Changes between Initial Version and Version 1 of Ticket #14858


Ignore:
Timestamp:
Apr 1, 2024, 10:58:27 AM (20 months ago)
Author:
Eric Pettersen
Comment:

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  • Ticket #14858

    • Property Component Unassigned → Structure Editing
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crash getting secondary structure IDs after deleting residues

  • Ticket #14858 – Description

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    2336     "name" : "_random.cpython-311-darwin.so"
    2337   },
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    2345     "name" : "_bisect.cpython-311-darwin.so"
    2346   },
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    2355   },
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    2492     "name" : "libffi.dylib"
    2493   },
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    2503     "name" : "Foundation",
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    2505   },
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    2510     "CFBundleShortVersionString" : "6.9",
    2511     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    2512     "size" : 4825085,
    2513     "uuid" : "fd59424c-be72-3201-b98c-0421b284ffbb",
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    2531   "sharedCache" : {
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    2535 },
    2536   "legacyInfo" : {
    2537   "threadTriggered" : {
    2538     "name" : "CrBrowserMain",
    2539     "queue" : "com.apple.main-thread"
    2540   }
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    2542   "logWritingSignature" : "52b84223808ce37e2896aa47bf84a0a6c443c96d",
    2543   "trialInfo" : {
    2544   "rollouts" : [
    2545     {
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    2547       "factorPackIds" : {
    2548 
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    2555 
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    2558     }
    2559   ],
    2560   "experiments" : [
    2561     {
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    2563       "experimentId" : "6384d56b96e8d228551ec182",
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    2565     }
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    2567 },
    2568   "reportNotes" : [
    2569   "PC register does not match crashing frame (0x0 vs 0x7FF896BAEA78)"
    2570 ]
    2571 }
    2572 ===== Log before crash start =====
    2573 Startup Messages 
    2574 --- 
    2575 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
    2576 bundle with that from NMRSTAR bundle 
    2577  
    2578 UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    2579 © 2016-2023 Regents of the University of California. All rights reserved. 
    2580 How to cite UCSF ChimeraX 
    2581 
    2582 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    2583 > evolution/Chimera models/Working models/RacGEF working1h.pdb" format pdb
    2584 
    2585 Chain information for RacGEF working1h.pdb #1 
    2586 --- 
    2587 Chain | Description 
    2588 C D F H I J L M | No description available 
    2589 E | No description available 
    2590 G | No description available 
    2591 K | No description available 
    2592 O | No description available 
    2593 Q | No description available 
    2594 R | No description available 
    2595  
    2596 
    2597 > set bgColor white
    2598 
    2599 > ui tool show "Show Sequence Viewer"
    2600 
    2601 > sequence chain /E
    2602 
    2603 Alignment identifier is 1/E 
    2604 
    2605 > select /E:165
    2606 
    2607 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2608 
    2609 > select /E:165
    2610 
    2611 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2612 
    2613 > interfaces #1 areaCutoff 20
    2614 
    2615 30 buried areas: R O 2213, R G 2211, F K 1724, C J 1274, F D 1246, C H 1177, F
    2616 M 1174, H L 1166, O Q 1094, R Q 1081, I D 1073, F C 699, O K 675, D K 614, F J
    2617 544, C D 522, J M 493, H D 492, O E 480, O D 478, O F 462, H I 452, F E 397, C
    2618 K 396, C E 321, D E 320, I L 310, E K 300, R D 298, H E 24 
    2619 
    2620 > select ::name="4IP"
    2621 
    2622 36 atoms, 36 bonds, 1 residue, 1 model selected 
    2623 
    2624 > select ::name="4IP"
    2625 
    2626 36 atoms, 36 bonds, 1 residue, 1 model selected 
    2627 
    2628 > delete atoms sel
    2629 
    2630 > delete bonds sel
    2631 
    2632 > interfaces #1 areaCutoff 20
    2633 
    2634 30 buried areas: R O 2213, R G 2211, F K 1724, C J 1274, F D 1246, C H 1177, F
    2635 M 1174, H L 1166, O Q 1094, R Q 1081, I D 1073, F C 699, O K 675, D K 614, F J
    2636 544, C D 522, J M 493, H D 492, O E 480, O D 478, O F 462, H I 452, F E 397, C
    2637 K 396, C E 321, D E 320, I L 310, E K 300, R D 298, H E 24 
    2638 
    2639 > ui tool show "Show Sequence Viewer"
    2640 
    2641 > sequence chain /C
    2642 
    2643 Alignment identifier is 1/C 
    2644 
    2645 > select /E
    2646 
    2647 2637 atoms, 2665 bonds, 166 residues, 1 model selected 
    2648 
    2649 > show sel cartoons
    2650 
    2651 > hide sel atoms
    2652 
    2653 > color N cornflowerblue atoms
    2654 
    2655 > color O hotpink atoms
    2656 
    2657 > color :arg,hic,his,lys & sidechain & N blue atoms
    2658 
    2659 > color :asp,glu & sidechain & O red atoms
    2660 
    2661 > color S yellow atoms
    2662 
    2663 > color P purple atoms
    2664 
    2665 > hide H atoms
    2666 
    2667 > select /E:165
    2668 
    2669 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2670 
    2671 > select /E:160-165
    2672 
    2673 93 atoms, 93 bonds, 6 residues, 1 model selected 
    2674 
    2675 > select /E:160
    2676 
    2677 24 atoms, 24 bonds, 1 residue, 1 model selected 
    2678 
    2679 > select /E:160
    2680 
    2681 24 atoms, 24 bonds, 1 residue, 1 model selected 
    2682 
    2683 > select /E:165
    2684 
    2685 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2686 
    2687 > select /E:152-165
    2688 
    2689 211 atoms, 211 bonds, 14 residues, 1 model selected 
    2690 
    2691 > select /E:151
    2692 
    2693 12 atoms, 11 bonds, 1 residue, 1 model selected 
    2694 
    2695 > select /E:0-151
    2696 
    2697 2426 atoms, 2453 bonds, 152 residues, 1 model selected 
    2698 
    2699 > show sel atoms
    2700 
    2701 > isolde sim start /E
    2702 
    2703 > set selectionWidth 4
    2704 
    2705 Done loading forcefield 
    2706 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2707 chains... 
    2708 Chain information for RacGEF working1h.pdb 
    2709 --- 
    2710 Chain | Description 
    2711 1.2/C 1.2/D 1.2/F 1.2/H 1.2/I 1.2/J 1.2/L 1.2/M | No description available 
    2712 1.2/E | No description available 
    2713 1.2/G | No description available 
    2714 1.2/K | No description available 
    2715 1.2/O | No description available 
    2716 1.2/Q | No description available 
    2717 1.2/R | No description available 
    2718  
    2719 
    2720 > isolde set simFidelityMode Medium/Medium
    2721 
    2722 ISOLDE: setting sim fidelity mode to Medium/Medium 
    2723 nonbonded_cutoff_distance = 0.900000 
    2724 use_gbsa = True 
    2725 gbsa_cutoff = 1.100000 
    2726 ISOLDE: started sim 
    2727 
    2728 > select /E:165
    2729 
    2730 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2731 
    2732 > select /E:165
    2733 
    2734 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2735 
    2736 > show sel cartoons
    2737 
    2738 > select
    2739 
    2740 74199 atoms, 74989 bonds, 12 pseudobonds, 4715 residues, 18 models selected 
    2741 
    2742 > show sel cartoons
    2743 
    2744 > isolde sim pause
    2745 
    2746 > select clear
    2747 
    2748 > select /E:165
    2749 
    2750 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2751 
    2752 > select /E:164-165
    2753 
    2754 30 atoms, 29 bonds, 2 residues, 1 model selected 
    2755 
    2756 > select /E:165
    2757 
    2758 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2759 
    2760 > select /E:153-165
    2761 
    2762 197 atoms, 197 bonds, 13 residues, 1 model selected 
    2763 
    2764 > select /E:165
    2765 
    2766 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2767 
    2768 > select /E:165
    2769 
    2770 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2771 
    2772 > ui mousemode right "isolde tug selection"
    2773 
    2774 > isolde sim resume
    2775 
    2776 > select
    2777 
    2778 74199 atoms, 74989 bonds, 12 pseudobonds, 4715 residues, 18 models selected 
    2779 
    2780 > hide sel cartoons
    2781 
    2782 > select clear
    2783 
    2784 > select /E:165
    2785 
    2786 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2787 
    2788 > select /E:163-165
    2789 
    2790 46 atoms, 45 bonds, 3 residues, 1 model selected 
    2791 
    2792 > ui mousemode right "isolde tug atom"
    2793 
    2794 > select /E:160
    2795 
    2796 24 atoms, 24 bonds, 1 residue, 1 model selected 
    2797 
    2798 > select /E:160
    2799 
    2800 24 atoms, 24 bonds, 1 residue, 1 model selected 
    2801 
    2802 > isolde sim stop
    2803 
    2804 Sim termination reason: None 
    2805 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2806 chains... 
    2807 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    2808 standards. 
    2809 ISOLDE: stopped sim 
    2810 
    2811 > select /F
    2812 
    2813 5848 atoms, 5912 bonds, 1 pseudobond, 377 residues, 2 models selected 
    2814 
    2815 > select /E
    2816 
    2817 2637 atoms, 2665 bonds, 166 residues, 1 model selected 
    2818 
    2819 > style sel sphere
    2820 
    2821 Changed 2637 atom styles 
    2822 
    2823 > select /E:160
    2824 
    2825 24 atoms, 24 bonds, 1 residue, 1 model selected 
    2826 
    2827 > select /E:160
    2828 
    2829 24 atoms, 24 bonds, 1 residue, 1 model selected 
    2830 
    2831 > select /E:165
    2832 
    2833 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2834 
    2835 > select /E:160-165
    2836 
    2837 93 atoms, 93 bonds, 6 residues, 1 model selected 
    2838 
    2839 > show sel atoms
    2840 
    2841 > color N cornflowerblue atoms
    2842 
    2843 > color O hotpink atoms
    2844 
    2845 > color :arg,hic,his,lys & sidechain & N blue atoms
    2846 
    2847 > color :asp,glu & sidechain & O red atoms
    2848 
    2849 > color S yellow atoms
    2850 
    2851 > color P purple atoms
    2852 
    2853 > hide H atoms
    2854 
    2855 > show sel atoms
    2856 
    2857 > show (#!1.2 & sel) target ab
    2858 
    2859 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    2860 > evolution/Chimera models/Working models/RacGEF working1i.pdb"
    2861 
    2862 > close session
    2863 
    2864 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    2865 > evolution/Chimera models/Working models/RacGEF working1i.pdb" format pdb
    2866 
    2867 Chain information for RacGEF working1i.pdb #1 
