Changes between Initial Version and Version 1 of Ticket #3308


Ignore:
Timestamp:
May 26, 2020, 10:17:58 AM (5 years ago)
Author:
Eric Pettersen
Comment:

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  • Ticket #3308

    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → User-supplied template does not match the residue

  • Ticket #3308 – Description

    initial v1  
    669669During handling of the above exception, another exception occurred: 
    670670 
    671 Traceback (most recent call last): 
    672 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    673 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    674 isolde.forcefield_mgr) 
    675 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    676 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    677 sim_params, residue_templates) 
    678 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    679 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    680 _create_openmm_system 
    681 sys = forcefield.createSystem(top, **system_params) 
    682 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    683 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    684 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    685 % (tname, res.index+1, res.name)) 
    686 Exception: User-supplied template GLYCAM_4YB does not match the residue 454
    687 (NAG) 
    688  
    689 During handling of the above exception, another exception occurred: 
    690  
    691 Traceback (most recent call last): 
    692 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    693 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    694 isolde.forcefield_mgr) 
    695 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    696 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    697 sim_params, residue_templates) 
    698 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    699 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    700 _create_openmm_system 
    701 sys = forcefield.createSystem(top, **system_params) 
    702 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    703 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    704 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    705 % (tname, res.index+1, res.name)) 
    706 Exception: User-supplied template GLYCAM_4YB does not match the residue 455
    707 (NAG) 
    708  
    709 During handling of the above exception, another exception occurred: 
    710  
    711 Traceback (most recent call last): 
    712 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    713 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    714 isolde.forcefield_mgr) 
    715 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    716 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    717 sim_params, residue_templates) 
    718 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    719 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    720 _create_openmm_system 
    721 sys = forcefield.createSystem(top, **system_params) 
    722 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    723 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    724 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    725 % (tname, res.index+1, res.name)) 
    726 Exception: User-supplied template GLYCAM_4YB does not match the residue 457
    727 (NAG) 
    728  
    729 During handling of the above exception, another exception occurred: 
    730  
    731 Traceback (most recent call last): 
    732 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    733 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    734 isolde.forcefield_mgr) 
    735 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    736 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    737 sim_params, residue_templates) 
    738 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    739 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    740 _create_openmm_system 
    741 sys = forcefield.createSystem(top, **system_params) 
    742 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    743 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    744 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    745 % (tname, res.index+1, res.name)) 
    746 Exception: User-supplied template GLYCAM_0YB does not match the residue 458
    747 (NAG) 
    748  
    749 During handling of the above exception, another exception occurred: 
    750  
    751 Traceback (most recent call last): 
    752 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    753 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    754 isolde.forcefield_mgr) 
    755 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    756 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    757 sim_params, residue_templates) 
    758 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    759 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    760 _create_openmm_system 
    761 sys = forcefield.createSystem(top, **system_params) 
    762 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    763 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    764 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    765 % (tname, res.index+1, res.name)) 
    766 Exception: User-supplied template GLYCAM_0YB does not match the residue 458
    767 (NAG) 
    768  
    769 During handling of the above exception, another exception occurred: 
    770  
    771 Traceback (most recent call last): 
    772 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    773 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    774 isolde.forcefield_mgr) 
    775 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    776 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    777 sim_params, residue_templates) 
    778 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    779 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    780 _create_openmm_system 
    781 sys = forcefield.createSystem(top, **system_params) 
    782 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    783 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    784 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    785 % (tname, res.index+1, res.name)) 
    786 Exception: User-supplied template CYS does not match the residue 716 (ASP) 
    787  
    788 During handling of the above exception, another exception occurred: 
    789  
    790 Traceback (most recent call last): 
    791 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    792 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    793 isolde.forcefield_mgr) 
    794 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    795 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    796 sim_params, residue_templates) 
    797 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    798 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    799 _create_openmm_system 
    800 sys = forcefield.createSystem(top, **system_params) 
    801 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    802 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    803 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    804 % (tname, res.index+1, res.name)) 
    805 Exception: User-supplied template CYS does not match the residue 716 (ASP) 
    806  
    807 During handling of the above exception, another exception occurred: 
    808  
    809 Traceback (most recent call last): 
    810 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    811 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    812 isolde.forcefield_mgr) 
    813 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    814 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    815 sim_params, residue_templates) 
    816 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    817 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    818 _create_openmm_system 
    819 sys = forcefield.createSystem(top, **system_params) 
    820 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    821 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    822 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    823 % (tname, res.index+1, res.name)) 
    824 Exception: User-supplied template CYS does not match the residue 716 (ASP) 
    825  
    826 During handling of the above exception, another exception occurred: 
    827  
    828 Traceback (most recent call last): 
    829 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    830 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    831 isolde.forcefield_mgr) 
    832 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    833 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    834 sim_params, residue_templates) 
    835 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    836 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    837 _create_openmm_system 
    838 sys = forcefield.createSystem(top, **system_params) 
    839 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    840 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    841 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    842 % (tname, res.index+1, res.name)) 
    843 Exception: User-supplied template CYS does not match the residue 731 (PRO) 
    844  
    845 During handling of the above exception, another exception occurred: 
    846  
    847 Traceback (most recent call last): 
    848 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    849 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    850 isolde.forcefield_mgr) 
    851 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    852 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    853 sim_params, residue_templates) 
    854 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    855 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    856 _create_openmm_system 
    857 sys = forcefield.createSystem(top, **system_params) 
    858 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    859 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    860 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    861 % (tname, res.index+1, res.name)) 
    862 Exception: User-supplied template CYS does not match the residue 731 (PRO) 
    863  
    864 During handling of the above exception, another exception occurred: 
    865  
    866 Traceback (most recent call last): 
    867 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    868 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    869 isolde.forcefield_mgr) 
    870 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    871 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    872 sim_params, residue_templates) 
    873 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    874 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    875 _create_openmm_system 
    876 sys = forcefield.createSystem(top, **system_params) 
    877 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    878 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    879 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    880 % (tname, res.index+1, res.name)) 
    881 Exception: User-supplied template CYS does not match the residue 731 (PRO) 
    882  
    883 During handling of the above exception, another exception occurred: 
    884  
    885 Traceback (most recent call last): 
    886 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    887 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    888 isolde.forcefield_mgr) 
    889 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    890 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    891 sim_params, residue_templates) 
    892 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    893 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    894 _create_openmm_system 
    895 sys = forcefield.createSystem(top, **system_params) 
    896 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    897 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    898 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    899 % (tname, res.index+1, res.name)) 
    900 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    901  
    902 During handling of the above exception, another exception occurred: 
    903  
    904 Traceback (most recent call last): 
    905 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    906 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    907 isolde.forcefield_mgr) 
    908 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    909 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    910 sim_params, residue_templates) 
    911 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    912 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    913 _create_openmm_system 
    914 sys = forcefield.createSystem(top, **system_params) 
    915 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    916 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    917 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    918 % (tname, res.index+1, res.name)) 
    919 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    920  
    921 During handling of the above exception, another exception occurred: 
    922  
    923 Traceback (most recent call last): 
    924 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    925 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    926 isolde.forcefield_mgr) 
    927 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    928 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    929 sim_params, residue_templates) 
    930 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    931 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    932 _create_openmm_system 
    933 sys = forcefield.createSystem(top, **system_params) 
    934 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    935 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    936 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    937 % (tname, res.index+1, res.name)) 
    938 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    939  
    940 During handling of the above exception, another exception occurred: 
    941  
    942 Traceback (most recent call last): 
    943 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    944 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    945 isolde.forcefield_mgr) 
    946 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    947 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    948 sim_params, residue_templates) 
    949 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    950 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    951 _create_openmm_system 
    952 sys = forcefield.createSystem(top, **system_params) 
    953 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    954 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    955 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    956 % (tname, res.index+1, res.name)) 
    957 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    958  
    959 During handling of the above exception, another exception occurred: 
    960  
    961 Traceback (most recent call last): 
    962 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    963 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    964 isolde.forcefield_mgr) 
    965 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    966 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    967 sim_params, residue_templates) 
    968 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    969 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    970 _create_openmm_system 
    971 sys = forcefield.createSystem(top, **system_params) 
    972 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    973 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    974 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    975 % (tname, res.index+1, res.name)) 
    976 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    977  
    978 During handling of the above exception, another exception occurred: 
    979  
    980 Traceback (most recent call last): 
    981 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    982 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    983 isolde.forcefield_mgr) 
    984 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    985 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    986 sim_params, residue_templates) 
    987 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    988 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    989 _create_openmm_system 
    990 sys = forcefield.createSystem(top, **system_params) 
    991 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    992 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    993 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    994 % (tname, res.index+1, res.name)) 
    995 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    996  
    997 During handling of the above exception, another exception occurred: 
    998  
    999 Traceback (most recent call last): 
    1000 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1001 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1002 isolde.forcefield_mgr) 
    1003 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1004 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1005 sim_params, residue_templates) 
    1006 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1007 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1008 _create_openmm_system 
    1009 sys = forcefield.createSystem(top, **system_params) 
    1010 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1011 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1012 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1013 % (tname, res.index+1, res.name)) 
    1014 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    1015  
    1016 During handling of the above exception, another exception occurred: 
    1017  
    1018 Traceback (most recent call last): 
    1019 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1020 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1021 isolde.forcefield_mgr) 
    1022 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1023 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1024 sim_params, residue_templates) 
    1025 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1026 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1027 _create_openmm_system 
    1028 sys = forcefield.createSystem(top, **system_params) 
    1029 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1030 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1031 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1032 % (tname, res.index+1, res.name)) 
    1033 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    1034  
    1035 During handling of the above exception, another exception occurred: 
    1036  
    1037 Traceback (most recent call last): 
    1038 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1039 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1040 isolde.forcefield_mgr) 
    1041 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1042 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1043 sim_params, residue_templates) 
    1044 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1045 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1046 _create_openmm_system 
    1047 sys = forcefield.createSystem(top, **system_params) 
    1048 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1049 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1050 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1051 % (tname, res.index+1, res.name)) 
    1052 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    1053  
    1054 During handling of the above exception, another exception occurred: 
    1055  
    1056 Traceback (most recent call last): 
    1057 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1058 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1059 isolde.forcefield_mgr) 
    1060 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1061 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1062 sim_params, residue_templates) 
    1063 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1064 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1065 _create_openmm_system 
    1066 sys = forcefield.createSystem(top, **system_params) 
    1067 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1068 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1069 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1070 % (tname, res.index+1, res.name)) 
    1071 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    1072  
    1073 During handling of the above exception, another exception occurred: 
    1074  
    1075 Traceback (most recent call last): 
    1076 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1077 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1078 isolde.forcefield_mgr) 
    1079 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1080 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1081 sim_params, residue_templates) 
    1082 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1083 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1084 _create_openmm_system 
    1085 sys = forcefield.createSystem(top, **system_params) 
    1086 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1087 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1088 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1089 % (tname, res.index+1, res.name)) 
    1090 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    1091  
    1092 During handling of the above exception, another exception occurred: 
    1093  
    1094 Traceback (most recent call last): 
    1095 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1096 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1097 isolde.forcefield_mgr) 
    1098 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1099 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1100 sim_params, residue_templates) 
    1101 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1102 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1103 _create_openmm_system 
    1104 sys = forcefield.createSystem(top, **system_params) 
    1105 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1106 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1107 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1108 % (tname, res.index+1, res.name)) 
    1109 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    1110  
    1111 During handling of the above exception, another exception occurred: 
    1112  
    1113 Traceback (most recent call last): 
    1114 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1115 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1116 isolde.forcefield_mgr) 
    1117 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1118 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1119 sim_params, residue_templates) 
    1120 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1121 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1122 _create_openmm_system 
    1123 sys = forcefield.createSystem(top, **system_params) 
    1124 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1125 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1126 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1127 % (tname, res.index+1, res.name)) 
    1128 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    1129  
    1130 During handling of the above exception, another exception occurred: 
    1131  
    1132 Traceback (most recent call last): 
    1133 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1134 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1135 isolde.forcefield_mgr) 
    1136 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1137 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1138 sim_params, residue_templates) 
    1139 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1140 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1141 _create_openmm_system 
    1142 sys = forcefield.createSystem(top, **system_params) 
    1143 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1144 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1145 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1146 % (tname, res.index+1, res.name)) 
    1147 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    1148  
    1149 During handling of the above exception, another exception occurred: 
    1150  
    1151 Traceback (most recent call last): 
    1152 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1153 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1154 isolde.forcefield_mgr) 
    1155 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1156 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1157 sim_params, residue_templates) 
    1158 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1159 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1160 _create_openmm_system 
    1161 sys = forcefield.createSystem(top, **system_params) 
    1162 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1163 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    1164 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    1165 % (tname, res.index+1, res.name)) 
    1166 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    1167  
    1168 During handling of the above exception, another exception occurred: 
    1169  
    1170 Traceback (most recent call last): 
    1171 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1172 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    1173 self.start_sim() 
    1174 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1175 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1176 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1177 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1178 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1179 if self._parse_explicit_template_error(e): 
    1180 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1181 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1182 _parse_explicit_template_error 
    1183 self.isolde._handle_bad_template(residue) 
    1184 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1185 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1186 self.start_sim() 
    1187 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1188 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1189 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1190 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1191 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1192 if self._parse_explicit_template_error(e): 
    1193 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1194 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1195 _parse_explicit_template_error 
    1196 self.isolde._handle_bad_template(residue) 
    1197 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1198 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1199 self.start_sim() 
    1200 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1201 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1202 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1203 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1204 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1205 if self._parse_explicit_template_error(e): 
    1206 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1207 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1208 _parse_explicit_template_error 
    1209 self.isolde._handle_bad_template(residue) 
    1210 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1211 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1212 self.start_sim() 
    1213 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1214 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1215 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1216 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1217 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1218 if self._parse_explicit_template_error(e): 
    1219 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1220 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1221 _parse_explicit_template_error 
    1222 self.isolde._handle_bad_template(residue) 
    1223 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1224 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1225 self.start_sim() 
    1226 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1227 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1228 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1229 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1230 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1231 if self._parse_explicit_template_error(e): 
    1232 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1233 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1234 _parse_explicit_template_error 
    1235 self.isolde._handle_bad_template(residue) 
    1236 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1237 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1238 self.start_sim() 
    1239 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1240 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1241 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1242 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1243 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1244 if self._parse_explicit_template_error(e): 
    1245 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1246 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1247 _parse_explicit_template_error 
    1248 self.isolde._handle_bad_template(residue) 
    1249 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1250 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1251 self.start_sim() 
    1252 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1253 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1254 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1255 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1256 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1257 if self._parse_explicit_template_error(e): 
    1258 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1259 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1260 _parse_explicit_template_error 
    1261 self.isolde._handle_bad_template(residue) 
    1262 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1263 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1264 self.start_sim() 
    1265 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1266 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1267 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1268 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1269 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1270 if self._parse_explicit_template_error(e): 
    1271 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1272 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1273 _parse_explicit_template_error 
    1274 self.isolde._handle_bad_template(residue) 
    1275 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1276 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1277 self.start_sim() 
    1278 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1279 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1280 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1281 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1282 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1283 if self._parse_explicit_template_error(e): 
    1284 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1285 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1286 _parse_explicit_template_error 
    1287 self.isolde._handle_bad_template(residue) 
    1288 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1289 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1290 self.start_sim() 
    1291 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1292 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1293 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1294 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1295 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1296 if self._parse_explicit_template_error(e): 
    1297 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1298 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1299 _parse_explicit_template_error 
    1300 self.isolde._handle_bad_template(residue) 
    1301 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1302 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1303 self.start_sim() 
    1304 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1305 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1306 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1307 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1308 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1309 if self._parse_explicit_template_error(e): 
    1310 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1311 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1312 _parse_explicit_template_error 
    1313 self.isolde._handle_bad_template(residue) 
    1314 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1315 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1316 self.start_sim() 
    1317 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1318 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1319 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1320 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1321 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1322 if self._parse_explicit_template_error(e): 
    1323 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1324 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1325 _parse_explicit_template_error 
    1326 self.isolde._handle_bad_template(residue) 
    1327 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1328 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1329 self.start_sim() 
    1330 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1331 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1332 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1333 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1334 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1335 if self._parse_explicit_template_error(e): 
    1336 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1337 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1338 _parse_explicit_template_error 
    1339 self.isolde._handle_bad_template(residue) 
    1340 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1341 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1342 self.start_sim() 
    1343 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1344 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1345 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1346 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1347 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1348 if self._parse_explicit_template_error(e): 
    1349 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1350 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1351 _parse_explicit_template_error 
    1352 self.isolde._handle_bad_template(residue) 
    1353 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1354 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1355 self.start_sim() 
    1356 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1357 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1358 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1359 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1360 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1361 if self._parse_explicit_template_error(e): 
    1362 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1363 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1364 _parse_explicit_template_error 
    1365 self.isolde._handle_bad_template(residue) 
    1366 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1367 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1368 self.start_sim() 
    1369 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1370 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1371 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1372 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1373 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1374 if self._parse_explicit_template_error(e): 
    1375 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1376 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1377 _parse_explicit_template_error 
    1378 self.isolde._handle_bad_template(residue) 
    1379 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1380 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1381 self.start_sim() 
    1382 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1383 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1384 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1385 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1386 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1387 if self._parse_explicit_template_error(e): 
    1388 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1389 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1390 _parse_explicit_template_error 
    1391 self.isolde._handle_bad_template(residue) 
    1392 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1393 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1394 self.start_sim() 
    1395 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1396 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1397 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1398 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1399 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1400 if self._parse_explicit_template_error(e): 
    1401 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1402 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1403 _parse_explicit_template_error 
    1404 self.isolde._handle_bad_template(residue) 
    1405 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1406 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1407 self.start_sim() 
    1408 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1409 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1410 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1411 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1412 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1413 if self._parse_explicit_template_error(e): 
    1414 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1415 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1416 _parse_explicit_template_error 
    1417 self.isolde._handle_bad_template(residue) 
    1418 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1419 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1420 self.start_sim() 
    1421 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1422 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1423 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1424 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1425 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1426 if self._parse_explicit_template_error(e): 
    1427 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1428 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1429 _parse_explicit_template_error 
    1430 self.isolde._handle_bad_template(residue) 
    1431 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1432 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1433 self.start_sim() 
    1434 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1435 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1436 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1437 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1438 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1439 if self._parse_explicit_template_error(e): 
    1440 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1441 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1442 _parse_explicit_template_error 
    1443 self.isolde._handle_bad_template(residue) 
    1444 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1445 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1446 self.start_sim() 
    1447 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1448 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1449 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1450 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1451 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1452 if self._parse_explicit_template_error(e): 
    1453 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1454 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1455 _parse_explicit_template_error 
    1456 self.isolde._handle_bad_template(residue) 
    1457 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1458 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1459 self.start_sim() 
    1460 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1461 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1462 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1463 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1464 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1465 if self._parse_explicit_template_error(e): 
    1466 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1467 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1468 _parse_explicit_template_error 
    1469 self.isolde._handle_bad_template(residue) 
    1470 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1471 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1472 self.start_sim() 
    1473 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1474 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1475 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1476 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1477 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1478 if self._parse_explicit_template_error(e): 
    1479 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1480 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1481 _parse_explicit_template_error 
    1482 self.isolde._handle_bad_template(residue) 
    1483 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1484 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1485 self.start_sim() 
    1486 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1487 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1488 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1489 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1490 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1491 if self._parse_explicit_template_error(e): 
    1492 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1493 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1494 _parse_explicit_template_error 
    1495 self.isolde._handle_bad_template(residue) 
    1496 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1497 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1498 self.start_sim() 
    1499 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1500 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1501 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1502 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1503 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1504 if self._parse_explicit_template_error(e): 
    1505 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1506 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1507 _parse_explicit_template_error 
    1508 self.isolde._handle_bad_template(residue) 
    1509 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1510 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1511 self.start_sim() 
    1512 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1513 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1514 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1515 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1516 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1517 if self._parse_explicit_template_error(e): 
    1518 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1519 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1520 _parse_explicit_template_error 
    1521 self.isolde._handle_bad_template(residue) 
    1522 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1523 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1524 self.start_sim() 
    1525 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1526 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1527 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1528 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1529 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1530 if self._parse_explicit_template_error(e): 
    1531 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1532 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1533 _parse_explicit_template_error 
    1534 self.isolde._handle_bad_template(residue) 
    1535 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1536 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1537 self.start_sim() 
    1538 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1539 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1540 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1541 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1542 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1543 if self._parse_explicit_template_error(e): 
    1544 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1545 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1546 _parse_explicit_template_error 
    1547 self.isolde._handle_bad_template(residue) 
    1548 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1549 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1550 self.start_sim() 
    1551 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1552 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1553 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1554 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1555 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1556 if self._parse_explicit_template_error(e): 
    1557 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1558 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1559 _parse_explicit_template_error 
    1560 self.isolde._handle_bad_template(residue) 
    1561 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1562 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1563 self.start_sim() 
    1564 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1565 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1566 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1567 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1568 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1569 if self._parse_explicit_template_error(e): 
    1570 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1571 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1572 _parse_explicit_template_error 
    1573 self.isolde._handle_bad_template(residue) 
    1574 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1575 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1576 self.start_sim() 
    1577 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1578 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1579 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1580 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1581 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1582 if self._parse_explicit_template_error(e): 
    1583 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1584 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1585 _parse_explicit_template_error 
    1586 self.isolde._handle_bad_template(residue) 
    1587 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1588 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1589 self.start_sim() 
    1590 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1591 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1592 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1593 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1594 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1595 if self._parse_explicit_template_error(e): 
    1596 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1597 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1598 _parse_explicit_template_error 
    1599 self.isolde._handle_bad_template(residue) 
    1600 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1601 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1602 self.start_sim() 
    1603 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1604 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1605 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1606 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1607 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1608 if self._parse_explicit_template_error(e): 
    1609 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1610 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1611 _parse_explicit_template_error 
    1612 self.isolde._handle_bad_template(residue) 
    1613 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1614 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1615 self.start_sim() 
    1616 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1617 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1618 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1619 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1620 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1621 if self._parse_explicit_template_error(e): 
    1622 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1623 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1624 _parse_explicit_template_error 
    1625 self.isolde._handle_bad_template(residue) 
    1626 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1627 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1628 self.start_sim() 
    1629 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1630 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1631 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1632 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1633 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1634 if self._parse_explicit_template_error(e): 
    1635 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1636 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1637 _parse_explicit_template_error 
    1638 self.isolde._handle_bad_template(residue) 
    1639 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1640 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1641 self.start_sim() 
    1642 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1643 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1644 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1645 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1646 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1647 if self._parse_explicit_template_error(e): 
    1648 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1649 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1650 _parse_explicit_template_error 
    1651 self.isolde._handle_bad_template(residue) 
    1652 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1653 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1654 self.start_sim() 
    1655 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1656 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1657 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1658 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1659 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1660 if self._parse_explicit_template_error(e): 
    1661 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1662 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1663 _parse_explicit_template_error 
    1664 self.isolde._handle_bad_template(residue) 
    1665 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1666 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1667 self.start_sim() 
    1668 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1669 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1670 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1671 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1672 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    1673 if self._parse_explicit_template_error(e): 
    1674 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1675 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    1676 _parse_explicit_template_error 
    1677 self.isolde._handle_bad_template(residue) 
    1678 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1679 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    1680 self.start_sim() 
    1681 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1682 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1683 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1684 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1685 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    1686 raise e 
    1687 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1688 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1689 isolde.forcefield_mgr) 
    1690 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1691 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1692 sim_params, residue_templates) 
    1693 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1694 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1695 _create_openmm_system 
    1696 sys = forcefield.createSystem(top, **system_params) 
    1697 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1698 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    1699 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    1700 ignoreExternalBonds=ignoreExternalBonds) 
    1701 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1702 packages/simtk/openmm/app/forcefield.py", line 893, in
    1703 _getResidueTemplateMatches 
    1704 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1705 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1706 Exception: Multiple matching templates found for residue 1468 (NAG):
    1707 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1708 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1709  
    1710 Exception: Multiple matching templates found for residue 1468 (NAG):
    1711 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1712 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1713  
    1714 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1715 packages/simtk/openmm/app/forcefield.py", line 893, in
    1716 _getResidueTemplateMatches 
    1717 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1718 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1719  
    1720 See log for complete Python traceback. 
    1721  
    1722 Traceback (most recent call last): 
    1723 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1724 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    1725 self.start_sim() 
    1726 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1727 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1728 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1729 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1730 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    1731 raise e 
    1732 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1733 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1734 isolde.forcefield_mgr) 
    1735 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1736 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1737 sim_params, residue_templates) 
    1738 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1739 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1740 _create_openmm_system 
    1741 sys = forcefield.createSystem(top, **system_params) 
    1742 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1743 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    1744 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    1745 ignoreExternalBonds=ignoreExternalBonds) 
    1746 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1747 packages/simtk/openmm/app/forcefield.py", line 893, in
    1748 _getResidueTemplateMatches 
    1749 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1750 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1751 Exception: Multiple matching templates found for residue 1468 (NAG):
    1752 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1753 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1754  
    1755 Exception: Multiple matching templates found for residue 1468 (NAG):
    1756 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1757 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1758  
    1759 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1760 packages/simtk/openmm/app/forcefield.py", line 893, in
    1761 _getResidueTemplateMatches 
    1762 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1763 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1764  
