4) relative to
+apo_HNH_cent_sharp.mrc (#9) coordinates:
+Matrix rotation and translation
+-0.99666193 0.08128198 -0.00763119 294.01909484
+-0.08106989 -0.99639770 -0.02488551 320.13744438
+-0.00962645 -0.02418378 0.99966118 6.22053499
+Axis 0.00432191 0.01228865 -0.99991515
+Axis point 153.53195307 154.12916032 0.00000000
+Rotation angle (degrees) 175.34344235
+Shift along axis -1.01522796
+> close session
+> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+opened ChimeraX session
+> show #!14 models
+> log metadata #3
+No models had metadata
+> log chains #3
+Chain information for postcleavage_HNH_outwards.pdb #3
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> show #!1 models
+> show #!3 models
+> show #!4 models
+> show #!7 models
+> show #!15 models
+> show #!32 models
+> show #!22 models
+> show #!25 models
+> matchmaker #22/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with apo_HNH_inwards.pdb, chain A
+(#22), sequence alignment score = 1518.4
+RMSD between 77 pruned atom pairs is 1.474 angstroms; (across all 340 pairs:
+.274)
+> matchmaker #25/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with
+apo_HNH_outwards_refined.pdb, chain A (#25), sequence alignment score = 1501.9
+RMSD between 82 pruned atom pairs is 1.427 angstroms; (across all 336 pairs:
+.925)
+> matchmaker #7/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with halfcleaved_HNH_inwards.pdb,
+chain A (#7), sequence alignment score = 1519
+RMSD between 63 pruned atom pairs is 1.325 angstroms; (across all 340 pairs:
+.974)
+> matchmaker #32/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with
+halfcleaved_HNH_center_main_model.pdb, chain A (#32), sequence alignment score
+= 1526.2
+RMSD between 181 pruned atom pairs is 1.066 angstroms; (across all 340 pairs:
+.116)
+> matchmaker #15/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with
+halfcleaved_HNH_outwards.pdb, chain A (#15), sequence alignment score = 1484.2
+RMSD between 67 pruned atom pairs is 1.302 angstroms; (across all 340 pairs:
+.332)
+> matchmaker #1/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with
+postcleavage_HNH_inwards.pdb, chain A (#1), sequence alignment score = 1501.2
+RMSD between 65 pruned atom pairs is 1.199 angstroms; (across all 338 pairs:
+.667)
+> matchmaker #3/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with
+postcleavage_HNH_outwards.pdb, chain A (#3), sequence alignment score = 1520.2
+RMSD between 70 pruned atom pairs is 1.370 angstroms; (across all 340 pairs:
+.928)
+> matchmaker #4/A to #14/A
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker apo_HNH_center.pdb, chain A (#14) with postcleavage_HNH_center.pdb,
+chain A (#4), sequence alignment score = 1511.2
+RMSD between 184 pruned atom pairs is 1.025 angstroms; (across all 340 pairs:
+.799)
+> dssp
+> graphics silhouettes true
+> graphics silhouettes width 1
+> lighting multiShadow 600
+> save /Users/gmontoya/Downloads/cas8_movment2.cxs
+> hide #!15 models
+> hide #!14 models
+> hide #!7 models
+> hide #!4 models
+> hide #!3 models
+> hide #!1 models
+> hide #!22 models
+> hide #!25 models
+> select #32/J-L
+atoms, 2659 bonds, 1 pseudobond, 115 residues, 2 models selected
+> show sel cartoons
+> close session
+> open /Users/gmontoya/Documents/Anders/map_continuousTS.cxs format session
+Opened halfcleaved_HNH_center_fullTS_sharp.mrc as #2, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_fullTS_sharp.mrc zone as #3, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_fullTS_sharp.mrc zone as #4, grid size
+,420,420, pixel 0.725, shown at level 0.041, step 1, values float32
+Opened halfcleaved_HNH_center_fullTS_sharp.mrc zone as #5, grid size
+,420,420, pixel 0.725, shown at level 0.0211, step 1, values float32
+opened ChimeraX session
+> show #!1 models
+> hide #!4 models
+> hide #!5 models
+> select #1/A,K
+atoms, 3827 bonds, 386 residues, 1 model selected
+> save /Users/gmontoya/Downloads/fullTS.pdb selectedOnly true
+> close session
+> open /Users/gmontoya/Downloads/cas8_movment2.cxs format session
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+opened ChimeraX session
+> open /Users/gmontoya/Downloads/fullTS.pdb
+Summary of feedback from opening /Users/gmontoya/Downloads/fullTS.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 PRO D 64 GLU D 70 1 7
+Start residue of secondary structure not found: HELIX 2 2 TYR D 112 GLU D 128
+17
+Start residue of secondary structure not found: HELIX 3 3 LEU D 132 ALA D 143
+12
+Start residue of secondary structure not found: HELIX 4 4 SER D 174 SER D 176
+3
+Start residue of secondary structure not found: HELIX 5 5 ALA D 187 ALA D 201
+15
+messages similar to the above omitted
+Chain information for fullTS.pdb #8
+---
+Chain | Description
+A | No description available
+K | No description available
+> matchmaker #8/A to #14/A
+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 apo_HNH_center.pdb, chain A (#14) with fullTS.pdb, chain A (#8),
+sequence alignment score = 1528.6
+RMSD between 181 pruned atom pairs is 1.066 angstroms; (across all 340 pairs:
+.131)
+> select add #8
+atoms, 3827 bonds, 386 residues, 1 model selected
+> hide #!1 models
+> hide #!3 models
+> hide #!4 models
+> hide #!7 models
+> hide #!14 models
+> hide #!15 models
+> hide #!22 models
+> hide #!25 models
+> hide #!32 models
+> color bychain
+> select clear
+> select #1/K
+atoms, 538 bonds, 24 residues, 1 model selected
+> nucleotides #8 ladder
+> select #1/K
+atoms, 538 bonds, 24 residues, 1 model selected
+> hide #8 cartoons
+> hide #8 atoms
+> show #8 atoms
+> undo
+> show #8 cartoons
+> show #8 atoms
+> hide #8 atoms
+> select #1/K
+atoms, 538 bonds, 24 residues, 1 model selected
+> show #8 atoms
+> nucleotides #8 stubs
+> select #1/K
+atoms, 538 bonds, 24 residues, 1 model selected
+> hide #8 cartoons
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> nucleotides sel stubs
+> nucleotides sel tube/slab shape muffler
+> hide sel atoms
+> undo
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> hide sel cartoons
+> hide sel atoms
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> show sel cartoons
+> select #8/A
+atoms, 2786 bonds, 340 residues, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> show #!22 models
+> show #!14 models
+> show #!25 models
+> hide #!25 models
+> hide #!22 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> close session
+> open /Users/gmontoya/Downloads/cas8_movment2.cxs format session
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+opened ChimeraX session
+> open /Users/gmontoya/Downloads/fullTS.pdb
+Summary of feedback from opening /Users/gmontoya/Downloads/fullTS.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 PRO D 64 GLU D 70 1 7
+Start residue of secondary structure not found: HELIX 2 2 TYR D 112 GLU D 128
+17
+Start residue of secondary structure not found: HELIX 3 3 LEU D 132 ALA D 143
+12
+Start residue of secondary structure not found: HELIX 4 4 SER D 174 SER D 176
+3
+Start residue of secondary structure not found: HELIX 5 5 ALA D 187 ALA D 201
+15
+messages similar to the above omitted
+Chain information for fullTS.pdb #8
+---
+Chain | Description
+A | No description available
+K | No description available
+> select add #8
+atoms, 3827 bonds, 386 residues, 1 model selected
+> color byattribute chain
+No known/registered numeric attribute chain
+> color bychain
+> undo
+> select subtract #8
+Nothing selected
+> select #8 color bychain
+Expected a keyword
+> select #8 color sel bychain
+Expected a keyword
+> select #8
+atoms, 3827 bonds, 386 residues, 1 model selected
+> colorsel bychain
+Unknown command: colorsel bychain
+> color sel bychain
+> select clear
+> matchmaker #8/A to #14/A
+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 apo_HNH_center.pdb, chain A (#14) with fullTS.pdb, chain A (#8),
+sequence alignment score = 1528.6
+RMSD between 181 pruned atom pairs is 1.066 angstroms; (across all 340 pairs:
+.131)
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> nucleotides sel stubs
+> nucleotides sel ladder
+> select clear
+> hide #!32 models
+> hide #!25 models
+> hide #!22 models
+> hide #!15 models
+> hide #!7 models
+> hide #!4 models
+> hide #!3 models
+> hide #!1 models
+> select #14/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #22/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #25/A:1-215
+atoms, 1717 bonds, 211 residues, 1 model selected
+> hide sel cartoons
+> select #7/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #32/A:1-215
+atoms, 1736 bonds, 1 pseudobond, 213 residues, 2 models selected
+> hide sel cartoons
+> select #15/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #1/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #3/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #4/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #8/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> cartoon style tube
+Expected an atoms specifier or a keyword
+> cartoon sel style tube
+Expected a keyword
+> cartoon sel style tube
+Expected a keyword
+> cartoon style sel modeHelix tube sides 20
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> nucleotides sel ladder
+> nucleotides sel stubs
+> hide sel atoms
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> cartoon style width 1.5 thickness 0.3
+> cartoon style width 1 thickness 0.3
+> cartoon #8/K width 1 thick 0.3
+Expected a keyword
+> hide sel atoms
+> select add #8
+atoms, 3827 bonds, 386 residues, 1 model selected
+> select subtract #8
+Nothing selected
+> select add #8
+atoms, 3827 bonds, 386 residues, 1 model selected
+> select clear
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> cartoon sel style nucleic oval
+Expected a keyword
+> cartoon style sel oval
+Expected a keyword
+> cartoon sel width 1
+Expected a keyword
+> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
+> cartoon style sel modeHelix tube sides 20
+> nucleotides sel stubs
+> nucleotides sel ladder
+> nucleotides sel tube/slab shape box
+> show sel atoms
+> nucleotides sel atoms
+> style nucleic & sel stick
+Changed 933 atom styles
+> nucleotides sel fill
+> style nucleic & sel stick
+Changed 933 atom styles
+> nucleotides sel slab
+> style nucleic & sel stick
+Changed 933 atom styles
+> nucleotides sel tube/slab shape box
+> nucleotides sel tube/slab shape ellipsoid
+> nucleotides sel tube/slab shape muffler
+> nucleotides sel ladder
+> nucleotides sel stubs
+> select clear
+> show #!1 models
+> hide #!1 models
+> hide #!14 models
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> cartoon tube
+Expected an atoms specifier or a keyword
+> cartoon sel tube
+Expected a keyword
+> hide sel atoms
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> cartoon sel tube
+Expected a keyword
+> cartoon byattribute worm
+No known/registered numeric attribute worm
+> cartoon byattribute sel
+No known/registered numeric attribute sel
+> cartoon byattribute #8/K
+No known/registered numeric attribute #8/K
+> cartoon style width 1.5 thickness 0.3
+> cartoon sel style width 1.0 thick 0.3
+Expected a keyword
+> cartoon style #8/k width 1.0 thickness 0.3
+> cartoon style #8/k width 0.5 thickness 0.3
+> select #8/K:10-46
+atoms, 836 bonds, 37 residues, 1 model selected
+> hide sel cartoons
+> lighting soft
+> ui tool show "Side View"
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> show #!22 models
+> color #22 #ff2600ff
+> color #22 #ff9300ff
+> show #!25 models
+> hide #!25 models
+> hide #!22 models
+> show #!32 models
+> hide #!14 models
+> hide #!32 models
+> show #!14 models
+> show #!22 models
+> show #!25 models
+> hide #!22 models
+> hide #!14 models
+> hide #8 models
+> hide #!25 models
+> show #!14 models
+> show #8 models
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> color sel dark gray
+> select clear
+> select #8/K
+atoms, 1041 bonds, 46 residues, 1 model selected
+> color sel black
+> select clear
+> hide #8 models
+> select #14/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #14/cyan
+> select #14/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #14/ cyan
+> select #14/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #14/A cyan
+> show #!1 models
+> show #!4 models
+> show #!3 models
+> show #!22 models
+> show #!25 models
+> show #!7 models
+> show #!32 models
+> show #!15 models
+> select #1/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #1/A lavender
+> select #4/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #4/A cyan
+> select #3/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #3/A tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> select #22/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #22/A lavender
+> select #14/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #14/A cyan
+> select #25/A:1-215
+atoms, 1717 bonds, 211 residues, 1 model selected
+> hide sel cartoons
+> color #25/A Tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> select #7/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #7/A lavender
+> select #32/A:1-215
+atoms, 1736 bonds, 1 pseudobond, 213 residues, 2 models selected
+> hide sel cartoons
+> color #32/A cyan
+> select #15/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #15/A Tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #15/A Tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> hide #!7 models
+> hide #!14 models
+> hide #!15 models
+> hide #!22 models
+> hide #!25 models
+> hide #!32 models
+> select add #15
+atoms, 24866 bonds, 2 pseudobonds, 2797 residues, 2 models selected
+> select subtract #15
+Nothing selected
+> select #3/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select 3/A:215-400
+Expected an objects specifier or a keyword
+> color #3/A tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #3/A tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #3/A tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> hide #!4 models
+> hide #!1 models
+> select 3/A:215-400
+Expected an objects specifier or a keyword
+> color #3/A tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color sel tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> select #3/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> select 3/A:215-400
+Expected an objects specifier or a keyword
+> color sel tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> select #3/A216-400
+Nothing selected
+> select #3/A:216-400
+atoms, 1049 bonds, 127 residues, 1 model selected
+> color sel tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color sel gray
+> select 3/A:215-400
+Expected an objects specifier or a keyword
+> color sel tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> select 3/A:215-400,
+Expected an objects specifier or a keyword
+> color sel tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> select #3/A:216-400
+atoms, 1049 bonds, 127 residues, 1 model selected
+> color sel tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color sel tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> select 3/A:215-400
+Expected an objects specifier or a keyword
+> color sel red
+> select 3/A:215-400
+Expected an objects specifier or a keyword
+> color sel Tangerine
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color sel orange
+> ui tool show "Color Actions"
+> show #!1 models
+> show #!4 models
+> show #!7 models
+> show #!15 models
+> show #!14 models
+> show #!22 models
+> show #!25 models
+> show #!32 models
+> select #1/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #1/A plum
+> select #4/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #4/A sky blue
+> select #3/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #3/A orange
+> select #22/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #22/A plum
+> select #14/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #14/A sky blue
+> select #25/A:1-215
+atoms, 1717 bonds, 211 residues, 1 model selected
+> hide sel cartoons
+> color #25/A orange
+> select #7/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #7/A plum
+> select #32/A:1-215
+atoms, 1736 bonds, 1 pseudobond, 213 residues, 2 models selected
+> hide sel cartoons
+> color #32/A sky blue
+> select #15/A:1-215
+atoms, 1736 bonds, 213 residues, 1 model selected
+> hide sel cartoons
+> color #15/A orange
+> show #8 models
+> hide #!1 models
+> hide #!3 models
+> hide #!4 models
+> hide #!7 models
+> hide #!15 models
+> hide #!32 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> hide #!22 models
+> hide #!25 models
+> select #8/A
+atoms, 2786 bonds, 340 residues, 1 model selected
+> color sel sky blue
+> select clear
+> select #8/A
+atoms, 2786 bonds, 340 residues, 1 model selected
+> color sel lime
+> select clear
+> select #8/A
+atoms, 2786 bonds, 340 residues, 1 model selected
+> color sel chartreuse
+> select clear
+> lighting soft
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting soft
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting soft
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> show #!32 models
+> hide #!32 models
+> hide #!4 models
+> show #!25 models
+> show #!22 models
+> show #!2 models
+> hide #!2 models
+> show #!1 models
+> show #!3 models
+> show #!4 models
+> show #!32 models
+> show #!15 models
+> hide #!32 models
+> hide #!25 models
+> hide #!22 models
+> hide #!15 models
+> hide #!4 models
+> hide #!3 models
+> hide #!1 models
+> save /Users/gmontoya/Downloads/fig4.2_apo.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> undo
+> hide #!14 models
+> hide #!3 models
+> hide #!1 models
+> show #!22 models
+> hide #8 models
+> save /Users/gmontoya/Downloads/fig4.1_apo.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> hide #!22 models
+> show #!24 models
+> hide #!24 models
+> show #!25 models
+> save /Users/gmontoya/Downloads/fig4.3_apo.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> hide #!25 models
+> show #!7 models
+> save /Users/gmontoya/Downloads/fig4.4_ntscle.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> hide #!7 models
+> show #!32 models
+> show #8 models
+> save /Users/gmontoya/Downloads/fig4.5_ntscle.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> hide #8 models
+> show #!15 models
+> hide #!32 models
+> save /Users/gmontoya/Downloads/fig4.6_ntscle.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> hide #!15 models
+> show #!1 models
+> save /Users/gmontoya/Downloads/fig4.7_post.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> hide #!1 models
+> show #!4 models
+> show #8 models
+> save /Users/gmontoya/Downloads/fig4.8_post.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> hide #!4 models
+> show #!3 models
+> hide #8 models
+> save /Users/gmontoya/Downloads/fig4.9_post.png width 3000 height 2589
+> supersample 4 transparentBackground true
+> show #!1 models
+> hide #!1 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/A
+Alignment identifier is 1/A
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/B
+Alignment identifier is 1/B
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/C
+Alignment identifier is 1/C
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/D
+Alignment identifier is 1/D
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/E
+Alignment identifier is 1/E
+===== Log before crash end =====
+Log:
+UCSF ChimeraX version: 1.10.dev202412070146 (2024-12-07)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open /Users/gmontoya/Downloads/cas8_movment2.cxs
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Log from Wed May 28 15:04:16 2025UCSF ChimeraX version: 1.10.dev202412070146
+(2024-12-07)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
+Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Log from Wed May 28 12:25:00 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_movement.cxs"
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
+at level 0.00199, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725,
+shown at level 0.02, step 2, values float32
+Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 2, values float32
+Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 2, values float32
+Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
+at level 0.00342, step 2, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
+.725, shown at level 0.00328, step 2, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+Log from Sat May 17 13:40:51 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs"
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
+pixel 0.725, shown at level 0.04, step 1, values float32
+Log from Wed May 14 12:43:12 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725,
+shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel
+.725, shown at level 0.05, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown
+at level 0.05, step 1, values float32
+Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown
+at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown
+at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 0 as #34.1, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 1 as #34.2, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 2 as #34.3, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 3 as #34.4, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 4 as #34.5, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 5 as #34.6, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 6 as #34.7, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 7 as #34.8, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 8 as #34.9, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 9 as #34.10, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 10 as #34.11, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 11 as #34.12, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 12 as #34.13, grid size
+,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
+Log from Mon May 12 14:04:47 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.03, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725,
+shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel
+.725, shown at level 0.002, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 1, values float32
+Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 1, values float32
+Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.07, step 1, values float32
+Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Log from Thu May 1 15:38:06 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.03, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Log from Fri Apr 25 19:29:02 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs" format session
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
+shown at level 0.01, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened J620_abinitio_map.mrc as #29, grid size 128,128,128, pixel 2.38, shown
+at level 0.218, step 1, values float32
+Opened half_hetref_J623_map.mrc as #30, grid size 128,128,128, pixel 2.38,
+shown at level 0.33, step 1, values float32
+Log from Wed Apr 23 13:09:57 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
+shown at level 0.01, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Log from Mon Mar 31 18:07:43 2025UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
+shown at level 0.01, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Log from Thu Mar 27 17:05:34 2025UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
+.725, shown at level 0.02, step 1, values float32
+Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
+shown at level 0.01, step 1, values float32
+Log from Wed Mar 26 12:19:53 2025UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.05, step 1, values float32
+Log from Tue Mar 25 00:19:58 2025UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.09, step 1, values float32
+Log from Mon Mar 24 13:31:18 2025UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.09, step 1, values float32
+Log from Mon Mar 24 00:43:04 2025 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 1imp
+Summary of feedback from opening 1imp fetched from pdb
+---
+note | Fetching compressed mmCIF 1imp from http://files.rcsb.org/download/1imp.cif
+imp title:
+Colicin E9 immunity protein IM9, NMR, 21 structures [more info...]
+Chain information for 1imp
+---
+Chain | Description | UniProt
+.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A | IM9 | IMM9_ECOLI 1-86
+> hide #1.1 models
+> show #1.1 models
+> hide models
+> show #1.1 models
+> open 1fsj
+Summary of feedback from opening 1fsj fetched from pdb
+---
+note | Fetching compressed mmCIF 1fsj from http://files.rcsb.org/download/1fsj.cif
+fsj title:
+Crystal structure of the E9 DNAse domain [more info...]
+Chain information for 1fsj #2
+---
+Chain | Description | UniProt
+B C D E | COLICIN E9 | CEA9_ECOLI 2-134 202-334 402-434 602-734
+Non-standard residues in 1fsj #2
+---
+PO4 — phosphate ion
+ZN — zinc ion
+fsj mmCIF Assemblies
+---
+| author_defined_assembly
+| author_defined_assembly
+| author_defined_assembly
+| author_defined_assembly
+> hide #!1 models
+Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds
+> hide #2 cartoons
+> show sel cartoons
+Drag select of 60 atoms, 4 pseudobonds, 55 bonds
+> hide sel atoms
+Drag select of 141 atoms, 8 pseudobonds, 127 bonds
+> hide sel atoms
+> select clear
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #3
+---
+Chain | Description
+Aa | No description available
+Ba | No description available
+Ca | No description available
+DA | No description available
+Da | No description available
+Db | No description available
+Dc | No description available
+Dd | No description available
+De | No description available
+Df | No description available
+EA | No description available
+FA | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
+pixel 0.725, shown at level 0.0319, step 2, values float32
+> volume #4 level 0.07
+> volume #4 step 1
+> hide #!4 models
+> style stick
+Changed 56061 atom styles
+> color #3/DA light gray
+> color #3/EA dim gray
+> color #3/FA dark red
+> color #3/Ca rebecca purple
+> color #3/Ba forest green
+> color #3/Da,Db,Dc,Dd,De,Df khaki
+> color #3/Aa steel blue
+> color #3/Aa:232-350 dark turquoise
+> hide #3 atoms
+> show #3 cartoons
+Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds
+> ui mousemode right "rotate selected models"
+> view matrix models #2,1,0,0,82.662,0,1,0,181.25,0,0,1,114.9
+> view matrix models
+> #2,1,0.0013443,-0.0025868,85.9,-0.0013444,1,-6.0428e-05,181.66,0.0025868,6.3905e-05,1,96.743
+> mmaker sel to #3/Aa:230-350
+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 halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
+fsj, chain E (#2), sequence alignment score = 97
+RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 97 pairs:
+.295)
+> color #2 yellow
+> color #2 byhetero
+> hide #!3 models
+> select subtract #2/E:700
+atoms, 43 bonds, 4 pseudobonds, 135 residues, 2 models selected
+> select subtract #2/E:701
+atoms, 39 bonds, 4 pseudobonds, 134 residues, 2 models selected
+> select subtract #2/E:702
+atoms, 32 bonds, 3 pseudobonds, 133 residues, 2 models selected
+> select subtract #2/E:703
+atoms, 25 bonds, 3 pseudobonds, 132 residues, 2 models selected
+> select subtract #2/E:719
+atoms, 25 bonds, 3 pseudobonds, 131 residues, 2 models selected
+> select subtract #2/E:720
+atoms, 25 bonds, 3 pseudobonds, 130 residues, 2 models selected
+> select subtract #2/E:721
+atoms, 25 bonds, 3 pseudobonds, 129 residues, 2 models selected
+> select subtract #2/E:722
+atoms, 25 bonds, 3 pseudobonds, 128 residues, 2 models selected
+> select clear
+> select add #2/E:700
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #2/E:701
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #2/E:702
+atoms, 25 bonds, 3 residues, 1 model selected
+> select add #2/E:703
+atoms, 35 bonds, 4 residues, 1 model selected
+> select add #2/E:719
+atoms, 43 bonds, 5 residues, 1 model selected
+> select add #2/E:720
+atoms, 53 bonds, 6 residues, 1 model selected
+> select add #2/E:721
+atoms, 59 bonds, 7 residues, 1 model selected
+> select add #2/E:722
+atoms, 65 bonds, 8 residues, 1 model selected
+> hide #!2 models
+> show #!3 models
+> mmaker sel to #3/Aa:300-325
+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 halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
+fsj, chain E (#2), sequence alignment score = 33.3
+RMSD between 6 pruned atom pairs is 0.986 angstroms; (across all 8 pairs:
+.082)
+> show #!2 models
+> view matrix models
+> #2,0.97297,-0.22873,-0.031935,103.66,0.22967,0.94372,0.23802,167.46,-0.024305,-0.23892,0.97073,110.17
+> view matrix models
+> #2,0.97551,-0.19874,-0.094297,106.33,0.21196,0.96388,0.16128,171.49,0.058839,-0.17731,0.98239,106.64
+> view matrix models
+> #2,0.97749,-0.14562,0.15266,94.724,0.17631,0.96123,-0.21202,189.82,-0.11586,0.23416,0.96527,111.65
+> select clear
+> select #2/E:702
+atoms, 10 bonds, 1 residue, 1 model selected
+> view matrix models
+> #2,0.98567,-0.047376,0.16189,94.269,0.055707,0.99733,-0.047316,185.39,-0.15921,0.055656,0.98567,112.54
+> select #2/E:700
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #2/E:701
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #2/E:702
+atoms, 25 bonds, 3 residues, 1 model selected
+> select add #2/E:703
+atoms, 35 bonds, 4 residues, 1 model selected
+> select add #2/E:704
+atoms, 42 bonds, 5 residues, 1 model selected
+> select add #2/E:706
+atoms, 49 bonds, 6 residues, 1 model selected
+> select add #2/E:707
+atoms, 56 bonds, 7 residues, 1 model selected
+> select add #2/E:708
+atoms, 61 bonds, 8 residues, 1 model selected
+> select add #2/E:709
+atoms, 69 bonds, 9 residues, 1 model selected
+> select add #2/E:710
+atoms, 72 bonds, 10 residues, 1 model selected
+> mmaker sel to #3/Aa:300-314
+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 halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
+fsj, chain E (#2), sequence alignment score = 46.3
+RMSD between 10 pruned atom pairs is 0.499 angstroms; (across all 10 pairs:
+.499)
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> select #3/Aa:280
+atoms, 10 bonds, 1 residue, 1 model selected
+> show #3/Aa:305,280,328,304
+> select #3/Aa:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show #!4 models
+> transparency 50
+> hide #!4 models
+> hide #!3 models
+> hide #!2 models
+> select clear
+> show #!3 models
+> show #!2 models
+> combine #2
+> hide #!2 models
+> hide #!3 models
+> show #5 cartoons
+> select #5/C:273
+atoms, 7 bonds, 1 residue, 1 model selected
+> select up
+atoms, 72 bonds, 10 residues, 1 model selected
+> select up
+atoms, 1071 bonds, 132 residues, 1 model selected
+> delete sel
+> select #5/D:407
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #5/B:6
+atoms, 15 bonds, 2 residues, 1 model selected
+> select up
+atoms, 84 bonds, 10 residues, 1 model selected
+> select up
+atoms, 2159 bonds, 266 residues, 1 model selected
+> delete sel
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Structure/1fsj_E9_nuclease_HNH_like.pdb" models #5
+> select #5/E:904@ZN
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 4 bonds, 2 residues, 1 model selected
+> select #5
+atoms, 1087 bonds, 7 pseudobonds, 457 residues, 2 models selected
+> select subtract #5/E:804@P
+atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected
+> select subtract #5/E:804@O2
+atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected
+> select subtract #5/E:804@O3
+atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected
+> select subtract #5/E:804@O1
+atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected
+> select subtract #5/E:804@O4
+atoms, 1083 bonds, 6 pseudobonds, 456 residues, 2 models selected
+> select subtract #5/E:904@ZN
+atoms, 1083 bonds, 3 pseudobonds, 455 residues, 2 models selected
+> delete sel
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Structure/zn_phosphate_from_1fsj.pdb" models #5
+> hide #!5 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!2 models
+> hide #!2 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined_with_water.pdb"
+Chain information for halfcleaved_HNH_center_main_model_refined_with_water.pdb
+#6
+---
+Chain | Description
+Aa | No description available
+Ba | No description available
+Ca | No description available
+DA | No description available
+Da | No description available
+Db | No description available
+Dc | No description available
+Dd | No description available
+De | No description available
+Df | No description available
+EA | No description available
+FA | No description available
+> style stick
+Changed 80248 atom styles
+> hide #6 atoms
+> show #6 cartoons
+> show #6/B atoms
+> show #6/D atoms
+> show #6/C atoms
+> show #6/A atoms
+> color #6/DA light gray
+> color #6/EA dim gray
+> color #6/FA dark red
+> color #6/Ca rebecca purple
+> color #6/Ba forest green
+> color #6/Da,Db,Dc,Dd,De,Df khaki
+> color #6/Aa steel blue
+> color #6/Aa:232-350 dark turquoise
+> color #6 byhetero
+> show #6/Aa:305,280,328
+> show #6/Aa:304,280,328
+> show #!5 models
+> hide #!5 models
+> show #!2 models
+> select #6/Aa:303
+atoms, 6 bonds, 1 residue, 1 model selected
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> volume #4 level 0.09
+> hide #!2 models
+> show #!2 models
+> hide #!4 models
+> select #6/Aa:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> lighting soft
+> lighting simple
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> select #6/Aa:302
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #2/E:700
+atoms, 16 bonds, 2 residues, 2 models selected
+> show sel atoms
+> select #2/E:723
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #6/Aa:324
+atoms, 11 bonds, 2 residues, 2 models selected
+> show sel atoms
+> open 1v14
+Summary of feedback from opening 1v14 fetched from pdb
+---
+note | Fetching compressed mmCIF 1v14 from http://files.rcsb.org/download/1v14.cif
+v14 title:
+Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2
+and dsDNA (resolution 2.9A) [more info...]