    2868 --- 
    2869 Chain | Description 
    2870 C D F H I J L M | No description available 
    2871 E | No description available 
    2872 G | No description available 
    2873 K | No description available 
    2874 O | No description available 
    2875 Q | No description available 
    2876 R | No description available 
    2877  
    2878 
    2879 > color N cornflowerblue atoms
    2880 
    2881 > color O hotpink atoms
    2882 
    2883 > color :arg,hic,his,lys & sidechain & N blue atoms
    2884 
    2885 > color :asp,glu & sidechain & O red atoms
    2886 
    2887 > color S yellow atoms
    2888 
    2889 > color P purple atoms
    2890 
    2891 > hide H atoms
    2892 
    2893 > select up
    2894 
    2895 24 atoms, 23 bonds, 1 residue, 1 model selected 
    2896 
    2897 > ui tool show "Color Actions"
    2898 
    2899 > color sel red target apf
    2900 
    2901 > select clear
    2902 
    2903 > interfaces #1 areaCutoff 20
    2904 
    2905 29 buried areas: R O 2213, R G 2211, F K 1730, C J 1274, F D 1246, C H 1177, F
    2906 M 1174, H L 1166, O Q 1094, R Q 1081, I D 1073, F C 699, O K 673, D K 614, F J
    2907 544, C D 522, J M 493, H D 492, O E 489, O D 477, O F 459, H I 452, F E 412, C
    2908 K 396, E K 327, I L 310, C E 303, R D 298, D E 285 
    2909 
    2910 > ui tool show "Show Sequence Viewer"
    2911 
    2912 > sequence chain /E
    2913 
    2914 Alignment identifier is 1/E 
    2915 
    2916 > select /E:165
    2917 
    2918 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2919 
    2920 > select /E:165
    2921 
    2922 15 atoms, 14 bonds, 1 residue, 1 model selected 
    2923 
    2924 > select /R
    2925 
    2926 9136 atoms, 9223 bonds, 564 residues, 1 model selected 
    2927 
    2928 > select /R
    2929 
    2930 9136 atoms, 9223 bonds, 564 residues, 1 model selected 
    2931 
    2932 > hide sel atoms
    2933 
    2934 > ui tool show "Show Sequence Viewer"
    2935 
    2936 > sequence chain /O
    2937 
    2938 Alignment identifier is 1/O 
    2939 
    2940 > select /E
    2941 
    2942 2637 atoms, 2665 bonds, 166 residues, 1 model selected 
    2943 
    2944 > hide sel atoms
    2945 
    2946 > combine /C,K name K2
    2947 
    2948 > ui tool show Matchmaker
    2949 
    2950 > select clear
    2951 
    2952 > select add #2
    2953 
    2954 74199 atoms, 74989 bonds, 12 pseudobonds, 4715 residues, 2 models selected 
    2955 
    2956 > select subtract #2/C
    2957 
    2958 68352 atoms, 69078 bonds, 11 pseudobonds, 4338 residues, 2 models selected 
    2959 
    2960 > select subtract #2/K
    2961 
    2962 66159 atoms, 66870 bonds, 11 pseudobonds, 4197 residues, 2 models selected 
    2963 
    2964 > delete atoms (#!2 & sel)
    2965 
    2966 > delete bonds (#!2 & sel)
    2967 
    2968 > ui tool show Matchmaker
    2969 
    2970 > matchmaker #2/C to #1/D pairing ss
    2971 
    2972 Parameters 
    2973 --- 
    2974 Chain pairing | ss 
    2975 Alignment algorithm | Needleman-Wunsch 
    2976 Similarity matrix | BLOSUM-62 
    2977 SS fraction | 0.3 
    2978 Gap open (HH/SS/other) | 18/18/6 
    2979 Gap extend | 1 
    2980 SS matrix |  |  | H | S | O 
    2981 ---|---|---|--- 
    2982 H | 6 | -9 | -6 
    2983 S |  | 6 | -6 
    2984 O |  |  | 4 
    2985 Iteration cutoff | 2 
    2986  
    2987 Matchmaker RacGEF working1i.pdb, chain D (#1) with K2, chain C (#2), sequence
    2988 alignment score = 1843.3 
    2989 RMSD between 204 pruned atom pairs is 1.175 angstroms; (across all 374 pairs:
    2990 3.061) 
    2991  
    2992 
    2993 > select #1/E
    2994 
    2995 2637 atoms, 2665 bonds, 166 residues, 1 model selected 
    2996 
    2997 > show sel cartoons
    2998 
    2999 > matchmaker #2/C to #1/F pairing ss
    3000 
    3001 Parameters 
    3002 --- 
    3003 Chain pairing | ss 
    3004 Alignment algorithm | Needleman-Wunsch 
    3005 Similarity matrix | BLOSUM-62 
    3006 SS fraction | 0.3 
    3007 Gap open (HH/SS/other) | 18/18/6 
    3008 Gap extend | 1 
    3009 SS matrix |  |  | H | S | O 
    3010 ---|---|---|--- 
    3011 H | 6 | -9 | -6 
    3012 S |  | 6 | -6 
    3013 O |  |  | 4 
    3014 Iteration cutoff | 2 
    3015  
    3016 Matchmaker RacGEF working1i.pdb, chain F (#1) with K2, chain C (#2), sequence
    3017 alignment score = 1791.7 
    3018 RMSD between 252 pruned atom pairs is 1.233 angstroms; (across all 374 pairs:
    3019 2.046) 
    3020  
    3021 
    3022 > show sel atoms
    3023 
    3024 > hide #!2 models
    3025 
    3026 > show #!2 models
    3027 
    3028 > matchmaker #2/C to #1/I pairing ss
    3029 
    3030 Parameters 
    3031 --- 
    3032 Chain pairing | ss 
    3033 Alignment algorithm | Needleman-Wunsch 
    3034 Similarity matrix | BLOSUM-62 
    3035 SS fraction | 0.3 
    3036 Gap open (HH/SS/other) | 18/18/6 
    3037 Gap extend | 1 
    3038 SS matrix |  |  | H | S | O 
    3039 ---|---|---|--- 
    3040 H | 6 | -9 | -6 
    3041 S |  | 6 | -6 
    3042 O |  |  | 4 
    3043 Iteration cutoff | 2 
    3044  
    3045 Matchmaker RacGEF working1i.pdb, chain I (#1) with K2, chain C (#2), sequence
    3046 alignment score = 1809.7 
    3047 RMSD between 289 pruned atom pairs is 1.066 angstroms; (across all 374 pairs:
    3048 1.772) 
    3049  
    3050 
    3051 > matchmaker #2/C to #1/F pairing ss
    3052 
    3053 Parameters 
    3054 --- 
    3055 Chain pairing | ss 
    3056 Alignment algorithm | Needleman-Wunsch 
    3057 Similarity matrix | BLOSUM-62 
    3058 SS fraction | 0.3 
    3059 Gap open (HH/SS/other) | 18/18/6 
    3060 Gap extend | 1 
    3061 SS matrix |  |  | H | S | O 
    3062 ---|---|---|--- 
    3063 H | 6 | -9 | -6 
    3064 S |  | 6 | -6 
    3065 O |  |  | 4 
    3066 Iteration cutoff | 2 
    3067  
    3068 Matchmaker RacGEF working1i.pdb, chain F (#1) with K2, chain C (#2), sequence
    3069 alignment score = 1791.7 
    3070 RMSD between 252 pruned atom pairs is 1.233 angstroms; (across all 374 pairs:
    3071 2.046) 
    3072  
    3073 
    3074 > hide sel atoms
    3075 
    3076 > hide sel cartoons
    3077 
    3078 > show sel atoms
    3079 
    3080 > select clear
    3081 
    3082 > matchmaker #2/C to #1/D pairing ss
    3083 
    3084 Parameters 
    3085 --- 
    3086 Chain pairing | ss 
    3087 Alignment algorithm | Needleman-Wunsch 
    3088 Similarity matrix | BLOSUM-62 
    3089 SS fraction | 0.3 
    3090 Gap open (HH/SS/other) | 18/18/6 
    3091 Gap extend | 1 
    3092 SS matrix |  |  | H | S | O 
    3093 ---|---|---|--- 
    3094 H | 6 | -9 | -6 
    3095 S |  | 6 | -6 
    3096 O |  |  | 4 
    3097 Iteration cutoff | 2 
    3098  
    3099 Matchmaker RacGEF working1i.pdb, chain D (#1) with K2, chain C (#2), sequence
    3100 alignment score = 1843.3 
    3101 RMSD between 204 pruned atom pairs is 1.175 angstroms; (across all 374 pairs:
    3102 3.061) 
    3103  
    3104 
    3105 > select #1/E
    3106 
    3107 2637 atoms, 2665 bonds, 166 residues, 1 model selected 
    3108 
    3109 > hide sel atoms
    3110 
    3111 > show sel cartoons
    3112 
    3113 > select #2/K
    3114 
    3115 2193 atoms, 2208 bonds, 141 residues, 1 model selected 
    3116 
    3117 > hide sel atoms
    3118 
    3119 > show sel cartoons
    3120 
    3121 > select #1/G:15@CA
    3122 
    3123 1 atom, 1 residue, 1 model selected 
    3124 
    3125 > select #1/E
    3126 
    3127 2637 atoms, 2665 bonds, 166 residues, 1 model selected 
    3128 
    3129 > hide sel cartoons
    3130 
    3131 > select clear
    3132 
    3133 > matchmaker #2/C to #1/F pairing ss
    3134 
    3135 Parameters 
    3136 --- 
    3137 Chain pairing | ss 
    3138 Alignment algorithm | Needleman-Wunsch 
    3139 Similarity matrix | BLOSUM-62 
    3140 SS fraction | 0.3 
    3141 Gap open (HH/SS/other) | 18/18/6 
    3142 Gap extend | 1 
    3143 SS matrix |  |  | H | S | O 
    3144 ---|---|---|--- 
    3145 H | 6 | -9 | -6 
    3146 S |  | 6 | -6 
    3147 O |  |  | 4 
    3148 Iteration cutoff | 2 
    3149  
    3150 Matchmaker RacGEF working1i.pdb, chain F (#1) with K2, chain C (#2), sequence
    3151 alignment score = 1791.7 
    3152 RMSD between 252 pruned atom pairs is 1.233 angstroms; (across all 374 pairs:
    3153 2.046) 
    3154  
    3155 
    3156 > ui tool show "Show Sequence Viewer"
    3157 
    3158 > sequence chain #1/K
    3159 
    3160 Alignment identifier is 1/K 
    3161 
    3162 > select #1/K:802
    3163 
    3164 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3165 
    3166 > select #1/K:802-822
    3167 
    3168 274 atoms, 275 bonds, 21 residues, 1 model selected 
    3169 
    3170 > show sel atoms
    3171 
    3172 > hide sel atoms
    3173 
    3174 > ui tool show "Show Sequence Viewer"
    3175 
    3176 > sequence chain #2/K
    3177 
    3178 Alignment identifier is 2/K 
    3179 
    3180 > select #2/K:803
    3181 
    3182 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3183 
    3184 > select #2/K:803-822
    3185 
    3186 259 atoms, 260 bonds, 20 residues, 1 model selected 
    3187 
    3188 > show sel atoms
    3189 
    3190 > close session
    3191 
    3192 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3193 > evolution/Chimera models/Working models/RacGEF working1i.pdb" format pdb
    3194 
    3195 Chain information for RacGEF working1i.pdb #1 
    3196 --- 
    3197 Chain | Description 
    3198 C D F H I J L M | No description available 
    3199 E | No description available 
    3200 G | No description available 
    3201 K | No description available 
    3202 O | No description available 
    3203 Q | No description available 
    3204 R | No description available 
    3205  
    3206 
    3207 > close session
    3208 
    3209 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3210 > evolution/Chimera models/Working models/SOS-DHa.pdb" format pdb
    3211 
    3212 Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
    3213 also early evolution/Chimera models/Working models/SOS-DHa.pdb 
    3214 --- 
    3215 warnings | Cannot find LINK/SSBOND residue SER (1263 ) 
    3216 Cannot find LINK/SSBOND residue MSE (1264 ) 
    3217 Cannot find LINK/SSBOND residue HIS (1333 ) 
    3218 Cannot find LINK/SSBOND residue MSE (1334 ) 
    3219 Cannot find LINK/SSBOND residue LEU (1062 ) 
    3220 35 messages similar to the above omitted 
    3221 Start residue of secondary structure not found: HELIX 1 1 ASP A 1037 GLN A
    3222 1071 1 35 
    3223 Start residue of secondary structure not found: HELIX 2 2 GLN A 1078 PHE A
    3224 1085 1 8 
    3225 Start residue of secondary structure not found: HELIX 3 3 LEU A 1088 ARG A
    3226 1107 1 20 
    3227 Start residue of secondary structure not found: HELIX 4 4 LEU A 1112 LYS A
    3228 1114 1 3 
    3229 Start residue of secondary structure not found: HELIX 5 5 VAL A 1118 TYR A
    3230 1135 1 18 
    3231 7 messages similar to the above omitted 
    3232  
    3233 SOS-DHa.pdb title: 
    3234 Crystal structure of RAC1 In complex with the guanine nucleotide exchange
    3235 region of TIAM1 [more info...] 