    1765 See log for complete Python traceback. 
    1766  
    1767 Traceback (most recent call last): 
    1768 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1769 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    1770 self.start_sim() 
    1771 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1772 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1773 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1774 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1775 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    1776 raise e 
    1777 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1778 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1779 isolde.forcefield_mgr) 
    1780 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1781 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1782 sim_params, residue_templates) 
    1783 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1784 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1785 _create_openmm_system 
    1786 sys = forcefield.createSystem(top, **system_params) 
    1787 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1788 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    1789 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    1790 ignoreExternalBonds=ignoreExternalBonds) 
    1791 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1792 packages/simtk/openmm/app/forcefield.py", line 893, in
    1793 _getResidueTemplateMatches 
    1794 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1795 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1796 Exception: Multiple matching templates found for residue 1468 (NAG):
    1797 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1798 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1799  
    1800 Exception: Multiple matching templates found for residue 1468 (NAG):
    1801 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1802 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1803  
    1804 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1805 packages/simtk/openmm/app/forcefield.py", line 893, in
    1806 _getResidueTemplateMatches 
    1807 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1808 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1809  
    1810 See log for complete Python traceback. 
    1811  
    1812 Traceback (most recent call last): 
    1813 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1814 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    1815 self.start_sim() 
    1816 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1817 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1818 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1819 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1820 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    1821 raise e 
    1822 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1823 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1824 isolde.forcefield_mgr) 
    1825 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1826 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1827 sim_params, residue_templates) 
    1828 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1829 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1830 _create_openmm_system 
    1831 sys = forcefield.createSystem(top, **system_params) 
    1832 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1833 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    1834 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    1835 ignoreExternalBonds=ignoreExternalBonds) 
    1836 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1837 packages/simtk/openmm/app/forcefield.py", line 893, in
    1838 _getResidueTemplateMatches 
    1839 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1840 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1841 Exception: Multiple matching templates found for residue 1468 (NAG):
    1842 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1843 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1844  
    1845 Exception: Multiple matching templates found for residue 1468 (NAG):
    1846 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1847 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1848  
    1849 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1850 packages/simtk/openmm/app/forcefield.py", line 893, in
    1851 _getResidueTemplateMatches 
    1852 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1853 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1854  
    1855 See log for complete Python traceback. 
    1856  
    1857 Traceback (most recent call last): 
    1858 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1859 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    1860 self.start_sim() 
    1861 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1862 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    1863 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    1864 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1865 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    1866 raise e 
    1867 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1868 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    1869 isolde.forcefield_mgr) 
    1870 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1871 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    1872 sim_params, residue_templates) 
    1873 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    1874 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    1875 _create_openmm_system 
    1876 sys = forcefield.createSystem(top, **system_params) 
    1877 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1878 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    1879 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    1880 ignoreExternalBonds=ignoreExternalBonds) 
    1881 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1882 packages/simtk/openmm/app/forcefield.py", line 893, in
    1883 _getResidueTemplateMatches 
    1884 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1885 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1886 Exception: Multiple matching templates found for residue 1468 (NAG):
    1887 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1888 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1889  
    1890 Exception: Multiple matching templates found for residue 1468 (NAG):
    1891 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    1892 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    1893  
    1894 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    1895 packages/simtk/openmm/app/forcefield.py", line 893, in
    1896 _getResidueTemplateMatches 
    1897 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    1898 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    1899  
    1900 See log for complete Python traceback. 
    1901  
    1902 
    1903 > close session
    1904 
    1905 Deleting atomic symmetry model... 
    1906 
    1907 > open2
    1908 > /home/kartikmanne/Documents/VRC40/VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    1909 
    1910 Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb #1 
    1911 --- 
    1912 Chain | Description 
    1913 A E I | No description available 
    1914 A E I | No description available 
    1915 B F J | No description available 
    1916 C G K | No description available 
    1917 D H L | No description available 
    1918  
    1919 Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb 
    1920 --- 
    1921 Chain | Description 
    1922 1.2/A 1.2/E 1.2/I | No description available 
    1923 1.2/A 1.2/E 1.2/I | No description available 
    1924 1.2/B 1.2/F 1.2/J | No description available 
    1925 1.2/C 1.2/G 1.2/K | No description available 
    1926 1.2/D 1.2/H 1.2/L | No description available 
    1927  
    1928 
    1929 > open2
    1930 > /home/kartikmanne/Documents/VRC40/cryosparc_P4_J12_008_volume_map_sharp_local-
    1931 > zflip.mrc
    1932 
    1933 Opened cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc, grid size
    1934 320,320,320, pixel 1.08, shown at level 0.667, step 2, values float32 
    1935 
    1936 > addh
    1937 
    1938 Summary of feedback from adding hydrogens to
    1939 VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb #1.2 
    1940 --- 
    1941 notes | No usable SEQRES records for
    1942 VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb (#1.2) chain A; guessing
    1943 termini instead 
    1944 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    1945 (#1.2) chain A; guessing termini instead 
    1946 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    1947 (#1.2) chain B; guessing termini instead 
    1948 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    1949 (#1.2) chain C; guessing termini instead 
    1950 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    1951 (#1.2) chain D; guessing termini instead 
    1952 10 messages similar to the above omitted 
    1953 Chain-initial residues that are actual N termini: /A ALA 32, /A MAN 520, /B
    1954 ALA 512, /C GLN 1, /D GLN 1, /E ALA 32, /E MAN 520, /F ALA 512, /G GLN 1, /H
    1955 GLN 1, /I ALA 32, /I MAN 520, /J ALA 512, /K GLN 1, /L GLN 1 
    1956 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    1957 /A ASP 412, /A MAN 526, /A NAG 541, /A NAG 543, /C ALA 129, /C ALA 151, /C THR
    1958 175, /C TYR 209, /E HIS 67, /E LYS 190, /E ASP 412, /E MAN 526, /E NAG 541, /E
    1959 NAG 543, /G ALA 129, /G ALA 151, /G THR 175, /G TYR 209, /I HIS 67, /I LYS
    1960 190, /I ASP 412, /I MAN 526, /I NAG 541, /I NAG 543, /K ALA 129, /K ALA 151,
    1961 /K THR 175, /K TYR 209 
    1962 Chain-final residues that are actual C termini: /A NAG 544, /E NAG 544, /I NAG
    1963 544 
    1964 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    1965 GLN 184, /A ILE 396, /A MAN 521, /A MAN 528, /A NAG 541, /B ASP 664, /C SER
    1966 230, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505,
    1967 /E ALA 59, /E GLN 184, /E ILE 396, /E MAN 521, /E MAN 528, /E NAG 541, /F ASP
    1968 664, /G SER 230, /G SER 127, /G SER 143, /G GLY 172, /G THR 198, /H CYS 214,
    1969 /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396, /I MAN 521, /I MAN 528, /I NAG
    1970 541, /J ASP 664, /K SER 230, /K SER 127, /K SER 143, /K GLY 172, /K THR 198,
    1971 /L CYS 214 
    1972 2421 hydrogen bonds 
    1973 /A VAL 505 is not terminus, removing H atom from 'C' 
    1974 /A ALA 59 is not terminus, removing H atom from 'C' 
    1975 /A GLN 184 is not terminus, removing H atom from 'C' 
    1976 /A ILE 396 is not terminus, removing H atom from 'C' 
    1977 /B ASP 664 is not terminus, removing H atom from 'C' 
    1978 28 messages similar to the above omitted 
    1979 1452 hydrogens added 
    1980  
    1981 
    1982 > clipper associate #2 toModel #1
    1983 
    1984 > isolde start
    1985 
    1986 > select #1
    1987 
    1988 50082 atoms, 50682 bonds, 57 pseudobonds, 13 models selected 
    1989 
    1990 No template found for residue A506 (NAG) 
    1991 
    1992 Adding hydrogens 
    1993 Summary of feedback from adding hydrogens to
    1994 VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb #1.2 
    1995 --- 
    1996 notes | No usable SEQRES records for
    1997 VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb (#1.2) chain A; guessing
    1998 termini instead 
    1999 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2000 (#1.2) chain A; guessing termini instead 
    2001 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2002 (#1.2) chain B; guessing termini instead 
    2003 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2004 (#1.2) chain C; guessing termini instead 
    2005 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2006 (#1.2) chain D; guessing termini instead 
    2007 10 messages similar to the above omitted 
    2008 Chain-initial residues that are actual N termini: /A ALA 32, /A MAN 520, /B
    2009 ALA 512, /C GLN 1, /D GLN 1, /E ALA 32, /E MAN 520, /F ALA 512, /G GLN 1, /H
    2010 GLN 1, /I ALA 32, /I MAN 520, /J ALA 512, /K GLN 1, /L GLN 1 
    2011 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    2012 /A ASP 412, /A MAN 526, /A NAG 541, /A NAG 543, /C ALA 129, /C ALA 151, /C THR
    2013 175, /C TYR 209, /E HIS 67, /E LYS 190, /E ASP 412, /E MAN 526, /E NAG 541, /E
    2014 NAG 543, /G ALA 129, /G ALA 151, /G THR 175, /G TYR 209, /I HIS 67, /I LYS
    2015 190, /I ASP 412, /I MAN 526, /I NAG 541, /I NAG 543, /K ALA 129, /K ALA 151,
    2016 /K THR 175, /K TYR 209 
    2017 Chain-final residues that are actual C termini: /A NAG 544, /E NAG 544, /I NAG
    2018 544 
    2019 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    2020 GLN 184, /A ILE 396, /A MAN 521, /A MAN 528, /A NAG 541, /B ASP 664, /C SER
    2021 230, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505,
    2022 /E ALA 59, /E GLN 184, /E ILE 396, /E MAN 521, /E MAN 528, /E NAG 541, /F ASP
    2023 664, /G SER 230, /G SER 127, /G SER 143, /G GLY 172, /G THR 198, /H CYS 214,
    2024 /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396, /I MAN 521, /I MAN 528, /I NAG
    2025 541, /J ASP 664, /K SER 230, /K SER 127, /K SER 143, /K GLY 172, /K THR 198,
    2026 /L CYS 214 
    2027 2329 hydrogen bonds 
    2028 /A VAL 505 is not terminus, removing H atom from 'C' 
    2029 /A ALA 59 is not terminus, removing H atom from 'C' 
    2030 /A GLN 184 is not terminus, removing H atom from 'C' 
    2031 /A ILE 396 is not terminus, removing H atom from 'C' 
    2032 /B ASP 664 is not terminus, removing H atom from 'C' 
    2033 28 messages similar to the above omitted 
    2034 0 hydrogens added 
    2035  
    2036 
    2037 No template found for residue A506 (NAG) 
    2038 
    2039 Adding hydrogens 
    2040 Summary of feedback from adding hydrogens to
    2041 VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb #1.2 
    2042 --- 
    2043 notes | No usable SEQRES records for
    2044 VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb (#1.2) chain A; guessing
    2045 termini instead 
    2046 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2047 (#1.2) chain A; guessing termini instead 
    2048 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2049 (#1.2) chain B; guessing termini instead 
    2050 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2051 (#1.2) chain C; guessing termini instead 
    2052 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.pdb
    2053 (#1.2) chain D; guessing termini instead 
    2054 10 messages similar to the above omitted 
    2055 Chain-initial residues that are actual N termini: /A ALA 32, /A MAN 520, /B
    2056 ALA 512, /C GLN 1, /D GLN 1, /E ALA 32, /E MAN 520, /F ALA 512, /G GLN 1, /H
    2057 GLN 1, /I ALA 32, /I MAN 520, /J ALA 512, /K GLN 1, /L GLN 1 
    2058 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    2059 /A ASP 412, /A MAN 526, /A NAG 541, /A NAG 543, /C ALA 129, /C ALA 151, /C THR
    2060 175, /C TYR 209, /E HIS 67, /E LYS 190, /E ASP 412, /E MAN 526, /E NAG 541, /E
    2061 NAG 543, /G ALA 129, /G ALA 151, /G THR 175, /G TYR 209, /I HIS 67, /I LYS
    2062 190, /I ASP 412, /I MAN 526, /I NAG 541, /I NAG 543, /K ALA 129, /K ALA 151,
    2063 /K THR 175, /K TYR 209 
    2064 Chain-final residues that are actual C termini: /A NAG 544, /E NAG 544, /I NAG
    2065 544 
    2066 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    2067 GLN 184, /A ILE 396, /A MAN 521, /A MAN 528, /A NAG 541, /B ASP 664, /C SER
    2068 230, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505,
    2069 /E ALA 59, /E GLN 184, /E ILE 396, /E MAN 521, /E MAN 528, /E NAG 541, /F ASP
    2070 664, /G SER 230, /G SER 127, /G SER 143, /G GLY 172, /G THR 198, /H CYS 214,
    2071 /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396, /I MAN 521, /I MAN 528, /I NAG
    2072 541, /J ASP 664, /K SER 230, /K SER 127, /K SER 143, /K GLY 172, /K THR 198,
    2073 /L CYS 214 
    2074 2329 hydrogen bonds 
    2075 /A VAL 505 is not terminus, removing H atom from 'C' 
    2076 /A ALA 59 is not terminus, removing H atom from 'C' 
    2077 /A GLN 184 is not terminus, removing H atom from 'C' 
    2078 /A ILE 396 is not terminus, removing H atom from 'C' 
    2079 /B ASP 664 is not terminus, removing H atom from 'C' 
    2080 28 messages similar to the above omitted 
    2081 0 hydrogens added 
    2082  
    2083 
    2084 No template found for residue A506 (NAG) 
    2085 
    2086 Excluding residue 
    2087 
    2088 No template found for residue A509 (NAG) 
    2089 
    2090 Excluding residue 
    2091 
    2092 No template found for residue A512 (NAG) 
    2093 
    2094 Excluding residue 
    2095 
    2096 No template found for residue A515 (NAG) 
    2097 
    2098 Excluding residue 
    2099 
    2100 No template found for residue A517 (NAG) 
    2101 
    2102 Excluding residue 
    2103 
    2104 No template found for residue A519 (BMA) 
    2105 
    2106 Excluding residue 
    2107 Traceback (most recent call last): 
    2108 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2109 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2110 isolde.forcefield_mgr) 
    2111 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2112 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2113 sim_params, residue_templates) 
    2114 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2115 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2116 _create_openmm_system 
    2117 sys = forcefield.createSystem(top, **system_params) 
    2118 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2119 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2120 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2121 % (tname, res.index+1, res.name)) 
    2122 Exception: User-supplied template GLYCAM_4YB does not match the residue 440
    2123 (NAG) 
    2124  
    2125 During handling of the above exception, another exception occurred: 
    2126  
    2127 Traceback (most recent call last): 
    2128 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2129 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2130 isolde.forcefield_mgr) 
    2131 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2132 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2133 sim_params, residue_templates) 
    2134 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2135 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2136 _create_openmm_system 
    2137 sys = forcefield.createSystem(top, **system_params) 
    2138 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2139 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2140 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2141 % (tname, res.index+1, res.name)) 
    2142 Exception: User-supplied template GLYCAM_4YB does not match the residue 440
    2143 (NAG) 
    2144  
    2145 During handling of the above exception, another exception occurred: 
    2146  
    2147 Traceback (most recent call last): 
    2148 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2149 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2150 isolde.forcefield_mgr) 
    2151 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2152 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2153 sim_params, residue_templates) 
    2154 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2155 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2156 _create_openmm_system 
    2157 sys = forcefield.createSystem(top, **system_params) 
    2158 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2159 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2160 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2161 % (tname, res.index+1, res.name)) 
    2162 Exception: User-supplied template GLYCAM_4YB does not match the residue 440
    2163 (NAG) 
    2164  
    2165 During handling of the above exception, another exception occurred: 
    2166  
    2167 Traceback (most recent call last): 
    2168 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2169 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2170 isolde.forcefield_mgr) 
    2171 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2172 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2173 sim_params, residue_templates) 
    2174 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2175 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2176 _create_openmm_system 
    2177 sys = forcefield.createSystem(top, **system_params) 
    2178 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2179 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2180 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2181 % (tname, res.index+1, res.name)) 
    2182 Exception: User-supplied template GLYCAM_4YB does not match the residue 442
    2183 (NAG) 
    2184  
    2185 During handling of the above exception, another exception occurred: 
    2186  
    2187 Traceback (most recent call last): 
    2188 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2189 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2190 isolde.forcefield_mgr) 
    2191 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2192 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2193 sim_params, residue_templates) 
    2194 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2195 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2196 _create_openmm_system 
    2197 sys = forcefield.createSystem(top, **system_params) 
    2198 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2199 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2200 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2201 % (tname, res.index+1, res.name)) 
    2202 Exception: User-supplied template GLYCAM_4YB does not match the residue 444
    2203 (NAG) 
    2204  
    2205 During handling of the above exception, another exception occurred: 
    2206  
    2207 Traceback (most recent call last): 
    2208 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2209 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2210 isolde.forcefield_mgr) 
    2211 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2212 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2213 sim_params, residue_templates) 
    2214 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2215 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2216 _create_openmm_system 
    2217 sys = forcefield.createSystem(top, **system_params) 
    2218 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2219 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2220 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2221 % (tname, res.index+1, res.name)) 
    2222 Exception: User-supplied template GLYCAM_4YB does not match the residue 446
    2223 (NAG) 
    2224  
    2225 During handling of the above exception, another exception occurred: 
    2226  
    2227 Traceback (most recent call last): 
    2228 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2229 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2230 isolde.forcefield_mgr) 
    2231 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2232 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2233 sim_params, residue_templates) 
    2234 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2235 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2236 _create_openmm_system 
    2237 sys = forcefield.createSystem(top, **system_params) 
    2238 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2239 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2240 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2241 % (tname, res.index+1, res.name)) 
    2242 Exception: User-supplied template GLYCAM_4YB does not match the residue 447
    2243 (NAG) 
    2244  
    2245 During handling of the above exception, another exception occurred: 
    2246  
    2247 Traceback (most recent call last): 
    2248 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2249 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2250 isolde.forcefield_mgr) 
    2251 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2252 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2253 sim_params, residue_templates) 
    2254 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2255 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2256 _create_openmm_system 
    2257 sys = forcefield.createSystem(top, **system_params) 
    2258 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2259 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2260 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2261 % (tname, res.index+1, res.name)) 
    2262 Exception: User-supplied template GLYCAM_3MB does not match the residue 448
    2263 (BMA) 
    2264  
    2265 During handling of the above exception, another exception occurred: 
    2266  
    2267 Traceback (most recent call last): 
    2268 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2269 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    2270 self.start_sim() 
    2271 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2272 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2273 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2274 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2275 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2276 if self._parse_explicit_template_error(e): 
    2277 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2278 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2279 _parse_explicit_template_error 
    2280 self.isolde._handle_bad_template(residue) 
    2281 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2282 packages/chimerax/isolde/isolde.py", line 2791, in _handle_bad_template 
    2283 self.start_sim() 
    2284 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2285 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2286 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2287 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2288 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2289 if self._parse_explicit_template_error(e): 
    2290 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2291 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2292 _parse_explicit_template_error 
    2293 self.isolde._handle_bad_template(residue) 
    2294 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2295 packages/chimerax/isolde/isolde.py", line 2791, in _handle_bad_template 
    2296 self.start_sim() 
    2297 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2298 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2299 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2300 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2301 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2302 if self._parse_explicit_template_error(e): 
    2303 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2304 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2305 _parse_explicit_template_error 
    2306 self.isolde._handle_bad_template(residue) 
    2307 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2308 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    2309 self.start_sim() 
    2310 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2311 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2312 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2313 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2314 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2315 if self._parse_explicit_template_error(e): 
    2316 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2317 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2318 _parse_explicit_template_error 
    2319 self.isolde._handle_bad_template(residue) 
    2320 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2321 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    2322 self.start_sim() 
    2323 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2324 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2325 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2326 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2327 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2328 if self._parse_explicit_template_error(e): 
    2329 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2330 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2331 _parse_explicit_template_error 
    2332 self.isolde._handle_bad_template(residue) 
    2333 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2334 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    2335 self.start_sim() 
    2336 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2337 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2338 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2339 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2340 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2341 if self._parse_explicit_template_error(e): 
    2342 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2343 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2344 _parse_explicit_template_error 
    2345 self.isolde._handle_bad_template(residue) 
    2346 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2347 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    2348 self.start_sim() 
    2349 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2350 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2351 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2352 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2353 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2354 if self._parse_explicit_template_error(e): 
    2355 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2356 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2357 _parse_explicit_template_error 
    2358 self.isolde._handle_bad_template(residue) 
    2359 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2360 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    2361 self.start_sim() 
    2362 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2363 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2364 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2365 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2366 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    2367 if self._parse_explicit_template_error(e): 
    2368 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2369 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    2370 _parse_explicit_template_error 
    2371 self.isolde._handle_bad_template(residue) 
    2372 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2373 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    2374 self.start_sim() 
    2375 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2376 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    2377 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    2378 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2379 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    2380 raise e 
    2381 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2382 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2383 isolde.forcefield_mgr) 
    2384 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2385 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2386 sim_params, residue_templates) 
    2387 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2388 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2389 _create_openmm_system 
    2390 sys = forcefield.createSystem(top, **system_params) 
    2391 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2392 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    2393 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    2394 ignoreExternalBonds=ignoreExternalBonds) 
    2395 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2396 packages/simtk/openmm/app/forcefield.py", line 893, in
    2397 _getResidueTemplateMatches 
    2398 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    2399 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    2400 Exception: Multiple matching templates found for residue 448 (MAN):
    2401 GLYCAM_0EA, GLYCAM_0EB, GLYCAM_0GA, GLYCAM_0GB, GLYCAM_0KA, GLYCAM_0KB,
    2402 GLYCAM_0LA, GLYCAM_0LB, GLYCAM_0MA, GLYCAM_0MB, GLYCAM_0NA, GLYCAM_0NB,
    2403 GLYCAM_0TA, GLYCAM_0TB, GLYCAM_0eA, GLYCAM_0eB, GLYCAM_0gA, GLYCAM_0gB,
    2404 GLYCAM_0kA, GLYCAM_0kB, GLYCAM_0lA, GLYCAM_0lB, GLYCAM_0mA, GLYCAM_0mB,
    2405 GLYCAM_0nA, GLYCAM_0nB, GLYCAM_0tA, GLYCAM_0tB. 
    2406  
    2407 Exception: Multiple matching templates found for residue 448 (MAN):
    2408 GLYCAM_0EA, GLYCAM_0EB, GLYCAM_0GA, GLYCAM_0GB, GLYCAM_0KA, GLYCAM_0KB,
    2409 GLYCAM_0LA, GLYCAM_0LB, GLYCAM_0MA, GLYCAM_0MB, GLYCAM_0NA, GLYCAM_0NB,
    2410 GLYCAM_0TA, GLYCAM_0TB, GLYCAM_0eA, GLYCAM_0eB, GLYCAM_0gA, GLYCAM_0gB,
    2411 GLYCAM_0kA, GLYCAM_0kB, GLYCAM_0lA, GLYCAM_0lB, GLYCAM_0mA, GLYCAM_0mB,
    2412 GLYCAM_0nA, GLYCAM_0nB, GLYCAM_0tA, GLYCAM_0tB. 
    2413  
    2414 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2415 packages/simtk/openmm/app/forcefield.py", line 893, in
    2416 _getResidueTemplateMatches 
    2417 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    2418 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    2419  
    2420 See log for complete Python traceback. 
    2421  
    2422 
    2423 > close session
    2424 
    2425 Deleting atomic symmetry model... 
    2426 
    2427 > open2
    2428 > /home/kartikmanne/Documents/VRC40/VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2429 
    2430 Summary of feedback from opening
    2431 /home/kartikmanne/Documents/VRC40/VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif 
    2432 --- 
    2433 warnings | Skipping chem_comp category: Missing column 'type' near line 1674 
