2644 | | Traceback (most recent call last): |
2645 | | File |
2646 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2647 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
2648 | | return self._func(self._name, data) |
2649 | | File |
2650 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2651 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
2652 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
2653 | | File |
2654 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2655 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
2656 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
2657 | | File |
2658 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2659 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
2660 | | self.seq_canvas.assoc_mod(aseq) |
2661 | | File |
2662 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2663 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
2664 | | self.lead_block.assoc_mod(aseq) |
2665 | | File |
2666 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2667 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
2668 | | label_text.setFont(self._label_font(aseq)) |
2669 | | File |
2670 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2671 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
2672 | | if self.has_associated_structures(line): |
2673 | | File |
2674 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2675 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2676 | | has_associated_structures |
2677 | | and [chain for chain in line.match_maps.keys() if not |
2678 | | chain.structure.deleted]: |
2679 | | File |
2680 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2681 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2682 | | and [chain for chain in line.match_maps.keys() if not |
2683 | | chain.structure.deleted]: |
2684 | | File |
2685 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2686 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
2687 | | return look_in_class._attr_registration.get_attr(attr_name) |
2688 | | File |
2689 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2690 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2691 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2692 | | (self.class_.__name__, attr_name)) from None |
2693 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2694 | | |
2695 | | Error processing trigger "changes done": |
2696 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2697 | | |
2698 | | File |
2699 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2700 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2701 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2702 | | (self.class_.__name__, attr_name)) from None |
2703 | | |
2704 | | See log for complete Python traceback. |
2705 | | |
2706 | | Traceback (most recent call last): |
2707 | | File |
2708 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2709 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
2710 | | return self._func(self._name, data) |
2711 | | File |
2712 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2713 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
2714 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
2715 | | File |
2716 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2717 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
2718 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
2719 | | File |
2720 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2721 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
2722 | | self.seq_canvas.assoc_mod(aseq) |
2723 | | File |
2724 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2725 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
2726 | | self.lead_block.assoc_mod(aseq) |
2727 | | File |
2728 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2729 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
2730 | | label_text.setFont(self._label_font(aseq)) |
2731 | | File |
2732 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2733 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
2734 | | if self.has_associated_structures(line): |
2735 | | File |
2736 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2737 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2738 | | has_associated_structures |
2739 | | and [chain for chain in line.match_maps.keys() if not |
2740 | | chain.structure.deleted]: |
2741 | | File |
2742 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2743 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2744 | | and [chain for chain in line.match_maps.keys() if not |
2745 | | chain.structure.deleted]: |
2746 | | File |
2747 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2748 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
2749 | | return look_in_class._attr_registration.get_attr(attr_name) |
2750 | | File |
2751 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2752 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2753 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2754 | | (self.class_.__name__, attr_name)) from None |
2755 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2756 | | |
2757 | | Error processing trigger "changes done": |
2758 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2759 | | |
2760 | | File |
2761 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2762 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2763 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2764 | | (self.class_.__name__, attr_name)) from None |
2765 | | |
2766 | | See log for complete Python traceback. |
2767 | | |
2768 | | Traceback (most recent call last): |
2769 | | File |
2770 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2771 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
2772 | | return self._func(self._name, data) |
2773 | | File |
2774 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2775 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
2776 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
2777 | | File |
2778 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2779 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
2780 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
2781 | | File |
2782 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2783 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
2784 | | self.seq_canvas.assoc_mod(aseq) |
2785 | | File |
2786 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2787 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
2788 | | self.lead_block.assoc_mod(aseq) |
2789 | | File |
2790 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2791 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
2792 | | label_text.setFont(self._label_font(aseq)) |
2793 | | File |
2794 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2795 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
2796 | | if self.has_associated_structures(line): |
2797 | | File |
2798 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2799 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2800 | | has_associated_structures |
2801 | | and [chain for chain in line.match_maps.keys() if not |
2802 | | chain.structure.deleted]: |
2803 | | File |
2804 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2805 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2806 | | and [chain for chain in line.match_maps.keys() if not |
2807 | | chain.structure.deleted]: |
2808 | | File |
2809 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2810 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
2811 | | return look_in_class._attr_registration.get_attr(attr_name) |
2812 | | File |
2813 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2814 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2815 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2816 | | (self.class_.__name__, attr_name)) from None |
2817 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2818 | | |
2819 | | Error processing trigger "changes done": |
2820 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2821 | | |
2822 | | File |
2823 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2824 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2825 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2826 | | (self.class_.__name__, attr_name)) from None |
2827 | | |
2828 | | See log for complete Python traceback. |
2829 | | |
2830 | | |
2831 | | > mmaker #1 to #2 |
2832 | | |
2833 | | Parameters |
2834 | | --- |
2835 | | Chain pairing | bb |
2836 | | Alignment algorithm | Needleman-Wunsch |
2837 | | Similarity matrix | BLOSUM-62 |
2838 | | SS fraction | 0.3 |
2839 | | Gap open (HH/SS/other) | 18/18/6 |
2840 | | Gap extend | 1 |
2841 | | SS matrix | | | H | S | O |
2842 | | ---|---|---|--- |
2843 | | H | 6 | -9 | -6 |
2844 | | S | | 6 | -6 |
2845 | | O | | | 4 |
2846 | | Iteration cutoff | 2 |
2847 | | |
2848 | | Matchmaker ranked_1.pdb, chain A (#2) with ranked_0.pdb, chain A (#1), |
2849 | | sequence alignment score = 1458.1 |
2850 | | RMSD between 266 pruned atom pairs is 0.503 angstroms; (across all 300 pairs: |
2851 | | 3.708) |
2852 | | |
2853 | | Traceback (most recent call last): |
2854 | | File |
2855 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2856 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
2857 | | return self._func(self._name, data) |
2858 | | File |
2859 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2860 | | packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb |
2861 | | if chain.structure in changes.modified_structures(): |
2862 | | File |
2863 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2864 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
2865 | | return look_in_class._attr_registration.get_attr(attr_name) |
2866 | | File |
2867 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2868 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2869 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2870 | | (self.class_.__name__, attr_name)) from None |
2871 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2872 | | |
2873 | | Error processing trigger "changes": |
2874 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2875 | | |
2876 | | File |
2877 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2878 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2879 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2880 | | (self.class_.__name__, attr_name)) from None |
2881 | | |
2882 | | See log for complete Python traceback. |
2883 | | |
2884 | | Traceback (most recent call last): |
2885 | | File |
2886 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2887 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
2888 | | return self._func(self._name, data) |
2889 | | File |
2890 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2891 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
2892 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
2893 | | File |
2894 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2895 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
2896 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
2897 | | File |
2898 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2899 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
2900 | | self.seq_canvas.assoc_mod(aseq) |
2901 | | File |
2902 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2903 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
2904 | | self.lead_block.assoc_mod(aseq) |
2905 | | File |
2906 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2907 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
2908 | | label_text.setFont(self._label_font(aseq)) |
2909 | | File |
2910 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2911 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
2912 | | if self.has_associated_structures(line): |
2913 | | File |
2914 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2915 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2916 | | has_associated_structures |
2917 | | and [chain for chain in line.match_maps.keys() if not |
2918 | | chain.structure.deleted]: |
2919 | | File |
2920 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2921 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2922 | | and [chain for chain in line.match_maps.keys() if not |