    3236  
    3237 Chain information for SOS-DHa.pdb 
    3238 --- 
    3239 Chain | Description | UniProt 
    3240 1.1/A | T-lymphoma invasion and metastasis inducing protein 1 | TIAM1_MOUSE
    3241 1030-1406 
    3242 1.2/A | T-lymphoma invasion and metastasis inducing protein 1 | TIAM1_MOUSE
    3243 1030-1406 
    3244 1.2/B | ras-related C3 botulinum toxin substrate | RAC1_HUMAN 1-177 
    3245  
    3246 
    3247 > close session
    3248 
    3249 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3250 > evolution/Chimera models/Working models/RacGEF working1h.cxs"
    3251 
    3252 opened ChimeraX session 
    3253 
    3254 > close session
    3255 
    3256 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3257 > evolution/Chimera models/Working models/RacGEF working1h.cxs"
    3258 
    3259 opened ChimeraX session 
    3260 
    3261 > select ::name="4IP"
    3262 
    3263 36 atoms, 36 bonds, 1 residue, 1 model selected 
    3264 
    3265 > view sel
    3266 
    3267 > close session
    3268 
    3269 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3270 > evolution/Chimera models/Working models/RacGEF working1g.cxs" format session
    3271 
    3272 opened ChimeraX session 
    3273 
    3274 > show #2.3 models
    3275 
    3276 > hide #1.3,5#!1.1,4,6-8,10-11 target m
    3277 
    3278 > hide #!6 models
    3279 
    3280 > hide #1.12 models
    3281 
    3282 > show #2.4 models
    3283 
    3284 > show #1.13#2.1,3-4#!1.14#!8.2 cartoons
    3285 
    3286 > ui tool show Matchmaker
    3287 
    3288 > matchmaker #2.4/D to #1.12/O pairing ss
    3289 
    3290 Parameters 
    3291 --- 
    3292 Chain pairing | ss 
    3293 Alignment algorithm | Needleman-Wunsch 
    3294 Similarity matrix | BLOSUM-62 
    3295 SS fraction | 0.3 
    3296 Gap open (HH/SS/other) | 18/18/6 
    3297 Gap extend | 1 
    3298 SS matrix |  |  | H | S | O 
    3299 ---|---|---|--- 
    3300 H | 6 | -9 | -6 
    3301 S |  | 6 | -6 
    3302 O |  |  | 4 
    3303 Iteration cutoff | 2 
    3304  
    3305 Matchmaker RacGEF working1b.pdb O, chain O (#1.12) with SOS1-AF-split.pdb D,
    3306 chain D (#2.4), sequence alignment score = 2416 
    3307 RMSD between 197 pruned atom pairs is 1.301 angstroms; (across all 483 pairs:
    3308 4.276) 
    3309  
    3310 
    3311 > show #1.12 models
    3312 
    3313 > hide #1.12-13#2.1,3-4#!1.14#!8.2 atoms
    3314 
    3315 > ui tool show "Show Sequence Viewer"
    3316 
    3317 > sequence chain #2.4/D
    3318 
    3319 Alignment identifier is 2.4/D 
    3320 
    3321 > select #2.4/D:819
    3322 
    3323 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3324 
    3325 > select #2.4/D:819
    3326 
    3327 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3328 
    3329 > select #2.4/D:819-864
    3330 
    3331 385 atoms, 390 bonds, 46 residues, 1 model selected 
    3332 
    3333 > matchmaker #2.4/D & sel to #1.12/O pairing ss
    3334 
    3335 Parameters 
    3336 --- 
    3337 Chain pairing | ss 
    3338 Alignment algorithm | Needleman-Wunsch 
    3339 Similarity matrix | BLOSUM-62 
    3340 SS fraction | 0.3 
    3341 Gap open (HH/SS/other) | 18/18/6 
    3342 Gap extend | 1 
    3343 SS matrix |  |  | H | S | O 
    3344 ---|---|---|--- 
    3345 H | 6 | -9 | -6 
    3346 S |  | 6 | -6 
    3347 O |  |  | 4 
    3348 Iteration cutoff | 2 
    3349  
    3350 Matchmaker RacGEF working1b.pdb O, chain O (#1.12) with SOS1-AF-split.pdb D,
    3351 chain D (#2.4), sequence alignment score = 239.8 
    3352 RMSD between 46 pruned atom pairs is 0.632 angstroms; (across all 46 pairs:
    3353 0.632) 
    3354  
    3355 
    3356 > select #2.1/A:23
    3357 
    3358 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3359 
    3360 > select #2.1/A:1-23
    3361 
    3362 196 atoms, 202 bonds, 23 residues, 1 model selected 
    3363 Drag select of 143 residues 
    3364 
    3365 > select clear
    3366 
    3367 Drag select of 59 residues 
    3368 
    3369 > show sel atoms
    3370 
    3371 > style sel stick
    3372 
    3373 Changed 644 atom styles 
    3374 
    3375 > select
    3376 
    3377 95223 atoms, 96417 bonds, 13 pseudobonds, 6996 residues, 56 models selected 
    3378 
    3379 > select
    3380 > ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="MSE"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
    3381 
    3382 94465 atoms, 95650 bonds, 6929 residues, 22 models selected 
    3383 
    3384 > hide sel & #1.12#2.1,3-4#!1.14#!8.2 atoms
    3385 
    3386 > close session
    3387 
    3388 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3389 > evolution/Chimera models/Working models/RacGEF working1h.pdb"
    3390 
    3391 Chain information for RacGEF working1h.pdb #1 
    3392 --- 
    3393 Chain | Description 
    3394 C D F H I J L M | No description available 
    3395 E | No description available 
    3396 G | No description available 
    3397 K | No description available 
    3398 O | No description available 
    3399 Q | No description available 
    3400 R | No description available 
    3401  
    3402 
    3403 > color N cornflowerblue atoms
    3404 
    3405 > color O hotpink atoms
    3406 
    3407 > color :arg,hic,his,lys & sidechain & N blue atoms
    3408 
    3409 > color :asp,glu & sidechain & O red atoms
    3410 
    3411 > color S yellow atoms
    3412 
    3413 > color P purple atoms
    3414 
    3415 > hide H atoms
    3416 
    3417 > select /Q
    3418 
    3419 2653 atoms, 2672 bonds, 4 pseudobonds, 168 residues, 2 models selected 
    3420 
    3421 > show sel cartoons
    3422 
    3423 > hide sel atoms
    3424 
    3425 > close session
    3426 
    3427 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3428 > evolution/Chimera models/Working models/RacGEF working1h.cxs"
    3429 
    3430 opened ChimeraX session 
    3431 
    3432 > close session
    3433 
    3434 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3435 > evolution/Chimera models/Working models/RacGEF working1h.pdb" format pdb
    3436 
    3437 Chain information for RacGEF working1h.pdb #1 
    3438 --- 
    3439 Chain | Description 
    3440 C D F H I J L M | No description available 
    3441 E | No description available 
    3442 G | No description available 
    3443 K | No description available 
    3444 O | No description available 
    3445 Q | No description available 
    3446 R | No description available 
    3447  
    3448 
    3449 > select ::name="4IP"
    3450 
    3451 36 atoms, 36 bonds, 1 residue, 1 model selected 
    3452 
    3453 > close session
    3454 
    3455 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3456 > evolution/Chimera models/Working models/RacGEF working1h.cxs" format session
    3457 
    3458 opened ChimeraX session 
    3459 
    3460 > interfaces #1 areaCutoff 20
    3461 
    3462 30 buried areas: R O 2401, R G 2318, F K 1861, C J 1315, F D 1285, F M 1219, C
    3463 H 1216, H L 1210, O Q 1179, R Q 1177, I D 1131, F C 766, O K 748, D K 672, F J
    3464 587, C D 585, O D 536, H D 533, J M 525, O E 524, O F 498, H I 491, C K 438, F
    3465 E 419, I L 355, C E 350, R D 347, D E 333, E K 320, H E 27 
    3466 
    3467 > close session
    3468 
    3469 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3470 > evolution/Chimera models/Working models/RacGEF working1g.cxs"
    3471 
    3472 opened ChimeraX session 
    3473 
    3474 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    3475 > evolution/Chimera models/Working models/RacGEF working1g.pdb"
    3476 
    3477 > close #3
    3478 
    3479 > close #5#4
    3480 
    3481 > close #7
    3482 
    3483 > close #2.2
    3484 
    3485 > close #2.5
    3486 
    3487 > close #8.2
    3488 
    3489 Deleting atomic symmetry model... 
    3490 Deleting atomic symmetry model... 
    3491 
    3492 > close #8
    3493 
    3494 Deleting atomic symmetry model... 
    3495 
    3496 > combine 1,2,6 close true name working
    3497 
    3498 Expected a keyword 
    3499 
    3500 > combine #1,2,6 close true name working
    3501 
    3502 Remapping chain ID 'C' in SOS1-AF-split.pdb C #2.3 to 'D' 
    3503 Remapping chain ID 'D' in SOS1-AF-split.pdb D #2.4 to 'K' 
    3504 Remapping chain ID 'D' in RacGEF working1b.pdb #6 to 'N' 
    3505 
    3506 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    3507 > evolution/Chimera models/Working models/RacGEF working1g.pdb" relModel #1
    3508 
    3509 > close session
    3510 
    3511 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3512 > evolution/Chimera models/Working models/RacGEF working1g.pdb" format pdb
    3513 
    3514 Chain information for RacGEF working1g.pdb #1 
    3515 --- 
    3516 Chain | Description 
    3517 A | No description available 
    3518 C F H I J L M N | No description available 
    3519 D | No description available 
    3520 E | No description available 
    3521 G | No description available 
    3522 K | No description available 
    3523 O | No description available 
    3524 Q | No description available 
    3525 R | No description available 
    3526  
    3527 
    3528 > split #1
    3529 
    3530 Split RacGEF working1g.pdb (#1) into 17 models 
    3531 Chain information for RacGEF working1g.pdb A #1.1 
    3532 --- 
    3533 Chain | Description 
    3534 A | No description available 
    3535  
    3536 Chain information for RacGEF working1g.pdb C #1.2 
    3537 --- 
    3538 Chain | Description 
    3539 C | No description available 
    3540  
    3541 Chain information for RacGEF working1g.pdb D #1.3 
    3542 --- 
    3543 Chain | Description 
    3544 D | No description available 
    3545  
    3546 Chain information for RacGEF working1g.pdb E #1.4 
    3547 --- 
    3548 Chain | Description 
    3549 E | No description available 
    3550  
    3551 Chain information for RacGEF working1g.pdb F #1.5 
    3552 --- 
    3553 Chain | Description 
    3554 F | No description available 
    3555  
    3556 Chain information for RacGEF working1g.pdb G #1.6 
    3557 --- 
    3558 Chain | Description 
    3559 G | No description available 
    3560  
    3561 Chain information for RacGEF working1g.pdb H #1.7 
    3562 --- 
    3563 Chain | Description 
    3564 H | No description available 
    3565  
    3566 Chain information for RacGEF working1g.pdb I #1.8 
    3567 --- 
    3568 Chain | Description 
    3569 I | No description available 
    3570  
    3571 Chain information for RacGEF working1g.pdb J #1.9 
    3572 --- 
    3573 Chain | Description 
    3574 J | No description available 
    3575  
    3576 Chain information for RacGEF working1g.pdb K #1.10 
    3577 --- 
    3578 Chain | Description 
    3579 K | No description available 
    3580  
    3581 Chain information for RacGEF working1g.pdb L #1.11 
    3582 --- 
    3583 Chain | Description 
    3584 L | No description available 
    3585  
    3586 Chain information for RacGEF working1g.pdb M #1.12 
    3587 --- 
    3588 Chain | Description 
    3589 M | No description available 
    3590  
    3591 Chain information for RacGEF working1g.pdb N #1.13 
    3592 --- 
    3593 Chain | Description 
    3594 N | No description available 
    3595  
    3596 Chain information for RacGEF working1g.pdb O #1.14 
    3597 --- 
    3598 Chain | Description 
    3599 O | No description available 
    3600  
    3601 Chain information for RacGEF working1g.pdb Q #1.16 
    3602 --- 
    3603 Chain | Description 
    3604 Q | No description available 
    3605  
    3606 Chain information for RacGEF working1g.pdb R #1.17 
    3607 --- 
    3608 Chain | Description 
    3609 R | No description available 
    3610  
    3611 
    3612 > hide #1.1 models
    3613 
    3614 > select add #1.1
    3615 
    3616 1426 atoms, 1455 bonds, 176 residues, 1 model selected 
    3617 
    3618 > show #1.1 models
    3619 
    3620 > select subtract #1.1
    3621 
    3622 Nothing selected 
    3623 
    3624 > hide #!1.2 models
    3625 
    3626 > show #!1.2 models
    3627 
    3628 > close #1.3#1.2
    3629 
    3630 > hide #1.4,6#!1.5,7-9 target m
    3631 
    3632 > close #1.4,6#1.5,7-9
    3633 
    3634 > close #1.11-12
    3635 
    3636 > hide #!1.13 models
    3637 
    3638 > show #!1.13 models
    3639 
    3640 > close #1.13
    3641 
    3642 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3643 > evolution/Chimera models/Alphafold models/SOS1-AF-split.pdb"
    3644 
    3645 Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
    3646 also early evolution/Chimera models/Alphafold models/SOS1-AF-split.pdb 
    3647 --- 
    3648 warning | Ignored bad PDB record found on line 38 
    3649 DBREF XXXX A 1 176 UNP Q07889 SOS1_HUMAN 1 1333 
    3650  
    3651 SOS1-AF-split.pdb title: 
    3652 Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889)
    3653 [more info...] 
