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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