2923 | | chain.structure.deleted]: |
2924 | | File |
2925 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2926 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
2927 | | return look_in_class._attr_registration.get_attr(attr_name) |
2928 | | File |
2929 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2930 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2931 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2932 | | (self.class_.__name__, attr_name)) from None |
2933 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2934 | | |
2935 | | Error processing trigger "changes done": |
2936 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2937 | | |
2938 | | File |
2939 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2940 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2941 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2942 | | (self.class_.__name__, attr_name)) from None |
2943 | | |
2944 | | See log for complete Python traceback. |
2945 | | |
2946 | | Traceback (most recent call last): |
2947 | | File |
2948 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2949 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
2950 | | return self._func(self._name, data) |
2951 | | File |
2952 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2953 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
2954 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
2955 | | File |
2956 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2957 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
2958 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
2959 | | File |
2960 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2961 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
2962 | | self.seq_canvas.assoc_mod(aseq) |
2963 | | File |
2964 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2965 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
2966 | | self.lead_block.assoc_mod(aseq) |
2967 | | File |
2968 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2969 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
2970 | | label_text.setFont(self._label_font(aseq)) |
2971 | | File |
2972 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2973 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
2974 | | if self.has_associated_structures(line): |
2975 | | File |
2976 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2977 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2978 | | has_associated_structures |
2979 | | and [chain for chain in line.match_maps.keys() if not |
2980 | | chain.structure.deleted]: |
2981 | | File |
2982 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2983 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
2984 | | and [chain for chain in line.match_maps.keys() if not |
2985 | | chain.structure.deleted]: |
2986 | | File |
2987 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2988 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
2989 | | return look_in_class._attr_registration.get_attr(attr_name) |
2990 | | File |
2991 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
2992 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
2993 | | raise AttributeError("'%s' object has no attribute '%s'" % |
2994 | | (self.class_.__name__, attr_name)) from None |
2995 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2996 | | |
2997 | | Error processing trigger "changes done": |
2998 | | AttributeError: 'Sequence' object has no attribute 'structure' |
2999 | | |
3000 | | File |
3001 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3002 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3003 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3004 | | (self.class_.__name__, attr_name)) from None |
3005 | | |
3006 | | See log for complete Python traceback. |
3007 | | |
3008 | | Traceback (most recent call last): |
3009 | | File |
3010 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3011 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3012 | | return self._func(self._name, data) |
3013 | | File |
3014 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3015 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3016 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3017 | | File |
3018 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3019 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3020 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3021 | | File |
3022 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3023 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3024 | | self.seq_canvas.assoc_mod(aseq) |
3025 | | File |
3026 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3027 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3028 | | self.lead_block.assoc_mod(aseq) |
3029 | | File |
3030 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3031 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3032 | | label_text.setFont(self._label_font(aseq)) |
3033 | | File |
3034 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3035 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3036 | | if self.has_associated_structures(line): |
3037 | | File |
3038 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3039 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3040 | | has_associated_structures |
3041 | | and [chain for chain in line.match_maps.keys() if not |
3042 | | chain.structure.deleted]: |
3043 | | File |
3044 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3045 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3046 | | and [chain for chain in line.match_maps.keys() if not |
3047 | | chain.structure.deleted]: |
3048 | | File |
3049 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3050 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3051 | | return look_in_class._attr_registration.get_attr(attr_name) |
3052 | | File |
3053 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3054 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3055 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3056 | | (self.class_.__name__, attr_name)) from None |
3057 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3058 | | |
3059 | | Error processing trigger "changes done": |
3060 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3061 | | |
3062 | | File |
3063 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3064 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3065 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3066 | | (self.class_.__name__, attr_name)) from None |
3067 | | |
3068 | | See log for complete Python traceback. |
3069 | | |
3070 | | |
3071 | | > mmaker #3 to #2 |
3072 | | |
3073 | | Parameters |
3074 | | --- |
3075 | | Chain pairing | bb |
3076 | | Alignment algorithm | Needleman-Wunsch |
3077 | | Similarity matrix | BLOSUM-62 |
3078 | | SS fraction | 0.3 |
3079 | | Gap open (HH/SS/other) | 18/18/6 |
3080 | | Gap extend | 1 |
3081 | | SS matrix | | | H | S | O |
3082 | | ---|---|---|--- |
3083 | | H | 6 | -9 | -6 |
3084 | | S | | 6 | -6 |
3085 | | O | | | 4 |
3086 | | Iteration cutoff | 2 |
3087 | | |
3088 | | Matchmaker ranked_1.pdb, chain A (#2) with combination, chain A (#3), sequence |
3089 | | alignment score = 85.1 |
3090 | | RMSD between 59 pruned atom pairs is 0.450 angstroms; (across all 100 pairs: |
3091 | | 10.984) |
3092 | | |
3093 | | Traceback (most recent call last): |
3094 | | File |
3095 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3096 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3097 | | return self._func(self._name, data) |
3098 | | File |
3099 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3100 | | packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb |
3101 | | if chain.structure in changes.modified_structures(): |
3102 | | File |
3103 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3104 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3105 | | return look_in_class._attr_registration.get_attr(attr_name) |
3106 | | File |
3107 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3108 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3109 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3110 | | (self.class_.__name__, attr_name)) from None |
3111 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3112 | | |
3113 | | Error processing trigger "changes": |
3114 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3115 | | |
3116 | | File |
3117 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3118 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3119 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3120 | | (self.class_.__name__, attr_name)) from None |
3121 | | |
3122 | | See log for complete Python traceback. |
3123 | | |
3124 | | Traceback (most recent call last): |
3125 | | File |
3126 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3127 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3128 | | return self._func(self._name, data) |
3129 | | File |
3130 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3131 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3132 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3133 | | File |
3134 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3135 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3136 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3137 | | File |
3138 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3139 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3140 | | self.seq_canvas.assoc_mod(aseq) |
3141 | | File |
3142 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3143 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3144 | | self.lead_block.assoc_mod(aseq) |
3145 | | File |
3146 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3147 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3148 | | label_text.setFont(self._label_font(aseq)) |
3149 | | File |
3150 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3151 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3152 | | if self.has_associated_structures(line): |
3153 | | File |
3154 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3155 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3156 | | has_associated_structures |
3157 | | and [chain for chain in line.match_maps.keys() if not |
3158 | | chain.structure.deleted]: |
3159 | | File |
3160 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3161 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3162 | | and [chain for chain in line.match_maps.keys() if not |
3163 | | chain.structure.deleted]: |
3164 | | File |
3165 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3166 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3167 | | return look_in_class._attr_registration.get_attr(attr_name) |
3168 | | File |
3169 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3170 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3171 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3172 | | (self.class_.__name__, attr_name)) from None |
3173 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3174 | | |
3175 | | Error processing trigger "changes done": |
3176 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3177 | | |
3178 | | File |
3179 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3180 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3181 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3182 | | (self.class_.__name__, attr_name)) from None |
3183 | | |
3184 | | See log for complete Python traceback. |
3185 | | |
3186 | | Traceback (most recent call last): |
3187 | | File |
3188 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3189 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3190 | | return self._func(self._name, data) |
3191 | | File |
3192 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3193 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3194 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3195 | | File |
3196 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3197 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3198 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3199 | | File |
