Changes between Initial Version and Version 1 of Ticket #3163


Ignore:
Timestamp:
May 8, 2020, 9:09:33 AM (6 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #3163

    • Property Platform → all
    • Property Project → ChimeraX
    • Property Resolution → duplicate
    • Property Status new → closed
    • Property Summary ChimeraX bug report submission → Model panel problem

  • Ticket #3163 – Description

    initial v1  
    24162416> volume #19 color #cccccc4e
    24172417
    2418 > volume #19 color #cccccc45
    2419 
    2420 > volume #19 color #cccccc43
    2421 
    2422 > volume #19 color #cccccc3f
    2423 
    2424 > volume #19 color #cccccc3e
    2425 
    2426 > volume #19 color #cccccc3d
    2427 
    2428 > volume #19 color #cccccc3b
    2429 
    2430 > volume #19 color #cccccc38
    2431 
    2432 > volume #19 color #cccccc36
    2433 
    2434 > volume #19 color #cccccc35
    2435 
    2436 > volume #19 color #cccccc33
    2437 
    2438 > volume #19 color #cccccc32
    2439 
    2440 > volume #19 color #cccccc30
    2441 
    2442 > volume #19 color #cccccc2f
    2443 
    2444 > volume #19 color #cccccc2e
    2445 
    2446 > select clear
    2447 
    2448 > lighting soft
    2449 
    2450 > lighting soft
    2451 
    2452 > lighting full
    2453 
    2454 > select clear
    2455 
    2456 > lighting shadows false
    2457 
    2458 > lighting full
    2459 
    2460 > lighting soft
    2461 
    2462 > lighting soft
    2463 
    2464 > lighting full
    2465 
    2466 > select clear
    2467 
    2468 > volume #19 color #cccccc2f
    2469 
    2470 > volume #19 color #cccccc36
    2471 
    2472 > volume #19 color #cccccc53
    2473 
    2474 > volume #19 color #cccccc5a
    2475 
    2476 > volume #19 color #cccccc5b
    2477 
    2478 > volume #19 color #cccccc62
    2479 
    2480 > volume #19 color #cccccc65
    2481 
    2482 > volume #19 color #cccccc68
    2483 
    2484 > volume #19 color #cccccc6d
    2485 
    2486 > volume #19 color #cccccc6e
    2487 
    2488 > volume #19 color #cccccc6f
    2489 
    2490 > volume #19 color #cccccc72
    2491 
    2492 > volume #19 color #cccccc73
    2493 
    2494 > volume #19 color #cccccc77
    2495 
    2496 > volume #19 color #cccccc7b
    2497 
    2498 > volume #19 color #cccccc7c
    2499 
    2500 > volume #19 color #cccccc7e
    2501 
    2502 > volume #19 color #cccccc80
    2503 
    2504 > volume #19 color #cccccc89
    2505 
    2506 > volume #19 color #cccccc8b
    2507 
    2508 > volume #19 color #cccccc90
    2509 
    2510 > volume #19 color #cccccc91
    2511 
    2512 > save image /Users/chunyan/2020/20200506-Figure5-6.tif pixelSize 0.1
    2513 > supersample 4 transparentBackground true
    2514 
    2515 > volume #19 color #ccccb291
    2516 
    2517 > volume #19 color #cca9b291
    2518 
    2519 > volume #19 color #b7a9b291
    2520 
    2521 > volume #19 color #a6a9b291
    2522 
    2523 > volume #19 color #95a9b291
    2524 
    2525 > volume #19 color #9596b291
    2526 
    2527 > volume #19 color #95969b91
    2528 
    2529 > volume #19 color #95968e91
    2530 
    2531 > volume #19 color #95963291
    2532 
    2533 > volume #19 color #9596a091
    2534 
    2535 > volume #19 color #95a0a091
    2536 
    2537 > volume #19 color #a0a0a091
    2538 
    2539 > volume #19 color #3ca0a091
    2540 
    2541 > volume #19 color #a0a0a091
    2542 
    2543 > volume #19 color #a0a0a099
    2544 
    2545 > save image /Users/chunyan/2020/20200506-Figure5-6.tif pixelSize 0.1
    2546 > supersample 4 transparentBackground true
    2547 
    2548 > save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
    2549 
    2550 > view
    2551 
    2552 > volume #11 level 0.004921
    2553 
    2554 > surface dust #11 size 40
    2555 
    2556 > volume #11 level 0.005853
    2557 
    2558 > volume #11 color #ffff66cd
    2559 
    2560 > volume #11 color #d4ff66cd
    2561 
    2562 > volume #11 color #d4d766cd
    2563 
    2564 > volume #11 color #d4d7d3cd
    2565 
    2566 > volume #11 color #bfd7d3cd
    2567 
    2568 > volume #11 color #bfbdd3cd
    2569 
    2570 > volume #11 color #bfbdc0cd
    2571 
    2572 > volume #11 color #bfbdc0cc
    2573 
    2574 > volume #11 color #bfbdc0c4
    2575 
    2576 > volume #11 color #bfbdc088
    2577 
    2578 > volume #11 color #bfbdc084
    2579 
    2580 > volume #11 color #bfbdc080
    2581 
    2582 > volume #11 color #bfbdc07e
    2583 
    2584 > volume #11 color #bfbdc07b
    2585 
    2586 > volume #11 color #bfbdc076
    2587 
    2588 > volume #11 color #bfbdc075
    2589 
    2590 > volume #11 color #bfbdc073
    2591 
    2592 > volume #11 color #bfbdc071
    2593 
    2594 > volume #11 color #bfbdc06f
    2595 
    2596 > volume #11 color #bfbdc070
    2597 
    2598 Traceback (most recent call last): 
    2599 File
    2600 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2601 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2602 return self._func(self._name, data) 
    2603 File
    2604 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2605 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    2606 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    2607 File
    2608 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2609 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2610 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2611 IndexError: list index out of range 
    2612  
    2613 Error processing trigger "new frame": 
    2614 IndexError: list index out of range 
    2615  
    2616 File
    2617 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2618 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2619 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2620  
    2621 See log for complete Python traceback. 
    2622  
    2623 
    2624 > volume #41 level 0.009946
    2625 
    2626 > volume #41 level 0.009589
    2627 
    2628 > select clear
    2629 
    2630 > select #37:300-400
    2631 
    2632 9360 atoms, 9480 bonds, 1 model selected 
    2633 
    2634 > show sel cartoons
    2635 
    2636 > show sel cartoons
    2637 
    2638 > show sel cartoons
    2639 
    2640 > hide sel atoms
    2641 
    2642 > show sel cartoons
    2643 
    2644 > select clear
    2645 
    2646 > volume #11 level 0.005586
    2647 
    2648 > surface dust #11 size 40
    2649 
    2650 > select clear
    2651 
    2652 > select #37
    2653 
    2654 49008 atoms, 49740 bonds, 1 model selected 
    2655 
    2656 > hide sel cartoons
    2657 
    2658 > select clear
    2659 
    2660 > volume #23 color #21ffa9
    2661 
    2662 > volume #23 color #21b1a9
    2663 
    2664 > volume #23 color #abb1a9
    2665 
    2666 > volume #23 color #abb1a9ad
    2667 
    2668 > volume #23 color #abb1a996
    2669 
    2670 > volume #23 color #abb1a997
    2671 
    2672 > volume #10 color #fd808b
    2673 
    2674 > volume #10 color #fdd48b
    2675 
    2676 > volume #10 color #d7d48b
    2677 
    2678 > volume #10 color #d7d4d4
    2679 
    2680 > volume #10 color #d7d4d47f
    2681 
    2682 > volume #10 color #d7d4d480
    2683 
    2684 > volume #41 level 0.009114
    2685 
    2686 > volume #10 color #d7d4d4bb
    2687 
    2688 > volume #10 color #d7d4d486
    2689 
    2690 > volume #10 color #d7d4d487
    2691 
    2692 > volume #10 color #c9d4d487
    2693 
    2694 > volume #10 color #d2d4d487
    2695 
    2696 > volume #10 color #d2d3d487
    2697 
    2698 > volume #10 color #d2d2d487
    2699 
    2700 > volume #10 color #d2d2d387
    2701 
    2702 > volume #10 color #d2d2d287
    2703 
    2704 > volume #10 color #d2d2d299
    2705 
    2706 > volume #23 color #abb1a999
    2707 
    2708 > volume #23 color #d2b1a999
    2709 
    2710 > volume #23 color #d2d2a999
    2711 
    2712 > volume #23 color #d2d2d299
    2713 
    2714 > surface dust #11 size 40
    2715 
    2716 > surface dust #10 size 40
    2717 
    2718 > surface dust #23 size 40
    2719 
    2720 Traceback (most recent call last): 
    2721 File
    2722 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2723 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2724 return self._func(self._name, data) 
    2725 File
    2726 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2727 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    2728 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    2729 File
    2730 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2731 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2732 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2733 IndexError: list index out of range 
    2734  
    2735 Error processing trigger "new frame": 
    2736 IndexError: list index out of range 
    2737  
    2738 File
    2739 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2740 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2741 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2742  
    2743 See log for complete Python traceback. 
    2744  
    2745 
    2746 > volume #23 color #d2ead299
    2747 
    2748 > volume #23 color #d2fbd299
    2749 
    2750 > volume #23 color #32fbd299
    2751 
    2752 > volume #23 color #18fbd299
    2753 
    2754 > volume #23 color #11fbd299
    2755 
    2756 > volume #23 color #00fbd299
    2757 
    2758 > volume #23 color #00fbe199
    2759 
    2760 > volume #23 color #00fbe499
    2761 
    2762 > volume #23 color #00fbfe99
    2763 
    2764 > volume #23 color #00fbdd99
    2765 
    2766 > volume #23 color #00fb8d99
    2767 
    2768 > volume #23 color #00fb5e99
    2769 
    2770 > volume #23 color #00fb3799
    2771 
    2772 > volume #23 color #00fb1d99
    2773 
    2774 > volume #23 color #00fb0e99
    2775 
    2776 > volume #23 color #00fb0b99
    2777 
    2778 > volume #23 color #00fb0199
    2779 
    2780 > volume #23 color #00fb0099
    2781 
    2782 > volume #23 color #00fb0098
    2783 
    2784 > volume #23 color #00fb008a
    2785 
    2786 > volume #23 color #00fb0080
    2787 
    2788 > volume #23 color #00fb0076
    2789 
    2790 > volume #23 color #00fb0075
    2791 
    2792 > volume #23 color #00fb0076
    2793 
    2794 > volume #23 color #00fb0080
    2795 
    2796 > volume #23 color #d2fb0080
    2797 
    2798 > volume #23 color #d2d20080
    2799 
    2800 > volume #23 color #d2d2d280
    2801 
    2802 > volume #23 color #d2d2d299
    2803 
    2804 > select clear
    2805 
    2806 > volume #11 color #d2bdc070
    2807 
    2808 > volume #11 color #d2d2c070
    2809 
    2810 > volume #11 color #d2d2d270
    2811 
    2812 > volume #11 color #d2d2d299
    2813 
    2814 > volume #11 color #d2d2d266
    2815 
    2816 > volume #10 color #d2d2d266
    2817 
    2818 > volume #23 color #d2d2d266
    2819 
    2820 > select clear
    2821 
    2822 > save image /Users/chunyan/2020/20200507-Figure5-1.tif pixelSize 0.1
    2823 > supersample 4 transparentBackground true
    2824 
    2825 > view name p1
    2826 
    2827 Traceback (most recent call last): 
    2828 File
    2829 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2830 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2831 return self._func(self._name, data) 
    2832 File
    2833 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2834 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    2835 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    2836 File
    2837 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2838 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2839 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2840 IndexError: list index out of range 
    2841  
    2842 Error processing trigger "new frame": 
    2843 IndexError: list index out of range 
    2844  
    2845 File
    2846 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2847 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2848 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2849  
    2850 See log for complete Python traceback. 
    2851  
    2852 
    2853 > volume #19 color #d2a0a099
    2854 
    2855 > volume #19 color #d2d2a099
    2856 
    2857 > volume #19 color #d2d2d299
    2858 
    2859 > volume #19 color #d2d2d266
    2860 
    2861 > volume #19 level 0.006746
    2862 
    2863 Traceback (most recent call last): 
    2864 File
    2865 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2866 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2867 return self._func(self._name, data) 
    2868 File
    2869 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2870 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    2871 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    2872 File
    2873 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2874 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2875 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2876 IndexError: list index out of range 
    2877  
    2878 Error processing trigger "new frame": 
    2879 IndexError: list index out of range 
    2880  
    2881 File
    2882 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2883 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2884 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2885  
    2886 See log for complete Python traceback. 
    2887  
    2888 Traceback (most recent call last): 
    2889 File
    2890 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2891 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2892 return self._func(self._name, data) 
    2893 File
    2894 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2895 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    2896 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    2897 File
    2898 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2899 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2900 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2901 IndexError: list index out of range 
    2902  
    2903 Error processing trigger "new frame": 
    2904 IndexError: list index out of range 
    2905  
    2906 File
    2907 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2908 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2909 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2910  
    2911 See log for complete Python traceback. 
    2912  
    2913 Traceback (most recent call last): 
    2914 File
    2915 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2916 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2917 return self._func(self._name, data) 
    2918 File
    2919 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2920 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    2921 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    2922 File
    2923 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2924 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2925 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2926 IndexError: list index out of range 
    2927  
    2928 Error processing trigger "new frame": 
    2929 IndexError: list index out of range 
    2930  
    2931 File
    2932 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2933 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2934 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2935  
    2936 See log for complete Python traceback. 
    2937  
    2938 
    2939 > surface dust #19 size 40
    2940 
    2941 > surface dust #19 size 30
    2942 
    2943 > surface dust #19 size 50
    2944 
    2945 > surface dust #19 size 40
    2946 
    2947 > save image /Users/chunyan/2020/20200507-Figure5-2.tif pixelSize 0.1
    2948 > supersample 4 transparentBackground true
    2949 
    2950 > select #37:300-400
    2951 
    2952 9360 atoms, 9480 bonds, 1 model selected 
    2953 
    2954 > show sel cartoons
    2955 
    2956 > select clear
    2957 
    2958 Traceback (most recent call last): 
    2959 File
    2960 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2961 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2962 return self._func(self._name, data) 
    2963 File
    2964 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2965 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    2966 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    2967 File
    2968 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2969 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2970 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2971 IndexError: list index out of range 
    2972  
    2973 Error processing trigger "new frame": 
    2974 IndexError: list index out of range 
    2975  
    2976 File
    2977 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    2978 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    2979 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    2980  