+Chain information for 1v14 #7
+---
+Chain | Description | UniProt
+A B C D | COLICIN E9 | CEA9_ECOLI 2-134
+E F G H I J K L | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' |
+Non-standard residues in 1v14 #7
+---
+MG — magnesium ion
+v14 mmCIF Assemblies
+---
+| author_and_software_defined_assembly
+| author_and_software_defined_assembly
+| author_and_software_defined_assembly
+| author_and_software_defined_assembly
+> hide #!2 models
+> hide #!6 models
+> view
+> select add #7
+atoms, 5524 bonds, 73 pseudobonds, 623 residues, 5 models selected
+> select clear
+> select add #7
+atoms, 5513 bonds, 73 pseudobonds, 621 residues, 3 models selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> select add #7/G:8
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #7/H:12
+atoms, 43 bonds, 2 residues, 1 model selected
+> select add #7/J:11
+atoms, 67 bonds, 3 residues, 1 model selected
+> select add #7/I:8
+atoms, 87 bonds, 4 residues, 1 model selected
+> select add #7/C:80
+atoms, 92 bonds, 5 residues, 1 model selected
+> select add #7/B:123
+atoms, 98 bonds, 6 residues, 1 model selected
+> select add #7/E:5
+atoms, 119 bonds, 7 residues, 1 model selected
+> select add #7/F:12
+atoms, 142 bonds, 8 residues, 1 model selected
+> select add #7/A:53
+atoms, 153 bonds, 9 residues, 1 model selected
+> select up
+atoms, 1247 bonds, 77 residues, 1 model selected
+> select up
+atoms, 4147 bonds, 438 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #7/D:100
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #7/D:101
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #7/D:102
+atoms, 25 bonds, 3 residues, 1 model selected
+> select add #7/D:103
+atoms, 29 bonds, 4 residues, 1 model selected
+> select add #7/D:104
+atoms, 36 bonds, 5 residues, 1 model selected
+> select add #7/D:105
+atoms, 44 bonds, 6 residues, 1 model selected
+> select add #7/D:106
+atoms, 51 bonds, 7 residues, 1 model selected
+> select add #7/D:107
+atoms, 58 bonds, 8 residues, 1 model selected
+> show #!6 models
+> mmaker sel to #6/Aa:300-310
+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 halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa
+(#6) with 1v14, chain D (#7), sequence alignment score = 23.8
+RMSD between 8 pruned atom pairs is 0.406 angstroms; (across all 8 pairs:
+.406)
+> color #7 yellow
+> color #7 byhetero
+> select clear
+> select #7/K:6
+atoms, 20 bonds, 1 residue, 1 model selected
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> show sel atoms
+> select #7/K:5
+atoms, 21 bonds, 1 residue, 1 model selected
+> show sel atoms
+> view sel
+> select #7/D:5
+atoms, 10 bonds, 1 residue, 1 model selected
+> hide #!4 models
+> select #7/D:102
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #7/D:6
+atoms, 17 bonds, 2 residues, 1 model selected
+> select subtract #7/D:6
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #7/D:5
+atoms, 20 bonds, 2 residues, 1 model selected
+> select add #7/D:103
+atoms, 24 bonds, 3 residues, 1 model selected
+> select add #7/D:100
+atoms, 32 bonds, 4 residues, 1 model selected
+> select add #7/D:127
+atoms, 42 bonds, 5 residues, 1 model selected
+> show sel atoms
+> style stick
+Changed 85576 atom styles
+> select add #7/K:4
+atoms, 65 bonds, 6 residues, 1 model selected
+> select #7/K:5
+atoms, 21 bonds, 1 residue, 1 model selected
+> select add #7/K:6
+atoms, 41 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> show #!4 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb" models #7
+> hide #!4 models
+> hide #!6 models
+> hide #!7 models
+> show #!7 models
+> show #7 cartoons
+> view
+> select #7/H:12
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #7/G:8
+atoms, 43 bonds, 2 residues, 1 model selected
+> select add #7/F:13
+atoms, 64 bonds, 3 residues, 1 model selected
+> select add #7/E:7
+atoms, 88 bonds, 4 residues, 1 model selected
+> select add #7/A:102
+atoms, 98 bonds, 5 residues, 1 model selected
+> select add #7/J:12
+atoms, 121 bonds, 6 residues, 1 model selected
+> select add #7/I:7
+atoms, 145 bonds, 7 residues, 1 model selected
+> select add #7/C:78
+atoms, 150 bonds, 8 residues, 1 model selected
+> select up
+atoms, 1055 bonds, 56 residues, 1 model selected
+> select up
+atoms, 3079 bonds, 306 residues, 1 model selected
+> select up
+atoms, 3079 bonds, 328 residues, 1 model selected
+> select up
+atoms, 5513 bonds, 621 residues, 1 model selected
+> select down
+atoms, 3079 bonds, 328 residues, 1 model selected
+> delete sel
+> select #7/B:89
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 42 bonds, 5 residues, 1 model selected
+> select up
+atoms, 1068 bonds, 132 residues, 1 model selected
+> delete sel
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb" models #7
+> hide #!7 models
+> open 1emv
+Summary of feedback from opening 1emv fetched from pdb
+---
+note | Fetching compressed mmCIF 1emv from http://files.rcsb.org/download/1emv.cif
+emv title:
+Crystal structure of colicin E9 DNAse domain with its cognate immunity protein
+IM9 (1.7 angstroms) [more info...]
+Chain information for 1emv #8
+---
+Chain | Description | UniProt
+A | IMMUNITY PROTEIN IM9 | IMM9_ECOLI 1-86
+B | COLICIN E9 | CEA9_ECOLI 2-134
+Non-standard residues in 1emv #8
+---
+PO4 — phosphate ion
+> view
+> select #8/A:71
+atoms, 6 bonds, 1 residue, 1 model selected
+> select up
+atoms, 123 bonds, 16 residues, 1 model selected
+> select up
+atoms, 664 bonds, 83 residues, 1 model selected
+> delete sel
+> mmaker #8/B:100-110 to #6/Aa:300-310
+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 halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa
+(#6) with 1emv, chain B (#8), sequence alignment score = 35.4
+RMSD between 9 pruned atom pairs is 0.264 angstroms; (across all 9 pairs:
+.264)
+> view
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #8 models
+> show #8 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> select #8/B:127
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> select #8/B:100
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide #8 models
+> hide #!6 models
+> show #!5 models
+> hide #!5 models
+> show #!2 models
+> show #!6 models
+> select #6/Aa:303
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/E:704
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/Aa:306
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/E:706
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/Ba:128
+atoms, 6 bonds, 1 residue, 1 model selected
+> select clear
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> show #!4 models
+> lighting simple
+> lighting soft
+> lighting simple
+> hide #!4 models
+> hide #!2 models
+> hide #!6 models
+> show #8 models
+> set chain
+Expected a keyword
+> set chain #8/B A
+Expected a keyword
+> set chain #8/B to A
+Expected a keyword
+> set chain A #8/B
+Expected a keyword
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_refined2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #9
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> color #9/L light gray
+> color #9/K dim gray
+> color #9/J dark red
+> color #9/I rebecca purple
+> color #9/B forest green
+> color #9/C,D,E,F,G,H khaki
+> color #9/A steel blue
+> color #9/A:232-350 dark turquoise
+> style stick
+Changed 106889 atom styles
+> hide #9 atoms
+> show #9 cartoons
+> hide #!9 models
+> show #!3 models
+> hide #!3 models
+> show #!6 models
+> hide #!6 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> show #8 models
+> show #9/M atoms
+> show #9/N atoms
+> hide #!9 models
+> show #!9 models
+> hide #8 models
+> show #8 models
+> hide #8 models
+> hide #!9 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #10
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #10 atoms
+> show #10 cartoons
+> cartoon style nucleic xsection oval width 1.6 thickness 1.6
+> color #10/L light gray
+> color #10/K dim gray
+> color #10/J dark red
+> color #10/I rebecca purple
+> color #10/B forest green
+> color #10/C,D,E,F,G,H khaki
+> color #10/A steel blue
+> color #10/A:232-350 dark turquoise
+> show #10/K atoms
+> style stick
+Changed 131055 atom styles
+> show #10 & nucleic atoms
+> select #10
+atoms, 24925 bonds, 3 pseudobonds, 2803 residues, 2 models selected
+> nucleotides sel ladder
+> select clear
+> show #!4 models
+> volume #4 level 0.06
+> show #10/M,N,O atoms
+> select clear
+> select #10/K:4
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #10/K:3
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #10/K:2
+atoms, 47 bonds, 3 residues, 1 model selected
+> select add #10/K:1
+atoms, 56 bonds, 4 residues, 1 model selected
+> hide sel cartoons
+> nucleotides sel atoms
+> style nucleic & sel stick
+Changed 54 atom styles
+> select clear
+> color zone #4 near #10 distance 10
+> transparency 50
+> volume #4 level 0.05
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #10/L light gray
+> color #10/K dim gray
+> color #10/J dark red
+> color #10/I rebecca purple
+> color #10/B forest green
+> color #10/C,D,E,F,G,H khaki
+> color #10/A steel blue
+> color #10/A:232-350 dark turquoise
+> color zone #4 near #10 distance 10
+> hide #!10 models
+> hide #!4 models
+> show #!10 models
+> select #10/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select #10/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select clear
+> color zone #4 near #10 distance 10
+> show #!4 models
+> hide #!10 models
+> color zone #4 near #10 distance 5
+> volume #4 level 0.09
+> lighting soft
+> lighting full
+> lighting soft
+> color zone #4 near #10 distance 4
+> color zone #4 near #10 distance 3
+> volume #4 level 0.07
+> surface zone #4 nearAtoms #10 distance 2.5
+> surface zone #4 nearAtoms #10 distance 3
+> select add #4
+models selected
+> ui tool show "Color Actions"
+> color sel navajo white
+> set bgColor white
+> lighting simple
+> transparency sel 50
+> show #!10 models
+> volume #4 level 0.05
+> volume #4 level 0.09
+> volume #4 level 0.08
+> color #10 byhetero
+> select clear
+> select #10/K:1@N9
+atom, 1 residue, 1 model selected
+> select up
+atoms, 9 bonds, 1 residue, 1 model selected
+> select add #10/K:2@OP2
+atoms, 9 bonds, 2 residues, 1 model selected
+> select up
+atoms, 31 bonds, 2 residues, 1 model selected
+> select down
+atoms, 9 bonds, 2 residues, 1 model selected
+> select add #10/K:2@OP1
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #10/K:2@O2
+atoms, 17 bonds, 2 residues, 1 model selected
+> select add #10/K:2@O4
+atoms, 20 bonds, 2 residues, 1 model selected
+> select add #10/K:2@C5
+atoms, 21 bonds, 2 residues, 1 model selected
+> select add #10/K:2@C7
+atoms, 24 bonds, 2 residues, 1 model selected
+> select add #10/K:3@N6
+atoms, 25 bonds, 3 residues, 1 model selected
+> select up
+atoms, 27 bonds, 3 residues, 1 model selected
+> select up
+atoms, 55 bonds, 3 residues, 1 model selected
+> hide #!4 models
+> select subtract #10/K:3@OP1
+atoms, 53 bonds, 3 residues, 1 model selected
+> select subtract #10/K:3@P
+atoms, 51 bonds, 3 residues, 1 model selected
+> select subtract #10/K:3@OP2
+atoms, 51 bonds, 3 residues, 1 model selected
+> select add #10/K:4@P
+atoms, 51 bonds, 4 residues, 1 model selected
+> select add #10/K:4@OP1
+atoms, 52 bonds, 4 residues, 1 model selected
+> select add #10/K:4@OP2
+atoms, 54 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@O3'
+atoms, 53 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C4'
+atoms, 50 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@O4'
+atoms, 48 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C3'
+atoms, 48 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C2'
+atoms, 47 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C1'
+atoms, 46 bonds, 4 residues, 1 model selected
+> select subtract #10/K:2@C5'
+atoms, 46 bonds, 4 residues, 1 model selected
+> hide sel atoms
+> show #10/K:3 atoms
+> hide sel atoms
+> select #10/K:3@C5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #10/K:3@C4'
+atom, 1 residue, 1 model selected
+> select add #10/K:3@O3'
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C2'
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@O4'
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select #10/K:3@C3'
+atom, 1 residue, 1 model selected
+> select add #10/K:3@C1'
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C8
+atoms, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select down
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N3
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C4
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C5
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N7
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C6
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N6
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@N1
+atoms, 1 residue, 1 model selected
+> select add #10/K:3@C2
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select #10/K:3@N9
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> select #10/K:2@C5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> volume #4 level 0.07
+> show #10/A:305,304,280,328
+> volume #4 level 0.09
+> select #10/K:4@O5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> color #10/M red
+> color #10/O blue
+> color #10/O dark blue
+> color #10/O blue
+> volume #4 level 0.07
+> show #10/K:2 atoms
+> volume #4 level 0.06
+> show #10/K:1-2 atoms
+> show #!5 models
+> hide #!5 models
+> show #!2 models
+> hide #!2 models
+> hide #!4 models
+> hide #!10 models
+> show #!10 models
+> select #10/K:1@O5'
+atom, 1 residue, 1 model selected
+> select add #10/K:1@C5'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C4'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@O4'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C1'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@N9
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C2'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@C3'
+atoms, 1 residue, 1 model selected
+> select add #10/K:1@O3'
+atoms, 1 residue, 1 model selected
+> select add #10/K:2@P
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@OP2
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@OP1
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@O5'
+atoms, 2 residues, 1 model selected
+> select add #10/K:2@C5'
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> show #!4 models
+> hide #!4 models
+> ui tool show Distances
+> select #10/O:1@O
+atom, 1 residue, 1 model selected
+> select #10/K:3@OP2
+atom, 1 residue, 1 model selected
+> select add #10/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #10/K:3@OP2 #10/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/K DA 3 OP2
+and /O HOH 1 O: 2.479Å
+> select #10/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #10/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #10/A:304@ND1 #10/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 304 ND1
+and /M MG 1 MG: 2.377Å
+> select #10/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #10/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #10/A:328@NE2 #10/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 328 NE2
+and /M MG 1 MG: 2.352Å
+> select #10/M:1@MG
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP1
+atoms, 2 residues, 1 model selected
+> distance #10/M:1@MG #10/K:3@OP1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/M MG 1 MG and
+/K DA 3 OP1: 3.166Å
+> select #10/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #10/A:280@NH2 #10/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH2
+and /K DA 3 OP2: 2.389Å
+> select #10/A:280@NH1
+atom, 1 residue, 1 model selected
+> select add #10/K:3@O5'
+atoms, 2 residues, 1 model selected
+> distance #10/A:280@NH1 #10/K:3@O5'
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH1
+and /K DA 3 O5': 2.765Å
+> select #10/A:238
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #10/A:319
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #10/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #10/A:305@ND1 #10/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
+and /K DA 3 OP2: 3.592Å
+> select #10/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> select #10/A:309@N
+atom, 1 residue, 1 model selected
+> select add #10/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #10/A:309@N #10/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A LEU 309 N
+and /O HOH 1 O: 3.104Å
+> select #10/A:309@N
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> view
+> select #10/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #10/K:3@OP1
+atoms, 2 residues, 1 model selected
+> distance #10/A:305@ND1 #10/K:3@OP1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
+and /K DA 3 OP1: 3.734Å
+> delete sel
+> ~distance #10/A:305@ND1 #10/K:3@OP1
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 155221 atom styles
+> hide #12 atoms
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> hide #!11 models
+> show #!11 models
+> close #11
+> show #12 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> show #12/K:2-3 atoms
+> hide #12/K:1-3 cartoons
+> select clear
+> select #12/K:2@OP1
+atom, 1 residue, 1 model selected
+> select add #12/K:2@OP2
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@P
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:3@C5'
+atoms, 2 residues, 1 model selected
+> select add #12/K:3@C4'
+atoms, 2 residues, 1 model selected
+> select add #12/K:3@C3'
+atoms, 2 residues, 1 model selected
+> select add #12/K:4
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@O4'
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C2'
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C1'
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N9
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C8
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C4
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C5
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N7
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C6
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N6
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N1
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@C2
+atoms, 3 bonds, 3 residues, 1 model selected
+> select add #12/K:3@N3
+atoms, 3 bonds, 3 residues, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select #12/K:3@O3'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> select #12/K:2@O5'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show #12/M,O atoms
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select clear
+> show #12/A:304-305,328,280
+> select #12/A:319
+atoms, 7 bonds, 1 residue, 1 model selected
+> select ~sel & ##selected
+atoms, 24918 bonds, 3 pseudobonds, 2802 residues, 2 models selected
+> show #12/A:304-305,328,280,319
+> color #12 byhetero
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> select add #12/M:1@MG
+atoms, 2 residues, 1 model selected
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select clear
+> select #12/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/A:305@ND1 #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 305 ND1
+and /K DA 3 OP2: 3.159Å
+> select #12/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/A:280@NH2 #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH2
+and /K DA 3 OP2: 2.389Å
+> select #12/A:280@NH1
+atom, 1 residue, 1 model selected
+> select add #12/K:3@O5'
+atoms, 2 residues, 1 model selected
+> distance #12/A:280@NH1 #12/K:3@O5'
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH1
+and /K DA 3 O5': 2.765Å
+> view
+> select #12/K:3@OP1
+atom, 1 residue, 1 model selected
+> select add #12/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP1 #12/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP1
+and /M MG 1 MG: 3.166Å
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> select add #12/A:304@ND1
+atoms, 2 residues, 1 model selected
+> distance #12/M:1@MG #12/A:304@ND1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/M MG 1 MG and
+/A HIS 304 ND1: 2.377Å
+> select #12/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #12/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #12/A:328@NE2 #12/M:1@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 328 NE2
+and /M MG 1 MG: 2.352Å
+> select clear
+> color sel maroon
+> color sel teal
+> color sel cornflower blue
+> color sel dark salmon
+> color sel dark khaki
+> color sel peru
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> color sel indigo
+> color sel red
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> select #12/K:3@OP2
+atom, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP2 #12/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP2
+and /O HOH 1 O: 2.479Å
+> color sel indigo
+> select clear
+> color sel dark blue
+[Repeated 1 time(s)]
+> select clear
+> select #12/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 7 bonds, 2 residues, 1 model selected
+Exactly two atoms must be selected!
+> select clear
+> select #12/A LEU 309 N
+Expected a keyword
+> select #12/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> select #12/A:309@N
+atom, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #12/A:309@N #12/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A LEU 309 N
+and /O HOH 1 O: 3.104Å
+> distance style decimalPlaces 2
+[Repeated 2 time(s)]
+> distance style decimalPlaces 1
+[Repeated 2 time(s)]
+> select subtract #12/O:1@O
+atom, 1 residue, 1 model selected
+> select ~sel & ##selected
+atoms, 24925 bonds, 11 pseudobonds, 2803 residues, 3 models selected
+> hide #12/A:309 atoms
+> show #12/A:309 cartoons
+> select clear
+> show #!4 models
+> volume #4 level 0.07
+> volume #4 level 0.08
+> select #12/K:2@N3
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> select down
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> surface dust #4 size 7.25
+[Repeated 1 time(s)]
+> surface dust #4 1
+Expected a keyword
+> surface dust #4 size 1
+> show (sel-residues & sidechain) target ab
+> hide sel atoms
+> select clear
+> select #12/K:3@O5'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> show #12/K:2 atoms
+> select #12/K:2@C2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide #!4 models
+> select subtract #12/K:2@O3'
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> volume #4 level 0.06
+> volume #4 level 0.08
+> volume #4 level 0.09
+> volume #4 level 0.08
+> view matrix models
+> #12,0.95038,0.072866,-0.30245,40.949,-0.29386,-0.10887,-0.94963,361.72,-0.10212,0.99138,-0.082056,19.143
+> show #!10 models
+> hide #!10 models
+> mmaker #12 to #10
+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 halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#10) with
+halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#12), sequence alignment
+score = 1753
+RMSD between 340 pruned atom pairs is 0.001 angstroms; (across all 340 pairs:
+.001)
+> ui tool show "Side View"
+> hide #11.1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3 transparentBackground true
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!4 models
+> select #2/E:804@O1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #2/E:731@CG
+atoms, 4 bonds, 2 residues, 1 model selected
+> select up
+atoms, 14 bonds, 2 residues, 1 model selected
+> select up
+atoms, 15 bonds, 3 residues, 1 model selected
+> select up
+atoms, 16 bonds, 4 residues, 1 model selected
+> select add #12/A:319@OD1
+atoms, 16 bonds, 5 residues, 2 models selected
+> select up
+atoms, 35 bonds, 5 residues, 2 models selected
+> select add #2/E:31@O
+atoms, 35 bonds, 6 residues, 2 models selected
+> select add #2/E:298@O
+atoms, 35 bonds, 7 residues, 2 models selected
+> select subtract #2/E:298@O
+atoms, 35 bonds, 6 residues, 2 models selected
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> show #2.1 models
+> hide #2.1 models
+> select add #12
+atoms, 24953 bonds, 11 pseudobonds, 2808 residues, 4 models selected
+> select subtract #12
+atoms, 28 bonds, 5 residues, 1 model selected
+> hide sel atoms
+> select #2/E:701@CB
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #12/A:319@OD1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/E:298@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> color sel dark blue
+> select clear
+> show #!4 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!12 models
+> hide #!4 models
+> show #!2 models
+> select #2/E:904@ZN
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> hide #!2 models
+> show #!12 models
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel silver
+> color sel metallic
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color sel dark gray
+> color sel dim gray
+> select clear
+> color sel red
+> select #12/M:1@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> color sel dim gray
+> select clear
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> color sel red
+> color #12/M red
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!4 models
+> color sel tan
+> color sel dim gray
+[Repeated 1 time(s)]
+> show #!4 models
+> select clear
+> hide #!2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> hide #!4 models
+> show #!2 models
+> hide #!11 models
+> color #2 yellow
+> sle #2/E
+Unknown command: sle #2/E
+> select #2/E
+atoms, 1075 bonds, 4 pseudobonds, 190 residues, 2 models selected
+> select clear
+> ui tool show "Show Sequence Viewer"
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> hide #!2 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #13
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #13 atoms
+> show #13 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #13/DA light gray
+> color #13/EA dim gray
+> color #13/FA dark red
+> color #13/Ca rebecca purple
+> color #13/Ba forest green
+> color #13/Da,Db,Dc,Dd,De,Df khaki
+> color #13/Aa steel blue
+> color #13/Aa:232-350 dark turquoise
+> hide #!12 models
+> show #!12 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> color #13/L light gray
+> color #13/K dim gray
+> color #13/J dark red
+> color #13/I rebecca purple
+> color #13/B forest green
+> color #13/C,D,E,F,G,H khaki
+> color #13/A steel blue
+> color #13/A:232-350 dark turquoise
+> color #13 byhetero
+> hide #!12 models
+> color #13/M red
+> show #13/K:2 atoms
+> style stick
+Changed 179387 atom styles
+> select #13/K:3
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #13/K:4
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #13/K:2
+atoms, 47 bonds, 3 residues, 1 model selected
+> hide sel cartoons
+> show #13/K:3 atoms
+> select subtract #13/K:3@O5'
+atoms, 45 bonds, 3 residues, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 44 bonds, 3 residues, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 43 bonds, 3 residues, 1 model selected
+> select subtract #13/K:2@O3'
+atoms, 42 bonds, 3 residues, 1 model selected
+> select subtract #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> select add #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> select subtract #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> select add #13/K:2@C3'
+atoms, 40 bonds, 3 residues, 1 model selected
+> hide sel atoms
+> select #13/K:2@O3'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> show sel atoms
+> select #13/K:4@O5'
+atom, 1 residue, 1 model selected
+> select add #13/K:4@OP1
+atoms, 1 residue, 1 model selected
+> select add #13/K:3@O3'
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 27 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@O5'
+atoms, 25 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@P
+atoms, 23 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 23 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 23 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select up
+atoms, 24 bonds, 3 residues, 1 model selected
+> select up
+atoms, 49 bonds, 3 residues, 1 model selected
+> select down
+atoms, 24 bonds, 3 residues, 1 model selected
+> select #13/K:2@N1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select subtract #13/K:2@O3'
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #13/A:304-305,328,280
+> show #13/M,O
+> select #13/O:1@O
+atom, 1 residue, 1 model selected
+> color sel blue
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!4 models
+> show #!12 models
+> hide #!12 models
+> select #13/K:1
+atoms, 9 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select #13/K:1@O5'
+atom, 1 residue, 1 model selected
+> select add #13/K:1@C5'
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select Mg
+atoms, 6 residues, 6 models selected
+> select Zn
+atoms, 5 residues, 2 models selected
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> select add #2
+atoms, 4317 bonds, 16 pseudobonds, 856 residues, 3 models selected
+> select subtract #2
+atom, 1 residue, 1 model selected
+> hide #!4 models
+> select add #5
+atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> select add #5
+atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
+> select subtract #5
+Nothing selected
+> hide #!5 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select Zn
+atoms, 5 residues, 2 models selected
+> select add #5
+atoms, 4 bonds, 1 pseudobond, 6 residues, 3 models selected
+> select subtract #5
+atoms, 4 residues, 1 model selected
+> show sel atoms
+> show #!2 models
+> select water
+Expected an objects specifier or a keyword
+> ui tool show "Check Waters"
+> hbonds #13/O interModel false reveal true restrict any name "water H-bonds"
+The following atoms were skipped as donors/acceptors due to missing heavy-atom
+bond partners: halfcleaved_HNH_center_main_model_temp2.pdb #13/K DG 1 N9
+hydrogen bonds found
+> show #4 models
+> select #13/O
+atom, 1 residue, 1 model selected
+> display #13/O :<4
+> view #13/O @<4
+> select add #13/K:3@N7
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 23 bonds, 2 residues, 1 model selected
+> hide #!2 models
+> hide #!4 models
+> select subtract #13/K:3@O5'
+atoms, 21 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 20 bonds, 2 residues, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 19 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select #13/K:3@O5'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@P
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@OP1
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@OP2
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #13/K:3@O5'
+atoms, 19 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select subtract #13/K:2@O3'
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 9 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #13/A:308@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> hide sel cartoons
+> select #13/A:309@N
+atom, 1 residue, 1 model selected
+> show #13/O atoms
+> show #!11 models
+> hide #!11 models
+> close #11
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> hide sel
+> select #13/O:1@O
+atom, 1 residue, 1 model selected
+> select add #13/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #13/O:1@O #13/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/O HOH 1 O and
+/K DA 3 OP2: 2.5Å
+> select #13/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> show sel atoms
+> select #13/A:309@N
+atom, 1 residue, 1 model selected
+> select add #13/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #13/A:309@N #13/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LEU 309 N
+and /O HOH 1 O: 3.1Å
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> hide #11.1 models
+> select #13/M:2@MG
+atom, 1 residue, 1 model selected
+> select add #13/K:2@O3'
+atoms, 2 residues, 1 model selected
+> distance #13/M:2@MG #13/K:2@O3'
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/M MG 2 MG and
+/K DT 2 O3': 2.9Å
+> select #13/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #13/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #13/A:304@ND1 #13/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 304 ND1
+and /M MG 2 MG: 2.6Å
+> select #13/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #13/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #13/A:328@NE2 #13/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 328 NE2
+and /M MG 2 MG: 2.0Å
+> select clear
+> select #13/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #13/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #13/A:305@ND1 #13/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 305 ND1
+and /K DA 3 OP2: 3.2Å
+> select #13/K:3@O5'
+atom, 1 residue, 1 model selected
+> select add #13/A:280@NH1
+atoms, 2 residues, 1 model selected
+> distance #13/K:3@O5' #13/A:280@NH1
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 O5'
+and /A ARG 280 NH1: 2.8Å
+> select #13/K:3@OP2
+atom, 1 residue, 1 model selected
+> select add #13/A:280@NH2
+atoms, 2 residues, 1 model selected
+> distance #13/K:3@OP2 #13/A:280@NH2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 OP2
+and /A ARG 280 NH2: 2.4Å
+> select add #11
+pseudobonds, 2 models selected
+> color sel dim gray
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> unsel
+Unknown command: unsel
+> select
+atoms, 183813 bonds, 57 pseudobonds, 19979 residues, 49 models selected
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
+> 1210 supersample 3
+> show #!2 models
+> hide #!4 models
+> hide #!11 models
+> select #2/E:31@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
+> 1210 supersample 3
+> lighting soft
+> show #!4 models
+> hide #!2 models
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> show #!2 models
+> hide #!4 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
+> 1210 supersample 3
+> hide #!2 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> volume #4 level 0.09
+> volume #4 level 0.1
+> volume #4 level 0.95
+> volume #4 level 0.095
+> volume #4 level 0.09
+> volume #4 level 0.08
+> volume #4 level 0.09
+> select #13/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> show #13/L atoms
+> select clear
+> show #13/L,J atoms
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Mon Mar 24 00:43:04 2025 ———
+opened ChimeraX session
+> volume #4 level 0.08
+> hide #13/J,L atoms
+> hide #13/K:6-46 atoms
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_zoom_out.tif" width 1984 height
+> 1210 supersample 3
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> volume #4 level 0.06
+> show #13/A:83,85 atoms
+> show #13/K:39-40 atoms
+> show #13/L:6-7 atoms
+> select clear
+> show #13/L,J #13/K:7-46 atoms
+> color #13/L light gray
+> color #13/K dim gray
+> color #13/J dark red
+> color #13/I rebecca purple
+> color #13/B forest green
+> color #13/C,D,E,F,G,H khaki
+> color #13/A steel blue
+> color #13/A:232-350 dark turquoise
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoom_out.tif" width 1984 height
+> 1210 supersample 3
+> color #13/A. byhet
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #13/A byhetero
+> ui tool show "Side View"
+> hide #13/K:7-46 #13/L cartoons
+> hide #13/K:7-46 #13/L atoms
+> show #13/K:39-40 #13/L:6-7 atoms
+> ui tool show Distances
+> show #!11 models
+Exactly two atoms must be selected!
