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#2997 closed defect (duplicate)
settings error-reporting using non-existent attribute
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-03-08)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warnings | No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Figure
No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Session
UCSF ChimeraX version: 0.92 (2020-03-08)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig3/Fig3_humPolD-
> interface.cxs
opened ChimeraX session
> close #2
> close #4
> close #5
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> hide sel atoms
> show sel cartoons
> show #!3 models
> select #3
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #3/F:119-128
77 atoms, 76 bonds, 1 model selected
> color sel firebrick
> undo
> redo
> show #!1 models
> save session "/Users/fengwei.zheng/Documents/Draft_PolD/Session/PolD-
> interface comparison.cxs"
> hide #!3 models
> hide #!1 models
> select #3
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> ~select #3
Nothing selected
> interfaces #1 & protein
5 buried areas: B C 2542, A B 2353, A H 1505, H F 745, H G 591
> show #!1 models
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> ~select #1
Nothing selected
> hide #!1 models
> show #!1 models
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> show sel atoms
> color #1/A & ~sel grey
> style sel sphere
Changed 428 atom styles
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> hide sel atoms
> show sel cartoons
> show #1/t,p atoms
> select clear
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/ystPolD-
> interface.cxs
> hide #!1 models
> show #!3 models
> show #3/t,p atoms
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/humanPolD-
> interface.cxs
> show #!1 models
> hide #!3 models
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/ystPolD-
> interface.tif width 1200 height 900
> show #!3 models
> hide #!1 models
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/humanPolD-
> interface.tif width 1200 height 900
> show #!1 models
> hide #!3 models
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> show sel cartoons
> hide sel cartoons
> show sel atoms
> show #1/t,p cartoons
> interfaces #3 & protein
8 buried areas: B C 2606, A B 2015, A F 1022, A D 711, F G 671, E F 614, E G
512, B D 510
> hide #!1 models
> show #!3 models
> select #3
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> hide sel cartoons
> show sel atoms
> show #3/t,p cartoons
> style sel sphere
Changed 296 atom styles
> select clear
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> color #3 & ~sel linen
> select clear
> show #!1 models
> hide #!3 models
> color #1 & ~sel grey
> show #!3 models
> hide #!1 models
> select #3
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> ~select #3
Nothing selected
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/ystPolD-
> interface_detached.tif width 1200 height 900
> hide #!1 models
> show #!3 models
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/humanPolD-
> interface_detached.tif width 1200 height 900
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/humanPolD-
> interface_detached.cxs
> show #!1 models
> hide #!3 models
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/ystPolD-
> interface_detached.cxs
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> ~select #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> style sel stick
Changed 219 atom styles
> turn x -1 90
> hide #1 & ~sel
> undo
> hide #1/f-h & ~sel
> select clear
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/ystPolD-
> interface_detached_A.cxs
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/ystPolD-
> interface_detached_A.tif width 1200 height 900
> undo
> undo
> undo
> undo
> style sel sphere
Changed 219 atom styles
> select clear
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/ystPolD-
> interface_sphere.cxs
> style sel stick
Changed 209 atom styles
> turn x 1 90
> hide #1/a-c & ~sel
> select clear
> hide #1/a-c,t,p & ~sel
> undo
> hide #1/a-c,t,p & ~sel
> undo
> hide #1/t,p
Expected ',' or a keyword
> hide #1/t,p cartoons
> select clear
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/ystPolD-
> interface_detached_B.cxs
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/ystPolD-
> interface_detached_B.tif width 1200 height 900
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> select clear
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/humanPolD-
> interface_sphere.cxs
> style sel stick
Changed 158 atom styles
> turn x -1 90
> hide #1/e-g & ~sel
> undo
> hide #3/e-g & ~sel
> select clear
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/humanPolD-
> interface_detached_A.cxs
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/humanPolD-
> interface_detached_A.tif width 1200 height 900
> undo
> undo
> undo
> undo
> undo
> select clear
> turn x 1 90
> hide #3/a-d & ~sel
Expected an objects specifier or a keyword
> select #3/t,p
1024 atoms, 1147 bonds, 1 model selected
> hide sel
> hide sel cartoons
> save image /Users/fengwei.zheng/Documents/Draft_PolD/Figure/humanPolD-
> interface_detached_B.tif width 1200 height 900
> save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/humanPolD-
> interface_detached_B.cxs
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> hide #!3 models
> show #!1 models
> show #!3 models
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> ~select #1
Nothing selected
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> select #1
16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected
> ~select #1
Nothing selected
> style sel stick
Changed 428 atom styles
> color sel byhetero
> hide ~sel
> hide cartoons
> show #!3 models
> hide #!1 models
> select #3
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> show #3
> hide #3 & ~sel
> style sel stick
Changed 296 atom styles
> color sel byhetero
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> toolshed show H-Bonds
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
4 hydrogen bonds found
> select clear
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Atom specifier selects no atoms
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
4 hydrogen bonds found
> select clear
> show #!3 models
> hide #!1 models
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> show #3/A:991-995 atoms
> show #3/A:991-995
> select #3/A:991-995
37 atoms, 36 bonds, 1 model selected
> show sel atoms
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel cartoons
> show sel atoms
> select #3/A:991-995
37 atoms, 36 bonds, 1 model selected
> show sel atoms
> hide sel cartoons
> ui mousemode rightMode distance
> distance #3/A:991@O #3/F:120@N
Distance between 409-humPolDcplx.pdb #3/A CYS 991 O and /F ASP 120 N: 3.353Å
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> close #2
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!3 models
> toolshed show H-Bonds
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.9 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.9 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A THR 993 N 409-humPolDcplx.pdb #3/F ASP 120 O no hydrogen 3.787 N/A
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A CYS 1011 SG 409-humPolDcplx.pdb #3/F GLU 124 OE1 no hydrogen 4.377 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
