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Opened 6 years ago
Closed 6 years ago
#2996 closed defect (fixed)
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.
OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → settings error-reporting using non-existent attribute |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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