+> hide #!4 models
+> show #13/K:39-41 #13/L:6-7 atoms
+> select #13/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #13/K:40@N2
+atoms, 2 residues, 1 model selected
+> distance #13/A:83@OD1 #13/K:40@N2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
+and /K DG 40 N2: 3.013Å
+> distance style color black
+[Repeated 2 time(s)]
+> ui tool show "Color Actions"
+> distance style color dimgrey
+[Repeated 2 time(s)]
+> select #13/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #13/K:41@O2
+atoms, 2 residues, 1 model selected
+> distance #13/A:85@NZ #13/K:41@O2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
+and /K DC 41 O2: 3.020Å
+> select #13/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #13/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #13/A:85@NZ #13/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
+and /L DG 6 N2: 3.258Å
+> select #13/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #13/A:85@NZ
+atoms, 2 residues, 1 model selected
+> distance #13/A:83@OD1 #13/A:85@NZ
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
+and LYS 85 NZ: 2.939Å
+> select add #11
+atoms, 12 pseudobonds, 2 residues, 3 models selected
+> color sel dim gray
+> select clear
+> select add #13/A:85
+atoms, 9 bonds, 1 residue, 1 model selected
+> select add #13/A:83
+atoms, 15 bonds, 2 residues, 1 model selected
+> color sel steel blue
+> color sel byhetero
+> color sel dim gray
+> select clear
+> show #!4 models
+> volume #4 level 0.08
+> volume #4 level 0.07
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
+> 1210 supersample 3
+> hide #!4 models
+> hide #13/K:39 atoms
+> show #!4 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
+> 1210 supersample 3
+> show #11.1 models
+> distance style decimalPlaces 1
+[Repeated 2 time(s)]
+> hide #11.1 models
+> view #13/L
+> volume #4 level 0.06
+> show #13/k,l cartoons
+> show #13/k:7-46 #13/l atoms
+> hide #!4 models
+> select #13/A:178
+atoms, 12 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #13/A:193
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show #!4 models
+> hide #!11 models
+> hide #13/A:83,85 atoms
+> select clear
+> surface dust #4 size 7.25
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
+> 1984 height 1210 supersample 3
+> show #13/A:191 atoms
+> select #13/A:193@OD1
+atom, 1 residue, 1 model selected
+> select add #13/L:9@N2
+atoms, 2 residues, 1 model selected
+> distance #13/A:193@OD1 #13/L:9@N2
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASN 193 OD1
+and /L DG 9 N2: 2.6Å
+> show #!11 models
+> select #13/K:39
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> hide #!4 models
+> select #13/K:39@OP1
+atom, 1 residue, 1 model selected
+> select add #13/A:191@OG
+atoms, 2 residues, 1 model selected
+> distance #13/K:39@OP1 #13/A:191@OG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DC 39 OP1
+and /A SER 191 OG: 2.9Å
+> show sel cartoons
+> show #!4 models
+> color sel dim gray
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
+> 1984 height 1210 supersample 3
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!13 models
+> show #!13 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> volume #4 level 0.09
+> volume #4 level 0.05
+> volume #4 level 0.06
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
+> 1984 height 1210 supersample 3
+> hide #!4 models
+> show #!4 models
+> hide #!11 models
+> select #13/K:4
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #13/K:3
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #13/K:2
+atoms, 47 bonds, 3 residues, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> select down
+atoms, 47 bonds, 3 residues, 1 model selected
+> hide #!4 models
+> select add #13/K:1
+atoms, 56 bonds, 4 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #13/K:3@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select up
+atoms, 986 bonds, 45 residues, 1 model selected
+> select down
+atoms, 23 bonds, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select up
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #13/K:2@O3'
+atoms, 23 bonds, 2 residues, 1 model selected
+> select up
+atoms, 45 bonds, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> select #13/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #13/A:295
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #13/I:140
+atoms, 10 bonds, 2 residues, 1 model selected
+> show sel atoms
+> show #!4 models
+> hide #!4 models
+> select #13/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> select add #13/K:7
+atoms, 45 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> show #!4 models
+> volume #4 level 0.09
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 24 bonds, 1 residue, 1 model selected
+> hide #!4 models
+> select subtract #13/K:6@O3'
+atoms, 23 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> hide #!4 models
+> select #13/K:7@OP1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> select #13/K:6@O3'
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show #!4 models
+> hide #!4 models
+> select #13/I:50
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #13/I:51
+atoms, 16 bonds, 2 residues, 1 model selected
+> show sel atoms
+> show #!4 models
+> volume #4 level 0.06
+> volume #4 level 0.08
+> select #13/I:51@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 9 bonds, 2 residues, 1 model selected
+> select up
+atoms, 17 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> volume #4 level 0.1
+> color #13/i byhetero
+> select clear
+> select #13/K:7
+atoms, 21 bonds, 1 residue, 1 model selected
+> volume #4 level 0.07
+> select clear
+> volume #4 level 0.09
+> show #!2 models
+> hide #!2 models
+> hide #!4 models
+> select #13/A:295@SG
+atom, 1 residue, 1 model selected
+> select add #13/I:140@SG
+atoms, 2 residues, 1 model selected
+> distance #13/A:295@SG #13/I:140@SG
+Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A CYS 295 SG
+and /I CYS 140 SG: 3.9Å
+> show #!11 models
+> color sel dim gray
+> select clear
+> hide #13/A:230-350 atoms
+> hide #13/o atoms
+> select #13/A:295
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> show #!4 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/cas8_cas6_cys_pair_0p09.tif" width
+> 1984 height 1210 supersample 3
+> hide #!4 models
+> show #11.1 models
+> hide #11.1 models
+> show #!2 models
+> select #2/E:706@CG
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/E:706@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+[Repeated 1 time(s)]
+> select clear
+> select #2/E:706@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/E:707@CD1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+[Repeated 1 time(s)]
+> select clear
+> select #13/I:140@SG
+atom, 1 residue, 1 model selected
+> select add #13/A:295@SG
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 10 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> show #13/A:305,304,280,328
+> select #2/E:718
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #13/A:319
+atoms, 14 bonds, 2 residues, 2 models selected
+> show sel atoms
+> show #13/O
+> select clear
+> hide #!11 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj_2.tif" width 1984
+> height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Mon Mar 24 13:31:18 2025 ———
+opened ChimeraX session
+> hide #!2 models
+> ui tool show "Side View"
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!13 models
+> close #12
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #12 atoms
+> show #12 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/M red
+> color #12/o blue
+> select clear
+> select #12/K:6
+atoms, 24 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> style stick
+Changed 179387 atom styles
+> select clear
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> select #12/K:7
+atoms, 21 bonds, 1 residue, 1 model selected
+> hide #12/K cartoons
+> show #12/k atoms
+> select clear
+> volume #4 level 0.06
+> hide #!4 models
+> select #12/A:295
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #12/I:50
+atoms, 13 bonds, 2 residues, 1 model selected
+> select add #12/I:140
+atoms, 18 bonds, 3 residues, 1 model selected
+> show sel atoms
+> show #!4 models
+> hide #!4 models
+> select #12/A:290
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show #!4 models
+> volume #4 level 0.08
+> hide #!4 models
+> select #12/A:296
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #12/I:51
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> show #!4 models
+> volume #4 level 0.07
+> volume #4 level 0.09
+> volume #4 level 0.05
+> surface dust #4 size 7.25
+> color #12/K:1-4 red
+> show #12/m,o atoms
+> select clear
+> close #13
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Tue Mar 25 00:19:58 2025 ———
+opened ChimeraX session
+> close #12
+> hide #!4 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp.pdb #12
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 155168 atom styles
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> cartoon style nucleic xsection oval width 1 thickness 1
+> show #12 cartoons
+> hide #12 atoms
+> hide #12/k:1-6 cartoons
+> show #12/k:1-6 atoms
+> show #12/m,o atoms
+> color #12/m red
+> color #12/o blue
+> select clear
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_center_sharp3Å.mrc"
+Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
+pixel 0.725, shown at level 0.00305, step 2, values float32
+> volume #13 step 1
+> volume #13 level 0.01
+> volume #13 level 0.02
+> transparency #13.1 50
+> color zone #13 near #12 distance 5
+> select subtract #11
+Nothing selected
+> hide #!12 models
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 near #12/m,o dis
+> 1
+Repeated keyword argument "near"
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 #12/m,o dis 1
+Expected a keyword
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3
+> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3.5
+> color zone #13 near #12/ dis 3.5
+Expected a keyword
+> color zone #13 near #12 distance 3.5
+> color zone #13 near #12 distance 3
+> color zone #13 near #12 distance 1
+> color zone #13 near #12 distance 1.5
+> color zone #13 near #12 distance 2
+> color zone #13 near #12 distance 2.4
+> color zone #13 near #12 distance 2.5
+> color zone #13 near #12 distance 3
+> color zone #13 near #12 distance 4
+> color zone #13 near #12 distance 4.5
+> color zone #13 near #12 distance 5
+> lighting soft
+> hide #!13 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_in_sharp3Å.mrc"
+Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 2, values float32
+> volume #14 step 1
+> volume #14 level 0.02
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
+Chain information for halfcleaved_HNH_inwards_refined.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> color #15/L light gray
+> color #15/K dim gray
+> color #15/J dark red
+> color #15/I rebecca purple
+> color #15/B forest green
+> color #15/C,D,E,F,G,H khaki
+> color #15/A steel blue
+> color #15/A:232-350 dark turquoise
+> hide #15 atoms
+> show #!14 models
+> color zone #14 near #15 distance 5
+> hide #!15 models
+> show #!15 models
+> hide #!14 models
+> show #!14 models
+> show cartoons #15
+Expected ',' or a keyword
+> show #15 cartoons
+> hide #!14 models
+> combine #15
+> delete #15/b,c,d,e,f,g,h,j,k,l
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> delete #15/b,c,d,e,f,g,h,j,k,l,i
+> delete #15/a:1-230
+> delete #15/a:1-231
+> show #!14 models
+> transparency #14.1 50
+> fitmap #15 inMap #14
+Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
+halfcleaved_HNH_in_sharp3Å.mrc (#14) using 897 atoms
+average map value = 0.1033, steps = 48
+shifted from previous position = 0.103
+rotated from previous position = 0.723 degrees
+atoms outside contour = 296, contour level = 0.02
+Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
+halfcleaved_HNH_in_sharp3Å.mrc (#14) coordinates:
+Matrix rotation and translation
+.99995867 0.00821061 0.00390412 -2.00149362
+-0.00817612 0.99992812 -0.00876986 2.45517496
+-0.00397584 0.00873757 0.99995392 -1.09279831
+Axis 0.69359957 0.31218363 -0.64920029
+Axis point 0.00000000 120.00927253 275.85141597
+Rotation angle (degrees) 0.72313237
+Shift along axis 0.08767530
+> hide #!14 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_refined.pdb"
+Chain information for postcleavage_HNH_inwards_refined.pdb #17
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_3p93Å.mrc"
+Opened postcleavage_HNH_inwards_3p93Å.mrc as #18, grid size 420,420,420,
+pixel 0.725, shown at level 0.0417, step 2, values float32
+> close #18
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_in_sharp_4p5.mrc"
+Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 2, values float32
+> volume #18 step 1
+> hide #!15 models
+> show #!15 models
+> hide #!17 models
+> transparency #18.1 50
+> lighting simple
+> fitmap #15 inMap #18
+Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
+post_HNH_in_sharp_4p5.mrc (#18) using 897 atoms
+average map value = 0.1722, steps = 88
+shifted from previous position = 5.79
+rotated from previous position = 18.5 degrees
+atoms outside contour = 305, contour level = 0.025678
+Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
+post_HNH_in_sharp_4p5.mrc (#18) coordinates:
+Matrix rotation and translation
+.98515450 -0.14232903 -0.09598467 36.22127193
+.16215106 0.95508370 0.24803662 -52.49007293
+.05637058 -0.25991841 0.96398381 44.34612442
+Axis -0.83066353 -0.24914793 0.49791908
+Axis point 0.00000000 129.04516803 229.89711725
+Rotation angle (degrees) 17.80344657
+Shift along axis 5.07088499
+> hide #17 atoms
+> show #17 cartoons
+> show #!17 models
+> hide #!17 models
+> hide #!15 models
+> show #!15 models
+> show #!16 models
+> hide #!16 models
+> hide #!15 models
+> show #!16 models
+> hide #!16 models
+> show #!17 models
+> select add #18
+models selected
+> ui tool show "Color Actions"
+> color sel navajo white
+> lighting simple
+> lighting soft
+> lighting simple
+> color #17/DA light gray
+> color #17/EA dim gray
+> color #17/FA dark red
+> color #17/Ca rebecca purple
+> color #17/Ba forest green
+> color #17/Da,Db,Dc,Dd,De,Df khaki
+> color #17/Aa steel blue
+> color #17/Aa:232-350 dark turquoise
+> color #17/L light gray
+> color #17/K dim gray
+> color #17/J dark red
+> color #17/I rebecca purple
+> color #17/B forest green
+> color #17/C,D,E,F,G,H khaki
+> color #17/A steel blue
+> color #17/A:232-350 dark turquoise
+> select subtract #18
+Nothing selected
+> hide #!18 models
+> show #!18 models
+> hide #!17 models
+> hide #!18 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
+shown at level 0.00149, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #20
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #20 atoms
+> show #20 cartoons
+> volume #19 step 1
+> volume #19 level 0.07
+> volume #19 level 0.05
+> volume #19 level 0.02
+> volume #19 level 0.01
+> combine #19
+No structures specified
+> combine #20
+> hide #!20 models
+> delete #21/a,b,c,d,e,f,g,h,k,l
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2726 atoms
+average map value = 0.1694, steps = 2000
+shifted from previous position = 0.186
+rotated from previous position = 0.199 degrees
+atoms outside contour = 1261, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999396 0.00180060 0.00297193 -0.76393106
+-0.00180072 0.99999838 0.00003869 0.16921571
+-0.00297185 -0.00004404 0.99999558 0.56555929
+Axis -0.01190446 0.85519891 -0.51816321
+Axis point 165.64366772 0.00000000 257.94336417
+Rotation angle (degrees) 0.19910813
+Shift along axis -0.13924475
+> select #21/J:51
+atoms, 25 bonds, 1 residue, 1 model selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #21,0.99951,0.00060373,-0.031401,4.2416,-0.0016237,0.99947,-0.032468,6.0991,0.031365,0.032503,0.99898,-9.4868
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2726 atoms
+average map value = 0.1688, steps = 2000
+shifted from previous position = 1.36
+rotated from previous position = 2.61 degrees
+atoms outside contour = 1266, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999350 0.00327561 0.00150351 -0.76518814
+-0.00327402 0.99999408 -0.00105700 0.62813683
+-0.00150696 0.00105207 0.99999831 -0.07731006
+Axis 0.28081232 0.40083125 -0.87205433
+Axis point 178.64402650 242.89942515 0.00000000
+Rotation angle (degrees) 0.21516256
+Shift along axis 0.10432118
+> delete #21/i:119-133
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1781, steps = 2000
+shifted from previous position = 0.132
+rotated from previous position = 0.117 degrees
+atoms outside contour = 1140, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999500 0.00239001 0.00207238 -0.60674616
+-0.00239146 0.99999689 0.00070090 0.14244066
+-0.00207070 -0.00070585 0.99999761 0.40363617
+Axis -0.21704908 0.63924101 -0.73774021
+Axis point 79.27931343 260.84792943 -0.00000000
+Rotation angle (degrees) 0.18567412
+Shift along axis -0.07503103
+> show #21/j atoms
+> style stick
+Changed 229983 atom styles
+> select clear
+> select #21/J:44
+atoms, 21 bonds, 1 residue, 1 model selected
+> view matrix models
+> #21,0.99372,-0.10871,0.026365,13.992,0.10722,0.99284,0.052567,-20.988,-0.031891,-0.04941,0.99827,11.548
+> select up
+atoms, 1444 bonds, 60 residues, 1 model selected
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1752, steps = 2000
+shifted from previous position = 4.3
+rotated from previous position = 7.23 degrees
+atoms outside contour = 1149, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99998549 0.00368109 0.00393188 -1.30544186
+-0.00367497 0.99999203 -0.00156309 0.73010434
+-0.00393760 0.00154862 0.99999105 0.48740849
+Axis 0.27751762 0.70184056 -0.65605168
+Axis point 94.79211019 0.00000000 320.39166369
+Rotation angle (degrees) 0.32121992
+Shift along axis -0.16963143
+> view matrix models
+> #21,0.95316,-0.16312,0.2547,-4.7007,0.14,0.98441,0.10651,-33.244,-0.2681,-0.065869,0.96114,54.875
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1731, steps = 2000
+shifted from previous position = 0.932
+rotated from previous position = 18.4 degrees
+atoms outside contour = 1177, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99994904 -0.00778267 -0.00643051 1.98761314
+.00779564 0.99996762 0.00199459 -1.51674316
+.00641478 -0.00204462 0.99997733 -0.91523181
+Axis -0.19616124 -0.62382235 0.75654904
+Axis point 206.49736911 250.60632995 0.00000000
+Rotation angle (degrees) 0.58990690
+Shift along axis -0.13613214
+> view matrix models
+> #21,0.99995,-0.0077827,-0.0064305,3.3447,0.0077956,0.99997,0.0019946,-2.7803,0.0064148,-0.0020446,0.99998,0.39857
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 2605 atoms
+average map value = 0.1778, steps = 2000
+shifted from previous position = 1.77
+rotated from previous position = 0.414 degrees
+atoms outside contour = 1144, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99999337 -0.00330202 -0.00153324 0.70289684
+.00330074 0.99999420 -0.00083994 -0.52418630
+.00153600 0.00083487 0.99999847 -0.38974171
+Axis 0.22416395 -0.41079927 0.88373892
+Axis point 155.63582398 210.62363526 0.00000000
+Rotation angle (degrees) 0.21403999
+Shift along axis 0.02846957
+> delete #21/j:1-41
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02377, steps = 68
+shifted from previous position = 0.607
+rotated from previous position = 0.441 degrees
+atoms outside contour = 1066, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99996474 -0.00055599 -0.00837886 1.69415235
+.00053058 0.99999525 -0.00303455 0.64823116
+.00838051 0.00303000 0.99996029 -1.81624530
+Axis 0.33963693 -0.93858608 0.06085174
+Axis point 216.66154710 0.00000000 207.10057130
+Rotation angle (degrees) 0.51154276
+Shift along axis -0.14354572
+> view matrix models
+> #21,0.95152,0.063441,0.30097,-58.133,0.017073,0.9661,-0.25762,48.854,-0.30711,0.25027,0.91818,-0.5168
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.01942, steps = 92
+shifted from previous position = 1.42
+rotated from previous position = 9.42 degrees
+atoms outside contour = 1173, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.97435965 -0.00668895 0.22489671 -33.93326133
+.03560741 0.99154562 -0.12477740 17.25587377
+-0.22216072 0.12958605 0.96636022 5.49530082
+Axis 0.49286534 0.86623732 0.08195521
+Axis point 2.77043250 0.00000000 148.29261146
+Rotation angle (degrees) 14.95412576
+Shift along axis -1.32647815
+> view matrix models
+> #21,0.90553,-0.2837,0.31547,16.944,0.29673,0.95494,0.0070231,-29.813,-0.30325,0.08725,0.94891,27.343
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.01933, steps = 104
+shifted from previous position = 2.05
+rotated from previous position = 9.43 degrees
+atoms outside contour = 1170, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.94411256 -0.12450182 0.30520610 -21.00938346
+.14744888 0.98763632 -0.05322902 -8.92619050
+-0.29480552 0.09525648 0.95079751 24.92749364
+Axis 0.21988344 0.88852194 0.40271582
+Axis point 74.52306659 0.00000000 80.67313058
+Rotation angle (degrees) 19.73351564
+Shift along axis -2.51203568
+> view matrix models
+> #21,0.94411,-0.1245,0.30521,-17.873,0.14745,0.98764,-0.053229,-5.6643,-0.29481,0.095256,0.9508,23.681
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.01942, steps = 156
+shifted from previous position = 3.04
+rotated from previous position = 8.27 degrees
+atoms outside contour = 1166, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.97438343 -0.01578899 0.22433822 -31.97489437
+.04417306 0.99153739 -0.12207515 15.64761333
+-0.22051229 0.12885771 0.96683505 5.34685589
+Axis 0.48795736 0.86504446 0.11660060
+Axis point 3.97780903 0.00000000 139.84528015
+Rotation angle (degrees) 14.89958612
+Shift along axis -1.44305704
+> view matrix models
+> #21,0.97881,0.079073,-0.18889,14.498,-0.093393,0.99329,-0.068145,23.787,0.18223,0.084342,0.97963,-36.826
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02378, steps = 112
+shifted from previous position = 4.26
+rotated from previous position = 12.1 degrees
+atoms outside contour = 1061, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99995850 -0.00058011 -0.00909169 1.82468704
+.00055786 0.99999684 -0.00244989 0.54145676
+.00909308 0.00244471 0.99995567 -1.79847577
+Axis 0.25943577 -0.96387493 0.06031750
+Axis point 197.73964432 0.00000000 204.27550886
+Rotation angle (degrees) 0.54048814
+Shift along axis -0.15698708
+> select clear
+> select #21/J:50
+atoms, 21 bonds, 1 residue, 1 model selected
+> view matrix models
+> #21,0.96924,-0.18193,0.16576,13.795,0.16697,0.98085,0.10023,-33.405,-0.18082,-0.069465,0.98106,39.844
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02378, steps = 120
+shifted from previous position = 0.698
+rotated from previous position = 15.5 degrees
+atoms outside contour = 1064, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99996372 -0.00034050 -0.00851103 1.66866582
+.00031330 0.99999484 -0.00319750 0.69973282
+.00851207 0.00319472 0.99995867 -1.87660250
+Axis 0.35130930 -0.93556970 0.03593210
+Axis point 220.86482619 0.00000000 200.72582758
+Rotation angle (degrees) 0.52126798
+Shift along axis -0.13586127
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> view matrix models
+> #21,0.94284,-0.16526,0.28937,-7.4067,0.16063,0.98621,0.039865,-23.627,-0.29196,0.0088937,0.95639,41.501
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1727 atoms
+average map value = 0.02377, steps = 140
+shifted from previous position = 0.641
+rotated from previous position = 19.9 degrees
+atoms outside contour = 1065, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99996409 -0.00060556 -0.00845233 1.72034129
+.00057980 0.99999518 -0.00304995 0.64758353
+.00845413 0.00304494 0.99995963 -1.83001040
+Axis 0.33840585 -0.93869583 0.06581501
+Axis point 216.32111144 0.00000000 208.46719481
+Rotation angle (degrees) 0.51597228
+Shift along axis -0.14615257
+> hide #!20 models
+> delete #21/i:107-118
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1617 atoms
+average map value = 0.025, steps = 44
+shifted from previous position = 0.0515
+rotated from previous position = 0.51 degrees
+atoms outside contour = 976, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99991658 -0.00665991 -0.01106673 3.46514203
+.00669212 0.99997347 0.00287541 -1.15618478
+.01104728 -0.00294923 0.99993463 -0.94027532
+Axis -0.21995713 -0.83509609 0.50421561
+Axis point 74.57354161 0.00000000 307.17000003
+Rotation angle (degrees) 0.75864102
+Shift along axis -0.27075880
+> view matrix models
+> #21,0.9761,-0.050009,0.2115,-22.223,0.037779,0.99739,0.061477,-14.46,-0.21402,-0.052017,0.97544,41.647
+> fitmap #21 inMap #19
+Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
+post_HNH_cent_sharp.mrc (#19) using 1617 atoms
+average map value = 0.025, steps = 112
+shifted from previous position = 0.714
+rotated from previous position = 13.5 degrees
+atoms outside contour = 978, contour level = 0.01
+Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
+post_HNH_cent_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+.99991534 -0.00691325 -0.01102344 3.51324748
+.00694686 0.99997133 0.00301354 -1.20471924
+.01100229 -0.00308986 0.99993470 -0.89660439
+Axis -0.22833637 -0.82401113 0.51852498
+Axis point 70.41448246 0.00000000 312.48223472
+Rotation angle (degrees) 0.76577763
+Shift along axis -0.27441187
+> hide #!21 models
+> hide #!19 models
+> show #!19 models
+> show #!18 models
+> hide #!18 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!19 models
+> show #!18 models
+> hide #!18 models
+> hide #!17 models
+> show #!16 models
+> hide #!16 models
+> show #!14 models
+> select add #14
+atoms, 21 bonds, 1 residue, 3 models selected
+> transparency sel 0
+> select clear
+> show #!13 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!4 models
+> lighting soft
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> hide #!13 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Wed Mar 26 12:19:53 2025 ———
+opened ChimeraX session
+> show #!13 models
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color #13 navajo white
+> show #!12 models
+> transparency #13.1 50
+> lighting simple
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> view
+> lighting soft
+> lighting simple
+> hide #12/l,k cartoons
+> show #12/k:39-40
+> show #12/l:6-7
+> show #12/l:6-8
+> hide #12/l:6 atoms
+> show #12/a:83,85 atoms
+> color #12/a:83,85 byhetero
+> ui tool show "Side View"
+> show #12/l:6-7
+> hide #12/l:8 atoms
+> hide #12/k:39 atoms
+> show #12/k:41 atoms
+> hide #!13 models
+> show #11 models
+> ui tool show Distances
+> select #12/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #12/A:83@OD1
+atoms, 2 residues, 1 model selected
+> distance #12/A:85@NZ #12/A:83@OD1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
+and ASP 83 OD1: 2.939Å
+> select #12/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #12/K:41@O2
+atoms, 2 residues, 1 model selected
+> distance #12/A:85@NZ #12/K:41@O2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
+and /K DC 41 O2: 3.020Å
+> select #12/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #12/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #12/A:85@NZ #12/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
+and /L DG 6 N2: 3.258Å
+> select #12/K:40@N2
+atom, 1 residue, 1 model selected
+> select add #12/A:83@OD1
+atoms, 2 residues, 1 model selected
+> distance #12/K:40@N2 #12/A:83@OD1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DG 40 N2 and
+/A ASP 83 OD1: 3.013Å
+> select add #11
+atoms, 4 pseudobonds, 2 residues, 3 models selected
+> color sel dim gray
+> select clear
+> show #!13 models
+> hide #11.1 models
+> lighting soft
+> lighting full
+> lighting simple
+> color #12/a byhetero
+> surface zone #13 nearAtoms #12/a,k,l
+> surface zone #13 nearAtoms #12/a,k,l distance 10
+> surface zone #13 nearAtoms #12/a,k,l distance 5
+> surface zone #13 nearAtoms #12/a,k,l distance 10
+> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 10
+> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 5
+> hide #12/b,c cartoons
+> hide #12/b,c,d cartoons
+> lighting soft
+> lighting simple
+> lighting full
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp.tif" width 1984 height
+> 1210 supersample 3
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #12 cartoons
+> show #12/j,k,l atoms
+> select #12
+atoms, 24865 bonds, 7 pseudobonds, 2801 residues, 3 models selected
+> nucleotides sel ladder
+> select clear
+> hide #12 cartoons
+> show #12 cartoons
+> surface zone #13 nearAtoms #12 distance 10
+> surface dust #13 size 7.25
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out.tif" width 1984
+> height 1210 supersample 3
+> hide #!13 models
+> hide #!12 models
+> show #!12 models
+> show #!13 models
+> hide #12/l,k,j cartoons
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 tube/slab shape ellipsoid
+> nucleotides #!12 tube/slab shape box
+> nucleotides #!12 slab
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 fill
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> nucleotides #!12 atoms
+> style nucleic & #!12 stick
+Changed 2368 atom styles
+> lighting soft
+> lighting simple
+> hide #12/a:83,85 atoms
+> hide #!13 models
+> select #12/A:178
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #12/A:193
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #12/A:192
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #12/A:191
+atoms, 17 bonds, 3 residues, 1 model selected
+> select add #12/A:178
+atoms, 29 bonds, 4 residues, 1 model selected
+> show sel atoms
+> show #!13 models
+> hide #!13 models
+> select #12/A:191@OG
+atom, 1 residue, 1 model selected
+> select add #12/K:39@OP1
+atoms, 2 residues, 1 model selected
+> distance #12/A:191@OG #12/K:39@OP1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A SER 191 OG
+and /K DC 39 OP1: 2.884Å
+> select #12/A:193@OD1
+atom, 1 residue, 1 model selected
+> select add #12/L:9@N2