7 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.9
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.9 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A THR 993 N 409-humPolDcplx.pdb #3/F ASP 120 O no hydrogen 3.787 N/A
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A CYS 1011 SG 409-humPolDcplx.pdb #3/F GLU 124 OE1 no hydrogen 4.377 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
7 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false angleSlop 25.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 25 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false angleSlop 28.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 28 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false angleSlop 28.0
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 28 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.41
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.41 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.44
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.44 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.49
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.49 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
3 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> twoColors true intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
0 strict hydrogen bonds found
> show #!1 models
> hide #!3 models
> select #1
16769 atoms, 17166 bonds, 46 pseudobonds, 4 models selected
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> twoColors true intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A ILE 988 N 409-ystPolDcplx_156-679.pdb #1/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
2 strict hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A ILE 988 N 409-ystPolDcplx_156-679.pdb #1/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
4 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A ILE 988 N 409-ystPolDcplx_156-679.pdb #1/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
> select clear
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> twoColors true intraMol false intraRes false reveal true log true
Atom specifier selects no atoms
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> twoColors true intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A ILE 988 N 409-ystPolDcplx_156-679.pdb #1/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
2 strict hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #1/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #1/A ILE 988 N 409-ystPolDcplx_156-679.pdb #1/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #1/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #1/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #1/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #1/H GLU 129 N 409-ystPolDcplx_156-679.pdb #1/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
> hide #!1 models
> show #!3 models
> hide #3 & ~sel
> show #!1 models
> hide #!3 models
> ~label
> hide #!1 models
> show #!3 models
> select clear
> select #3
19722 atoms, 20206 bonds, 30 pseudobonds, 4 models selected
> ~select #3
Nothing selected
> toolshed show H-Bonds
> hbonds showDist true interModel false distSlop 0.5 saltOnly true intraMol
> false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
3 409-humPolDcplx.pdb
6 409-humPolDcplx_1.pdb
22 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 674 NH1 409-ystPolDcplx_156-679.pdb #1/A D3T 1102 O1G no hydrogen 2.316 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 701 NZ 409-ystPolDcplx_156-679.pdb #1/A D3T 1102 O2A no hydrogen 3.068 N/A
409-ystPolDcplx_156-679.pdb #1/A HIS 903 NE2 409-ystPolDcplx_156-679.pdb #1/P DA 21 OP1 no hydrogen 3.082 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 934 NZ 409-ystPolDcplx_156-679.pdb #1/T DA 10 OP2 no hydrogen 2.835 N/A
409-ystPolDcplx_156-679.pdb #1/A ARG 1051 NH1 409-ystPolDcplx_156-679.pdb #1/B GLU 121 OE1 no hydrogen 2.872 N/A
409-ystPolDcplx_156-679.pdb #1/A ARG 1051 NH2 409-ystPolDcplx_156-679.pdb #1/B GLU 121 OE1 no hydrogen 2.984 N/A
409-ystPolDcplx_156-679.pdb #1/C LYS 45 NZ 409-ystPolDcplx_156-679.pdb #1/B ASP 11 OD1 no hydrogen 2.995 N/A
409-ystPolDcplx_156-679.pdb #1/G LYS 20 NZ 409-ystPolDcplx_156-679.pdb #1/T DT 15 OP1 no hydrogen 3.342 N/A
409-humPolDcplx.pdb #3/A ARG 667 NH1 409-humPolDcplx.pdb #3/A TTP 1203 O2G no hydrogen 3.067 N/A
409-humPolDcplx.pdb #3/A ARG 667 NH2 409-humPolDcplx.pdb #3/A TTP 1203 O2G no hydrogen 3.361 N/A
409-humPolDcplx.pdb #3/A LYS 694 NZ 409-humPolDcplx.pdb #3/A TTP 1203 O1A no hydrogen 3.185 N/A
409-humPolDcplx.pdb #3/A LYS 694 NZ 409-humPolDcplx.pdb #3/A TTP 1203 O3G no hydrogen 3.489 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/B ARG 44 NH2 409-humPolDcplx.pdb #3/A GLU 1048 OE2 no hydrogen 2.841 N/A
409-humPolDcplx.pdb #3/C LYS 24 NZ 409-humPolDcplx.pdb #3/B ASP 220 OD1 no hydrogen 3.549 N/A
409-humPolDcplx_1.pdb #6/A ARG 667 NH1 409-humPolDcplx_1.pdb #6/A TTP 1203 O2G no hydrogen 3.067 N/A
409-humPolDcplx_1.pdb #6/A ARG 667 NH2 409-humPolDcplx_1.pdb #6/A TTP 1203 O2G no hydrogen 3.361 N/A
409-humPolDcplx_1.pdb #6/A LYS 694 NZ 409-humPolDcplx_1.pdb #6/A TTP 1203 O1A no hydrogen 3.185 N/A
409-humPolDcplx_1.pdb #6/A LYS 694 NZ 409-humPolDcplx_1.pdb #6/A TTP 1203 O3G no hydrogen 3.489 N/A
409-humPolDcplx_1.pdb #6/A ARG 1016 NH2 409-humPolDcplx_1.pdb #6/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx_1.pdb #6/B ARG 44 NH2 409-humPolDcplx_1.pdb #6/A GLU 1048 OE2 no hydrogen 2.841 N/A
409-humPolDcplx_1.pdb #6/C LYS 24 NZ 409-humPolDcplx_1.pdb #6/B ASP 220 OD1 no hydrogen 3.549 N/A
22 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> saltOnly true intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
1 hydrogen bonds found
> hide #3 & ~sel
> hbonds showDist true interModel false distSlop 0.5 saltOnly true intraMol
> false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 409-ystPolDcplx_156-679.pdb
3 409-humPolDcplx.pdb
6 409-humPolDcplx_1.pdb
22 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #1/A ARG 674 NH1 409-ystPolDcplx_156-679.pdb #1/A D3T 1102 O1G no hydrogen 2.316 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 701 NZ 409-ystPolDcplx_156-679.pdb #1/A D3T 1102 O2A no hydrogen 3.068 N/A
409-ystPolDcplx_156-679.pdb #1/A HIS 903 NE2 409-ystPolDcplx_156-679.pdb #1/P DA 21 OP1 no hydrogen 3.082 N/A
409-ystPolDcplx_156-679.pdb #1/A LYS 934 NZ 409-ystPolDcplx_156-679.pdb #1/T DA 10 OP2 no hydrogen 2.835 N/A
409-ystPolDcplx_156-679.pdb #1/A ARG 1051 NH1 409-ystPolDcplx_156-679.pdb #1/B GLU 121 OE1 no hydrogen 2.872 N/A
409-ystPolDcplx_156-679.pdb #1/A ARG 1051 NH2 409-ystPolDcplx_156-679.pdb #1/B GLU 121 OE1 no hydrogen 2.984 N/A
409-ystPolDcplx_156-679.pdb #1/C LYS 45 NZ 409-ystPolDcplx_156-679.pdb #1/B ASP 11 OD1 no hydrogen 2.995 N/A
409-ystPolDcplx_156-679.pdb #1/G LYS 20 NZ 409-ystPolDcplx_156-679.pdb #1/T DT 15 OP1 no hydrogen 3.342 N/A
409-humPolDcplx.pdb #3/A ARG 667 NH1 409-humPolDcplx.pdb #3/A TTP 1203 O2G no hydrogen 3.067 N/A
409-humPolDcplx.pdb #3/A ARG 667 NH2 409-humPolDcplx.pdb #3/A TTP 1203 O2G no hydrogen 3.361 N/A
409-humPolDcplx.pdb #3/A LYS 694 NZ 409-humPolDcplx.pdb #3/A TTP 1203 O1A no hydrogen 3.185 N/A