    2981 See log for complete Python traceback. 
    2982  
    2983 
    2984 > volume #19 level 0.005287
    2985 
    2986 > volume #41 level 0.00953
    2987 
    2988 > select #37:300-400
    2989 
    2990 9360 atoms, 9480 bonds, 1 model selected 
    2991 
    2992 > hide sel cartoons
    2993 
    2994 > fitmap #41 inMap #19
    2995 
    2996 Fit map gp8-asym-300-400-part-genome.mrc in map gp8-asym-manmade.mrc using
    2997 7783 points 
    2998 correlation = 0.9278, correlation about mean = 0.784, overlap = 1.745 
    2999 steps = 1056, shift = 11.7, angle = 79.2 degrees 
    3000  
    3001 Position of gp8-asym-300-400-part-genome.mrc (#41) relative to gp8-asym-
    3002 manmade.mrc (#19) coordinates: 
    3003 Matrix rotation and translation 
    3004 0.99798290 0.06336786 -0.00382899 -12.14584535 
    3005 -0.06335537 0.99798558 0.00330033 13.07674362 
    3006 0.00403041 -0.00305108 0.99998723 -0.19283028 
    3007 Axis -0.04996174 -0.06182390 -0.99683581 
    3008 Axis point 200.09681520 198.04885876 0.00000000 
    3009 Rotation angle (degrees) 3.64433341 
    3010 Shift along axis -0.00940760 
    3011  
    3012 
    3013 > select clear
    3014 
    3015 > select clear
    3016 
    3017 > volume #11 level 0.00572
    3018 
    3019 > save image /Users/chunyan/2020/20200507-Figure5-1.tif pixelSize 0.1
    3020 > supersample 4 transparentBackground true
    3021 
    3022 Traceback (most recent call last): 
    3023 File
    3024 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3025 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3026 return self._func(self._name, data) 
    3027 File
    3028 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3029 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3030 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3031 File
    3032 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3033 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3034 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3035 IndexError: list index out of range 
    3036  
    3037 Error processing trigger "new frame": 
    3038 IndexError: list index out of range 
    3039  
    3040 File
    3041 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3042 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3043 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3044  
    3045 See log for complete Python traceback. 
    3046  
    3047 
    3048 > surface dust #19 size 50
    3049 
    3050 > surface dust #19 size 20
    3051 
    3052 > surface dust #19 size 10
    3053 
    3054 > surface dust #19 size 15
    3055 
    3056 > surface dust #19 size 19
    3057 
    3058 > save image /Users/chunyan/2020/20200507-Figure5-2.tif pixelSize 0.1
    3059 > supersample 4 transparentBackground true
    3060 
    3061 > open /Users/chunyan/2020/gp8-asym/part/gp8-asym-360-383-part.mrc
    3062 
    3063 Opened gp8-asym-360-383-part.mrc, grid size 400,400,400, pixel 1.05, shown at
    3064 level 5.35e-06, step 2, values float32 
    3065 Traceback (most recent call last): 
    3066 File
    3067 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3068 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3069 return self._func(self._name, data) 
    3070 File
    3071 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3072 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3073 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3074 File
    3075 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3076 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3077 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3078 IndexError: list index out of range 
    3079  
    3080 Error processing trigger "new frame": 
    3081 IndexError: list index out of range 
    3082  
    3083 File
    3084 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3085 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3086 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3087  
    3088 See log for complete Python traceback. 
    3089  
    3090 
    3091 > volume #34 level 0.004485
    3092 
    3093 > volume #34 step 1
    3094 
    3095 > select #34
    3096 
    3097 2 models selected 
    3098 
    3099 > ui mousemode rightMode "translate selected models"
    3100 
    3101 > ui mousemode rightMode "rotate selected models"
    3102 
    3103 > volume #34 color #b2b254
    3104 
    3105 > volume #34 color #f0b254
    3106 
    3107 > volume #34 color #f1b254
    3108 
    3109 > volume #34 color #f4b254
    3110 
    3111 > volume #34 color #f5b254
    3112 
    3113 > volume #34 color #f9b254
    3114 
    3115 > volume #34 color #feb254
    3116 
    3117 > volume #34 color #ffb254
    3118 
    3119 > volume #34 color #ffff54
    3120 
    3121 > volume #34 color #ffff53
    3122 
    3123 > volume #34 color #ffff51
    3124 
    3125 > volume #34 color #ffff4c
    3126 
    3127 > volume #34 color #ffff44
    3128 
    3129 > volume #34 color #ffff3e
    3130 
    3131 > volume #34 color #ffff37
    3132 
    3133 > volume #34 color #ffff32
    3134 
    3135 > volume #34 color #ffff2f
    3136 
    3137 > volume #34 color #ffff2d
    3138 
    3139 > volume #34 color #ffff2c
    3140 
    3141 > volume #34 color #ffff26
    3142 
    3143 > volume #34 color #ffff21
    3144 
    3145 > volume #34 color #ffff1e
    3146 
    3147 > volume #34 color #ffff1b
    3148 
    3149 > volume #34 color #ffff19
    3150 
    3151 > volume #34 color #ffff17
    3152 
    3153 > volume #34 color #ffff15
    3154 
    3155 > volume #34 color #ffff14
    3156 
    3157 > volume #34 color #ffff13
    3158 
    3159 > volume #34 color #ffff12
    3160 
    3161 > volume #34 color #ffff10
    3162 
    3163 > volume #34 color #ffff0e
    3164 
    3165 > volume #34 color #ffff0d
    3166 
    3167 > lighting flat
    3168 
    3169 > volume #34 color #ffff05
    3170 
    3171 > volume #34 color yellow
    3172 
    3173 > lighting flat
    3174 
    3175 > ui mousemode rightMode "rotate selected models"
    3176 
    3177 > ui mousemode rightMode "translate selected models"
    3178 
    3179 > ui mousemode rightMode "translate selected models"
    3180 
    3181 > ui mousemode rightMode "rotate selected models"
    3182 
    3183 > ui mousemode rightMode "translate selected models"
    3184 
    3185 > ui mousemode rightMode "rotate selected models"
    3186 
    3187 > fitmap #34 inMap #19
    3188 
    3189 Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
    3190 points 
    3191 correlation = 0.557, correlation about mean = 0.3042, overlap = 1.757 
    3192 steps = 76, shift = 6.81, angle = 6.29 degrees 
    3193  
    3194 Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
    3195 (#19) coordinates: 
    3196 Matrix rotation and translation 
    3197 0.06655295 0.97230064 -0.22405845 27.34578043 
    3198 -0.84899906 -0.06278820 -0.52465060 488.71519810 
    3199 -0.52418634 0.22514246 0.82130358 100.13786168 
    3200 Axis 0.37633884 0.15064127 -0.91415332 
    3201 Axis point 279.72434579 237.46857280 0.00000000 
    3202 Rotation angle (degrees) 95.01783476 
    3203 Shift along axis -7.62940078 
    3204  
    3205 
    3206 > volume #19 color #d2d2d2b9
    3207 
    3208 > volume #19 color #d2d2d2da
    3209 
    3210 > volume #19 color #d2d2d2d9
    3211 
    3212 > lighting soft
    3213 
    3214 Traceback (most recent call last): 
    3215 File
    3216 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3217 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3218 return self._func(self._name, data) 
    3219 File
    3220 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3221 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3222 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3223 File
    3224 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3225 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3226 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3227 IndexError: list index out of range 
    3228  
    3229 Error processing trigger "new frame": 
    3230 IndexError: list index out of range 
    3231  
    3232 File
    3233 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3234 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3235 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3236  
    3237 See log for complete Python traceback. 
    3238  
    3239 
    3240 > ui mousemode rightMode "rotate selected models"
    3241 
    3242 > ui mousemode rightMode "translate selected models"
    3243 
    3244 > ui mousemode rightMode "rotate selected models"
    3245 
    3246 > fitmap #34 inMap #19
    3247 
    3248 Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
    3249 points 
    3250 correlation = 0.8733, correlation about mean = 0.6888, overlap = 3.359 
    3251 steps = 112, shift = 9.76, angle = 4.84 degrees 
    3252  
    3253 Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
    3254 (#19) coordinates: 
    3255 Matrix rotation and translation 
    3256 0.50448478 0.86341311 -0.00359559 -76.70631138 
    3257 -0.86341923 0.50448701 -0.00032550 285.28025861 
    3258 0.00153289 0.00326871 0.99999349 -1.24790332 
    3259 Axis 0.00208137 -0.00296986 -0.99999342 
    3260 Axis point 210.19328550 209.47190344 0.00000000 
    3261 Rotation angle (degrees) 59.70298563 
    3262 Shift along axis 0.24099930 
    3263  
    3264 
    3265 > ui mousemode rightMode "rotate selected models"
    3266 
    3267 > fitmap #34 inMap #19
    3268 
    3269 Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
    3270 points 
    3271 correlation = 0.9353, correlation about mean = 0.8283, overlap = 3.769 
    3272 steps = 56, shift = 0.772, angle = 2.52 degrees 
    3273  
    3274 Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
    3275 (#19) coordinates: 
    3276 Matrix rotation and translation 
    3277 0.86730538 0.49777078 -0.00237426 -76.24261085 
    3278 -0.49777315 0.86730713 -0.00050043 132.39955696 
    3279 0.00181011 0.00161587 0.99999706 -0.81475401 
    3280 Axis 0.00212575 -0.00420305 -0.99998891 
    3281 Axis point 210.21552119 209.20730927 0.00000000 
    3282 Rotation angle (degrees) 29.85306801 
    3283 Shift along axis 0.09619043 
    3284  
    3285 
    3286 > ui mousemode rightMode "rotate selected models"
    3287 
    3288 > fitmap #34 inMap #19
    3289 
    3290 Fit map gp8-asym-360-383-part.mrc in map gp8-asym-manmade.mrc using 28648
    3291 points 
    3292 correlation = 0.9994, correlation about mean = 0.9978, overlap = 4.311 
    3293 steps = 76, shift = 0.751, angle = 3.2 degrees 
    3294  
    3295 Position of gp8-asym-360-383-part.mrc (#34) relative to gp8-asym-manmade.mrc
    3296 (#19) coordinates: 
    3297 Matrix rotation and translation 
    3298 0.99999991 0.00033577 0.00029514 -0.11132430 
    3299 -0.00033564 0.99999987 -0.00041694 0.16480008 
    3300 -0.00029528 0.00041684 0.99999988 0.08422849 
    3301 Axis 0.68201519 0.48294647 -0.54919759 
    3302 Axis point 0.00000000 -145.80624871 444.64506118 
    3303 Rotation angle (degrees) 0.03502295 
    3304 Shift along axis -0.04259333 
    3305  
    3306 
    3307 > surface dust #34 size 40
    3308 
    3309 > surface dust #19 size 40
    3310 
    3311 > select #19
    3312 
    3313 3 models selected 
    3314 
    3315 > select clear
    3316 
    3317 Traceback (most recent call last): 
    3318 File
    3319 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3320 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3321 return self._func(self._name, data) 
    3322 File
    3323 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3324 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3325 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3326 File
    3327 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3328 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3329 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3330 IndexError: list index out of range 
    3331  
    3332 Error processing trigger "new frame": 
    3333 IndexError: list index out of range 
    3334  
    3335 File
    3336 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3337 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3338 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3339  
    3340 See log for complete Python traceback. 
    3341  
    3342 
    3343 > volume #19 color #d2d2bbd9
    3344 
    3345 > volume #19 color #d2d2acd9
    3346 
    3347 > volume #19 color #d2d2ddd9
    3348 
    3349 > volume #19 color #d2d2d2d9
    3350 
    3351 > volume #19 color #d2d2d266
    3352 
    3353 > volume #34 level 0.003799
    3354 
    3355 > volume #34 level 0.002151
    3356 
    3357 > volume #34 level 0.003799
    3358 
    3359 > volume #34 level 0.003661
    3360 
    3361 > volume #34 level 0.003661
    3362 
    3363 > volume #34 level 0.003387
    3364 
    3365 > volume #34 level 0.0007783
    3366 
    3367 > volume #34 level 0.0002292
    3368 
    3369 > volume #34 level 0.002151
    3370 
    3371 Traceback (most recent call last): 
    3372 File
    3373 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3374 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3375 return self._func(self._name, data) 
    3376 File
    3377 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3378 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3379 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3380 File
    3381 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3382 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3383 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3384 IndexError: list index out of range 
    3385  
    3386 Error processing trigger "new frame": 
    3387 IndexError: list index out of range 
    3388  
    3389 File
    3390 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3391 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3392 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3393  
    3394 See log for complete Python traceback. 
    3395  
    3396 Traceback (most recent call last): 
    3397 File
    3398 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3399 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3400 return self._func(self._name, data) 
    3401 File
    3402 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3403 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3404 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3405 File
    3406 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3407 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3408 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3409 IndexError: list index out of range 
    3410  
    3411 Error processing trigger "new frame": 
    3412 IndexError: list index out of range 
    3413  
    3414 File
    3415 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3416 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3417 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3418  
    3419 See log for complete Python traceback. 
    3420  
    3421 Traceback (most recent call last): 
    3422 File
    3423 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3424 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3425 return self._func(self._name, data) 
    3426 File
    3427 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3428 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3429 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3430 File
    3431 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3432 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3433 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3434 IndexError: list index out of range 
    3435  
    3436 Error processing trigger "new frame": 
    3437 IndexError: list index out of range 
    3438  
    3439 File
    3440 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3441 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3442 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3443  