    3654  
    3655 Chain information for SOS1-AF-split.pdb #2 
    3656 --- 
    3657 Chain | Description 
    3658 A | son of sevenless homolog 1 
    3659 B | No description available 
    3660 C | No description available 
    3661 D | No description available 
    3662 E | No description available 
    3663  
    3664 
    3665 > split #2
    3666 
    3667 Split SOS1-AF-split.pdb (#2) into 5 models 
    3668 Chain information for SOS1-AF-split.pdb A #2.1 
    3669 --- 
    3670 Chain | Description 
    3671 A | No description available 
    3672  
    3673 Chain information for SOS1-AF-split.pdb B #2.2 
    3674 --- 
    3675 Chain | Description 
    3676 B | No description available 
    3677  
    3678 Chain information for SOS1-AF-split.pdb C #2.3 
    3679 --- 
    3680 Chain | Description 
    3681 C | No description available 
    3682  
    3683 Chain information for SOS1-AF-split.pdb D #2.4 
    3684 --- 
    3685 Chain | Description 
    3686 D | No description available 
    3687  
    3688 Chain information for SOS1-AF-split.pdb E #2.5 
    3689 --- 
    3690 Chain | Description 
    3691 E | No description available 
    3692  
    3693 
    3694 > close #2.5
    3695 
    3696 > ui tool show Matchmaker
    3697 
    3698 > ui tool show "Show Sequence Viewer"
    3699 
    3700 > sequence chain #1.1/A
    3701 
    3702 Alignment identifier is 1.1/A 
    3703 
    3704 > sequence chain #1.10/K
    3705 
    3706 Alignment identifier is 1.10/K 
    3707 
    3708 > sequence chain #1.14/O
    3709 
    3710 Alignment identifier is 1.14/O 
    3711 
    3712 > sequence chain #1.16/Q
    3713 
    3714 Alignment identifier is 1.16/Q 
    3715 
    3716 > sequence chain #1.17/R
    3717 
    3718 Alignment identifier is 1.17/R 
    3719 
    3720 > sequence chain #2.1/A
    3721 
    3722 Alignment identifier is 2.1/A 
    3723 
    3724 > select #1.14/O:819
    3725 
    3726 14 atoms, 14 bonds, 1 residue, 1 model selected 
    3727 
    3728 > select #1.14/O:819-864
    3729 
    3730 786 atoms, 791 bonds, 46 residues, 1 model selected 
    3731 
    3732 > matchmaker #2.4/D & sel to #1.14/O pairing ss
    3733 
    3734 No molecules/chains to match specified 
    3735 
    3736 > matchmaker #2.4/D to #1.14/O & sel pairing ss
    3737 
    3738 Parameters 
    3739 --- 
    3740 Chain pairing | ss 
    3741 Alignment algorithm | Needleman-Wunsch 
    3742 Similarity matrix | BLOSUM-62 
    3743 SS fraction | 0.3 
    3744 Gap open (HH/SS/other) | 18/18/6 
    3745 Gap extend | 1 
    3746 SS matrix |  |  | H | S | O 
    3747 ---|---|---|--- 
    3748 H | 6 | -9 | -6 
    3749 S |  | 6 | -6 
    3750 O |  |  | 4 
    3751 Iteration cutoff | 2 
    3752  
    3753 Matchmaker RacGEF working1g.pdb O, chain O (#1.14) with SOS1-AF-split.pdb D,
    3754 chain D (#2.4), sequence alignment score = 239.8 
    3755 RMSD between 46 pruned atom pairs is 0.632 angstroms; (across all 46 pairs:
    3756 0.632) 
    3757  
    3758 
    3759 > matchmaker #1.1/A to #1.17/R pairing ss
    3760 
    3761 Parameters 
    3762 --- 
    3763 Chain pairing | ss 
    3764 Alignment algorithm | Needleman-Wunsch 
    3765 Similarity matrix | BLOSUM-62 
    3766 SS fraction | 0.3 
    3767 Gap open (HH/SS/other) | 18/18/6 
    3768 Gap extend | 1 
    3769 SS matrix |  |  | H | S | O 
    3770 ---|---|---|--- 
    3771 H | 6 | -9 | -6 
    3772 S |  | 6 | -6 
    3773 O |  |  | 4 
    3774 Iteration cutoff | 2 
    3775  
    3776 Matchmaker RacGEF working1g.pdb R, chain R (#1.17) with RacGEF working1g.pdb
    3777 A, chain A (#1.1), sequence alignment score = 822.2 
    3778 RMSD between 99 pruned atom pairs is 1.129 angstroms; (across all 176 pairs:
    3779 9.119) 
    3780  
    3781 
    3782 > matchmaker #2.2/B to #1.17/R pairing ss
    3783 
    3784 Parameters 
    3785 --- 
    3786 Chain pairing | ss 
    3787 Alignment algorithm | Needleman-Wunsch 
    3788 Similarity matrix | BLOSUM-62 
    3789 SS fraction | 0.3 
    3790 Gap open (HH/SS/other) | 18/18/6 
    3791 Gap extend | 1 
    3792 SS matrix |  |  | H | S | O 
    3793 ---|---|---|--- 
    3794 H | 6 | -9 | -6 
    3795 S |  | 6 | -6 
    3796 O |  |  | 4 
    3797 Iteration cutoff | 2 
    3798  
    3799 Matchmaker RacGEF working1g.pdb R, chain R (#1.17) with SOS1-AF-split.pdb B,
    3800 chain B (#2.2), sequence alignment score = 1025.4 
    3801 RMSD between 34 pruned atom pairs is 1.097 angstroms; (across all 231 pairs:
    3802 19.032) 
    3803  
    3804 
    3805 > matchmaker #2.3/C to #1.17/R pairing ss
    3806 
    3807 Parameters 
    3808 --- 
    3809 Chain pairing | ss 
    3810 Alignment algorithm | Needleman-Wunsch 
    3811 Similarity matrix | BLOSUM-62 
    3812 SS fraction | 0.3 
    3813 Gap open (HH/SS/other) | 18/18/6 
    3814 Gap extend | 1 
    3815 SS matrix |  |  | H | S | O 
    3816 ---|---|---|--- 
    3817 H | 6 | -9 | -6 
    3818 S |  | 6 | -6 
    3819 O |  |  | 4 
    3820 Iteration cutoff | 2 
    3821  
    3822 Matchmaker RacGEF working1g.pdb R, chain R (#1.17) with SOS1-AF-split.pdb C,
    3823 chain C (#2.3), sequence alignment score = 786.4 
    3824 RMSD between 77 pruned atom pairs is 1.241 angstroms; (across all 157 pairs:
    3825 5.489) 
    3826  
    3827 
    3828 > hide #1.17 models
    3829 
    3830 > hide #1.1 models
    3831 
    3832 > show #1.1 models
    3833 
    3834 > ui tool show "Side View"
    3835 
    3836 > ui tool show Matchmaker
    3837 
    3838 > matchmaker #2.1/A to #1.17/R pairing ss
    3839 
    3840 Parameters 
    3841 --- 
    3842 Chain pairing | ss 
    3843 Alignment algorithm | Needleman-Wunsch 
    3844 Similarity matrix | BLOSUM-62 
    3845 SS fraction | 0.3 
    3846 Gap open (HH/SS/other) | 18/18/6 
    3847 Gap extend | 1 
    3848 SS matrix |  |  | H | S | O 
    3849 ---|---|---|--- 
    3850 H | 6 | -9 | -6 
    3851 S |  | 6 | -6 
    3852 O |  |  | 4 
    3853 Iteration cutoff | 2 
    3854  
    3855 Matchmaker RacGEF working1g.pdb R, chain R (#1.17) with SOS1-AF-split.pdb A,
    3856 chain A (#2.1), sequence alignment score = 822.2 
    3857 RMSD between 99 pruned atom pairs is 1.129 angstroms; (across all 176 pairs:
    3858 9.119) 
    3859  
    3860 
    3861 > select clear
    3862 
    3863 > view
    3864 
    3865 > color N cornflowerblue atoms
    3866 
    3867 > color O hotpink atoms
    3868 
    3869 > color :arg,hic,his,lys & sidechain & N blue atoms
    3870 
    3871 > color :asp,glu & sidechain & O red atoms
    3872 
    3873 > color S yellow atoms
    3874 
    3875 > color P purple atoms
    3876 
    3877 > hide H atoms
    3878 
    3879 Drag select of 124 atoms, 28 bonds 
    3880 
    3881 > ui tool show "Show Sequence Viewer"
    3882 
    3883 > sequence chain #2.1/A
    3884 
    3885 Destroying pre-existing alignment with identifier 2.1/A 
    3886 Alignment identifier is 2.1/A 
    3887 
    3888 > select up
    3889 
    3890 277 atoms, 265 bonds, 25 residues, 5 models selected 
    3891 
    3892 > select #2.1/A:151
    3893 
    3894 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3895 
    3896 > select #2.1/A:150-151
    3897 
    3898 19 atoms, 18 bonds, 2 residues, 1 model selected 
    3899 
    3900 > select #2.1/A:155
    3901 
    3902 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3903 
    3904 > select #2.1/A:155
    3905 
    3906 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3907 
    3908 > hide #1.10 models
    3909 
    3910 > show #1.10 models
    3911 
    3912 > hide #!1.16 models
    3913 
    3914 > show #!1.16 models
    3915 
    3916 > hide #2.2 models
    3917 
    3918 > hide #2.4 models
    3919 
    3920 > show #2.4 models
    3921 
    3922 > hide #2.4 models
    3923 
    3924 > show #2.4 models
    3925 
    3926 > hide #1.14 models
    3927 
    3928 > ui tool show "Show Sequence Viewer"
    3929 
    3930 > sequence chain #1.1/A
    3931 
    3932 Destroying pre-existing alignment with identifier 1.1/A 
    3933 Alignment identifier is 1.1/A 
    3934 
    3935 > sequence chain #1.10/K
    3936 
    3937 Destroying pre-existing alignment with identifier 1.10/K 
    3938 Alignment identifier is 1.10/K 
    3939 
    3940 > ui tool show "Show Sequence Viewer"
    3941 
    3942 > sequence chain #1.14/O
    3943 
    3944 Alignment identifier is 1.14/O 
    3945 
    3946 > hide #1.1 models
    3947 
    3948 > hide #1.15 models
    3949 
    3950 > hide #!1.16 models
    3951 
    3952 > hide #2.1 models
    3953 
    3954 > hide #2.3 models
    3955 
    3956 > show #1.14 models
    3957 
    3958 Drag select of 12007 atoms 
    3959 
    3960 > hide sel atoms
    3961 
    3962 > show sel cartoons
    3963 
    3964 > select clear
    3965 
    3966 > close #1.10
    3967 
    3968 > show #1.1 models
    3969 
    3970 > show #!1.16 models
    3971 
    3972 > show #2.1 models
    3973 
    3974 > hide #2.1 models
    3975 
    3976 > show #2.1 models
    3977 
    3978 > hide #1.1 models
    3979 
    3980 > hide #2.1 models
    3981 
    3982 > show #1.1 models
    3983 
    3984 > show #2.1 models
    3985 
    3986 > hide #1.1 models
    3987 
    3988 > show #1.1 models
    3989 
    3990 > hide #1.1 models
    3991 
    3992 > close #1.1
    3993 
    3994 > select add #2.1
    3995 
    3996 1426 atoms, 1455 bonds, 176 residues, 1 model selected 
    3997 
    3998 > hide sel atoms
    3999 
    4000 > show sel cartoons
    4001 
    4002 > select #2.1/A:176
    4003 
    4004 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4005 
    4006 > select #2.1/A:24-176
    4007 
    4008 1230 atoms, 1252 bonds, 153 residues, 1 model selected 
    4009 
    4010 > show sel atoms
    4011 
    4012 > select clear
    4013 
    4014 > select add #2.1
    4015 
    4016 1426 atoms, 1455 bonds, 176 residues, 1 model selected 
    4017 
    4018 > ui mousemode right "translate selected models"
    4019 
    4020 > view matrix models
    4021 > #2.1,0.17068,0.54934,-0.81798,318.84,-0.9487,0.31585,0.014162,343.48,0.26614,0.77361,0.57507,360.73
    4022 
    4023 > ui mousemode right "rotate selected models"
    4024 
    4025 > view matrix models
    4026 > #2.1,0.10598,0.56231,-0.82011,316.47,-0.95727,0.28088,0.06888,342.72,0.26908,0.77776,0.56805,360.89
    4027 
    4028 > select clear
    4029 
    4030 > select add #2.4
    4031 
    4032 4003 atoms, 4102 bonds, 484 residues, 1 model selected 
    4033 
    4034 > ui mousemode right zoom
    4035 
    4036 > show sel atoms
    4037 
    4038 > hide sel cartoons
    4039 
    4040 > select clear
    4041 
    4042 > hide #1.14 models
    4043 
    4044 > select add #2.1
    4045 
    4046 1426 atoms, 1455 bonds, 176 residues, 1 model selected 
    4047 
    4048 > combine #2/A name HH2
    4049 
    4050 > ui tool show "Show Sequence Viewer"
    4051 
    4052 > sequence chain #3/A
    4053 
    4054 Alignment identifier is 3/A 
    4055 
    4056 > select #3/A:24
    4057 
    4058 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4059 
    4060 > select #3/A:24-176
    4061 
    4062 1230 atoms, 1252 bonds, 153 residues, 1 model selected 
    4063 
    4064 > hide sel atoms
    4065 
    4066 > hide sel cartoons
    4067 
    4068 > hide #2.1 models
    4069 
    4070 > select #3/A:23
    4071 
    4072 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4073 
    4074 > select #3/A:1-23
    4075 
    4076 196 atoms, 202 bonds, 23 residues, 1 model selected 
    4077 
    4078 > show sel atoms
    4079 
    4080 > style sel stick
    4081 
    4082 Changed 196 atom styles 
    4083 
    4084 > select #3/A:18
    4085 
    4086 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4087 
    4088 > select #3/A:18-20
    4089 
    4090 34 atoms, 35 bonds, 3 residues, 1 model selected 
    4091 
    4092 > style sel sphere
    4093 
    4094 Changed 34 atom styles 
    4095 
    4096 > select #3/A:21
    4097 
    4098 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4099 
    4100 > select #3/A:21
    4101 
    4102 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4103 
    4104 > cofr sel
    4105 
    4106 > ui mousemode right "rotate selected models"
    4107 
    4108 > view matrix models
    4109 > #3,-0.72646,0.55151,0.41,277.31,-0.41402,-0.82742,0.37942,346.72,0.5485,0.10588,0.82942,360.98
    4110 
    4111 > ui mousemode right "translate selected models"
    4112 
    4113 > view matrix models
    4114 > #3,-0.72646,0.55151,0.41,297.17,-0.41402,-0.82742,0.37942,343.23,0.5485,0.10588,0.82942,360.05
    4115 
    4116 > view matrix models
    4117 > #3,-0.72646,0.55151,0.41,297.09,-0.41402,-0.82742,0.37942,342.59,0.5485,0.10588,0.82942,359.52
    4118 
    4119 > select #3/A:15
    4120 
    4121 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4122 
    4123 > select #3/A:15
    4124 
    4125 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4126 
    4127 > ui tool show "Selection Inspector"
    4128 
    4129 > setattr sel r psi 100
    4130 
    4131 Assigning psi attribute to 1 item 
    4132 
    4133 > setattr sel r omega 180
    4134 
    4135 Assigning omega attribute to 1 item 
    4136 
    4137 > select clear
    4138 
    4139 > select add #2.1
    4140 
    4141 1426 atoms, 1455 bonds, 176 residues, 1 model selected 
    4142 
    4143 > select clear
    4144 
    4145 > select add #3
    4146 
    4147 1426 atoms, 1455 bonds, 176 residues, 1 model selected 
    4148 
    4149 > view matrix models
    4150 > #3,-0.72646,0.55151,0.41,305.49,-0.41402,-0.82742,0.37942,353.45,0.5485,0.10588,0.82942,368.37
    4151 
    4152 > view matrix models
    4153 > #3,-0.72646,0.55151,0.41,306.78,-0.41402,-0.82742,0.37942,355.38,0.5485,0.10588,0.82942,369.95
    4154 
    4155 > view matrix models
    4156 > #3,-0.72646,0.55151,0.41,304.37,-0.41402,-0.82742,0.37942,350.22,0.5485,0.10588,0.82942,365.66
    4157 
    4158 > view matrix models
    4159 > #3,-0.72646,0.55151,0.41,299.25,-0.41402,-0.82742,0.37942,340.69,0.5485,0.10588,0.82942,357.76
    4160 
    4161 > select #3/A:19
    4162 
    4163 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4164 
    4165 > select #3/A:19
    4166 
    4167 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4168 
    4169 > ui tool show Rotamers
    4170 
    4171 > swapaa interactive sel TRP rotLib Dunbrack
    4172 
    4173 HH2 #3/A TRP 19: phi -109.3, psi -36.1 trans 
    4174 Changed 468 bond radii 
    4175 
    4176 > select clear