+atoms, 2 residues, 1 model selected
+> distance #12/A:193@OD1 #12/L:9@N2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ASN 193 OD1
+and /L DG 9 N2: 2.565Å
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> select #12/A:205
+atoms, 8 bonds, 1 residue, 1 model selected
+> show #12/a:205 atoms
+> show #!13 models
+> hide #12/a:205 atoms
+> color zone #13 near #12 distance 10
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> volume #!13 style image
+> volume #!13 style surface
+> transparency #13.1 0
+> transparency #13.1 50
+> color #12 white
+[Repeated 1 time(s)]
+> color #12 black
+> color #12 gray
+> color #12 dim gray
+> color #12 light gray
+> color #12 dim gray
+> color #12 red
+> orange
+Unknown command: orange
+> color #12 orange
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #13 navajo white
+> transparency #13.1 50
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #13 navajo white
+> transparency #13 50
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12/DA light gray
+> color #12/EA dim gray
+> color #12/FA dark red
+> color #12/Ca rebecca purple
+> color #12/Ba forest green
+> color #12/Da,Db,Dc,Dd,De,Df khaki
+> color #12/Aa steel blue
+> color #12/Aa:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 dim gray
+> transparency #13 50
+> color #12 rosy brown
+> color #12 orange
+> color #12 sienna
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 sienna
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 sienna
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #13 navajo white
+> transparency #13 50
+> select clear
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 sienna
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 peru
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 khaki
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 violet
+> transparency #13 50
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color zone #13 near #12 distance 10
+> color #12 alice blue
+> transparency #13 50
+> select #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> color sel violet
+> select subtract #12
+Nothing selected
+> select add #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> select subtract #12
+Nothing selected
+> select add #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> select subtract #12
+Nothing selected
+> select add #12
+atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
+> color sel lemon chiffon
+> color sel light coral
+> color sel burly wood
+> color sel pale green
+> color sel gray
+> select clear
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/o blue
+> color zone #13 near #12/o distance 1
+> surface dust #13 size 7.25
+> surface dust #13 size 0
+> transparency #13 50
+> color zone #13 near #12
+> color zone #13 near #12 distance 10
+> transparency #13 50
+> surface dust #13 size 7.25
+> color #12 byhetero
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/a byhetero
+> hide #12/a:192 atoms
+> select add #11
+pseudobonds, 2 models selected
+> color sel white
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel yellow
+> color sel dark orange
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel orange red
+> select clear
+> hide #12/j atoms
+> hide #12/c,d,e,f,g,h,i cartoons
+> color #12 red
+> color #12 blue
+> color #12 green
+> color #12 cyan
+> select clear
+> color #12/a byhetero
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel dark red
+> color sel red
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding_shar_colormap.tif"
+> width 1984 height 1210 supersample 3
+> hide #12 atoms
+> show #12/k:39,40 atoms
+> show #12/l:7-8 atoms
+> select #13
+models selected
+> select clear
+> show #12/a:83,85 atoms
+> show #12/k:40-41 atoms
+> show #12/l:6 atoms
+> hide #12/k:39 #12/l:8 atoms
+> select clear
+> hide #12 cartoons
+> show #12/a:32-86 cartoons
+> lighting soft
+> lighting simple
+> lighting full
+> lighting simple
+> lighting full
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_colormap.tif" width 1984
+> height 1210 supersample 3
+> view
+> show #12 cartoons
+> select clear
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> hide #!11 models
+> hide #!13 models
+> lighting soft
+> lighting simple
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> show #!13 models
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+[Repeated 1 time(s)]
+> lighting soft
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out_colormap.tif"
+> width 1984 height 1210 supersample 3
+> color #12/m,o turquoise
+> color zone #13 near #12 distance 10
+> surface dust #13 size 0
+> color zone #13 near #12 distance 10
+> color #12/o blue
+> color zone #13 near #12 distance 1
+> color zone #13 near #12 distance 10
+> color #12/o blue
+> color zone #13 near #12/o distance 1
+> color blue zon #13 nea #12/o
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select #13 & zon 5 #12
+Expected a keyword
+> zone #13 within 5 of #12
+Expected a keyword
+> select zone #13 nea #12 dis 5
+Missing or invalid "range" argument: Expected a number
+> zone #13 nea #12 dis 5
+Expected a keyword
+> zone #13 nea #12 dis 5
+Expected a keyword
+> color zone #13 near #12 distance 5
+> split map #13
+Expected a structures specifier or a keyword
+> volume copy #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy as #22, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!22 models
+> show #!22 models
+> color #22 nea #12 dis 5
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color zone #22 near #12 distance 5
+> split map #22 nea #12
+Expected a structures specifier or a keyword
+> color zone #13 near #12 distance 5 split map
+Expected a keyword
+> split map zon #22 nea #12 dis 5
+Expected a structures specifier or a keyword
+> ui tool show "Color Zone"
+> volume splitbyzone #22
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 0 as #23.1, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 1 as #23.2, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 2 as #23.3, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 3 as #23.4, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 4 as #23.5, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 5 as #23.6, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 6 as #23.7, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 7 as #23.8, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 8 as #23.9, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 9 as #23.10, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc copy 10 as #23.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> show #!22 models
+> hide #!22 models
+> hide #!23 models
+> show #!23 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.2 models
+> show #!23.2 models
+> hide #!23.2 models
+> show #!23.2 models
+> hide #!23.2 models
+> show #!23.2 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> hide #!23.3 models
+> show #!23.3 models
+> hide #!12 models
+> hide #!23.11 models
+> show #!23.11 models
+> hide #!23.11 models
+> show #!23.11 models
+> hide #!23.10 models
+> show #!23.10 models
+> hide #!23.10 models
+> show #!23.10 models
+> select add #23.10
+models selected
+> color sel turquoise
+> select subtract #23.10
+Nothing selected
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.8 models
+> show #!23.8 models
+> hide #!23.8 models
+> show #!23.8 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23 models
+> show #!23 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> hide #!23.2 models
+> hide #!23.3 models
+> hide #!23.4 models
+> hide #!23.5 models
+> hide #!23.6 models
+> hide #!23.9 models
+> show #!23.9 models
+> hide #!23.8 models
+> show #!23.8 models
+> hide #!23.8 models
+> show #!23.8 models
+> show #!23.6 models
+> show #!23.5 models
+> show #!23.4 models
+> show #!23.3 models
+> show #!23.2 models
+> show #!23.1 models
+> show #!22 models
+> show #!21 models
+> show #!20 models
+> show #!19 models
+> show #!18 models
+> hide #!18 models
+> hide #!19 models
+> hide #!20 models
+> hide #!21 models
+> hide #!22 models
+> close #22
+> hide #!23.1 models
+> show #!23.1 models
+> hide #!23.1 models
+> show #!23.1 models
+> close #23
+> color zone #13 near #12
+> show #!13 models
+> color zone #13 near #12 distance 4
+> color zone #13 near #12 distance 4.25
+> color zone #13 near #12 distance 5
+> volume splitbyzone #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 10 as #22.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> hide #!22 models
+> show #!22 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> view
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.8 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> select add #22.10
+models selected
+> color sel turquoise
+> select subtract #22.10
+Nothing selected
+> select #22.10
+models selected
+> color sel dark turquoise
+> select clear
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> show #!22.3 models
+> lighting soft
+> lighting simple
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> volume #22.1-11 hide
+> volume #22.2 show
+> show #!22.3 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.9 models
+> show #!22.7 models
+> hide #!22.7 models
+> show #!22.8 models
+> show #!22.7 models
+> show #!22.10 models
+> show #!22.11 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> transparency #22 50
+> show #!13 models
+> hide #!13 models
+> show #!12 models
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide #12/k:1-3 atoms
+> hide #12/k:1-3 cartoons
+> show #12/a:280,304-305,319,328 atoms
+> color #12/a byhetero
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!22.10 models
+> color #22.10 #ff2600ff models
+> select add #22.10
+atoms, 8 bonds, 1 residue, 3 models selected
+> color sel dark turquoise
+> select clear
+> select add #22.10
+models selected
+> transparency sel 50
+> select clear
+> show #12/o,m atoms
+> color #12/m red
+> select clear
+> volume #22 hide
+> select #12/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> select #12/A:309@N
+atom, 1 residue, 1 model selected
+> select add #12/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #12/A:309@N #12/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LEU 309 N
+and /O HOH 1 O: 3.004Å
+> distance #12/A:309@N #12/O:1@O
+Distance already exists; modify distance properties with 'distance style'
+> show #!11 models
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> show #12/k:1-3 atoms
+> select #12/K:2@O3'
+atom, 1 residue, 1 model selected
+> select add #12/K:2@C3'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C2'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O5'
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> show sel atoms
+> select subtract #12/K:2@O3'
+atoms, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select down
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select #12/K:2@O3'
+atom, 1 residue, 1 model selected
+> color sel dim gray
+> select clear
+> hide #12.1 models
+> select #12/O:1@O
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/O:1@O #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/O HOH 1 O and
+/K DA 3 OP2: 2.868Å
+> select #12/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #12/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #12/A:280@NH2 #12/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ARG 280 NH2
+and /K DA 3 OP2: 2.709Å
+> select #12/K:3@OP1
+atom, 1 residue, 1 model selected
+> select add #12/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP1 #12/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP1 and
+/M MG 2 MG: 2.496Å
+> select #12/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #12/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #12/A:328@NE2 #12/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A HIS 328 NE2
+and /M MG 2 MG: 1.829Å
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> select add #12/A:304@ND1
+atoms, 2 residues, 1 model selected
+> distance #12/M:2@MG #12/A:304@ND1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/M MG 2 MG and
+/A HIS 304 ND1: 2.331Å
+> select #12/A:305@ND1
+atom, 1 residue, 1 model selected
+> select #12/K:3@OP2
+atom, 1 residue, 1 model selected
+Exactly two atoms must be selected!
+> select add #12/A:305@ND1
+atoms, 2 residues, 1 model selected
+> distance #12/K:3@OP2 #12/A:305@ND1
+Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP2 and
+/A HIS 305 ND1: 2.858Å
+> select clear
+> volume #22 show
+> color #12/k byhetero
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel orange red
+> select clear
+> hide #12/a cartoons
+> show #12/a cartoons
+> select #12/K:6
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #12/K:7
+atoms, 32 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #22.8
+models selected
+> select clear
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> color zone #22.8 near #12/a distance 5
+> color #12/a:232-350 dark turquoise
+> color zone #22.8 near #12/a distance 5
+> transparency
+> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
+> 0
+> transparency
+> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
+> 50
+> combine #12
+> hide #!12 models
+> hide #!22 models
+> hide #!23 models
+> show #!23 models
+> select #23/K:2@O3'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select clear
+> close #23
+> show #12 models
+> show #12 cartoons
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #12/K:3
+atoms, 11 bonds, 2 residues, 1 model selected
+> color darkred turqoise
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color sel darkred turqoise
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select clear
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #12/K:3
+atoms, 11 bonds, 2 residues, 1 model selected
+> color sel dark turquoise
+> select clear
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> color sel darkred turqoise
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> select clear
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> color sel dark turquoise
+> select clear
+> close #22
+> color zone #13 near #12 distance 5
+> volume splitbyzone #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 10 as #22.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 11 as #22.12, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 12 as #22.13, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 13 as #22.14, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> close #22
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H khaki
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #12/K:3
+atoms, 11 bonds, 2 residues, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select up
+atoms, 24865 bonds, 2801 residues, 1 model selected
+> select down
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 11 bonds, 2 residues, 1 model selected
+> select down
+atoms, 11 bonds, 2 residues, 1 model selected
+> select down
+atoms, 11 bonds, 2 residues, 1 model selected
+> select clear
+> select add #12/K:3
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #12/K:2
+atoms, 11 bonds, 2 residues, 1 model selected
+> color sel dark turquoise
+[Repeated 1 time(s)]
+> select clear
+> color zone #13 near #12 distance 5
+> hide #!12 models
+> show #!13 models
+> volume splitbyzone #13
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
+pixel 0.725, shown at level 0.02, step 1, values float32
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!22.6 models
+> show #!22.6 models
+> transparency
+> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 50
+> show #12 models
+> color #12/a byhetero
+> select #12/K:2
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide #12/k:1-6 cartoons
+> show #12/k:1-3 atoms
+> volume #22 hide
+> select subtract #12/K:2@O3'
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #12/K:2@O3'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #12/K:3@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #12/K:2@O3'
+atoms, 3 bonds, 2 residues, 1 model selected
+> color sel dim gray
+> color sel byhetero
+> select clear
+> select #12/M:2@MG
+atom, 1 residue, 1 model selected
+> color sel red
+> select clear
+> volume #22 show
+> transparency #22 90
+> transparency #22 80
+> transparency #22 75
+> hide #12/a cartoons
+> show #12/a cartoons
+> lighting soft
+> lighting simple
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_colormap.tif" width 1729
+> height 1210 supersample 3
+> view
+> view #22
+> hide #12 atoms
+> transparency #22 10
+> transparency #22 25
+> transparency #22 40
+> transparency #22 50
+> transparency #22 60
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_zoom_out_colormap.tif"
+> width 1729 height 1210 supersample 3
+> show #12/k:6 atoms
+> show #12/k:6-7 atoms
+> hide #12/k cartoons
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22 models
+> show #!13 models
+> transparency #13.1 0
+> transparency #13.1 50
+> hide #!13 models
+> select #12/I:140
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #12/A:295
+atoms, 10 bonds, 2 residues, 1 model selected
+> show sel atoms
+> color sel byhetero
+> select clear
+> show #!13 models
+> hide #12.1 models
+> color #12 cyan
+> transparency #13 90
+> transparency #13 75
+> color #12 dim gray
+> color #12 khaki
+> select #12
+atoms, 24865 bonds, 16 pseudobonds, 2801 residues, 3 models selected
+> color sel light salmon
+> color sel dark goldenrod
+> color sel olive
+> color sel green
+> color sel olive
+> color sel misty rose
+> color sel lavender blush
+> color sel snow
+> color sel dark green
+> color sel white
+> color sel light yellow
+> color sel ghost white
+> color sel mint cream
+> color sel white smoke
+> color sel papaya whip
+> color sel moccasin
+> color sel navajo white
+> select clear
+> color #12 byhetero
+> select #12/K:6@C5'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> color sel pale goldenrod
+> color #12 pale goldenrod
+> color #12/a,i byhetero
+> select clear
+> color #12 ivory
+> color #12 orange red
+> color #12 chocolate
+> select clear
+> color #12 goldenrod
+> select clear
+> color #12/a,i byhetero
+> select clear
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!12 models
+> hide #!11 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 253112 atom styles
+> close #23
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 253112 atom styles
+> color #23/j red
+> colse #23
+Unknown command: colse #23
+> close #23
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stu
+Expected a keyword
+> style stick
+Changed 253111 atom styles
+> select #23/J:61@P
+atom, 1 residue, 1 model selected
+> select add #23/J:60@O3'
+atoms, 2 residues, 1 model selected
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> close #23
+> show #!22 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.1 models
+> transparency
+> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 0
+> view
+> lighting soft
+> hide #!22.2 models
+> hide #!22.6 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.4 models
+> hide #!22.5 models
+> show #!22.2 models
+> hide #!22.3 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!12 models
+> show #12 cartoons
+> show #12/j,k,l atoms
+> hide #12/j,k,l cartoons
+> hide #12 cartoons
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.7 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.7 models
+> hide #12/k,l atoms
+> show #!22.3 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.4 models
+> hide #!22.2 models
+> hide #!12 models
+> show #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.4 models
+> hide #!22.3 models
+> hide #!22.7 models
+> show #!22.7 models
+> show #!22.3 models
+> show #!22.4 models
+> hide #!22.8 models
+> show #!22.9 models
+> show #!22.5 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!22.6 models
+> volume #22 copy
+Expected a keyword
+> volume copy #22
+Opened halfcleaved_HNH_center_sharp3Å.mrc 0 copy as #23, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 copy as #24, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 2 copy as #25, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 3 copy as #26, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 4 copy as #27, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 6 copy as #29, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 7 copy as #30, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 9 copy as #32, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+> close #23-27-29,30,32
+Expected a models specifier or a keyword
+> close #23-27,29,30,32
+> select add #31
+models selected
+> select add #28
+models selected
+> ui mousemode right "rotate selected models"
+Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy , 31
+halfcleaved_HNH_center_sharp3Å.mrc 8 copy
+> select clear
+> select add #28
+models selected
+> select add #31
+models selected
+> view matrix models
+> #28,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558,#31,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> show #!22.9 models
+> show #!22.6 models
+Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy
+> view matrix models #28,1,0,0,-26.099,0,1,0,28.092,0,0,1,69.137
+> undo
+> view matrix models #28,1,0,0,-27.45,0,1,0,25.948,0,0,1,59.885
+> undo
+> view matrix models
+> #28,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812,#31,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812
+> view matrix models
+> #28,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175,#31,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07,#31,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68,#31,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27,#31,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56,#31,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56
+> view matrix models
+> #28,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3,#31,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3
+> hide #!28 models
+> hide #!22.6 models
+> select clear
+> show #!28 models
+> volume copy #28,31
+Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
+,420,420, pixel 0.725, shown at step 1, values float32
+> select add #24
+models selected
+> select add #23
+models selected
+> hide #!23 models
+> view matrix models
+> #23,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77,#24,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77
+> view matrix models
+> #23,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97,#24,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97
+> view matrix models
+> #23,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07,#24,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07
+> view matrix models
+> #23,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16,#24,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16
+> view matrix models
+> #23,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3,#24,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3
+> view matrix models
+> #23,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159,#24,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159
+> view matrix models
+> #23,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62,#24,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62
+> show #!31 models
+> show #!22.3 models
+> hide #!22.3 models
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59,#24,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55,#24,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41,#24,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41
+> view
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68,#24,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68
+> show #!22.3 models
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71,#24,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21,#24,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21
+> view matrix models
+> #23,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137,#24,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137
+> hide #!22.3 models
+> select clear
+> show #!23 models
+> show #!28 models
+> show #!22.6 models
+> hide #!28 models
+> hide #!23 models
+> hide #!22.6 models
+> show #!22.3 models
+> show #!28 models
+> hide #!28 models
+> show #!23 models
+> show #!22.4 models
+> show #!22.6 models
+> show #!28 models
+> hide #!28 models
+> hide #!23 models
+> hide #!22.3 models
+> hide #!22.4 models
+> show #!22.2 models
+> show #!28 models
+> show #!23 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Thu Mar 27 17:05:34 2025 ———
+opened ChimeraX session
+> hide #!22.6 models
+> hide #!22.2 models
+> show #!22.6 models
+> hide #!22.6 models
+> hide #!23 models
+> hide #!28 models
+> show #!28 models
+> select add #28
+models selected
+> select add #31
+models selected
+> ui mousemode right "rotate selected models"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> view matrix models
+> #28,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74,#31,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74
+> show #!23 models
+> show #!22.6 models
+> hide #!28 models
+> hide #!23 models
+> hide #!22.6 models
+> select clear
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #25
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> volume #22 hide
+> volume #24-25 hide
+> volume #31 hide
+> style stick
+Changed 253111 atom styles
+> show #25 cartoons
+> hide #25
+> show #25 & nucleic
+> color #25/L light gray
+> color #25/K dim gray
+> color #25/J dark red
+> color #25/I rebecca purple
+> color #25/B forest green
+> color #25/C,D,E,F,G,H khaki
+> color #25/A steel blue
+> color #25/A:232-350 dark turquoise
+> hide #25 & nucleic cartoons
+> show #25
+> hide #25
+> show #25 & nucleic
+> show #25/j
+> open 3i4h
+Summary of feedback from opening 3i4h fetched from pdb
+---
+note | Fetching compressed mmCIF 3i4h from http://files.rcsb.org/download/3i4h.cif
+i4h title:
+Crystal structure of Cas6 in Pyrococcus furiosus [more info...]
+Chain information for 3i4h #26
+---
+Chain | Description | UniProt
+X | endoribonuclease | Q8U1S4_PYRFU 8-270
+> hide #!22 models
+> hide #!26 models
+> show #!26 models
+> hide #!25 models
+> show #!25 models
+> select #26/X:34
+atoms, 3 bonds, 1 residue, 1 model selected
+> view matrix models #26,1,0,0,11.063,0,1,0,112.94,0,0,1,76.569
+Drag select of 48 residues
+> view matrix models #26,1,0,0,25.302,0,1,0,250.11,0,0,1,200.98
+> view matrix models #26,1,0,0,73.305,0,1,0,249.54,0,0,1,132.47
+> view matrix models
+> #26,0.6118,0.31311,-0.72641,89.838,-0.77626,0.41421,-0.47524,242.91,0.15208,0.85463,0.49646,158
+> view matrix models
+> #26,0.20919,0.21723,-0.95344,137.17,-0.96272,0.21674,-0.16184,238.54,0.17149,0.95175,0.25447,203.29
+> view matrix models
+> #26,-0.18257,0.38275,-0.90563,144.87,-0.7876,0.49443,0.36774,240.71,0.58852,0.78041,0.21118,199.4
+> view matrix models
+> #26,0.24049,0.042201,-0.96973,126.99,-0.49179,0.86663,-0.084247,255.09,0.83685,0.49716,0.22917,198.15
+> view matrix models
+> #26,0.24049,0.042201,-0.96973,115.81,-0.49179,0.86663,-0.084247,256.61,0.83685,0.49716,0.22917,201.79
+> select #26 & name="tyr"
+Expected a keyword
+> select ::name="TYR"
+atoms, 15721 bonds, 1261 residues, 36 models selected
+> select #26::name="tyr"
+atoms, 193 bonds, 16 residues, 1 model selected
+> select #26::name="tyr" #26::name=lys
+atoms, 373 bonds, 38 residues, 1 model selected
+> select #26::name="tyr" #26::name=lys,his
+atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
+> select #26::name="tyr" #26::name=lys
+atoms, 373 bonds, 38 residues, 1 model selected
+> select #26::name=lys
+atoms, 178 bonds, 22 residues, 1 model selected
+> select #26::name=his
+atoms, 82 bonds, 8 residues, 1 model selected
+> view matrix models
+> #26,-0.89794,0.08841,0.43115,111.17,0.14503,0.98434,0.10021,254.49,-0.41554,0.15251,-0.8967,209.66
+> select #26::name="his,lys"
+Nothing selected
+> select #26::name=his,lys
+atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
+> select #26::name=his::name=lys
+atoms, 260 bonds, 30 residues, 1 model selected
+> select #26::name=his::name=lys::name=tyr
+atoms, 455 bonds, 46 residues, 1 model selected
+> show sel
+> select clear
+> mmaker #26 to #25/i
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain I (#25)
+with 3i4h, chain X (#26), sequence alignment score = 33.6
+RMSD between 6 pruned atom pairs is 1.546 angstroms; (across all 156 pairs:
+.266)
+> hide #!26 models
+> hide #!25 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 279140 atom styles
+> hide #27
+> show #27 cartoons
+> show #27/j,k,l
+> hide #27/j,k,l cartoons
+> color #27/L light gray
+> color #27/K dim gray
+> color #27/J dark red
+> color #27/I rebecca purple
+> color #27/B forest green
+> color #27/C,D,E,F,G,H khaki
+> color #27/A steel blue
+> color #27/A:232-350 dark turquoise
+> color #27/O blue
+> color #27/M red
+> volume #13 show
+> color zone #13 near #27 distance 10
+> color zone #13 near #27 distance 6
+> color zone #13 near #27 distance 4
+> color zone #13 near #27 distance 8
+> transparency #13 50
+> volume #13 hide
+> hide #27 models
+> close #27
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 279111 atom styles
+> hide #27
+> show #27 cartoons
+> show #27 & nucleic
+> color #27/L light gray
+> color #27/K dim gray
+> color #27/J dark red
+> color #27/I rebecca purple
+> color #27/B forest green
+> color #27/C,D,E,F,G,H khaki
+> color #27/A steel blue
+> color #27/A:232-350 dark turquoise
+> color #27/O blue
+> color #27/M red
+> hide #27& nucleic
+> hide #27& nucleic cartoons
+> hide #27& nucleic
+> show #27 & nucleic
+> select clear
+> select P
+atoms, 1108 residues, 15 models selected
+> color sel byhetero
+> select clear
+> hide #!27 models
+> open 3pkm
+Summary of feedback from opening 3pkm fetched from pdb
+---
+note | Fetching compressed mmCIF 3pkm from http://files.rcsb.org/download/3pkm.cif
+pkm title:
+Crystal structure of Cas6 with its substrate RNA [more info...]
