The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/bsahoo/Downloads/cl2_prot-backbone.cxs
Log from Fri May 9 15:50:15 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/clust0_chimera/clust0_intraRNA.cxs"
Log from Fri May 9 14:26:47 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/clust0_chimera/clust0_orient_trans_57-65.cxs"
> format session
Log from Fri May 9 13:26:45 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 "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/chained_frame_20
> copy.pdb"
Summary of feedback from opening /Users/alexeykovalenko/University of Michigan
Dropbox/Alexey
Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/chained_frame_20
copy.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK THIS IS A SIMULATION BOX
chained_frame_20 copy.pdb title:
Title in water t= 1000000.00000 step= 250000000 [more info...]
Chain information for chained_frame_20 copy.pdb #1
---
Chain | Description
A B C D E F | No description available
G | No description available
> show cartoons
> hide atoms
> show target m
> select add #1
8885 atoms, 9121 bonds, 3 pseudobonds, 444 residues, 2 models selected
> color (#!1 & sel) blue
> undo
> select subtract #1
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D /E /F
Alignment identifier is 1
> sequence chain /G
Alignment identifier is 1/G
> select /A-F:1
114 atoms, 105 bonds, 3 pseudobonds, 6 residues, 2 models selected
> select /A-F
5916 atoms, 5913 bonds, 3 pseudobonds, 354 residues, 2 models selected
> color (#!1 & sel) red
> ui tool show "Color Actions"
> color (#!1 & sel) #c7ffffff
> color (#!1 & sel) #c7a3ffff
> color (#!1 & sel) #c7a3ecff
> ui tool show "Show Sequence Viewer"
> sequence chain /G
Destroying pre-existing alignment with identifier 1/G
Alignment identifier is 1/G
> select /G:1-2
66 atoms, 71 bonds, 2 residues, 1 model selected
> select /G:1-5
165 atoms, 178 bonds, 5 residues, 1 model selected
> select /G:90
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /G
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> color sel #f5a3ecff
> color sel #f599ecff
> color sel #f59900ff
> select /G:2
34 atoms, 36 bonds, 1 residue, 1 model selected
> select /G:2-4
102 atoms, 110 bonds, 3 residues, 1 model selected
> save /Users/alexeykovalenko/Desktop/cl0_colored.cxs
> select /G:14-15
68 atoms, 73 bonds, 2 residues, 1 model selected
> select /G:14-16
102 atoms, 110 bonds, 3 residues, 1 model selected
> select /G:1
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /G:1
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /G:1-7
230 atoms, 248 bonds, 7 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel ball
Changed 230 atom styles
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
5 hydrogen bonds found
> hbonds sel restrict cross intraMol false intraRes false reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
5 hydrogen bonds found
> hide sel atoms
> show sel atoms
> style sel ball
Changed 230 atom styles
> select all
8885 atoms, 9121 bonds, 8 pseudobonds, 444 residues, 3 models selected
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D /E /F
Alignment identifier is 1
> select /G:1-7
230 atoms, 248 bonds, 7 residues, 1 model selected
> style sel stick
Changed 230 atom styles
> show sel atoms
> hide sel atoms
> undo
[Repeated 1 time(s)]
> hide #1.2 models
> select ~sel & ##selected
8655 atoms, 8873 bonds, 8 pseudobonds, 437 residues, 3 models selected
> select ~sel & ##selected
230 atoms, 248 bonds, 7 residues, 1 model selected
> select ~sel & ##selected
8655 atoms, 8873 bonds, 8 pseudobonds, 437 residues, 3 models selected
> select /G:66-72
229 atoms, 246 bonds, 7 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 229 atom styles
> ui tool show H-Bonds
[Repeated 1 time(s)]
> hbonds sel color #0056cd showDist true restrict cross intraMol false
> intraRes false select true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 3 NH1 /G GUA 70 O1P /B ARG 3 HH11 2.736 1.758
/B LYS 50 NZ /G GUA 67 O1P /B LYS 50 HZ1 2.697 1.663
/B LYS 54 NZ /G CYT 66 O2P /B LYS 54 HZ1 2.698 1.667
/D THR 2 N /G CYT 72 O2' /D THR 2 HN 2.894 2.021
/D ARG 11 NH2 /G GUA 67 O6 /D ARG 11 HH22 3.040 2.149
/D LYS 25 NZ /G GUA 70 N7 /D LYS 25 HZ1 2.850 1.855
/G CYT 66 O2' /D ASP 20 OD1 /G CYT 66 H2' 2.654 1.709
7 hydrogen bonds found
> show sel atoms
> style sel ball
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> select ~sel & ##selected
8871 atoms, 9121 bonds, 3 pseudobonds, 444 residues, 2 models selected
> select ~sel & ##selected
14 atoms, 7 pseudobonds, 11 residues, 2 models selected
> select ~sel & ##selected
8871 atoms, 9121 bonds, 3 pseudobonds, 444 residues, 2 models selected
> select ~sel & ##selected
14 atoms, 7 pseudobonds, 11 residues, 2 models selected
> select up
270 atoms, 270 bonds, 7 pseudobonds, 11 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 270 atom styles
> undo
[Repeated 9 time(s)]
> select /G:66-72
229 atoms, 246 bonds, 7 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0056cd showDist true restrict cross intraMol false
> intraRes false select true reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 3 NH1 /G GUA 70 O1P /B ARG 3 HH11 2.736 1.758
/B LYS 50 NZ /G GUA 67 O1P /B LYS 50 HZ1 2.697 1.663
/B LYS 54 NZ /G CYT 66 O2P /B LYS 54 HZ1 2.698 1.667
/D THR 2 N /G CYT 72 O2' /D THR 2 HN 2.894 2.021
/D ARG 11 NH2 /G GUA 67 O6 /D ARG 11 HH22 3.040 2.149
/D LYS 25 NZ /G GUA 70 N7 /D LYS 25 HZ1 2.850 1.855
/G CYT 66 O2' /D ASP 20 OD1 /G CYT 66 H2' 2.654 1.709
7 hydrogen bonds found
> undo
> show #!1.2 models
> undo
> hide sel atoms