409-humPolDcplx.pdb #3/A LYS 694 NZ 409-humPolDcplx.pdb #3/A TTP 1203 O3G no hydrogen 3.489 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/B ARG 44 NH2 409-humPolDcplx.pdb #3/A GLU 1048 OE2 no hydrogen 2.841 N/A
409-humPolDcplx.pdb #3/C LYS 24 NZ 409-humPolDcplx.pdb #3/B ASP 220 OD1 no hydrogen 3.549 N/A
409-humPolDcplx_1.pdb #6/A ARG 667 NH1 409-humPolDcplx_1.pdb #6/A TTP 1203 O2G no hydrogen 3.067 N/A
409-humPolDcplx_1.pdb #6/A ARG 667 NH2 409-humPolDcplx_1.pdb #6/A TTP 1203 O2G no hydrogen 3.361 N/A
409-humPolDcplx_1.pdb #6/A LYS 694 NZ 409-humPolDcplx_1.pdb #6/A TTP 1203 O1A no hydrogen 3.185 N/A
409-humPolDcplx_1.pdb #6/A LYS 694 NZ 409-humPolDcplx_1.pdb #6/A TTP 1203 O3G no hydrogen 3.489 N/A
409-humPolDcplx_1.pdb #6/A ARG 1016 NH2 409-humPolDcplx_1.pdb #6/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx_1.pdb #6/B ARG 44 NH2 409-humPolDcplx_1.pdb #6/A GLU 1048 OE2 no hydrogen 2.841 N/A
409-humPolDcplx_1.pdb #6/C LYS 24 NZ 409-humPolDcplx_1.pdb #6/B ASP 220 OD1 no hydrogen 3.549 N/A
22 hydrogen bonds found
> hide #3 & ~sel
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> saltOnly true intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
1 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false saltOnly true
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> show #!1 models
> hide #!3 models
> hide #1 & ~sel
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select clear
> ui mousemode rightMode distance
> distance #1/H:122@OD2 #1/A:1013@NZ
Distance between 409-ystPolDcplx_156-679.pdb #1/H ASP 122 OD2 and /A LYS 1013
NZ: 4.648Å
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #6
> close #2
> select #1
16769 atoms, 17166 bonds, 50 pseudobonds, 5 models selected
> show sel cartoons
> hide sel cartoons
> open
> /Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_156-679.pdb
Summary of feedback from opening
/Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_156-679.pdb
---
warning | Ignored bad PDB record found on line 171
SSBOND *** CYS C 58 CYS C 83
Chain information for 409-ystPolDcplx_156-679.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
F | No description available
G | No description available
H | No description available
P | No description available
T | No description available
> interfaces #2 & protein
5 buried areas: B C 2542, A B 2353, A H 1503, H F 745, H G 591
> hide #2 & ~sel
> style sel stick
Changed 428 atom styles
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> toolshed show H-Bonds
> hbonds sel restrict both showDist true interModel false saltOnly true
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
1 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false twoColors true
> saltOnly true intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
1 hydrogen bonds found
0 strict hydrogen bonds found
> hbonds sel restrict both showDist true interModel false saltOnly true
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
1 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> select #1
16769 atoms, 17166 bonds, 50 pseudobonds, 5 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel atoms
> undo
> undo
> undo
> undo
> ~select #1
Nothing selected
> hide #1 & ~sel
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2/A:984-1030 blue
> 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
> color #2/H #ffb2ff
> color #2/H:118-134 firebrick
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2/A:835-985 chocolate
> hide #!2 models
> show #!2 models
> undo
> show #!2 models
> undo
> undo
> undo
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #2/A:835-983 chocolate
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2
16769 atoms, 17166 bonds, 64 pseudobonds, 5 models selected
> show sel atoms
> hide sel atoms
> hide #!1 models
> show #!1 models
> hide #!1 models
> show sel atoms
> color #2 & ~sel grey
> show sel atoms
> select #2
16769 atoms, 17166 bonds, 64 pseudobonds, 5 models selected
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel byhetero
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> save session "/Users/fengwei.zheng/Documents/Draft_PolD/Session/PolD-
> interface sticks.cxs"
> show sel cartoons
> hide sel cartoons
> toolshed show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x122d42390>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x168469850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x168d91d50>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x168469850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x1246cca50>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
> toolshed show H-Bonds
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> saltOnly true intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
1 hydrogen bonds found
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x16fff64d0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x1707bf6d0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x15aa5a0d0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
> toolshed show H-Bonds
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x16fff6f10>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
> toolshed show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.5 saltOnly true
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
1 hydrogen bonds found
> hbonds sel restrict both dashes 6 interModel false distSlop 0.5 saltOnly
> true intraMol false intraRes false reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
1 hydrogen bonds found
> hbonds sel restrict both dashes 6 interModel false distSlop 0.5 intraMol
> false intraRes false reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hbonds sel restrict both dashes 6 interModel false distSlop 0.5 intraMol
> false intraRes false reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hbonds sel restrict both dashes 6 interModel false distSlop 0.5 saltOnly
> true intraMol false intraRes false reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
1 hydrogen bonds found
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x15958af50>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
> select clear
> show #!3 models
> hide #!2 models
> close #1
> toolshed show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> toolshed show H-Bonds
> select clear
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> toolshed show H-Bonds
> toolshed show H-Bonds
> hbonds interModel false distSlop 0.6 intraMol false intraRes false reveal
> true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
2 409-ystPolDcplx_156-679.pdb
286 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A SER 443 OG 409-ystPolDcplx_156-679.pdb #2/T DA -1 O3' no hydrogen 3.487 N/A
409-ystPolDcplx_156-679.pdb #2/A SER 443 OG 409-ystPolDcplx_156-679.pdb #2/T DA 0 OP1 no hydrogen 3.454 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 554 NH1 409-ystPolDcplx_156-679.pdb #2/T DT -2 O5' no hydrogen 3.465 N/A
409-ystPolDcplx_156-679.pdb #2/A GLY 555 N 409-ystPolDcplx_156-679.pdb #2/T DA -1 OP1 no hydrogen 3.376 N/A
409-ystPolDcplx_156-679.pdb #2/A GLN 556 N 409-ystPolDcplx_156-679.pdb #2/T DA 0 OP1 no hydrogen 3.135 N/A
409-ystPolDcplx_156-679.pdb #2/A GLN 557 N 409-ystPolDcplx_156-679.pdb #2/T DA 0 OP2 no hydrogen 3.254 N/A
409-ystPolDcplx_156-679.pdb #2/A TYR 587 N 409-ystPolDcplx_156-679.pdb #2/T DC 2 OP1 no hydrogen 3.330 N/A
409-ystPolDcplx_156-679.pdb #2/A GLY 589 N 409-ystPolDcplx_156-679.pdb #2/T DA 3 OP1 no hydrogen 2.645 N/A