    2434 Unable to infer polymer connectivity due to unspecified label_seq_id for
    2435 residue "NAG" near line 1720 
    2436 Missing entity information. Treating each chain as a separate entity. 
    2437 Missing second residue in struct_conn "C00002" 
    2438 Missing first residue in struct_conn "C00020" 
    2439 Missing first residue in struct_conn "C00021" 
    2440 Missing first residue in struct_conn "C00022" 
    2441 Missing first residue in struct_conn "C00023" 
    2442 Missing first residue in struct_conn "C00024" 
    2443 57 messages similar to the above omitted 
    2444 Missing second residue in struct_conn "C00082" 
    2445 Missing second residue in struct_conn "C00083" 
    2446 Missing first residue in struct_conn "C00084" 
    2447 Missing first residue in struct_conn "C00085" 
    2448 Missing first residue in struct_conn "C00086" 
    2449 Missing first residue in struct_conn "C00087" 
    2450 Missing first residue in struct_conn "C00088" 
    2451 5 messages similar to the above omitted 
    2452 Missing second residue in struct_conn "C00094" 
    2453 Missing second residue in struct_conn "C00095" 
    2454 Missing first residue in struct_conn "C00096" 
    2455 Missing first residue in struct_conn "C00097" 
    2456 Missing first residue in struct_conn "C00098" 
    2457 Missing first residue in struct_conn "C00099" 
    2458 Missing first residue in struct_conn "C00100" 
    2459 13 messages similar to the above omitted 
    2460 Missing second residue in struct_conn "C00114" 
    2461 Missing second residue in struct_conn "C00115" 
    2462 Missing first residue in struct_conn "C00116" 
    2463 Missing first residue in struct_conn "C00117" 
    2464 Missing first residue in struct_conn "C00118" 
    2465 Missing first residue in struct_conn "C00119" 
    2466 Missing first residue in struct_conn "C00120" 
    2467 69 messages similar to the above omitted 
    2468 Missing second residue in struct_conn "C00228" 
    2469 Missing second residue in struct_conn "C00229" 
    2470 Missing first residue in struct_conn "C00230" 
    2471 Missing first residue in struct_conn "C00231" 
    2472 Missing first residue in struct_conn "C00232" 
    2473 Missing first residue in struct_conn "C00233" 
    2474 Missing first residue in struct_conn "C00234" 
    2475 8 messages similar to the above omitted 
    2476 Missing second residue in struct_conn "C00301" 
    2477 Missing first residue in struct_conn "C00319" 
    2478 Missing first residue in struct_conn "C00320" 
    2479 Missing first residue in struct_conn "C00321" 
    2480 Missing first residue in struct_conn "C00322" 
    2481 Missing first residue in struct_conn "C00323" 
    2482 57 messages similar to the above omitted 
    2483 Missing second residue in struct_conn "C00381" 
    2484 Missing second residue in struct_conn "C00382" 
    2485 Missing first residue in struct_conn "C00383" 
    2486 Missing first residue in struct_conn "C00384" 
    2487 Missing first residue in struct_conn "C00385" 
    2488 Missing first residue in struct_conn "C00386" 
    2489 Missing first residue in struct_conn "C00387" 
    2490 5 messages similar to the above omitted 
    2491 Missing second residue in struct_conn "C00393" 
    2492 Missing second residue in struct_conn "C00394" 
    2493 Missing first residue in struct_conn "C00395" 
    2494 Missing first residue in struct_conn "C00396" 
    2495 Missing first residue in struct_conn "C00397" 
    2496 Missing first residue in struct_conn "C00398" 
    2497 Missing first residue in struct_conn "C00399" 
    2498 13 messages similar to the above omitted 
    2499 Missing second residue in struct_conn "C00413" 
    2500 Missing second residue in struct_conn "C00414" 
    2501 Missing first residue in struct_conn "C00415" 
    2502 Missing first residue in struct_conn "C00416" 
    2503 Missing first residue in struct_conn "C00417" 
    2504 Missing first residue in struct_conn "C00418" 
    2505 Missing first residue in struct_conn "C00419" 
    2506 69 messages similar to the above omitted 
    2507 Missing second residue in struct_conn "C00527" 
    2508 Missing second residue in struct_conn "C00528" 
    2509 Missing first residue in struct_conn "C00529" 
    2510 Missing first residue in struct_conn "C00530" 
    2511 Missing first residue in struct_conn "C00531" 
    2512 Missing first residue in struct_conn "C00532" 
    2513 Missing first residue in struct_conn "C00533" 
    2514 8 messages similar to the above omitted 
    2515 Missing second residue in struct_conn "C00600" 
    2516 Missing first residue in struct_conn "C00618" 
    2517 Missing first residue in struct_conn "C00619" 
    2518 Missing first residue in struct_conn "C00620" 
    2519 Missing first residue in struct_conn "C00621" 
    2520 Missing first residue in struct_conn "C00622" 
    2521 57 messages similar to the above omitted 
    2522 Missing second residue in struct_conn "C00680" 
    2523 Missing second residue in struct_conn "C00681" 
    2524 Missing first residue in struct_conn "C00682" 
    2525 Missing first residue in struct_conn "C00683" 
    2526 Missing first residue in struct_conn "C00684" 
    2527 Missing first residue in struct_conn "C00685" 
    2528 Missing first residue in struct_conn "C00686" 
    2529 5 messages similar to the above omitted 
    2530 Missing second residue in struct_conn "C00692" 
    2531 Missing second residue in struct_conn "C00693" 
    2532 Missing first residue in struct_conn "C00694" 
    2533 Missing first residue in struct_conn "C00695" 
    2534 Missing first residue in struct_conn "C00696" 
    2535 Missing first residue in struct_conn "C00697" 
    2536 Missing first residue in struct_conn "C00698" 
    2537 13 messages similar to the above omitted 
    2538 Missing second residue in struct_conn "C00712" 
    2539 Missing second residue in struct_conn "C00713" 
    2540 Missing first residue in struct_conn "C00714" 
    2541 Missing first residue in struct_conn "C00715" 
    2542 Missing first residue in struct_conn "C00716" 
    2543 Missing first residue in struct_conn "C00717" 
    2544 Missing first residue in struct_conn "C00718" 
    2545 69 messages similar to the above omitted 
    2546 Missing second residue in struct_conn "C00826" 
    2547 Missing second residue in struct_conn "C00827" 
    2548 Missing first residue in struct_conn "C00828" 
    2549 Missing first residue in struct_conn "C00829" 
    2550 Missing first residue in struct_conn "C00830" 
    2551 Missing first residue in struct_conn "C00831" 
    2552 Missing first residue in struct_conn "C00832" 
    2553 8 messages similar to the above omitted 
    2554 Bad residue range for struct_conf "1" near line 110 
    2555 Bad residue range for struct_conf "2" near line 111 
    2556 Bad residue range for struct_conf "3" near line 112 
    2557 Bad residue range for struct_conf "4" near line 113 
    2558 Bad residue range for struct_conf "5" near line 114 
    2559 22 messages similar to the above omitted 
    2560 Invalid sheet range for struct_sheet_range "D 3" near line 1383 
    2561 Invalid sheet range for struct_sheet_range "I 3" near line 1402 
    2562 Invalid sheet range for struct_sheet_range "N 3" near line 1421 
    2563 Invalid sheet range for struct_sheet_range "A 2" near line 1425 
    2564 Invalid sheet range for struct_sheet_range "B 2" near line 1427 
    2565 4 messages similar to the above omitted 
    2566 Atom H1 is not in the residue template for ALA #32 in chain A 
    2567 Atom H1 is not in the residue template for ALA #512 in chain B 
    2568 Atom H1 is not in the residue template for GLN #1 in chain C 
    2569 Atom H1 is not in the residue template for GLN #1 in chain D 
    2570 Atom H1 is not in the residue template for ALA #32 in chain E 
    2571 7 messages similar to the above omitted 
    2572 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    2573 Skipping chem_comp category: Missing column 'type' near line 50550 
    2574 Skipping chem_comp category: Missing column 'type' near line 50714 
    2575 Skipping chem_comp category: Missing column 'type' near line 50878 
    2576  
    2577 Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1 
    2578 --- 
    2579 Chain | Description 
    2580 A E I | No description available 
    2581 B | No description available 
    2582 C | No description available 
    2583 D | No description available 
    2584  
    2585 Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif 
    2586 --- 
    2587 Chain | Description 
    2588 1.2/A 1.2/E 1.2/I | No description available 
    2589 1.2/B | No description available 
    2590 1.2/C | No description available 
    2591 1.2/D | No description available 
    2592  
    2593 
    2594 > addh
    2595 
    2596 Summary of feedback from adding hydrogens to
    2597 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1.2 
    2598 --- 
    2599 notes | No usable SEQRES records for
    2600 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif (#1.2) chain A; guessing
    2601 termini instead 
    2602 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2603 (#1.2) chain B; guessing termini instead 
    2604 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2605 (#1.2) chain C; guessing termini instead 
    2606 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2607 (#1.2) chain D; guessing termini instead 
    2608 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2609 (#1.2) chain E; guessing termini instead 
    2610 1 messages similar to the above omitted 
    2611 Chain-initial residues that are actual N termini: /A ALA 32, /B ALA 512, /C
    2612 GLN 1, /D GLN 1, /E ALA 32, /I ALA 32 
    2613 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    2614 /A ASP 412, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA
    2615 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209,
    2616 /E HIS 67, /E LYS 190, /E ASP 412, /I HIS 67, /I LYS 190, /I ASP 412 
    2617 Chain-final residues that are actual C termini: 
    2618 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    2619 GLN 184, /A ILE 396, /B ASP 664, /C SER 230, /C SER 127, /C SER 143, /C GLY
    2620 172, /C THR 198, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /C SER 127,
    2621 /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505, /E ALA 59, /E GLN
    2622 184, /E ILE 396, /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396 
    2623 2461 hydrogen bonds 
    2624 /A VAL 505 is not terminus, removing H atom from 'C' 
    2625 /A ALA 59 is not terminus, removing H atom from 'C' 
    2626 /A GLN 184 is not terminus, removing H atom from 'C' 
    2627 /A ILE 396 is not terminus, removing H atom from 'C' 
    2628 /B ASP 664 is not terminus, removing H atom from 'C' 
    2629 22 messages similar to the above omitted 
    2630 1530 hydrogens added 
    2631  
    2632 
    2633 > open2
    2634 > /home/kartikmanne/Documents/VRC40/cryosparc_P4_J12_008_volume_map_sharp_local-
    2635 > zflip.mrc
    2636 
    2637 Opened cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc, grid size
    2638 320,320,320, pixel 1.08, shown at level 0.667, step 2, values float32 
    2639 
    2640 > clipper associate #2 toModel #1
    2641 
    2642 > select #1
    2643 
    2644 50160 atoms, 50724 bonds, 321 pseudobonds, 13 models selected 
    2645 
    2646 No template found for residue A506 (NAG) 
    2647 
    2648 Excluding residue 
    2649 
    2650 No template found for residue A508 (NAG) 
    2651 
    2652 Excluding residue 
    2653 
    2654 No template found for residue A509 (NAG) 
    2655 
    2656 Excluding residue 
    2657 
    2658 No template found for residue A512 (NAG) 
    2659 
    2660 Excluding residue 
    2661 
    2662 No template found for residue A515 (NAG) 
    2663 
    2664 Excluding residue 
    2665 
    2666 No template found for residue A517 (NAG) 
    2667 
    2668 Excluding residue 
    2669 
    2670 No template found for residue A519 (BMA) 
    2671 
    2672 Excluding residue 
    2673 
    2674 No template found for residue A521 (MAN) 
    2675 
    2676 Excluding residue 
    2677 
    2678 No template found for residue A522 (NAG) 
    2679 
    2680 Excluding residue 
    2681 
    2682 No template found for residue A527 (MAN) 
    2683 
    2684 Excluding residue 
    2685 
    2686 No template found for residue A528 (MAN) 
    2687 
    2688 Excluding residue 
    2689 
    2690 No template found for residue A529 (NAG) 
    2691 
    2692 Excluding residue 
    2693 
    2694 No template found for residue A531 (NAG) 
    2695 
    2696 Excluding residue 
    2697 
    2698 No template found for residue A534 (NAG) 
    2699 
    2700 Excluding residue 
    2701 
    2702 No template found for residue A537 (NAG) 
    2703 
    2704 Excluding residue 
    2705 
    2706 No template found for residue A540 (NAG) 
    2707 
    2708 Excluding residue 
    2709 
    2710 No template found for residue A543 (NAG) 
    2711 
    2712 Excluding residue 
    2713 
    2714 No template found for residue A544 (NAG) 
    2715 
    2716 Excluding residue 
    2717 
    2718 No template found for residue B598 (CYS) 
    2719 
    2720 Excluding residue 
    2721 
    2722 No template found for residue B598 (CYS) 
    2723 
    2724 Excluding residue 
    2725 
    2726 No template found for residue B598 (CYS) 
    2727 
    2728 Excluding residue 
    2729 
    2730 No template found for residue B604 (CYS) 
    2731 
    2732 Excluding residue 
    2733 
    2734 No template found for residue B604 (CYS) 
    2735 
    2736 Excluding residue 
    2737 
    2738 No template found for residue B604 (CYS) 
    2739 
    2740 Excluding residue 
    2741 
    2742 No template found for residue B605 (CYS) 
    2743 
    2744 Adding hydrogens 
    2745 Summary of feedback from adding hydrogens to
    2746 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1.2 
    2747 --- 
    2748 notes | No usable SEQRES records for
    2749 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif (#1.2) chain A; guessing
    2750 termini instead 
    2751 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2752 (#1.2) chain B; guessing termini instead 
    2753 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2754 (#1.2) chain C; guessing termini instead 
    2755 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2756 (#1.2) chain D; guessing termini instead 
    2757 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2758 (#1.2) chain E; guessing termini instead 
    2759 1 messages similar to the above omitted 
    2760 Chain-initial residues that are actual N termini: /A ALA 32, /B ALA 512, /C
    2761 GLN 1, /D GLN 1, /E ALA 32, /I ALA 32 
    2762 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    2763 /A ASP 412, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA
    2764 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209,
    2765 /E HIS 67, /E LYS 190, /E ASP 412, /I HIS 67, /I LYS 190, /I ASP 412 
    2766 Chain-final residues that are actual C termini: 
    2767 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    2768 GLN 184, /A ILE 396, /B ASP 664, /C SER 230, /C SER 127, /C SER 143, /C GLY
    2769 172, /C THR 198, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /C SER 127,
    2770 /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505, /E ALA 59, /E GLN
    2771 184, /E ILE 396, /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396 
    2772 2360 hydrogen bonds 
    2773 /A VAL 505 is not terminus, removing H atom from 'C' 
    2774 /A ALA 59 is not terminus, removing H atom from 'C' 
    2775 /A GLN 184 is not terminus, removing H atom from 'C' 
    2776 /A ILE 396 is not terminus, removing H atom from 'C' 
    2777 /B ASP 664 is not terminus, removing H atom from 'C' 
    2778 22 messages similar to the above omitted 
    2779 0 hydrogens added 
    2780  
    2781 
    2782 No template found for residue B605 (CYS) 
    2783 
    2784 Adding hydrogens 
    2785 Summary of feedback from adding hydrogens to
    2786 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1.2 
    2787 --- 
    2788 notes | No usable SEQRES records for
    2789 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif (#1.2) chain A; guessing
    2790 termini instead 
    2791 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2792 (#1.2) chain B; guessing termini instead 
    2793 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2794 (#1.2) chain C; guessing termini instead 
    2795 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2796 (#1.2) chain D; guessing termini instead 
    2797 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2798 (#1.2) chain E; guessing termini instead 
    2799 1 messages similar to the above omitted 
    2800 Chain-initial residues that are actual N termini: /A ALA 32, /B ALA 512, /C
    2801 GLN 1, /D GLN 1, /E ALA 32, /I ALA 32 
    2802 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    2803 /A ASP 412, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA
    2804 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209,
    2805 /E HIS 67, /E LYS 190, /E ASP 412, /I HIS 67, /I LYS 190, /I ASP 412 
    2806 Chain-final residues that are actual C termini: 
    2807 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    2808 GLN 184, /A ILE 396, /B ASP 664, /C SER 230, /C SER 127, /C SER 143, /C GLY
    2809 172, /C THR 198, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /C SER 127,
    2810 /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505, /E ALA 59, /E GLN
    2811 184, /E ILE 396, /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396 
    2812 2360 hydrogen bonds 
    2813 /A VAL 505 is not terminus, removing H atom from 'C' 
    2814 /A ALA 59 is not terminus, removing H atom from 'C' 
    2815 /A GLN 184 is not terminus, removing H atom from 'C' 
    2816 /A ILE 396 is not terminus, removing H atom from 'C' 
    2817 /B ASP 664 is not terminus, removing H atom from 'C' 
    2818 22 messages similar to the above omitted 
    2819 0 hydrogens added 
    2820  
    2821 
    2822 No template found for residue B605 (CYS) 
    2823 
    2824 Doing nothing 
    2825 
    2826 No template found for residue C22 (CYS) 
    2827 
    2828 Adding hydrogens 
    2829 Summary of feedback from adding hydrogens to
    2830 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1.2 
    2831 --- 
    2832 notes | No usable SEQRES records for
    2833 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif (#1.2) chain A; guessing
    2834 termini instead 
    2835 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2836 (#1.2) chain B; guessing termini instead 
    2837 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2838 (#1.2) chain C; guessing termini instead 
    2839 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2840 (#1.2) chain D; guessing termini instead 
    2841 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    2842 (#1.2) chain E; guessing termini instead 
    2843 1 messages similar to the above omitted 
    2844 Chain-initial residues that are actual N termini: /A ALA 32, /B ALA 512, /C
    2845 GLN 1, /D GLN 1, /E ALA 32, /I ALA 32 
    2846 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    2847 /A ASP 412, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA
    2848 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209,
    2849 /E HIS 67, /E LYS 190, /E ASP 412, /I HIS 67, /I LYS 190, /I ASP 412 
    2850 Chain-final residues that are actual C termini: 
    2851 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    2852 GLN 184, /A ILE 396, /B ASP 664, /C SER 230, /C SER 127, /C SER 143, /C GLY
    2853 172, /C THR 198, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /C SER 127,
    2854 /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505, /E ALA 59, /E GLN
    2855 184, /E ILE 396, /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396 
    2856 2360 hydrogen bonds 
    2857 /A VAL 505 is not terminus, removing H atom from 'C' 
    2858 /A ALA 59 is not terminus, removing H atom from 'C' 
    2859 /A GLN 184 is not terminus, removing H atom from 'C' 
    2860 /A ILE 396 is not terminus, removing H atom from 'C' 
    2861 /B ASP 664 is not terminus, removing H atom from 'C' 
    2862 22 messages similar to the above omitted 
    2863 0 hydrogens added 
    2864  
    2865 
    2866 No template found for residue C22 (CYS) 
    2867 
    2868 Excluding residue 
    2869 
    2870 No template found for residue C101 (CYS) 
    2871 
    2872 Excluding residue 
    2873 
    2874 No template found for residue D23 (CYS) 
    2875 
    2876 Excluding residue 
    2877 
    2878 No template found for residue D88 (CYS) 
    2879 
    2880 Excluding residue 
    2881 
    2882 > select #1
    2883 
    2884 50160 atoms, 50724 bonds, 321 pseudobonds, 19 models selected 
    2885 
    2886 > show sel cartoons
    2887 
    2888 > show sel atoms
    2889 
    2890 No template found for residue B605 (CYS) 
    2891 
    2892 Excluding residue 
    2893 
    2894 No template found for residue B605 (CYS) 
    2895 
    2896 Excluding residue 
    2897 
    2898 No template found for residue B605 (CYS) 
    2899 
    2900 Excluding residue 
    2901 
    2902 No template found for residue C22 (CYS) 
    2903 
    2904 Excluding residue 
    2905 
    2906 No template found for residue C22 (CYS) 
    2907 
    2908 Excluding residue 
    2909 
    2910 No template found for residue C101 (CYS) 
    2911 
    2912 Excluding residue 
    2913 
    2914 No template found for residue C101 (CYS) 
    2915 
    2916 Excluding residue 
    2917 
    2918 No template found for residue C155 (CYS) 
    2919 
    2920 Excluding residue 
    2921 
    2922 No template found for residue C155 (CYS) 
    2923 
    2924 Excluding residue 
    2925 
    2926 No template found for residue C155 (CYS) 
    2927 
    2928 Excluding residue 
    2929 
    2930 No template found for residue C211 (CYS) 
    2931 
    2932 Excluding residue 
    2933 
    2934 No template found for residue C211 (CYS) 
    2935 
    2936 Excluding residue 
    2937 
    2938 No template found for residue C211 (CYS) 
    2939 
    2940 Excluding residue 
    2941 Traceback (most recent call last): 
    2942 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2943 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2944 isolde.forcefield_mgr) 
    2945 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2946 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2947 sim_params, residue_templates) 
    2948 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2949 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2950 _create_openmm_system 
    2951 sys = forcefield.createSystem(top, **system_params) 
    2952 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2953 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2954 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2955 % (tname, res.index+1, res.name)) 
    2956 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    2957  
    2958 During handling of the above exception, another exception occurred: 
    2959  
    2960 Traceback (most recent call last): 
    2961 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2962 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2963 isolde.forcefield_mgr) 
    2964 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2965 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2966 sim_params, residue_templates) 
    2967 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2968 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2969 _create_openmm_system 
    2970 sys = forcefield.createSystem(top, **system_params) 
    2971 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2972 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2973 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2974 % (tname, res.index+1, res.name)) 
    2975 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    2976  
    2977 During handling of the above exception, another exception occurred: 
    2978  
    2979 Traceback (most recent call last): 
    2980 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2981 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    2982 isolde.forcefield_mgr) 
    2983 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2984 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    2985 sim_params, residue_templates) 
    2986 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    2987 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    2988 _create_openmm_system 
    2989 sys = forcefield.createSystem(top, **system_params) 
    2990 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    2991 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    2992 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    2993 % (tname, res.index+1, res.name)) 
    2994 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    2995  
    2996 During handling of the above exception, another exception occurred: 
    2997  
    2998 Traceback (most recent call last): 
    2999 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3000 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3001 isolde.forcefield_mgr) 
    3002 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3003 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3004 sim_params, residue_templates) 
    3005 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3006 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3007 _create_openmm_system 
    3008 sys = forcefield.createSystem(top, **system_params) 
    3009 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3010 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3011 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3012 % (tname, res.index+1, res.name)) 
    3013 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    3014  
    3015 During handling of the above exception, another exception occurred: 
    3016  
    3017 Traceback (most recent call last): 
    3018 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3019 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3020 isolde.forcefield_mgr) 
    3021 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3022 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3023 sim_params, residue_templates) 
    3024 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3025 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3026 _create_openmm_system 
    3027 sys = forcefield.createSystem(top, **system_params) 
    3028 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3029 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3030 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3031 % (tname, res.index+1, res.name)) 
    3032 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    3033  
    3034 During handling of the above exception, another exception occurred: 
    3035  
    3036 Traceback (most recent call last): 
    3037 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3038 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3039 isolde.forcefield_mgr) 
    3040 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3041 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3042 sim_params, residue_templates) 
    3043 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3044 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3045 _create_openmm_system 
    3046 sys = forcefield.createSystem(top, **system_params) 
    3047 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3048 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3049 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3050 % (tname, res.index+1, res.name)) 
    3051 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    3052  
    3053 During handling of the above exception, another exception occurred: 
    3054  
    3055 Traceback (most recent call last): 
    3056 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3057 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3058 isolde.forcefield_mgr) 
    3059 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3060 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3061 sim_params, residue_templates) 
    3062 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3063 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3064 _create_openmm_system 
    3065 sys = forcefield.createSystem(top, **system_params) 
    3066 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3067 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3068 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3069 % (tname, res.index+1, res.name)) 
    3070 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    3071  
    3072 During handling of the above exception, another exception occurred: 
    3073  
    3074 Traceback (most recent call last): 
    3075 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3076 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3077 isolde.forcefield_mgr) 
    3078 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3079 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3080 sim_params, residue_templates) 
    3081 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3082 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3083 _create_openmm_system 
    3084 sys = forcefield.createSystem(top, **system_params) 
    3085 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3086 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3087 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3088 % (tname, res.index+1, res.name)) 
    3089 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    3090  
    3091 During handling of the above exception, another exception occurred: 
    3092  
    3093 Traceback (most recent call last): 
    3094 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3095 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3096 isolde.forcefield_mgr) 
    3097 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3098 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3099 sim_params, residue_templates) 
    3100 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3101 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3102 _create_openmm_system 
    3103 sys = forcefield.createSystem(top, **system_params) 
    3104 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3105 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3106 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3107 % (tname, res.index+1, res.name)) 
    3108 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    3109  
    3110 During handling of the above exception, another exception occurred: 
    3111  
    3112 Traceback (most recent call last): 
    3113 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3114 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3115 isolde.forcefield_mgr) 
    3116 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3117 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3118 sim_params, residue_templates) 
    3119 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3120 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3121 _create_openmm_system 
    3122 sys = forcefield.createSystem(top, **system_params) 
    3123 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3124 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3125 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3126 % (tname, res.index+1, res.name)) 
    3127 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    3128  
    3129 During handling of the above exception, another exception occurred: 
    3130  
    3131 Traceback (most recent call last): 
    3132 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3133 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3134 isolde.forcefield_mgr) 
    3135 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3136 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3137 sim_params, residue_templates) 
    3138 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3139 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3140 _create_openmm_system 
    3141 sys = forcefield.createSystem(top, **system_params) 
    3142 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3143 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3144 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3145 % (tname, res.index+1, res.name)) 
    3146 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    3147  
    3148 During handling of the above exception, another exception occurred: 
    3149  
    3150 Traceback (most recent call last): 
    3151 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3152 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3153 isolde.forcefield_mgr) 
    3154 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3155 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3156 sim_params, residue_templates) 
    3157 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3158 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3159 _create_openmm_system 
    3160 sys = forcefield.createSystem(top, **system_params) 
    3161 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3162 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3163 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3164 % (tname, res.index+1, res.name)) 
    3165 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    3166  
    3167 During handling of the above exception, another exception occurred: 
    3168  
    3169 Traceback (most recent call last): 
    3170 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3171 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3172 isolde.forcefield_mgr) 
    3173 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3174 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3175 sim_params, residue_templates) 
    3176 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3177 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3178 _create_openmm_system 
    3179 sys = forcefield.createSystem(top, **system_params) 
    3180 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3181 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3182 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3183 % (tname, res.index+1, res.name)) 
    3184 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    3185  
    3186 During handling of the above exception, another exception occurred: 
    3187  
    3188 Traceback (most recent call last): 
    3189 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3190 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    3191 self.start_sim() 
    3192 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3193 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3194 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3195 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3196 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3197 if self._parse_explicit_template_error(e): 
    3198 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3199 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3200 _parse_explicit_template_error 
    3201 self.isolde._handle_bad_template(residue) 
    3202 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3203 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3204 self.start_sim() 
    3205 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3206 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3207 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3208 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3209 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3210 if self._parse_explicit_template_error(e): 
    3211 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3212 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3213 _parse_explicit_template_error 
    3214 self.isolde._handle_bad_template(residue) 
    3215 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3216 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3217 self.start_sim() 
    3218 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3219 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3220 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3221 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3222 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3223 if self._parse_explicit_template_error(e): 
    3224 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3225 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3226 _parse_explicit_template_error 
    3227 self.isolde._handle_bad_template(residue) 
    3228 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3229 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3230 self.start_sim() 
    3231 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3232 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3233 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3234 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3235 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3236 if self._parse_explicit_template_error(e): 
    3237 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3238 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3239 _parse_explicit_template_error 
    3240 self.isolde._handle_bad_template(residue) 
    3241 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3242 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3243 self.start_sim() 
    3244 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3245 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3246 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3247 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3248 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3249 if self._parse_explicit_template_error(e): 
    3250 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3251 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3252 _parse_explicit_template_error 
    3253 self.isolde._handle_bad_template(residue) 
    3254 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3255 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3256 self.start_sim() 
    3257 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3258 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3259 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3260 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3261 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3262 if self._parse_explicit_template_error(e): 
    3263 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3264 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3265 _parse_explicit_template_error 
    3266 self.isolde._handle_bad_template(residue) 
    3267 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3268 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3269 self.start_sim() 
    3270 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3271 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3272 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3273 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3274 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3275 if self._parse_explicit_template_error(e): 
    3276 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3277 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3278 _parse_explicit_template_error 
    3279 self.isolde._handle_bad_template(residue) 
    3280 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3281 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3282 self.start_sim() 
    3283 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3284 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3285 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3286 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3287 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3288 if self._parse_explicit_template_error(e): 
    3289 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3290 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3291 _parse_explicit_template_error 
    3292 self.isolde._handle_bad_template(residue) 
    3293 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3294 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3295 self.start_sim() 
    3296 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3297 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3298 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3299 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3300 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3301 if self._parse_explicit_template_error(e): 
    3302 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3303 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3304 _parse_explicit_template_error 
    3305 self.isolde._handle_bad_template(residue) 
    3306 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3307 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3308 self.start_sim() 
    3309 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3310 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3311 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3312 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3313 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3314 if self._parse_explicit_template_error(e): 
    3315 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3316 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3317 _parse_explicit_template_error 
    3318 self.isolde._handle_bad_template(residue) 
    3319 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3320 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3321 self.start_sim() 
    3322 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3323 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3324 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3325 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3326 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3327 if self._parse_explicit_template_error(e): 
    3328 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3329 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3330 _parse_explicit_template_error 
    3331 self.isolde._handle_bad_template(residue) 
    3332 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3333 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3334 self.start_sim() 
    3335 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3336 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3337 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3338 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3339 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3340 if self._parse_explicit_template_error(e): 
    3341 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3342 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3343 _parse_explicit_template_error 
    3344 self.isolde._handle_bad_template(residue) 
    3345 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3346 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3347 self.start_sim() 
    3348 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3349 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3350 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3351 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3352 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    3353 if self._parse_explicit_template_error(e): 
    3354 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3355 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    3356 _parse_explicit_template_error 
    3357 self.isolde._handle_bad_template(residue) 
    3358 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3359 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    3360 self.start_sim() 
    3361 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3362 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    3363 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    3364 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3365 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    3366 raise e 
    3367 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3368 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3369 isolde.forcefield_mgr) 
    3370 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3371 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3372 sim_params, residue_templates) 
    3373 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3374 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3375 _create_openmm_system 
    3376 sys = forcefield.createSystem(top, **system_params) 
    3377 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3378 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    3379 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    3380 ignoreExternalBonds=ignoreExternalBonds) 
    3381 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3382 packages/simtk/openmm/app/forcefield.py", line 893, in
    3383 _getResidueTemplateMatches 
    3384 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    3385 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    3386 Exception: Multiple matching templates found for residue 1468 (NAG):
    3387 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    3388 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    3389  
    3390 Exception: Multiple matching templates found for residue 1468 (NAG):
    3391 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    3392 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    3393  
    3394 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3395 packages/simtk/openmm/app/forcefield.py", line 893, in
    3396 _getResidueTemplateMatches 
    3397 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    3398 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    3399  