> ui tool show H-Bonds
> hbonds sel color #0056cd showDist true restrict cross intraMol false
> intraRes false select true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 3 NH1 /G GUA 70 O1P /B ARG 3 HH11 2.736 1.758
/B LYS 50 NZ /D ASP 20 OD1 /B LYS 50 HZ3 2.616 1.624
/B LYS 50 NZ /G GUA 67 O1P /B LYS 50 HZ1 2.697 1.663
/B LYS 54 NZ /G CYT 66 O2P /B LYS 54 HZ1 2.698 1.667
/D THR 2 N /G CYT 72 O2' /D THR 2 HN 2.894 2.021
/D ARG 11 NH2 /G GUA 67 O6 /D ARG 11 HH22 3.040 2.149
/D LYS 25 NZ /G GUA 70 N7 /D LYS 25 HZ1 2.850 1.855
/G CYT 66 O2' /D ASP 20 OD1 /G CYT 66 H2' 2.654 1.709
8 hydrogen bonds found
> hide sel atoms
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select ~sel & ##selected
8870 atoms, 9121 bonds, 3 pseudobonds, 444 residues, 2 models selected
> select ~sel & ##selected
15 atoms, 8 pseudobonds, 11 residues, 2 models selected
> select up
270 atoms, 270 bonds, 8 pseudobonds, 11 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> style sel stick
Changed 270 atom styles
> show sel atoms
> show #!1.2 models
> select ~sel & ##selected
8615 atoms, 8851 bonds, 3 pseudobonds, 433 residues, 2 models selected
> select ~sel & ##selected
270 atoms, 270 bonds, 8 pseudobonds, 11 residues, 2 models selected
> select ~sel & ##selected
8615 atoms, 8851 bonds, 3 pseudobonds, 433 residues, 2 models selected
> select ~sel & ##selected
270 atoms, 270 bonds, 8 pseudobonds, 11 residues, 2 models selected
> select ~sel & ##selected
8615 atoms, 8851 bonds, 3 pseudobonds, 433 residues, 2 models selected
> select ~sel & ##selected
270 atoms, 270 bonds, 8 pseudobonds, 11 residues, 2 models selected
> select up
4277 atoms, 4514 bonds, 8 pseudobonds, 169 residues, 2 models selected
> select up
4941 atoms, 5180 bonds, 8 pseudobonds, 208 residues, 2 models selected
> select down
4277 atoms, 4514 bonds, 8 pseudobonds, 169 residues, 2 models selected
> select down
270 atoms, 270 bonds, 8 pseudobonds, 11 residues, 2 models selected
> ui tool show "Color Actions"
> set bgColor white
> ui tool show "Color Actions"
> color sel byelement target a
> label height 2.0
> label height 1.0
> color #1.2.1 #643ad0ff models
> color #1.2.1 black models
> hide #1.2.1 models
> label sel
> select up
4277 atoms, 4514 bonds, 8 pseudobonds, 169 residues, 2 models selected
> select up
4941 atoms, 5180 bonds, 8 pseudobonds, 208 residues, 2 models selected
> select down
4277 atoms, 4514 bonds, 8 pseudobonds, 169 residues, 2 models selected
> select down
270 atoms, 270 bonds, 8 pseudobonds, 11 residues, 2 models selected
> select down
15 atoms, 8 pseudobonds, 11 residues, 2 models selected
> select down
14 atoms, 8 pseudobonds, 11 residues, 2 models selected
> select down
14 atoms, 8 pseudobonds, 11 residues, 2 models selected
> select up
270 atoms, 270 bonds, 8 pseudobonds, 11 residues, 2 models selected
> label height 1.5
> hide #1.3 models
> show #1.3 models
> save /Users/alexeykovalenko/Desktop/cl0_label_orient_66-72.cxs
> hide #1.3 models
> select all
8885 atoms, 9121 bonds, 11 pseudobonds, 444 residues, 5 models selected
> cartoon style (#!1 & sel) xsection rectangle modeHelix default
> cartoon style (#!1 & sel & coil) xsection oval
> cartoon style (#!1 & sel) xsection barbell modeHelix default
> cartoon style (#!1 & sel) modeHelix tube sides 20
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2969 atom styles
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select all
8885 atoms, 9121 bonds, 11 pseudobonds, 444 residues, 5 models selected
> select ::name="CYT"::name="GUA"
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> ui tool show "Color Actions"
> cartoon style nucleic width 2.5 thickness 1.0
> cartoon style nucleic width 1.5 thickness 1.0
> cartoon style nucleic width 1.5 thickness 0.5
> cartoon style nucleic width 0.5 thickness 0.25
> cartoon style nucleic width 1 thickness 0.3
> show #1.3 models
> hide #1.3 models
> transparency protein 70 target r
> transparency nucleic 80 target r
> show #1.3 models
> hide #1.3 models
> save /Users/alexeykovalenko/Desktop/clust0_transparent.cxs
> select /G:57-65
297 atoms, 320 bonds, 9 residues, 1 model selected
> select down
14 atoms, 11 residues, 1 model selected
> select up
270 atoms, 270 bonds, 11 residues, 1 model selected
> select up
4277 atoms, 4514 bonds, 169 residues, 1 model selected
> select up
4941 atoms, 5180 bonds, 208 residues, 1 model selected
> select ~sel & ##selected
3944 atoms, 3941 bonds, 3 pseudobonds, 236 residues, 2 models selected
> select ~sel & ##selected
4941 atoms, 5180 bonds, 8 pseudobonds, 208 residues, 2 models selected
> select ~sel & ##selected
3944 atoms, 3941 bonds, 3 pseudobonds, 236 residues, 2 models selected
> select ~sel & ##selected
4941 atoms, 5180 bonds, 8 pseudobonds, 208 residues, 2 models selected
> select ~sel & ##selected
3944 atoms, 3941 bonds, 3 pseudobonds, 236 residues, 2 models selected
> select ~sel & ##selected
4941 atoms, 5180 bonds, 8 pseudobonds, 208 residues, 2 models selected
> select ~sel & ##selected
3944 atoms, 3941 bonds, 3 pseudobonds, 236 residues, 2 models selected
> select ~sel & ##selected
4941 atoms, 5180 bonds, 8 pseudobonds, 208 residues, 2 models selected
> select up
8885 atoms, 9121 bonds, 8 pseudobonds, 444 residues, 2 models selected
> hide sel atoms
> select /G:57-65
297 atoms, 320 bonds, 9 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0056cd showDist true restrict cross intraMol false
> intraRes false select true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 11 NH1 /G GUA 62 O2P /B ARG 11 HH12 2.889 1.937
/B ARG 11 NH2 /G GUA 62 O1P /B ARG 11 HH22 2.765 1.787