    4177 
    4178 > select add #2.1
    4179 
    4180 1426 atoms, 1455 bonds, 176 residues, 1 model selected 
    4181 
    4182 > select add #3
    4183 
    4184 3284 atoms, 3378 bonds, 388 residues, 39 models selected 
    4185 
    4186 > select subtract #2.1
    4187 
    4188 1858 atoms, 1923 bonds, 212 residues, 38 models selected 
    4189 
    4190 > ui mousemode right "rotate selected models"
    4191 
    4192 > view matrix models
    4193 > #3,-0.60169,0.56869,0.56085,307.94,-0.51229,-0.8135,0.27528,334.5,0.6128,-0.12169,0.78081,356.56
    4194 
    4195 > cofr sel
    4196 
    4197 > view matrix models
    4198 > #3,-0.0011605,-0.040014,0.9992,334.15,-0.95571,-0.29401,-0.012884,316.81,0.29429,-0.95496,-0.0379,315.28
    4199 
    4200 > view matrix models
    4201 > #3,-0.99512,-0.087469,-0.045593,268.42,0.060843,-0.90813,0.41425,364.62,-0.077638,0.40946,0.90902,331.18
    4202 
    4203 > view matrix models
    4204 > #3,-0.57009,0.61068,-0.54961,296.79,-0.63597,-0.75153,-0.17537,323.6,-0.52014,0.24956,0.81681,304.04
    4205 
    4206 > ui mousemode right "translate selected models"
    4207 
    4208 > view matrix models
    4209 > #3,-0.57009,0.61068,-0.54961,294,-0.63597,-0.75153,-0.17537,331.14,-0.52014,0.24956,0.81681,308.23
    4210 
    4211 > view matrix models
    4212 > #3,-0.57009,0.61068,-0.54961,297.48,-0.63597,-0.75153,-0.17537,330.31,-0.52014,0.24956,0.81681,316.07
    4213 
    4214 > select #!3/A:19@CZ3
    4215 
    4216 1 atom, 1 residue, 1 model selected 
    4217 
    4218 > cofr sel
    4219 
    4220 > roll z 180 1 models #3
    4221 
    4222 > select add #3
    4223 
    4224 1858 atoms, 1923 bonds, 212 residues, 38 models selected 
    4225 
    4226 > view matrix models
    4227 > #3,-0.88787,-0.34582,-0.30346,266.38,-0.23952,0.91057,-0.33689,375.39,0.39282,-0.22643,-0.8913,335.58
    4228 
    4229 > ui mousemode right "rotate selected models"
    4230 
    4231 > view matrix models
    4232 > #3,-0.896,-0.33912,-0.28666,266.28,-0.24114,0.91368,-0.32717,375.48,0.37287,-0.22402,-0.90043,334.47
    4233 
    4234 > undo
    4235 
    4236 > view matrix models
    4237 > #3,-0.81524,0.20603,-0.54124,276.95,0.34937,0.92033,-0.1759,408.43,0.46188,-0.33249,-0.82227,338.19
    4238 
    4239 > ui mousemode right "translate selected models"
    4240 
    4241 > view matrix models
    4242 > #3,-0.81524,0.20603,-0.54124,280.02,0.34937,0.92033,-0.1759,405.45,0.46188,-0.33249,-0.82227,337.18
    4243 
    4244 > clashes #!3 & ~#!3/A:19 & ~solvent radius 0.075 reveal true restrict #3.1 &
    4245 > ~@c,ca,n
    4246 
    4247 1042 clashes 
    4248 
    4249 > swapaa #!3/A:19 TRP criteria 3 rotLib Dunbrack retain false
    4250 
    4251 Using Dunbrack library 
    4252 HH2 #!3/A TRP 19: phi -109.3, psi -36.1 trans 
    4253 Applying TRP rotamer (chi angles: 60.9 -93.0) to HH2 #!3/A TRP 19 
    4254 
    4255 > ui tool show "Show Sequence Viewer"
    4256 
    4257 > sequence chain #1.16/Q
    4258 
    4259 Alignment identifier is 1.16/Q 
    4260 
    4261 > select #1.16/Q:46
    4262 
    4263 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4264 
    4265 > select #1.16/Q:40-46
    4266 
    4267 135 atoms, 135 bonds, 7 residues, 1 model selected 
    4268 
    4269 > view matrix models #1.16,1,0,0,-0.15577,0,1,0,-0.49524,0,0,1,0.22752
    4270 
    4271 > undo
    4272 
    4273 > ui mousemode right zoom
    4274 
    4275 > interfaces #1 areaCutoff 20
    4276 
    4277 3 buried areas: #1.17/R #1.14/O 2215, #1.14/O #1.16/Q 1094, #1.17/R #1.16/Q
    4278 1081 
    4279 
    4280 > show #1.14 models
    4281 
    4282 > hide #2.4 models
    4283 
    4284 > select clear
    4285 
    4286 > select add #1.14
    4287 
    4288 8016 atoms, 8115 bonds, 483 residues, 1 model selected 
    4289 
    4290 > show sel atoms
    4291 
    4292 > close #4
    4293 
    4294 > hide #3 models
    4295 
    4296 > show #3 models
    4297 
    4298 > select #1.16/Q:40
    4299 
    4300 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4301 
    4302 > select #1.16/Q:40-46
    4303 
    4304 135 atoms, 135 bonds, 7 residues, 1 model selected 
    4305 
    4306 > select #3/A:20
    4307 
    4308 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4309 
    4310 > select #3/A:20
    4311 
    4312 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4313 
    4314 > select #3/A:18
    4315 
    4316 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4317 
    4318 > select #3/A:18
    4319 
    4320 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4321 
    4322 > swapaa #1/Q:64 tyr
    4323 
    4324 Using Dunbrack library 
    4325 RacGEF working1g.pdb Q #1.16/Q ALA 64: phi -78.6, psi -7.7 trans 
    4326 Applying TYR rotamer (chi angles: -68.6 -18.1) to RacGEF working1g.pdb Q
    4327 #1.16/Q TYR 64 
    4328 
    4329 > select #1.16/Q:64-65
    4330 
    4331 25 atoms, 25 bonds, 2 residues, 1 model selected 
    4332 
    4333 > select #1.16/Q:64-65
    4334 
    4335 25 atoms, 25 bonds, 2 residues, 1 model selected 
    4336 
    4337 > select #1.16/Q:64
    4338 
    4339 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4340 
    4341 > select #1.16/Q:64
    4342 
    4343 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4344 
    4345 > select #1.16/Q:71
    4346 
    4347 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4348 
    4349 > select #1.16/Q:71
    4350 
    4351 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4352 
    4353 > select #1.16/Q:73
    4354 
    4355 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4356 
    4357 > select #1.16/Q:73
    4358 
    4359 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4360 
    4361 > select #1.14/O:884-885
    4362 
    4363 45 atoms, 45 bonds, 2 residues, 1 model selected 
    4364 
    4365 > select #1.14/O:884-885
    4366 
    4367 45 atoms, 45 bonds, 2 residues, 1 model selected 
    4368 
    4369 > select #1.14/O:884
    4370 
    4371 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4372 
    4373 > select #1.14/O:884
    4374 
    4375 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4376 
    4377 > ui tool show Rotamers
    4378 
    4379 > swapaa interactive sel TYR rotLib Dunbrack
    4380 
    4381 RacGEF working1g.pdb O #1.14/O TYR 884: phi -63.4, psi -29.0 trans 
    4382 Changed 180 bond radii 
    4383 
    4384 > swapaa #!1.14/O:884 TYR criteria 2 rotLib Dunbrack retain false
    4385 
    4386 Using Dunbrack library 
    4387 RacGEF working1g.pdb O #!1.14/O TYR 884: phi -63.4, psi -29.0 trans 
    4388 Applying TYR rotamer (chi angles: 72.9 89.3) to RacGEF working1g.pdb O
    4389 #!1.14/O TYR 884 
    4390 
    4391 > select #3/A:23
    4392 
    4393 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4394 
    4395 > select #3/A:1-23
    4396 
    4397 196 atoms, 202 bonds, 23 residues, 1 model selected 
    4398 
    4399 > select #3/A:24
    4400 
    4401 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4402 
    4403 > select #3/A:24-176
    4404 
    4405 1230 atoms, 1252 bonds, 153 residues, 1 model selected 
    4406 
    4407 > delete atoms sel
    4408 
    4409 > delete bonds sel
    4410 
    4411 > combine #1/Q,O#3 close true name HH2
    4412 
    4413 > ui tool show "Show Sequence Viewer"
    4414 
    4415 > sequence chain #3/A
    4416 
    4417 Alignment identifier is 3/A 
    4418 
    4419 > sequence chain #3/O
    4420 
    4421 Alignment identifier is 3/O 
    4422 
    4423 > sequence chain #3/Q
    4424 
    4425 Alignment identifier is 3/Q 
    4426 
    4427 > isolde sim start #3/A
    4428 
    4429 > set selectionWidth 4
    4430 
    4431 Done loading forcefield 
    4432 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4433 chains... 
    4434 ISOLDE: Corrected atom nomenclature of 5 residues in model #3 to IUPAC-IUB
    4435 standards. 
    4436 
    4437 > isolde set simFidelityMode Medium/Medium
    4438 
    4439 ISOLDE: setting sim fidelity mode to Medium/Medium 
    4440 nonbonded_cutoff_distance = 0.900000 
    4441 use_gbsa = True 
    4442 gbsa_cutoff = 1.100000 
    4443 Sim termination reason: None 
    4444 ISOLDE: stopped sim 
    4445 
    4446 > addh
    4447 
    4448 Summary of feedback from adding hydrogens to multiple structures 
    4449 --- 
    4450 warnings | Skipped 4 atom(s) with bad connectivities; see log for details 
    4451 Skipped 6 atom(s) with bad connectivities; see log for details 
    4452 notes | Chain-initial residues that are actual N termini: 
    4453 Chain-initial residues that are not actual N termini: 
    4454 Chain-final residues that are actual C termini: 
    4455 Chain-final residues that are not actual C termini: 
    4456 1 hydrogen bonds 
    4457 No usable SEQRES records for RacGEF working1g.pdb R (#1.17) chain R; guessing
    4458 termini instead 
    4459 Chain-initial residues that are actual N termini: RacGEF working1g.pdb R
    4460 #1.17/R MET 1 
    4461 Chain-initial residues that are not actual N termini: 
    4462 Chain-final residues that are actual C termini: 
    4463 Chain-final residues that are not actual C termini: RacGEF working1g.pdb R
    4464 #1.17/R GLU 564 
    4465 Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
    4466 GLY 280 O 
    4467 Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
    4468 #1.17/R GLY 280 O 
    4469  
    4470 Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
    4471 GLY 280 OXT 
    4472 Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
    4473 #1.17/R GLY 280 OXT 
    4474  
    4475 Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
    4476 GLY 280 O 
    4477 Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
    4478 #1.17/R GLY 280 O 
    4479  
    4480 Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
    4481 GLY 280 OXT 
    4482 Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
    4483 #1.17/R GLY 280 OXT 
    4484  
    4485 498 hydrogen bonds 
    4486 RacGEF working1g.pdb R #1.17/R GLU 564 is not terminus, removing H atom from
    4487 'C' 
    4488 No usable SEQRES records for SOS1-AF-split.pdb A (#2.1) chain A; guessing
    4489 termini instead 
    4490 Chain-initial residues that are actual N termini: SOS1-AF-split.pdb A #2.1/A
    4491 MET 1 
    4492 Chain-initial residues that are not actual N termini: 
    4493 Chain-final residues that are actual C termini: 
    4494 Chain-final residues that are not actual C termini: SOS1-AF-split.pdb A #2.1/A
    4495 PHE 176 
    4496 158 hydrogen bonds 
    4497 SOS1-AF-split.pdb A #2.1/A PHE 176 is not terminus, removing H atom from 'C' 
    4498 No usable SEQRES records for SOS1-AF-split.pdb B (#2.2) chain B; guessing
    4499 termini instead 
    4500 Chain-initial residues that are actual N termini: SOS1-AF-split.pdb B #2.2/B
    4501 HIS 177 
    4502 Chain-initial residues that are not actual N termini: 
    4503 Chain-final residues that are actual C termini: 
    4504 Chain-final residues that are not actual C termini: SOS1-AF-split.pdb B #2.2/B
    4505 PHE 407 
    4506 209 hydrogen bonds 
    4507 SOS1-AF-split.pdb B #2.2/B PHE 407 is not terminus, removing H atom from 'C' 
    4508 No usable SEQRES records for SOS1-AF-split.pdb C (#2.3) chain C; guessing
    4509 termini instead 
    4510 Chain-initial residues that are actual N termini: SOS1-AF-split.pdb C #2.3/C
    4511 TYR 408 
    4512 Chain-initial residues that are not actual N termini: 
    4513 Chain-final residues that are actual C termini: 
    4514 Chain-final residues that are not actual C termini: SOS1-AF-split.pdb C #2.3/C
    4515 GLU 564 
    4516 128 hydrogen bonds 
    4517 SOS1-AF-split.pdb C #2.3/C GLU 564 is not terminus, removing H atom from 'C' 
    4518 No usable SEQRES records for SOS1-AF-split.pdb D (#2.4) chain D; guessing
    4519 termini instead 
    4520 Chain-initial residues that are actual N termini: SOS1-AF-split.pdb D #2.4/D
    4521 GLU 565 
    4522 Chain-initial residues that are not actual N termini: 
    4523 Chain-final residues that are actual C termini: 
    4524 Chain-final residues that are not actual C termini: SOS1-AF-split.pdb D #2.4/D
    4525 GLY 1048 
    4526 467 hydrogen bonds 
    4527 SOS1-AF-split.pdb D #2.4/D GLY 1048 is not terminus, removing H atom from 'C' 
    4528 No usable SEQRES records for HH2 (#3.2) chain O; guessing termini instead 
    4529 No usable SEQRES records for HH2 (#3.2) chain Q; guessing termini instead 
    4530 No usable SEQRES records for HH2 (#3.2) chain A; guessing termini instead 
    4531 Chain-initial residues that are actual N termini: HH2 #3.2/Q MET 1, HH2 #3.2/A
    4532 MET 1 
    4533 Chain-initial residues that are not actual N termini: HH2 #3.2/O GLU 565 
    4534 Chain-final residues that are actual C termini: HH2 #3.2/O PRO 1047, HH2
    4535 #3.2/Q HIS 166 
    4536 Chain-final residues that are not actual C termini: HH2 #3.2/A LEU 23 
    4537 Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 OXT 
    4538 Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 OXT 
    4539  
    4540 Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 O 
    4541 Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 O 
    4542  
    4543 Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 OXT 
    4544 Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 OXT 
    4545  
    4546 Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 O 
    4547 Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 O 
    4548  
    4549 Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 OXT 
    4550 Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 OXT 
    4551  
    4552 1 messages similar to the above omitted 
    4553 684 hydrogen bonds 
    4554 HH2 #3.2/A LEU 23 is not terminus, removing H atom from 'C' 
    4555 8792 hydrogens added 
    4556  
    4557 
    4558 > isolde sim start #3/A
    4559 
    4560 > set selectionWidth 4
    4561 
    4562 Done loading forcefield 
    4563 
    4564 > isolde set simFidelityMode Medium/Medium
    4565 
    4566 ISOLDE: setting sim fidelity mode to Medium/Medium 
    4567 nonbonded_cutoff_distance = 0.900000 
    4568 use_gbsa = True 
    4569 gbsa_cutoff = 1.100000 
    4570 ISOLDE: started sim 
    4571 
    4572 > isolde sim stop discardTo start
    4573 
    4574 Sim termination reason: None 
    4575 reverting to start 
    4576 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4577 chains... 