    3400 See log for complete Python traceback. 
    3401  
    3402 
    3403 Not saving entity_poly_seq for non-authoritative sequences 
    3404 
    3405 Not saving entity_poly_seq for non-authoritative sequences 
    3406 
    3407 > close session
    3408 
    3409 Deleting atomic symmetry model... 
    3410 
    3411 > open2
    3412 > /home/kartikmanne/Documents/VRC40/VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    3413 
    3414 Summary of feedback from opening
    3415 /home/kartikmanne/Documents/VRC40/VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif 
    3416 --- 
    3417 warnings | Skipping chem_comp category: Missing column 'type' near line 1674 
    3418 Unable to infer polymer connectivity due to unspecified label_seq_id for
    3419 residue "NAG" near line 1720 
    3420 Missing entity information. Treating each chain as a separate entity. 
    3421 Missing second residue in struct_conn "C00002" 
    3422 Missing first residue in struct_conn "C00020" 
    3423 Missing first residue in struct_conn "C00021" 
    3424 Missing first residue in struct_conn "C00022" 
    3425 Missing first residue in struct_conn "C00023" 
    3426 Missing first residue in struct_conn "C00024" 
    3427 57 messages similar to the above omitted 
    3428 Missing second residue in struct_conn "C00082" 
    3429 Missing second residue in struct_conn "C00083" 
    3430 Missing first residue in struct_conn "C00084" 
    3431 Missing first residue in struct_conn "C00085" 
    3432 Missing first residue in struct_conn "C00086" 
    3433 Missing first residue in struct_conn "C00087" 
    3434 Missing first residue in struct_conn "C00088" 
    3435 5 messages similar to the above omitted 
    3436 Missing second residue in struct_conn "C00094" 
    3437 Missing second residue in struct_conn "C00095" 
    3438 Missing first residue in struct_conn "C00096" 
    3439 Missing first residue in struct_conn "C00097" 
    3440 Missing first residue in struct_conn "C00098" 
    3441 Missing first residue in struct_conn "C00099" 
    3442 Missing first residue in struct_conn "C00100" 
    3443 13 messages similar to the above omitted 
    3444 Missing second residue in struct_conn "C00114" 
    3445 Missing second residue in struct_conn "C00115" 
    3446 Missing first residue in struct_conn "C00116" 
    3447 Missing first residue in struct_conn "C00117" 
    3448 Missing first residue in struct_conn "C00118" 
    3449 Missing first residue in struct_conn "C00119" 
    3450 Missing first residue in struct_conn "C00120" 
    3451 69 messages similar to the above omitted 
    3452 Missing second residue in struct_conn "C00228" 
    3453 Missing second residue in struct_conn "C00229" 
    3454 Missing first residue in struct_conn "C00230" 
    3455 Missing first residue in struct_conn "C00231" 
    3456 Missing first residue in struct_conn "C00232" 
    3457 Missing first residue in struct_conn "C00233" 
    3458 Missing first residue in struct_conn "C00234" 
    3459 8 messages similar to the above omitted 
    3460 Missing second residue in struct_conn "C00301" 
    3461 Missing first residue in struct_conn "C00319" 
    3462 Missing first residue in struct_conn "C00320" 
    3463 Missing first residue in struct_conn "C00321" 
    3464 Missing first residue in struct_conn "C00322" 
    3465 Missing first residue in struct_conn "C00323" 
    3466 57 messages similar to the above omitted 
    3467 Missing second residue in struct_conn "C00381" 
    3468 Missing second residue in struct_conn "C00382" 
    3469 Missing first residue in struct_conn "C00383" 
    3470 Missing first residue in struct_conn "C00384" 
    3471 Missing first residue in struct_conn "C00385" 
    3472 Missing first residue in struct_conn "C00386" 
    3473 Missing first residue in struct_conn "C00387" 
    3474 5 messages similar to the above omitted 
    3475 Missing second residue in struct_conn "C00393" 
    3476 Missing second residue in struct_conn "C00394" 
    3477 Missing first residue in struct_conn "C00395" 
    3478 Missing first residue in struct_conn "C00396" 
    3479 Missing first residue in struct_conn "C00397" 
    3480 Missing first residue in struct_conn "C00398" 
    3481 Missing first residue in struct_conn "C00399" 
    3482 13 messages similar to the above omitted 
    3483 Missing second residue in struct_conn "C00413" 
    3484 Missing second residue in struct_conn "C00414" 
    3485 Missing first residue in struct_conn "C00415" 
    3486 Missing first residue in struct_conn "C00416" 
    3487 Missing first residue in struct_conn "C00417" 
    3488 Missing first residue in struct_conn "C00418" 
    3489 Missing first residue in struct_conn "C00419" 
    3490 69 messages similar to the above omitted 
    3491 Missing second residue in struct_conn "C00527" 
    3492 Missing second residue in struct_conn "C00528" 
    3493 Missing first residue in struct_conn "C00529" 
    3494 Missing first residue in struct_conn "C00530" 
    3495 Missing first residue in struct_conn "C00531" 
    3496 Missing first residue in struct_conn "C00532" 
    3497 Missing first residue in struct_conn "C00533" 
    3498 8 messages similar to the above omitted 
    3499 Missing second residue in struct_conn "C00600" 
    3500 Missing first residue in struct_conn "C00618" 
    3501 Missing first residue in struct_conn "C00619" 
    3502 Missing first residue in struct_conn "C00620" 
    3503 Missing first residue in struct_conn "C00621" 
    3504 Missing first residue in struct_conn "C00622" 
    3505 57 messages similar to the above omitted 
    3506 Missing second residue in struct_conn "C00680" 
    3507 Missing second residue in struct_conn "C00681" 
    3508 Missing first residue in struct_conn "C00682" 
    3509 Missing first residue in struct_conn "C00683" 
    3510 Missing first residue in struct_conn "C00684" 
    3511 Missing first residue in struct_conn "C00685" 
    3512 Missing first residue in struct_conn "C00686" 
    3513 5 messages similar to the above omitted 
    3514 Missing second residue in struct_conn "C00692" 
    3515 Missing second residue in struct_conn "C00693" 
    3516 Missing first residue in struct_conn "C00694" 
    3517 Missing first residue in struct_conn "C00695" 
    3518 Missing first residue in struct_conn "C00696" 
    3519 Missing first residue in struct_conn "C00697" 
    3520 Missing first residue in struct_conn "C00698" 
    3521 13 messages similar to the above omitted 
    3522 Missing second residue in struct_conn "C00712" 
    3523 Missing second residue in struct_conn "C00713" 
    3524 Missing first residue in struct_conn "C00714" 
    3525 Missing first residue in struct_conn "C00715" 
    3526 Missing first residue in struct_conn "C00716" 
    3527 Missing first residue in struct_conn "C00717" 
    3528 Missing first residue in struct_conn "C00718" 
    3529 69 messages similar to the above omitted 
    3530 Missing second residue in struct_conn "C00826" 
    3531 Missing second residue in struct_conn "C00827" 
    3532 Missing first residue in struct_conn "C00828" 
    3533 Missing first residue in struct_conn "C00829" 
    3534 Missing first residue in struct_conn "C00830" 
    3535 Missing first residue in struct_conn "C00831" 
    3536 Missing first residue in struct_conn "C00832" 
    3537 8 messages similar to the above omitted 
    3538 Bad residue range for struct_conf "1" near line 110 
    3539 Bad residue range for struct_conf "2" near line 111 
    3540 Bad residue range for struct_conf "3" near line 112 
    3541 Bad residue range for struct_conf "4" near line 113 
    3542 Bad residue range for struct_conf "5" near line 114 
    3543 22 messages similar to the above omitted 
    3544 Invalid sheet range for struct_sheet_range "D 3" near line 1383 
    3545 Invalid sheet range for struct_sheet_range "I 3" near line 1402 
    3546 Invalid sheet range for struct_sheet_range "N 3" near line 1421 
    3547 Invalid sheet range for struct_sheet_range "A 2" near line 1425 
    3548 Invalid sheet range for struct_sheet_range "B 2" near line 1427 
    3549 4 messages similar to the above omitted 
    3550 Atom H1 is not in the residue template for ALA #32 in chain A 
    3551 Atom H1 is not in the residue template for ALA #512 in chain B 
    3552 Atom H1 is not in the residue template for GLN #1 in chain C 
    3553 Atom H1 is not in the residue template for GLN #1 in chain D 
    3554 Atom H1 is not in the residue template for ALA #32 in chain E 
    3555 7 messages similar to the above omitted 
    3556 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    3557 Skipping chem_comp category: Missing column 'type' near line 50550 
    3558 Skipping chem_comp category: Missing column 'type' near line 50714 
    3559 Skipping chem_comp category: Missing column 'type' near line 50878 
    3560  
    3561 Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1 
    3562 --- 
    3563 Chain | Description 
    3564 A E I | No description available 
    3565 B | No description available 
    3566 C | No description available 
    3567 D | No description available 
    3568  
    3569 Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif 
    3570 --- 
    3571 Chain | Description 
    3572 1.2/A 1.2/E 1.2/I | No description available 
    3573 1.2/B | No description available 
    3574 1.2/C | No description available 
    3575 1.2/D | No description available 
    3576  
    3577 
    3578 > addh
    3579 
    3580 Summary of feedback from adding hydrogens to
    3581 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1.2 
    3582 --- 
    3583 notes | No usable SEQRES records for
    3584 VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif (#1.2) chain A; guessing
    3585 termini instead 
    3586 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    3587 (#1.2) chain B; guessing termini instead 
    3588 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    3589 (#1.2) chain C; guessing termini instead 
    3590 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    3591 (#1.2) chain D; guessing termini instead 
    3592 No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
    3593 (#1.2) chain E; guessing termini instead 
    3594 1 messages similar to the above omitted 
    3595 Chain-initial residues that are actual N termini: /A ALA 32, /B ALA 512, /C
    3596 GLN 1, /D GLN 1, /E ALA 32, /I ALA 32 
    3597 Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
    3598 /A ASP 412, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA
    3599 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209,
    3600 /E HIS 67, /E LYS 190, /E ASP 412, /I HIS 67, /I LYS 190, /I ASP 412 
    3601 Chain-final residues that are actual C termini: 
    3602 Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
    3603 GLN 184, /A ILE 396, /B ASP 664, /C SER 230, /C SER 127, /C SER 143, /C GLY
    3604 172, /C THR 198, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /C SER 127,
    3605 /C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505, /E ALA 59, /E GLN
    3606 184, /E ILE 396, /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396 
    3607 2461 hydrogen bonds 
    3608 /A VAL 505 is not terminus, removing H atom from 'C' 
    3609 /A ALA 59 is not terminus, removing H atom from 'C' 
    3610 /A GLN 184 is not terminus, removing H atom from 'C' 
    3611 /A ILE 396 is not terminus, removing H atom from 'C' 
    3612 /B ASP 664 is not terminus, removing H atom from 'C' 
    3613 22 messages similar to the above omitted 
    3614 1530 hydrogens added 
    3615  
    3616 
    3617 > open2
    3618 > /home/kartikmanne/Documents/VRC40/cryosparc_P4_J12_008_volume_map_sharp_local-
    3619 > zflip.mrc
    3620 
    3621 Opened cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc, grid size
    3622 320,320,320, pixel 1.08, shown at level 0.667, step 2, values float32 
    3623 
    3624 > clipper associate #2 toModel #1
    3625 
    3626 > isolde start
    3627 
    3628 > set selectionWidth 4
    3629 
    3630 Done loading forcefield 
    3631 
    3632 QWidget::repaint: Recursive repaint detected 
    3633 
    3634 > select #1
    3635 
    3636 50160 atoms, 50724 bonds, 321 pseudobonds, 13 models selected 
    3637 
    3638 No template found for residue A506 (NAG) 
    3639 
    3640 Excluding residue 
    3641 
    3642 No template found for residue A508 (NAG) 
    3643 
    3644 Excluding residue 
    3645 
    3646 No template found for residue A509 (NAG) 
    3647 
    3648 Excluding residue 
    3649 
    3650 No template found for residue A512 (NAG) 
    3651 
    3652 Excluding residue 
    3653 
    3654 No template found for residue A515 (NAG) 
    3655 
    3656 Excluding residue 
    3657 
    3658 No template found for residue A517 (NAG) 
    3659 
    3660 Excluding residue 
    3661 
    3662 No template found for residue A519 (BMA) 
    3663 
    3664 Excluding residue 
    3665 
    3666 No template found for residue A521 (MAN) 
    3667 
    3668 Excluding residue 
    3669 
    3670 No template found for residue A522 (NAG) 
    3671 
    3672 Excluding residue 
    3673 
    3674 No template found for residue A527 (MAN) 
    3675 
    3676 Excluding residue 
    3677 
    3678 No template found for residue A528 (MAN) 
    3679 
    3680 Excluding residue 
    3681 
    3682 No template found for residue A529 (NAG) 
    3683 
    3684 Excluding residue 
    3685 
    3686 No template found for residue A531 (NAG) 
    3687 
    3688 Excluding residue 
    3689 
    3690 No template found for residue A534 (NAG) 
    3691 
    3692 Excluding residue 
    3693 
    3694 No template found for residue A537 (NAG) 
    3695 
    3696 Excluding residue 
    3697 
    3698 No template found for residue A540 (NAG) 
    3699 
    3700 Excluding residue 
    3701 
    3702 No template found for residue A543 (NAG) 
    3703 
    3704 Excluding residue 
    3705 
    3706 No template found for residue A544 (NAG) 
    3707 
    3708 Excluding residue 
    3709 
    3710 No template found for residue B598 (CYS) 
    3711 
    3712 Excluding residue 
    3713 
    3714 No template found for residue B598 (CYS) 
    3715 
    3716 Excluding residue 
    3717 
    3718 No template found for residue B598 (CYS) 
    3719 
    3720 Excluding residue 
    3721 
    3722 No template found for residue B604 (CYS) 
    3723 
    3724 Excluding residue 
    3725 
    3726 No template found for residue B604 (CYS) 
    3727 
    3728 Excluding residue 
    3729 
    3730 No template found for residue B604 (CYS) 
    3731 
    3732 Excluding residue 
    3733 
    3734 No template found for residue B605 (CYS) 
    3735 
    3736 Excluding residue 
    3737 
    3738 No template found for residue B605 (CYS) 
    3739 
    3740 Excluding residue 
    3741 
    3742 No template found for residue B605 (CYS) 
    3743 
    3744 Excluding residue 
    3745 
    3746 No template found for residue C22 (CYS) 
    3747 
    3748 Excluding residue 
    3749 
    3750 No template found for residue C22 (CYS) 
    3751 
    3752 Excluding residue 
    3753 
    3754 No template found for residue C22 (CYS) 
    3755 
    3756 Excluding residue 
    3757 
    3758 No template found for residue C101 (CYS) 
    3759 
    3760 Excluding residue 
    3761 
    3762 No template found for residue C101 (CYS) 
    3763 
    3764 Excluding residue 
    3765 
    3766 No template found for residue C101 (CYS) 
    3767 
    3768 Excluding residue 
    3769 
    3770 No template found for residue C155 (CYS) 
    3771 
    3772 Excluding residue 
    3773 
    3774 No template found for residue C155 (CYS) 
    3775 
    3776 Excluding residue 
    3777 
    3778 No template found for residue C155 (CYS) 
    3779 
    3780 Excluding residue 
    3781 
    3782 No template found for residue C211 (CYS) 
    3783 
    3784 Excluding residue 
    3785 
    3786 No template found for residue C211 (CYS) 
    3787 
    3788 Excluding residue 
    3789 
    3790 No template found for residue C211 (CYS) 
    3791 
    3792 Excluding residue 
    3793 Traceback (most recent call last): 
    3794 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3795 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3796 isolde.forcefield_mgr) 
    3797 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3798 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3799 sim_params, residue_templates) 
    3800 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3801 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3802 _create_openmm_system 
    3803 sys = forcefield.createSystem(top, **system_params) 
    3804 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3805 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3806 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3807 % (tname, res.index+1, res.name)) 
    3808 Exception: User-supplied template GLYCAM_4YB does not match the residue 440
    3809 (NAG) 
    3810  
    3811 During handling of the above exception, another exception occurred: 
    3812  
    3813 Traceback (most recent call last): 
    3814 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3815 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3816 isolde.forcefield_mgr) 
    3817 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3818 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3819 sim_params, residue_templates) 
    3820 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3821 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3822 _create_openmm_system 
    3823 sys = forcefield.createSystem(top, **system_params) 
    3824 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3825 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3826 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3827 % (tname, res.index+1, res.name)) 
    3828 Exception: User-supplied template GLYCAM_0YB does not match the residue 441
    3829 (NAG) 
    3830  
    3831 During handling of the above exception, another exception occurred: 
    3832  
    3833 Traceback (most recent call last): 
    3834 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3835 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3836 isolde.forcefield_mgr) 
    3837 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3838 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3839 sim_params, residue_templates) 
    3840 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3841 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3842 _create_openmm_system 
    3843 sys = forcefield.createSystem(top, **system_params) 
    3844 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3845 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3846 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3847 % (tname, res.index+1, res.name)) 
    3848 Exception: User-supplied template GLYCAM_4YB does not match the residue 441
    3849 (NAG) 
    3850  
    3851 During handling of the above exception, another exception occurred: 
    3852  
    3853 Traceback (most recent call last): 
    3854 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3855 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3856 isolde.forcefield_mgr) 
    3857 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3858 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3859 sim_params, residue_templates) 
    3860 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3861 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3862 _create_openmm_system 
    3863 sys = forcefield.createSystem(top, **system_params) 
    3864 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3865 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3866 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3867 % (tname, res.index+1, res.name)) 
    3868 Exception: User-supplied template GLYCAM_4YB does not match the residue 443
    3869 (NAG) 
    3870  
    3871 During handling of the above exception, another exception occurred: 
    3872  
    3873 Traceback (most recent call last): 
    3874 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3875 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3876 isolde.forcefield_mgr) 
    3877 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3878 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3879 sim_params, residue_templates) 
    3880 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3881 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3882 _create_openmm_system 
    3883 sys = forcefield.createSystem(top, **system_params) 
    3884 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3885 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3886 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3887 % (tname, res.index+1, res.name)) 
    3888 Exception: User-supplied template GLYCAM_4YB does not match the residue 445
    3889 (NAG) 
    3890  
    3891 During handling of the above exception, another exception occurred: 
    3892  
    3893 Traceback (most recent call last): 
    3894 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3895 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3896 isolde.forcefield_mgr) 
    3897 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3898 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3899 sim_params, residue_templates) 
    3900 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3901 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3902 _create_openmm_system 
    3903 sys = forcefield.createSystem(top, **system_params) 
    3904 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3905 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3906 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3907 % (tname, res.index+1, res.name)) 
    3908 Exception: User-supplied template GLYCAM_4YB does not match the residue 446
    3909 (NAG) 
    3910  
    3911 During handling of the above exception, another exception occurred: 
    3912  
    3913 Traceback (most recent call last): 
    3914 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3915 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3916 isolde.forcefield_mgr) 
    3917 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3918 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3919 sim_params, residue_templates) 
    3920 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3921 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3922 _create_openmm_system 
    3923 sys = forcefield.createSystem(top, **system_params) 
    3924 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3925 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3926 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3927 % (tname, res.index+1, res.name)) 
    3928 Exception: User-supplied template GLYCAM_3MB does not match the residue 447
    3929 (BMA) 
    3930  
    3931 During handling of the above exception, another exception occurred: 
    3932  
    3933 Traceback (most recent call last): 
    3934 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3935 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3936 isolde.forcefield_mgr) 
    3937 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3938 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3939 sim_params, residue_templates) 
    3940 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3941 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3942 _create_openmm_system 
    3943 sys = forcefield.createSystem(top, **system_params) 
    3944 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3945 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3946 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3947 % (tname, res.index+1, res.name)) 
    3948 Exception: User-supplied template GLYCAM_0MA does not match the residue 448
    3949 (MAN) 
    3950  
    3951 During handling of the above exception, another exception occurred: 
    3952  
    3953 Traceback (most recent call last): 
    3954 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3955 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3956 isolde.forcefield_mgr) 
    3957 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3958 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3959 sim_params, residue_templates) 
    3960 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3961 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3962 _create_openmm_system 
    3963 sys = forcefield.createSystem(top, **system_params) 
    3964 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3965 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3966 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3967 % (tname, res.index+1, res.name)) 
    3968 Exception: User-supplied template GLYCAM_4YB does not match the residue 448
    3969 (NAG) 
    3970  
    3971 During handling of the above exception, another exception occurred: 
    3972  
    3973 Traceback (most recent call last): 
    3974 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3975 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3976 isolde.forcefield_mgr) 
    3977 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3978 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3979 sim_params, residue_templates) 
    3980 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3981 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    3982 _create_openmm_system 
    3983 sys = forcefield.createSystem(top, **system_params) 
    3984 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    3985 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    3986 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    3987 % (tname, res.index+1, res.name)) 
    3988 Exception: User-supplied template GLYCAM_0MA does not match the residue 452
    3989 (MAN) 
    3990  
    3991 During handling of the above exception, another exception occurred: 
    3992  
    3993 Traceback (most recent call last): 
    3994 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3995 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    3996 isolde.forcefield_mgr) 
    3997 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    3998 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    3999 sim_params, residue_templates) 
    4000 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4001 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4002 _create_openmm_system 
    4003 sys = forcefield.createSystem(top, **system_params) 
    4004 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4005 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4006 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4007 % (tname, res.index+1, res.name)) 
    4008 Exception: User-supplied template GLYCAM_0MA does not match the residue 452
    4009 (MAN) 
    4010  
    4011 During handling of the above exception, another exception occurred: 
    4012  
    4013 Traceback (most recent call last): 
    4014 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4015 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4016 isolde.forcefield_mgr) 
    4017 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4018 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4019 sim_params, residue_templates) 
    4020 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4021 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4022 _create_openmm_system 
    4023 sys = forcefield.createSystem(top, **system_params) 
    4024 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4025 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4026 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4027 % (tname, res.index+1, res.name)) 
    4028 Exception: User-supplied template GLYCAM_4YB does not match the residue 452
    4029 (NAG) 
    4030  
    4031 During handling of the above exception, another exception occurred: 
    4032  
    4033 Traceback (most recent call last): 
    4034 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4035 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4036 isolde.forcefield_mgr) 
    4037 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4038 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4039 sim_params, residue_templates) 
    4040 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4041 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4042 _create_openmm_system 
    4043 sys = forcefield.createSystem(top, **system_params) 
    4044 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4045 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4046 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4047 % (tname, res.index+1, res.name)) 
    4048 Exception: User-supplied template GLYCAM_4YB does not match the residue 453
    4049 (NAG) 
    4050  
    4051 During handling of the above exception, another exception occurred: 
    4052  
    4053 Traceback (most recent call last): 
    4054 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4055 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4056 isolde.forcefield_mgr) 
    4057 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4058 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4059 sim_params, residue_templates) 
    4060 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4061 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4062 _create_openmm_system 
    4063 sys = forcefield.createSystem(top, **system_params) 
    4064 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4065 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4066 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4067 % (tname, res.index+1, res.name)) 
    4068 Exception: User-supplied template GLYCAM_4YB does not match the residue 454
    4069 (NAG) 
    4070  
    4071 During handling of the above exception, another exception occurred: 
    4072  
    4073 Traceback (most recent call last): 
    4074 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4075 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4076 isolde.forcefield_mgr) 
    4077 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4078 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4079 sim_params, residue_templates) 
    4080 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4081 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4082 _create_openmm_system 
    4083 sys = forcefield.createSystem(top, **system_params) 
    4084 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4085 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4086 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4087 % (tname, res.index+1, res.name)) 
    4088 Exception: User-supplied template GLYCAM_4YB does not match the residue 455
    4089 (NAG) 
    4090  
    4091 During handling of the above exception, another exception occurred: 
    4092  
    4093 Traceback (most recent call last): 
    4094 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4095 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4096 isolde.forcefield_mgr) 
    4097 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4098 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4099 sim_params, residue_templates) 
    4100 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4101 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4102 _create_openmm_system 
    4103 sys = forcefield.createSystem(top, **system_params) 
    4104 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4105 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4106 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4107 % (tname, res.index+1, res.name)) 
    4108 Exception: User-supplied template GLYCAM_4YB does not match the residue 457
    4109 (NAG) 
    4110  
    4111 During handling of the above exception, another exception occurred: 
    4112  
    4113 Traceback (most recent call last): 
    4114 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4115 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4116 isolde.forcefield_mgr) 
    4117 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4118 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4119 sim_params, residue_templates) 
    4120 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4121 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4122 _create_openmm_system 
    4123 sys = forcefield.createSystem(top, **system_params) 
    4124 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4125 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4126 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4127 % (tname, res.index+1, res.name)) 
    4128 Exception: User-supplied template GLYCAM_0YB does not match the residue 458
    4129 (NAG) 
    4130  
    4131 During handling of the above exception, another exception occurred: 
    4132  
    4133 Traceback (most recent call last): 
    4134 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4135 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4136 isolde.forcefield_mgr) 
    4137 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4138 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4139 sim_params, residue_templates) 
    4140 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4141 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4142 _create_openmm_system 
    4143 sys = forcefield.createSystem(top, **system_params) 
    4144 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4145 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4146 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4147 % (tname, res.index+1, res.name)) 
    4148 Exception: User-supplied template GLYCAM_0YB does not match the residue 458
    4149 (NAG) 
    4150  
    4151 During handling of the above exception, another exception occurred: 
    4152  
    4153 Traceback (most recent call last): 
    4154 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4155 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4156 isolde.forcefield_mgr) 
    4157 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4158 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4159 sim_params, residue_templates) 
    4160 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4161 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4162 _create_openmm_system 
    4163 sys = forcefield.createSystem(top, **system_params) 
    4164 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4165 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4166 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4167 % (tname, res.index+1, res.name)) 
    4168 Exception: User-supplied template CYS does not match the residue 716 (ASP) 
    4169  
    4170 During handling of the above exception, another exception occurred: 
    4171  
    4172 Traceback (most recent call last): 
    4173 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4174 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4175 isolde.forcefield_mgr) 
    4176 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4177 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4178 sim_params, residue_templates) 
    4179 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4180 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4181 _create_openmm_system 
    4182 sys = forcefield.createSystem(top, **system_params) 
    4183 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4184 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4185 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4186 % (tname, res.index+1, res.name)) 
    4187 Exception: User-supplied template CYS does not match the residue 716 (ASP) 
    4188  
    4189 During handling of the above exception, another exception occurred: 
    4190  
    4191 Traceback (most recent call last): 
    4192 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4193 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4194 isolde.forcefield_mgr) 
    4195 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4196 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4197 sim_params, residue_templates) 
    4198 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4199 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4200 _create_openmm_system 
    4201 sys = forcefield.createSystem(top, **system_params) 
    4202 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4203 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4204 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4205 % (tname, res.index+1, res.name)) 
    4206 Exception: User-supplied template CYS does not match the residue 716 (ASP) 
    4207  
    4208 During handling of the above exception, another exception occurred: 
    4209  
    4210 Traceback (most recent call last): 
    4211 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4212 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4213 isolde.forcefield_mgr) 
    4214 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4215 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4216 sim_params, residue_templates) 
    4217 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4218 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4219 _create_openmm_system 
    4220 sys = forcefield.createSystem(top, **system_params) 
    4221 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4222 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4223 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4224 % (tname, res.index+1, res.name)) 
    4225 Exception: User-supplied template CYS does not match the residue 731 (PRO) 
    4226  
    4227 During handling of the above exception, another exception occurred: 
    4228  
    4229 Traceback (most recent call last): 
    4230 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4231 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4232 isolde.forcefield_mgr) 
    4233 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4234 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4235 sim_params, residue_templates) 
    4236 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4237 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4238 _create_openmm_system 
    4239 sys = forcefield.createSystem(top, **system_params) 
    4240 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4241 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4242 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4243 % (tname, res.index+1, res.name)) 
    4244 Exception: User-supplied template CYS does not match the residue 731 (PRO) 
    4245  
    4246 During handling of the above exception, another exception occurred: 
    4247  
    4248 Traceback (most recent call last): 
    4249 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4250 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4251 isolde.forcefield_mgr) 
    4252 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4253 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4254 sim_params, residue_templates) 
    4255 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4256 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4257 _create_openmm_system 
    4258 sys = forcefield.createSystem(top, **system_params) 
    4259 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4260 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4261 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4262 % (tname, res.index+1, res.name)) 
    4263 Exception: User-supplied template CYS does not match the residue 731 (PRO) 
    4264  
    4265 During handling of the above exception, another exception occurred: 
    4266  
    4267 Traceback (most recent call last): 
    4268 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4269 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4270 isolde.forcefield_mgr) 
    4271 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4272 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4273 sim_params, residue_templates) 
    4274 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4275 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4276 _create_openmm_system 
    4277 sys = forcefield.createSystem(top, **system_params) 
    4278 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4279 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4280 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4281 % (tname, res.index+1, res.name)) 
    4282 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    4283  
    4284 During handling of the above exception, another exception occurred: 
    4285  
    4286 Traceback (most recent call last): 
    4287 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4288 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4289 isolde.forcefield_mgr) 
    4290 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4291 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4292 sim_params, residue_templates) 
    4293 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4294 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4295 _create_openmm_system 
    4296 sys = forcefield.createSystem(top, **system_params) 
    4297 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4298 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4299 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4300 % (tname, res.index+1, res.name)) 
    4301 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    4302  
    4303 During handling of the above exception, another exception occurred: 
    4304  