/B LYS 13 NZ /G GUA 64 O2P /B LYS 13 HZ2 2.760 1.831
/B ASN 14 N /G GUA 63 O1P /B ASN 14 HN 2.803 1.810
/B ASN 14 ND2 /G GUA 63 O1P /B ASN 14 HD22 2.911 1.930
/B LYS 16 NZ /G GUA 62 O2' /B LYS 16 HZ3 2.939 1.970
/B ARG 39 NH2 /G GUA 64 O1P /B ARG 39 HH21 2.716 1.801
/B LYS 55 N /G CYT 65 O1P /B LYS 55 HN 3.025 2.046
/E LYS 47 NZ /G GUA 58 O1P /E LYS 47 HZ2 2.643 1.615
/E LYS 47 NZ /G CYT 59 O1P /E LYS 47 HZ3 2.678 1.652
/E LYS 50 NZ /G CYT 59 O2P /E LYS 50 HZ2 2.825 1.801
/E LYS 54 NZ /G GUA 58 N7 /E LYS 54 HZ1 3.022 2.124
/E LYS 54 NZ /G GUA 58 O6 /E LYS 54 HZ2 2.605 1.708
13 hydrogen bonds found
> select up
392 atoms, 398 bonds, 15 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 392 atom styles
> style sel stick
Changed 392 atom styles
> ui tool show "Color Actions"
> color sel byelement target a
> show #1.3 models
> hide #1.3 models
> label sel
> show #1.3 models
> hide #1.3 models
> label delete
> label sel
> save /Users/alexeykovalenko/Desktop/cl0_label_orient_57-65.cxs
> save "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/clust0_chimera/clust0_orient_trans_57-65.cxs"
——— End of log from Fri May 9 13:26:45 2025 ———
opened ChimeraX session
> label delete
> select nucleic
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel #f5ffffff
> color sel #f599ffff
> color sel #f59900ff
> select all
8885 atoms, 9121 bonds, 16 pseudobonds, 444 residues, 3 models selected
> hide sel atoms
> select nucleic
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0056cd restrict both interModel false intraRes false
> select true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
161 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/G GUA 1 O2' /G GUA 2 O4' /G GUA 1 H2' 2.814 1.952
/G GUA 1 O2' /G GUA 2 O5' /G GUA 1 H2' 3.133 2.461
/G GUA 2 N1 /G GUA 85 O4' /G GUA 2 H1 3.262 2.363
/G GUA 2 N2 /G GUA 85 O4' /G GUA 2 H21 3.593 2.984
/G GUA 2 N2 /G GUA 85 O5' /G GUA 2 H21 2.895 1.913
/G GUA 3 N1 /G CYT 90 N3 /G GUA 3 H1 2.840 1.850
/G GUA 3 N2 /G CYT 90 O2 /G GUA 3 H21 2.933 1.940
/G GUA 4 N1 /G CYT 89 N3 /G GUA 4 H1 2.930 1.946
/G GUA 4 N1 /G CYT 89 O2 /G GUA 4 H1 3.350 2.537
/G GUA 4 N2 /G CYT 89 O2 /G GUA 4 H22 3.049 2.079
/G CYT 5 N4 /G GUA 88 O6 /G CYT 5 H42 2.964 1.978
/G CYT 5 O2' /G CYT 6 O5' /G CYT 5 H2' 2.917 2.152
/G CYT 6 N4 /G GUA 87 O6 /G CYT 6 H41 3.048 2.085
/G GUA 9 N1 /G GUA 1 N7 /G GUA 9 H1 3.442 2.534
/G GUA 9 N1 /G GUA 1 O6 /G GUA 9 H1 3.015 2.229
/G GUA 9 N2 /G GUA 1 N7 /G GUA 9 H22 3.075 2.104
/G GUA 9 N2 /G CYT 84 O2 /G GUA 9 H21 2.636 1.700
/G GUA 9 O2' /G GUA 10 O4' /G GUA 9 H2' 3.104 2.253
/G GUA 9 O2' /G GUA 10 O5' /G GUA 9 H2' 3.187 2.511
/G CYT 11 N4 /G GUA 10 O2P /G CYT 11 H42 3.102 2.199
/G CYT 12 N4 /G GUA 10 O1P /G CYT 12 H42 2.840 1.981
/G CYT 12 N4 /G GUA 10 O3' /G CYT 12 H41 3.333 2.539
/G CYT 12 N4 /G CYT 11 O2P /G CYT 12 H41 2.976 2.062
/G GUA 15 O2' /G GUA 16 O4' /G GUA 15 H2' 3.281 2.560
/G GUA 15 O2' /G GUA 16 O5' /G GUA 15 H2' 2.946 2.149
/G GUA 16 O2' /G CYT 17 O4' /G GUA 16 H2' 3.026 2.079
/G CYT 17 N4 /G GUA 16 O2P /G CYT 17 H41 2.652 1.743
/G CYT 17 O2' /G CYT 18 O5' /G CYT 17 H2' 2.847 2.099
/G CYT 18 N4 /G GUA 15 O6 /G CYT 18 H42 3.335 2.377
/G CYT 18 N4 /G GUA 81 N7 /G CYT 18 H41 3.020 2.061
/G GUA 19 N2 /G GUA 80 N3 /G GUA 19 H21 3.317 2.334
/G GUA 19 N2 /G GUA 80 O2' /G GUA 19 H22 2.735 1.766
/G GUA 19 N2 /G GUA 81 O4' /G GUA 19 H22 3.646 2.984
/G GUA 21 O2' /G GUA 22 O4' /G GUA 21 H2' 3.359 2.531
/G GUA 22 N2 /G CYT 24 O2P /G GUA 22 H22 2.821 2.141
/G GUA 22 O2' /G CYT 23 O1P /G GUA 22 H2' 3.012 2.138
/G CYT 23 O2' /G CYT 24 O1P /G CYT 23 H2' 2.678 1.828
/G CYT 24 N4 /G CYT 23 O1P /G CYT 24 H42 3.249 2.396
/G GUA 25 N1 /G CYT 18 O2P /G GUA 25 H1 2.692 1.707
/G GUA 25 N2 /G CYT 18 O2P /G GUA 25 H21 2.935 2.172
/G GUA 26 N1 /G GUA 19 O2P /G GUA 26 H1 2.816 1.883
/G GUA 26 N2 /G GUA 19 O2P /G GUA 26 H22 2.860 2.041
/G GUA 27 N1 /G GUA 20 O2P /G GUA 27 H1 3.165 2.339
/G GUA 27 N2 /G GUA 19 O1P /G GUA 27 H21 3.238 2.489
/G GUA 27 N2 /G GUA 20 O2P /G GUA 27 H22 3.002 2.134
/G GUA 28 N2 /G GUA 20 O1P /G GUA 28 H21 2.919 1.945
/G GUA 28 N2 /G GUA 21 O2P /G GUA 28 H22 2.855 1.995
/G GUA 28 O2' /G CYT 29 O4' /G GUA 28 H2' 2.877 1.976
/G GUA 28 O2' /G CYT 29 O5' /G GUA 28 H2' 3.336 2.630
/G CYT 29 N4 /G GUA 21 O2P /G CYT 29 H41 2.711 1.718
/G CYT 29 O2' /G CYT 30 O4' /G CYT 29 H2' 2.874 2.230
/G CYT 29 O2' /G CYT 30 O5' /G CYT 29 H2' 2.945 2.164
/G GUA 31 N1 /G GUA 21 O1P /G GUA 31 H1 2.884 2.179
/G GUA 31 N2 /G GUA 21 O1P /G GUA 31 H21 2.739 1.862
/G GUA 31 O2' /G GUA 32 O4' /G GUA 31 H2' 3.005 2.126
/G GUA 32 N1 /G GUA 22 O1P /G GUA 32 H1 3.023 2.023
/G GUA 32 N2 /G GUA 21 O3' /G GUA 32 H22 3.012 2.034
/G GUA 33 O2' /G CYT 72 O1P /G GUA 33 H2' 2.532 1.598
/G CYT 35 N4 /G CYT 41 N3 /G CYT 35 H42 3.004 2.044
/G CYT 36 N4 /G GUA 34 O1P /G CYT 36 H41 2.964 2.217
/G CYT 36 N4 /G CYT 35 O2P /G CYT 36 H42 2.782 1.863
/G CYT 36 O2' /G GUA 37 O1P /G CYT 36 H2' 2.650 1.762
/G GUA 37 N1 /G CYT 41 O4' /G GUA 37 H1 2.901 1.972
/G GUA 37 N2 /G CYT 41 O4' /G GUA 37 H22 3.542 2.761
/G GUA 37 O2' /G CYT 36 O2P /G GUA 37 H2' 2.682 1.725
/G GUA 39 O2' /G GUA 40 O4' /G GUA 39 H2' 3.198 2.348
/G GUA 39 O2' /G GUA 40 O5' /G GUA 39 H2' 3.246 2.503
/G GUA 40 N2 /G GUA 69 N7 /G GUA 40 H21 3.127 2.350
/G GUA 40 N2 /G GUA 69 O1P /G GUA 40 H22 2.684 1.689
/G GUA 40 O2' /G GUA 68 N3 /G GUA 40 H2' 2.920 1.974
/G CYT 41 N4 /G GUA 33 O3' /G CYT 41 H42 3.389 2.562
/G CYT 41 N4 /G GUA 34 N7 /G CYT 41 H41 3.102 2.112
/G CYT 41 N4 /G GUA 34 O1P /G CYT 41 H42 3.307 2.664
/G CYT 41 O2' /G CYT 42 O4' /G CYT 41 H2' 3.233 2.503