    4578 ISOLDE: stopped sim 
    4579 
    4580 > isolde sim start #3/A,O,Q
    4581 
    4582 ISOLDE: started sim 
    4583 
    4584 > hide sel atoms
    4585 
    4586 > show sel cartoons
    4587 
    4588 > select #3.2/A
    4589 
    4590 383 atoms, 389 bonds, 23 residues, 1 model selected 
    4591 
    4592 > show sel atoms
    4593 
    4594 > ui tool show "Show Sequence Viewer"
    4595 
    4596 > sequence chain #3.2/A
    4597 
    4598 Alignment identifier is 3.2/A 
    4599 
    4600 > show sel atoms
    4601 
    4602 > select #3.2/O
    4603 
    4604 8016 atoms, 8115 bonds, 483 residues, 1 model selected 
    4605 
    4606 > style sel sphere
    4607 
    4608 Changed 8016 atom styles 
    4609 
    4610 > select #3.2/Q
    4611 
    4612 2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected 
    4613 
    4614 > style sel sphere
    4615 
    4616 Changed 2664 atom styles 
    4617 
    4618 > select #3.2/A:19
    4619 
    4620 24 atoms, 25 bonds, 1 residue, 1 model selected 
    4621 
    4622 > select #3.2/A:19
    4623 
    4624 24 atoms, 25 bonds, 1 residue, 1 model selected 
    4625 
    4626 > select #3.2/A:14-15
    4627 
    4628 29 atoms, 28 bonds, 2 residues, 1 model selected 
    4629 
    4630 > select #3.2/A:1-15
    4631 
    4632 244 atoms, 247 bonds, 15 residues, 1 model selected 
    4633 
    4634 > ui mousemode right "isolde tug selection"
    4635 
    4636 > select #3.2/A:20
    4637 
    4638 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4639 
    4640 > select #3.2/A:20
    4641 
    4642 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4643 
    4644 > select #3.2/A:18
    4645 
    4646 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4647 
    4648 > select #3.2/A:18
    4649 
    4650 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4651 
    4652 > select #3.2/A:1
    4653 
    4654 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4655 
    4656 > select #3.2/A:1
    4657 
    4658 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4659 
    4660 > select #3.2/A:8
    4661 
    4662 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4663 
    4664 > select #3.2/A:8
    4665 
    4666 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4667 
    4668 > color N cornflowerblue atoms
    4669 
    4670 > color O hotpink atoms
    4671 
    4672 > color :arg,hic,his,lys & sidechain & N blue atoms
    4673 
    4674 > color :asp,glu & sidechain & O red atoms
    4675 
    4676 > color S yellow atoms
    4677 
    4678 > color P purple atoms
    4679 
    4680 > select #3.2/O:799
    4681 
    4682 16 atoms, 15 bonds, 1 residue, 1 model selected 
    4683 
    4684 > select #3.2/O:668-799
    4685 
    4686 2231 atoms, 2260 bonds, 132 residues, 1 model selected 
    4687 
    4688 > select #3.2/A:1-2
    4689 
    4690 36 atoms, 35 bonds, 2 residues, 1 model selected 
    4691 
    4692 > select #3.2/A:1-2
    4693 
    4694 36 atoms, 35 bonds, 2 residues, 1 model selected 
    4695 
    4696 > select #3.2/A:23
    4697 
    4698 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4699 
    4700 > select #3.2/A:21-23
    4701 
    4702 45 atoms, 44 bonds, 3 residues, 1 model selected 
    4703 
    4704 > select #3.2/A:19
    4705 
    4706 24 atoms, 25 bonds, 1 residue, 1 model selected 
    4707 
    4708 > select #3.2/A:19
    4709 
    4710 24 atoms, 25 bonds, 1 residue, 1 model selected 
    4711 
    4712 > select #3.2/A:20
    4713 
    4714 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4715 
    4716 > select #3.2/A:20
    4717 
    4718 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4719 
    4720 > select #3.2/A:18
    4721 
    4722 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4723 
    4724 > select #3.2/A:18
    4725 
    4726 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4727 
    4728 > select #3.2/A:19
    4729 
    4730 24 atoms, 25 bonds, 1 residue, 1 model selected 
    4731 
    4732 > style sel sphere
    4733 
    4734 Changed 24 atom styles 
    4735 
    4736 > ui mousemode right "isolde tug atom"
    4737 
    4738 > select #3.2/A:20
    4739 
    4740 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4741 
    4742 > select #3.2/A:19-20
    4743 
    4744 48 atoms, 49 bonds, 2 residues, 1 model selected 
    4745 
    4746 > select #3.2/A:18
    4747 
    4748 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4749 
    4750 > select #3.2/A:18
    4751 
    4752 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4753 
    4754 > select #3.2/Q:40
    4755 
    4756 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4757 
    4758 > select #3.2/Q:40-46
    4759 
    4760 135 atoms, 135 bonds, 7 residues, 1 model selected 
    4761 
    4762 > style sel stick
    4763 
    4764 Changed 135 atom styles 
    4765 
    4766 > style sel sphere
    4767 
    4768 Changed 135 atom styles 
    4769 
    4770 > select #3.2/A:1
    4771 
    4772 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4773 
    4774 > select #3.2/A:1
    4775 
    4776 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4777 
    4778 > style sel sphere
    4779 
    4780 Changed 19 atom styles 
    4781 
    4782 > style sel sphere
    4783 
    4784 Changed 19 atom styles 
    4785 
    4786 > style sel sphere
    4787 
    4788 Changed 19 atom styles 
    4789 
    4790 > ui mousemode right "isolde tug selection"
    4791 
    4792 > select #3.2/A:19-20
    4793 
    4794 48 atoms, 49 bonds, 2 residues, 1 model selected 
    4795 
    4796 > select #3.2/A:19-20
    4797 
    4798 48 atoms, 49 bonds, 2 residues, 1 model selected 
    4799 
    4800 > ui mousemode right "isolde tug atom"
    4801 
    4802 > select #3.2/A:20
    4803 
    4804 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4805 
    4806 > select #3.2/A:20
    4807 
    4808 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4809 
    4810 > select #3.2/A:20
    4811 
    4812 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4813 
    4814 > select #3.2/A:20
    4815 
    4816 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4817 
    4818 > select #3.2/A:18-20
    4819 
    4820 70 atoms, 71 bonds, 3 residues, 1 model selected 
    4821 
    4822 > style sel sphere
    4823 
    4824 Changed 70 atom styles 
    4825 
    4826 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    4827 bonded heavy atom. 
    4828 
    4829 > select #3.2/A:22-23
    4830 
    4831 38 atoms, 37 bonds, 2 residues, 1 model selected 
    4832 
    4833 > select #3.2/A:21-23
    4834 
    4835 45 atoms, 44 bonds, 3 residues, 1 model selected 
    4836 
    4837 > style sel sphere
    4838 
    4839 Changed 45 atom styles 
    4840 
    4841 > select #3.2/A:1
    4842 
    4843 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4844 
    4845 > select #3.2/A:1
    4846 
    4847 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4848 
    4849 > style sel stick
    4850 
    4851 Changed 19 atom styles 
    4852 
    4853 > style sel stick
    4854 
    4855 Changed 17 atom styles 
    4856 
    4857 > style sel stick
    4858 
    4859 Changed 22 atom styles 
    4860 
    4861 > style sel stick
    4862 
    4863 Changed 14 atom styles 
    4864 
    4865 > style sel stick
    4866 
    4867 Changed 15 atom styles 
    4868 
    4869 > isolde sim stop
    4870 
    4871 Sim termination reason: None 
    4872 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4873 chains... 
    4874 ISOLDE: Corrected atom nomenclature of 21 residues in model #3.2 to IUPAC-IUB
    4875 standards. 
    4876 ISOLDE: stopped sim 
    4877 
    4878 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    4879 > evolution/Chimera models/Working models/temp.pdb"
    4880 
    4881 > close session
    4882 
    4883 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    4884 > evolution/Chimera models/Working models/temp.pdb" format pdb
    4885 
    4886 Chain information for temp.pdb 
    4887 --- 
    4888 Chain | Description 
    4889 1.3/A | No description available 
    4890 1.7/A | No description available 
    4891 1.4/B | No description available 
    4892 1.5/C | No description available 
    4893 1.6/D | No description available 
    4894 1.7/O | No description available 
    4895 1.7/Q | No description available 
    4896 1.2/R | No description available 
    4897  
    4898 
    4899 > select add #1.1
    4900 
    4901 36 atoms, 36 bonds, 1 residue, 1 model selected 
    4902 
    4903 > delete atoms sel
    4904 
    4905 > delete bonds sel
    4906 
    4907 > select add #1.2
    4908 
    4909 9136 atoms, 9223 bonds, 564 residues, 1 model selected 
    4910 
    4911 > hide #1.3 models
    4912 
    4913 > show #1.3 models
    4914 
    4915 > ui tool show "Show Sequence Viewer"
    4916 
    4917 > hide #1.2 models
    4918 
    4919 > hide #1.4 models
    4920 
    4921 > hide #1.5 models
    4922 
    4923 > hide #1.3 models
    4924 
    4925 > hide #1.6 models
    4926 
    4927 > select add #1.3
    4928 
    4929 12024 atoms, 12140 bonds, 740 residues, 2 models selected 
    4930 
    4931 > select subtract #1.3
    4932 
    4933 9136 atoms, 9223 bonds, 564 residues, 1 model selected 
    4934 
    4935 > select #1.3/A#1.7/A
    4936 
    4937 3271 atoms, 3306 bonds, 199 residues, 2 models selected 
    4938 
    4939 > ui tool show "Show Sequence Viewer"
    4940 
    4941 > sequence chain #1.7/A
    4942 
    4943 Alignment identifier is 1.7/A 
    4944 
    4945 > show sel & #!1.7 atoms
    4946 
    4947 > select #1.7/A:6
    4948 
    4949 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4950 
    4951 > select #1.7/A:1-6
    4952 
    4953 99 atoms, 98 bonds, 6 residues, 1 model selected 
    4954 
    4955 > select #1.7/A:7
    4956 
    4957 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4958 
    4959 > select #1.7/A:7
    4960 
    4961 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4962 
    4963 > select add #1.7
    4964 
    4965 11063 atoms, 11188 bonds, 4 pseudobonds, 674 residues, 2 models selected 
    4966 
    4967 > isolde sim start #1.7
    4968 
    4969 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4970 chains... 