+Chain information for 3pkm #29
+---
+Chain | Description | UniProt
+A X | CRISPR-associated endoribonuclease Cas6 | CAS6_PYRFU 8-270
+G | 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
+R | 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
+pkm mmCIF Assemblies
+---
+| author_defined_assembly
+| author_defined_assembly
+Drag select of 237 residues, 3 pseudobonds, 27 shapes
+> hide sel cartoons
+> select #29/A:106
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+Drag select of 71 atoms, 71 bonds, 27 shapes
+> hide sel
+Drag select of 13 atoms
+> hide sel
+> close #29
+> show #27 models
+> view
+> close #27
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style sty
+Expected a keyword
+> style stick
+Changed 279111 atom styles
+> hide #27
+> color #27/L light gray
+> color #27/K dim gray
+> color #27/J dark red
+> color #27/I rebecca purple
+> color #27/B forest green
+> color #27/C,D,E,F,G,H khaki
+> color #27/A steel blue
+> color #27/A:232-350 dark turquoise
+> color #27/O blue
+> color #27/M red
+> show #27 cartoons
+> show #27/j,k,l,m,o
+> hide #27 & nucleic cartoons
+> select P
+atoms, 1108 residues, 15 models selected
+> select #27::P
+Nothing selected
+> select #27::name=P
+Nothing selected
+> select #27 & P
+atoms, 111 residues, 1 model selected
+> color sel byhetero
+> select clear
+> hide #27 models
+> open /Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Phenix/eLBOW_54/elbow.001.pdb
+> view
+> close #29
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Mon Mar 31 18:07:43 2025 ———
+opened ChimeraX session
+> open /Users/zxc755/Downloads/J620_abinitio_map.mrc
+Opened J620_abinitio_map.mrc as #29, grid size 128,128,128, pixel 2.38, shown
+at level 0.218, step 1, values float32
+> hide #!29 models
+> show #!29 models
+> view
+> lighting soft
+> lighting simple
+> lighting soft
+> ui tool show "Color Actions"
+> select add #29
+models selected
+> color sel dark khaki
+[Repeated 1 time(s)]
+> color sel navajo white
+> select clear
+> lighting soft
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/half_abinitio.tif" width 1984 height
+> 1210 supersample 3 transparentBackground true
+> open /Users/zxc755/Downloads/half_hetref_J623_map.mrc
+Opened half_hetref_J623_map.mrc as #30, grid size 128,128,128, pixel 2.38,
+shown at level 0.227, step 1, values float32
+> select add #30
+models selected
+> color sel navajo white
+> hide #!29 models
+> select clear
+> volume #30 level 0.5
+> volume #30 level 0.3
+> volume #30 level 0.35
+> volume #30 level 0.33
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/half_hetref.tif" width 1984 height 1210
+> supersample 3
+> hide #!30 models
+Unsupported scale factor (0.000000) detected on Display0
+[Repeated 7 time(s)]
+> show #!31 models
+> hide #!31 models
+> show #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> hide #!29 models
+> show #!13 models
+> hide #!30 models
+> show #!30 models
+> hide #!30 models
+> color #12/L light gray
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H salmon
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/O blue
+> color #12/M red
+> color zone #13 near #12 distance 10
+> show #!22.1 models
+> hide #!22 models
+> hide #!22.1 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> color #22.2 salmon
+> show #!22.2 models
+> hide #!22.2 models
+> hide #!13 models
+> show #!22.2 models
+> show #!22.1 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.1 models
+> show #!22.1 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.1 models
+> show #!22.3 models
+> hide #!22.2 models
+> show #!22.2 models
+> surface dust #22.2-9 size 10
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.2 models
+> show #!22.4 models
+> hide #!22.3 models
+> show #!22.5 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.3 models
+> show #!22.7 models
+> hide #!22.7 models
+> surface dust #22.5 size 10
+> surface dust #22.4 size 10
+> surface dust #22.6 size 10
+> surface dust #22.7 size 10
+> surface dust #22.8 size 10
+> surface dust #22.9 size 10
+> show #!22.6 models
+> hide #!22.3 models
+> surface dust #22.6 size 10
+> hide #!22.4 models
+> hide #!22.5 models
+> show #!22.7 models
+> hide #!22.6 models
+> show #!22.8 models
+> show #!22.9 models
+> surface dust #22.7 size 10
+> surface dust #22.8 size 10
+> surface dust #22.9 size 10
+> show #!22.10 models
+> hide #!22.10 models
+> view
+> hide #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> show #!22.6 models
+> show #!22.9 models
+> hide #!22.9 models
+> hide #!22.6 models
+> show #!22.5 models
+> show #!22.4 models
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.2 models
+> hide #!22.4 models
+> hide #!22.3 models
+> show #!22.3 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.10 models
+> view
+[Repeated 1 time(s)]
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> volume #22 hide
+> show #12
+> hide #12
+> show #12 cartoons
+> show #12 & nucleic
+> volume #22 hide mod
+Expected a keyword
+> volume #22 hide model
+Expected a keyword
+> hide #22 models
+> show #22
+> hide #!22.1 models
+> hide #22 models
+> show #!13 models
+> hide #!13 models
+> show #22 models
+> hide #!22.1 models
+> transparency #22 70
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+> show #12/A:83,85
+> color #12/A byhetero
+> hide #12 & nucleic cartoons
+> ui tool show "Side View"
+> hide #!22.10 models
+> hide #!22.9 models
+> hide #!22.6 models
+> hide #!22.5 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.2 models
+> hide #12/c,d,e,f,g,h,i cartoons
+> show #!22.9 models
+> hide #!22.9 models
+> hide #12/c,d,e,f,g,h,i,j cartoons
+> hide #12/j
+> color #12/l wheat
+> color #22.7 wheat
+> show #!22.2 models
+> hide #!22.2 models
+> show #!21 models
+> hide #!21 models
+> show #!11 models
+> select add #11
+pseudobonds, 2 models selected
+> color sel black
+> color sel slate gray
+> color sel gray
+> color sel dim gray
+> select subtract #11
+Nothing selected
+> hide #!11 models
+> show #!11 models
+> show #!22.5 models
+> show #!22.2 models
+> show #!22.6 models
+> show #!22.9 models
+> show #!22.10 models
+> hide #!12 models
+> transparency #22 0
+> lighting soft
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> color #22.7 gold
+> color #22.7 khaki
+> color #22.7 dark khaki
+> color #22.7 olive
+> color #22.7 dark khaki
+> view
+> color #22.7 goldenrod
+> color #22.7 orange
+> color #22.7 dark orange
+> color #22.7 dark khaki
+> show #!12 models
+> transparency #22 70
+> graphics silhouettes true
+> lighting flat
+[Repeated 2 time(s)]
+> lighting soft
+> lighting flat
+> lighting soft
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> transparency #22 80
+> transparency #22 99
+> transparency #22 90
+> transparency #12/l:1-6 50
+> select add #11
+pseudobonds, 2 models selected
+> color sel crimson
+> color sel brown
+> color sel saddle brown
+> color sel indian red
+> color sel yellow
+> color sel gold
+[Repeated 1 time(s)]
+> color sel orange
+> color sel dark orange
+> color sel goldenrod
+> color sel salmon
+> color sel dark khaki
+> color sel peru
+> color sel dark goldenrod
+> select subtract #11
+Nothing selected
+> view
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> hide #!22.5 models
+> hide #!22.6 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22 models
+> show #!22 models
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+> volume #22.8 level 0.03
+> volume #22.8 level 0.02
+> volume #22 level 0.07
+> volume #22 level 0.05
+> hide #!22 models
+> show #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
+> 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
+> 1210 supersample 4
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
+[Repeated 1 time(s)]
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
+> 1210 supersample 3
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #12/a:83,85
+> volume #22 level 0.02
+> show #!22.5 models
+> show #!22.9 models
+> show #12/j
+> hide #12/a,b
+> hide #12/a,b cartoons
+> hide #!22.5 models
+> hide #!22.4 models
+> hide #!22.3 models
+> hide #!12 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #!32 models
+> show #!32 models
+> style ato
+Expected a keyword
+> style stick
+Changed 303224 atom styles
+> cki #32
+Unknown command: cki #32
+> close #32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 303277 atom styles
+> close #32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 303198 atom styles
+> hide #32
+> show #32 cartoons
+Computing secondary structure
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #32/L dark khaki
+> color #32/K dim gray
+> color #32/J dark red
+> color #32/I rebecca purple
+> color #32/B forest green
+> color #32/C,D,E,F,G,H salmon
+> color #32/A steel blue
+> color #32/A:232-350 dark turquoise
+> color #32/O blue
+> color #32/M red
+> hide #32 & nucleic cartoons
+> show #32 & nucleic
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> hide #!22.7 models
+> show #!22.7 models
+> show #!32 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> color #22.7 khaki
+> color #22.7 dark khaki
+> hide #!12 models
+> color #32/l khaki
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!32 models
+> show #!12 models
+> show #12/m,o
+> hide #!22.8 models
+> hide #!22.9 models
+> hide #!22.7 models
+> show #!22.5 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #12/a cartoons
+> hide #12/j
+> show #!22.4 models
+> show #12/a:304,305
+> hide #!22 models
+> select #12/A:280
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #12/A:319
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #12/A:280
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> select #12/K:2@C2'
+atom, 1 residue, 1 model selected
+> select add #12/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@O5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select add #12/K:2@C3'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select clear
+> select #12/K:3@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 3 bonds, 1 residue, 1 model selected
+> select up
+atoms, 926 bonds, 43 residues, 1 model selected
+> select down
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #12/K:2@O3'
+atoms, 3 bonds, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> select #12/A:328
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> show #!22 models
+> hide #!22 models
+> hide #!12 models
+> show #!12 models
+> show #!22 models
+> hide #!22 models
+> hide #!12 models
+> show #!22 models
+> show #!12 models
+> transparency #22 90
+> transparency #22 95
+> hide #!22 models
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows true intensity 0.5
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows false
+> lighting flat
+[Repeated 1 time(s)]
+> graphics silhouettes false
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting flat
+> graphics silhouettes false
+> show #!22 models
+> graphics silhouettes true
+> view
+> view orient
+[Repeated 1 time(s)]
+> show #12/a
+> volume #22 level 0.05
+> volume #22 level 0.09
+> volume #22 level 0.02
+> hide #12/a
+> hide #!12 models
+> show #!22.2 models
+> show #!22.3 models
+> hide #!22.4 models
+> hide #!22.5 models
+> hide #!22.2 models
+> show #!12 models
+> hide #12/a cartoons
+> show #12/b cartoons
+> hide #12/k,l
+> show #12/b
+> hide #12/b
+> hide #12/b cartoons
+> hide #!22.3 models
+> show #!22.2 models
+> show #12/c,d,e,f,g,h
+> show #12/c,d,e,f,g,h cartoons
+> hide #12/c,d,e,f,g,h
+> hide #!22.2 models
+> hide #12/c,d,e,f,g,h cartoons
+> show #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> show #12/j,k,l
+> hide #!12 models
+> show #!32 models
+> hide #!32 models
+> show #!12 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!22.2 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> hide #!22 models
+> hide #!32 models
+> show #!32 models
+> show #32/m,o
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> select #32/l
+atoms, 280 bonds, 1 pseudobond, 12 residues, 2 models selected
+> color sel khaki
+> color sel burly wood
+> color sel rosy brown
+> color sel midnight blue
+> color sel purple
+> color sel rebecca purple
+> color sel cornflower blue
+> color sel dodger blue
+> color sel peru
+> color sel dark goldenrod
+> color sel dark orange
+> color sel orange
+> color sel dark orange
+> color sel orange
+> color sel dark orange
+> select clear
+> show #!22.1 models
+> select add #22.7
+models selected
+> select subtract #22.7
+Nothing selected
+> select add #22.7
+models selected
+> color sel dark orange
+> select clear
+> hide #!22.1 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!13 models
+> hide #!13 models
+> hide #!11 models
+> show #!13 models
+> graphics silhouettes false
+> lighting simple
+> lighting soft
+> color zone #13 near #32 distance 10
+> hide #!13 models
+> show #!22.1 models
+> hide #!22 models
+> select #32/K:40@N1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> color sel indigo
+> color sel peru
+> color sel maroon
+> color sel hot pink
+> show #!22 models
+> view
+> select clear
+> hide #32/c,d,e,f,g,h,j, car
+> hide #32/c,d,e,f,g,h,j cartoons
+> hide #!22 models
+> show #!22 models
+> hide #!22.1 models
+> hide #!22.2 models
+> hide #!22.6 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #32/m,o
+> show #32/a:83,85
+> color #32/a byhetero
+> show #!11 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/chimera_session.cxs"
+——— End of log from Wed Apr 23 13:09:57 2025 ———
+opened ChimeraX session
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #!11 models
+> show #!11 models
+> ui tool show Distances
+> hide #!22 models
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /L DG 6 N2: 3.258Å
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.03
+[Repeated 2 time(s)]
+> distance style radius 0.02
+[Repeated 2 time(s)]
+> distance style radius 0.01
+[Repeated 2 time(s)]
+> distance style radius 0.02
+[Repeated 2 time(s)]
+> distance style radius 0.03
+[Repeated 2 time(s)]
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> distance style decimalPlaces 2
+[Repeated 2 time(s)]
+> distance style decimalPlaces 1
+[Repeated 2 time(s)]
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/K:41@O2
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/K:41@O2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /K DC 41 O2: 3.0Å
+> select #32/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #32/A:85@NZ
+atoms, 2 residues, 1 model selected
+> distance #32/A:83@OD1 #32/A:85@NZ
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
+OD1 and LYS 85 NZ: 2.9Å
+> select #32/K:40@N2
+atom, 1 residue, 1 model selected
+> select #32/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:83@OD1 #32/K:40@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
+OD1 and /K DG 40 N2: 3.0Å
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> select clear
+> select add #11
+pseudobonds, 2 models selected
+> color sel peru
+> color sel light salmon
+> color sel olive
+> color sel teal
+> select clear
+> close sel
+> delete sel
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> close #32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
+Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
+---
+Chain | Description
+A | No description available
+B | No description available
+C E | No description available
+D | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> style stick
+Changed 303202 atom styles
+> color #32/L dark orange
+> color #32/K dim gray
+> color #32/J dark red
+> color #32/I rebecca purple
+> color #32/B forest green
+> color #32/C,D,E,F,G,H salmon
+> color #32/A steel blue
+> color #32/A:232-350 dark turquoise
+> color #32/O blue
+> color #32/M red
+> color #32/k:40 hot pink
+> hide #32
+> show #32/k,l
+> show #32/a,b cartoons
+Computing secondary structure
+> color #32/a byhetero
+> show #32/a:83-85
+> select #32/A:83@OD1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:83@OD1 #32/K:40@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
+OD1 and /K DG 40 N2: 3.0Å
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/A:83@OD1
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/A:83@OD1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and ASP 83 OD1: 2.7Å
+> select #32/A:85@NZ
+atom, 1 residue, 1 model selected
+> select add #32/L:6@N2
+atoms, 2 residues, 1 model selected
+> distance #32/A:85@NZ #32/L:6@N2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /L DG 6 N2: 3.1Å
+> select #32/K:41@O2
+atom, 1 residue, 1 model selected
+> select add #32/A:85@NZ
+atoms, 2 residues, 1 model selected
+> distance #32/K:41@O2 #32/A:85@NZ
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DC
+O2 and /A LYS 85 NZ: 2.9Å
+> select add #11
+atoms, 17 pseudobonds, 2 residues, 3 models selected
+> color sel dark khaki
+> color sel teal
+> select clear
+> select #32/A:85
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel steel blue
+> color sel byhetero
+> select clear
+> select #32/K:41@O2
+atom, 1 residue, 1 model selected
+> color sel dim gray
+> select clear
+> select #32/L:7@C2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 20 bonds, 1 residue, 1 model selected
+> color sel hot pink
+> select clear
+> show #!22 models
+> hide #!22 models
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> show #11.1 models
+> hide #11.1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_nomap.tif" width 1984 height
+> 1210 supersample 3
+> show #!22 models
+> hide #!22 models
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
+> close #1-10
+> close #14-21
+> close #23-31
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
+> show #32 cartoons
+> hide #32/a
+> cartoon style nucleic xsection oval width 1 thickness 1
+> show #!22 models
+> show #!22.2 models
+> show #!22.6 models
+> show #!22.9 models
+> show #32/j
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout.tif" width 1984 height
+> 1210 supersample 3
+> hide #32/j,k,l cartoons
+> select clear
+> hide #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout_nomap.tif" width 1984
+> height 1210 supersample 3
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
+Chain information for halfcleaved_HNH_inwards_refined.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #1-2
+> hide #32/k:1-6
+> show #1-2 cartoons
+Computing secondary structure
+[Repeated 1 time(s)]
+> color #1,2/L dark orange
+> color #1,2/K dim gray
+> color #1,2/J dark red
+> color #1,2/I rebecca purple
+> color #1,2/B forest green
+> color #1,2/C,D,E,F,G,H salmon
+> color #1,2/A steel blue
+> color #1,2/A:232-350 dark turquoise
+> color #1,2/O blue
+> color #1,2/M red
+> cartoon style nucleic xsection oval width 1 thickness 1
+> hide #1-2 & nucleic cartoons
+> color #32/k dim gray
+> color #32/l dark orange
+> select clear
+> mmaker #1/a:150-200 to #32/a:150-200
+Computing secondary structure
+[Repeated 1 time(s)]  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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with halfcleaved_HNH_inwards_refined.pdb, chain A (#1), sequence alignment
+score = 253.2
+RMSD between 51 pruned atom pairs is 0.259 angstroms; (across all 51 pairs:
+.259)
+> mmaker #2/a:150-200 to #32/a:150-200
+Computing secondary structure
+[Repeated 1 time(s)]  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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with halfcleaved_HNH_outwards_refined.pdb, chain A (#2), sequence alignment
+score = 241.2
+RMSD between 51 pruned atom pairs is 0.283 angstroms; (across all 51 pairs:
+.283)
+> combine #1
+> combine #2
+> combine #32
+> morph #2 #32 #1 #5 #4
+Computed 201 frame morph #6
+> coordset #6 1,201
+> hide #!3 models
+> hide #!6 models
+> show #!6 models
+> show #6 & nucleic cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> nucleotides #!6 ladder
+> show #6 & nucleic
+> hide #!6 models
+> close #1-5
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
+Chain information for halfcleaved_HNH_inwards_refined.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #3
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> combine #32
+> hide #1-4
+> show #1-4 cartoons
+Computing secondary structure
+[Repeated 2 time(s)]
+> color #1-4/L dark orange
+> color #1-4/K dim gray
+> color #1-4/J dark red
+> color #1-4/I rebecca purple
+> color #1-4/B forest green
+> color #1-4/C,D,E,F,G,H salmon
+> color #1-4/A steel blue
+> color #1-4/A:232-350 dark turquoise
+> color #1-4/O blue
+> color #1-4/M red
+> hide #!4 models
+> hide #!3 models
+> hide #!2 models
+> hide #!1 models
+> morph #1 #3 #4 #32 #2
+Computed 201 frame morph #5
+> coordset #5 1,201
+> close #5
+> morph #1 #32 #2 #4 #3
+Computed 201 frame morph #5
+> coordset #5 1,201
+> hide #5/k:1-6
+> hide #5/k:1-6 cartoons
+> show #5 & nucleic
+> style stick
+Changed 192721 atom styles
+> nucleotides #!5 ladder
+> cartoon style nucleic xsection oval width 1 thickness 1
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> movie record
+> movie encode /Users/zxc755/Desktop/movie1.mp4 framerate 25.0
+Movie saved to /Users/zxc755/Desktop/movie1.mp4
+> hide #!5 models
+> show #!32 models
+> show #!22 models
+> show #32/k
+> hide #!22 models
+> select #32/K:2@O5'
+atom, 1 residue, 1 model selected
+> select add #32/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C2'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C3'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select #32/K:2@C5'
+atom, 1 residue, 1 model selected
+> hide sel
+> show #32/m,o
+> select clear
+> show #32/a:280,305,304
+> select #32/K:3@P
+atom, 1 residue, 1 model selected
+> select add #32/K:2@O3'
+atoms, 2 residues, 1 model selected
+> select add #32/K:3@OP1
+atoms, 2 residues, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> select add #32/K:3@O5'
+atoms, 2 residues, 1 model selected
+> color sel byhetero
+> select clear
+> hide #32.1 models
+> select #32/A:328
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> select #32/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #32/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #32/A:304@ND1 #32/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
+ND1 and /M MG 2 MG: 2.3Å
+> select #32/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #32/M:2@MG
+atoms, 2 residues, 1 model selected
+> distance #32/A:328@NE2 #32/M:2@MG
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
+NE2 and /M MG 2 MG: 1.8Å
+> hide #11.1 models
+> select #32/O:1@O
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #32/O:1@O #32/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/O HOH
+O and /K DA 3 OP2: 2.9Å
+> select #32/A:280@NH2
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance #32/A:280@NH2 #32/K:3@OP2
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ARG
+NH2 and /K DA 3 OP2: 2.7Å
+> select #32/A:308
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #32/A:309
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel
+> hide sel cartoons
+> select #32/A:309@N
+atom, 1 residue, 1 model selected
+> select add #32/O:1@O
+atoms, 2 residues, 1 model selected
+> distance #32/A:309@N #32/O:1@O
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LEU
+N and /O HOH 1 O: 3.0Å
+> select #32/A:309@CA
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> hide sel
+> select #32/M:2@MG
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/M:2@MG #32/K:3@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/M MG 2
+MG and /K DA 3 OP1: 2.5Å
+> color #11 teal
+> select clear
+> select #32/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> distance sel
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
+ND1 and /K DA 3 OP2: 2.9Å
+> color #11 teal
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 3
+[Repeated 2 time(s)]
+> distance style dashes 2
+[Repeated 2 time(s)]
+> distance style dashes 1
+[Repeated 2 time(s)]
+> distance style dashes 2
+[Repeated 2 time(s)]
+> distance style dashes 3
+[Repeated 2 time(s)]
+> distance style dashes 4
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style dashes 6
+[Repeated 2 time(s)]
+> distance style dashes 7
+[Repeated 2 time(s)]
+> distance style dashes 8
+[Repeated 2 time(s)]
+> distance style dashes 7
+[Repeated 2 time(s)]
+> distance style dashes 8
+[Repeated 2 time(s)]
+> distance style dashes 7
+[Repeated 2 time(s)]
+> distance style dashes 6
+[Repeated 2 time(s)]
+> distance style dashes 5
+[Repeated 2 time(s)]
+> select clear
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #32/a:319
+> show #!22 models
+> hide #!22 models
+> select #32/A:320
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #32/A:320
+atoms, 7 bonds, 1 residue, 1 model selected
+> select clear
+> ~distance #12/A:85@NZ #12/A:83@OD1
+> ~distance #12/K:3@OP2 #12/A:305@ND1
+> ~distance #12/M:2@MG #12/A:304@ND1
+> ~distance #12/K:40@N2 #12/A:83@OD1
+> ~distance #12/A:85@NZ #12/K:41@O2
+> ~distance #12/A:193@OD1 #12/L:9@N2
+> ~distance #12/A:280@NH2 #12/K:3@OP2
+> ~distance #12/A:85@NZ #12/L:6@N2
+> ~distance #12/A:191@OG #12/K:39@OP1
+> ~distance #12/A:328@NE2 #12/M:2@MG
+> ~distance #12/A:309@N #12/O:1@O
+> ~distance #12/K:3@OP1 #12/M:2@MG
+> ~distance #12/O:1@O #12/K:3@OP2
+> select #32/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 24845 bonds, 12 pseudobonds, 2799 residues, 3 models selected
+> select clear
+> select #32/A:305@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:3@OP2
+atoms, 2 residues, 1 model selected
+> ~distance sel
+> select #32/K:3@O5'
+atom, 1 residue, 1 model selected
+> select add #32/A:305@ND1
+atoms, 2 residues, 1 model selected
+> distance sel
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DA 3
+O5' and /A HIS 305 ND1: 2.9Å
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> color #11 teal
+> select clear
+> hide #32 cartoons
+> hide #32/j
+> show #32/a cartoons
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_nomap.tif" width 1984
+> height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs"
+> show #32 cartoons
+> hide #32/k:1-6 cartoons
+> select #32/J:48
+atoms, 25 bonds, 1 residue, 1 model selected
+> show #32/j
+> show #32/k:6 cartoons
+> select clear
+> hide #!11 models
+> hide #32/a
+> hide #32/m,o
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_zoomout_nomap.tif" width
+> 1984 height 1210 supersample 3
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> surface dust #13 size 10
+> hide #!32 models
+> lighting soft
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> view
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting soft
+> lighting flat
+> lighting soft
+> set bgColor gray
+> set bgColor white
+> view #13
+> show #!32 models
+> hide #!13 models
+> hide #!32 models
+> show #!12 models
+> color #12/L dark orange
+> color #12/K dim gray
+> color #12/J dark red
+> color #12/I rebecca purple
+> color #12/B forest green
+> color #12/C,D,E,F,G,H salmon
+> color #12/A steel blue
+> color #12/A:232-350 dark turquoise
+> color #12/O dark turquoise
+> color #12/M dark turquoise
+> color #12/k:1-3 dark turquoise
+> hide #!12 models
+> show #!13 models
+> color zone #13 near #12 distance 10
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> volume #13 level 0.05
+> volume #13 change image level 0.0001303,0 level 0.002946,0.8 level 1.983,1
+> volume #13 level 0.09
+> volume #13 level 0.06
+> volume #13 level 0.05
+> volume #13 level 0.03
+> turn x 90
+[Repeated 3 time(s)]
+> hide #!13 models
+> show #!32 models
+> hide #!32 models
+> show #!22 models
+> lighting soft
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting soft
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> show #!32 models
+> graphics silhouettes true
+> lighting flat
+> hide #!32 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript
+> save "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"
+——— End of log from Fri Apr 25 19:29:02 2025 ———
+opened ChimeraX session
+> hide #!32 models
+> show #!32 models
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #!32 models
+> show #!1 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> show #!32 models
+> hide #1,2,32 cartoons
+> hide #1,2,32
+> show #1,2,32/a
+> show #1,2,32/a cartoons
+> hide #1,2,32
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_fullTS_sharp.mrc"
+Opened halfcleaved_HNH_center_fullTS_sharp.mrc as #7, grid size 420,420,420,
+pixel 0.725, shown at level 0.00325, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_sharp.mrc"
+Opened halfcleaved_HNH_center_main_map_sharp.mrc as #8, grid size 420,420,420,
+pixel 0.725, shown at level 0.00305, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_in_sharp.mrc"
+Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725,
+shown at level 0.00277, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_out_sharp.mrc"
+Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+> close #7,8
+> hide #!2 models
+> hide #!1 models
+> color zone #9 near #2 distance 10
+> color zone #10 near #1 distance 10
+> ui tool show "Color Zone"
+> volume splitbyzone #9
+Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel
+.725, shown at level 0.00277, step 1, values float32
+> volume splitbyzone #10
+Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 1, values float32
+> hide #!7.1 models
+> show #!7.1 models
+> hide #!7.1 models
+> hide #!7.4 models
+> hide #!7.5 models
+> hide #!7.6 models
+> hide #!7.7 models
+> hide #!7.8 models
+> hide #!7.9 models
+> hide #!8.1 models
+> hide #!8.4 models
+> hide #!8.5 models
+> hide #!8.6 models
+> hide #!8.7 models
+> hide #!8.8 models
+> hide #!8.9 models
+> hide #!8 models
+> show #!2 models
+> transparency #7,8 90
+> volume dus #7,8 siz 10
+Expected a density maps specifier or a keyword
+> surface dust #7.2 size 7.25
+> surface dust #7.3 size 7.25
+> surface dust #8 size 10
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> hide #!7 models
+> show #!7 models
+> volume #7.2 level 0.002
+> volume #7 level 0.002
+> volume #8 level 0.002
+> hide #!2 models
+> hide #!7 models
+> show #!8 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!32 models
+> show #!7 models
+> show #!2 models
+> hide #!1 models
+> hide #!8 models
+> surface dust #7 size 10
+> show #!1 models
+> hide #!2 models
+> show #!8 models
+> hide #!7 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out.tif" width
+> 1984 height 1210 supersample 3 transparentBackground true
+> show #!2 models
+> hide #!1 models
+> show #!7 models
+> hide #!8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in.tif" width
+> 1984 height 1210 supersample 3
+> hide #!2 models
+> hide #!7 models
+> show #!22 models
+> show #!32 models