3200 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3201 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3202 | | self.seq_canvas.assoc_mod(aseq) |
3203 | | File |
3204 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3205 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3206 | | self.lead_block.assoc_mod(aseq) |
3207 | | File |
3208 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3209 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3210 | | label_text.setFont(self._label_font(aseq)) |
3211 | | File |
3212 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3213 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3214 | | if self.has_associated_structures(line): |
3215 | | File |
3216 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3217 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3218 | | has_associated_structures |
3219 | | and [chain for chain in line.match_maps.keys() if not |
3220 | | chain.structure.deleted]: |
3221 | | File |
3222 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3223 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3224 | | and [chain for chain in line.match_maps.keys() if not |
3225 | | chain.structure.deleted]: |
3226 | | File |
3227 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3228 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3229 | | return look_in_class._attr_registration.get_attr(attr_name) |
3230 | | File |
3231 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3232 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3233 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3234 | | (self.class_.__name__, attr_name)) from None |
3235 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3236 | | |
3237 | | Error processing trigger "changes done": |
3238 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3239 | | |
3240 | | File |
3241 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3242 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3243 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3244 | | (self.class_.__name__, attr_name)) from None |
3245 | | |
3246 | | See log for complete Python traceback. |
3247 | | |
3248 | | Traceback (most recent call last): |
3249 | | File |
3250 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3251 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3252 | | return self._func(self._name, data) |
3253 | | File |
3254 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3255 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3256 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3257 | | File |
3258 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3259 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3260 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3261 | | File |
3262 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3263 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3264 | | self.seq_canvas.assoc_mod(aseq) |
3265 | | File |
3266 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3267 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3268 | | self.lead_block.assoc_mod(aseq) |
3269 | | File |
3270 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3271 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3272 | | label_text.setFont(self._label_font(aseq)) |
3273 | | File |
3274 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3275 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3276 | | if self.has_associated_structures(line): |
3277 | | File |
3278 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3279 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3280 | | has_associated_structures |
3281 | | and [chain for chain in line.match_maps.keys() if not |
3282 | | chain.structure.deleted]: |
3283 | | File |
3284 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3285 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3286 | | and [chain for chain in line.match_maps.keys() if not |
3287 | | chain.structure.deleted]: |
3288 | | File |
3289 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3290 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3291 | | return look_in_class._attr_registration.get_attr(attr_name) |
3292 | | File |
3293 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3294 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3295 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3296 | | (self.class_.__name__, attr_name)) from None |
3297 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3298 | | |
3299 | | Error processing trigger "changes done": |
3300 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3301 | | |
3302 | | File |
3303 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3304 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3305 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3306 | | (self.class_.__name__, attr_name)) from None |
3307 | | |
3308 | | See log for complete Python traceback. |
3309 | | |
3310 | | |
3311 | | > mmaker #4 to #2 |
3312 | | |
3313 | | Parameters |
3314 | | --- |
3315 | | Chain pairing | bb |
3316 | | Alignment algorithm | Needleman-Wunsch |
3317 | | Similarity matrix | BLOSUM-62 |
3318 | | SS fraction | 0.3 |
3319 | | Gap open (HH/SS/other) | 18/18/6 |
3320 | | Gap extend | 1 |
3321 | | SS matrix | | | H | S | O |
3322 | | ---|---|---|--- |
3323 | | H | 6 | -9 | -6 |
3324 | | S | | 6 | -6 |
3325 | | O | | | 4 |
3326 | | Iteration cutoff | 2 |
3327 | | |
3328 | | Matchmaker ranked_1.pdb, chain A (#2) with ranked_2.pdb, chain C (#4), |
3329 | | sequence alignment score = 1458.1 |
3330 | | RMSD between 266 pruned atom pairs is 0.432 angstroms; (across all 300 pairs: |
3331 | | 3.208) |
3332 | | |
3333 | | Traceback (most recent call last): |
3334 | | File |
3335 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3336 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3337 | | return self._func(self._name, data) |
3338 | | File |
3339 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3340 | | packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb |
3341 | | if chain.structure in changes.modified_structures(): |
3342 | | File |
3343 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3344 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3345 | | return look_in_class._attr_registration.get_attr(attr_name) |
3346 | | File |
3347 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3348 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3349 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3350 | | (self.class_.__name__, attr_name)) from None |
3351 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3352 | | |
3353 | | Error processing trigger "changes": |
3354 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3355 | | |
3356 | | File |
3357 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3358 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3359 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3360 | | (self.class_.__name__, attr_name)) from None |
3361 | | |
3362 | | See log for complete Python traceback. |
3363 | | |
3364 | | Traceback (most recent call last): |
3365 | | File |
3366 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3367 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3368 | | return self._func(self._name, data) |
3369 | | File |
3370 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3371 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3372 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3373 | | File |
3374 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3375 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3376 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3377 | | File |
3378 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3379 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3380 | | self.seq_canvas.assoc_mod(aseq) |
3381 | | File |
3382 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3383 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3384 | | self.lead_block.assoc_mod(aseq) |
3385 | | File |
3386 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3387 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3388 | | label_text.setFont(self._label_font(aseq)) |
3389 | | File |
3390 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3391 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3392 | | if self.has_associated_structures(line): |
3393 | | File |
3394 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3395 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3396 | | has_associated_structures |
3397 | | and [chain for chain in line.match_maps.keys() if not |
3398 | | chain.structure.deleted]: |
3399 | | File |
3400 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3401 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3402 | | and [chain for chain in line.match_maps.keys() if not |
3403 | | chain.structure.deleted]: |
3404 | | File |
3405 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3406 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3407 | | return look_in_class._attr_registration.get_attr(attr_name) |
3408 | | File |
3409 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3410 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3411 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3412 | | (self.class_.__name__, attr_name)) from None |
3413 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3414 | | |
3415 | | Error processing trigger "changes done": |
3416 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3417 | | |
3418 | | File |
3419 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3420 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3421 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3422 | | (self.class_.__name__, attr_name)) from None |
3423 | | |
3424 | | See log for complete Python traceback. |
3425 | | |
3426 | | Traceback (most recent call last): |
3427 | | File |
3428 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3429 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3430 | | return self._func(self._name, data) |
3431 | | File |
3432 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3433 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3434 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3435 | | File |
3436 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3437 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3438 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3439 | | File |
3440 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3441 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3442 | | self.seq_canvas.assoc_mod(aseq) |
3443 | | File |
3444 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3445 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3446 | | self.lead_block.assoc_mod(aseq) |
3447 | | File |
3448 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3449 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3450 | | label_text.setFont(self._label_font(aseq)) |
3451 | | File |
3452 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3453 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3454 | | if self.has_associated_structures(line): |
3455 | | File |
3456 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3457 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3458 | | has_associated_structures |
3459 | | and [chain for chain in line.match_maps.keys() if not |
3460 | | chain.structure.deleted]: |
3461 | | File |
3462 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3463 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3464 | | and [chain for chain in line.match_maps.keys() if not |
3465 | | chain.structure.deleted]: |
3466 | | File |
3467 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3468 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3469 | | return look_in_class._attr_registration.get_attr(attr_name) |
3470 | | File |
3471 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3472 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3473 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3474 | | (self.class_.__name__, attr_name)) from None |
3475 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3476 | | |