409-ystPolDcplx_156-679.pdb #2/A LEU 612 N 409-ystPolDcplx_156-679.pdb #2/A D3T 1102 O1B no hydrogen 3.141 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 674 NH2 409-ystPolDcplx_156-679.pdb #2/A D3T 1102 O3G no hydrogen 2.569 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 701 NZ 409-ystPolDcplx_156-679.pdb #2/A D3T 1102 O3A no hydrogen 3.312 N/A
409-ystPolDcplx_156-679.pdb #2/A ASN 812 ND2 409-ystPolDcplx_156-679.pdb #2/T DT 6 OP1 no hydrogen 2.859 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 814 NZ 409-ystPolDcplx_156-679.pdb #2/P DG 24 N3 no hydrogen 3.632 N/A
409-ystPolDcplx_156-679.pdb #2/A TYR 816 OH 409-ystPolDcplx_156-679.pdb #2/P DC 25 OP1 no hydrogen 3.089 N/A
409-ystPolDcplx_156-679.pdb #2/A GLY 834 N 409-ystPolDcplx_156-679.pdb #2/P DG 24 OP2 no hydrogen 3.469 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 839 NH2 409-ystPolDcplx_156-679.pdb #2/P DA 21 N3 no hydrogen 3.621 N/A
409-ystPolDcplx_156-679.pdb #2/A THR 892 N 409-ystPolDcplx_156-679.pdb #2/P DT 22 OP1 no hydrogen 3.090 N/A
409-ystPolDcplx_156-679.pdb #2/A THR 892 OG1 409-ystPolDcplx_156-679.pdb #2/P DT 22 OP2 no hydrogen 3.461 N/A
409-ystPolDcplx_156-679.pdb #2/A TYR 897 OH 409-ystPolDcplx_156-679.pdb #2/P DA 21 OP1 no hydrogen 2.178 N/A
409-ystPolDcplx_156-679.pdb #2/A THR 898 N 409-ystPolDcplx_156-679.pdb #2/P DA 20 OP1 no hydrogen 2.563 N/A
409-ystPolDcplx_156-679.pdb #2/A THR 898 OG1 409-ystPolDcplx_156-679.pdb #2/P DG 19 O3' no hydrogen 2.825 N/A
409-ystPolDcplx_156-679.pdb #2/A THR 898 OG1 409-ystPolDcplx_156-679.pdb #2/P DA 20 OP1 no hydrogen 3.000 N/A
409-ystPolDcplx_156-679.pdb #2/A ASN 899 N 409-ystPolDcplx_156-679.pdb #2/P DA 20 OP1 no hydrogen 3.335 N/A
409-ystPolDcplx_156-679.pdb #2/A HIS 903 NE2 409-ystPolDcplx_156-679.pdb #2/P DA 21 OP1 no hydrogen 3.082 N/A
409-ystPolDcplx_156-679.pdb #2/A ASN 932 ND2 409-ystPolDcplx_156-679.pdb #2/H ASP 41 OD2 no hydrogen 3.752 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 934 NZ 409-ystPolDcplx_156-679.pdb #2/T DA 10 OP2 no hydrogen 2.835 N/A
409-ystPolDcplx_156-679.pdb #2/A TYR 936 N 409-ystPolDcplx_156-679.pdb #2/T DT 9 OP1 no hydrogen 3.100 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ASN 960 ND2 409-ystPolDcplx_156-679.pdb #2/T DG 8 OP1 no hydrogen 3.372 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 1043 NE 409-ystPolDcplx_156-679.pdb #2/B SER 306 O no hydrogen 2.682 N/A
409-ystPolDcplx_156-679.pdb #2/A TYR 1049 OH 409-ystPolDcplx_156-679.pdb #2/B TYR 49 O no hydrogen 2.869 N/A
409-ystPolDcplx_156-679.pdb #2/A SER 1050 OG 409-ystPolDcplx_156-679.pdb #2/B TYR 53 OH no hydrogen 2.310 N/A
409-ystPolDcplx_156-679.pdb #2/A SER 1050 OG 409-ystPolDcplx_156-679.pdb #2/B CYS 418 O no hydrogen 3.440 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 1051 NH1 409-ystPolDcplx_156-679.pdb #2/B GLU 121 OE1 no hydrogen 2.872 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 1051 NH2 409-ystPolDcplx_156-679.pdb #2/B GLU 121 OE1 no hydrogen 2.984 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 1058 NH1 409-ystPolDcplx_156-679.pdb #2/B PRO 116 O no hydrogen 2.916 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 1058 NH2 409-ystPolDcplx_156-679.pdb #2/B PRO 116 O no hydrogen 3.489 N/A
409-ystPolDcplx_156-679.pdb #2/A ARG 1058 NH2 409-ystPolDcplx_156-679.pdb #2/B ASP 414 O no hydrogen 3.433 N/A
409-ystPolDcplx_156-679.pdb #2/A LEU 1063 N 409-ystPolDcplx_156-679.pdb #2/B GLU 149 OE2 no hydrogen 3.519 N/A
409-ystPolDcplx_156-679.pdb #2/A HIS 1064 NE2 409-ystPolDcplx_156-679.pdb #2/B SER 107 OG no hydrogen 2.980 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1067 N 409-ystPolDcplx_156-679.pdb #2/B GLN 52 OE1 no hydrogen 3.399 N/A
409-ystPolDcplx_156-679.pdb #2/B ARG 25 N 409-ystPolDcplx_156-679.pdb #2/C THR 108 O no hydrogen 2.788 N/A
409-ystPolDcplx_156-679.pdb #2/B ARG 27 N 409-ystPolDcplx_156-679.pdb #2/C LYS 110 O no hydrogen 3.146 N/A
409-ystPolDcplx_156-679.pdb #2/B SER 107 OG 409-ystPolDcplx_156-679.pdb #2/A HIS 1064 NE2 no hydrogen 2.980 N/A
409-ystPolDcplx_156-679.pdb #2/B ARG 243 NH1 409-ystPolDcplx_156-679.pdb #2/C GLN 103 OE1 no hydrogen 3.353 N/A
409-ystPolDcplx_156-679.pdb #2/B ARG 243 NH1 409-ystPolDcplx_156-679.pdb #2/C CYS 106 O no hydrogen 2.931 N/A
409-ystPolDcplx_156-679.pdb #2/B ASN 246 ND2 409-ystPolDcplx_156-679.pdb #2/C ASP 82 OD2 no hydrogen 2.830 N/A
409-ystPolDcplx_156-679.pdb #2/B LYS 308 N 409-ystPolDcplx_156-679.pdb #2/A GLU 1046 OE1 no hydrogen 2.775 N/A
409-ystPolDcplx_156-679.pdb #2/B SER 309 N 409-ystPolDcplx_156-679.pdb #2/A GLU 1046 OE1 no hydrogen 3.641 N/A
409-ystPolDcplx_156-679.pdb #2/B ASN 329 ND2 409-ystPolDcplx_156-679.pdb #2/C LYS 116 O no hydrogen 3.367 N/A
409-ystPolDcplx_156-679.pdb #2/B ASP 486 N 409-ystPolDcplx_156-679.pdb #2/C ILE 65 O no hydrogen 2.953 N/A
409-ystPolDcplx_156-679.pdb #2/C SER 34 OG 409-ystPolDcplx_156-679.pdb #2/B ASP 16 OD2 no hydrogen 2.977 N/A
409-ystPolDcplx_156-679.pdb #2/C LYS 45 NZ 409-ystPolDcplx_156-679.pdb #2/B ASP 11 OD1 no hydrogen 2.995 N/A
409-ystPolDcplx_156-679.pdb #2/C CYS 59 SG 409-ystPolDcplx_156-679.pdb #2/B ILE 244 O no hydrogen 3.510 N/A
409-ystPolDcplx_156-679.pdb #2/C ILE 65 N 409-ystPolDcplx_156-679.pdb #2/B LYS 484 O no hydrogen 3.036 N/A
409-ystPolDcplx_156-679.pdb #2/C ASN 111 N 409-ystPolDcplx_156-679.pdb #2/B PRO 292 O no hydrogen 3.411 N/A
409-ystPolDcplx_156-679.pdb #2/C SER 112 OG 409-ystPolDcplx_156-679.pdb #2/B ILE 28 O no hydrogen 2.602 N/A
409-ystPolDcplx_156-679.pdb #2/F LYS 108 NZ 409-ystPolDcplx_156-679.pdb #2/H GLU 143 OE1 no hydrogen 3.684 N/A
409-ystPolDcplx_156-679.pdb #2/F ILE 111 N 409-ystPolDcplx_156-679.pdb #2/H ILE 181 O no hydrogen 3.396 N/A
409-ystPolDcplx_156-679.pdb #2/F GLU 113 N 409-ystPolDcplx_156-679.pdb #2/H SER 179 O no hydrogen 2.676 N/A
409-ystPolDcplx_156-679.pdb #2/F TYR 114 OH 409-ystPolDcplx_156-679.pdb #2/H ASP 150 OD1 no hydrogen 3.335 N/A
409-ystPolDcplx_156-679.pdb #2/F SER 115 N 409-ystPolDcplx_156-679.pdb #2/H SER 177 O no hydrogen 2.631 N/A
409-ystPolDcplx_156-679.pdb #2/F LYS 117 N 409-ystPolDcplx_156-679.pdb #2/H ILE 175 O no hydrogen 3.155 N/A
409-ystPolDcplx_156-679.pdb #2/F LYS 146 NZ 409-ystPolDcplx_156-679.pdb #2/G GLY 82 O no hydrogen 3.702 N/A
409-ystPolDcplx_156-679.pdb #2/G LYS 20 NZ 409-ystPolDcplx_156-679.pdb #2/T DT 15 OP1 no hydrogen 3.342 N/A
409-ystPolDcplx_156-679.pdb #2/G CYS 81 SG 409-ystPolDcplx_156-679.pdb #2/F ASP 150 OD2 no hydrogen 3.148 N/A
409-ystPolDcplx_156-679.pdb #2/G LYS 146 NZ 409-ystPolDcplx_156-679.pdb #2/H ASN 83 OD1 no hydrogen 2.580 N/A
409-ystPolDcplx_156-679.pdb #2/G SER 179 N 409-ystPolDcplx_156-679.pdb #2/H GLU 113 O no hydrogen 2.324 N/A
409-ystPolDcplx_156-679.pdb #2/G ILE 181 N 409-ystPolDcplx_156-679.pdb #2/H ILE 111 O no hydrogen 3.205 N/A
409-ystPolDcplx_156-679.pdb #2/H CYS 81 SG 409-ystPolDcplx_156-679.pdb #2/G ASP 150 O no hydrogen 3.737 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 113 N 409-ystPolDcplx_156-679.pdb #2/G SER 179 O no hydrogen 2.432 N/A
409-ystPolDcplx_156-679.pdb #2/H SER 115 N 409-ystPolDcplx_156-679.pdb #2/G SER 177 O no hydrogen 2.889 N/A
409-ystPolDcplx_156-679.pdb #2/H LYS 127 N 409-ystPolDcplx_156-679.pdb #2/A LYS 1004 O no hydrogen 3.551 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