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.6 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.9 models
+> hide #!22.10 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent.tif" width
+> 1984 height 1210 supersample 3
+> hide #!32 models
+> hide #!22.5 models
+> show #!22.5 models
+> hide #!22 models
+> show #!7 models
+> show #!8 models
+> hide #!7 models
+> show #!7 models
+> hide #!8 models
+> show #!7.4 models
+> show #!7.5 models
+> show #!7.6 models
+> show #!7.7 models
+> show #!7.8 models
+> show #!7.9 models
+> hide #!7.9 models
+> show #!7.9 models
+> hide #!7.4 models
+> hide #!7.5 models
+> hide #!7.6 models
+> hide #!7.7 models
+> hide #!7.8 models
+> hide #!7.9 models
+> show #!2 models
+> show #!1 models
+> show #!8 models
+> hide #!7 models
+> hide #!2 models
+> hide #!1 models
+> hide #!8 models
+> show #!22 models
+> show #!32 models
+> hide #!32 models
+> hide #!22 models
+> show #!7 models
+> show #!8 models
+> hide #!7 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out_2.tif" width
+> 1984 height 1210 supersample 3
+> hide #!8 models
+> show #!7 models
+> show #!2 models
+> hide #!1 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in_2.tif" width
+> 1984 height 1210 supersample 3
+> hide #!2 models
+> hide #!7 models
+> show #!22 models
+> show #!32 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent_2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!32 models
+> hide #!22 models
+> show #!22 models
+> show #!32 models
+> hide #!32 models
+> hide #!22 models
+> show #!1 models
+> show #!2 models
+> hide #!2 models
+> hide #!1 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_center_refined.pdb"
+Chain information for apo_HNH_center_refined.pdb #14
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_inwards_refined.pdb"
+Chain information for apo_HNH_inwards_refined.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+F G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ILE a 6 ALA a 9 1 4
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 SER a 30 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 THR a 44 1
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 VAL a 93 1
+messages similar to the above omitted
+Chain information for apo_HNH_outwards_refined.pdb #16
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F G | No description available
+H | No description available
+I | No description available
+J | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_cent_sharp.mrc"
+Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_in_sharp.mrc"
+Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown
+at level 0.00173, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_out_sharp.mrc"
+Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown
+at level 0.00214, step 2, values float32
+> hide #!19 models
+> hide #!18 models
+> hide #!17 models
+> color ##14/L dark orange;col ##14/K dim gray;col ##14/J dark red;col ##14/I
+> rebecca purple;col ##14/B forest green;col ##14/C,D,E,F,G,H salmon;col
+> ##14/A steel blue;col ##14/A:232-350 dark turquoise; col ##14/O blue; col
+> ##14/M red
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #14/L dark orange
+> color #14/K dim gray
+> color #14/J dark red
+> color #14/I rebecca purple
+> color #14/B forest green
+> color #14/C,D,E,F,G,H salmon
+> color #14/A steel blue
+> color #14/A:232-350 dark turquoise
+> color #14/O blue
+> color #14/M red
+> color #15/L dark orange
+> color #15/K dim gray
+> color #15/J dark red
+> color #15/I rebecca purple
+> color #15/B forest green
+> color #15/C,D,E,F,G,H salmon
+> color #15/A steel blue
+> color #15/A:232-350 dark turquoise
+> color #15/O blue
+> color #15/M red
+> color #16/L dark orange
+> color #16/K dim gray
+> color #16/J dark red
+> color #16/I rebecca purple
+> color #16/B forest green
+> color #16/C,D,E,F,G,H salmon
+> color #16/A steel blue
+> color #16/A:232-350 dark turquoise
+> color #16/O blue
+> color #16/M red
+> color zone #17 near #14 distance 10
+> color zone #18 near #15 distance 10
+> color zone #19 near #16 distance 10
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> hide #!15 models
+> hide #!14 models
+> show #!17 models
+> show #!18 models
+> show #!19 models
+> hide #!19 models
+> hide #!18 models
+> hide #!17 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #20
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_refined.pdb"
+Chain information for postcleavage_HNH_inwards_refined.pdb #21
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_outwards.pdb"
+Chain information for postcleavage_HNH_outwards.pdb #23
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_in_sharp.mrc"
+Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown
+at level 0.0257, step 2, values float32
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_out_sharp.mrc"
+Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 2, values float32
+> hide #!20 models
+> hide #!21 models
+> hide #!23 models
+> color #20/L dark orange
+> color #20/K dim gray
+> color #20/J dark red
+> color #20/I rebecca purple
+> color #20/B forest green
+> color #20/C,D,E,F,G,H salmon
+> color #20/A steel blue
+> color #20/A:232-350 dark turquoise
+> color #20/O blue
+> color #20/M red
+> color #21/L dark orange
+> color #21/K dim gray
+> color #21/J dark red
+> color #21/I rebecca purple
+> color #21/B forest green
+> color #21/C,D,E,F,G,H salmon
+> color #21/A steel blue
+> color #21/A:232-350 dark turquoise
+> color #21/O blue
+> color #21/M red
+> color #23/L dark orange
+> color #23/K dim gray
+> color #23/J dark red
+> color #23/I rebecca purple
+> color #23/B forest green
+> color #23/C,D,E,F,G,H salmon
+> color #23/A steel blue
+> color #23/A:232-350 dark turquoise
+> color #23/O blue
+> color #23/M red
+> color zone #24 near #20 distance 10
+> color zone #25 near #21 distance 10
+> color zone #26 near #23 distance 10
+> hide #!26 models
+> hide #!25 models
+> hide #!24 models
+> show #!17 models
+> hide #!17 models
+> volume splitbyzone #17
+Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 6 as #27.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+> hide #!27.1 models
+> hide #!27.4 models
+> hide #!27.5 models
+> hide #!27.6 models
+> hide #!27.7 models
+> volume splitbyzone #18
+Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 6 as #28.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+> hide #!28.1 models
+> hide #!28.4 models
+> hide #!28.5 models
+> hide #!28.6 models
+> hide #!28.7 models
+> volume splitbyzone #19
+Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 6 as #29.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+> hide #!29.1 models
+> hide #!29.4 models
+> show #!29.4 models
+> hide #!29.4 models
+> hide #!29.5 models
+> hide #!29.6 models
+> hide #!29.7 models
+> hide #!27 models
+> hide #!28 models
+> hide #!29 models
+> volume splitbyzone #24
+Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 8 as #30.9, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+> volume splitbyzone #25
+Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 8 as #31.9, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+> volume splitbyzone #26
+Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 8 as #33.9, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+> hide #!30.1 models
+> hide #!30.4 models
+> hide #!30.5 models
+> hide #!30.6 models
+> hide #!30.7 models
+> hide #!30.8 models
+> hide #!30.9 models
+> hide #!31.1 models
+> hide #!31.4 models
+> hide #!31.5 models
+> hide #!31.6 models
+> hide #!31.7 models
+> hide #!31.8 models
+> hide #!31.9 models
+> hide #!33.1 models
+> hide #!33.4 models
+> hide #!33.5 models
+> hide #!33.6 models
+> hide #!33.7 models
+> hide #!33.8 models
+> hide #!33.9 models
+> show #!32 models
+> hide #!32 models
+> show #!22 models
+> hide #!22 models
+> show #!29 models
+> show #!28 models
+> show #!27 models
+> transparency 90
+> surface dust siz 10
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #27-31 #33 size 10
+> hide #!33 models
+> hide #!31 models
+> hide #!30 models
+> hide #!29 models
+> hide #!28 models
+Must specify one map, got 10
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 53530 points
+correlation = 0, correlation about mean = 0, overlap = 0
+steps = 24, shift = 0, angle = 0 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.00000000 0.00000000 0.00000000 0.00000000
+.00000000 1.00000000 0.00000000 0.00000000
+.00000000 0.00000000 1.00000000 0.00000000
+Axis 0.00000000 0.00000000 1.00000000
+Axis point 0.00000000 0.00000000 0.00000000
+Rotation angle (degrees) 0.00000000
+Shift along axis 0.00000000
+> hide #!27.2 models
+> show #!27.2 models
+> hide #!27.2 models
+> show #!27.2 models
+> show #!22 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!27.2 models
+> show #!27.2 models
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 53530 points
+correlation = 0, correlation about mean = 0, overlap = 0
+steps = 24, shift = 0, angle = 0 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.00000000 0.00000000 0.00000000 0.00000000
+.00000000 1.00000000 0.00000000 0.00000000
+.00000000 0.00000000 1.00000000 0.00000000
+Axis 0.00000000 0.00000000 1.00000000
+Axis point 0.00000000 0.00000000 0.00000000
+Rotation angle (degrees) 0.00000000
+Shift along axis 0.00000000
+> select #27.2
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #27.2,-0.90481,-0.32416,-0.27613,332.21,0.31284,-0.94596,0.085389,229.16,-0.28888,-0.0091226,0.95732,44.701
+> view matrix models
+> #27.2,-0.97923,-0.19279,0.06285,325.19,0.18122,-0.97109,-0.15536,293.34,0.090985,-0.14075,0.98586,0.54729
+> undo
+[Repeated 2 time(s)]
+> close #27-31
+> close #33
+> color #14-16/a steel blue
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> show #!15 models
+> hide #!15 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> color #20,21,23/a steel blue
+> color zone #17 near #14 distance 10
+> color zone #18 near #15 distance 10
+> color zone #19 near #16 distance 10
+> color #24 nea #20 dis 10
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color zone #24 near #20 distance 10
+> color zone #25 near #21 distance 10
+> color zone #26 near #23 distance 10
+> volume splitbyzone #17
+Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00199, step 1, values float32
+> volume splitbyzone #18
+Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00173, step 1, values float32
+> volume splitbyzone #19
+Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00214, step 1, values float32
+> volume splitbyzone #24
+Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 1, values float32
+> volume splitbyzone #25
+Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.0257, step 1, values float32
+> volume splitbyzone #26
+Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
+shown at level 0.00342, step 1, values float32
+> hide #!33 models
+> hide #!33.1 models
+> hide #!33.3 models
+> show #!33 models
+> hide #!33.4 models
+> hide #!33.5 models
+> hide #!33.6 models
+> hide #!33.7 models
+> hide #!33.8 models
+> hide #!31.8 models
+> hide #!31.7 models
+> hide #!31.6 models
+> hide #!31.5 models
+> hide #!31.4 models
+> hide #!31.3 models
+> hide #!31.1 models
+> hide #!30.8 models
+> hide #!30.7 models
+> hide #!30.6 models
+> hide #!30.5 models
+> hide #!30.4 models
+> hide #!30.3 models
+> hide #!30.1 models
+> hide #!29.6 models
+> hide #!29.5 models
+> hide #!29.4 models
+> hide #!29.3 models
+> hide #!29.1 models
+> hide #!28.6 models
+> hide #!28.5 models
+> hide #!28.4 models
+> hide #!28.3 models
+> hide #!28.1 models
+> hide #!27.6 models
+> hide #!27.5 models
+> hide #!27.4 models
+> hide #!27.3 models
+> hide #!27.1 models
+> hide #!22 models
+> transparency #27-31,33 90
+> show #!22 models
+> hide #!28 models
+> hide #!29 models
+> hide #!30 models
+> hide #!31 models
+> hide #!33 models
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 82885 points
+correlation = 0, correlation about mean = 0, overlap = 0
+steps = 24, shift = 0, angle = 0 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.00000000 0.00000000 0.00000000 0.00000000
+.00000000 1.00000000 0.00000000 0.00000000
+.00000000 0.00000000 1.00000000 0.00000000
+Axis 0.00000000 0.00000000 1.00000000
+Axis point 0.00000000 0.00000000 0.00000000
+Rotation angle (degrees) 0.00000000
+Shift along axis 0.00000000
+> select #27.2
+models selected
+> select add #27
+models selected
+> view matrix models
+> #27,-0.9851,0.028378,0.1696,261.6,0.012815,-0.97143,0.23698,244.5,0.17148,0.23562,0.9566,-52.331
+Drag select of 27.2 apo_HNH_cent_sharp.mrc 1
+> view matrix models
+> #27.2,1,4.8572e-17,6.1062e-16,-14.27,8.32e-32,1,4.1633e-16,-23.71,3.8858e-16,1.6653e-16,1,-1.3138
+> view matrix models
+> #27.2,1,4.8572e-17,6.1062e-16,10.218,8.32e-32,1,4.1633e-16,-19.262,3.8858e-16,1.6653e-16,1,-23.993
+> color #27.2 red
+> view matrix models
+> #27.2,1,0.0011286,0.00024256,-17.671,-0.0011282,1,-0.001653,-23.156,-0.00024442,0.0016527,1,0.99344
+> view matrix models
+> #27.2,0.98647,0.15904,0.039716,-44.71,-0.15822,0.86043,0.48439,-45.115,0.042865,-0.48412,0.87395,80.037
+> surface dust #27-31,33 size 10
+> hide #!27 models
+> select add #27
+models selected
+> select subtract #27
+Nothing selected
+> hide #!22 models
+> show #!22 models
+> show #!30 models
+> select add #30
+models selected
+> color #30.2 green
+> view matrix models
+> #30,0.99278,0.11969,0.0075487,-17.819,-0.11662,0.97821,-0.17177,45.003,-0.027942,0.16965,0.98511,-26.609
+> select subtract #30
+Nothing selected
+> hide #!30 models
+> hide #!22 models
+> show #!2 models
+> hide #!2 models
+> show #!7 models
+> show #!28 models
+> color #28.2 red
+> color #29.2 red
+> color #31.2 green
+> color #33.2 green
+> select add #28
+models selected
+> view matrix models
+> #28,-0.93864,-0.18774,0.28933,282.81,0.11817,-0.96316,-0.24158,292.86,0.32402,-0.19257,0.92624,-7.1144
+> view matrix models
+> #28,-0.93864,-0.18774,0.28933,281.83,0.11817,-0.96316,-0.24158,308.33,0.32402,-0.19257,0.92624,-20.3
+> view matrix models
+> #28,-0.94765,-0.24867,0.20033,309.6,0.18207,-0.93615,-0.30078,306.85,0.26233,-0.24856,0.93242,-0.83323
+> view matrix models
+> #28,-0.95707,-0.19669,0.2129,302.83,0.13597,-0.95335,-0.26952,311.55,0.25597,-0.229,0.93917,-4.0077
+> view matrix models
+> #28,-0.95956,-0.22645,0.1672,313.45,0.18549,-0.95546,-0.22952,299.35,0.21173,-0.18923,0.95883,-5.8084
+> view matrix models
+> #28,-0.95956,-0.22645,0.1672,313,0.18549,-0.95546,-0.22952,299.82,0.21173,-0.18923,0.95883,-5.8642
+> view matrix models
+> #28,-0.94956,-0.28011,0.14095,322.64,0.23523,-0.93354,-0.2705,294.86,0.20736,-0.2237,0.95235,0.5275
+> select subtract #28
+Nothing selected
+> hide #!28 models
+> show #!31 models
+> select add #31
+models selected
+> view matrix models
+> #31,0.95745,0.28853,-0.0061963,-39.992,-0.2858,0.94498,-0.15916,77.745,-0.040066,0.15415,0.98723,-22.047
+> view matrix models
+> #31,0.98495,0.16362,0.055651,-31.707,-0.14812,0.9651,-0.21598,59.788,-0.089048,0.20449,0.97481,-20.953
+> view matrix models
+> #31,0.98502,0.15503,0.075475,-31.759,-0.13914,0.9732,-0.18309,50.935,-0.10184,0.16984,0.98019,-13.582
+> view matrix models
+> #31,0.98251,0.17881,0.052001,-31.724,-0.16394,0.96301,-0.21385,60.765,-0.088316,0.20159,0.97548,-20.561
+> view matrix models
+> #31,0.98782,0.1293,0.086525,-28.788,-0.10934,0.97261,-0.20513,49.258,-0.11068,0.19317,0.9749,-15.438
+> select subtract #31
+Nothing selected
+> hide #!31 models
+> hide #!7 models
+> show #!8 models
+> show #!29 models
+> select add #29
+models selected
+> view matrix models
+> #29,-0.96301,-0.11026,0.24587,268.61,0.020435,-0.93971,-0.34137,320.74,0.26869,-0.32372,0.9072,1.2682
+> view matrix models
+> #29,-0.92586,-0.36935,0.079794,337.56,0.33423,-0.89898,-0.28307,279.15,0.17629,-0.23541,0.95577,1.8338
+> view matrix models
+> #29,-0.9501,-0.28304,0.13113,324.32,0.24497,-0.93725,-0.24809,292.2,0.19312,-0.20359,0.95982,-2.6028
+> view matrix models
+> #29,-0.94885,-0.296,0.10988,328.51,0.25817,-0.9277,-0.26968,291.73,0.18176,-0.22752,0.95666,1.6234
+> view matrix models
+> #29,-0.95084,-0.25098,0.18144,313.28,0.21054,-0.95351,-0.21564,295.36,0.22712,-0.16684,0.95947,-11.512
+> view matrix models
+> #29,-0.94437,-0.26912,0.18906,314.35,0.22158,-0.94541,-0.23894,296.14,0.24304,-0.18376,0.95245,-10.94
+> hide #!29 models
+> select subtract #29
+Nothing selected
+> show #!33 models
+> select add #33
+models selected
+> view matrix models
+> #33,0.95382,0.29041,-0.076702,-29.712,-0.30037,0.92263,-0.24193,98.778,0.0005105,0.25379,0.96726,-42.939
+> view matrix models
+> #33,0.96865,0.24664,-0.029782,-31.412,-0.24842,0.96286,-0.10577,62.659,0.0025886,0.10985,0.99394,-24.767
+> view matrix models
+> #33,0.9728,0.17623,-0.15036,-2.5415,-0.20302,0.96116,-0.18696,65.208,0.11158,0.2124,0.97079,-60.099
+> view matrix models
+> #33,0.98074,0.15825,0.11447,-37.799,-0.13348,0.97094,-0.19866,54.576,-0.14258,0.17955,0.97336,-11.971
+> view matrix models
+> #33,0.98222,0.15787,0.10163,-34.87,-0.13329,0.96753,-0.21473,54.252,-0.13223,0.19737,0.97137,-14.291
+> view matrix models
+> #33,0.98222,0.15787,0.10163,-35.019,-0.13329,0.96753,-0.21473,54.238,-0.13223,0.19737,0.97137,-13.879
+> fitmap #33.2 inMap #8.4
+Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 3 using
+points
+correlation = 0.2302, correlation about mean = 0.1069, overlap = 657.4
+steps = 364, shift = 12.6, angle = 27.8 degrees
+Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
+halfcleaved_HNH_out_sharp.mrc 3 (#8.4) coordinates:
+Matrix rotation and translation
+.88487665 -0.11856540 -0.45048370 86.96048472
+.12698700 0.99183644 -0.01160897 -10.81407486
+.44818257 -0.04693306 0.89270917 -57.31875206
+Axis -0.03789003 -0.96394524 0.26338929
+Axis point 159.50208814 0.00000000 151.60629729
+Rotation angle (degrees) 27.78400581
+Shift along axis -7.96790445
+> fitmap #33.2 inMap #8.2
+Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
+points
+correlation = 0.7507, correlation about mean = 0.6577, overlap = 3498
+steps = 300, shift = 13.1, angle = 25.8 degrees
+Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
+halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
+Matrix rotation and translation
+.99883251 0.02105205 -0.04347916 3.28381267
+-0.01860045 0.99825524 0.05604021 -3.01589348
+.04458306 -0.05516605 0.99748136 2.36658331
+Axis -0.75501980 -0.59788649 -0.26921525
+Axis point 0.00000000 33.34610426 68.86626768
+Rotation angle (degrees) 4.22334809
+Shift along axis -1.31330194
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!33 models
+> show #!29 models
+> fitmap #29.2 inMap #8.2
+Fit map apo_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
+points
+correlation = 0.6154, correlation about mean = 0.4909, overlap = 1988
+steps = 108, shift = 0.371, angle = 3.89 degrees
+Position of apo_HNH_out_sharp.mrc 1 (#29.2) relative to
+halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
+Matrix rotation and translation
+.99774720 -0.00616969 0.06680170 -7.75363432
+.00547813 0.99992955 0.01053061 -2.15873626
+-0.06686197 -0.01014094 0.99771070 11.37852778
+Axis -0.15227290 0.98460707 0.08580135
+Axis point 165.97569556 0.00000000 121.59503582
+Rotation angle (degrees) 3.89203832
+Shift along axis 0.03145444
+> select subtract #33
+Nothing selected
+> hide #!29 models
+> hide #!8 models
+> show #!7 models
+> show #!28 models
+> fitmap #28.2 inMap #7.2
+Fit map apo_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
+points
+correlation = 0.6568, correlation about mean = 0.5566, overlap = 1483
+steps = 100, shift = 1.93, angle = 2.75 degrees
+Position of apo_HNH_in_sharp.mrc 1 (#28.2) relative to
+halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
+Matrix rotation and translation
+.99894275 -0.01608144 0.04306693 -3.27929226
+.01666443 0.99977384 -0.01321212 -2.52037376
+-0.04284472 0.01391584 0.99898482 4.13599960
+Axis 0.28299722 0.89622541 0.34160298
+Axis point 109.08725783 0.00000000 67.16502763
+Rotation angle (degrees) 2.74722295
+Shift along axis -1.77398382
+> hide #!28 models
+> show #!31 models
+> fitmap #31.2 inMap #7.2
+Fit map post_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
+points
+correlation = 0.5948, correlation about mean = 0.441, overlap = 2814
+steps = 152, shift = 1.12, angle = 4.52 degrees
+Position of post_HNH_in_sharp.mrc 1 (#31.2) relative to
+halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
+Matrix rotation and translation
+.99726035 0.04676217 -0.05731570 1.19747961
+-0.04518981 0.99857380 0.02842974 4.02672915
+.05856339 -0.02576177 0.99795123 -4.59092844
+Axis -0.34397877 -0.73553868 -0.58366211
+Axis point 85.75257186 0.00000000 12.62773521
+Rotation angle (degrees) 4.51795970
+Shift along axis -0.69417165
+> hide #!31 models
+> show #!22 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!7 models
+> show #!30 models
+> fitmap #30.2 inMap #22.4
+Fit map post_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 86342 points
+correlation = 0.7861, correlation about mean = 0.6973, overlap = 3404
+steps = 84, shift = 0.298, angle = 2.98 degrees
+Position of post_HNH_cent_sharp.mrc 1 (#30.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.99880892 0.03024374 0.03828920 -9.33094617
+-0.03093378 0.99936719 0.01755928 3.13913491
+-0.03773391 -0.01872279 0.99911241 9.35512683
+Axis -0.34850229 0.73022926 -0.58763201
+Axis point 242.75204382 0.00000000 250.82225024
+Rotation angle (degrees) 2.98383902
+Shift along axis 0.04677237
+> hide #!30 models
+> show #!27 models
+> fitmap #27.2 inMap #22.4
+Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
+using 82885 points
+correlation = 0.608, correlation about mean = 0.4719, overlap = 1708
+steps = 124, shift = 1.2, angle = 3.81 degrees
+Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
+halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
+Matrix rotation and translation
+.97832698 0.19020262 0.08184916 -54.13025495
+-0.20662179 0.87084737 0.44601826 -34.04774174
+.01355572 -0.45326352 0.89127348 78.28203288
+Axis -0.91268658 0.06931143 -0.40273953
+Axis point 0.00000000 156.71923356 124.12929737
+Rotation angle (degrees) 29.51532960
+Shift along axis 15.51679105
+> show #!14 models
+> style stick
+Changed 332211 atom styles
+> hide #14
+> show #14/a cartoons
+Computing secondary structure
+> color #14/a red
+> fitmap #14/a inMap #27.2
+Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
+(#27.2) using 2728 atoms
+average map value = 0.0141, steps = 2000
+shifted from previous position = 21.7
+rotated from previous position = 19 degrees
+atoms outside contour = 2485, contour level = 0.0019908
+Position of apo_HNH_center_refined.pdb (#14) relative to
+apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
+Matrix rotation and translation
+.87515076 -0.42346707 0.23406577 55.94220375
+.48348878 0.74666401 -0.45687137 70.79007602
+.01870149 0.51299950 0.85818516 -55.77887122
+Axis 0.72097898 0.16009669 0.67420944
+Axis point 0.00000000 146.26043027 68.91682292
+Rotation angle (degrees) 42.26858727
+Shift along axis 14.05976817
+> select #14/A:169
+atoms, 7 bonds, 1 residue, 1 model selected
+> view matrix models
+> #14,-0.60187,-0.59648,-0.531,396.65,0.776,-0.27978,-0.56529,167.42,0.18862,-0.75229,0.63126,115.81
+> fitmap #14/a inMap #27.2
+Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
+(#27.2) using 2728 atoms
+average map value = 0.04066, steps = 124
+shifted from previous position = 2.25
+rotated from previous position = 10.1 degrees
+atoms outside contour = 1852, contour level = 0.0019908
+Position of apo_HNH_center_refined.pdb (#14) relative to
+apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
+Matrix rotation and translation
+-0.82083116 -0.46116689 -0.33698869 392.52408221
+.45571980 -0.17311548 -0.87312688 269.72015669
+.34431924 -0.87026214 0.35226145 171.58912907
+Axis 0.00250785 -0.59643049 0.80266081
+Axis point 145.87352872 275.32026651 0.00000000
+Rotation angle (degrees) 145.16922813
+Shift along axis -22.15706392
+> view matrix models
+> #14,-0.91976,-0.13361,0.36905,259.57,0.12723,-0.991,-0.041693,295.14,0.3713,0.0086066,0.92847,-56.6
+> view matrix models
+> #14,-0.94601,-0.32105,-0.044503,348.25,0.30157,-0.82153,-0.48389,302.66,0.1188,-0.47119,0.874,58.735
+> fitmap #14/a inMap #27.2
+Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
+(#27.2) using 2728 atoms
+average map value = 0.1677, steps = 128
+shifted from previous position = 5.27
+rotated from previous position = 18.3 degrees
+atoms outside contour = 544, contour level = 0.0019908
+Position of apo_HNH_center_refined.pdb (#14) relative to
+apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
+Matrix rotation and translation
+-0.98941113 -0.04220312 0.13886890 304.43360331
+-0.05300114 -0.78565708 -0.61638777 392.25034981
+.13511682 -0.61722111 0.77510102 112.81565364
+Axis -0.07270707 0.32735899 -0.94209860
+Axis point 148.46002111 215.26270714 0.00000000
+Rotation angle (degrees) 179.67164584
+Shift along axis -0.01126639
+> select clear
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> hide #!27 models
+> show #!30 models
+> show #!20 models
+> hide #20
+> show #20/a
+> color #20/a green
+> hide #20
+> show #20/a cartoons
+Computing secondary structure
+> fitmap #20/a inMap #30.2
+Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
+post_HNH_cent_sharp.mrc 1 (#30.2) using 2728 atoms
+average map value = 0.2822, steps = 108
+shifted from previous position = 5.73
+rotated from previous position = 12.7 degrees
+atoms outside contour = 221, contour level = 0.0032808
+Position of postcleavage_HNH_center_refined.pdb (#20) relative to
+post_HNH_cent_sharp.mrc 1 (#30.2) coordinates:
+Matrix rotation and translation
+.99338756 0.11381514 0.01507534 -17.65419683
+-0.10945975 0.97851549 -0.17471692 44.27616892
+-0.03463688 0.17191148 0.98450329 -25.68733743
+Axis 0.83464546 0.11970190 -0.53762293
+Axis point 0.00000000 156.57774257 231.16518944
+Rotation angle (degrees) 11.98467665
+Shift along axis 4.37504802
+> show #!32 models
+> show #!14 models
+> show #!17 models
+> hide #!17 models
+> show #!27 models
+> hide #!20 models
+> hide #!22 models
+> hide #!27 models
+> hide #!30 models
+> hide #!32 models
+> hide #!14 models
+> show #!15 models
+> hide #15-6
+> hide #15
+> hide #15,16
+> show #15,16/a cartoons
+Computing secondary structure
+[Repeated 1 time(s)]
+> color #15,16/a red
+> show #!28 models
+> select #15/A:341
+atoms, 15 bonds, 1 residue, 1 model selected
+> view matrix models
+> #15,-0.93405,-0.34831,-0.078927,345.57,0.30616,-0.66712,-0.67913,293.42,0.1839,-0.65851,0.72976,90.717
+> fitmap #15/a nea #28.2
+Expected a keyword
+> fitmap #15/a inMap #28.2
+Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
+(#28.2) using 2728 atoms
+average map value = 0.02958, steps = 260
+shifted from previous position = 11.6
+rotated from previous position = 23.4 degrees
+atoms outside contour = 2054, contour level = 0.0017272
+Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
+(#28.2) coordinates:
+Matrix rotation and translation
+-0.79630665 -0.43561221 -0.41968766 386.18629814
+.58540743 -0.38030007 -0.71600978 230.23651908
+.15229535 -0.81585162 0.55784610 144.52477351
+Axis -0.08500291 -0.48697238 0.86927120
+Axis point 158.93131778 227.39289934 0.00000000
+Rotation angle (degrees) 144.03543017
+Shift along axis -19.31456020
+> view matrix models
+> #15,-0.94602,-0.14843,-0.28813,357.26,0.24355,-0.9121,-0.32979,304.65,-0.21385,-0.38217,0.89901,84.308
+> fitmap #15/a inMap #28.2
+Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
+(#28.2) using 2728 atoms
+average map value = 0.1223, steps = 184
+shifted from previous position = 7.42
+rotated from previous position = 24 degrees
+atoms outside contour = 707, contour level = 0.0017272
+Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
+(#28.2) coordinates:
+Matrix rotation and translation
+-0.96127242 -0.26981301 0.05618076 335.20428011
+.25014099 -0.93972629 -0.23311799 292.00968965
+.11569280 -0.21003679 0.97082425 10.38879106
+Axis 0.04406009 -0.11360351 0.99254871
+Axis point 147.82603778 169.13090853 0.00000000
+Rotation angle (degrees) 164.81546446
+Shift along axis -8.09281367
+> select clear
+> hide #!15 models
+> hide #!28 models
+> show #!31 models
+> show #!15 models
+> hide #!15 models
+> show #!21 models
+> show #!20 models
+> hide #!20 models
+> show #!23 models
+> hide #!23 models
+> hide #21,23
+> show #21,23/a cartoons
+Computing secondary structure
+[Repeated 1 time(s)]
+> color #21,23/a green
+> fitmap #21/a inMap #31.2
+Fit molecule postcleavage_HNH_inwards_refined.pdb (#21) to map
+post_HNH_in_sharp.mrc 1 (#31.2) using 2703 atoms
+average map value = 0.2685, steps = 112
+shifted from previous position = 5.5
+rotated from previous position = 13.7 degrees
+atoms outside contour = 520, contour level = 0.025678
+Position of postcleavage_HNH_inwards_refined.pdb (#21) relative to
+post_HNH_in_sharp.mrc 1 (#31.2) coordinates:
+Matrix rotation and translation
+.98616651 0.13380918 0.09783004 -31.07144516
+-0.11332146 0.97498229 -0.19122706 47.65695927
+-0.12097049 0.17749548 0.97665833 -11.51991642
+Axis 0.74507872 0.44213088 -0.49937760
+Axis point 0.00000000 84.76781023 229.63504986
+Rotation angle (degrees) 14.32599614
+Shift along axis 3.67272934
+> hide #!31 models
+> show #!33 models
+> show #!23 models
+> hide #!21 models
+> fitmap #23/a inMap #33.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
+(#33.2) using 2728 atoms
+average map value = 0.2713, steps = 180
+shifted from previous position = 7.21
+rotated from previous position = 13.7 degrees
+atoms outside contour = 230, contour level = 0.003418
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
+Matrix rotation and translation
+.98012633 0.16191619 0.11461028 -37.06976884
+-0.13594647 0.96898777 -0.20635229 53.55638420
+-0.14446774 0.18667045 0.97174236 -10.17466150
+Axis 0.70553647 0.46508503 -0.53470946
+Axis point 0.00000000 78.56032267 238.27779114
+Rotation angle (degrees) 16.17234589
+Shift along axis 4.19468674
+> show #!20 models
+> hide #!23 models
+> hide #!33 models
+> show #!30 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> hide #!30 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> show #!23 models
+> hide #!23 models
+> hide #!21 models
+> show #!14 models
+> show #!32 models
+> hide #!32 models
+> hide #!20 models
+> hide #!14 models
+> show #!15 models
+> show #!21 models
+> show #!2 models
+> hide #!2 models
+> hide #!15 models
+> hide #!21 models
+> show #!16 models