3477 | | Error processing trigger "changes done": |
3478 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3479 | | |
3480 | | File |
3481 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3482 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3483 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3484 | | (self.class_.__name__, attr_name)) from None |
3485 | | |
3486 | | See log for complete Python traceback. |
3487 | | |
3488 | | Traceback (most recent call last): |
3489 | | File |
3490 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3491 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3492 | | return self._func(self._name, data) |
3493 | | File |
3494 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3495 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3496 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3497 | | File |
3498 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3499 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3500 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3501 | | File |
3502 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3503 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3504 | | self.seq_canvas.assoc_mod(aseq) |
3505 | | File |
3506 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3507 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3508 | | self.lead_block.assoc_mod(aseq) |
3509 | | File |
3510 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3511 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3512 | | label_text.setFont(self._label_font(aseq)) |
3513 | | File |
3514 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3515 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3516 | | if self.has_associated_structures(line): |
3517 | | File |
3518 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3519 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3520 | | has_associated_structures |
3521 | | and [chain for chain in line.match_maps.keys() if not |
3522 | | chain.structure.deleted]: |
3523 | | File |
3524 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3525 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3526 | | and [chain for chain in line.match_maps.keys() if not |
3527 | | chain.structure.deleted]: |
3528 | | File |
3529 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3530 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3531 | | return look_in_class._attr_registration.get_attr(attr_name) |
3532 | | File |
3533 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3534 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3535 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3536 | | (self.class_.__name__, attr_name)) from None |
3537 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3538 | | |
3539 | | Error processing trigger "changes done": |
3540 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3541 | | |
3542 | | File |
3543 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3544 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3545 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3546 | | (self.class_.__name__, attr_name)) from None |
3547 | | |
3548 | | See log for complete Python traceback. |
3549 | | |
3550 | | |
3551 | | > mmaker #5 to #2 |
3552 | | |
3553 | | Parameters |
3554 | | --- |
3555 | | Chain pairing | bb |
3556 | | Alignment algorithm | Needleman-Wunsch |
3557 | | Similarity matrix | BLOSUM-62 |
3558 | | SS fraction | 0.3 |
3559 | | Gap open (HH/SS/other) | 18/18/6 |
3560 | | Gap extend | 1 |
3561 | | SS matrix | | | H | S | O |
3562 | | ---|---|---|--- |
3563 | | H | 6 | -9 | -6 |
3564 | | S | | 6 | -6 |
3565 | | O | | | 4 |
3566 | | Iteration cutoff | 2 |
3567 | | |
3568 | | Matchmaker ranked_1.pdb, chain A (#2) with ranked_3.pdb, chain C (#5), |
3569 | | sequence alignment score = 1445.5 |
3570 | | RMSD between 253 pruned atom pairs is 1.235 angstroms; (across all 300 pairs: |
3571 | | 4.402) |
3572 | | |
3573 | | Traceback (most recent call last): |
3574 | | File |
3575 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3576 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3577 | | return self._func(self._name, data) |
3578 | | File |
3579 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3580 | | packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb |
3581 | | if chain.structure in changes.modified_structures(): |
3582 | | File |
3583 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3584 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3585 | | return look_in_class._attr_registration.get_attr(attr_name) |
3586 | | File |
3587 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3588 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3589 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3590 | | (self.class_.__name__, attr_name)) from None |
3591 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3592 | | |
3593 | | Error processing trigger "changes": |
3594 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3595 | | |
3596 | | File |
3597 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3598 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3599 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3600 | | (self.class_.__name__, attr_name)) from None |
3601 | | |
3602 | | See log for complete Python traceback. |
3603 | | |
3604 | | Traceback (most recent call last): |
3605 | | File |
3606 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3607 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3608 | | return self._func(self._name, data) |
3609 | | File |
3610 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3611 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3612 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3613 | | File |
3614 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3615 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3616 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3617 | | File |
3618 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3619 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3620 | | self.seq_canvas.assoc_mod(aseq) |
3621 | | File |
3622 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3623 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3624 | | self.lead_block.assoc_mod(aseq) |
3625 | | File |
3626 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3627 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3628 | | label_text.setFont(self._label_font(aseq)) |
3629 | | File |
3630 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3631 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3632 | | if self.has_associated_structures(line): |
3633 | | File |
3634 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3635 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3636 | | has_associated_structures |
3637 | | and [chain for chain in line.match_maps.keys() if not |
3638 | | chain.structure.deleted]: |
3639 | | File |
3640 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3641 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3642 | | and [chain for chain in line.match_maps.keys() if not |
3643 | | chain.structure.deleted]: |
3644 | | File |
3645 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3646 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3647 | | return look_in_class._attr_registration.get_attr(attr_name) |
3648 | | File |
3649 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3650 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3651 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3652 | | (self.class_.__name__, attr_name)) from None |
3653 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3654 | | |
3655 | | Error processing trigger "changes done": |
3656 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3657 | | |
3658 | | File |
3659 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3660 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3661 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3662 | | (self.class_.__name__, attr_name)) from None |
3663 | | |
3664 | | See log for complete Python traceback. |
3665 | | |
3666 | | Traceback (most recent call last): |
3667 | | File |
3668 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3669 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3670 | | return self._func(self._name, data) |
3671 | | File |
3672 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3673 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3674 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3675 | | File |
3676 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3677 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3678 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3679 | | File |
3680 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3681 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3682 | | self.seq_canvas.assoc_mod(aseq) |
3683 | | File |
3684 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3685 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3686 | | self.lead_block.assoc_mod(aseq) |
3687 | | File |
3688 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3689 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3690 | | label_text.setFont(self._label_font(aseq)) |
3691 | | File |
3692 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3693 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3694 | | if self.has_associated_structures(line): |
3695 | | File |
3696 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3697 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3698 | | has_associated_structures |
3699 | | and [chain for chain in line.match_maps.keys() if not |
3700 | | chain.structure.deleted]: |
3701 | | File |
3702 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3703 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3704 | | and [chain for chain in line.match_maps.keys() if not |
3705 | | chain.structure.deleted]: |
3706 | | File |
3707 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3708 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3709 | | return look_in_class._attr_registration.get_attr(attr_name) |
3710 | | File |
3711 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3712 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3713 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3714 | | (self.class_.__name__, attr_name)) from None |
3715 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3716 | | |
3717 | | Error processing trigger "changes done": |
3718 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3719 | | |
3720 | | File |
3721 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3722 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3723 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3724 | | (self.class_.__name__, attr_name)) from None |
3725 | | |
3726 | | See log for complete Python traceback. |
3727 | | |
3728 | | Traceback (most recent call last): |
3729 | | File |
3730 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3731 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3732 | | return self._func(self._name, data) |
3733 | | File |
3734 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3735 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3736 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3737 | | File |
3738 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3739 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3740 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3741 | | File |
3742 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3743 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3744 | | self.seq_canvas.assoc_mod(aseq) |
3745 | | File |
3746 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3747 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3748 | | self.lead_block.assoc_mod(aseq) |
3749 | | File |
3750 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3751 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3752 | | label_text.setFont(self._label_font(aseq)) |
3753 | | File |
3754 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3755 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3756 | | if self.has_associated_structures(line): |