/G CYT 41 O2' /G CYT 42 O5' /G CYT 41 H2' 2.887 2.037
/G GUA 43 N1 /G GUA 33 O1P /G GUA 43 H1 2.952 2.056
/G GUA 43 N2 /G GUA 32 O1P /G GUA 43 H21 3.378 2.492
/G GUA 43 N2 /G GUA 33 O1P /G GUA 43 H22 2.829 1.861
/G GUA 44 N1 /G GUA 33 O4' /G GUA 44 H1 3.580 2.583
/G GUA 45 N2 /G GUA 33 O2' /G GUA 45 H22 3.061 2.247
/G CYT 47 N4 /G CYT 71 O1P /G CYT 47 H42 2.914 2.100
/G CYT 47 N4 /G GUA 74 O6 /G CYT 47 H41 3.053 2.147
/G CYT 47 O2' /G CYT 48 O4' /G CYT 47 H2' 3.248 2.405
/G CYT 47 O2' /G CYT 48 O5' /G CYT 47 H2' 2.897 2.135
/G CYT 48 N4 /G GUA 70 O2' /G CYT 48 H42 3.340 2.395
/G CYT 48 N4 /G GUA 73 O6 /G CYT 48 H41 2.688 1.700
/G GUA 49 N1 /G GUA 70 O2P /G GUA 49 H1 2.894 1.899
/G GUA 49 N2 /G GUA 69 O3' /G GUA 49 H21 3.241 2.330
/G GUA 49 O2' /G GUA 50 O4' /G GUA 49 H2' 2.697 1.855
/G GUA 50 N2 /G GUA 69 N3 /G GUA 50 H22 3.193 2.233
/G GUA 50 N2 /G GUA 69 O2' /G GUA 50 H21 2.880 2.028
/G GUA 50 O2' /G GUA 51 O4' /G GUA 50 H2' 2.695 1.906
/G GUA 50 O2' /G GUA 51 O5' /G GUA 50 H2' 3.080 2.293
/G GUA 51 O2' /G GUA 52 O4' /G GUA 51 H2' 2.826 1.974
/G GUA 51 O2' /G GUA 52 O5' /G GUA 51 H2' 3.013 2.274
/G GUA 52 N1 /G GUA 68 O2P /G GUA 52 H1 2.883 1.975
/G GUA 52 N2 /G GUA 68 O2P /G GUA 52 H21 2.847 1.997
/G GUA 52 O2' /G CYT 53 O2P /G GUA 52 H2' 2.650 1.714
/G CYT 53 O2' /G CYT 54 O1P /G CYT 53 H2' 3.019 2.118
/G CYT 54 N4 /G CYT 53 O2P /G CYT 54 H41 2.824 1.825
/G GUA 55 O2' /G GUA 56 O4' /G GUA 55 H2' 2.916 1.971
/G GUA 56 N1 /G CYT 65 O2' /G GUA 56 H1 3.330 2.367
/G GUA 56 N2 /G CYT 65 O4' /G GUA 56 H21 3.395 2.499
/G GUA 56 O2' /G GUA 57 O4' /G GUA 56 H2' 2.830 1.951
/G GUA 56 O2' /G GUA 57 O5' /G GUA 56 H2' 3.318 2.664
/G GUA 57 O2' /G GUA 64 O6 /G GUA 57 H2' 2.703 1.857
/G GUA 58 O2' /G CYT 59 O5' /G GUA 58 H2' 2.883 2.001
/G CYT 59 O2' /G CYT 60 O4' /G CYT 59 H2' 2.970 2.034
/G CYT 60 O2' /G GUA 61 O2P /G CYT 60 H2' 3.211 2.429
/G GUA 62 O2' /G GUA 63 O4' /G GUA 62 H2' 2.759 1.817
/G GUA 63 N2 /G GUA 57 N7 /G GUA 63 H22 3.332 2.700
/G GUA 63 N2 /G GUA 57 O6 /G GUA 63 H22 3.485 2.885
/G GUA 63 O2' /G GUA 64 O4' /G GUA 63 H2' 3.211 2.443
/G GUA 63 O2' /G GUA 64 O5' /G GUA 63 H2' 3.219 2.404
/G GUA 64 O2' /G CYT 65 O4' /G GUA 64 H2' 2.987 2.077
/G CYT 65 N4 /G GUA 64 O2P /G CYT 65 H41 2.817 1.823
/G CYT 65 O2' /G CYT 66 O1P /G CYT 65 H2' 2.986 2.071
/G GUA 67 O2' /G GUA 68 O4' /G GUA 67 H2' 3.215 2.500
/G GUA 67 O2' /G GUA 68 O5' /G GUA 67 H2' 2.971 2.110
/G GUA 68 O2' /G GUA 40 O2' /G GUA 68 H2' 2.892 1.962
/G GUA 69 O2' /G GUA 68 O1P /G GUA 69 H2' 2.518 1.593
/G GUA 70 N1 /G GUA 49 O2P /G GUA 70 H1 2.866 1.935
/G GUA 70 N2 /G GUA 49 O4' /G GUA 70 H22 2.854 2.214
/G GUA 70 N2 /G GUA 49 O5' /G GUA 70 H22 2.966 2.020
/G GUA 73 N1 /G CYT 48 N3 /G GUA 73 H1 2.956 1.970
/G GUA 73 N2 /G CYT 48 O2 /G GUA 73 H21 3.026 2.050
/G GUA 74 N1 /G CYT 47 N3 /G GUA 74 H1 2.916 1.932
/G GUA 74 N2 /G CYT 47 O2 /G GUA 74 H21 2.787 1.814
/G GUA 75 N1 /G GUA 46 O2P /G GUA 75 H1 3.264 2.371
/G GUA 75 N2 /G GUA 46 N7 /G GUA 75 H21 3.008 2.013
/G GUA 75 N2 /G GUA 46 O2P /G GUA 75 H22 2.749 1.787
/G GUA 75 O2' /G GUA 46 O6 /G GUA 75 H2' 2.747 1.838
/G GUA 76 N1 /G GUA 45 O2' /G GUA 76 H1 3.071 2.262
/G GUA 76 N1 /G GUA 45 O3' /G GUA 76 H1 3.333 2.520
/G GUA 76 N2 /G GUA 45 O3' /G GUA 76 H22 3.016 2.039
/G GUA 76 N2 /G GUA 46 O4' /G GUA 76 H21 3.205 2.524
/G CYT 77 N4 /G GUA 76 O2P /G CYT 77 H41 2.895 1.939
/G CYT 78 N4 /G GUA 76 O1P /G CYT 78 H41 2.801 1.832
/G CYT 78 N4 /G CYT 77 O2P /G CYT 78 H42 3.315 2.422
/G GUA 79 O2' /G CYT 78 O1P /G GUA 79 H2' 2.645 1.697
/G GUA 80 N1 /G GUA 13 O2P /G GUA 80 H1 3.223 2.244
/G GUA 80 O2' /G GUA 81 O4' /G GUA 80 H2' 2.753 2.049
/G GUA 80 O2' /G GUA 81 O5' /G GUA 80 H2' 2.955 2.167
/G GUA 81 N1 /G CYT 12 O2P /G GUA 81 H1 2.890 1.970
/G GUA 81 N2 /G CYT 12 O2P /G GUA 81 H22 2.681 1.749
/G GUA 81 O2' /G GUA 82 O4' /G GUA 81 H2' 2.889 2.046
/G GUA 81 O2' /G GUA 82 O5' /G GUA 81 H2' 3.420 2.668
/G CYT 83 N4 /G CYT 11 O1P /G CYT 83 H41 3.177 2.225
/G CYT 83 N4 /G GUA 82 O2P /G CYT 83 H42 3.168 2.468
/G CYT 84 N4 /G GUA 1 O2' /G CYT 84 H42 3.103 2.253
/G GUA 85 N1 /G GUA 3 O1P /G GUA 85 H1 2.725 1.723
/G GUA 85 O2' /G GUA 86 O4' /G GUA 85 H2' 2.807 2.004
/G GUA 85 O2' /G GUA 86 O5' /G GUA 85 H2' 3.059 2.281
/G GUA 86 N2 /G GUA 88 O6 /G GUA 86 H21 3.660 2.815
/G GUA 87 N1 /G CYT 6 N3 /G GUA 87 H1 3.012 2.016
/G GUA 87 N2 /G CYT 6 O2 /G GUA 87 H22 2.709 1.722
/G GUA 88 N1 /G CYT 5 N3 /G GUA 88 H1 3.000 1.981
/G GUA 88 N2 /G CYT 5 O2 /G GUA 88 H21 2.825 1.820
/G CYT 89 N4 /G GUA 4 O6 /G CYT 89 H41 2.881 1.920
/G CYT 89 O2' /G CYT 90 O4' /G CYT 89 H2' 3.206 2.409
/G CYT 90 N4 /G GUA 3 O6 /G CYT 90 H42 2.741 1.761
161 hydrogen bonds found
> show sel cartoons
> show sel atoms
> style sel stick
Changed 277 atom styles
> style sel stick
Changed 277 atom styles
> show sel atoms
> style sel stick
Changed 277 atom styles
> select up
2833 atoms, 3057 bonds, 86 residues, 1 model selected
> style sel stick
Changed 2833 atom styles
> select up
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> select up
8885 atoms, 9121 bonds, 444 residues, 1 model selected
> select up
8885 atoms, 9121 bonds, 444 residues, 1 model selected
> style sel stick
Changed 8885 atom styles
> show sel atoms
> undo
> select down
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> style sel stick
Changed 2969 atom styles
> show sel atoms
> undo
> select down
2833 atoms, 3057 bonds, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> select down
277 atoms, 86 residues, 1 model selected
> style sel stick
Changed 277 atom styles
> show sel atoms
> select up
2833 atoms, 3057 bonds, 86 residues, 1 model selected