    4971 Chain information for temp.pdb 
    4972 --- 
    4973 Chain | Description 
    4974 2.2/A | No description available 
    4975 2.2/O | No description available 
    4976 2.2/Q | No description available 
    4977  
    4978 ISOLDE: started sim 
    4979 
    4980 > isolde sim pause
    4981 
    4982 > select #2.2/O
    4983 
    4984 8016 atoms, 8115 bonds, 483 residues, 1 model selected 
    4985 
    4986 > style sel sphere
    4987 
    4988 Changed 8016 atom styles 
    4989 
    4990 > select #2.2/Q
    4991 
    4992 2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected 
    4993 
    4994 > show sel cartoons
    4995 
    4996 > hide sel atoms
    4997 
    4998 > select #2.2/A:7
    4999 
    5000 14 atoms, 14 bonds, 1 residue, 1 model selected 
    5001 
    5002 > select #2.2/A:7
    5003 
    5004 14 atoms, 14 bonds, 1 residue, 1 model selected 
    5005 
    5006 > select #2.2/A:1
    5007 
    5008 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5009 
    5010 > select #2.2/A:1
    5011 
    5012 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5013 
    5014 > ui mousemode right "isolde tug selection"
    5015 
    5016 > isolde sim resume
    5017 
    5018 > isolde sim stop
    5019 
    5020 Sim termination reason: None 
    5021 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5022 chains... 
    5023 ISOLDE: Corrected atom nomenclature of 17 residues in model #2.2 to IUPAC-IUB
    5024 standards. 
    5025 ISOLDE: stopped sim 
    5026 
    5027 > close session
    5028 
    5029 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    5030 > evolution/Chimera models/Working models/temp.pdb" format pdb
    5031 
    5032 Chain information for temp.pdb 
    5033 --- 
    5034 Chain | Description 
    5035 1.3/A | No description available 
    5036 1.7/A | No description available 
    5037 1.4/B | No description available 
    5038 1.5/C | No description available 
    5039 1.6/D | No description available 
    5040 1.7/O | No description available 
    5041 1.7/Q | No description available 
    5042 1.2/R | No description available 
    5043  
    5044 
    5045 > hide #1.1-6 target m
    5046 
    5047 > select #1.3/A
    5048 
    5049 2888 atoms, 2917 bonds, 176 residues, 1 model selected 
    5050 
    5051 > show #1.3 models
    5052 
    5053 > select subtract #1.3
    5054 
    5055 Nothing selected 
    5056 
    5057 > hide #1.3 models
    5058 
    5059 > select add #1.7
    5060 
    5061 11063 atoms, 11188 bonds, 4 pseudobonds, 674 residues, 2 models selected 
    5062 
    5063 > show sel atoms
    5064 
    5065 > style sel sphere
    5066 
    5067 Changed 11063 atom styles 
    5068 
    5069 > color N cornflowerblue atoms
    5070 
    5071 > color O hotpink atoms
    5072 
    5073 > color :arg,hic,his,lys & sidechain & N blue atoms
    5074 
    5075 > color :asp,glu & sidechain & O red atoms
    5076 
    5077 > color S yellow atoms
    5078 
    5079 > color P purple atoms
    5080 
    5081 > hide H atoms
    5082 
    5083 > select #1.7/A
    5084 
    5085 383 atoms, 389 bonds, 23 residues, 1 model selected 
    5086 
    5087 > ui tool show "Show Sequence Viewer"
    5088 
    5089 > sequence chain #1.7/A
    5090 
    5091 Alignment identifier is 1.7/A 
    5092 
    5093 > select #1.7/A:13
    5094 
    5095 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5096 
    5097 > select #1.7/A:13
    5098 
    5099 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5100 
    5101 > select #1.7/Q
    5102 
    5103 2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected 
    5104 
    5105 > select intersect C
    5106 
    5107 834 atoms, 660 bonds, 167 residues, 1 model selected 
    5108 
    5109 > ui tool show "Color Actions"
    5110 
    5111 > color sel orange target apf
    5112 
    5113 > select #1.7/A:17
    5114 
    5115 14 atoms, 14 bonds, 1 residue, 1 model selected 
    5116 
    5117 > select #1.7/A:1-17
    5118 
    5119 268 atoms, 272 bonds, 17 residues, 1 model selected 
    5120 
    5121 > select #1.7/A:1-17
    5122 
    5123 268 atoms, 272 bonds, 17 residues, 1 model selected 
    5124 
    5125 > style sel stick
    5126 
    5127 Changed 268 atom styles 
    5128 
    5129 > select #1.7/A:14
    5130 
    5131 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5132 
    5133 > select #1.7/A:14
    5134 
    5135 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5136 
    5137 > isolde sim start #1.7
    5138 
    5139 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5140 chains... 
    5141 Chain information for temp.pdb 
    5142 --- 
    5143 Chain | Description 
    5144 2.2/A | No description available 
    5145 2.2/O | No description available 
    5146 2.2/Q | No description available 
    5147  
    5148 ISOLDE: started sim 
    5149 
    5150 > isolde sim pause
    5151 
    5152 > select intersect #2.2/O
    5153 
    5154 8016 atoms, 8115 bonds, 483 residues, 1 model selected 
    5155 
    5156 > style sel sphere
    5157 
    5158 Changed 8016 atom styles 
    5159 
    5160 > style sel sphere
    5161 
    5162 Changed 8016 atom styles 
    5163 
    5164 > style sel sphere
    5165 
    5166 Changed 8016 atom styles 
    5167 
    5168 > select intersect #2.2/Q
    5169 
    5170 Nothing selected 
    5171 
    5172 > select #2.2/Q
    5173 
    5174 2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected 
    5175 
    5176 > style sel sphere
    5177 
    5178 Changed 2664 atom styles 
    5179 
    5180 > color N cornflowerblue atoms
    5181 
    5182 > color O hotpink atoms
    5183 
    5184 > color :arg,hic,his,lys & sidechain & N blue atoms
    5185 
    5186 > color :asp,glu & sidechain & O red atoms
    5187 
    5188 > color S yellow atoms
    5189 
    5190 > color P purple atoms
    5191 
    5192 > hide H atoms
    5193 
    5194 > ui tool show "Show Sequence Viewer"
    5195 
    5196 > sequence chain #2.2/A
    5197 
    5198 Alignment identifier is 2.2/A 
    5199 
    5200 > sequence chain #2.2/O
    5201 
    5202 Alignment identifier is 2.2/O 
    5203 
    5204 > sequence chain #2.2/Q
    5205 
    5206 Alignment identifier is 2.2/Q 
    5207 
    5208 > select #2.2/Q:166
    5209 
    5210 18 atoms, 18 bonds, 1 residue, 1 model selected 
    5211 
    5212 > select #2.2/Q:1-166
    5213 
    5214 2619 atoms, 2638 bonds, 166 residues, 1 model selected 
    5215 
    5216 > select clear
    5217 
    5218 > select #2.2/Q:1
    5219 
    5220 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5221 
    5222 > select #2.2/Q:1
    5223 
    5224 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5225 
    5226 > select #2.2/Q:46
    5227 
    5228 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5229 
    5230 > select #2.2/Q:40-46
    5231 
    5232 135 atoms, 135 bonds, 7 residues, 1 model selected 
    5233 
    5234 > style sel stick
    5235 
    5236 Changed 135 atom styles 
    5237 
    5238 > select clear
    5239 
    5240 > hide #!2.2 models
    5241 
    5242 > show #!2.2 models
    5243 
    5244 > select #2.2/A:15
    5245 
    5246 14 atoms, 13 bonds, 1 residue, 1 model selected 
    5247 
    5248 > select #2.2/A:15
    5249 
    5250 14 atoms, 13 bonds, 1 residue, 1 model selected 
    5251 
    5252 > style sel sphere
    5253 
    5254 Changed 14 atom styles 
    5255 
    5256 > style sel sphere
    5257 
    5258 Changed 14 atom styles 
    5259 
    5260 > select #2.2/A:19-20
    5261 
    5262 48 atoms, 49 bonds, 2 residues, 1 model selected 
    5263 
    5264 > select #2.2/A:18-20
    5265 
    5266 70 atoms, 71 bonds, 3 residues, 1 model selected 
    5267 
    5268 > style sel sphere
    5269 
    5270 Changed 70 atom styles 
    5271 
    5272 > select #2.2/A:15
    5273 
    5274 14 atoms, 13 bonds, 1 residue, 1 model selected 
    5275 
    5276 > select #2.2/A:15
    5277 
    5278 14 atoms, 13 bonds, 1 residue, 1 model selected 
    5279 
    5280 > select #2.2/A:11
    5281 
    5282 20 atoms, 20 bonds, 1 residue, 1 model selected 
    5283 
    5284 > select #2.2/A:11
    5285 
    5286 20 atoms, 20 bonds, 1 residue, 1 model selected 
    5287 
    5288 > ui mousemode right "isolde tug selection"
    5289 
    5290 > isolde sim resume
    5291 
    5292 > select #2.2/A:8
    5293 
    5294 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5295 
    5296 > select #2.2/A:8
    5297 
    5298 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5299 
    5300 > select #2.2/A:1-2
    5301 
    5302 36 atoms, 35 bonds, 2 residues, 1 model selected 
    5303 
    5304 > select #2.2/A:1-2
    5305 
    5306 36 atoms, 35 bonds, 2 residues, 1 model selected 
    5307 
    5308 > isolde sim stop discardTo start
    5309 
    5310 Sim termination reason: None 
    5311 reverting to start 
    5312 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5313 chains... 
    5314 ISOLDE: stopped sim 
    5315 
    5316 > isolde sim start #1.7
    5317 
    5318 No atoms selected! 
    5319 
    5320 > isolde sim start #2
    5321 
    5322 ISOLDE: started sim 
    5323 
    5324 > show sel atoms
    5325 
    5326 > select #2.2/O
    5327 
    5328 8016 atoms, 8115 bonds, 483 residues, 1 model selected 
    5329 
    5330 > style sel sphere
    5331 
    5332 Changed 8016 atom styles 
    5333 
    5334 > select #2.2/Q
    5335 
    5336 2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected 
    5337 
    5338 > style sel sphere
    5339 
    5340 Changed 2664 atom styles 
    5341 
    5342 > select clear
    5343 
    5344 > select #2.2/Q:46
    5345 
    5346 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5347 
    5348 > select #2.2/Q:40-46
    5349 
    5350 135 atoms, 135 bonds, 7 residues, 1 model selected 
    5351 
    5352 > style sel stick
    5353 
    5354 Changed 135 atom styles 
    5355 
    5356 > select #2.2/A:18
    5357 
    5358 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5359 
    5360 > select #2.2/A:18-23
    5361 
    5362 115 atoms, 116 bonds, 6 residues, 1 model selected 
    5363 
    5364 > style sel sphere
    5365 
    5366 Changed 115 atom styles 
    5367 
    5368 > select #2.2/A:1
    5369 
    5370 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5371 
    5372 > select #2.2/A:1
    5373 
    5374 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5375 
    5376 > ui mousemode right "isolde tug selection"
    5377 
    5378 > select #2.2/A:11
    5379 
    5380 20 atoms, 20 bonds, 1 residue, 1 model selected 
    5381 
    5382 > select #2.2/A:1-11
    5383 
    5384 189 atoms, 192 bonds, 11 residues, 1 model selected 
    5385 
    5386 > roll y -90 1
    5387 
    5388 > select #2.2/A:1
    5389 
    5390 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5391 
    5392 > select #2.2/A:1
    5393 
    5394 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5395 
    5396 > select #2.2/A:5
    5397 
    5398 17 atoms, 16 bonds, 1 residue, 1 model selected 
    5399 
    5400 > select #2.2/A:1-5
    5401 
    5402 80 atoms, 79 bonds, 5 residues, 1 model selected 
    5403 
    5404 > select #2.2/A:8
    5405 
    5406 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5407 
    5408 > select #2.2/A:8
    5409 
    5410 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5411 
    5412 > select #2.2/A:1
    5413 
    5414 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5415 
    5416 > select #2.2/A:1
    5417 
    5418 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5419 
    5420 > select #2.2/A:5
    5421 
    5422 17 atoms, 16 bonds, 1 residue, 1 model selected 
    5423 
    5424 > select #2.2/A:1-5
    5425 
    5426 80 atoms, 79 bonds, 5 residues, 1 model selected 
    5427 
    5428 > select #2.2/A:1-2
    5429 
    5430 36 atoms, 35 bonds, 2 residues, 1 model selected 
    5431 
    5432 > select #2.2/A:1-2
    5433 
    5434 36 atoms, 35 bonds, 2 residues, 1 model selected 
    5435 
    5436 > ui mousemode right "isolde tug atom"
    5437 
    5438 > select #2.2/A:20
    5439 
    5440 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5441 
    5442 > select #2.2/A:18-20
    5443 
    5444 70 atoms, 71 bonds, 3 residues, 1 model selected 
    5445 
    5446 > style sel stick
    5447 
    5448 Changed 70 atom styles 
    5449 
    5450 > style sel sphere
    5451 
    5452 Changed 70 atom styles 
    5453 
    5454 > color N cornflowerblue atoms
    5455 
    5456 > color O hotpink atoms
    5457 
    5458 > color :arg,hic,his,lys & sidechain & N blue atoms
    5459 
    5460 > color :asp,glu & sidechain & O red atoms
    5461 
    5462 > color S yellow atoms
    5463 
    5464 > color P purple atoms
    5465 
    5466 > hide H atoms
    5467 
    5468 > select #2.2/Q:113
    5469 
    5470 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5471 
    5472 > select #2.2/Q:62-113
    5473 
    5474 846 atoms, 853 bonds, 52 residues, 1 model selected 
    5475 
    5476 > select clear
    5477 
    5478 > select #2.2/A
    5479 
    5480 383 atoms, 389 bonds, 23 residues, 1 model selected 
    5481 
    5482 > show sel atoms
    5483 
    5484 > select #2.2/A:20
    5485 
    5486 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5487 
    5488 > select #2.2/A:20
    5489 
    5490 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5491 
    5492 > select #2.2/A:9
    5493 
    5494 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5495 
    5496 > select #2.2/A:9
    5497 
    5498 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5499 
    5500 > select #2.2/O
    5501 
    5502 8016 atoms, 8115 bonds, 483 residues, 1 model selected 
    5503 
    5504 > style sel sphere
    5505 
    5506 Changed 8016 atom styles 
    5507 
    5508 > style sel sphere
    5509 
    5510 Changed 8016 atom styles 
    5511 
    5512 > select #2.2/A:9
    5513 
    5514 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5515 
    5516 > select #2.2/A:9
    5517 
    5518 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5519 
    5520 > style sel sphere
    5521 
    5522 Changed 15 atom styles 
    5523 
    5524 > select #2.2/Q:49
    5525 
    5526 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5527 
    5528 > select #2.2/Q:35-49
    5529 
    5530 240 atoms, 240 bonds, 15 residues, 1 model selected 
    5531 
    5532 > select #2.2/A:15-16
    5533 
    5534 24 atoms, 23 bonds, 2 residues, 1 model selected 
    5535 
    5536 > select #2.2/A:1-16
    5537 
    5538 254 atoms, 257 bonds, 16 residues, 1 model selected 
    5539 
    5540 > select intersect backbone
    5541 
    5542 97 atoms, 96 bonds, 16 residues, 1 model selected 
    5543 
    5544 > style sel sphere
    5545 
    5546 Changed 97 atom styles 
    5547 
    5548 > select #2.2/Q:38
    5549 
    5550 12 atoms, 11 bonds, 1 residue, 1 model selected 
    5551 
    5552 > select #2.2/Q:38-40
    5553 
    5554 44 atoms, 44 bonds, 3 residues, 1 model selected 
    5555 
    5556 > select #2.2/Q:46
    5557 
    5558 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5559 
    5560 > select #2.2/Q:39-46
    5561 
    5562 146 atoms, 146 bonds, 8 residues, 1 model selected 
    5563 
    5564 > style sel sphere
    5565 
    5566 Changed 146 atom styles 
    5567 
    5568 > style sel stick
    5569 
    5570 Changed 146 atom styles 
    5571 
    5572 > select intersect backbone
    5573 
    5574 48 atoms, 47 bonds, 8 residues, 1 model selected 
    5575 
    5576 > style sel sphere
    5577 
    5578 Changed 48 atom styles 
    5579 
    5580 > select #2.2/Q:48-49
    5581 
    5582 22 atoms, 21 bonds, 2 residues, 1 model selected 
    5583 
    5584 > select #2.2/Q:49-56
    5585 
    5586 128 atoms, 127 bonds, 8 residues, 1 model selected 
    5587 
    5588 > select #2.2/Q:39
    5589 
    5590 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5591 
    5592 > select #2.2/Q:39-56
    5593 
    5594 293 atoms, 293 bonds, 18 residues, 1 model selected 
    5595 
    5596 > select intersect sideonly
    5597 
    5598 184 atoms, 168 bonds, 17 residues, 1 model selected 
    5599 
    5600 > style sel stick
    5601 
    5602 Changed 184 atom styles 
    5603 
    5604 > isolde sim stop
    5605 
    5606 Sim termination reason: None 
    5607 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5608 chains... 