    3444 See log for complete Python traceback. 
    3445  
    3446 
    3447 > volume #34 level 0.003524
    3448 
    3449 > volume #34 level 0.003799
    3450 
    3451 > open /Users/chunyan/2020/gp8-asym/part/gp8-asym-360-383-part-lp.mrc
    3452 
    3453 Opened gp8-asym-360-383-part-lp.mrc, grid size 400,400,400, pixel 1.05, shown
    3454 at level 2.07e-06, step 2, values float32 
    3455 Traceback (most recent call last): 
    3456 File
    3457 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3458 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3459 return self._func(self._name, data) 
    3460 File
    3461 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3462 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3463 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3464 File
    3465 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3466 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3467 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3468 IndexError: list index out of range 
    3469  
    3470 Error processing trigger "new frame": 
    3471 IndexError: list index out of range 
    3472  
    3473 File
    3474 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3475 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3476 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3477  
    3478 See log for complete Python traceback. 
    3479  
    3480 
    3481 > volume #40 level 0.004534
    3482 
    3483 > volume #40 step 1
    3484 
    3485 > select #40
    3486 
    3487 2 models selected 
    3488 
    3489 > ui mousemode rightMode "rotate selected models"
    3490 
    3491 > ui mousemode rightMode "translate selected models"
    3492 
    3493 Traceback (most recent call last): 
    3494 File
    3495 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3496 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3497 return self._func(self._name, data) 
    3498 File
    3499 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3500 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3501 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3502 File
    3503 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3504 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3505 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3506 IndexError: list index out of range 
    3507  
    3508 Error processing trigger "new frame": 
    3509 IndexError: list index out of range 
    3510  
    3511 File
    3512 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3513 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3514 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3515  
    3516 See log for complete Python traceback. 
    3517  
    3518 
    3519 > ui mousemode rightMode "rotate selected models"
    3520 
    3521 > ui mousemode rightMode "translate selected models"
    3522 
    3523 > volume #40 color #ffff4a
    3524 
    3525 > volume #40 color #ffff1b
    3526 
    3527 > volume #40 color #ffff13
    3528 
    3529 > volume #40 color #ffff02
    3530 
    3531 > volume #40 color yellow
    3532 
    3533 Traceback (most recent call last): 
    3534 File
    3535 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3536 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3537 return self._func(self._name, data) 
    3538 File
    3539 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3540 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3541 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3542 File
    3543 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3544 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3545 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3546 IndexError: list index out of range 
    3547  
    3548 Error processing trigger "new frame": 
    3549 IndexError: list index out of range 
    3550  
    3551 File
    3552 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3553 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3554 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3555  
    3556 See log for complete Python traceback. 
    3557  
    3558 
    3559 > fitmap #34 inMap #19
    3560 
    3561 No atoms or maps for #34 
    3562 
    3563 > fitmap #40 inMap #19
    3564 
    3565 Fit map gp8-asym-360-383-part-lp.mrc in map gp8-asym-manmade.mrc using 24638
    3566 points 
    3567 correlation = 0.9649, correlation about mean = 0.8708, overlap = 3.272 
    3568 steps = 76, shift = 3.71, angle = 8.87 degrees 
    3569  
    3570 Position of gp8-asym-360-383-part-lp.mrc (#40) relative to gp8-asym-
    3571 manmade.mrc (#19) coordinates: 
    3572 Matrix rotation and translation 
    3573 0.99999967 -0.00007102 0.00082066 -0.11388253 
    3574 0.00007134 0.99999993 -0.00038619 0.04669667 
    3575 -0.00082063 0.00038625 0.99999960 0.21626464 
    3576 Axis 0.42452417 0.90202945 0.07824381 
    3577 Axis point 262.44281744 0.00000000 144.41216470 
    3578 Rotation angle (degrees) 0.05212622 
    3579 Shift along axis 0.01069726 
    3580  
    3581 
    3582 > volume #40 level 0.003573
    3583 
    3584 > select clear
    3585 
    3586 > ui mousemode rightMode "rotate selected models"
    3587 
    3588 > select #40
    3589 
    3590 3 models selected 
    3591 
    3592 > ui mousemode rightMode "rotate selected models"
    3593 
    3594 > fitmap #40 inMap #19
    3595 
    3596 Fit map gp8-asym-360-383-part-lp.mrc in map gp8-asym-manmade.mrc using 31658
    3597 points 
    3598 correlation = 0.9581, correlation about mean = 0.8663, overlap = 3.415 
    3599 steps = 72, shift = 0.559, angle = 8.92 degrees 
    3600  
    3601 Position of gp8-asym-360-383-part-lp.mrc (#40) relative to gp8-asym-
    3602 manmade.mrc (#19) coordinates: 
    3603 Matrix rotation and translation 
    3604 0.99999938 -0.00026360 0.00108789 -0.11845285 
    3605 0.00026436 0.99999973 -0.00070115 0.07206661 
    3606 -0.00108771 0.00070144 0.99999917 0.21903891 
    3607 Axis 0.53091701 0.82352231 0.19984529 
    3608 Axis point 193.88534095 0.00000000 128.62943191 
    3609 Rotation angle (degrees) 0.07568272 
    3610 Shift along axis 0.04023372 
    3611  
    3612 
    3613 > select clear
    3614 
    3615 > volume #40 level 0.003786
    3616 
    3617 > save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
    3618 > supersample 4 transparentBackground true
    3619 
    3620 > volume #19 color #d2d2d2af
    3621 
    3622 > volume #19 color #d2d2d2d0
    3623 
    3624 > volume #19 color #d2d2d2d1
    3625 
    3626 > volume #19 color #d2d2d2d4
    3627 
    3628 > volume #19 color #d2d2d2e3
    3629 
    3630 > volume #19 color #d2d2d2ed
    3631 
    3632 > volume #19 color #d2d2d2f1
    3633 
    3634 > volume #19 color #d2d2d2f2
    3635 
    3636 > volume #19 color #d2d2d2f4
    3637 
    3638 > volume #19 color #d2d2d2f6
    3639 
    3640 > volume #19 color #d2d2d2f8
    3641 
    3642 > volume #19 color #d2d2d2fa
    3643 
    3644 > volume #19 color #d2d2d2fb
    3645 
    3646 > volume #19 color #d2d2d2fa
    3647 
    3648 > volume #19 color #d2d2d2f8
    3649 
    3650 > volume #19 color #d2d2d2e3
    3651 
    3652 > volume #19 color #d2d2d2c7
    3653 
    3654 > volume #19 color #d2d2d2b0
    3655 
    3656 > volume #19 color #d2d2d2a8
    3657 
    3658 > volume #19 color #d2d2d29e
    3659 
    3660 > volume #19 color #d2d2d297
    3661 
    3662 > volume #19 color #d2d2d292
    3663 
    3664 > volume #19 color #d2d2d28f
    3665 
    3666 > volume #19 color #d2d2d28c
    3667 
    3668 > volume #19 color #d2d2d28a
    3669 
    3670 > volume #19 color #d2d2d288
    3671 
    3672 > volume #19 color #d2d2d285
    3673 
    3674 > volume #19 color #d2d2d282
    3675 
    3676 > volume #19 color #d2d2d280
    3677 
    3678 > volume #19 color #d2d2d275
    3679 
    3680 > volume #19 color #d2d2d274
    3681 
    3682 > volume #19 color #d2d2d272
    3683 
    3684 > volume #19 color #d2d2d271
    3685 
    3686 > volume #19 color #d2d2d272
    3687 
    3688 > volume #19 color #d2d2d274
    3689 
    3690 > volume #19 color #d2d2d276
    3691 
    3692 > volume #19 color #d2d2d277
    3693 
    3694 > volume #19 color #d2d2d279
    3695 
    3696 > volume #19 color #d2d2d27a
    3697 
    3698 > volume #19 color #d2d2d27c
    3699 
    3700 > volume #19 color #d2d2d27e
    3701 
    3702 > volume #19 color #d2d2d28a
    3703 
    3704 > volume #19 color #d2d2d29b
    3705 
    3706 > volume #19 color #d2d2d2a5
    3707 
    3708 > volume #19 color #d2d2d2a6
    3709 
    3710 > volume #19 color #d2d2d2ac
    3711 
    3712 > volume #19 color #d2d2d2d9
    3713 
    3714 > volume #19 color #d2d2d2db
    3715 
    3716 > volume #19 color #d2d2d2dc
    3717 
    3718 > volume #19 color #d2d2d2df
    3719 
    3720 > volume #19 color #d2d2d2e1
    3721 
    3722 > volume #19 color #d2d2d2e3
    3723 
    3724 > volume #19 color #d2d2d2e4
    3725 
    3726 > volume #19 color #d2d2d2e3
    3727 
    3728 > volume #19 color #d2d2d2db
    3729 
    3730 > volume #19 color #d2d2d2d3
    3731 
    3732 > volume #19 color #d2d2d2d0
    3733 
    3734 > volume #19 color #d2d2d2cd
    3735 
    3736 > volume #19 color #d2d2d2ca
    3737 
    3738 > volume #19 color #d2d2d2c8
    3739 
    3740 > volume #19 color #d2d2d2c5
    3741 
    3742 > volume #19 color #d2d2d2c2
    3743 
    3744 > volume #19 color #d2d2d2c1
    3745 
    3746 > volume #19 color #d2d2d2c0
    3747 
    3748 > volume #19 color #d2d2d2bf
    3749 
    3750 > volume #19 color #d2d2d2bd
    3751 
    3752 > volume #19 color #d2d2d2bb
    3753 
    3754 > volume #19 color #d2d2d2ba
    3755 
    3756 > surface dust #19 size 40
    3757 
    3758 > surface dust #40 size 40
    3759 
    3760 > surface dust #40 size 10
    3761 
    3762 > surface dust #19 size 40
    3763 
    3764 > volume #40 level 0.004213
    3765 
    3766 > volume #19 level 0.006891
    3767 
    3768 > save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
    3769 > supersample 4 transparentBackground true
    3770 
    3771 > volume #19 color #d2d2d2cc
    3772 
    3773 > volume #19 color #b4d2d2cc
    3774 
    3775 > volume #19 color #b4b4d2cc
    3776 
    3777 > volume #19 color #b4b4b4cc
    3778 
    3779 > volume #19 color #b4b4b4cb
    3780 
    3781 > volume #19 color #b4b4b4b4
    3782 
    3783 > volume #19 color #b4b4b49c
    3784 
    3785 > volume #19 color #b4b4b49a
    3786 
    3787 > volume #19 color #b4b4b498
    3788 
    3789 > volume #19 color #b4b4b497
    3790 
    3791 > volume #19 color #b4b4b496
    3792 
    3793 > volume #19 color #b4b4b494
    3794 
    3795 > volume #19 color #b4b4b493
    3796 
    3797 > volume #19 color #b4b4b492
    3798 
    3799 > volume #19 color #b4b4b491
    3800 
    3801 > volume #19 color #b4b4b490
    3802 
    3803 > volume #19 color #b4b4b48f
    3804 
    3805 > volume #19 color #b4b4b48e
    3806 
    3807 > volume #19 color #b4b4b487
    3808 
    3809 > volume #19 color #b4b4b485
    3810 
    3811 > volume #19 color #b4b4b484
    3812 
    3813 > volume #19 color #b4b4b482
    3814 
    3815 > volume #19 color #b4b4b481
    3816 
    3817 > volume #19 color #b4b4b480
    3818 
    3819 > volume #19 color #b4b4b47f
    3820 
    3821 > volume #19 color #b4b4b47d
    3822 
    3823 > volume #19 color #b4b4b47c
    3824 
    3825 > volume #19 color #b4b4b47b
    3826 
    3827 > volume #19 color #b4b4b47a
    3828 
    3829 > volume #19 color #b4b4b479
    3830 
    3831 > volume #19 color #b4b4b475
    3832 
    3833 > volume #19 color #b4b4b466
    3834 
    3835 > save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
    3836 > supersample 4 transparentBackground true
    3837 
    3838 > save image /Users/chunyan/2020/20200507-Figure5-3.tif pixelSize 0.1
    3839 > supersample 4 transparentBackground true
    3840 
    3841 > select #37
    3842 
    3843 49008 atoms, 49740 bonds, 1 model selected 
    3844 
    3845 > show sel cartoons
    3846 
    3847 > hide sel atoms
    3848 
    3849 > select clear
    3850 
    3851 > save image /Users/chunyan/2020/20200507-Figure5-4.tif pixelSize 0.1
    3852 > supersample 4 transparentBackground true
    3853 
    3854 > lighting flat
    3855 
    3856 > open /Users/chunyan/2020/gp8-asym/terminal-genome-remodeling/Ideal-B-form-
    3857 > DNA-coot-0.pdb
    3858 
    3859 Chain information for Ideal-B-form-DNA-coot-0.pdb #34 
    3860 --- 
    3861 Chain | Description 
    3862 A | No description available 
    3863 B | No description available 
    3864  
    3865 Traceback (most recent call last): 
    3866 File
    3867 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3868 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3869 return self._func(self._name, data) 
    3870 File
    3871 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3872 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3873 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3874 File
    3875 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3876 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3877 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3878 IndexError: list index out of range 
    3879  
    3880 Error processing trigger "new frame": 
    3881 IndexError: list index out of range 
    3882  
    3883 File
    3884 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3885 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3886 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3887  
    3888 See log for complete Python traceback. 
    3889  
    3890 
    3891 > select #34
    3892 
    3893 1640 atoms, 1838 bonds, 1 model selected 
    3894 
    3895 > ui mousemode rightMode "translate selected models"
    3896 
    3897 > ui mousemode rightMode "rotate selected models"
    3898 
    3899 Traceback (most recent call last): 
    3900 File
    3901 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3902 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3903 return self._func(self._name, data) 
    3904 File
    3905 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3906 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    3907 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    3908 File
    3909 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3910 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3911 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3912 IndexError: list index out of range 
    3913  
    3914 Error processing trigger "new frame": 
    3915 IndexError: list index out of range 
    3916  
    3917 File
    3918 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    3919 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    3920 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    3921  