3757 | | File |
3758 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3759 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3760 | | has_associated_structures |
3761 | | and [chain for chain in line.match_maps.keys() if not |
3762 | | chain.structure.deleted]: |
3763 | | File |
3764 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3765 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3766 | | and [chain for chain in line.match_maps.keys() if not |
3767 | | chain.structure.deleted]: |
3768 | | File |
3769 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3770 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3771 | | return look_in_class._attr_registration.get_attr(attr_name) |
3772 | | File |
3773 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3774 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3775 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3776 | | (self.class_.__name__, attr_name)) from None |
3777 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3778 | | |
3779 | | Error processing trigger "changes done": |
3780 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3781 | | |
3782 | | File |
3783 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3784 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3785 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3786 | | (self.class_.__name__, attr_name)) from None |
3787 | | |
3788 | | See log for complete Python traceback. |
3789 | | |
3790 | | |
3791 | | > mmaker #6 to #2 |
3792 | | |
3793 | | Parameters |
3794 | | --- |
3795 | | Chain pairing | bb |
3796 | | Alignment algorithm | Needleman-Wunsch |
3797 | | Similarity matrix | BLOSUM-62 |
3798 | | SS fraction | 0.3 |
3799 | | Gap open (HH/SS/other) | 18/18/6 |
3800 | | Gap extend | 1 |
3801 | | SS matrix | | | H | S | O |
3802 | | ---|---|---|--- |
3803 | | H | 6 | -9 | -6 |
3804 | | S | | 6 | -6 |
3805 | | O | | | 4 |
3806 | | Iteration cutoff | 2 |
3807 | | |
3808 | | Matchmaker ranked_1.pdb, chain A (#2) with ranked_4.pdb, chain A (#6), |
3809 | | sequence alignment score = 1449.1 |
3810 | | RMSD between 127 pruned atom pairs is 0.188 angstroms; (across all 300 pairs: |
3811 | | 13.729) |
3812 | | |
3813 | | Traceback (most recent call last): |
3814 | | File |
3815 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3816 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3817 | | return self._func(self._name, data) |
3818 | | File |
3819 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3820 | | packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb |
3821 | | if chain.structure in changes.modified_structures(): |
3822 | | File |
3823 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3824 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3825 | | return look_in_class._attr_registration.get_attr(attr_name) |
3826 | | File |
3827 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3828 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3829 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3830 | | (self.class_.__name__, attr_name)) from None |
3831 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3832 | | |
3833 | | Error processing trigger "changes": |
3834 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3835 | | |
3836 | | File |
3837 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3838 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3839 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3840 | | (self.class_.__name__, attr_name)) from None |
3841 | | |
3842 | | See log for complete Python traceback. |
3843 | | |
3844 | | Traceback (most recent call last): |
3845 | | File |
3846 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3847 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3848 | | return self._func(self._name, data) |
3849 | | File |
3850 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3851 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3852 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3853 | | File |
3854 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3855 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3856 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3857 | | File |
3858 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3859 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3860 | | self.seq_canvas.assoc_mod(aseq) |
3861 | | File |
3862 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3863 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3864 | | self.lead_block.assoc_mod(aseq) |
3865 | | File |
3866 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3867 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3868 | | label_text.setFont(self._label_font(aseq)) |
3869 | | File |
3870 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3871 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3872 | | if self.has_associated_structures(line): |
3873 | | File |
3874 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3875 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3876 | | has_associated_structures |
3877 | | and [chain for chain in line.match_maps.keys() if not |
3878 | | chain.structure.deleted]: |
3879 | | File |
3880 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3881 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3882 | | and [chain for chain in line.match_maps.keys() if not |
3883 | | chain.structure.deleted]: |
3884 | | File |
3885 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3886 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3887 | | return look_in_class._attr_registration.get_attr(attr_name) |
3888 | | File |
3889 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3890 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3891 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3892 | | (self.class_.__name__, attr_name)) from None |
3893 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3894 | | |
3895 | | Error processing trigger "changes done": |
3896 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3897 | | |
3898 | | File |
3899 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3900 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3901 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3902 | | (self.class_.__name__, attr_name)) from None |
3903 | | |
3904 | | See log for complete Python traceback. |
3905 | | |
3906 | | Traceback (most recent call last): |
3907 | | File |
3908 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3909 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3910 | | return self._func(self._name, data) |
3911 | | File |
3912 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3913 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3914 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3915 | | File |
3916 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3917 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3918 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3919 | | File |
3920 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3921 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3922 | | self.seq_canvas.assoc_mod(aseq) |
3923 | | File |
3924 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3925 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3926 | | self.lead_block.assoc_mod(aseq) |
3927 | | File |
3928 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3929 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3930 | | label_text.setFont(self._label_font(aseq)) |
3931 | | File |
3932 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3933 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3934 | | if self.has_associated_structures(line): |
3935 | | File |
3936 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3937 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3938 | | has_associated_structures |
3939 | | and [chain for chain in line.match_maps.keys() if not |
3940 | | chain.structure.deleted]: |
3941 | | File |
3942 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3943 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
3944 | | and [chain for chain in line.match_maps.keys() if not |
3945 | | chain.structure.deleted]: |
3946 | | File |
3947 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3948 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
3949 | | return look_in_class._attr_registration.get_attr(attr_name) |
3950 | | File |
3951 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3952 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3953 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3954 | | (self.class_.__name__, attr_name)) from None |
3955 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3956 | | |
3957 | | Error processing trigger "changes done": |
3958 | | AttributeError: 'Sequence' object has no attribute 'structure' |
3959 | | |
3960 | | File |
3961 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3962 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
3963 | | raise AttributeError("'%s' object has no attribute '%s'" % |
3964 | | (self.class_.__name__, attr_name)) from None |
3965 | | |
3966 | | See log for complete Python traceback. |
3967 | | |
3968 | | Traceback (most recent call last): |
3969 | | File |
3970 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3971 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
3972 | | return self._func(self._name, data) |
3973 | | File |
3974 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3975 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
3976 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
3977 | | File |
3978 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3979 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
3980 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
3981 | | File |
3982 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3983 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
3984 | | self.seq_canvas.assoc_mod(aseq) |
3985 | | File |
3986 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3987 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
3988 | | self.lead_block.assoc_mod(aseq) |
3989 | | File |
3990 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3991 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
3992 | | label_text.setFont(self._label_font(aseq)) |
3993 | | File |
3994 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3995 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
3996 | | if self.has_associated_structures(line): |
3997 | | File |
3998 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
3999 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4000 | | has_associated_structures |
4001 | | and [chain for chain in line.match_maps.keys() if not |
4002 | | chain.structure.deleted]: |
4003 | | File |
4004 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4005 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4006 | | and [chain for chain in line.match_maps.keys() if not |
4007 | | chain.structure.deleted]: |
4008 | | File |
4009 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4010 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4011 | | return look_in_class._attr_registration.get_attr(attr_name) |
4012 | | File |
4013 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4014 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4015 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4016 | | (self.class_.__name__, attr_name)) from None |
4017 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4018 | | |
4019 | | Error processing trigger "changes done": |
4020 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4021 | | |
4022 | | File |
4023 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4024 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4025 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4026 | | (self.class_.__name__, attr_name)) from None |
4027 | | |
4028 | | See log for complete Python traceback. |
4029 | | |
4030 | | |
4031 | | > mmaker #7 to #2 |
4032 | | |
4033 | | No molecules/chains to match specified |
4034 | | |
4035 | | > hide #3 models |
4036 | | |
4037 | | Traceback (most recent call last): |
4038 | | File |