> style sel stick
Changed 2833 atom styles
> show sel atoms
> save /Users/alexeykovalenko/Desktop/clust0_intraRNA.cxs
> save "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/clust0_chimera/clust0_intraRNA.cxs"
——— End of log from Fri May 9 14:26:47 2025 ———
opened ChimeraX session
> hide sel atoms
> cartoon style nucleic width 1 thickness 0.3
> transparency nucleic 80 target r
> select /G:75-85
362 atoms, 390 bonds, 9 pseudobonds, 11 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #0056cd restrict cross intraMol false intraRes false select
> true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/C LYS 23 NZ /G CYT 83 N3 /C LYS 23 HZ2 2.915 1.926
/D ARG 36 NH1 /G CYT 77 O1P /D ARG 36 HH12 3.132 2.171
/D ARG 36 NH1 /G CYT 78 O2P /D ARG 36 HH11 2.638 1.687
/D ARG 36 NH2 /G CYT 78 O2P /D ARG 36 HH22 3.003 2.123
/G GUA 82 N2 /C SER 19 O /G GUA 82 H21 3.239 2.481
5 hydrogen bonds found
> style sel stick
Changed 9 atom styles
> show sel atoms
> select up
184 atoms, 188 bonds, 7 residues, 1 model selected
> style sel stick
Changed 184 atom styles
> show sel atoms
> undo
[Repeated 3 time(s)]
> select /G:70
34 atoms, 36 bonds, 1 residue, 1 model selected
> select up
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> select down
34 atoms, 36 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0056cd restrict cross intraMol false intraRes false select
> true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 3 NH1 /G GUA 70 O1P /B ARG 3 HH11 2.736 1.758
/D LYS 25 NZ /G GUA 70 N7 /D LYS 25 HZ1 2.850 1.855
2 hydrogen bonds found
> select up
80 atoms, 80 bonds, 3 residues, 1 model selected
> style sel stick
Changed 80 atom styles
> style sel stick
Changed 80 atom styles
> show sel atoms
> color sel byelement
> select up
4044 atoms, 4281 bonds, 156 residues, 1 model selected
> select up
4941 atoms, 5180 bonds, 208 residues, 1 model selected
> select down
4044 atoms, 4281 bonds, 156 residues, 1 model selected
> select down
80 atoms, 80 bonds, 3 residues, 1 model selected
> label sele
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label sel
> save "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/clust0_chimera/cl0_sel_72.cxs"
> undo
[Repeated 5 time(s)]
> label delete
> select /G:51-56
198 atoms, 213 bonds, 6 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0056cd restrict cross intraMol false intraRes false select
> true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/D ARG 11 N /G GUA 52 O1P /D ARG 11 HN 2.751 1.807
/D ARG 11 NE /G CYT 53 O1P /D ARG 11 HE 2.653 1.761
/D ARG 11 NH2 /G CYT 53 O1P /D ARG 11 HH21 2.998 2.122
/D LYS 13 NZ /G CYT 54 O2P /D LYS 13 HZ1 2.748 1.754
/D LYS 13 NZ /G GUA 55 O2P /D LYS 13 HZ3 2.730 1.693
/D ASN 14 ND2 /G GUA 55 O6 /D ASN 14 HD22 3.049 2.400
/E LYS 55 NZ /G GUA 56 O1P /E LYS 55 HZ3 2.609 1.625
/E LYS 59 NZ /G GUA 56 O1P /E LYS 59 HZ2 2.990 2.051
/F SER 41 OG /G CYT 53 O2 /F SER 41 HG1 2.548 1.690
9 hydrogen bonds found
> style sel stick
Changed 16 atom styles
> show sel atoms
> select up
280 atoms, 287 bonds, 11 residues, 1 model selected
> style sel stick
Changed 280 atom styles
> show sel atoms
> color sel byelement
> save "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/clust0_chimera/cl0_sel_51-56.cxs"
> undo
[Repeated 4 time(s)]
> label sel
> label delete
> select protein
5916 atoms, 5913 bonds, 3 pseudobonds, 354 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #0056cd restrict cross intraMol false intraRes false select
> true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
89 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 5 N /G GUA 87 O2' /A ASN 5 HN 2.885 1.962
/A ASN 5 ND2 /G GUA 88 O4' /A ASN 5 HD21 2.969 2.020
/A GLU 8 N /G GUA 88 O3' /A GLU 8 HN 2.933 1.971
/A GLU 8 N /G CYT 89 O1P /A GLU 8 HN 3.212 2.471
/A LEU 9 N /G GUA 88 O2' /A LEU 9 HN 3.048 2.100
/A SER 21 OG /G CYT 5 O2' /A SER 21 HG1 3.399 2.676
/A LYS 23 NZ /G CYT 6 O2P /A LYS 23 HZ2 2.715 1.684
/A GLY 24 N /G CYT 6 O3' /A GLY 24 HN 3.243 2.248
/A LYS 25 NZ /G GUA 7 O2' /A LYS 25 HZ1 3.016 2.142
/A ARG 26 NH2 /G GUA 88 N3 /A ARG 26 HH22 2.992 2.013
/B ARG 3 NH1 /G GUA 70 O1P /B ARG 3 HH11 2.736 1.758
/B ARG 7 NH1 /G GUA 49 O6 /B ARG 7 HH12 3.055 2.070
/B ARG 7 NH2 /G GUA 50 O6 /B ARG 7 HH22 3.030 2.311
/B ARG 11 NH1 /G GUA 62 O2P /B ARG 11 HH12 2.889 1.937
/B ARG 11 NH2 /G GUA 62 O1P /B ARG 11 HH22 2.765 1.787
/B LYS 13 NZ /G GUA 64 O2P /B LYS 13 HZ2 2.760 1.831
/B ASN 14 N /G GUA 63 O1P /B ASN 14 HN 2.803 1.810
/B ASN 14 ND2 /G GUA 63 O1P /B ASN 14 HD22 2.911 1.930
/B LYS 16 NZ /G GUA 62 O2' /B LYS 16 HZ3 2.939 1.970
/B ARG 39 NH2 /G GUA 64 O1P /B ARG 39 HH21 2.716 1.801
/B LYS 50 NZ /G GUA 67 O1P /B LYS 50 HZ1 2.697 1.663
/B LYS 54 NZ /G CYT 66 O2P /B LYS 54 HZ1 2.698 1.667
/B LYS 55 N /G CYT 65 O1P /B LYS 55 HN 3.025 2.046
/C MET 1 N /G GUA 26 O1P /C MET 1 HT1 2.630 1.591
/C ARG 7 NE /G GUA 28 O2P /C ARG 7 HE 3.139 2.226
/C ARG 7 NH1 /G CYT 29 O2P /C ARG 7 HH11 2.831 1.859
/C ARG 11 NE /G CYT 29 O3' /C ARG 11 HE 3.058 2.173
/C ARG 11 NE /G CYT 30 O1P /C ARG 11 HE 3.099 2.251
/C ARG 11 NH2 /G CYT 30 O1P /C ARG 11 HH21 2.639 1.697
/C LYS 13 NZ /G CYT 29 O2' /C LYS 13 HZ1 2.930 1.993
/C LYS 13 NZ /G CYT 30 O4' /C LYS 13 HZ1 3.391 2.600
/C LYS 23 NZ /G CYT 11 O1P /C LYS 23 HZ1 2.631 1.738
/C LYS 23 NZ /G CYT 83 N3 /C LYS 23 HZ2 2.915 1.926
/C ARG 26 NE /G GUA 14 O2' /C ARG 26 HE 2.713 1.709
/C ARG 26 NH2 /G GUA 14 O3' /C ARG 26 HH21 2.953 1.962
/C ARG 39 NE /G GUA 15 O1P /C ARG 39 HE 2.863 1.883
/C ARG 39 NH1 /G GUA 25 O2P /C ARG 39 HH12 2.743 1.885