    3922 See log for complete Python traceback. 
    3923  
    3924 
    3925 > ui mousemode rightMode "translate selected models"
    3926 
    3927 > ui mousemode rightMode "rotate selected models"
    3928 
    3929 > ui mousemode rightMode "translate selected models"
    3930 
    3931 > ui mousemode rightMode "rotate selected models"
    3932 
    3933 > select #34/B:40
    3934 
    3935 20 atoms, 21 bonds, 1 model selected 
    3936 
    3937 > select #34/A:31
    3938 
    3939 21 atoms, 23 bonds, 1 model selected 
    3940 
    3941 > select #34/A:31
    3942 
    3943 21 atoms, 23 bonds, 1 model selected 
    3944 
    3945 > select #37/G:344
    3946 
    3947 7 atoms, 6 bonds, 1 model selected 
    3948 
    3949 > select #34/B:1
    3950 
    3951 20 atoms, 21 bonds, 1 model selected 
    3952 
    3953 > select #34/B:1
    3954 
    3955 20 atoms, 21 bonds, 1 model selected 
    3956 
    3957 > ui mousemode rightMode "rotate selected models"
    3958 
    3959 > ui mousemode rightMode "translate selected models"
    3960 
    3961 > fitmap #34 inMap #41
    3962 
    3963 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    3964 genome.mrc (#41) using 1640 atoms 
    3965 average map value = 0.004446, steps = 84 
    3966 shifted from previous position = 8.22 
    3967 rotated from previous position = 6.66 degrees 
    3968 atoms outside contour = 1231, contour level = 0.0095301 
    3969  
    3970 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    3971 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    3972 Matrix rotation and translation 
    3973 0.42625311 -0.90240860 0.06298412 299.64749259 
    3974 0.90453614 0.42433433 -0.04188980 -62.82850166 
    3975 0.01107539 0.07482708 0.99713502 -23.89254867 
    3976 Axis 0.06443269 0.02865583 0.99751054 
    3977 Axis point 199.96101362 205.37050398 0.00000000 
    3978 Rotation angle (degrees) 64.92139561 
    3979 Shift along axis -6.32637712 
    3980  
    3981 
    3982 > lighting soft
    3983 
    3984 > lighting simple
    3985 
    3986 > lighting soft
    3987 
    3988 > lighting full
    3989 
    3990 > select clear
    3991 
    3992 > select clear
    3993 
    3994 > select clear
    3995 
    3996 > save image /Users/chunyan/2020/20200507-Figure5-5.tif pixelSize 0.1
    3997 > supersample 4 transparentBackground true
    3998 
    3999 > save image /Users/chunyan/2020/20200507-Figure5-5.tif pixelSize 0.1
    4000 > supersample 4 transparentBackground true
    4001 
    4002 > select #34:300-400
    4003 
    4004 Nothing selected 
    4005 
    4006 > select #37
    4007 
    4008 49008 atoms, 49740 bonds, 1 model selected 
    4009 
    4010 > hide sel cartoons
    4011 
    4012 > select #37:300-400
    4013 
    4014 9360 atoms, 9480 bonds, 1 model selected 
    4015 
    4016 > show sel cartoons
    4017 
    4018 > show sel cartoons
    4019 
    4020 > select clear
    4021 
    4022 > save image /Users/chunyan/2020/20200507-Figure5-6.tif pixelSize 0.1
    4023 > supersample 4 transparentBackground true
    4024 
    4025 > select #37/F
    4026 
    4027 4084 atoms, 4145 bonds, 1 model selected 
    4028 
    4029 > hide sel cartoons
    4030 
    4031 > select #37/L
    4032 
    4033 4084 atoms, 4145 bonds, 1 model selected 
    4034 
    4035 > hide sel cartoons
    4036 
    4037 > select #37/K
    4038 
    4039 4084 atoms, 4145 bonds, 1 model selected 
    4040 
    4041 > hide sel cartoons
    4042 
    4043 > select #37/B
    4044 
    4045 4084 atoms, 4145 bonds, 1 model selected 
    4046 
    4047 > hide sel cartoons
    4048 
    4049 > select #37/C
    4050 
    4051 4084 atoms, 4145 bonds, 1 model selected 
    4052 
    4053 > hide sel cartoons
    4054 
    4055 > save image /Users/chunyan/2020/20200507-Figure5-7.tif pixelSize 0.1
    4056 > supersample 4 transparentBackground true
    4057 
    4058 #34
    4059 
    4060 Unknown command: sequence #34 
    4061 
    4062 #34/A
    4063 
    4064 Unknown command: sequence #34/A 
    4065 
    4066 #34/A
    4067 
    4068 Unknown command: sequence #34/A 
    4069 
    4070 > select #34/B:27
    4071 
    4072 20 atoms, 21 bonds, 1 model selected 
    4073 
    4074 > select #34/B:28
    4075 
    4076 21 atoms, 23 bonds, 1 model selected 
    4077 
    4078 #34/G
    4079 
    4080 Unknown command: sequence #34/G 
    4081 
    4082 > select #34/G
    4083 
    4084 Nothing selected 
    4085 
    4086 > select #37/G
    4087 
    4088 4084 atoms, 4145 bonds, 1 model selected 
    4089 
    4090 > hide sel cartoons
    4091 
    4092 > select #37/H-J:368
    4093 
    4094 33 atoms, 30 bonds, 1 model selected 
    4095 
    4096 > color #37/H-J:368 red
    4097 
    4098 > show sel atoms
    4099 
    4100 > style sel stick
    4101 
    4102 Changed 33 atom styles 
    4103 
    4104 > style sel sphere
    4105 
    4106 Changed 33 atom styles 
    4107 
    4108 > style sel stick
    4109 
    4110 Changed 33 atom styles 
    4111 
    4112 > style sel ball
    4113 
    4114 Changed 33 atom styles 
    4115 
    4116 > color sel byhetero
    4117 
    4118 > hide sel atoms
    4119 
    4120 > select clear
    4121 
    4122 > color #37/H-J:368 blue
    4123 
    4124 > color #37/H-J:368 magenta
    4125 
    4126 > select clear
    4127 
    4128 > save image /Users/chunyan/2020/20200507-Figure5-7.tif pixelSize 0.1
    4129 > supersample 4 transparentBackground true
    4130 
    4131 Expected an objects specifier or a keyword 
    4132 
    4133 > select #37
    4134 
    4135 49008 atoms, 49740 bonds, 1 model selected 
    4136 
    4137 > show sel cartoons
    4138 
    4139 > select clear
    4140 
    4141 > hide #32,34,37#17.1,3#!25,27#!17.2 cartoons
    4142 
    4143 > select #34
    4144 
    4145 1640 atoms, 1838 bonds, 1 model selected 
    4146 
    4147 > hide sel atoms
    4148 
    4149 > show sel cartoons
    4150 
    4151 > show sel atoms
    4152 
    4153 > select #37:300-400
    4154 
    4155 9360 atoms, 9480 bonds, 1 model selected 
    4156 
    4157 > show sel cartoons
    4158 
    4159 > select clear
    4160 
    4161 > fitmap #34 inMap #41
    4162 
    4163 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4164 genome.mrc (#41) using 1640 atoms 
    4165 average map value = 0.004451, steps = 44 
    4166 shifted from previous position = 0.0135 
    4167 rotated from previous position = 1.03 degrees 
    4168 atoms outside contour = 1230, contour level = 0.0095301 
    4169  
    4170 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4171 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4172 Matrix rotation and translation 
    4173 0.41007729 -0.90966944 0.06586455 304.05920833 
    4174 0.91199125 0.40815477 -0.04100800 -61.13699070 
    4175 0.01042080 0.07688434 0.99698556 -24.16858650 
    4176 Axis 0.06455209 0.03035829 0.99745246 
    4177 Axis point 199.90398960 205.06379451 0.00000000 
    4178 Rotation angle (degrees) 65.94528781 
    4179 Shift along axis -6.33537287 
    4180  
    4181 
    4182 > select #37
    4183 
    4184 49008 atoms, 49740 bonds, 1 model selected 
    4185 
    4186 > hide sel cartoons
    4187 
    4188 > select #34
    4189 
    4190 1640 atoms, 1838 bonds, 1 model selected 
    4191 
    4192 > hide sel cartoons
    4193 
    4194 > hide sel atoms
    4195 
    4196 > show sel cartoons
    4197 
    4198 > ui mousemode rightMode "rotate selected models"
    4199 
    4200 > volume #41 level 0.008283
    4201 
    4202 > ui mousemode rightMode "rotate selected models"
    4203 
    4204 > ui mousemode rightMode "translate selected models"
    4205 
    4206 > fitmap #34 inMap #41
    4207 
    4208 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4209 genome.mrc (#41) using 1640 atoms 
    4210 average map value = 0.004447, steps = 100 
    4211 shifted from previous position = 3.3 
    4212 rotated from previous position = 2.64 degrees 
    4213 atoms outside contour = 1202, contour level = 0.0082828 
    4214  
    4215 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4216 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4217 Matrix rotation and translation 
    4218 0.42063165 -0.90497669 0.06392350 301.19950201 
    4219 0.90716627 0.41871105 -0.04159828 -62.24577642 
    4220 0.01087999 0.07548680 0.99708745 -23.98488873 
    4221 Axis 0.06444946 0.02919779 0.99749374 
    4222 Axis point 199.94459682 205.27147824 0.00000000 
    4223 Rotation angle (degrees) 65.27805103 
    4224 Shift along axis -6.33007116 
    4225  
    4226 
    4227 > ui mousemode rightMode "rotate selected models"
    4228 
    4229 > fitmap #34 inMap #41
    4230 
    4231 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4232 genome.mrc (#41) using 1640 atoms 
    4233 average map value = 0.004519, steps = 132 
    4234 shifted from previous position = 5.13 
    4235 rotated from previous position = 10.6 degrees 
    4236 atoms outside contour = 1186, contour level = 0.0082828 
    4237  
    4238 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4239 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4240 Matrix rotation and translation 
    4241 0.93547549 0.34489143 -0.07704237 -44.40030068 
    4242 -0.34464527 0.93858102 0.01689126 83.03529378 
    4243 0.07813616 0.01075093 0.99688473 -19.50503015 
    4244 Axis -0.00868740 -0.21954805 -0.97556301 
    4245 Axis point 211.68923829 168.31140960 0.00000000 
    4246 Rotation angle (degrees) 20.69569092 
    4247 Shift along axis 1.18387280 
    4248  
    4249 
    4250 > ui mousemode rightMode "translate selected models"
    4251 
    4252 > ui mousemode rightMode "rotate selected models"
    4253 
    4254 > fitmap #34 inMap #41
    4255 
    4256 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4257 genome.mrc (#41) using 1640 atoms 
    4258 average map value = 0.004556, steps = 96 
    4259 shifted from previous position = 1.91 
    4260 rotated from previous position = 4.58 degrees 
    4261 atoms outside contour = 1170, contour level = 0.0082828 
    4262  
    4263 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4264 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4265 Matrix rotation and translation 
    4266 0.82117216 0.56991607 -0.02952885 -77.47602396 
    4267 -0.56802441 0.82124170 0.05394755 147.54016646 
    4268 0.05499590 -0.02752711 0.99810707 -9.14699464 
    4269 Axis -0.07122033 -0.07388654 -0.99472028 
    4270 Axis point 198.03521668 197.61791594 0.00000000 
    4271 Rotation angle (degrees) 34.88912441 
    4272 Shift along axis 3.71533704 
    4273  
    4274 
    4275 > ui mousemode rightMode "translate selected models"
    4276 
    4277 > fitmap #34 inMap #41
    4278 
    4279 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4280 genome.mrc (#41) using 1640 atoms 
    4281 average map value = 0.003983, steps = 156 
    4282 shifted from previous position = 3.49 
    4283 rotated from previous position = 8.74 degrees 
    4284 atoms outside contour = 1257, contour level = 0.0082828 
    4285  
    4286 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4287 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4288 Matrix rotation and translation 
    4289 0.66300924 0.74771230 0.03667518 -96.77980539 
    4290 -0.74781153 0.65924187 0.07860078 212.81848276 
    4291 0.03459296 -0.07953916 0.99623133 -26.82893429 
    4292 Axis -0.10515581 0.00138458 -0.99445479 
    4293 Axis point 189.08756419 209.43060811 0.00000000 
    4294 Rotation angle (degrees) 48.75797096 
    4295 Shift along axis 37.15178598 
    4296  
    4297 
    4298 > ui mousemode rightMode "rotate selected models"
    4299 
    4300 > ui mousemode rightMode "translate selected models"
    4301 
    4302 > ui mousemode rightMode "rotate selected models"
    4303 
    4304 > ui mousemode rightMode "rotate selected models"
    4305 
    4306 > ui mousemode rightMode "translate selected models"
    4307 
    4308 > ui mousemode rightMode "rotate selected models"
    4309 
    4310 > ui mousemode rightMode "translate selected models"
    4311 
    4312 > ui mousemode rightMode "rotate selected models"
    4313 
    4314 > fitmap #34 inMap #41
    4315 
    4316 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4317 genome.mrc (#41) using 1640 atoms 
    4318 average map value = 0.004543, steps = 72 
    4319 shifted from previous position = 5.04 
    4320 rotated from previous position = 3.4 degrees 
    4321 atoms outside contour = 1185, contour level = 0.0082828 
    4322  
    4323 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4324 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4325 Matrix rotation and translation 
    4326 -0.08772293 0.99467753 -0.05404914 30.40851684 
    4327 -0.98904511 -0.08050292 0.12372979 414.18108330 
    4328 0.11872013 0.06431098 0.99084289 -44.92164954 
    4329 Axis -0.02982695 -0.08672641 -0.99578556 
    4330 Axis point 206.46391414 194.96895401 0.00000000 
    4331 Rotation angle (degrees) 95.08833309 
    4332 Shift along axis 7.90489774 
    4333  
    4334 
    4335 > fitmap #34 inMap #41
    4336 
    4337 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4338 genome.mrc (#41) using 1640 atoms 
    4339 average map value = 0.004505, steps = 224 
    4340 shifted from previous position = 2.63 
    4341 rotated from previous position = 7.74 degrees 
    4342 atoms outside contour = 1185, contour level = 0.0082828 
    4343  
    4344 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4345 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4346 Matrix rotation and translation 