409-ystPolDcplx_156-679.pdb #2/H LYS 146 NZ 409-ystPolDcplx_156-679.pdb #2/F CYS 81 O no hydrogen 3.136 N/A
409-ystPolDcplx_156-679.pdb #2/H LYS 146 NZ 409-ystPolDcplx_156-679.pdb #2/F ASN 83 O no hydrogen 3.454 N/A
409-ystPolDcplx_156-679.pdb #2/H SER 177 N 409-ystPolDcplx_156-679.pdb #2/F SER 115 O no hydrogen 3.315 N/A
409-ystPolDcplx_156-679.pdb #2/H SER 179 N 409-ystPolDcplx_156-679.pdb #2/F GLU 113 O no hydrogen 2.551 N/A
409-ystPolDcplx_156-679.pdb #2/H ILE 181 N 409-ystPolDcplx_156-679.pdb #2/F ILE 111 O no hydrogen 3.052 N/A
409-ystPolDcplx_156-679.pdb #2/H LYS 183 N 409-ystPolDcplx_156-679.pdb #2/F ASP 109 O no hydrogen 3.652 N/A
409-ystPolDcplx_156-679.pdb #2/P DT 6 N3 409-ystPolDcplx_156-679.pdb #2/T DA 20 N1 no hydrogen 2.575 N/A
409-ystPolDcplx_156-679.pdb #2/P DT 6 N3 409-ystPolDcplx_156-679.pdb #2/T DT 21 O2 no hydrogen 2.655 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 7 N1 409-ystPolDcplx_156-679.pdb #2/T DC 19 N3 no hydrogen 2.900 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 7 N2 409-ystPolDcplx_156-679.pdb #2/T DC 19 N3 no hydrogen 3.633 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 7 N2 409-ystPolDcplx_156-679.pdb #2/T DC 19 O2 no hydrogen 2.798 N/A
409-ystPolDcplx_156-679.pdb #2/P DA 8 N6 409-ystPolDcplx_156-679.pdb #2/T DT 18 O4 no hydrogen 3.032 N/A
409-ystPolDcplx_156-679.pdb #2/P DC 9 N4 409-ystPolDcplx_156-679.pdb #2/T DG 17 O6 no hydrogen 2.948 N/A
409-ystPolDcplx_156-679.pdb #2/P DC 10 N4 409-ystPolDcplx_156-679.pdb #2/T DT 15 O4 no hydrogen 3.747 N/A
409-ystPolDcplx_156-679.pdb #2/P DC 10 N4 409-ystPolDcplx_156-679.pdb #2/T DG 16 O6 no hydrogen 2.886 N/A
409-ystPolDcplx_156-679.pdb #2/P DA 11 N6 409-ystPolDcplx_156-679.pdb #2/T DT 15 O4 no hydrogen 3.010 N/A
409-ystPolDcplx_156-679.pdb #2/P DT 12 N3 409-ystPolDcplx_156-679.pdb #2/T DA 14 N1 no hydrogen 2.739 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 13 N1 409-ystPolDcplx_156-679.pdb #2/T DC 13 N3 no hydrogen 2.866 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 13 N2 409-ystPolDcplx_156-679.pdb #2/T DC 13 N3 no hydrogen 3.601 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 13 N2 409-ystPolDcplx_156-679.pdb #2/T DC 13 O2 no hydrogen 2.722 N/A
409-ystPolDcplx_156-679.pdb #2/P DA 14 N6 409-ystPolDcplx_156-679.pdb #2/T DT 12 O4 no hydrogen 3.021 N/A
409-ystPolDcplx_156-679.pdb #2/P DT 15 N3 409-ystPolDcplx_156-679.pdb #2/T DA 11 N1 no hydrogen 2.814 N/A
409-ystPolDcplx_156-679.pdb #2/P DT 16 N3 409-ystPolDcplx_156-679.pdb #2/T DA 10 N1 no hydrogen 2.771 N/A
409-ystPolDcplx_156-679.pdb #2/P DA 17 N6 409-ystPolDcplx_156-679.pdb #2/T DT 9 O4 no hydrogen 2.952 N/A
409-ystPolDcplx_156-679.pdb #2/P DC 18 N4 409-ystPolDcplx_156-679.pdb #2/T DG 8 O6 no hydrogen 2.969 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 19 N1 409-ystPolDcplx_156-679.pdb #2/T DC 7 N3 no hydrogen 2.886 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 19 N2 409-ystPolDcplx_156-679.pdb #2/T DC 7 N3 no hydrogen 3.594 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 19 N2 409-ystPolDcplx_156-679.pdb #2/T DC 7 O2 no hydrogen 2.728 N/A
409-ystPolDcplx_156-679.pdb #2/P DA 20 N6 409-ystPolDcplx_156-679.pdb #2/T DT 6 O4 no hydrogen 2.999 N/A
409-ystPolDcplx_156-679.pdb #2/P DA 21 N6 409-ystPolDcplx_156-679.pdb #2/T DT 5 O4 no hydrogen 2.910 N/A
409-ystPolDcplx_156-679.pdb #2/P DT 22 N3 409-ystPolDcplx_156-679.pdb #2/T DA 4 N1 no hydrogen 2.802 N/A
409-ystPolDcplx_156-679.pdb #2/P DT 23 N3 409-ystPolDcplx_156-679.pdb #2/T DA 3 N1 no hydrogen 2.789 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 24 N1 409-ystPolDcplx_156-679.pdb #2/T DC 2 N3 no hydrogen 2.824 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 24 N2 409-ystPolDcplx_156-679.pdb #2/T DC 2 N3 no hydrogen 3.195 N/A
409-ystPolDcplx_156-679.pdb #2/P DG 24 N2 409-ystPolDcplx_156-679.pdb #2/T DC 2 O2 no hydrogen 2.490 N/A
409-ystPolDcplx_156-679.pdb #2/P DC 25 N4 409-ystPolDcplx_156-679.pdb #2/T DG 1 O6 no hydrogen 2.899 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 1 N1 409-ystPolDcplx_156-679.pdb #2/P DC 25 N3 no hydrogen 2.992 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 1 N2 409-ystPolDcplx_156-679.pdb #2/P DC 25 N3 no hydrogen 3.609 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 1 N2 409-ystPolDcplx_156-679.pdb #2/P DC 25 O2 no hydrogen 2.974 N/A
409-ystPolDcplx_156-679.pdb #2/T DC 2 N4 409-ystPolDcplx_156-679.pdb #2/P DG 24 O6 no hydrogen 3.085 N/A
409-ystPolDcplx_156-679.pdb #2/T DA 3 N6 409-ystPolDcplx_156-679.pdb #2/P DT 23 O4 no hydrogen 3.038 N/A
409-ystPolDcplx_156-679.pdb #2/T DA 4 N6 409-ystPolDcplx_156-679.pdb #2/P DT 22 O4 no hydrogen 3.035 N/A
409-ystPolDcplx_156-679.pdb #2/T DT 5 N3 409-ystPolDcplx_156-679.pdb #2/P DA 21 N1 no hydrogen 2.808 N/A
409-ystPolDcplx_156-679.pdb #2/T DT 6 N3 409-ystPolDcplx_156-679.pdb #2/P DA 20 N1 no hydrogen 2.802 N/A
409-ystPolDcplx_156-679.pdb #2/T DC 7 N4 409-ystPolDcplx_156-679.pdb #2/P DG 19 O6 no hydrogen 2.938 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 8 N1 409-ystPolDcplx_156-679.pdb #2/P DC 18 N3 no hydrogen 2.889 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 8 N2 409-ystPolDcplx_156-679.pdb #2/P DC 18 N3 no hydrogen 3.602 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 8 N2 409-ystPolDcplx_156-679.pdb #2/P DC 18 O2 no hydrogen 2.709 N/A
409-ystPolDcplx_156-679.pdb #2/T DT 9 N3 409-ystPolDcplx_156-679.pdb #2/P DA 17 N1 no hydrogen 2.834 N/A
409-ystPolDcplx_156-679.pdb #2/T DA 10 N6 409-ystPolDcplx_156-679.pdb #2/P DT 16 O4 no hydrogen 2.929 N/A
409-ystPolDcplx_156-679.pdb #2/T DA 11 N6 409-ystPolDcplx_156-679.pdb #2/P DT 15 O4 no hydrogen 2.948 N/A
409-ystPolDcplx_156-679.pdb #2/T DT 12 N3 409-ystPolDcplx_156-679.pdb #2/P DA 14 N1 no hydrogen 2.820 N/A
409-ystPolDcplx_156-679.pdb #2/T DC 13 N4 409-ystPolDcplx_156-679.pdb #2/P DG 13 O6 no hydrogen 2.921 N/A
409-ystPolDcplx_156-679.pdb #2/T DA 14 N6 409-ystPolDcplx_156-679.pdb #2/P DT 12 O4 no hydrogen 3.027 N/A
409-ystPolDcplx_156-679.pdb #2/T DT 15 N3 409-ystPolDcplx_156-679.pdb #2/P DA 11 N1 no hydrogen 2.728 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 16 N1 409-ystPolDcplx_156-679.pdb #2/P DC 10 N3 no hydrogen 2.857 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 16 N2 409-ystPolDcplx_156-679.pdb #2/P DC 10 N3 no hydrogen 3.585 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 16 N2 409-ystPolDcplx_156-679.pdb #2/P DC 10 O2 no hydrogen 2.717 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 17 N1 409-ystPolDcplx_156-679.pdb #2/P DC 9 N3 no hydrogen 2.851 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 17 N2 409-ystPolDcplx_156-679.pdb #2/P DC 9 N3 no hydrogen 3.565 N/A
409-ystPolDcplx_156-679.pdb #2/T DG 17 N2 409-ystPolDcplx_156-679.pdb #2/P DC 9 O2 no hydrogen 2.656 N/A
409-ystPolDcplx_156-679.pdb #2/T DT 18 N3 409-ystPolDcplx_156-679.pdb #2/P DA 8 N1 no hydrogen 2.705 N/A
409-ystPolDcplx_156-679.pdb #2/T DC 19 N4 409-ystPolDcplx_156-679.pdb #2/P DG 7 O6 no hydrogen 2.901 N/A
409-ystPolDcplx_156-679.pdb #2/T DT 21 N3 409-ystPolDcplx_156-679.pdb #2/P DT 6 O4 no hydrogen 3.116 N/A
409-humPolDcplx.pdb #3/A ARG 224 NH2 409-humPolDcplx.pdb #3/T DT -3 OP2 no hydrogen 3.560 N/A
409-humPolDcplx.pdb #3/A LYS 323 NZ 409-humPolDcplx.pdb #3/D TYR 105 OH no hydrogen 3.276 N/A
409-humPolDcplx.pdb #3/A GLN 440 NE2 409-humPolDcplx.pdb #3/T DG 1 O6 no hydrogen 3.883 N/A