4039 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4040 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4041 | | return self._func(self._name, data) |
4042 | | File |
4043 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4044 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4045 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4046 | | File |
4047 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4048 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4049 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4050 | | File |
4051 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4052 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4053 | | self.seq_canvas.assoc_mod(aseq) |
4054 | | File |
4055 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4056 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4057 | | self.lead_block.assoc_mod(aseq) |
4058 | | File |
4059 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4060 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4061 | | label_text.setFont(self._label_font(aseq)) |
4062 | | File |
4063 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4064 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4065 | | if self.has_associated_structures(line): |
4066 | | File |
4067 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4068 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4069 | | has_associated_structures |
4070 | | and [chain for chain in line.match_maps.keys() if not |
4071 | | chain.structure.deleted]: |
4072 | | File |
4073 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4074 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4075 | | and [chain for chain in line.match_maps.keys() if not |
4076 | | chain.structure.deleted]: |
4077 | | File |
4078 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4079 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4080 | | return look_in_class._attr_registration.get_attr(attr_name) |
4081 | | File |
4082 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4083 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4084 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4085 | | (self.class_.__name__, attr_name)) from None |
4086 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4087 | | |
4088 | | Error processing trigger "changes done": |
4089 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4090 | | |
4091 | | File |
4092 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4093 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4094 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4095 | | (self.class_.__name__, attr_name)) from None |
4096 | | |
4097 | | See log for complete Python traceback. |
4098 | | |
4099 | | Traceback (most recent call last): |
4100 | | File |
4101 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4102 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4103 | | return self._func(self._name, data) |
4104 | | File |
4105 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4106 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4107 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4108 | | File |
4109 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4110 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4111 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4112 | | File |
4113 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4114 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4115 | | self.seq_canvas.assoc_mod(aseq) |
4116 | | File |
4117 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4118 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4119 | | self.lead_block.assoc_mod(aseq) |
4120 | | File |
4121 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4122 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4123 | | label_text.setFont(self._label_font(aseq)) |
4124 | | File |
4125 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4126 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4127 | | if self.has_associated_structures(line): |
4128 | | File |
4129 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4130 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4131 | | has_associated_structures |
4132 | | and [chain for chain in line.match_maps.keys() if not |
4133 | | chain.structure.deleted]: |
4134 | | File |
4135 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4136 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4137 | | and [chain for chain in line.match_maps.keys() if not |
4138 | | chain.structure.deleted]: |
4139 | | File |
4140 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4141 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4142 | | return look_in_class._attr_registration.get_attr(attr_name) |
4143 | | File |
4144 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4145 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4146 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4147 | | (self.class_.__name__, attr_name)) from None |
4148 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4149 | | |
4150 | | Error processing trigger "changes done": |
4151 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4152 | | |
4153 | | File |
4154 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4155 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4156 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4157 | | (self.class_.__name__, attr_name)) from None |
4158 | | |
4159 | | See log for complete Python traceback. |
4160 | | |
4161 | | Traceback (most recent call last): |
4162 | | File |
4163 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4164 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4165 | | return self._func(self._name, data) |
4166 | | File |
4167 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4168 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4169 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4170 | | File |
4171 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4172 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4173 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4174 | | File |
4175 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4176 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4177 | | self.seq_canvas.assoc_mod(aseq) |
4178 | | File |
4179 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4180 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4181 | | self.lead_block.assoc_mod(aseq) |
4182 | | File |
4183 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4184 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4185 | | label_text.setFont(self._label_font(aseq)) |
4186 | | File |
4187 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4188 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4189 | | if self.has_associated_structures(line): |
4190 | | File |
4191 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4192 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4193 | | has_associated_structures |
4194 | | and [chain for chain in line.match_maps.keys() if not |
4195 | | chain.structure.deleted]: |
4196 | | File |
4197 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4198 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4199 | | and [chain for chain in line.match_maps.keys() if not |
4200 | | chain.structure.deleted]: |
4201 | | File |
4202 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4203 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4204 | | return look_in_class._attr_registration.get_attr(attr_name) |
4205 | | File |
4206 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4207 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4208 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4209 | | (self.class_.__name__, attr_name)) from None |
4210 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4211 | | |
4212 | | Error processing trigger "changes done": |
4213 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4214 | | |
4215 | | File |
4216 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4217 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4218 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4219 | | (self.class_.__name__, attr_name)) from None |
4220 | | |
4221 | | See log for complete Python traceback. |
4222 | | |
4223 | | |
4224 | | > close #2 |
4225 | | |
4226 | | Traceback (most recent call last): |
4227 | | File |
4228 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4229 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4230 | | return self._func(self._name, data) |
4231 | | File |
4232 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4233 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4234 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4235 | | File |
4236 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4237 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4238 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4239 | | File |
4240 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4241 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4242 | | self.seq_canvas.assoc_mod(aseq) |
4243 | | File |
4244 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4245 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4246 | | self.lead_block.assoc_mod(aseq) |
4247 | | File |
4248 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4249 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4250 | | label_text.setFont(self._label_font(aseq)) |
4251 | | File |
4252 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4253 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4254 | | if self.has_associated_structures(line): |
4255 | | File |
4256 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4257 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4258 | | has_associated_structures |
4259 | | and [chain for chain in line.match_maps.keys() if not |
4260 | | chain.structure.deleted]: |
4261 | | File |
4262 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4263 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4264 | | and [chain for chain in line.match_maps.keys() if not |
4265 | | chain.structure.deleted]: |
4266 | | File |
4267 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4268 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4269 | | return look_in_class._attr_registration.get_attr(attr_name) |
4270 | | File |
4271 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4272 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4273 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4274 | | (self.class_.__name__, attr_name)) from None |
4275 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4276 | | |
4277 | | Error processing trigger "changes done": |
4278 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4279 | | |
4280 | | File |
4281 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4282 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4283 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4284 | | (self.class_.__name__, attr_name)) from None |
4285 | | |
4286 | | See log for complete Python traceback. |
4287 | | |
4288 | | Traceback (most recent call last): |
4289 | | File |
4290 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4291 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4292 | | return self._func(self._name, data) |
4293 | | File |
4294 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4295 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4296 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4297 | | File |
4298 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4299 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4300 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4301 | | File |
4302 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4303 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4304 | | self.seq_canvas.assoc_mod(aseq) |
4305 | | File |
4306 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4307 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4308 | | self.lead_block.assoc_mod(aseq) |
4309 | | File |
4310 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4311 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4312 | | label_text.setFont(self._label_font(aseq)) |