/C ARG 39 NH2 /G GUA 15 O2P /C ARG 39 HH22 3.052 2.110
/C ARG 39 NH2 /G GUA 25 O2P /C ARG 39 HH21 2.900 2.223
/C LYS 54 NZ /G GUA 38 O2' /C LYS 54 HZ1 3.361 2.483
/C LYS 54 NZ /G GUA 38 O3' /C LYS 54 HZ1 3.317 2.448
/D THR 2 N /G CYT 72 O2' /D THR 2 HN 2.894 2.021
/D ARG 11 N /G GUA 52 O1P /D ARG 11 HN 2.751 1.807
/D ARG 11 NE /G CYT 53 O1P /D ARG 11 HE 2.653 1.761
/D ARG 11 NH2 /G CYT 53 O1P /D ARG 11 HH21 2.998 2.122
/D ARG 11 NH2 /G GUA 67 O6 /D ARG 11 HH22 3.040 2.149
/D LYS 13 NZ /G CYT 54 O2P /D LYS 13 HZ1 2.748 1.754
/D LYS 13 NZ /G GUA 55 O2P /D LYS 13 HZ3 2.730 1.693
/D ASN 14 ND2 /G GUA 55 O6 /D ASN 14 HD22 3.049 2.400
/D LYS 23 NZ /G GUA 49 O2P /D LYS 23 HZ3 2.745 1.742
/D LYS 25 N /G CYT 48 O1P /D LYS 25 HN 2.655 1.671
/D LYS 25 NZ /G CYT 48 O2P /D LYS 25 HZ2 2.745 1.774
/D LYS 25 NZ /G GUA 70 N7 /D LYS 25 HZ1 2.850 1.855
/D ARG 36 NH1 /G CYT 77 O1P /D ARG 36 HH12 3.132 2.171
/D ARG 36 NH1 /G CYT 78 O2P /D ARG 36 HH11 2.638 1.687
/D ARG 36 NH2 /G CYT 78 O2P /D ARG 36 HH22 3.003 2.123
/D LYS 47 NZ /G GUA 31 O3' /D LYS 47 HZ2 2.964 1.978
/D GLN 48 N /G GUA 43 O2' /D GLN 48 HN 3.106 2.122
/D LYS 50 NZ /G GUA 32 O2P /D LYS 50 HZ1 2.608 1.614
/D LYS 54 NZ /G CYT 29 O1P /D LYS 54 HZ3 2.710 1.722
/E LYS 47 NZ /G GUA 58 O1P /E LYS 47 HZ2 2.643 1.615
/E LYS 47 NZ /G CYT 59 O1P /E LYS 47 HZ3 2.678 1.652
/E LYS 50 NZ /G CYT 59 O2P /E LYS 50 HZ2 2.825 1.801
/E LYS 54 NZ /G GUA 58 N7 /E LYS 54 HZ1 3.022 2.124
/E LYS 54 NZ /G GUA 58 O6 /E LYS 54 HZ2 2.605 1.708
/E LYS 55 NZ /G GUA 56 O1P /E LYS 55 HZ3 2.609 1.625
/E LYS 59 NZ /G GUA 56 O1P /E LYS 59 HZ2 2.990 2.051
/F MET 1 N /G GUA 39 O6 /F MET 1 HT3 2.788 1.755
/F ARG 3 N /G GUA 39 N7 /F ARG 3 HN 3.262 2.296
/F ARG 3 NE /G GUA 39 O2P /F ARG 3 HE 2.741 1.823
/F ARG 3 NH2 /G GUA 39 O2P /F ARG 3 HH21 3.196 2.495
/F ARG 3 NH2 /G GUA 39 O4' /F ARG 3 HH21 2.857 2.099
/F GLN 6 NE2 /G GUA 39 O1P /F GLN 6 HE21 3.249 2.316
/F LYS 13 NZ /G CYT 36 O1P /F LYS 13 HZ2 2.822 1.825
/F LYS 13 NZ /G GUA 38 O1P /F LYS 13 HZ3 2.743 1.756
/F ARG 26 NH1 /G GUA 37 O2P /F ARG 26 HH12 2.816 1.896
/F ARG 26 NH2 /G GUA 37 O2P /F ARG 26 HH22 2.878 1.919
/F ARG 27 NH2 /G GUA 40 O2P /F ARG 27 HH22 2.782 1.807
/F SER 41 OG /G CYT 53 O2 /F SER 41 HG1 2.548 1.690
/G CYT 6 O2' /A GLY 24 O /G CYT 6 H2' 3.035 2.122
/G GUA 13 N1 /C LYS 23 O /G GUA 13 H1 2.899 2.137
/G GUA 14 N1 /C VAL 22 O /G GUA 14 H1 2.959 2.060
/G GUA 14 N2 /C VAL 22 O /G GUA 14 H21 3.161 2.305
/G GUA 15 N2 /C ASP 20 O /G GUA 15 H21 3.423 2.613
/G CYT 24 O2' /C GLU 42 OE1 /G CYT 24 H2' 2.982 2.246
/G GUA 38 O2' /F GLN 6 OE1 /G GUA 38 H2' 2.837 1.886
/G GUA 46 O2' /D LEU 31 O /G GUA 46 H2' 2.590 1.680
/G CYT 66 O2' /D ASP 20 OD1 /G CYT 66 H2' 2.654 1.709
/G GUA 82 N2 /C SER 19 O /G GUA 82 H21 3.239 2.481
89 hydrogen bonds found
> select up
2641 atoms, 2704 bonds, 102 residues, 1 model selected
> style sel stick
Changed 2641 atom styles
> show sel atoms
> undo
> select protein
5916 atoms, 5913 bonds, 3 pseudobonds, 354 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #0056cd restrict cross intraMol false intraRes false log
> true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
89 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 5 N /G GUA 87 O2' /A ASN 5 HN 2.885 1.962
/A ASN 5 ND2 /G GUA 88 O4' /A ASN 5 HD21 2.969 2.020
/A GLU 8 N /G GUA 88 O3' /A GLU 8 HN 2.933 1.971
/A GLU 8 N /G CYT 89 O1P /A GLU 8 HN 3.212 2.471
/A LEU 9 N /G GUA 88 O2' /A LEU 9 HN 3.048 2.100
/A SER 21 OG /G CYT 5 O2' /A SER 21 HG1 3.399 2.676
/A LYS 23 NZ /G CYT 6 O2P /A LYS 23 HZ2 2.715 1.684
/A GLY 24 N /G CYT 6 O3' /A GLY 24 HN 3.243 2.248
/A LYS 25 NZ /G GUA 7 O2' /A LYS 25 HZ1 3.016 2.142
/A ARG 26 NH2 /G GUA 88 N3 /A ARG 26 HH22 2.992 2.013
/B ARG 3 NH1 /G GUA 70 O1P /B ARG 3 HH11 2.736 1.758
/B ARG 7 NH1 /G GUA 49 O6 /B ARG 7 HH12 3.055 2.070
/B ARG 7 NH2 /G GUA 50 O6 /B ARG 7 HH22 3.030 2.311
/B ARG 11 NH1 /G GUA 62 O2P /B ARG 11 HH12 2.889 1.937
/B ARG 11 NH2 /G GUA 62 O1P /B ARG 11 HH22 2.765 1.787
/B LYS 13 NZ /G GUA 64 O2P /B LYS 13 HZ2 2.760 1.831
/B ASN 14 N /G GUA 63 O1P /B ASN 14 HN 2.803 1.810
/B ASN 14 ND2 /G GUA 63 O1P /B ASN 14 HD22 2.911 1.930
/B LYS 16 NZ /G GUA 62 O2' /B LYS 16 HZ3 2.939 1.970
/B ARG 39 NH2 /G GUA 64 O1P /B ARG 39 HH21 2.716 1.801
/B LYS 50 NZ /G GUA 67 O1P /B LYS 50 HZ1 2.697 1.663
/B LYS 54 NZ /G CYT 66 O2P /B LYS 54 HZ1 2.698 1.667
/B LYS 55 N /G CYT 65 O1P /B LYS 55 HN 3.025 2.046
/C MET 1 N /G GUA 26 O1P /C MET 1 HT1 2.630 1.591
/C ARG 7 NE /G GUA 28 O2P /C ARG 7 HE 3.139 2.226
/C ARG 7 NH1 /G CYT 29 O2P /C ARG 7 HH11 2.831 1.859
/C ARG 11 NE /G CYT 29 O3' /C ARG 11 HE 3.058 2.173
/C ARG 11 NE /G CYT 30 O1P /C ARG 11 HE 3.099 2.251
/C ARG 11 NH2 /G CYT 30 O1P /C ARG 11 HH21 2.639 1.697
/C LYS 13 NZ /G CYT 29 O2' /C LYS 13 HZ1 2.930 1.993
/C LYS 13 NZ /G CYT 30 O4' /C LYS 13 HZ1 3.391 2.600
/C LYS 23 NZ /G CYT 11 O1P /C LYS 23 HZ1 2.631 1.738
/C LYS 23 NZ /G CYT 83 N3 /C LYS 23 HZ2 2.915 1.926
/C ARG 26 NE /G GUA 14 O2' /C ARG 26 HE 2.713 1.709
/C ARG 26 NH2 /G GUA 14 O3' /C ARG 26 HH21 2.953 1.962
/C ARG 39 NE /G GUA 15 O1P /C ARG 39 HE 2.863 1.883
/C ARG 39 NH1 /G GUA 25 O2P /C ARG 39 HH12 2.743 1.885
/C ARG 39 NH2 /G GUA 15 O2P /C ARG 39 HH22 3.052 2.110
/C ARG 39 NH2 /G GUA 25 O2P /C ARG 39 HH21 2.900 2.223
/C LYS 54 NZ /G GUA 38 O2' /C LYS 54 HZ1 3.361 2.483
/C LYS 54 NZ /G GUA 38 O3' /C LYS 54 HZ1 3.317 2.448
/D THR 2 N /G CYT 72 O2' /D THR 2 HN 2.894 2.021
/D ARG 11 N /G GUA 52 O1P /D ARG 11 HN 2.751 1.807
/D ARG 11 NE /G CYT 53 O1P /D ARG 11 HE 2.653 1.761
/D ARG 11 NH2 /G CYT 53 O1P /D ARG 11 HH21 2.998 2.122
/D ARG 11 NH2 /G GUA 67 O6 /D ARG 11 HH22 3.040 2.149