409-humPolDcplx.pdb #3/A SER 492 OG 409-humPolDcplx.pdb #3/D TYR 105 OH no hydrogen 3.453 N/A
409-humPolDcplx.pdb #3/A GLN 551 N 409-humPolDcplx.pdb #3/T DA 0 OP1 no hydrogen 3.103 N/A
409-humPolDcplx.pdb #3/A GLY 583 N 409-humPolDcplx.pdb #3/T DA 3 OP1 no hydrogen 2.711 N/A
409-humPolDcplx.pdb #3/A LEU 606 N 409-humPolDcplx.pdb #3/A TTP 1203 O2B no hydrogen 3.583 N/A
409-humPolDcplx.pdb #3/A TYR 607 N 409-humPolDcplx.pdb #3/A TTP 1203 O3' no hydrogen 2.709 N/A
409-humPolDcplx.pdb #3/A ARG 667 NH1 409-humPolDcplx.pdb #3/A TTP 1203 O2G no hydrogen 3.067 N/A
409-humPolDcplx.pdb #3/A ARG 667 NH2 409-humPolDcplx.pdb #3/A TTP 1203 O2G no hydrogen 3.361 N/A
409-humPolDcplx.pdb #3/A LYS 694 NZ 409-humPolDcplx.pdb #3/A TTP 1203 O1A no hydrogen 3.185 N/A
409-humPolDcplx.pdb #3/A LYS 694 NZ 409-humPolDcplx.pdb #3/A TTP 1203 O3A no hydrogen 3.258 N/A
409-humPolDcplx.pdb #3/A LYS 694 NZ 409-humPolDcplx.pdb #3/A TTP 1203 O3G no hydrogen 3.489 N/A
409-humPolDcplx.pdb #3/A LYS 806 NZ 409-humPolDcplx.pdb #3/T DA 4 OP1 no hydrogen 3.554 N/A
409-humPolDcplx.pdb #3/A TYR 809 OH 409-humPolDcplx.pdb #3/P DOC 25 OP1 no hydrogen 3.508 N/A
409-humPolDcplx.pdb #3/A GLY 828 N 409-humPolDcplx.pdb #3/P DG 24 OP1 no hydrogen 3.189 N/A
409-humPolDcplx.pdb #3/A ARG 833 NH1 409-humPolDcplx.pdb #3/P DT 22 O2 no hydrogen 3.691 N/A
409-humPolDcplx.pdb #3/A GLU 886 N 409-humPolDcplx.pdb #3/P DT 22 OP1 no hydrogen 3.519 N/A
409-humPolDcplx.pdb #3/A THR 888 OG1 409-humPolDcplx.pdb #3/P DA 21 OP1 no hydrogen 3.423 N/A
409-humPolDcplx.pdb #3/A THR 888 OG1 409-humPolDcplx.pdb #3/P DA 21 OP2 no hydrogen 3.414 N/A
409-humPolDcplx.pdb #3/A ALA 935 N 409-humPolDcplx.pdb #3/T DT 9 OP1 no hydrogen 2.931 N/A
409-humPolDcplx.pdb #3/A TYR 936 OH 409-humPolDcplx.pdb #3/T DA 10 OP1 no hydrogen 2.589 N/A
409-humPolDcplx.pdb #3/A ARG 968 NH2 409-humPolDcplx.pdb #3/T DT 6 O3' no hydrogen 3.554 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/A SER 1034 OG 409-humPolDcplx.pdb #3/B CYS 314 O no hydrogen 3.581 N/A
409-humPolDcplx.pdb #3/A GLN 1038 NE2 409-humPolDcplx.pdb #3/B SER 272 OG no hydrogen 3.110 N/A
409-humPolDcplx.pdb #3/A SER 1052 OG 409-humPolDcplx.pdb #3/B TYR 50 OH no hydrogen 2.697 N/A
409-humPolDcplx.pdb #3/A THR 1056 OG1 409-humPolDcplx.pdb #3/B PRO 379 O no hydrogen 3.765 N/A
409-humPolDcplx.pdb #3/A SER 1064 OG 409-humPolDcplx.pdb #3/B GLU 136 OE2 no hydrogen 3.529 N/A
409-humPolDcplx.pdb #3/A LEU 1065 N 409-humPolDcplx.pdb #3/B GLU 136 OE2 no hydrogen 2.897 N/A
409-humPolDcplx.pdb #3/A LYS 1083 NZ 409-humPolDcplx.pdb #3/D PRO 106 O no hydrogen 3.581 N/A
409-humPolDcplx.pdb #3/A ARG 1086 NH1 409-humPolDcplx.pdb #3/B ARG 48 O no hydrogen 3.251 N/A
409-humPolDcplx.pdb #3/A TTP 1203 N3 409-humPolDcplx.pdb #3/T DA 0 N1 no hydrogen 3.246 N/A
409-humPolDcplx.pdb #3/B PHE 24 N 409-humPolDcplx.pdb #3/C ALA 134 O no hydrogen 2.792 N/A
409-humPolDcplx.pdb #3/B ARG 40 NE 409-humPolDcplx.pdb #3/A PRO 1104 O no hydrogen 3.661 N/A
409-humPolDcplx.pdb #3/B ARG 40 NH2 409-humPolDcplx.pdb #3/A GLY 1103 O no hydrogen 3.739 N/A
409-humPolDcplx.pdb #3/B ARG 44 NH2 409-humPolDcplx.pdb #3/A GLU 1048 OE2 no hydrogen 2.841 N/A
409-humPolDcplx.pdb #3/B TYR 50 OH 409-humPolDcplx.pdb #3/A SER 1052 OG no hydrogen 2.697 N/A
409-humPolDcplx.pdb #3/B GLN 225 NE2 409-humPolDcplx.pdb #3/C CYS 129 O no hydrogen 3.279 N/A
409-humPolDcplx.pdb #3/B GLY 227 N 409-humPolDcplx.pdb #3/C HIS 99 NE2 no hydrogen 3.438 N/A
409-humPolDcplx.pdb #3/B ASP 228 N 409-humPolDcplx.pdb #3/C SER 97 OG no hydrogen 3.524 N/A
409-humPolDcplx.pdb #3/B GLN 232 NE2 409-humPolDcplx.pdb #3/C ASN 35 OD1 no hydrogen 3.213 N/A
409-humPolDcplx.pdb #3/B SER 451 N 409-humPolDcplx.pdb #3/C HIS 75 O no hydrogen 3.300 N/A
409-humPolDcplx.pdb #3/B SER 453 N 409-humPolDcplx.pdb #3/C VAL 77 O no hydrogen 3.318 N/A
409-humPolDcplx.pdb #3/B PHE 455 N 409-humPolDcplx.pdb #3/C VAL 79 O no hydrogen 3.146 N/A
409-humPolDcplx.pdb #3/C LYS 24 NZ 409-humPolDcplx.pdb #3/B ASP 220 OD1 no hydrogen 3.549 N/A
409-humPolDcplx.pdb #3/C ASN 35 ND2 409-humPolDcplx.pdb #3/B GLN 232 OE1 no hydrogen 3.569 N/A
409-humPolDcplx.pdb #3/C LYS 38 NZ 409-humPolDcplx.pdb #3/B GLN 225 O no hydrogen 3.465 N/A
409-humPolDcplx.pdb #3/C GLN 39 NE2 409-humPolDcplx.pdb #3/B THR 12 O no hydrogen 3.615 N/A
409-humPolDcplx.pdb #3/C SER 64 OG 409-humPolDcplx.pdb #3/B GLU 231 OE2 no hydrogen 2.876 N/A
409-humPolDcplx.pdb #3/C VAL 77 N 409-humPolDcplx.pdb #3/B SER 451 O no hydrogen 3.469 N/A
409-humPolDcplx.pdb #3/C SER 111 OG 409-humPolDcplx.pdb #3/B PHE 455 O no hydrogen 2.379 N/A
409-humPolDcplx.pdb #3/C SER 133 OG 409-humPolDcplx.pdb #3/B THR 223 O no hydrogen 3.061 N/A
409-humPolDcplx.pdb #3/C SER 133 OG 409-humPolDcplx.pdb #3/B GLY 224 O no hydrogen 3.674 N/A
409-humPolDcplx.pdb #3/C ALA 134 N 409-humPolDcplx.pdb #3/B GLY 224 O no hydrogen 3.359 N/A
409-humPolDcplx.pdb #3/C GLN 136 N 409-humPolDcplx.pdb #3/B PHE 24 O no hydrogen 3.693 N/A
409-humPolDcplx.pdb #3/C CYS 137 SG 409-humPolDcplx.pdb #3/B ALA 288 O no hydrogen 3.228 N/A
409-humPolDcplx.pdb #3/C CYS 137 SG 409-humPolDcplx.pdb #3/B SER 289 O no hydrogen 3.249 N/A
409-humPolDcplx.pdb #3/C ARG 143 N 409-humPolDcplx.pdb #3/B ALA 321 O no hydrogen 2.936 N/A
409-humPolDcplx.pdb #3/C ALA 144 N 409-humPolDcplx.pdb #3/B ALA 321 O no hydrogen 3.059 N/A
409-humPolDcplx.pdb #3/D GLN 51 NE2 409-humPolDcplx.pdb #3/A GLY 500 O no hydrogen 3.473 N/A
409-humPolDcplx.pdb #3/D ARG 72 NH1 409-humPolDcplx.pdb #3/B HIS 52 ND1 no hydrogen 3.199 N/A
409-humPolDcplx.pdb #3/D ARG 72 NH1 409-humPolDcplx.pdb #3/B TYR 388 O no hydrogen 3.171 N/A
409-humPolDcplx.pdb #3/D TYR 105 OH 409-humPolDcplx.pdb #3/A SER 492 OG no hydrogen 3.453 N/A
409-humPolDcplx.pdb #3/E CYS 81 SG 409-humPolDcplx.pdb #3/F ASP 150 O no hydrogen 4.038 N/A
409-humPolDcplx.pdb #3/E CYS 81 SG 409-humPolDcplx.pdb #3/F HIS 153 ND1 no hydrogen 4.017 N/A
409-humPolDcplx.pdb #3/E SER 183 N 409-humPolDcplx.pdb #3/G GLU 109 OE2 no hydrogen 3.653 N/A
409-humPolDcplx.pdb #3/F LYS 77 NZ 409-humPolDcplx.pdb #3/G HIS 153 O no hydrogen 3.375 N/A
409-humPolDcplx.pdb #3/F CYS 81 SG 409-humPolDcplx.pdb #3/G ASP 150 O no hydrogen 4.177 N/A
409-humPolDcplx.pdb #3/F CYS 81 SG 409-humPolDcplx.pdb #3/G HIS 153 ND1 no hydrogen 3.724 N/A
409-humPolDcplx.pdb #3/F GLU 115 N 409-humPolDcplx.pdb #3/G ASN 177 O no hydrogen 3.423 N/A
409-humPolDcplx.pdb #3/F LYS 117 NZ 409-humPolDcplx.pdb #3/G GLU 174 O no hydrogen 3.120 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
409-humPolDcplx.pdb #3/F ASN 179 N 409-humPolDcplx.pdb #3/E ASP 113 OD1 no hydrogen 3.306 N/A
409-humPolDcplx.pdb #3/F SER 183 N 409-humPolDcplx.pdb #3/E GLU 109 OE2 no hydrogen 2.879 N/A
409-humPolDcplx.pdb #3/F SER 183 OG 409-humPolDcplx.pdb #3/E GLU 109 OE1 no hydrogen 3.419 N/A
409-humPolDcplx.pdb #3/F SER 183 OG 409-humPolDcplx.pdb #3/E GLU 109 OE2 no hydrogen 3.541 N/A
409-humPolDcplx.pdb #3/G CYS 81 SG 409-humPolDcplx.pdb #3/E ASP 150 O no hydrogen 4.004 N/A
409-humPolDcplx.pdb #3/G ASN 177 N 409-humPolDcplx.pdb #3/F GLU 115 O no hydrogen 3.604 N/A
409-humPolDcplx.pdb #3/P DC 3 N4 409-humPolDcplx.pdb #3/T DG 23 O6 no hydrogen 2.962 N/A
409-humPolDcplx.pdb #3/P DT 4 N3 409-humPolDcplx.pdb #3/T DA 22 N1 no hydrogen 2.822 N/A
409-humPolDcplx.pdb #3/P DA 5 N6 409-humPolDcplx.pdb #3/T DT 21 O4 no hydrogen 2.983 N/A
409-humPolDcplx.pdb #3/P DT 6 N3 409-humPolDcplx.pdb #3/T DA 20 N1 no hydrogen 2.771 N/A