+> show #!23 models
+> show #!1 models
+> show #!29 models
+> select #16/A:287
+atoms, 4 bonds, 1 residue, 1 model selected
+> view matrix models
+> #16,0.62757,-0.044878,-0.77726,162.91,0.38861,0.88314,0.26278,-73.948,0.67464,-0.46696,0.57167,26.566
+> view matrix models
+> #16,-0.40419,-0.68046,-0.61123,393.44,0.90481,-0.39532,-0.15824,86.915,-0.13395,-0.617,0.77548,143.78
+> view matrix models
+> #16,-0.39826,-0.68007,-0.61555,393.45,0.90771,-0.38883,-0.1577,112.35,-0.1321,-0.62154,0.77216,126.84
+> fitmap #23/a inMap #29.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
+(#29.2) using 2728 atoms
+average map value = 0.1546, steps = 40
+shifted from previous position = 0.0804
+rotated from previous position = 0.183 degrees
+atoms outside contour = 645, contour level = 0.0021375
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+.98502518 0.17240574 0.00128825 -22.90899269
+-0.16981904 0.97148276 -0.16547731 53.93769403
+-0.02978076 0.16278055 0.98621276 -24.79677780
+Axis 0.69074579 0.06537784 -0.72013610
+Axis point 285.26360326 179.92837540 0.00000000
+Rotation angle (degrees) 13.74559352
+Shift along axis 5.55909429
+> view matrix models
+> #16,-0.89523,-0.41361,-0.16578,367.07,0.41729,-0.64769,-0.63747,283.05,0.15628,-0.63986,0.75243,90.762
+> fitmap #23/a inMap #29.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
+(#29.2) using 2728 atoms
+average map value = 0.1546, steps = 40
+shifted from previous position = 0.0116
+rotated from previous position = 0.0128 degrees
+atoms outside contour = 644, contour level = 0.0021375
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+.98500387 0.17252839 0.00115057 -22.91842576
+-0.16996614 0.97147812 -0.16535350 53.95165575
+-0.02964593 0.16267828 0.98623369 -24.80251774
+Axis 0.69024031 0.06480160 -0.72067265
+Axis point 285.13190470 179.83196787 0.00000000
+Rotation angle (degrees) 13.74619735
+Shift along axis 5.55142851
+> hide #!29 models
+> show #!29 models
+> view matrix models
+> #16,-0.88458,-0.38657,-0.26093,381.82,0.46041,-0.81307,-0.35627,265.27,-0.074434,-0.43529,0.89721,76.738
+> fitmap #23/a inMap #29.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
+(#29.2) using 2728 atoms
+average map value = 0.1546, steps = 28
+shifted from previous position = 0.0105
+rotated from previous position = 0.016 degrees
+atoms outside contour = 645, contour level = 0.0021375
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+.98502926 0.17238229 0.00130491 -22.90911466
+-0.16979162 0.97147864 -0.16552961 53.94066736
+-0.02980207 0.16282995 0.98620396 -24.80004337
+Axis 0.69090730 0.06545276 -0.71997434
+Axis point 285.31689662 179.95179673 0.00000000
+Rotation angle (degrees) 13.74665869
+Shift along axis 5.55788562
+> fitmap #16/A inMap #29.2
+Fit molecule apo_HNH_outwards_refined.pdb (#16) to map apo_HNH_out_sharp.mrc 1
+(#29.2) using 2684 atoms
+average map value = 0.1709, steps = 164
+shifted from previous position = 5.87
+rotated from previous position = 25 degrees
+atoms outside contour = 433, contour level = 0.0021375
+Position of apo_HNH_outwards_refined.pdb (#16) relative to
+apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
+Matrix rotation and translation
+-0.96402236 -0.25980162 0.05624954 334.31569824
+.23888339 -0.93953169 -0.24538732 293.59018493
+.11660025 -0.22312178 0.96779185 12.48674161
+Axis 0.04428161 -0.12002525 0.99178278
+Axis point 148.03200436 169.10595691 0.00000000
+Rotation angle (degrees) 165.43913121
+Shift along axis -8.05006265
+Must specify one map, got 0
+> fitmap #23/a inMap #33.2
+Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
+(#33.2) using 2728 atoms
+average map value = 0.2714, steps = 60
+shifted from previous position = 0.085
+rotated from previous position = 0.177 degrees
+atoms outside contour = 229, contour level = 0.003418
+Position of postcleavage_HNH_outwards.pdb (#23) relative to
+post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
+Matrix rotation and translation
+.98009236 0.16199252 0.11479281 -37.09053836
+-0.13597963 0.96897219 -0.20640359 53.56869743
+-0.14466688 0.18668509 0.97170992 -10.14527457
+Axis 0.70529698 0.46553397 -0.53463472
+Axis point 0.00000000 78.41673669 238.26776560
+Rotation angle (degrees) 16.18077713
+Shift along axis 4.20221993
+> show #!33 models
+> show #!8 models
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!33 models
+> hide #!29 models
+> hide #!8 models
+> color #1/a steel blue
+> color #8.3 steel blue
+> show #!8 models
+> hide #!8.3 models
+> show #!8.3 models
+> hide #!8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap.tif"
+> width 1984 height 1210 supersample 3
+> show #!8 models
+> show #!29 models
+> show #!33 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!33 models
+> hide #!29 models
+> hide #!23 models
+> hide #!16 models
+> hide #!8 models
+> hide #!1 models
+> show #!32 models
+> color #32/a steel blue
+> show #!22 models
+> color #22.4 steel blue
+> color #22.5 steel blue
+> show #!30 models
+> show #!29 models
+> hide #!29 models
+> show #!27 models
+> show #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!20 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!30 models
+> hide #!27 models
+> hide #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap.tif"
+> width 1984 height 1210 supersample 3
+> hide #!32 models
+> hide #!20 models
+> hide #!14 models
+> show #!2 models
+> color #2/a steel blue
+> show #!16 models
+> hide #!16 models
+> show #!15 models
+> show #!21 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
+> width 1984 height 1210 supersample 3
+> show #!31 models
+> show #!28 models
+> volume step 1
+> volume #31.2 level 0.03
+> volume #31.2 level 0.07
+> show #!7 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!2 models
+> hide #!7 models
+> hide #!31 models
+> hide #!28 models
+> hide #!21 models
+> hide #!15 models
+> show #!14 models
+> show #!32 models
+> show #!20 models
+> show #!30 models
+> show #!27 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!20 models
+> hide #!22 models
+> hide #!27 models
+> hide #!30 models
+> hide #!32 models
+> hide #!14 models
+> show #!16 models
+> show #!1 models
+> show #!23 models
+> show #!29 models
+> show #!33 models
+> show #!8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!8 models
+> hide #!16 models
+> hide #!23 models
+> hide #!29 models
+> hide #!33 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/chimerax_session.cxs"
+> show #!32 models
+> hide #!1 models
+> show #!22 models
+> transparency #22 100
+> transparency #22 90
+> hide #!22 models
+> hide #!32 models
+> show #!2 models
+> show #!7 models
+> color #7.3 steel blue
+> show #!15 models
+> show #!31 models
+> show #!28 models
+> show #!21 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
+> width 1984 height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
+> width 1984 height 1210 supersample 3
+> hide #!31 models
+> hide #!28 models
+> hide #!7 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
+> width 1984 height 1210 supersample 3
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/chimerax_session.cxs"
+——— End of log from Thu May 1 15:38:06 2025 ———
+opened ChimeraX session
+> hide #!2 models
+> hide #!15 models
+> hide #!21 models
+> show #!32 models
+> select #32/a:283
+atoms, 8 bonds, 1 residue, 1 model selected
+> select ::name="ASN"
+atoms, 13797 bonds, 1945 residues, 14 models selected
+> select clear
+> show #!16 models
+> hide #!16 models
+> show #!14 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!20 models
+> color #14/a salmon
+> ui tool show "Color Actions"
+> color #20/a orchid
+> color #20/a aquamarine
+> color #20/a sea green
+> color #20/a pale green
+> color #15/a salmon
+> color #16/a salmon
+> color #21/a pale green
+> color #23/a pale green
+> color #30.2 #31.2 #33.2 pale green
+> color #27.2 #28.2 #29.2 salmon
+> show #!27 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> hide #!30 models
+> show #!30 models
+> color #27.2 #28.2 #29.2 #14-16/a salmon
+> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
+> show #!22 models
+> color #27.2 #28.2 #29.2 #14-16/a hot pink
+> color #30.2 #31.2 #33.2 #20-21/a #23/a forest green
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> hide #!27 models
+> show #!27 models
+> color #27.2 #28.2 #29.2 #14-16/a plum
+> color #30.2 #31.2 #33.2 #20-21/a #23/a dark sea green
+> color #27.2 #28.2 #29.2 #14-16/a vermilion
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #27.2 #28.2 #29.2 #14-16/a dark orange
+> color #30.2 #31.2 #33.2 #20-21/a #23/a bluish green
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #27.2 #28.2 #29.2 #14-16/a warm beige
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #27.2 #28.2 #29.2 #14-16/a beige
+> color #30.2 #31.2 #33.2 #20-21/a #23/a sof gra
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #30.2 #31.2 #33.2 #20-21/a #23/a dim gray
+> color #30.2 #31.2 #33.2 #20-21/a #23/a light gray
+> color #30.2 #31.2 #33.2 #20-21/a #23/a gray
+> color #27.2 #28.2 #29.2 #14-16/a plum
+> transparency 70
+> transparency 100
+> transparency 80
+> color #27.2 #28.2 #29.2 #14-16/a dark gray
+> color #30.2 #31.2 #33.2 #20-21/a #23/a medium sea green
+> color #27.2 #28.2 #29.2 #14-16/a plum
+> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
+> color #30.2 #31.2 #33.2 #20-21/a #23/a dark gray
+> color #27.2 #28.2 #29.2 #14-16/a orange
+> color #30.2 #31.2 #33.2 #20-21/a #23/a teal
+> color #30.2 #31.2 #33.2 #20-21/a #23/a cyan
+> color #30.2 #31.2 #33.2 #20-21/a #23/a turquoise
+> color #27.2 #28.2 #29.2 #14-16/a chocolate
+> color #27.2 #28.2 #29.2 #14-16/a coral
+> color #30.2 #31.2 #33.2 #20-21/a #23/a olive
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!14 models
+> hide #!20 models
+> hide #!22 models
+> hide #!27 models
+> hide #!30 models
+> hide #!32 models
+> show #!15 models
+> show #!2 models
+> show #!21 models
+> show #!7 models
+> show #!28 models
+> show #!31 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!31 models
+> hide #!28 models
+> hide #!21 models
+> hide #!15 models
+> hide #!7 models
+> hide #!2 models
+> show #!1 models
+> show #!8 models
+> show #!16 models
+> show #!26 models
+> hide #!26 models
+> show #!29 models
+> show #!33 models
+> show #!23 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps2.tif"
+> width 1984 height 1210 supersample 3
+> hide #!8 models
+> hide #!16 models
+> hide #!23 models
+> hide #!29 models
+> hide #!33 models
+> hide #!1 models
+> show #!22 models
+> show #!22.3 models
+> show #!22.2 models
+> show #!22.6 models
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> transparency 100
+> show #!22.1 models
+> hide #!22.1 models
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.4 models
+> hide #!22.5 models
+> hide #!22.6 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.9 models
+> show #!22.4 models
+> show #!22.5 models
+> hide #!22.5 models
+> show #!22.5 models
+> hide #!22.5 models
+> show #!22.5 models
+> show #!22.3 models
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> transparency 80
+> show #!22.4 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.3 models
+> hide #!22.4 models
+> show #!22.3 models
+> hide #!22.3 models
+> hide #!22.2 models
+> show #!22.6 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> show #!22.7 models
+> show #!22.8 models
+> hide #!22.9 models
+> show #!22.2 models
+> show #!22.5 models
+> show #!22.4 models
+> show #!22.3 models
+> show #!22.9 models
+> transparency #22.2 100
+> transparency #22 100
+> show #!32 models
+> show #32 cartoons
+> hide #32 cartoons
+> hide #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> hide #!22.6 models
+> hide #!22.3 models
+> hide #!22.2 models
+> show #!22.2 models
+> show #!22.3 models
+> hide #!22.3 models
+> hide #!22.2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas8.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.3 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
+> width 1984 height 1210 supersample 3
+> hide #!22.3 models
+> show #!22.6 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas6.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.6 models
+> show #!22.3 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.3 models
+> show #!22.2 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> hide #!22.2 models
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.7 models
+> show #!22.2 models
+> show #32/c cartoons
+> color #32/c green
+> color zone #22.2 near #32 distance 10
+> volume splitbyzone #22.2
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 0 as #34.1, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 1 as #34.2, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 2 as #34.3, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 3 as #34.4, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 4 as #34.5, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 5 as #34.6, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 6 as #34.7, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 7 as #34.8, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 8 as #34.9, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 9 as #34.10, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 10 as #34.11, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 11 as #34.12, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+Opened halfcleaved_HNH_center_sharp3Å.mrc 1 12 as #34.13, grid size
+,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
+> hide #!22 models
+> hide #!34.1 models
+> hide #!34.2 models
+> hide #!34.4 models
+> show #!34.4 models
+> hide #!34.4 models
+> hide #!34.5 models
+> hide #!34.6 models
+> hide #!34.8 models
+> hide #!34.7 models
+> hide #!34.9 models
+> hide #!34.10 models
+> hide #!34.11 models
+> hide #!34.12 models
+> hide #!34.13 models
+> transparency 100
+> surface dust siz 10
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> dus siz 10
+Unknown command: dus siz 10
+> surface dust #34.3 size 7.25
+> hide #!32 models
+> show #!22 models
+> show #!22.8 models
+> hide #!22.9 models
+> hide #!22.8 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> show #!22.2 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.9 models
+> show #!22.8 models
+> show #!22.7 models
+> hide #!22.7 models
+> hide #!22.8 models
+> hide #!22.6 models
+> hide #!22.5 models
+> hide #!22.4 models
+> hide #!22.3 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x_2.tif"
+> width 1984 height 1210 supersample 3 transparentBackground true
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.3 models
+> show #!22.6 models
+> transparency 0
+> lighting soft
+> lighting simple
+> lighting soft
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> show (#22.2-9#34.3#!22,34 & sidechain) target ab
+> ui tool show "Side View"
+> turn x 90
+[Repeated 3 time(s)]
+> view
+> turn x -90
+> turn x 90
+> show #!17 models
+> hide #!17 models
+> show #!18 models
+> hide #!18 models
+> show #!26 models
+> hide #!26 models
+> show #!26 models
+> hide #!26 models
+> show #!26 models
+> hide #!26 models
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> view
+> turn x 90
+[Repeated 3 time(s)]
+> turn x -90
+> turn x 90
+> turn x -90
+> turn x 90
+> turn x -90
+> turn x 90
+> turn x -90
+> turn x 90
+> turn x -90
+[Repeated 1 time(s)]
+> turn x 90
+[Repeated 1 time(s)]
+> turn x -90
+> hide #!34.3 models
+> hide #!34 models
+> hide #!22 models
+> show #!22 models
+> show #!1 models
+> show #!2 models
+> hide #!22 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!1 models
+> show #!32 models
+> hide #32/b cartoons
+> hide #32/c cartoons
+> show #32/a cartoons
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> hide #!2 models
+> show #!32 models
+> show #!1 models
+> hide #!32 models
+> show #!32 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!2 models
+> show #!1 models
+> hide #!32 models
+> show #!2 models
+> hide #!2 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> select ~sel & ##selected
+Nothing selected
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #1/a cartoons
+> show #1/a cartoons
+> hide #32/a cartoons
+> show #32/a cartoons
+> hide #!1 models
+> show #!33 models
+> hide #!33 models
+> hide #!32 models
+> show #!25 models
+> view
+> surface dust siz 10
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #25 size 10
+> volume level 0.05
+> volume level 0.06
+> hide #!25 models
+> show #!24 models
+> hide #!24 models
+> show #!26 models
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> graphics silhouettes true
+> graphics silhouettes false
+> transparency 0
+> hide #!26 models
+> show #!22 models
+> volume #22 show
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.3 models
+> show #!22.3 models
+> hide #!22.4 models
+> show #!22.4 models
+> hide #!22.5 models
+> show #!22.5 models
+> hide #!22.6 models
+> show #!22.6 models
+> hide #!22.7 models
+> show #!22.7 models
+> hide #!22.8 models
+> show #!22.8 models
+> hide #!22.9 models
+> show #!22.9 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> hide #!22.2 models
+> show #!22.2 models
+> lighting soft
+> lighting simple
+> lighting soft
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> transparency 0
+> volume level 0.05
+> hide #!22.1 models
+> transparency 90
+> transparency 10
+> transparency 1
+> transparency 0
+> lighting simple
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting full
+> lighting simple
+> hide #!22.2 models
+> hide #!22.3 models
+> hide #!22.4 models
+> hide #!22.5 models
+> hide #!22.6 models
+> hide #!22.10 models
+> show #!22.10 models
+> hide #!22.10 models
+> show #!32 models
+> hide #32 cartoons
+> show #32/j,k,l
+> hide #32/k:1-3
+> transparency 90
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> volume #22 level 0.03
+> volume #22 level 0.02
+> volume #22 level 0.01
+> volume #22 level 0.005
+> volume #22 level 0.001
+> volume #22 level 0.0001
+> volume #22 level 0.02
+> hide #32
+> hide #!22.9 models
+> hide #!22.8 models
+> hide #!22.7 models
+> show #!22.6 models
+> hide #!22.6 models
+> show #!22.5 models
+> show #!22.4 models
+> show #32/a
+> hide #32
+> hide #!22.5 models
+> hide #!22.4 models
+> show #!22.3 models
+> show #32/b
+> hide #!22.3 models
+> show #!22.2 models
+> hide #32
+> show #32/c
+> color #32/c salmon
+> show #32/c-h
+> hide #32
+> hide #!22.2 models
+> show #!22.6 models
+> hide #!22.6 models
+> show #!22.6 models
+> show #32/i
+> hide #!22.6 models
+> show #!22.6 models
+> show #32/d,b
+> show #32/j:41-60
+> show #32/j:41-65
+> hide #32
+> hide #!22.6 models
+> show #!22.2 models
+> show #!22.3 models
+> show #!22.4 models
+> show #!22.5 models
+> show #!22.6 models
+> show #!22.7 models
+> show #!22.8 models
+> show #!22.9 models
+> show #!22.10 models
+> hide #!22.10 models
+> hide #!22 models
+> hide #!32 models
+> show #!32 models
+> show #32 cartoons
+> hide #32/k:1-3 cartoons
+> show #32/a:304
+> show #32/a:305
+> show #32/m,o
+> graphics silhouettes false
+> graphics silhouettes true
+> select ~sel & ##selected
+Nothing selected
+> show #32/a:328,319
+> show #32/a:328,319,280
+> show #32/k
+> select #32/A:281
+atoms, 8 bonds, 1 residue, 1 model selected
+> select clear
+> show #!11 models
+> show #32/a:83-85
+> show #32/l
+> color #32/k:40 #32/l:6 hot pink
+> color #32/k:40 #32/l:7 hot pink
+> color #32/l:7 orange
+> color #32/l:6 orange
+> color #32/l:7 hot pink
+> hide #32 & nucleic cartoons
+> show #32/j
+> show #!22 models
+> show #!22.10 models
+> hide #!22 models
+> hide #!32 models
+> show #!8 models
+> show #!8.4 models
+> show #!8.5 models
+> show #!8.6 models
+> show #!8.7 models
+> show #!8.8 models
+> show #!8.9 models
+> hide #!8.9 models
+> show #!8.9 models
+> show #!1 models
+> show #1 cartoons
+> hide #!8 models
+> select #1/I:140
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel
+> show #1/a:295
+> show #!8 models
+> show #1/a:319,304,305,328,280
+> color #1/a:319,304,305,328,280 byhetero
+> show #!2 models
+> hide #!1 models
+> hide #!8 models
+> show #!7 models
+> color #2/a:319,304,305,328,280 byhetero
+> show #2/a:319,304,305,328,280
+> show #2/a:295
+> volume #7 level 0.02
+> show #!7.4 models
+> show #!7.5 models
+> show #!7.6 models
+> show #!7.7 models
+> show #!7.8 models
+> show #!7.9 models
+> show #!7.1 models
+> hide #!7.1 models
+> volume #7 level 0.01
+> volume #7 level 0.02
+> hide #!7 models
+> show #!9 models
+> volume #9 level 0.02
+> volume #9 level 0.01
+> volume #9 level 0.002
+> show #2 cartoons
+> surface dust siz 5
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #9 size 5
+> hide #!2 models
+> show #!2 models
+> hide #!9 models
+Drag select of 3 atoms, 57 residues, 2 bonds
+> show sel
+> hide #!2 models
+> show #!1 models
+Drag select of 2 atoms, 16 residues
+> show sel
+> hide #!1 models
+> show #!12 models
+> hide #!12 models
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!9 models
+> hide #!9 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> show #2/i
+> color #2/i,a byhetero
+> hide #!2 models
+> show #!1 models
+> show #!10 models
+> hide #!10 models
+> show #!8 models
+> hide #!7 models
+> hide sel
+> select clear
+> show #1-2/j
+> hide #1-2 & nucleic cartoons
+> select clear
+> show #!2 models
+> hide #!1 models
+> show #!7 models
+> hide #!8 models
+> hide #1-2
+> show #1-2 cartoons
+> show #!1 models
+> show #!3 models
+> hide #!7 models
+> show #!8 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!2 models
+> hide #!8 models
+> hide #!1 models
+> show #!19 models
+> hide #!19 models
+> show #!10 models
+> hide #!10 models
+> show #!32 models
+> select #32/A:193
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:192
+atoms, 12 bonds, 2 residues, 1 model selected
+> show sel
+> select clear
+> hide #32/k 1-33
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> hide #32/k:1-33
+> select #32/K:34@P
+atom, 1 residue, 1 model selected
+> select add #32/K:34@OP1
+atoms, 1 residue, 1 model selected
+> select add #32/K:34@OP2
+atoms, 1 residue, 1 model selected
+> select add #32/K:34@O5'
+atoms, 1 residue, 1 model selected
+> select add #32/K:34@C5'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select #32/a:220-243
+atoms, 197 bonds, 24 residues, 1 model selected
+> show #32/k
+> select clear
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/chimerax_session.cxs"
+——— End of log from Mon May 12 14:04:47 2025 ———
+opened ChimeraX session
+> hide #!11 models
+> hide #!32 models
+> show #!16 models
+> hide #16 cartoons
+> show #16/j
+> show #!29 models
+> hide #!29 models
+> show #!29 models
+> show #!28 models
+> hide #!28 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> select #29.2
+models selected
+> hide #!29.2 models
+> show #!29.2 models
+> hide #!29.2 models
+> show #!29.6 models
+> volume #29 level 0.02
+> hide #!29.6 models
+> show #!27 models
+> hide #!27 models
+> show #!26 models
+> hide #!26 models
+> show #!19 models
+> hide #!16 models
+> hide #!19 models
+> show #!29.6 models
+> show #!16 models
+> show #!15 models
+> hide #!15 models
+> show #!14 models
+> show #!15 models
+> hide #!15 models
+> hide #!14 models
+> combine #16
+> hide #!16 models
+> hide #!35 models
+> show #!35 models
+> fitmap #35/j inMap #29.6
+Fit molecule copy of apo_HNH_outwards_refined.pdb (#35) to map
+apo_HNH_out_sharp.mrc 5 (#29.6) using 1288 atoms
+average map value = 0.3487, steps = 184
+shifted from previous position = 2.25
+rotated from previous position = 3.92 degrees
+atoms outside contour = 340, contour level = 0.02
+Position of copy of apo_HNH_outwards_refined.pdb (#35) relative to
+apo_HNH_out_sharp.mrc 5 (#29.6) coordinates:
+Matrix rotation and translation
+-0.94445333 -0.26862857 0.18933201 314.24147225
+.22085794 -0.94540525 -0.23964699 296.35999000
+.24337151 -0.18451992 0.95221989 -10.86743333
+Axis 0.11124727 -0.10905253 0.98779127
+Axis point 138.91057616 167.65489171 0.00000000
+Rotation angle (degrees) 165.65451579
+Shift along axis -8.09505614
+> volume #29 level 0.002
+> volume #29 level 0.0002
+> volume #29 level 0.002
+> hide #!35 models
+> hide #!29 models
+> show #!30 models
+> hide #!30.2 models
+> show #!30.8 models
+> show #!30.7 models
+> show #!30.6 models
+> hide #!30.6 models
+> show #!30.5 models
+> show #!1 models
+> show #!3 models
+> hide #!3 models
+> hide #1 cartoons
+> show #1/j-l
+> hide #!1 models
+> show #!20 models
+> hide #20 cartoons
+> show #20/j-l
+> fitmap #20/j inMap #30.8
+Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
+post_HNH_cent_sharp.mrc 7 (#30.8) using 1288 atoms
+average map value = 0.3259, steps = 228
+shifted from previous position = 2.32
+rotated from previous position = 3 degrees
+atoms outside contour = 457, contour level = 0.05
+Position of postcleavage_HNH_center_refined.pdb (#20) relative to
+post_HNH_cent_sharp.mrc 7 (#30.8) coordinates:
+Matrix rotation and translation
+.99292341 0.11846591 0.00830222 -17.69757193
+-0.11532901 0.97858172 -0.17051988 44.51738269
+-0.02832520 0.16835570 0.98531926 -26.31185417
+Axis 0.81987504 0.08861632 -0.56564306
+Axis point 0.00000000 162.56775146 238.40498938
+Rotation angle (degrees) 11.92686357
+Shift along axis 4.31828685
+> volume #30 level 0.002
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_post.tif"
+> width 1984 height 1210 supersample 3
+> hide #!30 models
+> hide #!20 models
+> show #!35 models
+> show #!19 models
+> hide #!19 models
+> show #!29 models
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_apo.tif"
+> width 1984 height 1210 supersample 3
+> hide #!29 models
+> hide #!35 models
+> show #!30 models
+> show #!20 models
+> select #20/l:1
+atoms, 19 bonds, 1 residue, 1 model selected
+> select clear
+> hide #!30 models
+> show #20 cartoons
+> cartoon style nucleic xsection oval width 1 thickness 1
+> color #20/L dark orange
+> color #20/K dim gray
+> color #20/J dark red
+> color #20/I rebecca purple
+> color #20/B forest green
+> color #20/C,D,E,F,G,H salmon
+> color #20/A steel blue
+> color #20/A:232-350 dark turquoise
+> color #20/O blue
+> color #20/M red
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/post_full_cartoon.tif" width 1984
+> height 1210 supersample 3
+> hide #!20 models
+> show #!16 models
+> show #16 cartoons
+> color #16/L dark orange
+> color #16/K dim gray
+> color #16/J dark red
+> color #16/I rebecca purple
+> color #16/B forest green
+> color #16/C,D,E,F,G,H salmon
+> color #16/A steel blue
+> color #16/A:232-350 dark turquoise
+> color #16/O blue
+> color #16/M red
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/apo_full_cartoon.tif" width 1984 height
+> 1210 supersample 3
+> hide #!16 models
+> show #!32 models
+> color #32/L dark orange
+> color #32/K dim gray
+> color #32/J dark red
+> color #32/I rebecca purple
+> color #32/B forest green
+> color #32/C,D,E,F,G,H salmon
+> color #32/A steel blue
+> color #32/A:232-350 dark turquoise
+> color #32/O blue
+> color #32/M red
+> show #32/m,o
+> show #32 cartoons
+> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/half_full_cartoon.tif" width 1984
+> height 1210 supersample 3
+> hide #!32 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> lighting simple
+> graphics silhouettes false
+> ui tool show "Surface Color"
+> color sample #13.1 map #13 palette #ff0000:#ffffff:#0000ff
+Map values for surface "surface": minimum 0.04997, mean 0.05, maximum 0.05003
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"
+Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #36, grid size
+,420,420, pixel 0.725, shown at level 0.0319, step 2, values float32
+> hide #!13 models
+> hide #!36 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/fsc_and_halfmaps/halfcleaved_HNH_center/J635_005_volume_map_half_A.mrc"
+Opened J635_005_volume_map_half_A.mrc as #37, grid size 420,420,420, pixel
+.725, shown at level 0.138, step 2, values float32
+> color sample #13.1 map #37 palette
+> 0.04997,#ff0000:0.05,#ffffff:0.05003,#0000ff
+Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
+.4275
+> show #!13 models
+> hide #!37 models
+> key red-white-blue :0.05 :0.05 :0.05 showTool true
+> ui mousemode right "color key"
+> color sample #13.1 map #37 palette 2,#ff0000:2.5,#ffffff:3,#0000ff
+Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
+.4275
+> color sample #13.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
+Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
+.4275
+> show #!37 models
+> hide #!37 models
+> show #!37 models
+> hide #!37 models
+> hide #38 models
+> show #38 models
+> hide #!13 models
+> show #!36 models
+> color sample #36.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> key red-white-blue :2.1 :2.3 :2.8 showTool true
+> key red-white-blue :2.1 :2.5 :3.0 showTool true
+[Repeated 1 time(s)]
+> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color single #36.1
+> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color single #36.1
+> color sample #36.1 map #37 palette 2.5,#ff0000:3,#ffffff:3.5,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3,#ffffff:3.5,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:3.5,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> key red-white-blue :3.0 :3.5 :4.0 showTool true
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color sample #36.1 map #37 palette 2,#ff0000:3.5,#ffffff:4,#0000ff
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> color single #36.1
+> key red-white-blue :2.0 :3.5 :4.0 showTool true
+> color sample #36.1 map #37 palette 2,#0433ff:2.5,#ffffff:3,#ff2600
+Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
+.3335
+> hide #38 models
+> hide #!36 models
+> ui mousemode right translate
+Unsupported scale factor (0.000000) detected on Display0
+[Repeated 9 time(s)]
+> show #!32 models
+> show #!22 models
+> color #32/a byhetero
+> hide #!32 models
+> show #!13 models
+> show #!32 models
+> hide #!22 models
+> hide #!13 models
+> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range 2
+> newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+Unknown or unsupported skia image format
+> transparency #39 90
+> close #39
+> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range
+> 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #39 90
+> hide #32/k cartoons
+> volume zone #13 nearAtoms #32/o range 2 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> volume #40 level 0.02
+> close #40
+> volume zone #13 nearAtoms #32/o range 0.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> volume #40 level 0.02
+> close #40