/D LYS 13 NZ /G CYT 54 O2P /D LYS 13 HZ1 2.748 1.754
/D LYS 13 NZ /G GUA 55 O2P /D LYS 13 HZ3 2.730 1.693
/D ASN 14 ND2 /G GUA 55 O6 /D ASN 14 HD22 3.049 2.400
/D LYS 23 NZ /G GUA 49 O2P /D LYS 23 HZ3 2.745 1.742
/D LYS 25 N /G CYT 48 O1P /D LYS 25 HN 2.655 1.671
/D LYS 25 NZ /G CYT 48 O2P /D LYS 25 HZ2 2.745 1.774
/D LYS 25 NZ /G GUA 70 N7 /D LYS 25 HZ1 2.850 1.855
/D ARG 36 NH1 /G CYT 77 O1P /D ARG 36 HH12 3.132 2.171
/D ARG 36 NH1 /G CYT 78 O2P /D ARG 36 HH11 2.638 1.687
/D ARG 36 NH2 /G CYT 78 O2P /D ARG 36 HH22 3.003 2.123
/D LYS 47 NZ /G GUA 31 O3' /D LYS 47 HZ2 2.964 1.978
/D GLN 48 N /G GUA 43 O2' /D GLN 48 HN 3.106 2.122
/D LYS 50 NZ /G GUA 32 O2P /D LYS 50 HZ1 2.608 1.614
/D LYS 54 NZ /G CYT 29 O1P /D LYS 54 HZ3 2.710 1.722
/E LYS 47 NZ /G GUA 58 O1P /E LYS 47 HZ2 2.643 1.615
/E LYS 47 NZ /G CYT 59 O1P /E LYS 47 HZ3 2.678 1.652
/E LYS 50 NZ /G CYT 59 O2P /E LYS 50 HZ2 2.825 1.801
/E LYS 54 NZ /G GUA 58 N7 /E LYS 54 HZ1 3.022 2.124
/E LYS 54 NZ /G GUA 58 O6 /E LYS 54 HZ2 2.605 1.708
/E LYS 55 NZ /G GUA 56 O1P /E LYS 55 HZ3 2.609 1.625
/E LYS 59 NZ /G GUA 56 O1P /E LYS 59 HZ2 2.990 2.051
/F MET 1 N /G GUA 39 O6 /F MET 1 HT3 2.788 1.755
/F ARG 3 N /G GUA 39 N7 /F ARG 3 HN 3.262 2.296
/F ARG 3 NE /G GUA 39 O2P /F ARG 3 HE 2.741 1.823
/F ARG 3 NH2 /G GUA 39 O2P /F ARG 3 HH21 3.196 2.495
/F ARG 3 NH2 /G GUA 39 O4' /F ARG 3 HH21 2.857 2.099
/F GLN 6 NE2 /G GUA 39 O1P /F GLN 6 HE21 3.249 2.316
/F LYS 13 NZ /G CYT 36 O1P /F LYS 13 HZ2 2.822 1.825
/F LYS 13 NZ /G GUA 38 O1P /F LYS 13 HZ3 2.743 1.756
/F ARG 26 NH1 /G GUA 37 O2P /F ARG 26 HH12 2.816 1.896
/F ARG 26 NH2 /G GUA 37 O2P /F ARG 26 HH22 2.878 1.919
/F ARG 27 NH2 /G GUA 40 O2P /F ARG 27 HH22 2.782 1.807
/F SER 41 OG /G CYT 53 O2 /F SER 41 HG1 2.548 1.690
/G CYT 6 O2' /A GLY 24 O /G CYT 6 H2' 3.035 2.122
/G GUA 13 N1 /C LYS 23 O /G GUA 13 H1 2.899 2.137
/G GUA 14 N1 /C VAL 22 O /G GUA 14 H1 2.959 2.060
/G GUA 14 N2 /C VAL 22 O /G GUA 14 H21 3.161 2.305
/G GUA 15 N2 /C ASP 20 O /G GUA 15 H21 3.423 2.613
/G CYT 24 O2' /C GLU 42 OE1 /G CYT 24 H2' 2.982 2.246
/G GUA 38 O2' /F GLN 6 OE1 /G GUA 38 H2' 2.837 1.886
/G GUA 46 O2' /D LEU 31 O /G GUA 46 H2' 2.590 1.680
/G CYT 66 O2' /D ASP 20 OD1 /G CYT 66 H2' 2.654 1.709
/G GUA 82 N2 /C SER 19 O /G GUA 82 H21 3.239 2.481
89 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #0056cd restrict cross intraMol false intraRes false select
> true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A MET 1 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 chained_frame_20 copy.pdb
89 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 5 N /G GUA 87 O2' /A ASN 5 HN 2.885 1.962
/A ASN 5 ND2 /G GUA 88 O4' /A ASN 5 HD21 2.969 2.020
/A GLU 8 N /G GUA 88 O3' /A GLU 8 HN 2.933 1.971
/A GLU 8 N /G CYT 89 O1P /A GLU 8 HN 3.212 2.471
/A LEU 9 N /G GUA 88 O2' /A LEU 9 HN 3.048 2.100
/A SER 21 OG /G CYT 5 O2' /A SER 21 HG1 3.399 2.676
/A LYS 23 NZ /G CYT 6 O2P /A LYS 23 HZ2 2.715 1.684
/A GLY 24 N /G CYT 6 O3' /A GLY 24 HN 3.243 2.248
/A LYS 25 NZ /G GUA 7 O2' /A LYS 25 HZ1 3.016 2.142
/A ARG 26 NH2 /G GUA 88 N3 /A ARG 26 HH22 2.992 2.013
/B ARG 3 NH1 /G GUA 70 O1P /B ARG 3 HH11 2.736 1.758
/B ARG 7 NH1 /G GUA 49 O6 /B ARG 7 HH12 3.055 2.070
/B ARG 7 NH2 /G GUA 50 O6 /B ARG 7 HH22 3.030 2.311
/B ARG 11 NH1 /G GUA 62 O2P /B ARG 11 HH12 2.889 1.937
/B ARG 11 NH2 /G GUA 62 O1P /B ARG 11 HH22 2.765 1.787
/B LYS 13 NZ /G GUA 64 O2P /B LYS 13 HZ2 2.760 1.831
/B ASN 14 N /G GUA 63 O1P /B ASN 14 HN 2.803 1.810
/B ASN 14 ND2 /G GUA 63 O1P /B ASN 14 HD22 2.911 1.930
/B LYS 16 NZ /G GUA 62 O2' /B LYS 16 HZ3 2.939 1.970
/B ARG 39 NH2 /G GUA 64 O1P /B ARG 39 HH21 2.716 1.801
/B LYS 50 NZ /G GUA 67 O1P /B LYS 50 HZ1 2.697 1.663
/B LYS 54 NZ /G CYT 66 O2P /B LYS 54 HZ1 2.698 1.667
/B LYS 55 N /G CYT 65 O1P /B LYS 55 HN 3.025 2.046
/C MET 1 N /G GUA 26 O1P /C MET 1 HT1 2.630 1.591
/C ARG 7 NE /G GUA 28 O2P /C ARG 7 HE 3.139 2.226
/C ARG 7 NH1 /G CYT 29 O2P /C ARG 7 HH11 2.831 1.859
/C ARG 11 NE /G CYT 29 O3' /C ARG 11 HE 3.058 2.173
/C ARG 11 NE /G CYT 30 O1P /C ARG 11 HE 3.099 2.251
/C ARG 11 NH2 /G CYT 30 O1P /C ARG 11 HH21 2.639 1.697
/C LYS 13 NZ /G CYT 29 O2' /C LYS 13 HZ1 2.930 1.993
/C LYS 13 NZ /G CYT 30 O4' /C LYS 13 HZ1 3.391 2.600
/C LYS 23 NZ /G CYT 11 O1P /C LYS 23 HZ1 2.631 1.738
/C LYS 23 NZ /G CYT 83 N3 /C LYS 23 HZ2 2.915 1.926
/C ARG 26 NE /G GUA 14 O2' /C ARG 26 HE 2.713 1.709
/C ARG 26 NH2 /G GUA 14 O3' /C ARG 26 HH21 2.953 1.962
/C ARG 39 NE /G GUA 15 O1P /C ARG 39 HE 2.863 1.883
/C ARG 39 NH1 /G GUA 25 O2P /C ARG 39 HH12 2.743 1.885
/C ARG 39 NH2 /G GUA 15 O2P /C ARG 39 HH22 3.052 2.110
/C ARG 39 NH2 /G GUA 25 O2P /C ARG 39 HH21 2.900 2.223
/C LYS 54 NZ /G GUA 38 O2' /C LYS 54 HZ1 3.361 2.483
/C LYS 54 NZ /G GUA 38 O3' /C LYS 54 HZ1 3.317 2.448
/D THR 2 N /G CYT 72 O2' /D THR 2 HN 2.894 2.021
/D ARG 11 N /G GUA 52 O1P /D ARG 11 HN 2.751 1.807
/D ARG 11 NE /G CYT 53 O1P /D ARG 11 HE 2.653 1.761
/D ARG 11 NH2 /G CYT 53 O1P /D ARG 11 HH21 2.998 2.122
/D ARG 11 NH2 /G GUA 67 O6 /D ARG 11 HH22 3.040 2.149
/D LYS 13 NZ /G CYT 54 O2P /D LYS 13 HZ1 2.748 1.754
/D LYS 13 NZ /G GUA 55 O2P /D LYS 13 HZ3 2.730 1.693
/D ASN 14 ND2 /G GUA 55 O6 /D ASN 14 HD22 3.049 2.400
/D LYS 23 NZ /G GUA 49 O2P /D LYS 23 HZ3 2.745 1.742
/D LYS 25 N /G CYT 48 O1P /D LYS 25 HN 2.655 1.671
/D LYS 25 NZ /G CYT 48 O2P /D LYS 25 HZ2 2.745 1.774
/D LYS 25 NZ /G GUA 70 N7 /D LYS 25 HZ1 2.850 1.855
/D ARG 36 NH1 /G CYT 77 O1P /D ARG 36 HH12 3.132 2.171
/D ARG 36 NH1 /G CYT 78 O2P /D ARG 36 HH11 2.638 1.687
/D ARG 36 NH2 /G CYT 78 O2P /D ARG 36 HH22 3.003 2.123
/D LYS 47 NZ /G GUA 31 O3' /D LYS 47 HZ2 2.964 1.978