409-humPolDcplx.pdb #3/P DG 7 N1 409-humPolDcplx.pdb #3/T DC 19 N3 no hydrogen 2.906 N/A
409-humPolDcplx.pdb #3/P DG 7 N2 409-humPolDcplx.pdb #3/T DC 19 N3 no hydrogen 3.625 N/A
409-humPolDcplx.pdb #3/P DG 7 N2 409-humPolDcplx.pdb #3/T DC 19 O2 no hydrogen 2.774 N/A
409-humPolDcplx.pdb #3/P DA 8 N6 409-humPolDcplx.pdb #3/T DT 18 O4 no hydrogen 2.927 N/A
409-humPolDcplx.pdb #3/P DC 9 N4 409-humPolDcplx.pdb #3/T DG 17 O6 no hydrogen 2.938 N/A
409-humPolDcplx.pdb #3/P DC 10 N4 409-humPolDcplx.pdb #3/T DG 16 O6 no hydrogen 2.888 N/A
409-humPolDcplx.pdb #3/P DA 11 N6 409-humPolDcplx.pdb #3/T DT 15 O4 no hydrogen 2.924 N/A
409-humPolDcplx.pdb #3/P DT 12 N3 409-humPolDcplx.pdb #3/T DA 14 N1 no hydrogen 2.961 N/A
409-humPolDcplx.pdb #3/P DG 13 N1 409-humPolDcplx.pdb #3/T DC 13 N3 no hydrogen 2.855 N/A
409-humPolDcplx.pdb #3/P DG 13 N2 409-humPolDcplx.pdb #3/T DC 13 N3 no hydrogen 3.625 N/A
409-humPolDcplx.pdb #3/P DG 13 N2 409-humPolDcplx.pdb #3/T DC 13 O2 no hydrogen 2.767 N/A
409-humPolDcplx.pdb #3/P DA 14 N6 409-humPolDcplx.pdb #3/T DT 12 O4 no hydrogen 2.974 N/A
409-humPolDcplx.pdb #3/P DT 15 N3 409-humPolDcplx.pdb #3/T DA 11 N1 no hydrogen 2.709 N/A
409-humPolDcplx.pdb #3/P DT 16 N3 409-humPolDcplx.pdb #3/T DA 10 N1 no hydrogen 3.030 N/A
409-humPolDcplx.pdb #3/P DA 17 N6 409-humPolDcplx.pdb #3/T DT 9 O4 no hydrogen 2.951 N/A
409-humPolDcplx.pdb #3/P DC 18 N4 409-humPolDcplx.pdb #3/T DG 8 O6 no hydrogen 2.973 N/A
409-humPolDcplx.pdb #3/P DG 19 N1 409-humPolDcplx.pdb #3/T DC 7 N3 no hydrogen 2.867 N/A
409-humPolDcplx.pdb #3/P DG 19 N2 409-humPolDcplx.pdb #3/T DC 7 N3 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/P DG 19 N2 409-humPolDcplx.pdb #3/T DC 7 O2 no hydrogen 2.821 N/A
409-humPolDcplx.pdb #3/P DA 20 N6 409-humPolDcplx.pdb #3/T DT 6 O4 no hydrogen 2.933 N/A
409-humPolDcplx.pdb #3/P DA 21 N6 409-humPolDcplx.pdb #3/T DT 5 O4 no hydrogen 3.022 N/A
409-humPolDcplx.pdb #3/P DT 22 N3 409-humPolDcplx.pdb #3/T DA 4 N1 no hydrogen 2.907 N/A
409-humPolDcplx.pdb #3/P DT 23 N3 409-humPolDcplx.pdb #3/T DA 3 N1 no hydrogen 2.945 N/A
409-humPolDcplx.pdb #3/P DG 24 N1 409-humPolDcplx.pdb #3/T DC 2 N3 no hydrogen 3.013 N/A
409-humPolDcplx.pdb #3/P DG 24 N2 409-humPolDcplx.pdb #3/T DC 2 N3 no hydrogen 3.705 N/A
409-humPolDcplx.pdb #3/P DG 24 N2 409-humPolDcplx.pdb #3/T DC 2 O2 no hydrogen 3.027 N/A
409-humPolDcplx.pdb #3/T DA 0 N6 409-humPolDcplx.pdb #3/A TTP 1203 O4 no hydrogen 3.274 N/A
409-humPolDcplx.pdb #3/T DG 1 N2 409-humPolDcplx.pdb #3/P DOC 25 O2 no hydrogen 3.062 N/A
409-humPolDcplx.pdb #3/T DC 2 N4 409-humPolDcplx.pdb #3/P DG 24 O6 no hydrogen 2.882 N/A
409-humPolDcplx.pdb #3/T DA 3 N6 409-humPolDcplx.pdb #3/P DT 23 O4 no hydrogen 3.039 N/A
409-humPolDcplx.pdb #3/T DA 4 N6 409-humPolDcplx.pdb #3/P DT 22 O4 no hydrogen 2.996 N/A
409-humPolDcplx.pdb #3/T DT 5 N3 409-humPolDcplx.pdb #3/P DA 21 N1 no hydrogen 2.934 N/A
409-humPolDcplx.pdb #3/T DT 6 N3 409-humPolDcplx.pdb #3/P DA 20 N1 no hydrogen 2.780 N/A
409-humPolDcplx.pdb #3/T DC 7 N4 409-humPolDcplx.pdb #3/P DG 19 O6 no hydrogen 2.820 N/A
409-humPolDcplx.pdb #3/T DG 8 N1 409-humPolDcplx.pdb #3/P DC 18 N3 no hydrogen 2.948 N/A
409-humPolDcplx.pdb #3/T DG 8 N2 409-humPolDcplx.pdb #3/P DC 18 N3 no hydrogen 3.688 N/A
409-humPolDcplx.pdb #3/T DG 8 N2 409-humPolDcplx.pdb #3/P DC 18 O2 no hydrogen 2.841 N/A
409-humPolDcplx.pdb #3/T DT 9 N3 409-humPolDcplx.pdb #3/P DA 17 N1 no hydrogen 2.885 N/A
409-humPolDcplx.pdb #3/T DA 10 N6 409-humPolDcplx.pdb #3/P DT 16 O4 no hydrogen 2.816 N/A
409-humPolDcplx.pdb #3/T DA 11 N6 409-humPolDcplx.pdb #3/P DT 15 O4 no hydrogen 2.795 N/A
409-humPolDcplx.pdb #3/T DT 12 N3 409-humPolDcplx.pdb #3/P DA 14 N1 no hydrogen 2.761 N/A
409-humPolDcplx.pdb #3/T DC 13 N4 409-humPolDcplx.pdb #3/P DT 12 O4 no hydrogen 3.835 N/A
409-humPolDcplx.pdb #3/T DC 13 N4 409-humPolDcplx.pdb #3/P DG 13 O6 no hydrogen 2.882 N/A
409-humPolDcplx.pdb #3/T DA 14 N6 409-humPolDcplx.pdb #3/P DT 12 O4 no hydrogen 3.017 N/A
409-humPolDcplx.pdb #3/T DT 15 N3 409-humPolDcplx.pdb #3/P DA 11 N1 no hydrogen 2.873 N/A
409-humPolDcplx.pdb #3/T DG 16 N1 409-humPolDcplx.pdb #3/P DC 10 N3 no hydrogen 2.868 N/A
409-humPolDcplx.pdb #3/T DG 16 N2 409-humPolDcplx.pdb #3/P DC 10 N3 no hydrogen 3.586 N/A
409-humPolDcplx.pdb #3/T DG 16 N2 409-humPolDcplx.pdb #3/P DC 10 O2 no hydrogen 2.774 N/A
409-humPolDcplx.pdb #3/T DG 17 N1 409-humPolDcplx.pdb #3/P DC 9 N3 no hydrogen 2.830 N/A
409-humPolDcplx.pdb #3/T DG 17 N2 409-humPolDcplx.pdb #3/P DC 9 N3 no hydrogen 3.567 N/A
409-humPolDcplx.pdb #3/T DG 17 N2 409-humPolDcplx.pdb #3/P DC 9 O2 no hydrogen 2.671 N/A
409-humPolDcplx.pdb #3/T DT 18 N3 409-humPolDcplx.pdb #3/P DA 8 N1 no hydrogen 3.017 N/A
409-humPolDcplx.pdb #3/T DC 19 N4 409-humPolDcplx.pdb #3/P DG 7 O6 no hydrogen 2.947 N/A
409-humPolDcplx.pdb #3/T DA 20 N6 409-humPolDcplx.pdb #3/P DT 6 O4 no hydrogen 3.026 N/A
409-humPolDcplx.pdb #3/T DT 21 N3 409-humPolDcplx.pdb #3/P DA 5 N1 no hydrogen 2.903 N/A
409-humPolDcplx.pdb #3/T DA 22 N6 409-humPolDcplx.pdb #3/P DT 4 O4 no hydrogen 3.000 N/A
409-humPolDcplx.pdb #3/T DG 23 N1 409-humPolDcplx.pdb #3/P DC 3 N3 no hydrogen 2.800 N/A
409-humPolDcplx.pdb #3/T DG 23 N2 409-humPolDcplx.pdb #3/P DC 3 N3 no hydrogen 3.465 N/A
409-humPolDcplx.pdb #3/T DG 23 N2 409-humPolDcplx.pdb #3/P DC 3 O2 no hydrogen 2.631 N/A
286 hydrogen bonds found
> hide #3 & ~sel
> hbonds sel restrict both interModel false distSlop 0.6 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.7 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.7 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
5 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.8 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A THR 993 N 409-humPolDcplx.pdb #3/F ASP 120 O no hydrogen 3.787 N/A
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
6 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.8 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A THR 993 N 409-humPolDcplx.pdb #3/F ASP 120 O no hydrogen 3.787 N/A
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
6 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 1.0 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A THR 993 N 409-humPolDcplx.pdb #3/F ASP 120 O no hydrogen 3.787 N/A
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A CYS 1011 SG 409-humPolDcplx.pdb #3/F GLU 124 OE1 no hydrogen 4.377 N/A
409-humPolDcplx.pdb #3/A CYS 1011 SG 409-humPolDcplx.pdb #3/F GLN 125 OE1 no hydrogen 4.636 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
8 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.8 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A THR 993 N 409-humPolDcplx.pdb #3/F ASP 120 O no hydrogen 3.787 N/A
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
6 hydrogen bonds found
> show #!2 models
> hide #!3 models
> hide #2 & ~sel
> hbonds sel restrict both interModel false distSlop 0.8 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 990 N 409-ystPolDcplx_156-679.pdb #2/H ILE 121 O no hydrogen 3.739 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H ASP 120 N 409-ystPolDcplx_156-679.pdb #2/A LYS 986 O no hydrogen 3.744 N/A
409-ystPolDcplx_156-679.pdb #2/H LYS 127 N 409-ystPolDcplx_156-679.pdb #2/A LYS 1004 O no hydrogen 3.551 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