4313 | | File |
4314 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4315 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4316 | | if self.has_associated_structures(line): |
4317 | | File |
4318 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4319 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4320 | | has_associated_structures |
4321 | | and [chain for chain in line.match_maps.keys() if not |
4322 | | chain.structure.deleted]: |
4323 | | File |
4324 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4325 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4326 | | and [chain for chain in line.match_maps.keys() if not |
4327 | | chain.structure.deleted]: |
4328 | | File |
4329 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4330 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4331 | | return look_in_class._attr_registration.get_attr(attr_name) |
4332 | | File |
4333 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4334 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4335 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4336 | | (self.class_.__name__, attr_name)) from None |
4337 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4338 | | |
4339 | | Error processing trigger "changes done": |
4340 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4341 | | |
4342 | | File |
4343 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4344 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4345 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4346 | | (self.class_.__name__, attr_name)) from None |
4347 | | |
4348 | | See log for complete Python traceback. |
4349 | | |
4350 | | Traceback (most recent call last): |
4351 | | File |
4352 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4353 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4354 | | return self._func(self._name, data) |
4355 | | File |
4356 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4357 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4358 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4359 | | File |
4360 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4361 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4362 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4363 | | File |
4364 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4365 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4366 | | self.seq_canvas.assoc_mod(aseq) |
4367 | | File |
4368 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4369 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4370 | | self.lead_block.assoc_mod(aseq) |
4371 | | File |
4372 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4373 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4374 | | label_text.setFont(self._label_font(aseq)) |
4375 | | File |
4376 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4377 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4378 | | if self.has_associated_structures(line): |
4379 | | File |
4380 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4381 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4382 | | has_associated_structures |
4383 | | and [chain for chain in line.match_maps.keys() if not |
4384 | | chain.structure.deleted]: |
4385 | | File |
4386 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4387 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4388 | | and [chain for chain in line.match_maps.keys() if not |
4389 | | chain.structure.deleted]: |
4390 | | File |
4391 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4392 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4393 | | return look_in_class._attr_registration.get_attr(attr_name) |
4394 | | File |
4395 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4396 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4397 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4398 | | (self.class_.__name__, attr_name)) from None |
4399 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4400 | | |
4401 | | Error processing trigger "changes done": |
4402 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4403 | | |
4404 | | File |
4405 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4406 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4407 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4408 | | (self.class_.__name__, attr_name)) from None |
4409 | | |
4410 | | See log for complete Python traceback. |
4411 | | |
4412 | | |
4413 | | > hide #4-6 target m |
4414 | | |
4415 | | Traceback (most recent call last): |
4416 | | File |
4417 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4418 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4419 | | return self._func(self._name, data) |
4420 | | File |
4421 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4422 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4423 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4424 | | File |
4425 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4426 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4427 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4428 | | File |
4429 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4430 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4431 | | self.seq_canvas.assoc_mod(aseq) |
4432 | | File |
4433 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4434 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4435 | | self.lead_block.assoc_mod(aseq) |
4436 | | File |
4437 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4438 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4439 | | label_text.setFont(self._label_font(aseq)) |
4440 | | File |
4441 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4442 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4443 | | if self.has_associated_structures(line): |
4444 | | File |
4445 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4446 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4447 | | has_associated_structures |
4448 | | and [chain for chain in line.match_maps.keys() if not |
4449 | | chain.structure.deleted]: |
4450 | | File |
4451 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4452 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4453 | | and [chain for chain in line.match_maps.keys() if not |
4454 | | chain.structure.deleted]: |
4455 | | File |
4456 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4457 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4458 | | return look_in_class._attr_registration.get_attr(attr_name) |
4459 | | File |
4460 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4461 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4462 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4463 | | (self.class_.__name__, attr_name)) from None |
4464 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4465 | | |
4466 | | Error processing trigger "changes done": |
4467 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4468 | | |
4469 | | File |
4470 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4471 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4472 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4473 | | (self.class_.__name__, attr_name)) from None |
4474 | | |
4475 | | See log for complete Python traceback. |
4476 | | |
4477 | | Traceback (most recent call last): |
4478 | | File |
4479 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4480 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4481 | | return self._func(self._name, data) |
4482 | | File |
4483 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4484 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4485 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4486 | | File |
4487 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4488 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4489 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4490 | | File |
4491 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4492 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4493 | | self.seq_canvas.assoc_mod(aseq) |
4494 | | File |
4495 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4496 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4497 | | self.lead_block.assoc_mod(aseq) |
4498 | | File |
4499 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4500 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4501 | | label_text.setFont(self._label_font(aseq)) |
4502 | | File |
4503 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4504 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4505 | | if self.has_associated_structures(line): |
4506 | | File |
4507 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4508 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4509 | | has_associated_structures |
4510 | | and [chain for chain in line.match_maps.keys() if not |
4511 | | chain.structure.deleted]: |
4512 | | File |
4513 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4514 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4515 | | and [chain for chain in line.match_maps.keys() if not |
4516 | | chain.structure.deleted]: |
4517 | | File |
4518 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4519 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4520 | | return look_in_class._attr_registration.get_attr(attr_name) |
4521 | | File |
4522 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4523 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4524 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4525 | | (self.class_.__name__, attr_name)) from None |
4526 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4527 | | |
4528 | | Error processing trigger "changes done": |
4529 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4530 | | |
4531 | | File |
4532 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4533 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4534 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4535 | | (self.class_.__name__, attr_name)) from None |
4536 | | |
4537 | | See log for complete Python traceback. |
4538 | | |
4539 | | Traceback (most recent call last): |
4540 | | File |
4541 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4542 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4543 | | return self._func(self._name, data) |
4544 | | File |
4545 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4546 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4547 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4548 | | File |
4549 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4550 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4551 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4552 | | File |
4553 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4554 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4555 | | self.seq_canvas.assoc_mod(aseq) |
4556 | | File |
4557 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4558 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4559 | | self.lead_block.assoc_mod(aseq) |
4560 | | File |
4561 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4562 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4563 | | label_text.setFont(self._label_font(aseq)) |
4564 | | File |
4565 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4566 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4567 | | if self.has_associated_structures(line): |
4568 | | File |
4569 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4570 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4571 | | has_associated_structures |
4572 | | and [chain for chain in line.match_maps.keys() if not |
4573 | | chain.structure.deleted]: |
4574 | | File |
4575 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4576 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4577 | | and [chain for chain in line.match_maps.keys() if not |
4578 | | chain.structure.deleted]: |
4579 | | File |
4580 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4581 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4582 | | return look_in_class._attr_registration.get_attr(attr_name) |
4583 | | File |