    4347 -0.31789315 0.94775299 0.02661256 72.56060229 
    4348 -0.93584472 -0.31815481 0.15156576 447.23106988 
    4349 0.15211382 0.02327649 0.98808886 -45.04347688 
    4350 Axis -0.06780157 -0.06632810 -0.99549160 
    4351 Axis point 198.56896202 198.82464526 0.00000000 
    4352 Rotation angle (degrees) 108.90376267 
    4353 Shift along axis 10.25669493 
    4354  
    4355 
    4356 > show sel atoms
    4357 
    4358 > hide sel cartoons
    4359 
    4360 > hide sel atoms
    4361 
    4362 > hide sel atoms
    4363 
    4364 > show sel cartoons
    4365 
    4366 > hide sel cartoons
    4367 
    4368 > select #34
    4369 
    4370 1640 atoms, 1838 bonds, 1 model selected 
    4371 
    4372 > ui mousemode rightMode "rotate selected models"
    4373 
    4374 > fitmap #34 inMap #41
    4375 
    4376 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4377 genome.mrc (#41) using 1640 atoms 
    4378 average map value = 0.004508, steps = 68 
    4379 shifted from previous position = 0.488 
    4380 rotated from previous position = 3.5 degrees 
    4381 atoms outside contour = 1183, contour level = 0.0082828 
    4382  
    4383 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4384 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4385 Matrix rotation and translation 
    4386 -0.28987221 0.95681841 0.02174035 65.63628670 
    4387 -0.94513990 -0.28976119 0.15082779 443.36651320 
    4388 0.15061432 0.02317312 0.98832097 -44.70401392 
    4389 Axis -0.06681431 -0.06745249 -0.99548280 
    4390 Axis point 198.76335963 198.63836369 0.00000000 
    4391 Rotation angle (degrees) 107.19689109 
    4392 Shift along axis 10.21045962 
    4393  
    4394 
    4395 > hide sel cartoons
    4396 
    4397 > hide sel atoms
    4398 
    4399 > volume #8 color #ce5c00e2
    4400 
    4401 > volume #8 color #cec000e2
    4402 
    4403 > volume #8 color #cebf00e2
    4404 
    4405 > volume #8 color #cebfb7e2
    4406 
    4407 > volume #8 color #cebfb7e1
    4408 
    4409 > save image /Users/chunyan/2020/20200507-Figure5-8.tif pixelSize 0.1
    4410 > supersample 4 transparentBackground true
    4411 
    4412 > select #37
    4413 
    4414 49008 atoms, 49740 bonds, 1 model selected 
    4415 
    4416 > volume #19 color #b4b4b4de
    4417 
    4418 > volume #19 color #b4b4b4f4
    4419 
    4420 > volume #19 color #b4b4b4
    4421 
    4422 > volume #19 color #b4b4b47c
    4423 
    4424 > volume #19 color #b4b4b461
    4425 
    4426 > volume #19 color #b4b4b4c9
    4427 
    4428 > volume #19 color #b4b4b499
    4429 
    4430 > volume #19 color #b4b4b495
    4431 
    4432 > volume #41 level 0.01001
    4433 
    4434 > select #37:300-400
    4435 
    4436 9360 atoms, 9480 bonds, 1 model selected 
    4437 
    4438 > show sel cartoons
    4439 
    4440 > select clear
    4441 
    4442 > select clear
    4443 
    4444 > save image /Users/chunyan/2020/20200507-Figure5-9.tif pixelSize 0.1
    4445 > supersample 4 transparentBackground true
    4446 
    4447 > select #37
    4448 
    4449 49008 atoms, 49740 bonds, 1 model selected 
    4450 
    4451 > show sel cartoons
    4452 
    4453 > select clear
    4454 
    4455 > select #37/A
    4456 
    4457 4084 atoms, 4145 bonds, 1 model selected 
    4458 
    4459 > hide sel cartoons
    4460 
    4461 > hide sel cartoons
    4462 
    4463 > select #37/B
    4464 
    4465 4084 atoms, 4145 bonds, 1 model selected 
    4466 
    4467 > select clear
    4468 
    4469 > select #37/E:393
    4470 
    4471 6 atoms, 5 bonds, 1 model selected 
    4472 
    4473 > select #37/E
    4474 
    4475 4084 atoms, 4145 bonds, 1 model selected 
    4476 
    4477 > hide sel cartoons
    4478 
    4479 > select #37/I:509
    4480 
    4481 5 atoms, 4 bonds, 1 model selected 
    4482 
    4483 > select #37/K:504
    4484 
    4485 4 atoms, 3 bonds, 1 model selected 
    4486 
    4487 > select #37/K:495
    4488 
    4489 9 atoms, 8 bonds, 1 model selected 
    4490 
    4491 > select #37/K
    4492 
    4493 4084 atoms, 4145 bonds, 1 model selected 
    4494 
    4495 > hide sel cartoons
    4496 
    4497 > hide sel cartoons
    4498 
    4499 > select #37/H:381
    4500 
    4501 8 atoms, 7 bonds, 1 model selected 
    4502 
    4503 > select #37/H
    4504 
    4505 4084 atoms, 4145 bonds, 1 model selected 
    4506 
    4507 > hide sel cartoons
    4508 
    4509 > select #37/I:377
    4510 
    4511 7 atoms, 6 bonds, 1 model selected 
    4512 
    4513 > select #37/I
    4514 
    4515 4084 atoms, 4145 bonds, 1 model selected 
    4516 
    4517 > hide sel cartoons
    4518 
    4519 > select #37/J:376
    4520 
    4521 12 atoms, 12 bonds, 1 model selected 
    4522 
    4523 > select #37/J
    4524 
    4525 4084 atoms, 4145 bonds, 1 model selected 
    4526 
    4527 > hide sel cartoons
    4528 
    4529 > save image /Users/chunyan/2020/20200507-Figure5-9.tif pixelSize 0.1
    4530 > supersample 4 transparentBackground true
    4531 
    4532 > select #34
    4533 
    4534 1640 atoms, 1838 bonds, 1 model selected 
    4535 
    4536 > show sel cartoons
    4537 
    4538 > show sel atoms
    4539 
    4540 > volume #41 level 0.008699
    4541 
    4542 > show sel cartoons
    4543 
    4544 > select clear
    4545 
    4546 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4547 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    4548 
    4549 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4550 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    4551 
    4552 > color #34/A #3DC5D3
    4553 
    4554 > color #34/B #3DC5D3
    4555 
    4556 > show #32,34,37#17.1,3#!25,27#!17.2 atoms
    4557 
    4558 > show #32,34,37#17.1,3#!25,27#!17.2 cartoons
    4559 
    4560 > hide #32,34,37#17.1,3#!25,27#!17.2 atoms
    4561 
    4562 > hide #32,34,37#17.1,3#!25,27#!17.2 atoms
    4563 
    4564 > select #32
    4565 
    4566 63576 atoms, 55608 bonds, 1 model selected 
    4567 
    4568 > hide sel cartoons
    4569 
    4570 > select #25
    4571 
    4572 3610 atoms, 3660 bonds, 1 model selected 
    4573 
    4574 > hide sel cartoons
    4575 
    4576 > select #27
    4577 
    4578 6313 atoms, 6474 bonds, 1 model selected 
    4579 
    4580 > hide sel cartoons
    4581 
    4582 > select #17
    4583 
    4584 60992 atoms, 61568 bonds, 64 pseudobonds, 5 models selected 
    4585 
    4586 > hide sel cartoons
    4587 
    4588 > select #34
    4589 
    4590 1640 atoms, 1838 bonds, 1 model selected 
    4591 
    4592 > show sel cartoons
    4593 
    4594 > show sel atoms
    4595 
    4596 Expected a keyword 
    4597 
    4598 > color #34/A green
    4599 
    4600 > select clear
    4601 
    4602 > color #34/A pink
    4603 
    4604 > volume #41 color #3debd3
    4605 
    4606 > volume #41 color #3dbcd3
    4607 
    4608 > volume #41 color #ccbcd3
    4609 
    4610 > volume #41 color #ccc9d3
    4611 
    4612 > volume #41 color #3dc5d3
    4613 
    4614 > color #34/A #3DC5DD
    4615 
    4616 > color #34/A #3DC500
    4617 
    4618 > save image /Users/chunyan/2020/20200507-Figure5-A1.tif pixelSize 0.1
    4619 > supersample 4 transparentBackground true
    4620 
    4621 > select #37
    4622 
    4623 49008 atoms, 49740 bonds, 1 model selected 
    4624 
    4625 > hide sel cartoons
    4626 
    4627 > hide sel cartoons
    4628 
    4629 > select #37:300-400
    4630 
    4631 9360 atoms, 9480 bonds, 1 model selected 
    4632 
    4633 > show sel cartoons
    4634 
    4635 > select clear
    4636 
    4637 > select #37:A368
    4638 
    4639 Nothing selected 
    4640 
    4641 > select #37:368
    4642 
    4643 132 atoms, 120 bonds, 1 model selected 
    4644 
    4645 > color #37:368 yellow
    4646 
    4647 > select clear
    4648 
    4649 > save image /Users/chunyan/2020/20200507-Figure5-A2.tif pixelSize 0.1
    4650 > supersample 4 transparentBackground true
    4651 
    4652 Traceback (most recent call last): 
    4653 File
    4654 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4655 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4656 return self._func(self._name, data) 
    4657 File
    4658 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4659 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    4660 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    4661 File
    4662 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4663 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4664 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4665 IndexError: list index out of range 
    4666  
    4667 Error processing trigger "new frame": 
    4668 IndexError: list index out of range 
    4669  
    4670 File
    4671 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4672 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4673 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4674  
    4675 See log for complete Python traceback. 
    4676  
    4677 
    4678 > save image /Users/chunyan/2020/20200507-Figure5-A3.tif pixelSize 0.1
    4679 > supersample 4 transparentBackground true
    4680 
    4681 > select #37
    4682 
    4683 49008 atoms, 49740 bonds, 1 model selected 
    4684 
    4685 > show sel cartoons
    4686 
    4687 > select clear
    4688 
    4689 > save image /Users/chunyan/2020/20200507-Figure5-A4.tif pixelSize 0.1
    4690 > supersample 4 transparentBackground true
    4691 
    4692 > select #37
    4693 
    4694 49008 atoms, 49740 bonds, 1 model selected 
    4695 
    4696 > hide sel cartoons
    4697 
    4698 > select #37:300-4--
    4699 
    4700 Nothing selected 
    4701 
    4702 > select #37:300-400
    4703 
    4704 9360 atoms, 9480 bonds, 1 model selected 
    4705 
    4706 > show sel cartoons
    4707 
    4708 > select clear
    4709 
    4710 > save image /Users/chunyan/2020/20200507-Figure5-A5.tif pixelSize 0.1
    4711 > supersample 4 transparentBackground true
    4712 
    4713 > lighting soft
    4714 
    4715 > lighting simple
    4716 
    4717 > lighting soft
    4718 
    4719 > lighting full
    4720 
    4721 > save image /Users/chunyan/2020/20200507-Figure5-A5.tif pixelSize 0.1
    4722 > supersample 4 transparentBackground true
    4723 
    4724 > save image /Users/chunyan/2020/20200507-Figure5-A6.tif pixelSize 0.1
    4725 > supersample 4 transparentBackground true
    4726 
    4727 Traceback (most recent call last): 
    4728 File
    4729 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4730 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4731 return self._func(self._name, data) 
    4732 File
    4733 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4734 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    4735 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    4736 File
    4737 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4738 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4739 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4740 IndexError: list index out of range 
    4741  
    4742 Error processing trigger "new frame": 
    4743 IndexError: list index out of range 
    4744  
    4745 File
    4746 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4747 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4748 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4749  
    4750 See log for complete Python traceback. 
    4751  
    4752 
    4753 > volume #41 level 0.009649
    4754 
    4755 > select #34
    4756 
    4757 1640 atoms, 1838 bonds, 1 model selected 
    4758 
    4759 > hide sel cartoons
    4760 
    4761 > hide sel atoms
    4762 
    4763 > select clear
    4764 
    4765 Traceback (most recent call last): 
    4766 File
    4767 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4768 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4769 return self._func(self._name, data) 
    4770 File
    4771 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4772 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    4773 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    4774 File
    4775 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4776 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4777 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4778 IndexError: list index out of range 
    4779  
    4780 Error processing trigger "new frame": 
    4781 IndexError: list index out of range 
    4782  
    4783 File
    4784 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4785 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4786 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4787  
    4788 See log for complete Python traceback. 
    4789  
    4790 Traceback (most recent call last): 
    4791 File
    4792 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4793 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4794 return self._func(self._name, data) 
    4795 File
    4796 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4797 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    4798 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    4799 File
    4800 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4801 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4802 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4803 IndexError: list index out of range 
    4804  
    4805 Error processing trigger "new frame": 
    4806 IndexError: list index out of range 
    4807  
    4808 File
    4809 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4810 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4811 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4812  