+> volume zone #13 nearAtoms #32/o range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> volume #40 level 0.02
+> transparency #40 90
+> color #40 blue
+> color #39 turquoise
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> color #32/k:3 byhetero
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> close #39
+> hide #!40 models
+> show #!40 models
+> select #32/A:280@CG
+atom, 1 residue, 1 model selected
+> select add #32/A:305@ND1
+atoms, 2 residues, 1 model selected
+> select add #32/A:319@CG
+atoms, 3 residues, 1 model selected
+> select add #32/A:304@ND1
+atoms, 4 residues, 1 model selected
+> select add #32/M:2@MG
+atoms, 1 bond, 5 residues, 1 model selected
+> select add #32/K:2@O5'
+atoms, 1 bond, 6 residues, 1 model selected
+> select add #32/K:3@P
+atoms, 1 bond, 7 residues, 1 model selected
+> select up
+atoms, 1 bond, 8 residues, 1 model selected
+> select up
+atoms, 60 bonds, 8 residues, 1 model selected
+> volume zone nea sel range 1.5 newmap tru
+Missing or invalid "volumes" argument: invalid density maps specifier
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> select clear
+> transparency #39 90
+> volume #39 level 0.03
+> volume #39 level 0.02
+> volume #39 level 0.002
+> surface dust #40 size 7.25
+> surface dust #39 size 7.25
+> surface dust siz 0
+Missing or invalid "surfaces" argument: invalid surfaces specifier
+> surface dust #39-40 size 0
+> volume #39 level 0.09
+> show #!11 models
+> volume #39 level 0.04054
+> hide #!39 models
+> hide #!40 models
+> select #32/A:280,304,305,319,328
+atoms, 48 bonds, 5 residues, 1 model selected
+> select #32/A:280,304,305,319,328 #32/k:1-3
+atoms, 60 bonds, 2 pseudobonds, 7 residues, 2 models selected
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #41, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> close #41
+> show #!39 models
+> show #!40 models
+> volume #39 level 0.04
+> volume #39 level 0.05
+> volume #49 level .03
+No volumes specified
+> volume #39 level .03
+> volume #39 level .04
+> volume #40 level .04
+> volume #40 level .03
+> volume #40 level .025
+> volume #40 level .021
+> volume #40 level .02
+> volume #40 level .01
+> volume #40 level .02
+> select clear
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> save "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/cat_pocket_with_nucleotide.tif"
+> width 1938 height 1210 supersample 3
+> save cat_pocket_with_nucleotide_test.tif supersample 3
+> save "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs" includeMaps
+> true
+> close #1-10,12,14-31,33-38
+> save HNH_cat_session.cxs includeMaps true
+——— End of log from Wed May 14 12:43:12 2025 ———
+opened ChimeraX session
+> hide #!39 models
+> select add /M:2@MG
+atom, 1 residue, 1 model selected
+> select add /A:304@ND1
+atoms, 2 residues, 1 model selected
+> select add /A:304@CE1
+atoms, 2 residues, 1 model selected
+> select add /A:304@NE2
+atoms, 2 residues, 1 model selected
+> select add /A:304@CD2
+atoms, 2 residues, 1 model selected
+> select add /A:304@CG
+atoms, 2 residues, 1 model selected
+> select add /A:304@CB
+atoms, 2 residues, 1 model selected
+> select add /A:328@CD2
+atoms, 3 residues, 1 model selected
+> select add /A:328@NE2
+atoms, 3 residues, 1 model selected
+> select add /A:328@CE1
+atoms, 3 residues, 1 model selected
+> select add /A:328@ND1
+atoms, 3 residues, 1 model selected
+> select add /A:328@CG
+atoms, 3 residues, 1 model selected
+> select add /A:328@CB
+atoms, 3 residues, 1 model selected
+> select add /A:319@ND2
+atoms, 4 residues, 1 model selected
+> select add /A:319@OD1
+atoms, 4 residues, 1 model selected
+> select add /A:319@CB
+atoms, 4 residues, 1 model selected
+> select add /A:305@CB
+atoms, 5 residues, 1 model selected
+> select add /A:305@CG
+atoms, 5 residues, 1 model selected
+> select add /A:305@CD2
+atoms, 5 residues, 1 model selected
+> select add /A:305@NE2
+atoms, 5 residues, 1 model selected
+> select add /A:305@CE1
+atoms, 5 residues, 1 model selected
+> select add /A:305@ND1
+atoms, 5 residues, 1 model selected
+> select add /K:3@OP2
+atoms, 6 residues, 1 model selected
+> select add /K:3@P
+atoms, 6 residues, 1 model selected
+> select add /K:3@O5'
+atoms, 6 residues, 1 model selected
+> select add /K:3@OP1
+atoms, 6 residues, 1 model selected
+> select subtract /K:3@P
+atoms, 6 residues, 1 model selected
+> select add /K:3@P
+atoms, 6 residues, 1 model selected
+> select add /K:2@O3'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C3'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C4'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C5'
+atoms, 7 residues, 1 model selected
+> select add /K:2@O5'
+atoms, 7 residues, 1 model selected
+> select add /K:2@O4'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C2'
+atoms, 7 residues, 1 model selected
+> select add /K:2@C1'
+atoms, 7 residues, 1 model selected
+> select add /A:280@NH2
+atoms, 8 residues, 1 model selected
+> select add /A:280@NH1
+atoms, 8 residues, 1 model selected
+> select add /A:280@CZ
+atoms, 8 residues, 1 model selected
+> select add /A:280@NE
+atoms, 8 residues, 1 model selected
+> select add /A:280@CD
+atoms, 8 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #1, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #1 90
+> select add /A:280@CG
+atoms, 8 residues, 1 model selected
+> select add /A:280@CB
+atoms, 8 residues, 1 model selected
+> close #1
+> volume zone #13 nearAtoms sel range 1.5 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #1, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #1 90
+> select clear
+> volume #1 level 0.02
+> show (#1,40#!11,32 & sidechain) target ab
+> ui tool show "Side View"
+> hide #32
+> show #32/a:280,304,305,319
+> show #32/a:280,304,305,319,328 #32/o,m
+> show #32/a:280,304,305,319,328 #32/o,m #32/k:1-3
+> hide #32 cartoons
+> show #32/a cartoons
+> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH
+Expected name of a folder to open/read; a name of 'browse' will bring up a
+file browser or a keyword
+> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/
+Expected name of a folder to open/read; a name of 'browse' will bring up a
+file browser or a keyword
+> cd "/Users/zxc755/OneDrive - University of Copenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH/"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> save cat_pocket_with_nucleotide_2.tif supersample 3
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7
+Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
+Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
+Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
+Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
+messages similar to the above omitted
+Chain information for halfcleaved_HNH_outwards_refined.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_out_sharp.mrc"
+Opened halfcleaved_HNH_out_sharp.mrc as #3, grid size 420,420,420, pixel
+.725, shown at level 0.0029, step 2, values float32
+> hide #!1 models
+> hide #!2 models
+> hide #!3 models
+> hide #!32 models
+> hide #!40 models
+> show #!3 models
+> show #!2 models
+> style stick
+Changed 48201 atom styles
+> hide #2
+> show #2 cartoons
+Computing secondary structure
+> transparency #3 90
+> color #2/L dark orange
+> color #2/K dim gray
+> color #2/J dark red
+> color #2/I rebecca purple
+> color #2/B forest green
+> color #2/C,D,E,F,G,H salmon
+> color #2/A steel blue
+> color #2/A:232-350 dark turquoise
+> color #2/O blue
+> color #2/M red
+> show #2/a:319,280,304,305
+> color #2/a byhetero
+> volume #3 level 0.005
+> volume #3 level 0.05
+> volume #3 level 0.09
+> show #2/a:328
+> hide #2 cartoons
+> show #2/a cartoons
+> hide #!3 models
+> hide #!2 models
+> show #!32 models
+> select #32/A:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel
+> select #32/A:333
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel
+> show #!13 models
+> volume #13 level 0.02
+> hide #!11 models
+> hide #!13 models
+> hide #!32 models
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #4
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+> hide #!5 models
+> style stick
+Changed 71932 atom styles
+> hide #4
+> show #4/a cartoons
+Computing secondary structure
+> show #4/m
+> color #4/L dark orange
+> color #4/K dim gray
+> color #4/J dark red
+> color #4/I rebecca purple
+> color #4/B forest green
+> color #4/C,D,E,F,G,H salmon
+> color #4/A steel blue
+> color #4/A:232-350 dark turquoise
+> color #4/O blue
+> color #4/M red
+> color #4/a byhetero
+> show #4/a:280,319,304,305
+> show #4/a:280,319,304,305,328
+> select #4/a280,319,304,305,328 #4/m
+atom, 1 residue, 1 model selected
+> select #4/a:280,319,304,305,328 #4/m
+atoms, 48 bonds, 6 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 1.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #6, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #6 90
+> volume #6 level 0.02
+> hide #!6 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> volume #6 level 0.09
+> volume zone #5 nearAtoms sel range 1 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> hide #!6 models
+> transparency #7 90
+> hide #!7 models
+> show #!6 models
+> volume #6 level 0.12
+> volume #6 level 0.1
+> volume #6 level 0.08
+> volume #6 level 0.06
+> select clear
+> show #!32 models
+> hide #!32 models
+> combine #4
+> hide #!4 models
+> hide #!6 models
+> show #!32 models
+> mmaker #8/a:220-350 to #32/a:220-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of postcleavage_HNH_center_refined.pdb, chain A (#8), sequence
+alignment score = 600
+RMSD between 122 pruned atom pairs is 0.599 angstroms; (across all 123 pairs:
+.646)
+> color #8/a salmon
+> hide #!32 models
+> hide #!8 models
+> show #!6 models
+> show #!4 models
+> show #!5 models
+> hide #!5 models
+> hide #!6 models
+> select add #4/A:328@NE2
+atom, 1 residue, 1 model selected
+> select add #4/A:304@ND1
+atoms, 2 residues, 1 model selected
+> select add #4/A:280@CZ
+atoms, 3 residues, 1 model selected
+> select add #4/A:305@CE1
+atoms, 4 residues, 1 model selected
+> select add #4/A:319@CG
+atoms, 5 residues, 1 model selected
+> select add #4/A:332
+atoms, 6 bonds, 6 residues, 1 model selected
+> select up
+atoms, 54 bonds, 6 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 1.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> close #9
+> select add #4/M:1@MG
+atoms, 54 bonds, 7 residues, 1 model selected
+> select up
+atoms, 415 bonds, 50 residues, 1 model selected
+> select down
+atoms, 54 bonds, 7 residues, 1 model selected
+> volume zone #5 nearAtoms sel range 1.5 newMap true
+Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
+shown at step 1, values float32
+> transparency #9 90
+> volume #9 level 0.06
+> select clear
+> hide #!9 models
+> select #4/A:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> show #!9 models
+> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/figures/structure/HNH"
+Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH
+> color #9 #ffcc99ff models
+> color #9 #ffd479ff models
+> color #9 white
+> transparency #9 90
+> ui tool show "Color Actions"
+> color #9 lavender
+> color #9 violet
+> color #9 navy
+> color #9 navajowhite
+> color #9 blanchedalmond
+> save cat_pocket_empty.tif supersample 3
+> hide #!9 models
+> show #!8 models
+> hide #!4 models
+> show #!32 models
+> color #8 salmon
+> select #32/K:2@C3'
+atom, 1 residue, 1 model selected
+> select add #32/K:2@C4'
+atoms, 1 residue, 1 model selected
+> select #32/K:2@C4'
+atom, 1 residue, 1 model selected
+> select add #32/K:2@C3'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C5'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@O5'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@O4'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C1'
+atoms, 1 residue, 1 model selected
+> select add #32/K:2@C2'
+atoms, 1 residue, 1 model selected
+> hide sel
+> select #32/K:2@O3'
+atom, 1 residue, 1 model selected
+> color sel byhetero
+> select clear
+> select #32/O:1@O
+atom, 1 residue, 1 model selected
+> hide sel
+> hide #!8 models
+> show #!8 models
+> select #8/A:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel
+> select clear
+> select add #8/A:332@CG2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 2 models selected
+> select up
+atoms, 12 bonds, 2 residues, 2 models selected
+> hide sel
+> select clear
+> combine #8
+> hide #!8 models
+> mmaker #10/a to #32/a
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
+sequence alignment score = 1678.6
+RMSD between 328 pruned atom pairs is 0.795 angstroms; (across all 340 pairs:
+.913)
+> mmaker #10/a:232-350 to #32/a:232-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
+sequence alignment score = 542.1
+RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
+.605)
+> save cat_half_post_superimpose.tif supersample 3
+> hide #!10 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> close #10
+> show #!4 models
+> hide #!4 models
+> hide #!32 models
+> show #!4 models
+> close #4
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_refined.pdb #4
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"
+Opened post_HNH_cent_sharp.mrc as #10, grid size 420,420,420, pixel 0.725,
+shown at level 0.00328, step 2, values float32
+> color #4/L dark orange
+> color #4/K dim gray
+> color #4/J dark red
+> color #4/I rebecca purple
+> color #4/B forest green
+> color #4/C,D,E,F,G,H salmon
+> color #4/A steel blue
+> color #4/A:232-350 dark turquoise
+> color #4/O blue
+> color #4/M red
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!10 models
+> hide #!4 models
+> show #!4 models
+> style stick
+Changed 95663 atom styles
+> hide #4
+> show #4/a cartoons
+Computing secondary structure
+> show #4/a:319,280,304,305 #4/m
+> show #4/a:319,280,304,305,328 #4/m
+> color #4/a byhetero
+> combine #4
+> hide #!4 models
+> mmaker #12/a:232-350 to #32/a:232-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with copy of postcleavage_HNH_center_refined.pdb, chain A (#12), sequence
+alignment score = 542.1
+RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
+.605)
+> color #12 salmon
+> show #!32 models
+> select #32/A:333@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> hide sel
+> save cat_half_post_superimpose_2.tif supersample 3
+> hide #!32 models
+> hide #!12 models
+> show #!12 models
+> show #!4 models
+> hide #!12 models
+> show #!8 models
+> hide #!8 models
+> show #!6 models
+> hide #!6 models
+> show #!7 models
+> hide #!7 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> show #!9 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> ui tool show Distances
+> show #!11 models
+> select #4/A:304@ND1
+atom, 1 residue, 1 model selected
+> select add #4/M:1@MG
+atoms, 2 residues, 1 model selected
+> distance #4/A:304@ND1 #4/M:1@MG
+Distance between postcleavage_HNH_center_refined.pdb #4/A HIS 304 ND1 and /M
+MG 1 MG: 3.141Å
+> distance style dashes 5
+[Repeated 2 time(s)]
+> distance style radius 0.09
+[Repeated 2 time(s)]
+> distance style radius 0.08
+[Repeated 2 time(s)]
+> distance style radius 0.07
+[Repeated 2 time(s)]
+> distance style radius 0.06
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> color #11 teal
+> select clear
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!9 models
+> save cat_pocket_empty_2.tif supersample 3
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting simple
+> lighting soft
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting full
+> graphics silhouettes false
+> lighting full
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> hide #!4 models
+> hide #!9 models
+> show #!32 models
+> show #32/a:232
+> show #!10 models
+> hide #!10 models
+> show #11.1 models
+> hide #11.1 models
+> hide #!32 models
+> show #!32 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!8 models
+> combine #32
+> hide #!32 models
+> hide #!14 models
+> show #!14 models
+> morph#8 #14
+Unknown command: morph#8 #14
+> morph #8 #14
+Computed 51 frame morph #15
+> coordset #15 1,51
+> show #!32 models
+> hide #!32 models
+> close #15
+> show #!12 models
+> hide #!12 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> close #14
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_with_TS_for_morph.pdb #14
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> color #14/L dark orange
+> color #14/K dim gray
+> color #14/J dark red
+> color #14/I rebecca purple
+> color #14/B forest green
+> color #14/C,D,E,F,G,H salmon
+> color #14/A steel blue
+> color #14/A:232-350 dark turquoise
+> color #14/O blue
+> color #14/M red
+> style stick
+Changed 142917 atom styles
+> hide #14
+> show #14/a cartoons
+Computing secondary structure
+> show #14/k:1-3
+> show #!32 models
+> mmaker #14/A:232-350 to #32/A:232-350
+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 halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
+with postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
+alignment score = 542.1
+RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
+.605)
+> show #14/a:280,304,305,317,328
+> show #14/a:280,304,305,319,328
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel
+> select clear
+> morph #14 #32
+Computed 51 frame morph #15
+> coordset #15 1,51
+> show #15/k:1-3
+> show #15/k
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
+Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #16
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+k | No description available
+> style stick
+Changed 190521 atom styles
+> hide #16
+> close #15
+> show #16/a cartoons
+> hide #!16 models
+> show #!16 models
+> show #16/a
+> view
+> hide #!16 models
+> show #!16 models
+> show #!14 models
+> hide #!14 models
+> hide #!16 models
+> show #!16 models
+> close #16
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
+Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+k | No description available
+> style stick
+Changed 167030 atom styles
+> hide #16
+> hide #15
+> show #15/a cartoons
+> hide #!15 models
+> show #!15 models
+> show #15
+> show #15/A cartoons
+Computing secondary structure
+> hide #15
+> show #15/Kk
+> show #15
+> select #15/k:2@C4'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 8 bonds, 1 residue, 1 model selected
+> select up
+atoms, 12 bonds, 2 residues, 1 model selected
+> hide #15
+> show sel
+> select clear
+> color #15/L dark orange
+> color #15/K dim gray
+> color #15/J dark red
+> color #15/I rebecca purple
+> color #15/B forest green
+> color #15/C,D,E,F,G,H salmon
+> color #15/A steel blue
+> color #15/A:232-350 dark turquoise
+> color #15/O blue
+> color #15/M red
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> select #15/k:2@O5'
+atom, 1 residue, 1 model selected
+> select add #15/k:2@C5'
+atoms, 1 residue, 1 model selected
+> delete sel
+> morph #14 #15
+models have different number of chains, 12 (Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
+(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
+> morph #14/A,Kk #15/A,Kk
+models have different number of chains, 12 (Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
+(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
+> close #14
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
+Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
+UniversityofCopenhagen/Type
+I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
+---
+warning | Ignored bad PDB record found on line 59
+SSBOND 1 CYS Aa 295 CYS Ca 140
+Chain information for postcleavage_HNH_center_with_TS_for_morph.pdb #14
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+> hide #!14 models
+> color #14/L dark orange
+> color #14/K dim gray
+> color #14/J dark red
+> color #14/I rebecca purple
+> color #14/B forest green
+> color #14/C,D,E,F,G,H salmon
+> color #14/A steel blue
+> color #14/A:232-350 dark turquoise
+> color #14/O blue
+> color #14/M red
+> show #!14 models
+> hide #!14 models
+> style #14 stick
+Changed 23523 atom styles
+> hide #14
+> show #14/A cartoons
+Computing secondary structure
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> mmaker #14/A:232-350 to #15/A:232-250
+Computing secondary structure
+[Repeated 1 time(s)]  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 halfcleaved_HNH_center_main_model_for_cat_morph.pdb, chain A (#15)
+with postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
+alignment score = 94.9
+RMSD between 19 pruned atom pairs is 0.653 angstroms; (across all 19 pairs:
+.653)
+> show #14,15/A:280
+> show #14,15/A:280,319,304,305,329
+> show #14,15/A:280,319,304,305,328
+> hide #14-15/A:329
+> show #14/Kk:1-3
+> morph #14 #15
+models have different number of chains, 12 (Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
+postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
+(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
+#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
+> close #15
+> open "/Users/zxc755/Library/CloudStorage/OneDrive-
+> UniversityofCopenhagen/Type
+> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
+Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+J | No description available
+K | No description available
+L | No description available
+k | No description available
+> close #15
+> hide #!14 models
+> show #!32 models
+> hide #!32 models
+> show #!14 models
+> hide #!14 models
+> show #!32 models
+> hide #32
+> show #32/b cartoons
+> hide #32/b cartoons
+> show #32/k,l
+> show #32/a:83,85
+> color #32/k:40 #32/l:7 hot pink
+> select add #32/A:85@CE
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 15 bonds, 2 residues, 1 model selected
+> volume zone #13 nearAtoms rang 1 new tru
+Invalid "nearAtoms" argument: invalid atoms specifier
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #15, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency #15 90
+> hide #32/a:200-350 cartoons
+> hide #32/k:1-38
+> hide #32/l:9-12
+> select #32/L:7@N3
+atom, 1 residue, 1 model selected
+> select add #32/K:40@O6
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #16, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> select up
+atoms, 2 bonds, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #17, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> transparency 16-17 90
+Missing or invalid "percent" argument: Expected a number
+> transparency #16-17 90
+> hide #11.1 models
+> hide #32/a:1-20
+> hide #32/a:1-20 cartoons
+> hide #32/a:87-200 cartoons
+Drag select of 163 atoms, 183 bonds
+> select up
+atoms, 185 bonds, 10 residues, 1 model selected
+> select up
+atoms, 225 bonds, 10 residues, 1 model selected
+Drag select of 133 atoms, 152 bonds
+> select up
+atoms, 154 bonds, 8 residues, 1 model selected
+> select up
+atoms, 179 bonds, 8 residues, 1 model selected
+> hide sel
+> select #15
+models selected
+> color sel steel blue
+> select #16
+models selected
+> color sel hot pink
+> select clear
+> select #17
+models selected
+> color zone sel near #32
+> transparency sel 90
+> select clear
+> select #32/L:5@C4'
+atom, 1 residue, 1 model selected
+> select add #32/K:42@C4
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> hide sel
+Drag select of 8 residues
+> select #32/A:47
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #32/A:48
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #32/A:46
+atoms, 18 bonds, 3 residues, 1 model selected
+> select add #32/A:49
+atoms, 25 bonds, 4 residues, 1 model selected
+> show sel
+> select clear
+> show #32/b:95
+> select #32/K:39@C4
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> hide sel
+> volume zone #13 nearAtoms #32 range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> color zone #18 near #32 distance 10
+> volume #18 level 0.01
+> hide #!32 models
+> hide #!17 models
+> hide #!16 models
+> hide #!15 models
+> show #!15 models
+> show #!16 models
+> show #!17 models
+> show #!32 models
+> volume #18 level 0.0001
+> lighting soft
+> lighting flat
+> close #18
+> select #32/A:47@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel
+> show #32/b:90-100 cartoons
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 10 bonds, 1 residue, 1 model selected
+> color byhetero
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select add #32/A:49@CD
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 13 bonds, 2 residues, 1 model selected
+> hide sel
+> show #32/a:32
+> show #32/a:42
+> select clear
+[Repeated 1 time(s)]
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel
+> select clear
+> show #32/a:82
+> show #32/K:42
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!15 models
+> show #!15 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> select add #32/K:41@P
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select #32/K:41@C1'
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> select add #32/K:42@P
+atoms, 44 bonds, 3 residues, 1 model selected
+> select add #32/K:42@OP1
+atoms, 44 bonds, 3 residues, 1 model selected
+> select add #32/K:42@OP2
+atoms, 44 bonds, 3 residues, 1 model selected
+> select add #32/K:42@O5'
+atoms, 44 bonds, 3 residues, 1 model selected
+> select up
+atoms, 66 bonds, 3 residues, 1 model selected
+> select down
+atoms, 44 bonds, 3 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> hide #!18 models
+> show #!17 models
+> hide #!17 models
+> show #!18 models
+> hide #!18 models
+> show #!17 models
+> show #!18 models
+> hide #!17 models
+> transparency #18 90
+> hide #!18 models
+> select #32/K:42@C4
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@OP2
+atoms, 20 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@OP1
+atoms, 19 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@P
+atoms, 18 bonds, 1 residue, 1 model selected
+> select subtract #32/K:42@O5'
+atoms, 17 bonds, 1 residue, 1 model selected
+> hide sel
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 24 bonds, 1 residue, 1 model selected
+> color sel orange
+> color sel dark orange
+> select #32/K:41@C4
+atom, 1 residue, 1 model selected
+> select up
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #32/K:42@P
+atoms, 20 bonds, 2 residues, 1 model selected
+> select up
+atoms, 42 bonds, 2 residues, 1 model selected
+> color sel dim gray
+> hide #!16 models
+> select add #32/K:40@C6
+atom, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 44 bonds, 2 residues, 1 model selected
+> color sel hot pink
+> select clear
+> show #!16 models
+> show #!18 models
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select down
+bond, 1 model selected
+> select #32/B:95@CB
+atom, 1 residue, 1 model selected
+> select add #32/B:95@CG
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@ND1
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@CE1
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@NE2
+atoms, 1 residue, 1 model selected
+> select add #32/B:95@CD2
+atoms, 1 residue, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #19, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> color zone #19 near #32
+> hide #!19 models
+> show #!19 models
+> select ~sel & ##selected
+atoms, 24839 bonds, 13 pseudobonds, 2799 residues, 3 models selected
+> color #19 forest green
+> transparency #19 90
+> select clear
+> select add #32/A:82@OD1
+atom, 1 residue, 1 model selected
+> select add #32/A:82@ND2
+atoms, 1 residue, 1 model selected
+> select add #32/A:82@CG
+atoms, 1 residue, 1 model selected
+> select add #32/A:82@CB
+atoms, 1 residue, 1 model selected
+> select add #32/A:42@NZ
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CE
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CD
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CG
+atoms, 2 residues, 1 model selected
+> select add #32/A:42@CB
+atoms, 2 residues, 1 model selected
+> select add #32/A:46@OG1
+atoms, 3 residues, 1 model selected
+> select add #32/A:46@CB
+atoms, 3 residues, 1 model selected
+> select add #32/A:46@CG2
+atoms, 3 residues, 1 model selected
+> hide #!15 models
+> select add #32/A:85@NZ
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CE
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CD
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CG
+atoms, 4 residues, 1 model selected
+> select add #32/A:85@CB
+atoms, 4 residues, 1 model selected
+> select add #32/A:83@CB
+atoms, 5 residues, 1 model selected
+> select add #32/A:83@CG
+atoms, 5 residues, 1 model selected
+> select add #32/A:83@OD2
+atoms, 5 residues, 1 model selected
+> select add #32/A:83@OD1
+atoms, 5 residues, 1 model selected
+> volume zone #13 nearAtoms sel range 1 newMap true
+Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420,
+pixel 0.725, shown at step 1, values float32
+> color #20 steel blue
+> transparency #20 90
+> select #18
+models selected
+> color zone sel near #32
+> color #32/:l dar ora
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #32/:L dark ora
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> color #32/:L ora
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> hide #!18 models
+> select #32/L:6@OP2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 24 bonds, 1 residue, 1 model selected
+> color sel orange
+> color sel dark orange
+> color #32/L dark orange
+> color #32/L:7 hot pink
+> show #!18 models
+> select #18
+models selected
+> color zone sel near #32
+> transparency sel 90
+> select clear
+> ui tool show Distances
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> hide #!18 models
+> hide #!19 models
+> hide #!20 models
+> show #!17 models
+> hide #!17 models
+> select #32/A:82@ND2
+atom, 1 residue, 1 model selected
+> select add #32/K:42@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/A:82@ND2 #32/K:42@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASN
+ND2 and /K DT 42 OP1: 2.690Å
+> distance style radius 0.04
+[Repeated 2 time(s)]
+> distance style radius 0.05
+[Repeated 2 time(s)]
+> select #32/A:42@NZ
+atom, 1 residue, 1 model selected
+> select add #32/K:41@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/A:42@NZ #32/K:41@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
+NZ and /K DC 41 OP1: 2.885Å
+> select #32/A:46@OG1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/A:46@OG1 #32/K:40@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A THR
+OG1 and /K DG 40 OP1: 2.817Å
+> select #32/B:95@ND1
+atom, 1 residue, 1 model selected
+> select add #32/K:40@OP1
+atoms, 2 residues, 1 model selected
+> distance #32/B:95@ND1 #32/K:40@OP1
+Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/B HIS
+ND1 and /K DG 40 OP1: 2.646Å
+[deleted to fit within ticket limits]
 > distance style radius 0.04