    4305 Traceback (most recent call last): 
    4306 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4307 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4308 isolde.forcefield_mgr) 
    4309 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4310 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4311 sim_params, residue_templates) 
    4312 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4313 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4314 _create_openmm_system 
    4315 sys = forcefield.createSystem(top, **system_params) 
    4316 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4317 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4318 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4319 % (tname, res.index+1, res.name)) 
    4320 Exception: User-supplied template CYS does not match the residue 731 (VAL) 
    4321  
    4322 During handling of the above exception, another exception occurred: 
    4323  
    4324 Traceback (most recent call last): 
    4325 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4326 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4327 isolde.forcefield_mgr) 
    4328 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4329 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4330 sim_params, residue_templates) 
    4331 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4332 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4333 _create_openmm_system 
    4334 sys = forcefield.createSystem(top, **system_params) 
    4335 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4336 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4337 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4338 % (tname, res.index+1, res.name)) 
    4339 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    4340  
    4341 During handling of the above exception, another exception occurred: 
    4342  
    4343 Traceback (most recent call last): 
    4344 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4345 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4346 isolde.forcefield_mgr) 
    4347 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4348 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4349 sim_params, residue_templates) 
    4350 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4351 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4352 _create_openmm_system 
    4353 sys = forcefield.createSystem(top, **system_params) 
    4354 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4355 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4356 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4357 % (tname, res.index+1, res.name)) 
    4358 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    4359  
    4360 During handling of the above exception, another exception occurred: 
    4361  
    4362 Traceback (most recent call last): 
    4363 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4364 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4365 isolde.forcefield_mgr) 
    4366 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4367 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4368 sim_params, residue_templates) 
    4369 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4370 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4371 _create_openmm_system 
    4372 sys = forcefield.createSystem(top, **system_params) 
    4373 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4374 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4375 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4376 % (tname, res.index+1, res.name)) 
    4377 Exception: User-supplied template CYX does not match the residue 971 (LEU) 
    4378  
    4379 During handling of the above exception, another exception occurred: 
    4380  
    4381 Traceback (most recent call last): 
    4382 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4383 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4384 isolde.forcefield_mgr) 
    4385 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4386 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4387 sim_params, residue_templates) 
    4388 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4389 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4390 _create_openmm_system 
    4391 sys = forcefield.createSystem(top, **system_params) 
    4392 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4393 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4394 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4395 % (tname, res.index+1, res.name)) 
    4396 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    4397  
    4398 During handling of the above exception, another exception occurred: 
    4399  
    4400 Traceback (most recent call last): 
    4401 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4402 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4403 isolde.forcefield_mgr) 
    4404 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4405 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4406 sim_params, residue_templates) 
    4407 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4408 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4409 _create_openmm_system 
    4410 sys = forcefield.createSystem(top, **system_params) 
    4411 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4412 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4413 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4414 % (tname, res.index+1, res.name)) 
    4415 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    4416  
    4417 During handling of the above exception, another exception occurred: 
    4418  
    4419 Traceback (most recent call last): 
    4420 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4421 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4422 isolde.forcefield_mgr) 
    4423 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4424 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4425 sim_params, residue_templates) 
    4426 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4427 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4428 _create_openmm_system 
    4429 sys = forcefield.createSystem(top, **system_params) 
    4430 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4431 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4432 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4433 % (tname, res.index+1, res.name)) 
    4434 Exception: User-supplied template CYX does not match the residue 1205 (ILE) 
    4435  
    4436 During handling of the above exception, another exception occurred: 
    4437  
    4438 Traceback (most recent call last): 
    4439 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4440 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4441 isolde.forcefield_mgr) 
    4442 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4443 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4444 sim_params, residue_templates) 
    4445 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4446 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4447 _create_openmm_system 
    4448 sys = forcefield.createSystem(top, **system_params) 
    4449 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4450 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4451 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4452 % (tname, res.index+1, res.name)) 
    4453 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    4454  
    4455 During handling of the above exception, another exception occurred: 
    4456  
    4457 Traceback (most recent call last): 
    4458 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4459 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4460 isolde.forcefield_mgr) 
    4461 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4462 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4463 sim_params, residue_templates) 
    4464 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4465 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4466 _create_openmm_system 
    4467 sys = forcefield.createSystem(top, **system_params) 
    4468 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4469 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4470 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4471 % (tname, res.index+1, res.name)) 
    4472 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    4473  
    4474 During handling of the above exception, another exception occurred: 
    4475  
    4476 Traceback (most recent call last): 
    4477 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4478 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4479 isolde.forcefield_mgr) 
    4480 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4481 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4482 sim_params, residue_templates) 
    4483 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4484 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4485 _create_openmm_system 
    4486 sys = forcefield.createSystem(top, **system_params) 
    4487 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4488 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4489 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4490 % (tname, res.index+1, res.name)) 
    4491 Exception: User-supplied template CYS does not match the residue 1340 (ALA) 
    4492  
    4493 During handling of the above exception, another exception occurred: 
    4494  
    4495 Traceback (most recent call last): 
    4496 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4497 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4498 isolde.forcefield_mgr) 
    4499 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4500 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4501 sim_params, residue_templates) 
    4502 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4503 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4504 _create_openmm_system 
    4505 sys = forcefield.createSystem(top, **system_params) 
    4506 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4507 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4508 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4509 % (tname, res.index+1, res.name)) 
    4510 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    4511  
    4512 During handling of the above exception, another exception occurred: 
    4513  
    4514 Traceback (most recent call last): 
    4515 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4516 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4517 isolde.forcefield_mgr) 
    4518 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4519 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4520 sim_params, residue_templates) 
    4521 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4522 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4523 _create_openmm_system 
    4524 sys = forcefield.createSystem(top, **system_params) 
    4525 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4526 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4527 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4528 % (tname, res.index+1, res.name)) 
    4529 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    4530  
    4531 During handling of the above exception, another exception occurred: 
    4532  
    4533 Traceback (most recent call last): 
    4534 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4535 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    4536 isolde.forcefield_mgr) 
    4537 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4538 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    4539 sim_params, residue_templates) 
    4540 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4541 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    4542 _create_openmm_system 
    4543 sys = forcefield.createSystem(top, **system_params) 
    4544 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4545 packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem 
    4546 raise Exception('User-supplied template %s does not match the residue %d (%s)'
    4547 % (tname, res.index+1, res.name)) 
    4548 Exception: User-supplied template CYS does not match the residue 1469 (NAG) 
    4549  
    4550 During handling of the above exception, another exception occurred: 
    4551  
    4552 Traceback (most recent call last): 
    4553 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4554 packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause 
    4555 self.start_sim() 
    4556 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4557 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4558 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4559 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4560 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4561 if self._parse_explicit_template_error(e): 
    4562 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4563 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4564 _parse_explicit_template_error 
    4565 self.isolde._handle_bad_template(residue) 
    4566 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4567 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4568 self.start_sim() 
    4569 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4570 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4571 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4572 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4573 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4574 if self._parse_explicit_template_error(e): 
    4575 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4576 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4577 _parse_explicit_template_error 
    4578 self.isolde._handle_bad_template(residue) 
    4579 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4580 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4581 self.start_sim() 
    4582 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4583 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4584 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4585 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4586 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4587 if self._parse_explicit_template_error(e): 
    4588 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4589 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4590 _parse_explicit_template_error 
    4591 self.isolde._handle_bad_template(residue) 
    4592 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4593 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4594 self.start_sim() 
    4595 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4596 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4597 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4598 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4599 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4600 if self._parse_explicit_template_error(e): 
    4601 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4602 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4603 _parse_explicit_template_error 
    4604 self.isolde._handle_bad_template(residue) 
    4605 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4606 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4607 self.start_sim() 
    4608 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4609 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4610 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4611 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4612 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4613 if self._parse_explicit_template_error(e): 
    4614 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4615 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4616 _parse_explicit_template_error 
    4617 self.isolde._handle_bad_template(residue) 
    4618 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4619 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4620 self.start_sim() 
    4621 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4622 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4623 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4624 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4625 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4626 if self._parse_explicit_template_error(e): 
    4627 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4628 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4629 _parse_explicit_template_error 
    4630 self.isolde._handle_bad_template(residue) 
    4631 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4632 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4633 self.start_sim() 
    4634 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4635 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4636 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4637 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4638 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4639 if self._parse_explicit_template_error(e): 
    4640 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4641 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4642 _parse_explicit_template_error 
    4643 self.isolde._handle_bad_template(residue) 
    4644 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4645 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4646 self.start_sim() 
    4647 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4648 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4649 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4650 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4651 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4652 if self._parse_explicit_template_error(e): 
    4653 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4654 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4655 _parse_explicit_template_error 
    4656 self.isolde._handle_bad_template(residue) 
    4657 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4658 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4659 self.start_sim() 
    4660 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4661 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4662 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4663 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4664 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4665 if self._parse_explicit_template_error(e): 
    4666 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4667 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4668 _parse_explicit_template_error 
    4669 self.isolde._handle_bad_template(residue) 
    4670 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4671 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4672 self.start_sim() 
    4673 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4674 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4675 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4676 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4677 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4678 if self._parse_explicit_template_error(e): 
    4679 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4680 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4681 _parse_explicit_template_error 
    4682 self.isolde._handle_bad_template(residue) 
    4683 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4684 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4685 self.start_sim() 
    4686 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4687 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4688 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4689 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4690 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4691 if self._parse_explicit_template_error(e): 
    4692 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4693 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4694 _parse_explicit_template_error 
    4695 self.isolde._handle_bad_template(residue) 
    4696 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4697 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4698 self.start_sim() 
    4699 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4700 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4701 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4702 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4703 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4704 if self._parse_explicit_template_error(e): 
    4705 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4706 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4707 _parse_explicit_template_error 
    4708 self.isolde._handle_bad_template(residue) 
    4709 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4710 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4711 self.start_sim() 
    4712 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4713 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4714 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4715 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4716 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4717 if self._parse_explicit_template_error(e): 
    4718 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4719 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4720 _parse_explicit_template_error 
    4721 self.isolde._handle_bad_template(residue) 
    4722 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4723 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4724 self.start_sim() 
    4725 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4726 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4727 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4728 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4729 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4730 if self._parse_explicit_template_error(e): 
    4731 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4732 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4733 _parse_explicit_template_error 
    4734 self.isolde._handle_bad_template(residue) 
    4735 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4736 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4737 self.start_sim() 
    4738 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4739 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4740 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4741 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4742 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4743 if self._parse_explicit_template_error(e): 
    4744 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4745 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4746 _parse_explicit_template_error 
    4747 self.isolde._handle_bad_template(residue) 
    4748 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4749 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4750 self.start_sim() 
    4751 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4752 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4753 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4754 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4755 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4756 if self._parse_explicit_template_error(e): 
    4757 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4758 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4759 _parse_explicit_template_error 
    4760 self.isolde._handle_bad_template(residue) 
    4761 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4762 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4763 self.start_sim() 
    4764 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4765 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4766 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4767 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4768 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4769 if self._parse_explicit_template_error(e): 
    4770 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4771 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4772 _parse_explicit_template_error 
    4773 self.isolde._handle_bad_template(residue) 
    4774 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4775 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4776 self.start_sim() 
    4777 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4778 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4779 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4780 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4781 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4782 if self._parse_explicit_template_error(e): 
    4783 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4784 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4785 _parse_explicit_template_error 
    4786 self.isolde._handle_bad_template(residue) 
    4787 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4788 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4789 self.start_sim() 
    4790 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4791 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4792 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4793 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4794 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4795 if self._parse_explicit_template_error(e): 
    4796 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4797 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4798 _parse_explicit_template_error 
    4799 self.isolde._handle_bad_template(residue) 
    4800 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4801 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4802 self.start_sim() 
    4803 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4804 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4805 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4806 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4807 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4808 if self._parse_explicit_template_error(e): 
    4809 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4810 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4811 _parse_explicit_template_error 
    4812 self.isolde._handle_bad_template(residue) 
    4813 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4814 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4815 self.start_sim() 
    4816 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4817 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4818 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4819 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4820 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4821 if self._parse_explicit_template_error(e): 
    4822 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4823 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4824 _parse_explicit_template_error 
    4825 self.isolde._handle_bad_template(residue) 
    4826 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4827 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4828 self.start_sim() 
    4829 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4830 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4831 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4832 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4833 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4834 if self._parse_explicit_template_error(e): 
    4835 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4836 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4837 _parse_explicit_template_error 
    4838 self.isolde._handle_bad_template(residue) 
    4839 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4840 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4841 self.start_sim() 
    4842 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4843 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4844 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4845 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4846 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4847 if self._parse_explicit_template_error(e): 
    4848 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4849 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4850 _parse_explicit_template_error 
    4851 self.isolde._handle_bad_template(residue) 
    4852 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4853 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4854 self.start_sim() 
    4855 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4856 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4857 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4858 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4859 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4860 if self._parse_explicit_template_error(e): 
    4861 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4862 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4863 _parse_explicit_template_error 
    4864 self.isolde._handle_bad_template(residue) 
    4865 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4866 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4867 self.start_sim() 
    4868 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4869 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4870 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4871 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4872 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4873 if self._parse_explicit_template_error(e): 
    4874 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4875 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4876 _parse_explicit_template_error 
    4877 self.isolde._handle_bad_template(residue) 
    4878 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4879 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4880 self.start_sim() 
    4881 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4882 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4883 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4884 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4885 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4886 if self._parse_explicit_template_error(e): 
    4887 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4888 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4889 _parse_explicit_template_error 
    4890 self.isolde._handle_bad_template(residue) 
    4891 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4892 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4893 self.start_sim() 
    4894 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4895 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4896 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4897 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4898 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4899 if self._parse_explicit_template_error(e): 
    4900 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4901 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4902 _parse_explicit_template_error 
    4903 self.isolde._handle_bad_template(residue) 
    4904 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4905 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4906 self.start_sim() 
    4907 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4908 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4909 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4910 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4911 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4912 if self._parse_explicit_template_error(e): 
    4913 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4914 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4915 _parse_explicit_template_error 
    4916 self.isolde._handle_bad_template(residue) 
    4917 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4918 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4919 self.start_sim() 
    4920 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4921 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4922 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4923 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4924 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4925 if self._parse_explicit_template_error(e): 
    4926 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4927 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4928 _parse_explicit_template_error 
    4929 self.isolde._handle_bad_template(residue) 
    4930 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4931 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4932 self.start_sim() 
    4933 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4934 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4935 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4936 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4937 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4938 if self._parse_explicit_template_error(e): 
    4939 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4940 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4941 _parse_explicit_template_error 
    4942 self.isolde._handle_bad_template(residue) 
    4943 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4944 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4945 self.start_sim() 
    4946 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4947 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4948 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4949 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4950 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4951 if self._parse_explicit_template_error(e): 
    4952 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4953 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4954 _parse_explicit_template_error 
    4955 self.isolde._handle_bad_template(residue) 
    4956 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4957 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4958 self.start_sim() 
    4959 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4960 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4961 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4962 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4963 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4964 if self._parse_explicit_template_error(e): 
    4965 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4966 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4967 _parse_explicit_template_error 
    4968 self.isolde._handle_bad_template(residue) 
    4969 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4970 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4971 self.start_sim() 
    4972 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4973 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4974 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4975 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4976 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4977 if self._parse_explicit_template_error(e): 
    4978 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4979 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4980 _parse_explicit_template_error 
    4981 self.isolde._handle_bad_template(residue) 
    4982 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4983 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4984 self.start_sim() 
    4985 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4986 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    4987 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    4988 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4989 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    4990 if self._parse_explicit_template_error(e): 
    4991 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4992 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    4993 _parse_explicit_template_error 
    4994 self.isolde._handle_bad_template(residue) 
    4995 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4996 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    4997 self.start_sim() 
    4998 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    4999 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    5000 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    5001 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5002 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    5003 if self._parse_explicit_template_error(e): 
    5004 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5005 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    5006 _parse_explicit_template_error 
    5007 self.isolde._handle_bad_template(residue) 
    5008 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5009 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    5010 self.start_sim() 
    5011 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5012 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    5013 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    5014 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5015 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    5016 if self._parse_explicit_template_error(e): 
    5017 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5018 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    5019 _parse_explicit_template_error 
    5020 self.isolde._handle_bad_template(residue) 
    5021 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5022 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    5023 self.start_sim() 
    5024 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5025 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    5026 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    5027 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5028 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    5029 if self._parse_explicit_template_error(e): 
    5030 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5031 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    5032 _parse_explicit_template_error 
    5033 self.isolde._handle_bad_template(residue) 
    5034 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5035 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    5036 self.start_sim() 
    5037 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5038 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    5039 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    5040 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5041 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    5042 if self._parse_explicit_template_error(e): 
    5043 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5044 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    5045 _parse_explicit_template_error 
    5046 self.isolde._handle_bad_template(residue) 
    5047 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5048 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    5049 self.start_sim() 
    5050 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5051 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    5052 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    5053 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5054 packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__ 
    5055 if self._parse_explicit_template_error(e): 
    5056 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5057 packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
    5058 _parse_explicit_template_error 
    5059 self.isolde._handle_bad_template(residue) 
    5060 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5061 packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template 
    5062 self.start_sim() 
    5063 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5064 packages/chimerax/isolde/isolde.py", line 2699, in start_sim 
    5065 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    5066 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5067 packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__ 
    5068 raise e 
    5069 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5070 packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__ 
    5071 isolde.forcefield_mgr) 
    5072 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5073 packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__ 
    5074 sim_params, residue_templates) 
    5075 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5076 packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
    5077 _create_openmm_system 
    5078 sys = forcefield.createSystem(top, **system_params) 
    5079 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5080 packages/simtk/openmm/app/forcefield.py", line 1117, in createSystem 
    5081 [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
    5082 ignoreExternalBonds=ignoreExternalBonds) 
    5083 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5084 packages/simtk/openmm/app/forcefield.py", line 893, in
    5085 _getResidueTemplateMatches 
    5086 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    5087 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    5088 Exception: Multiple matching templates found for residue 1468 (NAG):
    5089 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    5090 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    5091  