    4813 See log for complete Python traceback. 
    4814  
    4815 
    4816 > select #44
    4817 
    4818 Nothing selected 
    4819 
    4820 > select #41
    4821 
    4822 3 models selected 
    4823 
    4824 > ui mousemode rightMode "rotate selected models"
    4825 
    4826 > volume #41 level 0.008699
    4827 
    4828 > ui mousemode rightMode "translate selected models"
    4829 
    4830 > fitmap #41 inMap #15
    4831 
    4832 Fit map gp8-asym-300-400-part-genome.mrc in map tail-3.4-with-gp17N.mrc using
    4833 8254 points 
    4834 correlation = 0.9787, correlation about mean = 0.8204, overlap = 1.878 
    4835 steps = 828, shift = 2.58, angle = 63.6 degrees 
    4836  
    4837 Position of gp8-asym-300-400-part-genome.mrc (#41) relative to tail-3.4-with-
    4838 gp17N.mrc (#15) coordinates: 
    4839 Matrix rotation and translation 
    4840 0.99967047 0.02564450 -0.00115134 -5.11732562 
    4841 -0.02564356 0.99967083 0.00081819 5.31212695 
    4842 0.00117194 -0.00078840 0.99999901 -0.11592871 
    4843 Axis -0.03127735 -0.04523009 -0.99848684 
    4844 Axis point 204.62035890 202.13476675 0.00000000 
    4845 Rotation angle (degrees) 1.47168305 
    4846 Shift along axis 0.03554170 
    4847  
    4848 
    4849 > select #34
    4850 
    4851 1640 atoms, 1838 bonds, 1 model selected 
    4852 
    4853 > hide sel cartoons
    4854 
    4855 > hide sel cartoons
    4856 
    4857 > hide sel atoms
    4858 
    4859 > select #34
    4860 
    4861 1640 atoms, 1838 bonds, 1 model selected 
    4862 
    4863 > select #37
    4864 
    4865 49008 atoms, 49740 bonds, 1 model selected 
    4866 
    4867 > hide sel cartoons
    4868 
    4869 > select #34
    4870 
    4871 1640 atoms, 1838 bonds, 1 model selected 
    4872 
    4873 > show sel cartoons
    4874 
    4875 > ui mousemode rightMode "rotate selected models"
    4876 
    4877 > lighting flat
    4878 
    4879 > fitmap #34 inMap #41
    4880 
    4881 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#34) to map gp8-asym-300-400-part-
    4882 genome.mrc (#41) using 1640 atoms 
    4883 average map value = 0.004499, steps = 156 
    4884 shifted from previous position = 3.15 
    4885 rotated from previous position = 7.9 degrees 
    4886 atoms outside contour = 1193, contour level = 0.0086986 
    4887  
    4888 Position of Ideal-B-form-DNA-coot-0.pdb (#34) relative to
    4889 gp8-asym-300-400-part-genome.mrc (#41) coordinates: 
    4890 Matrix rotation and translation 
    4891 0.30568357 0.95194111 -0.01912283 -51.34197856 
    4892 -0.94579986 0.30590167 0.10902665 325.68893073 
    4893 0.10963665 -0.01524129 0.99385488 -25.83545717 
    4894 Axis -0.06519285 -0.06754918 -0.99558375 
    4895 Axis point 199.07452745 198.64871664 0.00000000 
    4896 Rotation angle (degrees) 72.37895029 
    4897 Shift along axis 7.06847102 
    4898  
    4899 
    4900 > lighting soft
    4901 
    4902 > hide sel cartoons
    4903 
    4904 > lighting soft
    4905 
    4906 > select #37:300-400
    4907 
    4908 9360 atoms, 9480 bonds, 1 model selected 
    4909 
    4910 > show sel cartoons
    4911 
    4912 > show sel surfaces
    4913 
    4914 Traceback (most recent call last): 
    4915 File
    4916 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4917 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4918 return self._func(self._name, data) 
    4919 File
    4920 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4921 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    4922 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    4923 File
    4924 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4925 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4926 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4927 IndexError: list index out of range 
    4928  
    4929 Error processing trigger "new frame": 
    4930 IndexError: list index out of range 
    4931  
    4932 File
    4933 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    4934 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    4935 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    4936  
    4937 See log for complete Python traceback. 
    4938  
    4939 
    4940 > hide sel surfaces
    4941 
    4942 > select clear
    4943 
    4944 > save image /Users/chunyan/2020/20200507-Figure5-A7.tif pixelSize 0.1
    4945 > supersample 4 transparentBackground true
    4946 
    4947 > select #34
    4948 
    4949 1640 atoms, 1838 bonds, 1 model selected 
    4950 
    4951 > show sel cartoons
    4952 
    4953 > hide sel cartoons
    4954 
    4955 > hide sel cartoons
    4956 
    4957 > select #34/B:39
    4958 
    4959 21 atoms, 23 bonds, 1 model selected 
    4960 
    4961 > select #34/A:31
    4962 
    4963 21 atoms, 23 bonds, 1 model selected 
    4964 
    4965 > hide sel cartoons
    4966 
    4967 > volume #41 color #3dc5d355
    4968 
    4969 > volume #41 level 0.008283
    4970 
    4971 > volume #41 color #b2c5d355
    4972 
    4973 > volume #41 color #d2c5d355
    4974 
    4975 > volume #41 color #d2d2d355
    4976 
    4977 > volume #41 color #d2d2d255
    4978 
    4979 > volume #41 color #d2b3d255
    4980 
    4981 > volume #41 color #d2b3b855
    4982 
    4983 > volume #41 color #b6b3b855
    4984 
    4985 > volume #41 color #b6b3b755
    4986 
    4987 > volume #41 color #b6b4b755
    4988 
    4989 > volume #41 color #b4b4b755
    4990 
    4991 > volume #41 color #b4b4b455
    4992 
    4993 > volume #41 level 0.009768
    4994 
    4995 > select #34
    4996 
    4997 1640 atoms, 1838 bonds, 1 model selected 
    4998 
    4999 > show sel atoms
    5000 
    5001 > select clear
    5002 
    5003 > select clear
    5004 
    5005 > select clear
    5006 
    5007 > hide sel atoms
    5008 
    5009 Traceback (most recent call last): 
    5010 File
    5011 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5012 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5013 return self._func(self._name, data) 
    5014 File
    5015 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5016 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5017 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5018 File
    5019 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5020 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5021 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5022 IndexError: list index out of range 
    5023  
    5024 Error processing trigger "new frame": 
    5025 IndexError: list index out of range 
    5026  
    5027 File
    5028 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5029 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5030 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5031  
    5032 See log for complete Python traceback. 
    5033  
    5034 
    5035 > hide sel atoms
    5036 
    5037 > hide sel atoms
    5038 
    5039 Traceback (most recent call last): 
    5040 File
    5041 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5042 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5043 return self._func(self._name, data) 
    5044 File
    5045 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5046 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5047 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5048 File
    5049 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5050 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5051 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5052 IndexError: list index out of range 
    5053  
    5054 Error processing trigger "new frame": 
    5055 IndexError: list index out of range 
    5056  
    5057 File
    5058 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5059 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5060 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5061  
    5062 See log for complete Python traceback. 
    5063  
    5064 
    5065 > select clear
    5066 
    5067 > hide sel atoms
    5068 
    5069 > hide sel atoms
    5070 
    5071 > select clear
    5072 
    5073 > volume #41 level 0.009649
    5074 
    5075 > select clear
    5076 
    5077 > save image /Users/chunyan/2020/20200507-Figure5-A8.tif pixelSize 0.1
    5078 > supersample 4 transparentBackground true
    5079 
    5080 > select #37:36
    5081 
    5082 108 atoms, 96 bonds, 1 model selected 
    5083 
    5084 > select #37:368
    5085 
    5086 132 atoms, 120 bonds, 1 model selected 
    5087 
    5088 > color #37:368 magenta
    5089 
    5090 > select clear
    5091 
    5092 > select #37/L:371
    5093 
    5094 5 atoms, 4 bonds, 1 model selected 
    5095 
    5096 > select #37/F:371
    5097 
    5098 5 atoms, 4 bonds, 1 model selected 
    5099 
    5100 > select #37/F:371
    5101 
    5102 5 atoms, 4 bonds, 1 model selected 
    5103 
    5104 > select clear
    5105 
    5106 > view name p1
    5107 
    5108 > save image /Users/chunyan/2020/20200507-Figure5-A9.tif pixelSize 0.1
    5109 > supersample 4 transparentBackground true
    5110 
    5111 > select #34
    5112 
    5113 1640 atoms, 1838 bonds, 1 model selected 
    5114 
    5115 > hide sel cartoons
    5116 
    5117 > hide sel atoms
    5118 
    5119 > select #37
    5120 
    5121 49008 atoms, 49740 bonds, 1 model selected 
    5122 
    5123 > show sel cartoons
    5124 
    5125 > select #37
    5126 
    5127 49008 atoms, 49740 bonds, 1 model selected 
    5128 
    5129 > hide sel cartoons
    5130 
    5131 > select #37/B
    5132 
    5133 4084 atoms, 4145 bonds, 1 model selected 
    5134 
    5135 > show sel cartoons
    5136 
    5137 > select #37/C
    5138 
    5139 4084 atoms, 4145 bonds, 1 model selected 
    5140 
    5141 > show sel cartoons
    5142 
    5143 > show sel cartoons
    5144 
    5145 > hide sel cartoons
    5146 
    5147 > select #37/H
    5148 
    5149 4084 atoms, 4145 bonds, 1 model selected 
    5150 
    5151 > show sel cartoons
    5152 
    5153 > hide sel cartoons
    5154 
    5155 > select #37/He
    5156 
    5157 Nothing selected 
    5158 
    5159 > select #37/E
    5160 
    5161 4084 atoms, 4145 bonds, 1 model selected 
    5162 
    5163 > show sel cartoons
    5164 
    5165 > hide sel cartoons
    5166 
    5167 > select #37/H
    5168 
    5169 4084 atoms, 4145 bonds, 1 model selected 
    5170 
    5171 > show sel cartoons
    5172 
    5173 Expected an objects specifier or a keyword 
    5174 
    5175 > select #37
    5176 
    5177 49008 atoms, 49740 bonds, 1 model selected 
    5178 
    5179 > show sel cartoons
    5180 
    5181 > hide sel cartoons
    5182 
    5183 > select #37/A-B
    5184 
    5185 8168 atoms, 8290 bonds, 1 model selected 
    5186 
    5187 > show sel cartoons
    5188 
    5189 > hide sel cartoons
    5190 
    5191 > select #37/A,C
    5192 
    5193 8168 atoms, 8290 bonds, 1 model selected 
    5194 
    5195 > show sel cartoons
    5196 
    5197 Expected an objects specifier or a keyword 
    5198 
    5199 > select #37
    5200 
    5201 49008 atoms, 49740 bonds, 1 model selected 
    5202 
    5203 > show sel cartoons
    5204 
    5205 > hide sel cartoons
    5206 
    5207 > hide sel cartoons
    5208 
    5209 > select #37/E
    5210 
    5211 4084 atoms, 4145 bonds, 1 model selected 
    5212 
    5213 > show sel cartoons
    5214 
    5215 > select #37/G
    5216 
    5217 4084 atoms, 4145 bonds, 1 model selected 
    5218 
    5219 > show sel cartoons
    5220 
    5221 > select #34
    5222 
    5223 1640 atoms, 1838 bonds, 1 model selected 
    5224 
    5225 > show sel cartoons
    5226 
    5227 > show sel atoms
    5228 
    5229 > hide sel cartoons
    5230 
    5231 > hide sel atoms
    5232 
    5233 > save image /Users/chunyan/2020/20200507-Figure5-A10.tif pixelSize 0.1
    5234 > supersample 4 transparentBackground true
    5235 
    5236 > color #37:368 yellow
    5237 
    5238 > hide sel cartoons
    5239 
    5240 > save image /Users/chunyan/2020/20200507-Figure5-A10.tif pixelSize 0.1
    5241 > supersample 4 transparentBackground true
    5242 
    5243 > select #37/E:384
    5244 
    5245 7 atoms, 6 bonds, 1 model selected 
    5246 
    5247 > select #37/E:355
    5248 
    5249 5 atoms, 4 bonds, 1 model selected 
    5250 
    5251 > select #37/E:356
    5252 
    5253 11 atoms, 11 bonds, 1 model selected 
    5254 
    5255 > select #37/E:383
    5256 
    5257 8 atoms, 7 bonds, 1 model selected 
    5258 
    5259 > open /Users/chunyan/2020/gp8-asym/terminal-genome-
    5260 > remodeling/gp8-asym-300-400-part-genome-lp.mrc
    5261 > /Users/chunyan/2020/gp8-asym/terminal-genome-remodeling/Ideal-B-form-DNA-
    5262 > coot-0.pdb
    5263 
    5264 Opened gp8-asym-300-400-part-genome-lp.mrc, grid size 400,400,400, pixel 1.05,
    5265 shown at level 1.54e-06, step 2, values float32 
    5266  
    5267 Chain information for Ideal-B-form-DNA-coot-0.pdb 
    5268 --- 
    5269 Chain | Description 
    5270 42.2/A | No description available 
    5271 42.2/B | No description available 
    5272  
    5273 Traceback (most recent call last): 
    5274 File
    5275 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5276 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5277 return self._func(self._name, data) 
    5278 File
    5279 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5280 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5281 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5282 File
    5283 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5284 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5285 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5286 IndexError: list index out of range 
    5287  
    5288 Error processing trigger "new frame": 
    5289 IndexError: list index out of range 
    5290  
    5291 File
    5292 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5293 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5294 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5295  
    5296 See log for complete Python traceback. 
    5297  
    5298 
    5299 > select #37
    5300 
    5301 49008 atoms, 49740 bonds, 1 model selected 
    5302 
    5303 > hide sel cartoons
    5304 
    5305 Traceback (most recent call last): 
    5306 File
    5307 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5308 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5309 return self._func(self._name, data) 
    5310 File
    5311 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5312 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5313 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5314 File
    5315 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5316 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5317 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5318 IndexError: list index out of range 
    5319  
    5320 Error processing trigger "new frame": 
    5321 IndexError: list index out of range 
    5322  
    5323 File
    5324 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5325 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5326 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5327  
    5328 See log for complete Python traceback. 
    5329  
    5330 
    5331 > select clear
    5332 
    5333 Expected an objects specifier or a keyword 
    5334 
    5335 > select #42
    5336 
    5337 1640 atoms, 1838 bonds, 4 models selected 
    5338 
    5339 > select #42.2/B:39
    5340 
    5341 21 atoms, 23 bonds, 1 model selected 
    5342 
    5343 > select clear
    5344 
    5345 > volume #42.1 level 0.0007187
    5346 
    5347 > select #42.1
    5348 
    5349 2 models selected 
    5350 
    5351 > volume #42.1 color #b2ffffd0
    5352 
    5353 > volume #42.1 color #b2ffffcc
    5354 
    5355 > volume #42.1 color #b2ffffba
    5356 
    5357 > select clear
    5358 
    5359 Traceback (most recent call last): 
    5360 File
    5361 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5362 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5363 return self._func(self._name, data) 
    5364 File
    5365 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5366 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5367 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5368 File
    5369 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5370 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5371 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5372 IndexError: list index out of range 
    5373  
    5374 Error processing trigger "new frame": 
    5375 IndexError: list index out of range 
    5376  
    5377 File
    5378 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5379 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5380 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5381  