    5609 ISOLDE: Corrected atom nomenclature of 10 residues in model #2.2 to IUPAC-IUB
    5610 standards. 
    5611 ISOLDE: stopped sim 
    5612 
    5613 > select #2.2/A:23
    5614 
    5615 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5616 
    5617 > select #2.2/A:18-23
    5618 
    5619 115 atoms, 116 bonds, 6 residues, 1 model selected 
    5620 
    5621 > show sel atoms
    5622 
    5623 > style sel sphere
    5624 
    5625 Changed 115 atom styles 
    5626 
    5627 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    5628 > evolution/Chimera models/Working models/temp.pdb"
    5629 
    5630 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    5631 > evolution/Chimera models/Working models/temp.cxs"
    5632 
    5633 > close session
    5634 
    5635 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    5636 > evolution/Chimera models/Working models/temp.pdb" format pdb
    5637 
    5638 Chain information for temp.pdb 
    5639 --- 
    5640 Chain | Description 
    5641 1.3/A | No description available 
    5642 1.7/A | No description available 
    5643 1.4/B | No description available 
    5644 1.5/C | No description available 
    5645 1.6/D | No description available 
    5646 1.7/O | No description available 
    5647 1.7/Q | No description available 
    5648 1.2/R | No description available 
    5649  
    5650 
    5651 > hide #!1 models
    5652 
    5653 > show #!1 models
    5654 
    5655 > hide #1.1 models
    5656 
    5657 > show #1.1 models
    5658 
    5659 > hide #1.1 models
    5660 
    5661 > hide #1.2 models
    5662 
    5663 > hide #1.4 models
    5664 
    5665 > hide #1.5 models
    5666 
    5667 > hide #1.6 models
    5668 
    5669 > hide #1.3 models
    5670 
    5671 > show #1.3 models
    5672 
    5673 > show sel atoms
    5674 
    5675 > ui tool show "Show Sequence Viewer"
    5676 
    5677 > hide #1.3 models
    5678 
    5679 > ui tool show "Show Sequence Viewer"
    5680 
    5681 > sequence chain #1.7/A
    5682 
    5683 Alignment identifier is 1.7/A 
    5684 
    5685 > sequence chain #1.7/O
    5686 
    5687 Alignment identifier is 1.7/O 
    5688 
    5689 > sequence chain #1.7/Q
    5690 
    5691 Alignment identifier is 1.7/Q 
    5692 
    5693 > select #1.7/A:20
    5694 
    5695 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5696 
    5697 > select #1.7/A:18-20
    5698 
    5699 70 atoms, 71 bonds, 3 residues, 1 model selected 
    5700 
    5701 > show sel atoms
    5702 
    5703 > style sel sphere
    5704 
    5705 Changed 70 atom styles 
    5706 
    5707 > select #1.7/O:868
    5708 
    5709 20 atoms, 20 bonds, 1 residue, 1 model selected 
    5710 
    5711 > select #1.7/O:868-911
    5712 
    5713 699 atoms, 706 bonds, 44 residues, 1 model selected 
    5714 
    5715 > show sel atoms
    5716 
    5717 > style sel sphere
    5718 
    5719 Changed 699 atom styles 
    5720 
    5721 > select ::name="GTP"
    5722 
    5723 44 atoms, 46 bonds, 1 residue, 1 model selected 
    5724 
    5725 > select add ::name="MG"
    5726 
    5727 45 atoms, 46 bonds, 2 residues, 1 model selected 
    5728 
    5729 > select add sel : select #1.7/A
    5730 
    5731 383 atoms, 389 bonds, 23 residues, 1 model selected 
    5732 
    5733 > isolde sim start #1.7
    5734 
    5735 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5736 chains... 
    5737 Chain information for temp.pdb 
    5738 --- 
    5739 Chain | Description 
    5740 2.2/A | No description available 
    5741 2.2/O | No description available 
    5742 2.2/Q | No description available 
    5743  
    5744 ISOLDE: started sim 
    5745 
    5746 > isolde sim pause
    5747 
    5748 > select #2.2/A:13
    5749 
    5750 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5751 
    5752 > select #2.2/A:11-13
    5753 
    5754 46 atoms, 46 bonds, 3 residues, 1 model selected 
    5755 
    5756 > isolde sim resume
    5757 
    5758 > ui mousemode right "isolde tug selection"
    5759 
    5760 > select
    5761 
    5762 37393 atoms, 37789 bonds, 4 pseudobonds, 2287 residues, 25 models selected 
    5763 
    5764 > show sel & #!2.2 cartoons
    5765 
    5766 > hide sel & #!2.2 atoms
    5767 
    5768 > select #2.2/A:3
    5769 
    5770 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5771 
    5772 > select #2.2/A:2-3
    5773 
    5774 27 atoms, 26 bonds, 2 residues, 1 model selected 
    5775 
    5776 > select #2.2/A:7
    5777 
    5778 14 atoms, 14 bonds, 1 residue, 1 model selected 
    5779 
    5780 > select #2.2/A:1-7
    5781 
    5782 113 atoms, 113 bonds, 7 residues, 1 model selected 
    5783 
    5784 > select #2.2/A:20
    5785 
    5786 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5787 
    5788 > select #2.2/A:18-20
    5789 
    5790 70 atoms, 71 bonds, 3 residues, 1 model selected 
    5791 
    5792 > select sel : isolde sim stop
    5793 
    5794 Sim termination reason: None 
    5795 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5796 chains... 
    5797 ISOLDE: Corrected atom nomenclature of 10 residues in model #2.2 to IUPAC-IUB
    5798 standards. 
    5799 ISOLDE: stopped sim 
    5800 
    5801 > dssp
    5802 
    5803 > select #2.2/A
    5804 
    5805 383 atoms, 389 bonds, 23 residues, 1 model selected 
    5806 
    5807 > select sel : select #2.2/A:14
    5808 
    5809 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5810 
    5811 > select #2.2/A:13-14
    5812 
    5813 30 atoms, 29 bonds, 2 residues, 1 model selected 
    5814 
    5815 > select sel : select #2.2/A:11
    5816 
    5817 20 atoms, 20 bonds, 1 residue, 1 model selected 
    5818 
    5819 > select #2.2/A:10-11
    5820 
    5821 40 atoms, 41 bonds, 2 residues, 1 model selected 
    5822 
    5823 > select sel : show sel & #!2.2 atoms
    5824 
    5825 > select #2.2/A
    5826 
    5827 383 atoms, 389 bonds, 23 residues, 1 model selected 
    5828 
    5829 > select sel : save "/Users/tmckeithan/Desktop/Cell biology and also early
    5830 > evolution/Chimera models/Working models/RacGEF HH a.pdb"
    5831 
    5832 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    5833 > evolution/Chimera models/Working models/RacGEF HH a.pdb" models #2
    5834 
    5835 > close session
    5836 
    5837 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    5838 > evolution/Chimera models/Working models/RacGEF HH a.pdb" format pdb
    5839 
    5840 Chain information for RacGEF HH a.pdb #1 
    5841 --- 
    5842 Chain | Description 
    5843 A | No description available 
    5844 O | No description available 
    5845 Q | No description available 
    5846  
    5847 
    5848 > ui tool show H-Bonds
    5849 
    5850 > hbonds radius 0.2 dashes 0 reveal true
    5851 
    5852 Skipping possible acceptor with bad geometry: /O GLU 565 OXT 
    5853 Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 OXT 
    5854  
    5855 Skipping possible acceptor with bad geometry: /O GLU 565 O 
    5856 Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 O 
    5857  
    5858 Skipping possible acceptor with bad geometry: /O GLU 565 OXT 
    5859 Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 OXT 
    5860  
    5861 Skipping possible acceptor with bad geometry: /O GLU 565 O 
    5862 Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 O 
    5863  
    5864 Skipping possible acceptor with bad geometry: /O GLU 565 OXT 
    5865 Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 OXT 
    5866  
    5867 
    5868 Skipped 8 atom(s) with bad connectivities; see log for details 
    5869 
    5870 684 hydrogen bonds found 
    5871 
    5872 > select /A
    5873 
    5874 383 atoms, 389 bonds, 6 pseudobonds, 23 residues, 2 models selected 
    5875 
    5876 > show sel atoms
    5877 
    5878 > select
    5879 
    5880 11063 atoms, 11188 bonds, 688 pseudobonds, 674 residues, 3 models selected 
    5881 
    5882 > show sel atoms
    5883 
    5884 > select clear
    5885 
    5886 > select /O
    5887 
    5888 8016 atoms, 8115 bonds, 497 pseudobonds, 483 residues, 2 models selected 
    5889 
    5890 > hide sel atoms
    5891 
    5892 > select clear
    5893 
    5894 > select /A
    5895 
    5896 383 atoms, 389 bonds, 6 pseudobonds, 23 residues, 2 models selected 
    5897 
    5898 > select intersect C
    5899 
    5900 128 atoms, 107 bonds, 23 residues, 1 model selected 
    5901 
    5902 > ui tool show "Color Actions"
    5903 
    5904 > color sel forest green target acpf
    5905 
    5906 > select clear
    5907 
    5908 > ui tool show "Show Sequence Viewer"
    5909 
    5910 > sequence chain /A
    5911 
    5912 Alignment identifier is 1/A 
    5913 
    5914 > sequence chain /O
    5915 
    5916 Alignment identifier is 1/O 
    5917 
    5918 > sequence chain /Q
    5919 
    5920 Alignment identifier is 1/Q 
    5921 
    5922 > interfaces #1
    5923 
    5924 3 buried areas: O Q 1230, Q A 890, O A 301 
    5925 
    5926 > select /Q:46
    5927 
    5928 19 atoms, 18 bonds, 1 residue, 1 model selected 
     559[deleted to fit within ticket limits]
    5929560
    5930561> select /Q:25-46