/D GLN 48 N /G GUA 43 O2' /D GLN 48 HN 3.106 2.122
/D LYS 50 NZ /G GUA 32 O2P /D LYS 50 HZ1 2.608 1.614
/D LYS 54 NZ /G CYT 29 O1P /D LYS 54 HZ3 2.710 1.722
/E LYS 47 NZ /G GUA 58 O1P /E LYS 47 HZ2 2.643 1.615
/E LYS 47 NZ /G CYT 59 O1P /E LYS 47 HZ3 2.678 1.652
/E LYS 50 NZ /G CYT 59 O2P /E LYS 50 HZ2 2.825 1.801
/E LYS 54 NZ /G GUA 58 N7 /E LYS 54 HZ1 3.022 2.124
/E LYS 54 NZ /G GUA 58 O6 /E LYS 54 HZ2 2.605 1.708
/E LYS 55 NZ /G GUA 56 O1P /E LYS 55 HZ3 2.609 1.625
/E LYS 59 NZ /G GUA 56 O1P /E LYS 59 HZ2 2.990 2.051
/F MET 1 N /G GUA 39 O6 /F MET 1 HT3 2.788 1.755
/F ARG 3 N /G GUA 39 N7 /F ARG 3 HN 3.262 2.296
/F ARG 3 NE /G GUA 39 O2P /F ARG 3 HE 2.741 1.823
/F ARG 3 NH2 /G GUA 39 O2P /F ARG 3 HH21 3.196 2.495
/F ARG 3 NH2 /G GUA 39 O4' /F ARG 3 HH21 2.857 2.099
/F GLN 6 NE2 /G GUA 39 O1P /F GLN 6 HE21 3.249 2.316
/F LYS 13 NZ /G CYT 36 O1P /F LYS 13 HZ2 2.822 1.825
/F LYS 13 NZ /G GUA 38 O1P /F LYS 13 HZ3 2.743 1.756
/F ARG 26 NH1 /G GUA 37 O2P /F ARG 26 HH12 2.816 1.896
/F ARG 26 NH2 /G GUA 37 O2P /F ARG 26 HH22 2.878 1.919
/F ARG 27 NH2 /G GUA 40 O2P /F ARG 27 HH22 2.782 1.807
/F SER 41 OG /G CYT 53 O2 /F SER 41 HG1 2.548 1.690
/G CYT 6 O2' /A GLY 24 O /G CYT 6 H2' 3.035 2.122
/G GUA 13 N1 /C LYS 23 O /G GUA 13 H1 2.899 2.137
/G GUA 14 N1 /C VAL 22 O /G GUA 14 H1 2.959 2.060
/G GUA 14 N2 /C VAL 22 O /G GUA 14 H21 3.161 2.305
/G GUA 15 N2 /C ASP 20 O /G GUA 15 H21 3.423 2.613
/G CYT 24 O2' /C GLU 42 OE1 /G CYT 24 H2' 2.982 2.246
/G GUA 38 O2' /F GLN 6 OE1 /G GUA 38 H2' 2.837 1.886
/G GUA 46 O2' /D LEU 31 O /G GUA 46 H2' 2.590 1.680
/G CYT 66 O2' /D ASP 20 OD1 /G CYT 66 H2' 2.654 1.709
/G GUA 82 N2 /C SER 19 O /G GUA 82 H21 3.239 2.481
89 hydrogen bonds found
> select up
2641 atoms, 2704 bonds, 102 residues, 1 model selected
> style sel stick
Changed 2641 atom styles
> show sel atoms
> color sel byelement
> select nucleic
2969 atoms, 3208 bonds, 90 residues, 1 model selected
> hide sel atoms
> lighting simple
> save "/Users/alexeykovalenko/University of Michigan Dropbox/Alexey
> Kovalenko/Simulations/Pics/15repRNA_serf/structures/snap_clust0/clust0_chimera/cl0_prot-
> backbone.cxs"
——— End of log from Fri May 9 15:50:15 2025 ———
opened ChimeraX session
> select clear
> open J:\BS-data\amyloid_G4\Data\docking\5oph_out_old.pdbqt format pdbqt
Summary of feedback from opening J:\BS-
data\amyloid_G4\Data\docking\5oph_out_old.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!
Ignored bad PDB record found on line 4
REMARK 152 active torsions:
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: O5'_1 and C5'_2
4162 messages similar to the above omitted
Chain information for 5oph_out_old.pdb
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A | No description available
Opened 5oph_out_old.pdbqt containing 9 structures (5076 atoms, 5535 bonds)
Computing secondary structure
[Repeated 8 time(s)]
> viewdockx #!2.1-9
> hide #!1 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.8 models
> hide #!2.7 models
> hide #!2.6 models
> hide #!2.5 models
> hide #!2.4 models
> hide #!2.9 models
> hide #!2 models
> show #!2.1 models
> close #1
> show #!2.9 models
> show #!2.5 models
> show #!2.4 models
> show #!2.3 models
> show #!2.2 models
> show #!2.6 models
> show #!2.7 models
> show #!2.8 models
> close #2
> open C:/Users/bsahoo/Downloads/7mkf-prep1.pdb
Chain information for 7mkf-prep1.pdb #1
---
Chain | Description
A B C D E F G H I J | No description available
> open C:/Users/bsahoo/Downloads/5oph_out_old.pdbqt
Summary of feedback from opening C:/Users/bsahoo/Downloads/5oph_out_old.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!
Ignored bad PDB record found on line 4
REMARK 152 active torsions:
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: O5'_1 and C5'_2
4162 messages similar to the above omitted
Chain information for 5oph_out_old.pdb
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A | No description available
Opened 5oph_out_old.pdbqt containing 9 structures (5076 atoms, 5535 bonds)
Computing secondary structure
[Repeated 8 time(s)]
> viewdockx #!2.1-9
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.4 models
> hide #!2.5 models
> hide #!2.6 models
> hide #!2.7 models
> hide #!2.8 models
> hide #!2.9 models
> show #!2.1 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11420 atom styles
Computing secondary structure
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select nucleic acid
Expected a keyword
> select nucleic
5076 atoms, 5535 bonds, 72 pseudobonds, 270 residues, 18 models selected
> ui tool show H-Bonds
> hbonds sel color #ff0000 restrict cross intraModel false intraMol false
> intraRes false select true reveal true
donor: 7mkf-prep1.pdb #1/I SER 341 OG acceptor: 5oph_out_old.pdb #2.4/A DG 9
N3
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\tool.py", line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hbonds sel color #ff0000 intraModel false intraMol false intraRes false
> select true reveal true
donor: 7mkf-prep1.pdb #1/I SER 341 OG acceptor: 5oph_out_old.pdb #2.4/A DG 9
N3
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\tool.py", line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\cmd.py", line 94, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 556.12
OpenGL renderer: NVIDIA GeForce RTX 2060 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 8940
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 68,440,993,792
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900 CPU @ 2.80GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Works for standard 5oph entry