    5382 See log for complete Python traceback. 
    5383  
    5384 
    5385 > toolshed show "Side View"
    5386 
    5387 > view
    5388 
    5389 > ui mousemode rightMode "translate selected models"
    5390 
    5391 > ui mousemode rightMode "rotate selected models"
    5392 
    5393 > ui mousemode rightMode "translate selected models"
    5394 
    5395 > ui mousemode rightMode "rotate selected models"
    5396 
    5397 > ui mousemode rightMode "translate selected models"
    5398 
    5399 > ui mousemode rightMode "translate selected models"
    5400 
    5401 > select clear
    5402 
    5403 > select clear
    5404 
    5405 > volume #42.1 color #b2fffff6
    5406 
    5407 > volume #42.1 color #b2fffff8
    5408 
    5409 > volume #42.1 color #b2fffffe
    5410 
    5411 > volume #42.1 color #b2ffff
    5412 
    5413 > volume #41 color #3dc5db55
    5414 
    5415 > volume #41 color #3dc5dbca
    5416 
    5417 > volume #41 color #3dc5dbcc
    5418 
    5419 > volume #41 color #3dc5db
    5420 
    5421 > volume #42.1 color #3dc5db
    5422 
    5423 > select #42.2
    5424 
    5425 1640 atoms, 1838 bonds, 1 model selected 
    5426 
    5427 > ui mousemode rightMode "rotate selected models"
    5428 
    5429 > fitmap #42.2 inMap #42.1
    5430 
    5431 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
    5432 genome-lp.mrc (#42.1) using 1640 atoms 
    5433 average map value = 0.004499, steps = 136 
    5434 shifted from previous position = 0.239 
    5435 rotated from previous position = 8.4 degrees 
    5436 atoms outside contour = 709, contour level = 0.00071868 
    5437  
    5438 Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
    5439 gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates: 
    5440 Matrix rotation and translation 
    5441 0.99873794 -0.05021764 0.00084651 10.69268753 
    5442 0.05021922 0.99873630 -0.00196013 -9.89928782 
    5443 -0.00074701 0.00200016 0.99999772 -0.15730335 
    5444 Axis 0.03939510 0.01585163 0.99909797 
    5445 Axis point 202.38327616 207.75661272 0.00000000 
    5446 Rotation angle (degrees) 2.88111567 
    5447 Shift along axis 0.10715811 
    5448  
    5449 
    5450 > select clear
    5451 
    5452 Traceback (most recent call last): 
    5453 File
    5454 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5455 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5456 return self._func(self._name, data) 
    5457 File
    5458 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5459 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5460 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5461 File
    5462 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5463 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5464 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5465 IndexError: list index out of range 
    5466  
    5467 Error processing trigger "new frame": 
    5468 IndexError: list index out of range 
    5469  
    5470 File
    5471 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5472 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5473 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5474  
    5475 See log for complete Python traceback. 
    5476  
    5477 Traceback (most recent call last): 
    5478 File
    5479 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5480 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5481 return self._func(self._name, data) 
    5482 File
    5483 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5484 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5485 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5486 File
    5487 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5488 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5489 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5490 IndexError: list index out of range 
    5491  
    5492 Error processing trigger "new frame": 
    5493 IndexError: list index out of range 
    5494  
    5495 File
    5496 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5497 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5498 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5499  
    5500 See log for complete Python traceback. 
    5501  
    5502 
    5503 > volume #41 level 0.01066
    5504 
    5505 Traceback (most recent call last): 
    5506 File
    5507 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5508 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5509 return self._func(self._name, data) 
    5510 File
    5511 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5512 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5513 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5514 File
    5515 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5516 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5517 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5518 IndexError: list index out of range 
    5519  
    5520 Error processing trigger "new frame": 
    5521 IndexError: list index out of range 
    5522  
    5523 File
    5524 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5525 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5526 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5527  
    5528 See log for complete Python traceback. 
    5529  
    5530 
    5531 > view
    5532 
    5533 > select #42.2
    5534 
    5535 1640 atoms, 1838 bonds, 1 model selected 
    5536 
    5537 > ui mousemode rightMode "rotate selected models"
    5538 
    5539 > ui mousemode rightMode "translate selected models"
    5540 
    5541 > ui mousemode rightMode "translate selected models"
    5542 
    5543 > ui mousemode rightMode "rotate selected models"
    5544 
    5545 > volume #15 level 0.01821
    5546 
    5547 Traceback (most recent call last): 
    5548 File
    5549 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5550 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5551 return self._func(self._name, data) 
    5552 File
    5553 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5554 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5555 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5556 File
    5557 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5558 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5559 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5560 IndexError: list index out of range 
    5561  
    5562 Error processing trigger "new frame": 
    5563 IndexError: list index out of range 
    5564  
    5565 File
    5566 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5567 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5568 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5569  
    5570 See log for complete Python traceback. 
    5571  
    5572 
    5573 > volume #15 level 0.01276
    5574 
    5575 > lighting flat
    5576 
    5577 > fitmap #42.2 inMap #42.1
    5578 
    5579 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
    5580 genome-lp.mrc (#42.1) using 1640 atoms 
    5581 average map value = 0.004347, steps = 320 
    5582 shifted from previous position = 0.6 
    5583 rotated from previous position = 15.1 degrees 
    5584 atoms outside contour = 823, contour level = 0.00071868 
    5585  
    5586 Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
    5587 gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates: 
    5588 Matrix rotation and translation 
    5589 -0.18236091 -0.97704616 0.11011492 435.41937537 
    5590 0.98291778 -0.18398541 -0.00469014 42.41735540 
    5591 0.02484202 0.10737861 0.99390779 -29.77959578 
    5592 Axis 0.05703197 0.04339552 0.99742879 
    5593 Axis point 200.89472016 202.71517927 0.00000000 
    5594 Rotation angle (degrees) 100.73222639 
    5595 Shift along axis -3.02948046 
    5596  
    5597 
    5598 > fitmap #42.2 inMap #42.1
    5599 
    5600 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
    5601 genome-lp.mrc (#42.1) using 1640 atoms 
    5602 average map value = 0.004504, steps = 120 
    5603 shifted from previous position = 3.2 
    5604 rotated from previous position = 4.01 degrees 
    5605 atoms outside contour = 706, contour level = 0.00071868 
    5606  
    5607 Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
    5608 gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates: 
    5609 Matrix rotation and translation 
    5610 0.99944996 -0.03316067 0.00036586 7.02156618 
    5611 0.03316116 0.99944901 -0.00141842 -6.58165157 
    5612 -0.00031862 0.00142977 0.99999892 -0.16636008 
    5613 Axis 0.04290318 0.01031048 0.99902603 
    5614 Axis point 201.95672256 208.30701193 0.00000000 
    5615 Rotation angle (degrees) 1.90218229 
    5616 Shift along axis 0.06718951 
    5617  
    5618 
    5619 > volume #42.1 color #4dddd3
    5620 
    5621 > lighting soft
    5622 
    5623 > volume #42.1 color #dfddd3
    5624 
    5625 > volume #42.1 color #dfddd39d
    5626 
    5627 > volume #42.1 color #c8ddd39d
    5628 
    5629 > volume #42.1 color #c8c2d39d
    5630 
    5631 > volume #42.1 color #c8c1d39d
    5632 
    5633 > volume #42.1 color #c8c1d3ca
    5634 
    5635 > volume #42.1 color #c8c1d3d6
    5636 
    5637 Missing or invalid "chains" argument: only initial part "#42" of atom
    5638 specifier valid 
    5639 
    5640 > sequence chain #42.1
    5641 
    5642 Chains must have same sequence 
    5643 
    5644 > select #42.2/A
    5645 
    5646 820 atoms, 922 bonds, 1 model selected 
    5647 
    5648 > color #42.2/A green
    5649 
    5650 > select #34
    5651 
    5652 1640 atoms, 1838 bonds, 1 model selected 
    5653 
    5654 > show sel cartoons
    5655 
    5656 > volume #42.1 color #8fc1d3d6
    5657 
    5658 > volume #42.1 color #7fc1d3d6
    5659 
    5660 > volume #42.1 color #7fced3d6
    5661 
    5662 > volume #42.1 color #7fced3d9
    5663 
    5664 > volume #42.1 color #7fced3
    5665 
    5666 > volume #42.1 color #4aced3
    5667 
    5668 > volume #42.1 color #08ced3
    5669 
    5670 > volume #42.1 color #08ce35
    5671 
    5672 > volume #42.1 color #08ce07
    5673 
    5674 > select #42.2/A
    5675 
    5676 820 atoms, 922 bonds, 1 model selected 
    5677 
    5678 > color #42.2/A green
    5679 
    5680 > volume #42.1 color #08ced6
    5681 
    5682 > volume #42.1 color #cbced6
    5683 
    5684 > volume #42.1 color #cbced698
    5685 
    5686 > select #42.2/B
    5687 
    5688 820 atoms, 916 bonds, 1 model selected 
    5689 
    5690 > select #34
    5691 
    5692 1640 atoms, 1838 bonds, 1 model selected 
    5693 
    5694 > hide sel cartoons
    5695 
    5696 > select #42.2/a
    5697 
    5698 820 atoms, 922 bonds, 1 model selected 
    5699 
    5700 > select #42.2/A
    5701 
    5702 820 atoms, 922 bonds, 1 model selected 
    5703 
    5704 > color #42.2/A green
    5705 
    5706 > color #42.2/B #4DDDD3
    5707 
    5708 > select clear
    5709 
    5710 > select #42.2
    5711 
    5712 1640 atoms, 1838 bonds, 1 model selected 
    5713 
    5714 > show sel atoms
    5715 
    5716 > show sel atoms
    5717 
    5718 > show sel cartoons
    5719 
    5720 > show sel atoms
    5721 
    5722 > select clear
    5723 
    5724 > select #34
    5725 
    5726 1640 atoms, 1838 bonds, 1 model selected 
    5727 
    5728 > show sel cartoons
    5729 
    5730 > hide sel cartoons
    5731 
    5732 > volume #42.1 color #cb50d698
    5733 
    5734 > volume #42.1 color #5750d698
    5735 
    5736 > volume #42.1 color #57a7d698
    5737 
    5738 > volume #42.1 color #57e8d698
    5739 
    5740 > volume #42.1 color #57e80298
    5741 
    5742 > volume #42.1 color #57e80198
    5743 
    5744 > volume #42.1 color #57e80098
    5745 
    5746 > volume #42.1 color #57e90098
    5747 
    5748 > volume #42.1 color #57f60098
    5749 
    5750 > volume #42.1 color #57ff0098
    5751 
    5752 > volume #42.1 color #57ff00
    5753 
    5754 > volume #42.1 color #57de00
    5755 
    5756 > volume #42.1 color #57df00
    5757 
    5758 > volume #42.1 color #d8df00
    5759 
    5760 > volume #42.1 color #d8dfdf
    5761 
    5762 > volume #42.1 color #d8dfdf9a
    5763 
    5764 > volume #42.1 color #d8dfde9a
    5765 
    5766 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    5767 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    5768 
    5769 > color #42.2/A #D58F00
    5770 
    5771 > volume #42.1 color #56dfde9a
    5772 
    5773 > volume #42.1 color #56df059a
    5774 
    5775 > volume #42.1 color #56df049a
    5776 
    5777 > volume #42.1 color #56df009a
    5778 
    5779 > volume #42.1 color #04df009a
    5780 
    5781 > volume #42.1 color #03df009a
    5782 
    5783 > volume #42.1 color #00df009a
    5784 
    5785 > volume #42.1 color #00e0009a
    5786 
    5787 > volume #42.1 color #00e5009a
    5788 
    5789 > volume #42.1 color #00ee009a
    5790 
    5791 > volume #42.1 color #00f6009a
    5792 
    5793 > volume #42.1 color #00fd009a
    5794 
    5795 > volume #42.1 color #00ff009a
    5796 
    5797 > color #42.2/A #00FF00
    5798 
    5799 > volume #42.1 color #00d5009a
    5800 
    5801 > volume #42.1 color #ced5009a
    5802 
    5803 > volume #42.1 color #ced5d49a
    5804 
    5805 > select clear
    5806 
    5807 > save image /Users/chunyan/2020/20200507-Figure5-A11.tif pixelSize 0.1
    5808 > supersample 4 transparentBackground true
    5809 
    5810 Traceback (most recent call last): 
    5811 File
    5812 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5813 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5814 return self._func(self._name, data) 
    5815 File
    5816 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5817 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5818 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5819 File
    5820 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5821 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5822 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5823 IndexError: list index out of range 
    5824  
    5825 Error processing trigger "new frame": 
    5826 IndexError: list index out of range 
    5827  
    5828 File
    5829 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5830 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5831 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5832  
    5833 See log for complete Python traceback. 
    5834  
    5835 Traceback (most recent call last): 
    5836 File
    5837 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5838 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5839 return self._func(self._name, data) 
    5840 File
    5841 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5842 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5843 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5844 File
    5845 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5846 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5847 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5848 IndexError: list index out of range 
    5849  
    5850 Error processing trigger "new frame": 
    5851 IndexError: list index out of range 
    5852  
    5853 File
    5854 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5855 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5856 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5857  
    5858 See log for complete Python traceback. 
    5859  
    5860 
    5861 > volume #23 color #d2d2d28f
    5862 
    5863 > lighting flat
    5864 
    5865 > volume #42.1 color #ced5d4f9
    5866 
    5867 > volume #42.1 color #ced5d4
    5868 
    5869 > volume #42.1 color #4dddd3
    5870 
    5871 > lighting soft
    5872 
    5873 > select #37
    5874 
    5875 49008 atoms, 49740 bonds, 1 model selected 
    5876 
    5877 > show sel cartoons
    5878 
    5879 > hide sel cartoons
    5880 
    5881 > select #37:300-400
    5882 
    5883 9360 atoms, 9480 bonds, 1 model selected 
    5884 
    5885 > show sel cartoons
    5886 
    5887 > open /Users/chunyan/2020/gp8-asym/part/gp8-asym-lp.mrc
    5888 
    5889 Opened gp8-asym-lp.mrc, grid size 400,400,400, pixel 1.05, shown at level
    5890 0.02, step 2, values float32 
    5891 Traceback (most recent call last): 
    5892 File
    5893 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5894 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5895 return self._func(self._name, data) 
    5896 File
    5897 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5898 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5899 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5900 File
    5901 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5902 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5903 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5904 IndexError: list index out of range 
    5905  
    5906 Error processing trigger "new frame": 
    5907 IndexError: list index out of range 
    5908  
    5909 File
    5910 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5911 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5912 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5913  