    5092 Exception: Multiple matching templates found for residue 1468 (NAG):
    5093 GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
    5094 GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB. 
    5095  
    5096 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5097 packages/simtk/openmm/app/forcefield.py", line 893, in
    5098 _getResidueTemplateMatches 
    5099 raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
    5100 (res.index+1, res.name, ', '.join(match[0].name for match in allMatches))) 
    5101  
    5102 See log for complete Python traceback. 
    5103  
    5104 
    5105 No template found for residue D23 (CYS) 
    5106 
    5107 Excluding residue 
    5108 
    5109 No template found for residue D88 (CYS) 
    5110 
    5111 Excluding residue 
    5112 Traceback (most recent call last): 
    5113 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5114 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5115 return self._func(self._name, data) 
    5116 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5117 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5118 _model_changed_cb 
    5119 self.update_scatter() 
    5120 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5121 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5122 if not self.visible: 
    5123 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5124 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5125 return self.parent.isVisible() 
    5126 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5127 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5128 return self.container.parentWidget() 
    5129 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5130  
    5131 Error processing trigger "changes": 
    5132 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5133  
    5134 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5135 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5136 return self.container.parentWidget() 
    5137  
    5138 See log for complete Python traceback. 
    5139  
    5140 Traceback (most recent call last): 
    5141 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5142 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5143 return self._func(self._name, data) 
    5144 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5145 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5146 _model_changed_cb 
    5147 self.update_scatter() 
    5148 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5149 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5150 if not self.visible: 
    5151 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5152 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5153 return self.parent.isVisible() 
    5154 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5155 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5156 return self.container.parentWidget() 
    5157 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5158  
    5159 Error processing trigger "changes": 
    5160 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5161  
    5162 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5163 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5164 return self.container.parentWidget() 
    5165  
    5166 See log for complete Python traceback. 
    5167  
    5168 Traceback (most recent call last): 
    5169 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5170 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5171 return self._func(self._name, data) 
    5172 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5173 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5174 _model_changed_cb 
    5175 self.update_scatter() 
    5176 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5177 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5178 if not self.visible: 
    5179 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5180 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5181 return self.parent.isVisible() 
    5182 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5183 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5184 return self.container.parentWidget() 
    5185 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5186  
    5187 Error processing trigger "changes": 
    5188 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5189  
    5190 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5191 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5192 return self.container.parentWidget() 
    5193  
    5194 See log for complete Python traceback. 
    5195  
    5196 Traceback (most recent call last): 
    5197 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5198 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5199 return self._func(self._name, data) 
    5200 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5201 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5202 _model_changed_cb 
    5203 self.update_scatter() 
    5204 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5205 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5206 if not self.visible: 
    5207 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5208 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5209 return self.parent.isVisible() 
    5210 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5211 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5212 return self.container.parentWidget() 
    5213 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5214  
    5215 Error processing trigger "changes": 
    5216 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5217  
    5218 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5219 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5220 return self.container.parentWidget() 
    5221  
    5222 See log for complete Python traceback. 
    5223  
    5224 Traceback (most recent call last): 
    5225 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5226 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5227 return self._func(self._name, data) 
    5228 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5229 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5230 _model_changed_cb 
    5231 self.update_scatter() 
    5232 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5233 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5234 if not self.visible: 
    5235 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5236 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5237 return self.parent.isVisible() 
    5238 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5239 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5240 return self.container.parentWidget() 
    5241 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5242  
    5243 Error processing trigger "changes": 
    5244 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5245  
    5246 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5247 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5248 return self.container.parentWidget() 
    5249  
    5250 See log for complete Python traceback. 
    5251  
    5252 Traceback (most recent call last): 
    5253 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5254 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5255 return self._func(self._name, data) 
    5256 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5257 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5258 _model_changed_cb 
    5259 self.update_scatter() 
    5260 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5261 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5262 if not self.visible: 
    5263 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5264 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5265 return self.parent.isVisible() 
    5266 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5267 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5268 return self.container.parentWidget() 
    5269 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5270  
    5271 Error processing trigger "changes": 
    5272 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5273  
    5274 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5275 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5276 return self.container.parentWidget() 
    5277  
    5278 See log for complete Python traceback. 
    5279  
    5280 Traceback (most recent call last): 
    5281 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5282 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5283 return self._func(self._name, data) 
    5284 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5285 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5286 _model_changed_cb 
    5287 self.update_scatter() 
    5288 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5289 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5290 if not self.visible: 
    5291 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5292 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5293 return self.parent.isVisible() 
    5294 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5295 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5296 return self.container.parentWidget() 
    5297 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5298  
    5299 Error processing trigger "changes": 
    5300 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5301  
    5302 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5303 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5304 return self.container.parentWidget() 
    5305  
    5306 See log for complete Python traceback. 
    5307  
    5308 Traceback (most recent call last): 
    5309 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5310 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5311 return self._func(self._name, data) 
    5312 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5313 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5314 _model_changed_cb 
    5315 self.update_scatter() 
    5316 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5317 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5318 if not self.visible: 
    5319 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5320 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5321 return self.parent.isVisible() 
    5322 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5323 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5324 return self.container.parentWidget() 
    5325 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5326  
    5327 Error processing trigger "changes": 
    5328 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5329  
    5330 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5331 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5332 return self.container.parentWidget() 
    5333  
    5334 See log for complete Python traceback. 
    5335  
    5336 Traceback (most recent call last): 
    5337 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5338 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5339 return self._func(self._name, data) 
    5340 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5341 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5342 _model_changed_cb 
    5343 self.update_scatter() 
    5344 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5345 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5346 if not self.visible: 
    5347 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5348 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5349 return self.parent.isVisible() 
    5350 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5351 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5352 return self.container.parentWidget() 
    5353 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5354  
    5355 Error processing trigger "changes": 
    5356 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5357  
    5358 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5359 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5360 return self.container.parentWidget() 
    5361  
    5362 See log for complete Python traceback. 
    5363  
    5364 Traceback (most recent call last): 
    5365 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5366 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5367 return self._func(self._name, data) 
    5368 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5369 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5370 _model_changed_cb 
    5371 self.update_scatter() 
    5372 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5373 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5374 if not self.visible: 
    5375 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5376 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5377 return self.parent.isVisible() 
    5378 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5379 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5380 return self.container.parentWidget() 
    5381 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5382  
    5383 Error processing trigger "changes": 
    5384 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5385  
    5386 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5387 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5388 return self.container.parentWidget() 
    5389  
    5390 See log for complete Python traceback. 
    5391  
    5392 Traceback (most recent call last): 
    5393 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5394 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5395 return self._func(self._name, data) 
    5396 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5397 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5398 _model_changed_cb 
    5399 self.update_scatter() 
    5400 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5401 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5402 if not self.visible: 
    5403 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5404 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5405 return self.parent.isVisible() 
    5406 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5407 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5408 return self.container.parentWidget() 
    5409 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5410  
    5411 Error processing trigger "changes": 
    5412 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5413  
    5414 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5415 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5416 return self.container.parentWidget() 
    5417  
    5418 See log for complete Python traceback. 
    5419  
    5420 Traceback (most recent call last): 
    5421 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5422 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5423 return self._func(self._name, data) 
    5424 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5425 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5426 _model_changed_cb 
    5427 self.update_scatter() 
    5428 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5429 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5430 if not self.visible: 
    5431 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5432 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5433 return self.parent.isVisible() 
    5434 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5435 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5436 return self.container.parentWidget() 
    5437 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5438  
    5439 Error processing trigger "changes": 
    5440 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5441  
    5442 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5443 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5444 return self.container.parentWidget() 
    5445  
    5446 See log for complete Python traceback. 
    5447  
    5448 Traceback (most recent call last): 
    5449 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5450 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5451 return self._func(self._name, data) 
    5452 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5453 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5454 _model_changed_cb 
    5455 self.update_scatter() 
    5456 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5457 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5458 if not self.visible: 
    5459 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5460 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5461 return self.parent.isVisible() 
    5462 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5463 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5464 return self.container.parentWidget() 
    5465 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5466  
    5467 Error processing trigger "changes": 
    5468 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5469  
    5470 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5471 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5472 return self.container.parentWidget() 
    5473  
    5474 See log for complete Python traceback. 
    5475  
    5476 Traceback (most recent call last): 
    5477 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5478 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5479 return self._func(self._name, data) 
    5480 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5481 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5482 _model_changed_cb 
    5483 self.update_scatter() 
    5484 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5485 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5486 if not self.visible: 
    5487 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5488 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5489 return self.parent.isVisible() 
    5490 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5491 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5492 return self.container.parentWidget() 
    5493 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5494  
    5495 Error processing trigger "changes": 
    5496 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5497  
    5498 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5499 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5500 return self.container.parentWidget() 
    5501  
    5502 See log for complete Python traceback. 
    5503  
    5504 Traceback (most recent call last): 
    5505 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5506 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5507 return self._func(self._name, data) 
    5508 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5509 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5510 _model_changed_cb 
    5511 self.update_scatter() 
    5512 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5513 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5514 if not self.visible: 
    5515 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5516 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5517 return self.parent.isVisible() 
    5518 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5519 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5520 return self.container.parentWidget() 
    5521 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5522  
    5523 Error processing trigger "changes": 
    5524 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5525  
    5526 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5527 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5528 return self.container.parentWidget() 
    5529  
    5530 See log for complete Python traceback. 
    5531  
    5532 Traceback (most recent call last): 
    5533 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5534 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5535 return self._func(self._name, data) 
    5536 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5537 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5538 _model_changed_cb 
    5539 self.update_scatter() 
    5540 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5541 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5542 if not self.visible: 
    5543 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5544 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5545 return self.parent.isVisible() 
    5546 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5547 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5548 return self.container.parentWidget() 
    5549 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5550  
    5551 Error processing trigger "changes": 
    5552 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5553  
    5554 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5555 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5556 return self.container.parentWidget() 
    5557  
    5558 See log for complete Python traceback. 
    5559  
    5560 Traceback (most recent call last): 
    5561 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5562 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5563 return self._func(self._name, data) 
    5564 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5565 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5566 _model_changed_cb 
    5567 self.update_scatter() 
    5568 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5569 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5570 if not self.visible: 
    5571 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5572 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5573 return self.parent.isVisible() 
    5574 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5575 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5576 return self.container.parentWidget() 
    5577 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5578  
    5579 Error processing trigger "changes": 
    5580 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5581  
    5582 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5583 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5584 return self.container.parentWidget() 
    5585  
    5586 See log for complete Python traceback. 
    5587  
    5588 Traceback (most recent call last): 
    5589 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5590 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5591 return self._func(self._name, data) 
    5592 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5593 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5594 _model_changed_cb 
    5595 self.update_scatter() 
    5596 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5597 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5598 if not self.visible: 
    5599 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5600 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5601 return self.parent.isVisible() 
    5602 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5603 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5604 return self.container.parentWidget() 
    5605 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5606  
    5607 Error processing trigger "changes": 
    5608 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5609  
    5610 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5611 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5612 return self.container.parentWidget() 
    5613  
    5614 See log for complete Python traceback. 
    5615  
    5616 Traceback (most recent call last): 
    5617 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5618 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5619 return self._func(self._name, data) 
    5620 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5621 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5622 _model_changed_cb 
    5623 self.update_scatter() 
    5624 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5625 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5626 if not self.visible: 
    5627 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5628 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5629 return self.parent.isVisible() 
    5630 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5631 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5632 return self.container.parentWidget() 
    5633 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5634  
    5635 Error processing trigger "changes": 
    5636 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5637  
    5638 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5639 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5640 return self.container.parentWidget() 
    5641  
    5642 See log for complete Python traceback. 
    5643  
    5644 Traceback (most recent call last): 
    5645 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5646 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5647 return self._func(self._name, data) 
    5648 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5649 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5650 _model_changed_cb 
    5651 self.update_scatter() 
    5652 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5653 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5654 if not self.visible: 
    5655 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5656 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5657 return self.parent.isVisible() 
    5658 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5659 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5660 return self.container.parentWidget() 
    5661 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5662  
    5663 Error processing trigger "changes": 
    5664 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5665  
    5666 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5667 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5668 return self.container.parentWidget() 
    5669  
    5670 See log for complete Python traceback. 
    5671  
    5672 Traceback (most recent call last): 
    5673 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5674 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5675 return self._func(self._name, data) 
    5676 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5677 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5678 _model_changed_cb 
    5679 self.update_scatter() 
    5680 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5681 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5682 if not self.visible: 
    5683 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5684 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5685 return self.parent.isVisible() 
    5686 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5687 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5688 return self.container.parentWidget() 
    5689 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5690  
    5691 Error processing trigger "changes": 
    5692 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5693  
    5694 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5695 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5696 return self.container.parentWidget() 
    5697  
    5698 See log for complete Python traceback. 
    5699  
    5700 Traceback (most recent call last): 
    5701 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5702 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5703 return self._func(self._name, data) 
    5704 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5705 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5706 _model_changed_cb 
    5707 self.update_scatter() 
    5708 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5709 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5710 if not self.visible: 
    5711 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5712 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5713 return self.parent.isVisible() 
    5714 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5715 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5716 return self.container.parentWidget() 
    5717 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5718  
    5719 Error processing trigger "changes": 
    5720 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5721  
    5722 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5723 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5724 return self.container.parentWidget() 
    5725  
    5726 See log for complete Python traceback. 
    5727  
    5728 Traceback (most recent call last): 
    5729 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5730 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5731 return self._func(self._name, data) 
    5732 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5733 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5734 _model_changed_cb 
    5735 self.update_scatter() 
    5736 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5737 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5738 if not self.visible: 
    5739 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5740 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5741 return self.parent.isVisible() 
    5742 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5743 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5744 return self.container.parentWidget() 
    5745 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5746  
    5747 Error processing trigger "changes": 
    5748 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5749  
    5750 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5751 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5752 return self.container.parentWidget() 
    5753  
    5754 See log for complete Python traceback. 
    5755  
    5756 Traceback (most recent call last): 
    5757 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5758 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5759 return self._func(self._name, data) 
    5760 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5761 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5762 _model_changed_cb 
    5763 self.update_scatter() 
    5764 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5765 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5766 if not self.visible: 
    5767 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5768 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5769 return self.parent.isVisible() 
    5770 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5771 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5772 return self.container.parentWidget() 
    5773 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5774  
    5775 Error processing trigger "changes": 
    5776 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5777  
    5778 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5779 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5780 return self.container.parentWidget() 
    5781  
    5782 See log for complete Python traceback. 
    5783  
    5784 Traceback (most recent call last): 
    5785 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5786 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5787 return self._func(self._name, data) 
    5788 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5789 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5790 _model_changed_cb 
    5791 self.update_scatter() 
    5792 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5793 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5794 if not self.visible: 
    5795 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5796 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5797 return self.parent.isVisible() 
    5798 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5799 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5800 return self.container.parentWidget() 
    5801 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5802  
    5803 Error processing trigger "changes": 
    5804 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5805  
    5806 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5807 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5808 return self.container.parentWidget() 
    5809  
    5810 See log for complete Python traceback. 
    5811  
    5812 Traceback (most recent call last): 
    5813 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5814 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5815 return self._func(self._name, data) 
    5816 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5817 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5818 _model_changed_cb 
    5819 self.update_scatter() 
    5820 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5821 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5822 if not self.visible: 
    5823 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5824 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5825 return self.parent.isVisible() 
    5826 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5827 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5828 return self.container.parentWidget() 
    5829 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5830  
    5831 Error processing trigger "changes": 
    5832 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5833  
    5834 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5835 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5836 return self.container.parentWidget() 
    5837  
    5838 See log for complete Python traceback. 
    5839  
    5840 Traceback (most recent call last): 
    5841 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5842 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5843 return self._func(self._name, data) 
    5844 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5845 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5846 _model_changed_cb 
    5847 self.update_scatter() 
    5848 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5849 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5850 if not self.visible: 
    5851 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5852 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5853 return self.parent.isVisible() 
    5854 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5855 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5856 return self.container.parentWidget() 
    5857 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5858  
    5859 Error processing trigger "changes": 
    5860 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5861  
    5862 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5863 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5864 return self.container.parentWidget() 
    5865  
    5866 See log for complete Python traceback. 
    5867  
    5868 Traceback (most recent call last): 
    5869 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5870 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5871 return self._func(self._name, data) 
    5872 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5873 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5874 _model_changed_cb 
    5875 self.update_scatter() 
    5876 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5877 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5878 if not self.visible: 
    5879 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5880 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5881 return self.parent.isVisible() 
    5882 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5883 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5884 return self.container.parentWidget() 
    5885 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5886  
    5887 Error processing trigger "changes": 
    5888 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5889  
    5890 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5891 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5892 return self.container.parentWidget() 
    5893  
    5894 See log for complete Python traceback. 
    5895  
    5896 Traceback (most recent call last): 
    5897 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5898 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5899 return self._func(self._name, data) 
    5900 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5901 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5902 _model_changed_cb 
    5903 self.update_scatter() 
    5904 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5905 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5906 if not self.visible: 
    5907 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5908 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5909 return self.parent.isVisible() 
    5910 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5911 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5912 return self.container.parentWidget() 
    5913 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5914  
    5915 Error processing trigger "changes": 
    5916 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5917  
    5918 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5919 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5920 return self.container.parentWidget() 
    5921  
    5922 See log for complete Python traceback. 
    5923  
    5924 Traceback (most recent call last): 
    5925 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5926 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5927 return self._func(self._name, data) 
    5928 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5929 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5930 _model_changed_cb 
    5931 self.update_scatter() 
    5932 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5933 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5934 if not self.visible: 
    5935 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5936 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5937 return self.parent.isVisible() 
    5938 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5939 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5940 return self.container.parentWidget() 
    5941 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5942  
    5943 Error processing trigger "changes": 
    5944 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5945  
    5946 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5947 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5948 return self.container.parentWidget() 
    5949  
    5950 See log for complete Python traceback. 
    5951  
    5952 Traceback (most recent call last): 
    5953 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5954 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5955 return self._func(self._name, data) 
    5956 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5957 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5958 _model_changed_cb 
    5959 self.update_scatter() 
    5960 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5961 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5962 if not self.visible: 
    5963 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5964 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5965 return self.parent.isVisible() 
    5966 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5967 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5968 return self.container.parentWidget() 
    5969 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5970  
    5971 Error processing trigger "changes": 
    5972 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5973  
    5974 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5975 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5976 return self.container.parentWidget() 
    5977  
    5978 See log for complete Python traceback. 
    5979  
    5980 Traceback (most recent call last): 
    5981 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    5982 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5983 return self._func(self._name, data) 
    5984 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5985 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    5986 _model_changed_cb 
    5987 self.update_scatter() 
    5988 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5989 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    5990 if not self.visible: 
    5991 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5992 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    5993 return self.parent.isVisible() 
    5994 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    5995 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    5996 return self.container.parentWidget() 
    5997 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    5998  
    5999 Error processing trigger "changes": 
    6000 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6001  
    6002 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6003 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6004 return self.container.parentWidget() 
    6005  
    6006 See log for complete Python traceback. 
    6007  
    6008 Traceback (most recent call last): 
    6009 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6010 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6011 return self._func(self._name, data) 
    6012 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6013 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6014 _model_changed_cb 
    6015 self.update_scatter() 
    6016 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6017 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6018 if not self.visible: 
    6019 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6020 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6021 return self.parent.isVisible() 
    6022 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6023 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6024 return self.container.parentWidget() 
    6025 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6026  
    6027 Error processing trigger "changes": 
    6028 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6029  
    6030 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6031 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6032 return self.container.parentWidget() 
    6033  
    6034 See log for complete Python traceback. 
    6035  
    6036 Traceback (most recent call last): 
    6037 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6038 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6039 return self._func(self._name, data) 
    6040 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6041 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6042 _model_changed_cb 
    6043 self.update_scatter() 
    6044 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6045 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6046 if not self.visible: 
    6047 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6048 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6049 return self.parent.isVisible() 
    6050 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6051 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6052 return self.container.parentWidget() 
    6053 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6054  
    6055 Error processing trigger "changes": 
    6056 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6057  
    6058 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6059 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6060 return self.container.parentWidget() 
    6061  
    6062 See log for complete Python traceback. 
    6063  
    6064 Traceback (most recent call last): 
    6065 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6066 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6067 return self._func(self._name, data) 
    6068 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6069 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6070 _model_changed_cb 
    6071 self.update_scatter() 
    6072 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6073 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6074 if not self.visible: 
    6075 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6076 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6077 return self.parent.isVisible() 
    6078 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6079 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6080 return self.container.parentWidget() 
    6081 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6082  
    6083 Error processing trigger "changes": 
    6084 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6085  
    6086 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6087 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6088 return self.container.parentWidget() 
    6089  
    6090 See log for complete Python traceback. 
    6091  
    6092 Traceback (most recent call last): 
    6093 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6094 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6095 return self._func(self._name, data) 
    6096 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6097 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6098 _model_changed_cb 
    6099 self.update_scatter() 
    6100 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6101 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6102 if not self.visible: 
    6103 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6104 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6105 return self.parent.isVisible() 
    6106 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6107 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6108 return self.container.parentWidget() 
    6109 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6110  
    6111 Error processing trigger "changes": 
    6112 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6113  
    6114 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6115 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6116 return self.container.parentWidget() 
    6117  
    6118 See log for complete Python traceback. 
    6119  
    6120 Traceback (most recent call last): 
    6121 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6122 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6123 return self._func(self._name, data) 
    6124 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6125 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6126 _model_changed_cb 
    6127 self.update_scatter() 
    6128 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6129 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6130 if not self.visible: 
    6131 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6132 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6133 return self.parent.isVisible() 
    6134 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6135 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6136 return self.container.parentWidget() 
    6137 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6138  
    6139 Error processing trigger "changes": 
    6140 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6141  
    6142 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6143 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6144 return self.container.parentWidget() 
    6145  
    6146 See log for complete Python traceback. 
    6147  
    6148 Traceback (most recent call last): 
    6149 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6150 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6151 return self._func(self._name, data) 
    6152 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6153 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6154 _model_changed_cb 
    6155 self.update_scatter() 
    6156 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6157 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6158 if not self.visible: 
    6159 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6160 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6161 return self.parent.isVisible() 
    6162 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6163 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6164 return self.container.parentWidget() 
    6165 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6166  
    6167 Error processing trigger "changes": 
    6168 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6169  
    6170 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6171 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6172 return self.container.parentWidget() 
    6173  
    6174 See log for complete Python traceback. 
    6175  
    6176 Traceback (most recent call last): 
    6177 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6178 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6179 return self._func(self._name, data) 
    6180 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6181 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6182 _model_changed_cb 
    6183 self.update_scatter() 
    6184 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6185 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6186 if not self.visible: 
    6187 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6188 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6189 return self.parent.isVisible() 
    6190 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6191 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6192 return self.container.parentWidget() 
    6193 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6194  
    6195 Error processing trigger "changes": 
    6196 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6197  
    6198 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6199 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6200 return self.container.parentWidget() 