9 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
5 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hide #!2 models
> show #!3 models
> hbonds sel restrict both interModel false distSlop 0.6 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.6 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.7 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.7 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
5 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.8 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A THR 993 N 409-humPolDcplx.pdb #3/F ASP 120 O no hydrogen 3.787 N/A
409-humPolDcplx.pdb #3/A LEU 995 N 409-humPolDcplx.pdb #3/F ASP 122 O no hydrogen 3.742 N/A
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
6 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> show #!2 models
> hide #!3 models
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> hide #!2 models
> show #!3 models
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both showDist true interModel false distSlop 0.5
> intraMol false intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
3 409-humPolDcplx.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-humPolDcplx.pdb #3/A ARG 1009 N 409-humPolDcplx.pdb #3/F GLN 125 O no hydrogen 3.531 N/A
409-humPolDcplx.pdb #3/A ARG 1016 NH2 409-humPolDcplx.pdb #3/F ASP 122 OD2 no hydrogen 3.647 N/A
409-humPolDcplx.pdb #3/F ASP 120 N 409-humPolDcplx.pdb #3/A CYS 991 O no hydrogen 3.353 N/A
409-humPolDcplx.pdb #3/F ASP 122 N 409-humPolDcplx.pdb #3/A THR 993 O no hydrogen 3.446 N/A
4 hydrogen bonds found
> show #!2 models
> hide #!3 models
> hbonds sel restrict both interModel false distSlop 0.5 intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
2 409-ystPolDcplx_156-679.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
409-ystPolDcplx_156-679.pdb #2/A ARG 955 NH2 409-ystPolDcplx_156-679.pdb #2/H GLN 24 OE1 no hydrogen 3.273 N/A
409-ystPolDcplx_156-679.pdb #2/A ILE 988 N 409-ystPolDcplx_156-679.pdb #2/H ASP 120 O no hydrogen 3.534 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1004 N 409-ystPolDcplx_156-679.pdb #2/H LYS 127 O no hydrogen 2.711 N/A
409-ystPolDcplx_156-679.pdb #2/A VAL 1006 N 409-ystPolDcplx_156-679.pdb #2/H PHE 125 O no hydrogen 2.945 N/A
409-ystPolDcplx_156-679.pdb #2/A LYS 1013 NZ 409-ystPolDcplx_156-679.pdb #2/H ASP 122 OD1 no hydrogen 3.443 N/A
409-ystPolDcplx_156-679.pdb #2/H GLU 129 N 409-ystPolDcplx_156-679.pdb #2/A PHE 1002 O no hydrogen 3.432 N/A
6 hydrogen bonds found
> select clear
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> save session "/Users/fengwei.zheng/Documents/Draft_PolD/Session/ystPolD-
> interface sticks.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2401, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12b842fd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x12b9ae790>
'409-ystPolDcplx_156-679.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-ystPolDcplx_156-679.pdb'
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2401, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 935, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 651, in file_save_cb
self.save_dialog.display(self, session)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display
fmt.save(session, filename)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save
run(session, cmd)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session
save(session, filename, **kw)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export
result = self.export_func(session, path, **kw)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12b842fd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x12b9ae790>
'409-ystPolDcplx_156-679.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-ystPolDcplx_156-679.pdb'
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
> save session "/Users/fengwei.zheng/Documents/Draft_PolD/Session/ystPolD-
> interface sticks.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2401, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12b842fd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x12b9ae790>
'409-ystPolDcplx_156-679.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-ystPolDcplx_156-679.pdb'
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2401, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 159, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 935, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 651, in file_save_cb
self.save_dialog.display(self, session)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display
fmt.save(session, filename)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save
run(session, cmd)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session
save(session, filename, **kw)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export
result = self.export_func(session, path, **kw)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12b842fd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x12b9ae790>
'409-ystPolDcplx_156-679.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'409-ystPolDcplx_156-679.pdb'
File
"/Applications/ChimeraX-0.92.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Attachments (1)
Change History (5)
comment:1 by , 6 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Reporter: | changed from to |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → settings error-reporting using non-existent attribute |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
follow-up: 3 comment:3 by , 6 years ago
Dear Eric,
Thank you so much for your fellowing! Yeah, I tried to change the default pseudobonds color (sky blue) to yellow (Pls see the figure below), it seems always failed~ But finally I found I can select the pseudobonds that I want to change color, and then achieve this via command, Many thanks and have a good one!
[cid:ce962e29-c636-4dba-878a-033eedd68605]
Best,
Fengwei
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, March 31, 2020 13:04
Cc: Zheng, Fengwei <Fengwei.Zheng@vai.org>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [External] Re: [ChimeraX] #2997: settings error-reporting using non-existent attribute
#2997: settings error-reporting using non-existent attribute
--------------------------------------+----------------------------
Reporter: Fengwei.Zheng@… | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Core | Version:
Resolution: duplicate | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
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Changes (by Eric Pettersen):
* status: accepted => closed
* resolution: => duplicate
Comment:
Hi Fengwei,
I have fixed the main error in this report, which was a bug in the
error reporting! Anyway, that bug was hiding an underlying issue where it
seems that you were using some value or setting in the H-bond interface
that wasn't legal. Do you remember what you were doing there?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
(duplicate of #2966, which is fixed)
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2997#comment:2>
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comment:4 by , 6 years ago
Okay, also fixed the problem with changing the color from the default. Fix will be in tomorrow's build.
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Hi Fengwei,
--Eric
(duplicate of #2996, which is fixed)