4584 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4585 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4586 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4587 | | (self.class_.__name__, attr_name)) from None |
4588 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4589 | | |
4590 | | Error processing trigger "changes done": |
4591 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4592 | | |
4593 | | File |
4594 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4595 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4596 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4597 | | (self.class_.__name__, attr_name)) from None |
4598 | | |
4599 | | See log for complete Python traceback. |
4600 | | |
4601 | | |
4602 | | > close #4-6 |
4603 | | |
4604 | | Traceback (most recent call last): |
4605 | | File |
4606 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4607 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4608 | | return self._func(self._name, data) |
4609 | | File |
4610 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4611 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4612 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4613 | | File |
4614 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4615 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4616 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4617 | | File |
4618 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4619 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4620 | | self.seq_canvas.assoc_mod(aseq) |
4621 | | File |
4622 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4623 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4624 | | self.lead_block.assoc_mod(aseq) |
4625 | | File |
4626 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4627 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4628 | | label_text.setFont(self._label_font(aseq)) |
4629 | | File |
4630 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4631 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4632 | | if self.has_associated_structures(line): |
4633 | | File |
4634 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4635 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4636 | | has_associated_structures |
4637 | | and [chain for chain in line.match_maps.keys() if not |
4638 | | chain.structure.deleted]: |
4639 | | File |
4640 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4641 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4642 | | and [chain for chain in line.match_maps.keys() if not |
4643 | | chain.structure.deleted]: |
4644 | | File |
4645 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4646 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4647 | | return look_in_class._attr_registration.get_attr(attr_name) |
4648 | | File |
4649 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4650 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4651 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4652 | | (self.class_.__name__, attr_name)) from None |
4653 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4654 | | |
4655 | | Error processing trigger "changes done": |
4656 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4657 | | |
4658 | | File |
4659 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4660 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4661 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4662 | | (self.class_.__name__, attr_name)) from None |
4663 | | |
4664 | | See log for complete Python traceback. |
4665 | | |
4666 | | Traceback (most recent call last): |
4667 | | File |
4668 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4669 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4670 | | return self._func(self._name, data) |
4671 | | File |
4672 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4673 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4674 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4675 | | File |
4676 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4677 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4678 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4679 | | File |
4680 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4681 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4682 | | self.seq_canvas.assoc_mod(aseq) |
4683 | | File |
4684 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4685 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4686 | | self.lead_block.assoc_mod(aseq) |
4687 | | File |
4688 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4689 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4690 | | label_text.setFont(self._label_font(aseq)) |
4691 | | File |
4692 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4693 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4694 | | if self.has_associated_structures(line): |
4695 | | File |
4696 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4697 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4698 | | has_associated_structures |
4699 | | and [chain for chain in line.match_maps.keys() if not |
4700 | | chain.structure.deleted]: |
4701 | | File |
4702 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4703 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4704 | | and [chain for chain in line.match_maps.keys() if not |
4705 | | chain.structure.deleted]: |
4706 | | File |
4707 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4708 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4709 | | return look_in_class._attr_registration.get_attr(attr_name) |
4710 | | File |
4711 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4712 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4713 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4714 | | (self.class_.__name__, attr_name)) from None |
4715 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4716 | | |
4717 | | Error processing trigger "changes done": |
4718 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4719 | | |
4720 | | File |
4721 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4722 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4723 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4724 | | (self.class_.__name__, attr_name)) from None |
4725 | | |
4726 | | See log for complete Python traceback. |
4727 | | |
4728 | | Traceback (most recent call last): |
4729 | | File |
4730 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4731 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4732 | | return self._func(self._name, data) |
4733 | | File |
4734 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4735 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4736 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4737 | | File |
4738 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4739 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4740 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4741 | | File |
4742 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4743 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4744 | | self.seq_canvas.assoc_mod(aseq) |
4745 | | File |
4746 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4747 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4748 | | self.lead_block.assoc_mod(aseq) |
4749 | | File |
4750 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4751 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4752 | | label_text.setFont(self._label_font(aseq)) |
4753 | | File |
4754 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4755 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4756 | | if self.has_associated_structures(line): |
4757 | | File |
4758 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4759 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4760 | | has_associated_structures |
4761 | | and [chain for chain in line.match_maps.keys() if not |
4762 | | chain.structure.deleted]: |
4763 | | File |
4764 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4765 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4766 | | and [chain for chain in line.match_maps.keys() if not |
4767 | | chain.structure.deleted]: |
4768 | | File |
4769 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4770 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4771 | | return look_in_class._attr_registration.get_attr(attr_name) |
4772 | | File |
4773 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4774 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4775 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4776 | | (self.class_.__name__, attr_name)) from None |
4777 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4778 | | |
4779 | | Error processing trigger "changes done": |
4780 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4781 | | |
4782 | | File |
4783 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4784 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4785 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4786 | | (self.class_.__name__, attr_name)) from None |
4787 | | |
4788 | | See log for complete Python traceback. |
4789 | | |
4790 | | |
4791 | | > show #3 models |
4792 | | |
4793 | | Traceback (most recent call last): |
4794 | | File |
4795 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4796 | | packages/chimerax/core/triggerset.py", line 134, in invoke |
4797 | | return self._func(self._name, data) |
4798 | | File |
4799 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4800 | | packages/chimerax/seqalign/alignment.py", line 444, in _delay_disassoc |
4801 | | self._notify_observers(self.NOTE_DEL_ASSOC, data) |
4802 | | File |
4803 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4804 | | packages/chimerax/seqalign/alignment.py", line 669, in _notify_observers |
4805 | | recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data)) |
4806 | | File |
4807 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4808 | | packages/chimerax/seq-view/tool.py", line 465, in alignment_notification |
4809 | | self.seq_canvas.assoc_mod(aseq) |
4810 | | File |
4811 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4812 | | packages/chimerax/seq-view/seq_canvas.py", line 420, in assoc_mod |
4813 | | self.lead_block.assoc_mod(aseq) |
4814 | | File |
4815 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4816 | | packages/chimerax/seq-view/seq_canvas.py", line 1641, in assoc_mod |
4817 | | label_text.setFont(self._label_font(aseq)) |
4818 | | File |
4819 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4820 | | packages/chimerax/seq-view/seq_canvas.py", line 2110, in _label_font |
4821 | | if self.has_associated_structures(line): |
4822 | | File |
4823 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4824 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4825 | | has_associated_structures |
4826 | | and [chain for chain in line.match_maps.keys() if not |
4827 | | chain.structure.deleted]: |
4828 | | File |
4829 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4830 | | packages/chimerax/seq-view/seq_canvas.py", line 2054, in |
4831 | | and [chain for chain in line.match_maps.keys() if not |
4832 | | chain.structure.deleted]: |
4833 | | File |
4834 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4835 | | packages/chimerax/core/attributes.py", line 57, in _getattr_ |
4836 | | return look_in_class._attr_registration.get_attr(attr_name) |
4837 | | File |
4838 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4839 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4840 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4841 | | (self.class_.__name__, attr_name)) from None |
4842 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4843 | | |
4844 | | Error processing trigger "changes done": |
4845 | | AttributeError: 'Sequence' object has no attribute 'structure' |
4846 | | |
4847 | | File |
4848 | | "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- |
4849 | | packages/chimerax/core/attributes.py", line 85, in get_attr |
4850 | | raise AttributeError("'%s' object has no attribute '%s'" % |
4851 | | (self.class_.__name__, attr_name)) from None |
4852 | | |
4853 | | See log for complete Python traceback. |
4854 | | |
| 2644 | |
| 2645 | [had to delete a bunch of stuff to get within ticket limits] |
| 2646 | |