    6201  
    6202 See log for complete Python traceback. 
    6203  
    6204 Traceback (most recent call last): 
    6205 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6206 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6207 return self._func(self._name, data) 
    6208 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6209 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6210 _model_changed_cb 
    6211 self.update_scatter() 
    6212 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6213 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6214 if not self.visible: 
    6215 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6216 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6217 return self.parent.isVisible() 
    6218 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6219 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6220 return self.container.parentWidget() 
    6221 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6222  
    6223 Error processing trigger "changes": 
    6224 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6225  
    6226 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6227 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6228 return self.container.parentWidget() 
    6229  
    6230 See log for complete Python traceback. 
    6231  
    6232 Traceback (most recent call last): 
    6233 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6234 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6235 return self._func(self._name, data) 
    6236 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6237 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6238 _model_changed_cb 
    6239 self.update_scatter() 
    6240 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6241 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6242 if not self.visible: 
    6243 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6244 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6245 return self.parent.isVisible() 
    6246 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6247 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6248 return self.container.parentWidget() 
    6249 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6250  
    6251 Error processing trigger "changes": 
    6252 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6253  
    6254 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6255 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6256 return self.container.parentWidget() 
    6257  
    6258 See log for complete Python traceback. 
    6259  
    6260 Traceback (most recent call last): 
    6261 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6262 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6263 return self._func(self._name, data) 
    6264 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6265 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6266 _model_changed_cb 
    6267 self.update_scatter() 
    6268 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6269 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6270 if not self.visible: 
    6271 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6272 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6273 return self.parent.isVisible() 
    6274 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6275 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6276 return self.container.parentWidget() 
    6277 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6278  
    6279 Error processing trigger "changes": 
    6280 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6281  
    6282 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6283 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6284 return self.container.parentWidget() 
    6285  
    6286 See log for complete Python traceback. 
    6287  
    6288 Traceback (most recent call last): 
    6289 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6290 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6291 return self._func(self._name, data) 
    6292 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6293 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6294 _model_changed_cb 
    6295 self.update_scatter() 
    6296 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6297 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6298 if not self.visible: 
    6299 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6300 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6301 return self.parent.isVisible() 
    6302 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6303 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6304 return self.container.parentWidget() 
    6305 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6306  
    6307 Error processing trigger "changes": 
    6308 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6309  
    6310 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6311 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6312 return self.container.parentWidget() 
    6313  
    6314 See log for complete Python traceback. 
    6315  
    6316 Traceback (most recent call last): 
    6317 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6318 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6319 return self._func(self._name, data) 
    6320 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6321 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6322 _model_changed_cb 
    6323 self.update_scatter() 
    6324 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6325 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6326 if not self.visible: 
    6327 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6328 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6329 return self.parent.isVisible() 
    6330 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6331 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6332 return self.container.parentWidget() 
    6333 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6334  
    6335 Error processing trigger "changes": 
    6336 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6337  
    6338 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6339 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6340 return self.container.parentWidget() 
    6341  
    6342 See log for complete Python traceback. 
    6343  
    6344 Traceback (most recent call last): 
    6345 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6346 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6347 return self._func(self._name, data) 
    6348 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6349 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6350 _model_changed_cb 
    6351 self.update_scatter() 
    6352 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6353 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6354 if not self.visible: 
    6355 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6356 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6357 return self.parent.isVisible() 
    6358 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6359 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6360 return self.container.parentWidget() 
    6361 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6362  
    6363 Error processing trigger "changes": 
    6364 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6365  
    6366 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6367 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6368 return self.container.parentWidget() 
    6369  
    6370 See log for complete Python traceback. 
    6371  
    6372 Traceback (most recent call last): 
    6373 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6374 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6375 return self._func(self._name, data) 
    6376 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6377 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6378 _model_changed_cb 
    6379 self.update_scatter() 
    6380 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6381 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6382 if not self.visible: 
    6383 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6384 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6385 return self.parent.isVisible() 
    6386 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6387 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6388 return self.container.parentWidget() 
    6389 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6390  
    6391 Error processing trigger "changes": 
    6392 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6393  
    6394 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6395 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6396 return self.container.parentWidget() 
    6397  
    6398 See log for complete Python traceback. 
    6399  
    6400 Traceback (most recent call last): 
    6401 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6402 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6403 return self._func(self._name, data) 
    6404 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6405 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6406 _model_changed_cb 
    6407 self.update_scatter() 
    6408 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6409 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6410 if not self.visible: 
    6411 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6412 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6413 return self.parent.isVisible() 
    6414 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6415 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6416 return self.container.parentWidget() 
    6417 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6418  
    6419 Error processing trigger "changes": 
    6420 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6421  
    6422 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6423 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6424 return self.container.parentWidget() 
    6425  
    6426 See log for complete Python traceback. 
    6427  
    6428 Traceback (most recent call last): 
    6429 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6430 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6431 return self._func(self._name, data) 
    6432 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6433 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6434 _model_changed_cb 
    6435 self.update_scatter() 
    6436 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6437 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6438 if not self.visible: 
    6439 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6440 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6441 return self.parent.isVisible() 
    6442 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6443 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6444 return self.container.parentWidget() 
    6445 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6446  
    6447 Error processing trigger "changes": 
    6448 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6449  
    6450 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6451 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6452 return self.container.parentWidget() 
    6453  
    6454 See log for complete Python traceback. 
    6455  
    6456 Traceback (most recent call last): 
    6457 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6458 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6459 return self._func(self._name, data) 
    6460 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6461 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6462 _model_changed_cb 
    6463 self.update_scatter() 
    6464 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6465 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6466 if not self.visible: 
    6467 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6468 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6469 return self.parent.isVisible() 
    6470 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6471 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6472 return self.container.parentWidget() 
    6473 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6474  
    6475 Error processing trigger "changes": 
    6476 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6477  
    6478 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6479 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6480 return self.container.parentWidget() 
    6481  
    6482 See log for complete Python traceback. 
    6483  
    6484 Traceback (most recent call last): 
    6485 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6486 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6487 return self._func(self._name, data) 
    6488 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6489 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6490 _model_changed_cb 
    6491 self.update_scatter() 
    6492 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6493 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6494 if not self.visible: 
    6495 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6496 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6497 return self.parent.isVisible() 
    6498 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6499 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6500 return self.container.parentWidget() 
    6501 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6502  
    6503 Error processing trigger "changes": 
    6504 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6505  
    6506 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6507 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6508 return self.container.parentWidget() 
    6509  
    6510 See log for complete Python traceback. 
    6511  
    6512 Traceback (most recent call last): 
    6513 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6514 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6515 return self._func(self._name, data) 
    6516 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6517 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6518 _model_changed_cb 
    6519 self.update_scatter() 
    6520 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6521 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6522 if not self.visible: 
    6523 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6524 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6525 return self.parent.isVisible() 
    6526 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6527 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6528 return self.container.parentWidget() 
    6529 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6530  
    6531 Error processing trigger "changes": 
    6532 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6533  
    6534 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6535 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6536 return self.container.parentWidget() 
    6537  
    6538 See log for complete Python traceback. 
    6539  
    6540 Traceback (most recent call last): 
    6541 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6542 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6543 return self._func(self._name, data) 
    6544 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6545 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6546 _model_changed_cb 
    6547 self.update_scatter() 
    6548 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6549 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6550 if not self.visible: 
    6551 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6552 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6553 return self.parent.isVisible() 
    6554 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6555 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6556 return self.container.parentWidget() 
    6557 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6558  
    6559 Error processing trigger "changes": 
    6560 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6561  
    6562 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6563 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6564 return self.container.parentWidget() 
    6565  
    6566 See log for complete Python traceback. 
    6567  
    6568 Traceback (most recent call last): 
    6569 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6570 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6571 return self._func(self._name, data) 
    6572 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6573 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6574 _model_changed_cb 
    6575 self.update_scatter() 
    6576 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6577 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6578 if not self.visible: 
    6579 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6580 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6581 return self.parent.isVisible() 
    6582 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6583 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6584 return self.container.parentWidget() 
    6585 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6586  
    6587 Error processing trigger "changes": 
    6588 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6589  
    6590 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6591 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6592 return self.container.parentWidget() 
    6593  
    6594 See log for complete Python traceback. 
    6595  
    6596 Traceback (most recent call last): 
    6597 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6598 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6599 return self._func(self._name, data) 
    6600 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6601 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6602 _model_changed_cb 
    6603 self.update_scatter() 
    6604 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6605 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6606 if not self.visible: 
    6607 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6608 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6609 return self.parent.isVisible() 
    6610 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6611 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6612 return self.container.parentWidget() 
    6613 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6614  
    6615 Error processing trigger "changes": 
    6616 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6617  
    6618 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6619 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6620 return self.container.parentWidget() 
    6621  
    6622 See log for complete Python traceback. 
    6623  
    6624 Traceback (most recent call last): 
    6625 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6626 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6627 return self._func(self._name, data) 
    6628 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6629 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6630 _model_changed_cb 
    6631 self.update_scatter() 
    6632 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6633 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6634 if not self.visible: 
    6635 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6636 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6637 return self.parent.isVisible() 
    6638 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6639 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6640 return self.container.parentWidget() 
    6641 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6642  
    6643 Error processing trigger "changes": 
    6644 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6645  
    6646 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6647 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6648 return self.container.parentWidget() 
    6649  
    6650 See log for complete Python traceback. 
    6651  
    6652 Traceback (most recent call last): 
    6653 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6654 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6655 return self._func(self._name, data) 
    6656 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6657 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6658 _model_changed_cb 
    6659 self.update_scatter() 
    6660 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6661 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6662 if not self.visible: 
    6663 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6664 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6665 return self.parent.isVisible() 
    6666 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6667 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6668 return self.container.parentWidget() 
    6669 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6670  
    6671 Error processing trigger "changes": 
    6672 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6673  
    6674 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6675 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6676 return self.container.parentWidget() 
    6677  
    6678 See log for complete Python traceback. 
    6679  
    6680 Traceback (most recent call last): 
    6681 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6682 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6683 return self._func(self._name, data) 
    6684 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6685 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6686 _model_changed_cb 
    6687 self.update_scatter() 
    6688 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6689 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6690 if not self.visible: 
    6691 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6692 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6693 return self.parent.isVisible() 
    6694 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6695 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6696 return self.container.parentWidget() 
    6697 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6698  
    6699 Error processing trigger "changes": 
    6700 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6701  
    6702 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6703 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6704 return self.container.parentWidget() 
    6705  
    6706 See log for complete Python traceback. 
    6707  
    6708 Traceback (most recent call last): 
    6709 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6710 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6711 return self._func(self._name, data) 
    6712 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6713 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6714 _model_changed_cb 
    6715 self.update_scatter() 
    6716 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6717 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6718 if not self.visible: 
    6719 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6720 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6721 return self.parent.isVisible() 
    6722 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6723 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6724 return self.container.parentWidget() 
    6725 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6726  
    6727 Error processing trigger "changes": 
    6728 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6729  
    6730 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6731 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6732 return self.container.parentWidget() 
    6733  
    6734 See log for complete Python traceback. 
    6735  
    6736 Traceback (most recent call last): 
    6737 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6738 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6739 return self._func(self._name, data) 
    6740 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6741 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6742 _model_changed_cb 
    6743 self.update_scatter() 
    6744 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6745 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6746 if not self.visible: 
    6747 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6748 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6749 return self.parent.isVisible() 
    6750 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6751 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6752 return self.container.parentWidget() 
    6753 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6754  
    6755 Error processing trigger "changes": 
    6756 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6757  
    6758 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6759 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6760 return self.container.parentWidget() 
    6761  
    6762 See log for complete Python traceback. 
    6763  
    6764 Traceback (most recent call last): 
    6765 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6766 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6767 return self._func(self._name, data) 
    6768 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6769 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6770 _model_changed_cb 
    6771 self.update_scatter() 
    6772 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6773 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6774 if not self.visible: 
    6775 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6776 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6777 return self.parent.isVisible() 
    6778 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6779 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6780 return self.container.parentWidget() 
    6781 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6782  
    6783 Error processing trigger "changes": 
    6784 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6785  
    6786 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6787 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6788 return self.container.parentWidget() 
    6789  
    6790 See log for complete Python traceback. 
    6791  
    6792 Traceback (most recent call last): 
    6793 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6794 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6795 return self._func(self._name, data) 
    6796 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6797 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6798 _model_changed_cb 
    6799 self.update_scatter() 
    6800 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6801 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6802 if not self.visible: 
    6803 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6804 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6805 return self.parent.isVisible() 
    6806 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6807 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6808 return self.container.parentWidget() 
    6809 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6810  
    6811 Error processing trigger "changes": 
    6812 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6813  
    6814 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6815 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6816 return self.container.parentWidget() 
    6817  
    6818 See log for complete Python traceback. 
    6819  
    6820 Traceback (most recent call last): 
    6821 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6822 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6823 return self._func(self._name, data) 
    6824 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6825 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6826 _model_changed_cb 
    6827 self.update_scatter() 
    6828 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6829 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6830 if not self.visible: 
    6831 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6832 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6833 return self.parent.isVisible() 
    6834 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6835 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6836 return self.container.parentWidget() 
    6837 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6838  
    6839 Error processing trigger "changes": 
    6840 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6841  
    6842 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6843 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6844 return self.container.parentWidget() 
    6845  
    6846 See log for complete Python traceback. 
    6847  
    6848 Traceback (most recent call last): 
    6849 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6850 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6851 return self._func(self._name, data) 
    6852 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6853 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6854 _model_changed_cb 
    6855 self.update_scatter() 
    6856 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6857 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6858 if not self.visible: 
    6859 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6860 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6861 return self.parent.isVisible() 
    6862 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6863 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6864 return self.container.parentWidget() 
    6865 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6866  
    6867 Error processing trigger "changes": 
    6868 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6869  
    6870 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6871 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6872 return self.container.parentWidget() 
    6873  
    6874 See log for complete Python traceback. 
    6875  
    6876 Traceback (most recent call last): 
    6877 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6878 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6879 return self._func(self._name, data) 
    6880 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6881 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6882 _model_changed_cb 
    6883 self.update_scatter() 
    6884 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6885 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6886 if not self.visible: 
    6887 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6888 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6889 return self.parent.isVisible() 
    6890 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6891 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6892 return self.container.parentWidget() 
    6893 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6894  
    6895 Error processing trigger "changes": 
    6896 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6897  
    6898 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6899 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6900 return self.container.parentWidget() 
    6901  
    6902 See log for complete Python traceback. 
    6903  
    6904 Traceback (most recent call last): 
    6905 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6906 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6907 return self._func(self._name, data) 
    6908 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6909 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6910 _model_changed_cb 
    6911 self.update_scatter() 
    6912 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6913 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6914 if not self.visible: 
    6915 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6916 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6917 return self.parent.isVisible() 
    6918 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6919 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6920 return self.container.parentWidget() 
    6921 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6922  
    6923 Error processing trigger "changes": 
    6924 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6925  
    6926 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6927 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6928 return self.container.parentWidget() 
    6929  
    6930 See log for complete Python traceback. 
    6931  
    6932 Traceback (most recent call last): 
    6933 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6934 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6935 return self._func(self._name, data) 
    6936 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6937 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6938 _model_changed_cb 
    6939 self.update_scatter() 
    6940 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6941 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6942 if not self.visible: 
    6943 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6944 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6945 return self.parent.isVisible() 
    6946 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6947 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6948 return self.container.parentWidget() 
    6949 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6950  
    6951 Error processing trigger "changes": 
    6952 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6953  
    6954 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6955 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6956 return self.container.parentWidget() 
    6957  
    6958 See log for complete Python traceback. 
    6959  
    6960 Traceback (most recent call last): 
    6961 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6962 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6963 return self._func(self._name, data) 
    6964 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6965 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6966 _model_changed_cb 
    6967 self.update_scatter() 
    6968 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6969 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6970 if not self.visible: 
    6971 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6972 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    6973 return self.parent.isVisible() 
    6974 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6975 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6976 return self.container.parentWidget() 
    6977 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6978  
    6979 Error processing trigger "changes": 
    6980 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    6981  
    6982 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6983 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    6984 return self.container.parentWidget() 
    6985  
    6986 See log for complete Python traceback. 
    6987  
    6988 Traceback (most recent call last): 
    6989 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    6990 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6991 return self._func(self._name, data) 
    6992 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6993 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    6994 _model_changed_cb 
    6995 self.update_scatter() 
    6996 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    6997 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    6998 if not self.visible: 
    6999 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7000 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7001 return self.parent.isVisible() 
    7002 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7003 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7004 return self.container.parentWidget() 
    7005 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7006  
    7007 Error processing trigger "changes": 
    7008 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7009  
    7010 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7011 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7012 return self.container.parentWidget() 
    7013  
    7014 See log for complete Python traceback. 
    7015  
    7016 Traceback (most recent call last): 
    7017 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7018 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7019 return self._func(self._name, data) 
    7020 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7021 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7022 _model_changed_cb 
    7023 self.update_scatter() 
    7024 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7025 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7026 if not self.visible: 
    7027 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7028 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7029 return self.parent.isVisible() 
    7030 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7031 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7032 return self.container.parentWidget() 
    7033 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7034  
    7035 Error processing trigger "changes": 
    7036 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7037  
    7038 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7039 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7040 return self.container.parentWidget() 
    7041  
    7042 See log for complete Python traceback. 
    7043  
    7044 Traceback (most recent call last): 
    7045 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7046 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7047 return self._func(self._name, data) 
    7048 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7049 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7050 _model_changed_cb 
    7051 self.update_scatter() 
    7052 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7053 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7054 if not self.visible: 
    7055 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7056 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7057 return self.parent.isVisible() 
    7058 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7059 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7060 return self.container.parentWidget() 
    7061 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7062  
    7063 Error processing trigger "changes": 
    7064 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7065  
    7066 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7067 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7068 return self.container.parentWidget() 
    7069  
    7070 See log for complete Python traceback. 
    7071  
    7072 Traceback (most recent call last): 
    7073 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7074 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7075 return self._func(self._name, data) 
    7076 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7077 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7078 _model_changed_cb 
    7079 self.update_scatter() 
    7080 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7081 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7082 if not self.visible: 
    7083 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7084 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7085 return self.parent.isVisible() 
    7086 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7087 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7088 return self.container.parentWidget() 
    7089 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7090  
    7091 Error processing trigger "changes": 
    7092 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7093  
    7094 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7095 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7096 return self.container.parentWidget() 
    7097  
    7098 See log for complete Python traceback. 
    7099  
    7100 Traceback (most recent call last): 
    7101 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7102 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7103 return self._func(self._name, data) 
    7104 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7105 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7106 _model_changed_cb 
    7107 self.update_scatter() 
    7108 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7109 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7110 if not self.visible: 
    7111 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7112 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7113 return self.parent.isVisible() 
    7114 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7115 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7116 return self.container.parentWidget() 
    7117 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7118  
    7119 Error processing trigger "changes": 
    7120 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7121  
    7122 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7123 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7124 return self.container.parentWidget() 
    7125  
    7126 See log for complete Python traceback. 
    7127  
    7128 Traceback (most recent call last): 
    7129 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7130 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7131 return self._func(self._name, data) 
    7132 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7133 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7134 _model_changed_cb 
    7135 self.update_scatter() 
    7136 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7137 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7138 if not self.visible: 
    7139 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7140 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7141 return self.parent.isVisible() 
    7142 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7143 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7144 return self.container.parentWidget() 
    7145 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7146  
    7147 Error processing trigger "changes": 
    7148 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7149  
    7150 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7151 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7152 return self.container.parentWidget() 
    7153  
    7154 See log for complete Python traceback. 
    7155  
    7156 Traceback (most recent call last): 
    7157 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7158 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7159 return self._func(self._name, data) 
    7160 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7161 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7162 _model_changed_cb 
    7163 self.update_scatter() 
    7164 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7165 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7166 if not self.visible: 
    7167 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7168 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7169 return self.parent.isVisible() 
    7170 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7171 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7172 return self.container.parentWidget() 
    7173 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7174  
    7175 Error processing trigger "changes": 
    7176 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7177  
    7178 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7179 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7180 return self.container.parentWidget() 
    7181  
    7182 See log for complete Python traceback. 
    7183  
    7184 Traceback (most recent call last): 
    7185 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7186 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7187 return self._func(self._name, data) 
    7188 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7189 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7190 _model_changed_cb 
    7191 self.update_scatter() 
    7192 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7193 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7194 if not self.visible: 
    7195 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7196 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7197 return self.parent.isVisible() 
    7198 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7199 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7200 return self.container.parentWidget() 
    7201 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7202  
    7203 Error processing trigger "changes": 
    7204 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7205  
    7206 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7207 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7208 return self.container.parentWidget() 
    7209  
    7210 See log for complete Python traceback. 
    7211  
    7212 Traceback (most recent call last): 
    7213 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7214 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7215 return self._func(self._name, data) 
    7216 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7217 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7218 _model_changed_cb 
    7219 self.update_scatter() 
    7220 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7221 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7222 if not self.visible: 
    7223 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7224 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7225 return self.parent.isVisible() 
    7226 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7227 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7228 return self.container.parentWidget() 
    7229 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7230  
    7231 Error processing trigger "changes": 
    7232 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7233  
    7234 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7235 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7236 return self.container.parentWidget() 
    7237  
    7238 See log for complete Python traceback. 
    7239  
    7240 Traceback (most recent call last): 
    7241 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7242 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7243 return self._func(self._name, data) 
    7244 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7245 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7246 _model_changed_cb 
    7247 self.update_scatter() 
    7248 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7249 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7250 if not self.visible: 
    7251 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7252 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7253 return self.parent.isVisible() 
    7254 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7255 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7256 return self.container.parentWidget() 
    7257 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7258  
    7259 Error processing trigger "changes": 
    7260 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7261  
    7262 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7263 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7264 return self.container.parentWidget() 
    7265  
    7266 See log for complete Python traceback. 
    7267  
    7268 Traceback (most recent call last): 
    7269 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7270 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7271 return self._func(self._name, data) 
    7272 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7273 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7274 _model_changed_cb 
    7275 self.update_scatter() 
    7276 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7277 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7278 if not self.visible: 
    7279 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7280 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7281 return self.parent.isVisible() 
    7282 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7283 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7284 return self.container.parentWidget() 
    7285 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7286  
    7287 Error processing trigger "changes": 
    7288 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7289  
    7290 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7291 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7292 return self.container.parentWidget() 
    7293  
    7294 See log for complete Python traceback. 
    7295  
    7296 Traceback (most recent call last): 
    7297 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7298 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7299 return self._func(self._name, data) 
    7300 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7301 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7302 _model_changed_cb 
    7303 self.update_scatter() 
    7304 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7305 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7306 if not self.visible: 
    7307 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7308 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7309 return self.parent.isVisible() 
    7310 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7311 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7312 return self.container.parentWidget() 
    7313 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7314  
    7315 Error processing trigger "changes": 
    7316 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7317  
    7318 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7319 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7320 return self.container.parentWidget() 
    7321  
    7322 See log for complete Python traceback. 
    7323  
    7324 Traceback (most recent call last): 
    7325 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7326 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7327 return self._func(self._name, data) 
    7328 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7329 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7330 _model_changed_cb 
    7331 self.update_scatter() 
    7332 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7333 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7334 if not self.visible: 
    7335 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7336 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7337 return self.parent.isVisible() 
    7338 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7339 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7340 return self.container.parentWidget() 
    7341 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7342  
    7343 Error processing trigger "changes": 
    7344 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7345  
    7346 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7347 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7348 return self.container.parentWidget() 
    7349  
    7350 See log for complete Python traceback. 
    7351  
    7352 Traceback (most recent call last): 
    7353 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7354 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7355 return self._func(self._name, data) 
    7356 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7357 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7358 _model_changed_cb 
    7359 self.update_scatter() 
    7360 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7361 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7362 if not self.visible: 
    7363 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7364 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7365 return self.parent.isVisible() 
    7366 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7367 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7368 return self.container.parentWidget() 
    7369 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7370  
    7371 Error processing trigger "changes": 
    7372 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7373  
    7374 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7375 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7376 return self.container.parentWidget() 
    7377  
    7378 See log for complete Python traceback. 
    7379  
    7380 Traceback (most recent call last): 
    7381 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7382 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7383 return self._func(self._name, data) 
    7384 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7385 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7386 _model_changed_cb 
    7387 self.update_scatter() 
    7388 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7389 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7390 if not self.visible: 
    7391 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7392 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7393 return self.parent.isVisible() 
    7394 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7395 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7396 return self.container.parentWidget() 
    7397 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7398  
    7399 Error processing trigger "changes": 
    7400 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7401  
    7402 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7403 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7404 return self.container.parentWidget() 
    7405  
    7406 See log for complete Python traceback. 
    7407  
    7408 Traceback (most recent call last): 
    7409 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7410 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7411 return self._func(self._name, data) 
    7412 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7413 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7414 _model_changed_cb 
    7415 self.update_scatter() 
    7416 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7417 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7418 if not self.visible: 
    7419 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7420 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7421 return self.parent.isVisible() 
    7422 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7423 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7424 return self.container.parentWidget() 
    7425 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7426  
    7427 Error processing trigger "changes": 
    7428 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7429  
    7430 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7431 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7432 return self.container.parentWidget() 
