Opened 6 years ago

Closed 6 years ago

#2996 closed defect (fixed)

settings error-reporting using non-existent attribute

Reported by: chimerax-bug-report@… 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 Eric Pettersen, 6 years ago

Component: UnassignedCore
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionsettings error-reporting using non-existent attribute

comment:2 by Eric Pettersen, 6 years ago

Resolution: fixed
Status: acceptedclosed
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