    7433  
    7434 See log for complete Python traceback. 
    7435  
    7436 Traceback (most recent call last): 
    7437 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7438 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7439 return self._func(self._name, data) 
    7440 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7441 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7442 _model_changed_cb 
    7443 self.update_scatter() 
    7444 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7445 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7446 if not self.visible: 
    7447 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7448 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7449 return self.parent.isVisible() 
    7450 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7451 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7452 return self.container.parentWidget() 
    7453 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7454  
    7455 Error processing trigger "changes": 
    7456 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7457  
    7458 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7459 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7460 return self.container.parentWidget() 
    7461  
    7462 See log for complete Python traceback. 
    7463  
    7464 Traceback (most recent call last): 
    7465 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7466 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7467 return self._func(self._name, data) 
    7468 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7469 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7470 _model_changed_cb 
    7471 self.update_scatter() 
    7472 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7473 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7474 if not self.visible: 
    7475 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7476 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7477 return self.parent.isVisible() 
    7478 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7479 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7480 return self.container.parentWidget() 
    7481 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7482  
    7483 Error processing trigger "changes": 
    7484 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7485  
    7486 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7487 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7488 return self.container.parentWidget() 
    7489  
    7490 See log for complete Python traceback. 
    7491  
    7492 Traceback (most recent call last): 
    7493 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7494 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7495 return self._func(self._name, data) 
    7496 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7497 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7498 _model_changed_cb 
    7499 self.update_scatter() 
    7500 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7501 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7502 if not self.visible: 
    7503 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7504 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7505 return self.parent.isVisible() 
    7506 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7507 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7508 return self.container.parentWidget() 
    7509 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7510  
    7511 Error processing trigger "changes": 
    7512 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7513  
    7514 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7515 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7516 return self.container.parentWidget() 
    7517  
    7518 See log for complete Python traceback. 
    7519  
    7520 Traceback (most recent call last): 
    7521 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7522 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7523 return self._func(self._name, data) 
    7524 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7525 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7526 _model_changed_cb 
    7527 self.update_scatter() 
    7528 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7529 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7530 if not self.visible: 
    7531 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7532 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7533 return self.parent.isVisible() 
    7534 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7535 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7536 return self.container.parentWidget() 
    7537 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7538  
    7539 Error processing trigger "changes": 
    7540 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7541  
    7542 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7543 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7544 return self.container.parentWidget() 
    7545  
    7546 See log for complete Python traceback. 
    7547  
    7548 Traceback (most recent call last): 
    7549 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7550 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7551 return self._func(self._name, data) 
    7552 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7553 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7554 _model_changed_cb 
    7555 self.update_scatter() 
    7556 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7557 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7558 if not self.visible: 
    7559 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7560 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7561 return self.parent.isVisible() 
    7562 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7563 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7564 return self.container.parentWidget() 
    7565 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7566  
    7567 Error processing trigger "changes": 
    7568 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7569  
    7570 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7571 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7572 return self.container.parentWidget() 
    7573  
    7574 See log for complete Python traceback. 
    7575  
    7576 Traceback (most recent call last): 
    7577 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7578 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7579 return self._func(self._name, data) 
    7580 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7581 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7582 _model_changed_cb 
    7583 self.update_scatter() 
    7584 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7585 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7586 if not self.visible: 
    7587 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7588 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7589 return self.parent.isVisible() 
    7590 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7591 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7592 return self.container.parentWidget() 
    7593 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7594  
    7595 Error processing trigger "changes": 
    7596 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7597  
    7598 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7599 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7600 return self.container.parentWidget() 
    7601  
    7602 See log for complete Python traceback. 
    7603  
    7604 Traceback (most recent call last): 
    7605 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7606 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7607 return self._func(self._name, data) 
    7608 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7609 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7610 _model_changed_cb 
    7611 self.update_scatter() 
    7612 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7613 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7614 if not self.visible: 
    7615 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7616 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7617 return self.parent.isVisible() 
    7618 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7619 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7620 return self.container.parentWidget() 
    7621 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7622  
    7623 Error processing trigger "changes": 
    7624 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7625  
    7626 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7627 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7628 return self.container.parentWidget() 
    7629  
    7630 See log for complete Python traceback. 
    7631  
    7632 Traceback (most recent call last): 
    7633 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7634 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7635 return self._func(self._name, data) 
    7636 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7637 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7638 _model_changed_cb 
    7639 self.update_scatter() 
    7640 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7641 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7642 if not self.visible: 
    7643 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7644 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7645 return self.parent.isVisible() 
    7646 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7647 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7648 return self.container.parentWidget() 
    7649 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7650  
    7651 Error processing trigger "changes": 
    7652 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7653  
    7654 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7655 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7656 return self.container.parentWidget() 
    7657  
    7658 See log for complete Python traceback. 
    7659  
    7660 Traceback (most recent call last): 
    7661 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7662 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7663 return self._func(self._name, data) 
    7664 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7665 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7666 _model_changed_cb 
    7667 self.update_scatter() 
    7668 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7669 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7670 if not self.visible: 
    7671 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7672 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7673 return self.parent.isVisible() 
    7674 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7675 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7676 return self.container.parentWidget() 
    7677 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7678  
    7679 Error processing trigger "changes": 
    7680 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7681  
    7682 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7683 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7684 return self.container.parentWidget() 
    7685  
    7686 See log for complete Python traceback. 
    7687  
    7688 Traceback (most recent call last): 
    7689 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7690 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7691 return self._func(self._name, data) 
    7692 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7693 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7694 _model_changed_cb 
    7695 self.update_scatter() 
    7696 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7697 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7698 if not self.visible: 
    7699 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7700 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7701 return self.parent.isVisible() 
    7702 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7703 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7704 return self.container.parentWidget() 
    7705 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7706  
    7707 Error processing trigger "changes": 
    7708 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7709  
    7710 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7711 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7712 return self.container.parentWidget() 
    7713  
    7714 See log for complete Python traceback. 
    7715  
    7716 Traceback (most recent call last): 
    7717 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7718 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7719 return self._func(self._name, data) 
    7720 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7721 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7722 _model_changed_cb 
    7723 self.update_scatter() 
    7724 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7725 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7726 if not self.visible: 
    7727 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7728 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7729 return self.parent.isVisible() 
    7730 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7731 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7732 return self.container.parentWidget() 
    7733 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7734  
    7735 Error processing trigger "changes": 
    7736 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7737  
    7738 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7739 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7740 return self.container.parentWidget() 
    7741  
    7742 See log for complete Python traceback. 
    7743  
    7744 Traceback (most recent call last): 
    7745 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7746 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7747 return self._func(self._name, data) 
    7748 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7749 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7750 _model_changed_cb 
    7751 self.update_scatter() 
    7752 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7753 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7754 if not self.visible: 
    7755 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7756 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7757 return self.parent.isVisible() 
    7758 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7759 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7760 return self.container.parentWidget() 
    7761 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7762  
    7763 Error processing trigger "changes": 
    7764 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7765  
    7766 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7767 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7768 return self.container.parentWidget() 
    7769  
    7770 See log for complete Python traceback. 
    7771  
    7772 Traceback (most recent call last): 
    7773 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7774 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7775 return self._func(self._name, data) 
    7776 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7777 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7778 _model_changed_cb 
    7779 self.update_scatter() 
    7780 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7781 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7782 if not self.visible: 
    7783 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7784 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7785 return self.parent.isVisible() 
    7786 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7787 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7788 return self.container.parentWidget() 
    7789 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7790  
    7791 Error processing trigger "changes": 
    7792 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7793  
    7794 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7795 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7796 return self.container.parentWidget() 
    7797  
    7798 See log for complete Python traceback. 
    7799  
    7800 Traceback (most recent call last): 
    7801 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7802 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7803 return self._func(self._name, data) 
    7804 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7805 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7806 _model_changed_cb 
    7807 self.update_scatter() 
    7808 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7809 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7810 if not self.visible: 
    7811 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7812 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7813 return self.parent.isVisible() 
    7814 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7815 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7816 return self.container.parentWidget() 
    7817 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7818  
    7819 Error processing trigger "changes": 
    7820 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7821  
    7822 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7823 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7824 return self.container.parentWidget() 
    7825  
    7826 See log for complete Python traceback. 
    7827  
    7828 Traceback (most recent call last): 
    7829 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7830 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7831 return self._func(self._name, data) 
    7832 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7833 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7834 _model_changed_cb 
    7835 self.update_scatter() 
    7836 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7837 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7838 if not self.visible: 
    7839 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7840 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7841 return self.parent.isVisible() 
    7842 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7843 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7844 return self.container.parentWidget() 
    7845 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7846  
    7847 Error processing trigger "changes": 
    7848 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7849  
    7850 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7851 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7852 return self.container.parentWidget() 
    7853  
    7854 See log for complete Python traceback. 
    7855  
    7856 Traceback (most recent call last): 
    7857 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7858 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7859 return self._func(self._name, data) 
    7860 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7861 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7862 _model_changed_cb 
    7863 self.update_scatter() 
    7864 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7865 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7866 if not self.visible: 
    7867 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7868 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7869 return self.parent.isVisible() 
    7870 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7871 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7872 return self.container.parentWidget() 
    7873 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7874  
    7875 Error processing trigger "changes": 
    7876 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7877  
    7878 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7879 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7880 return self.container.parentWidget() 
    7881  
    7882 See log for complete Python traceback. 
    7883  
    7884 Traceback (most recent call last): 
    7885 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7886 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7887 return self._func(self._name, data) 
    7888 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7889 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7890 _model_changed_cb 
    7891 self.update_scatter() 
    7892 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7893 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7894 if not self.visible: 
    7895 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7896 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7897 return self.parent.isVisible() 
    7898 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7899 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7900 return self.container.parentWidget() 
    7901 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7902  
    7903 Error processing trigger "changes": 
    7904 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7905  
    7906 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7907 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7908 return self.container.parentWidget() 
    7909  
    7910 See log for complete Python traceback. 
    7911  
    7912 Traceback (most recent call last): 
    7913 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7914 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7915 return self._func(self._name, data) 
    7916 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7917 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7918 _model_changed_cb 
    7919 self.update_scatter() 
    7920 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7921 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7922 if not self.visible: 
    7923 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7924 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7925 return self.parent.isVisible() 
    7926 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7927 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7928 return self.container.parentWidget() 
    7929 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7930  
    7931 Error processing trigger "changes": 
    7932 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7933  
    7934 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7935 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7936 return self.container.parentWidget() 
    7937  
    7938 See log for complete Python traceback. 
    7939  
    7940 Traceback (most recent call last): 
    7941 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7942 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7943 return self._func(self._name, data) 
    7944 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7945 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7946 _model_changed_cb 
    7947 self.update_scatter() 
    7948 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7949 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7950 if not self.visible: 
    7951 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7952 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7953 return self.parent.isVisible() 
    7954 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7955 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7956 return self.container.parentWidget() 
    7957 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7958  
    7959 Error processing trigger "changes": 
    7960 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7961  
    7962 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7963 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7964 return self.container.parentWidget() 
    7965  
    7966 See log for complete Python traceback. 
    7967  
    7968 Traceback (most recent call last): 
    7969 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7970 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7971 return self._func(self._name, data) 
    7972 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7973 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    7974 _model_changed_cb 
    7975 self.update_scatter() 
    7976 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7977 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    7978 if not self.visible: 
    7979 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7980 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    7981 return self.parent.isVisible() 
    7982 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7983 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7984 return self.container.parentWidget() 
    7985 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7986  
    7987 Error processing trigger "changes": 
    7988 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    7989  
    7990 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    7991 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    7992 return self.container.parentWidget() 
    7993  
    7994 See log for complete Python traceback. 
    7995  
    7996 Traceback (most recent call last): 
    7997 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    7998 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7999 return self._func(self._name, data) 
    8000 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8001 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8002 _model_changed_cb 
    8003 self.update_scatter() 
    8004 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8005 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8006 if not self.visible: 
    8007 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8008 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8009 return self.parent.isVisible() 
    8010 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8011 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8012 return self.container.parentWidget() 
    8013 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8014  
    8015 Error processing trigger "changes": 
    8016 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8017  
    8018 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8019 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8020 return self.container.parentWidget() 
    8021  
    8022 See log for complete Python traceback. 
    8023  
    8024 Traceback (most recent call last): 
    8025 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8026 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8027 return self._func(self._name, data) 
    8028 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8029 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8030 _model_changed_cb 
    8031 self.update_scatter() 
    8032 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8033 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8034 if not self.visible: 
    8035 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8036 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8037 return self.parent.isVisible() 
    8038 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8039 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8040 return self.container.parentWidget() 
    8041 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8042  
    8043 Error processing trigger "changes": 
    8044 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8045  
    8046 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8047 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8048 return self.container.parentWidget() 
    8049  
    8050 See log for complete Python traceback. 
    8051  
    8052 Traceback (most recent call last): 
    8053 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8054 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8055 return self._func(self._name, data) 
    8056 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8057 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8058 _model_changed_cb 
    8059 self.update_scatter() 
    8060 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8061 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8062 if not self.visible: 
    8063 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8064 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8065 return self.parent.isVisible() 
    8066 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8067 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8068 return self.container.parentWidget() 
    8069 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8070  
    8071 Error processing trigger "changes": 
    8072 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8073  
    8074 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8075 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8076 return self.container.parentWidget() 
    8077  
    8078 See log for complete Python traceback. 
    8079  
    8080 Traceback (most recent call last): 
    8081 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8082 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8083 return self._func(self._name, data) 
    8084 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8085 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8086 _model_changed_cb 
    8087 self.update_scatter() 
    8088 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8089 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8090 if not self.visible: 
    8091 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8092 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8093 return self.parent.isVisible() 
    8094 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8095 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8096 return self.container.parentWidget() 
    8097 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8098  
    8099 Error processing trigger "changes": 
    8100 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8101  
    8102 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8103 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8104 return self.container.parentWidget() 
    8105  
    8106 See log for complete Python traceback. 
    8107  
    8108 Traceback (most recent call last): 
    8109 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8110 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8111 return self._func(self._name, data) 
    8112 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8113 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8114 _model_changed_cb 
    8115 self.update_scatter() 
    8116 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8117 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8118 if not self.visible: 
    8119 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8120 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8121 return self.parent.isVisible() 
    8122 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8123 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8124 return self.container.parentWidget() 
    8125 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8126  
    8127 Error processing trigger "changes": 
    8128 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8129  
    8130 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8131 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8132 return self.container.parentWidget() 
    8133  
    8134 See log for complete Python traceback. 
    8135  
    8136 Traceback (most recent call last): 
    8137 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8138 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8139 return self._func(self._name, data) 
    8140 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8141 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8142 _model_changed_cb 
    8143 self.update_scatter() 
    8144 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8145 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8146 if not self.visible: 
    8147 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8148 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8149 return self.parent.isVisible() 
    8150 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8151 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8152 return self.container.parentWidget() 
    8153 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8154  
    8155 Error processing trigger "changes": 
    8156 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8157  
    8158 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8159 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8160 return self.container.parentWidget() 
    8161  
    8162 See log for complete Python traceback. 
    8163  
    8164 Traceback (most recent call last): 
    8165 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8166 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8167 return self._func(self._name, data) 
    8168 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8169 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8170 _model_changed_cb 
    8171 self.update_scatter() 
    8172 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8173 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8174 if not self.visible: 
    8175 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8176 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8177 return self.parent.isVisible() 
    8178 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8179 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8180 return self.container.parentWidget() 
    8181 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8182  
    8183 Error processing trigger "changes": 
    8184 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8185  
    8186 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8187 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8188 return self.container.parentWidget() 
    8189  
    8190 See log for complete Python traceback. 
    8191  
    8192 Traceback (most recent call last): 
    8193 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8194 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8195 return self._func(self._name, data) 
    8196 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8197 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8198 _model_changed_cb 
    8199 self.update_scatter() 
    8200 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8201 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8202 if not self.visible: 
    8203 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8204 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8205 return self.parent.isVisible() 
    8206 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8207 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8208 return self.container.parentWidget() 
    8209 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8210  
    8211 Error processing trigger "changes": 
    8212 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8213  
    8214 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8215 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8216 return self.container.parentWidget() 
    8217  
    8218 See log for complete Python traceback. 
    8219  
    8220 Traceback (most recent call last): 
    8221 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8222 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8223 return self._func(self._name, data) 
    8224 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8225 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8226 _model_changed_cb 
    8227 self.update_scatter() 
    8228 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8229 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8230 if not self.visible: 
    8231 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8232 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8233 return self.parent.isVisible() 
    8234 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8235 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8236 return self.container.parentWidget() 
    8237 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8238  
    8239 Error processing trigger "changes": 
    8240 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8241  
    8242 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8243 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8244 return self.container.parentWidget() 
    8245  
    8246 See log for complete Python traceback. 
    8247  
    8248 Traceback (most recent call last): 
    8249 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8250 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8251 return self._func(self._name, data) 
    8252 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8253 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8254 _model_changed_cb 
    8255 self.update_scatter() 
    8256 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8257 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8258 if not self.visible: 
    8259 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8260 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8261 return self.parent.isVisible() 
    8262 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8263 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8264 return self.container.parentWidget() 
    8265 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8266  
    8267 Error processing trigger "changes": 
    8268 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8269  
    8270 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8271 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8272 return self.container.parentWidget() 
    8273  
    8274 See log for complete Python traceback. 
    8275  
    8276 Traceback (most recent call last): 
    8277 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8278 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8279 return self._func(self._name, data) 
    8280 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8281 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8282 _model_changed_cb 
    8283 self.update_scatter() 
    8284 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8285 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8286 if not self.visible: 
    8287 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8288 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8289 return self.parent.isVisible() 
    8290 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8291 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8292 return self.container.parentWidget() 
    8293 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8294  
    8295 Error processing trigger "changes": 
    8296 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8297  
    8298 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8299 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8300 return self.container.parentWidget() 
    8301  
    8302 See log for complete Python traceback. 
    8303  
    8304 Traceback (most recent call last): 
    8305 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8306 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8307 return self._func(self._name, data) 
    8308 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8309 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8310 _model_changed_cb 
    8311 self.update_scatter() 
    8312 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8313 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8314 if not self.visible: 
    8315 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8316 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8317 return self.parent.isVisible() 
    8318 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8319 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8320 return self.container.parentWidget() 
    8321 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8322  
    8323 Error processing trigger "changes": 
    8324 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8325  
    8326 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8327 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8328 return self.container.parentWidget() 
    8329  
    8330 See log for complete Python traceback. 
    8331  
    8332 Traceback (most recent call last): 
    8333 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8334 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8335 return self._func(self._name, data) 
    8336 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8337 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8338 _model_changed_cb 
    8339 self.update_scatter() 
    8340 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8341 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8342 if not self.visible: 
    8343 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8344 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8345 return self.parent.isVisible() 
    8346 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8347 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8348 return self.container.parentWidget() 
    8349 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8350  
    8351 Error processing trigger "changes": 
    8352 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8353  
    8354 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8355 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8356 return self.container.parentWidget() 
    8357  
    8358 See log for complete Python traceback. 
    8359  
    8360 Traceback (most recent call last): 
    8361 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8362 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8363 return self._func(self._name, data) 
    8364 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8365 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8366 _model_changed_cb 
    8367 self.update_scatter() 
    8368 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8369 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8370 if not self.visible: 
    8371 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8372 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8373 return self.parent.isVisible() 
    8374 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8375 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8376 return self.container.parentWidget() 
    8377 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8378  
    8379 Error processing trigger "changes": 
    8380 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8381  
    8382 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8383 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8384 return self.container.parentWidget() 
    8385  
    8386 See log for complete Python traceback. 
    8387  
    8388 Traceback (most recent call last): 
    8389 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8390 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8391 return self._func(self._name, data) 
    8392 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8393 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8394 _model_changed_cb 
    8395 self.update_scatter() 
    8396 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8397 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8398 if not self.visible: 
    8399 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8400 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8401 return self.parent.isVisible() 
    8402 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8403 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8404 return self.container.parentWidget() 
    8405 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8406  
    8407 Error processing trigger "changes": 
    8408 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8409  
    8410 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8411 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8412 return self.container.parentWidget() 
    8413  
    8414 See log for complete Python traceback. 
    8415  
    8416 Traceback (most recent call last): 
    8417 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8418 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8419 return self._func(self._name, data) 
    8420 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8421 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8422 _model_changed_cb 
    8423 self.update_scatter() 
    8424 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8425 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8426 if not self.visible: 
    8427 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8428 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8429 return self.parent.isVisible() 
    8430 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8431 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8432 return self.container.parentWidget() 
    8433 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8434  
    8435 Error processing trigger "changes": 
    8436 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8437  
    8438 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8439 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8440 return self.container.parentWidget() 
    8441  
    8442 See log for complete Python traceback. 
    8443  
    8444 Traceback (most recent call last): 
    8445 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8446 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8447 return self._func(self._name, data) 
    8448 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8449 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8450 _model_changed_cb 
    8451 self.update_scatter() 
    8452 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8453 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8454 if not self.visible: 
    8455 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8456 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8457 return self.parent.isVisible() 
    8458 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8459 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8460 return self.container.parentWidget() 
    8461 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8462  
    8463 Error processing trigger "changes": 
    8464 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8465  
    8466 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8467 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8468 return self.container.parentWidget() 
    8469  
    8470 See log for complete Python traceback. 
    8471  
    8472 Traceback (most recent call last): 
    8473 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8474 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8475 return self._func(self._name, data) 
    8476 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8477 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8478 _model_changed_cb 
    8479 self.update_scatter() 
    8480 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8481 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8482 if not self.visible: 
    8483 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8484 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8485 return self.parent.isVisible() 
    8486 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8487 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8488 return self.container.parentWidget() 
    8489 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8490  
    8491 Error processing trigger "changes": 
    8492 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8493  
    8494 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8495 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8496 return self.container.parentWidget() 
    8497  
    8498 See log for complete Python traceback. 
    8499  
    8500 Traceback (most recent call last): 
    8501 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8502 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8503 return self._func(self._name, data) 
    8504 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8505 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8506 _model_changed_cb 
    8507 self.update_scatter() 
    8508 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8509 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8510 if not self.visible: 
    8511 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8512 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8513 return self.parent.isVisible() 
    8514 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8515 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8516 return self.container.parentWidget() 
    8517 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8518  
    8519 Error processing trigger "changes": 
    8520 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8521  
    8522 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8523 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8524 return self.container.parentWidget() 
    8525  
    8526 See log for complete Python traceback. 
    8527  
    8528 Traceback (most recent call last): 
    8529 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8530 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8531 return self._func(self._name, data) 
    8532 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8533 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8534 _model_changed_cb 
    8535 self.update_scatter() 
    8536 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8537 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8538 if not self.visible: 
    8539 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8540 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8541 return self.parent.isVisible() 
    8542 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8543 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8544 return self.container.parentWidget() 
    8545 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8546  
    8547 Error processing trigger "changes": 
    8548 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8549  
    8550 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8551 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8552 return self.container.parentWidget() 
    8553  
    8554 See log for complete Python traceback. 
    8555  
    8556 Traceback (most recent call last): 
    8557 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8558 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8559 return self._func(self._name, data) 
    8560 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8561 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8562 _model_changed_cb 
    8563 self.update_scatter() 
    8564 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8565 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8566 if not self.visible: 
    8567 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8568 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8569 return self.parent.isVisible() 
    8570 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8571 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8572 return self.container.parentWidget() 
    8573 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8574  
    8575 Error processing trigger "changes": 
    8576 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8577  
    8578 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8579 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8580 return self.container.parentWidget() 
    8581  
    8582 See log for complete Python traceback. 
    8583  
    8584 Traceback (most recent call last): 
    8585 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8586 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8587 return self._func(self._name, data) 
    8588 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8589 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8590 _model_changed_cb 
    8591 self.update_scatter() 
    8592 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8593 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8594 if not self.visible: 
    8595 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8596 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8597 return self.parent.isVisible() 
    8598 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8599 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8600 return self.container.parentWidget() 
    8601 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8602  
    8603 Error processing trigger "changes": 
    8604 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8605  
    8606 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8607 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8608 return self.container.parentWidget() 
    8609  
    8610 See log for complete Python traceback. 
    8611  
    8612 Traceback (most recent call last): 
    8613 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8614 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8615 return self._func(self._name, data) 
    8616 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8617 packages/chimerax/isolde/validation/ramaplot.py", line 275, in
    8618 _model_changed_cb 
    8619 self.update_scatter() 
    8620 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8621 packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter 
    8622 if not self.visible: 
    8623 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8624 packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible 
    8625 return self.parent.isVisible() 
    8626 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8627 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8628 return self.container.parentWidget() 
    8629 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8630  
    8631 Error processing trigger "changes": 
    8632 RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted 
    8633  
    8634 File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
    8635 packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent 
    8636 return self.container.parentWidget() 
    8637  
    8638 See log for complete Python traceback. 
    8639  
    8640 Traceback (most recent call last): 
     671[nuked center of log for length]
     672
    8641673File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    8642674packages/chimerax/core/triggerset.py", line 130, in invoke