    5914 See log for complete Python traceback. 
    5915  
    5916 Traceback (most recent call last): 
    5917 File
    5918 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5919 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5920 return self._func(self._name, data) 
    5921 File
    5922 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5923 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5924 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5925 File
    5926 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5927 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5928 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5929 IndexError: list index out of range 
    5930  
    5931 Error processing trigger "new frame": 
    5932 IndexError: list index out of range 
    5933  
    5934 File
    5935 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5936 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5937 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5938  
    5939 See log for complete Python traceback. 
    5940  
    5941 
    5942 > volume #43 level 0.008651
    5943 
    5944 > lighting flat
    5945 
    5946 > select #43
    5947 
    5948 3 models selected 
    5949 
    5950 > ui mousemode rightMode "rotate selected models"
    5951 
    5952 Traceback (most recent call last): 
    5953 File
    5954 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5955 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5956 return self._func(self._name, data) 
    5957 File
    5958 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5959 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    5960 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    5961 File
    5962 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5963 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5964 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5965 IndexError: list index out of range 
    5966  
    5967 Error processing trigger "new frame": 
    5968 IndexError: list index out of range 
    5969  
    5970 File
    5971 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    5972 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    5973 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    5974  
    5975 See log for complete Python traceback. 
    5976  
    5977 
    5978 > ui mousemode rightMode "rotate selected models"
    5979 
    5980 > ui mousemode rightMode "rotate selected models"
    5981 
    5982 > ui mousemode rightMode "translate selected models"
    5983 
    5984 > ui mousemode rightMode "rotate selected models"
    5985 
    5986 > ui mousemode rightMode "translate selected models"
    5987 
    5988 > ui mousemode rightMode "rotate selected models"
    5989 
    5990 > ui mousemode rightMode "translate selected models"
    5991 
    5992 > ui mousemode rightMode "rotate selected models"
    5993 
    5994 > fitmap #43 inMap #23
    5995 
    5996 Fit map gp8-asym-lp.mrc in map gp12-new.mrc using 1456064 points 
    5997 correlation = 0.1995, correlation about mean = 0.124, overlap = 10.24 
    5998 steps = 2000, shift = 51.6, angle = 23.8 degrees 
    5999  
    6000 Position of gp8-asym-lp.mrc (#43) relative to gp12-new.mrc (#23) coordinates: 
    6001 Matrix rotation and translation 
    6002 0.40696140 -0.91344510 -0.00066381 106.40439805 
    6003 -0.91344420 -0.40695962 -0.00188189 277.92196286 
    6004 0.00144886 0.00137221 -0.99999800 210.81785650 
    6005 Axis 0.83873705 -0.54453659 0.00023232 
    6006 Axis point 0.00000000 173.37975011 105.53535540 
    6007 Rotation angle (degrees) 179.88885292 
    6008 Shift along axis -62.04438986 
    6009  
    6010 
    6011 > volume #43 color #b2b2b6
    6012 
    6013 > volume #43 color #b2b2b6a2
    6014 
    6015 > volume #43 color #b2b2b680
    6016 
    6017 > volume #43 color #b2b2b580
    6018 
    6019 > volume #43 color #b2b2b480
    6020 
    6021 > volume #43 color #b2b2b380
    6022 
    6023 > fitmap #42.1 inMap #43
    6024 
    6025 Fit map gp8-asym-300-400-part-genome-lp.mrc in map gp8-asym-lp.mrc using 1667
    6026 points 
    6027 correlation = 0.9298, correlation about mean = 0.9033, overlap = 0.1757 
    6028 steps = 1056, shift = 1.89, angle = 79.6 degrees 
    6029  
    6030 Position of gp8-asym-300-400-part-genome-lp.mrc (#42.1) relative to gp8-asym-
    6031 lp.mrc (#43) coordinates: 
    6032 Matrix rotation and translation 
    6033 0.99082847 -0.13499437 0.00595422 29.27059608 
    6034 0.13502393 0.99083033 -0.00487730 -25.60878619 
    6035 -0.00524121 0.00563653 0.99997037 0.24372855 
    6036 Axis 0.03887465 0.04139482 0.99838631 
    6037 Axis point 203.53926969 202.90732245 0.00000000 
    6038 Rotation angle (degrees) 7.77176754 
    6039 Shift along axis 0.32114826 
    6040  
    6041 
    6042 > fitmap #42.2 inMap #42.1
    6043 
    6044 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
    6045 genome-lp.mrc (#42.1) using 1640 atoms 
    6046 average map value = 0.004369, steps = 348 
    6047 shifted from previous position = 6.57 
    6048 rotated from previous position = 17.7 degrees 
    6049 atoms outside contour = 813, contour level = 0.00071868 
    6050  
    6051 Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
    6052 gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates: 
    6053 Matrix rotation and translation 
    6054 0.39874175 -0.91455788 0.06774138 307.15876655 
    6055 0.91700257 0.39677637 -0.04092407 -59.81831363 
    6056 0.01054925 0.07843715 0.99686324 -24.46895053 
    6057 Axis 0.06499965 0.03114469 0.99739915 
    6058 Axis point 199.82629197 204.93099831 0.00000000 
    6059 Rotation angle (degrees) 66.65974546 
    6060 Shift along axis -6.30312184 
    6061  
    6062 
    6063 > fitmap #37 inMap #43
    6064 
    6065 Fit molecule gp8-new-assembled.pdb (#37) to map gp8-asym-lp.mrc (#43) using
    6066 49008 atoms 
    6067 average map value = 0.007408, steps = 52 
    6068 shifted from previous position = 0.589 
    6069 rotated from previous position = 0.379 degrees 
    6070 atoms outside contour = 32763, contour level = 0.0086506 
    6071  
    6072 Position of gp8-new-assembled.pdb (#37) relative to gp8-asym-lp.mrc (#43)
    6073 coordinates: 
    6074 Matrix rotation and translation 
    6075 -0.00550842 -0.99998038 0.00297801 420.47849047 
    6076 0.99998479 -0.00550910 -0.00022072 1.20334395 
    6077 0.00023713 0.00297674 0.99999553 -2.23188863 
    6078 Axis 0.00159876 0.00137046 0.99999778 
    6079 Axis point 209.64160107 209.68869631 0.00000000 
    6080 Rotation angle (degrees) 90.31575837 
    6081 Shift along axis -1.55799090 
    6082  
    6083 
    6084 > select #42.2
    6085 
    6086 1640 atoms, 1838 bonds, 1 model selected 
    6087 
    6088 > ui mousemode rightMode "rotate selected models"
    6089 
    6090 > fitmap #42.2 inMap #42.1
    6091 
    6092 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
    6093 genome-lp.mrc (#42.1) using 1640 atoms 
    6094 average map value = 0.004365, steps = 252 
    6095 shifted from previous position = 0.144 
    6096 rotated from previous position = 16.1 degrees 
    6097 atoms outside contour = 811, contour level = 0.00071868 
    6098  
    6099 Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
    6100 gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates: 
    6101 Matrix rotation and translation 
    6102 0.43194805 -0.89974929 0.06222611 298.03003881 
    6103 0.90182219 0.42998487 -0.04277546 -63.30728183 
    6104 0.01173090 0.07459366 0.99714501 -23.97935667 
    6105 Axis 0.06498496 0.02795820 0.99749451 
    6106 Axis point 199.88992538 205.49390475 0.00000000 
    6107 Rotation angle (degrees) 64.56169474 
    6108 Shift along axis -6.32176333 
    6109  
    6110 
    6111 > volume #43 step 1
    6112 
    6113 > lighting soft
    6114 
    6115 > lighting flat
    6116 
    6117 > volume #43 step 2
    6118 
    6119 > select #42.3
    6120 
    6121 Nothing selected 
    6122 
    6123 > select #43
    6124 
    6125 4 models selected 
    6126 
    6127 > ui mousemode rightMode "rotate selected models"
    6128 
    6129 > fitmap #43 inMap #23
    6130 
    6131 Fit map gp8-asym-lp.mrc in map gp12-new.mrc using 1456064 points 
    6132 correlation = 0.1995, correlation about mean = 0.1245, overlap = 10.27 
    6133 steps = 2000, shift = 2.89, angle = 27.9 degrees 
    6134  
    6135 Position of gp8-asym-lp.mrc (#43) relative to gp12-new.mrc (#23) coordinates: 
    6136 Matrix rotation and translation 
    6137 -0.58760139 -0.80914968 0.00117414 293.10936819 
    6138 -0.80915053 0.58760087 -0.00078318 46.88503539 
    6139 -0.00005622 -0.00141025 -0.99999900 211.67207040 
    6140 Axis -0.45409174 0.89095472 -0.00061587 
    6141 Axis point 158.54360138 0.00000000 105.80349757 
    6142 Rotation angle (degrees) 179.96043891 
    6143 Shift along axis -91.45646384 
    6144  
    6145 
    6146 > select #37
    6147 
    6148 49008 atoms, 49740 bonds, 1 model selected 
    6149 
    6150 > hide sel cartoons
    6151 
    6152 > volume #43 level 0.004727
    6153 
    6154 > show sel cartoons
    6155 
    6156 > show sel cartoons
    6157 
    6158 > fitmap #37 inMap #43
    6159 
    6160 Fit molecule gp8-new-assembled.pdb (#37) to map gp8-asym-lp.mrc (#43) using
    6161 49008 atoms 
    6162 average map value = 0.007438, steps = 48 
    6163 shifted from previous position = 0.201 
    6164 rotated from previous position = 0.0765 degrees 
    6165 atoms outside contour = 14728, contour level = 0.004727 
    6166  
    6167 Position of gp8-new-assembled.pdb (#37) relative to gp8-asym-lp.mrc (#43)
    6168 coordinates: 
    6169 Matrix rotation and translation 
    6170 0.86332314 -0.50464305 0.00292023 134.01356052 
    6171 0.50464654 0.86332586 -0.00056369 -77.09876795 
    6172 -0.00223665 0.00196033 0.99999557 -1.50301816 
    6173 Axis 0.00250074 0.00510934 0.99998382 
    6174 Axis point 209.33152145 208.87376160 0.00000000 
    6175 Rotation angle (degrees) 30.30831817 
    6176 Shift along axis -1.56178425 
    6177  
    6178 
    6179 > fitmap #42.1 inMap #43
    6180 
    6181 Fit map gp8-asym-300-400-part-genome-lp.mrc in map gp8-asym-lp.mrc using 1667
    6182 points 
    6183 correlation = 0.931, correlation about mean = 0.9059, overlap = 0.1758 
    6184 steps = 852, shift = 0.704, angle = 45.8 degrees 
    6185  
    6186 Position of gp8-asym-300-400-part-genome-lp.mrc (#42.1) relative to gp8-asym-
    6187 lp.mrc (#43) coordinates: 
    6188 Matrix rotation and translation 
    6189 0.99360833 0.11286291 -0.00210474 -21.97002251 
    6190 -0.11285188 0.99360031 0.00478170 24.19417980 
    6191 0.00263095 -0.00451361 0.99998634 0.14833026 
    6192 Axis -0.04113774 -0.02095848 -0.99893365 
    6193 Axis point 202.74999257 206.05268258 0.00000000 
    6194 Rotation angle (degrees) 6.48700546 
    6195 Shift along axis 0.24855187 
    6196  
    6197 
    6198 > volume #43 level 0.005539
    6199 
    6200 > select #37
    6201 
    6202 49008 atoms, 49740 bonds, 1 model selected 
    6203 
    6204 > hide sel cartoons
    6205 
    6206 > save session /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs
    6207 
    6208 > select clear
    6209 
    6210 > lighting soft
    6211 
    6212 > select #37
    6213 
    6214 49008 atoms, 49740 bonds, 1 model selected 
    6215 
    6216 > select #42.2
    6217 
    6218 1640 atoms, 1838 bonds, 1 model selected 
    6219 
    6220 > ui mousemode rightMode "rotate selected models"
    6221 
    6222 > ui mousemode rightMode "translate selected models"
    6223 
    6224 > fitmap #42.2 inMap #42.1
    6225 
    6226 Fit molecule Ideal-B-form-DNA-coot-0.pdb (#42.2) to map gp8-asym-300-400-part-
    6227 genome-lp.mrc (#42.1) using 1640 atoms 
    6228 average map value = 0.004498, steps = 172 
    6229 shifted from previous position = 3.86 
    6230 rotated from previous position = 11.7 degrees 
    6231 atoms outside contour = 708, contour level = 0.00071868 
    6232  
    6233 Position of Ideal-B-form-DNA-coot-0.pdb (#42.2) relative to
    6234 gp8-asym-300-400-part-genome-lp.mrc (#42.1) coordinates: 
    6235 Matrix rotation and translation 
    6236 0.99843386 -0.05593555 0.00101059 11.93622326 
    6237 0.05593765 0.99843186 -0.00218753 -10.99074593 
    6238 -0.00088665 0.00224063 0.99999709 -0.16246687 
    6239 Axis 0.03954532 0.01694311 0.99907412 
    6240 Axis point 202.34037066 207.63984332 0.00000000 
    6241 Rotation angle (degrees) 3.20957956 
    6242 Shift along axis 0.12348789 
    6243  
    6244 
    6245 > select clear
    6246 
    6247 Traceback (most recent call last): 
    6248 File
    6249 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    6250 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6251 return self._func(self._name, data) 
    6252 File
    6253 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    6254 packages/chimerax/model_panel/tool.py", line 158, in <lambda> 
    6255 lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) 
    6256 File
    6257 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    6258 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    6259 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    6260 IndexError: list index out of range 
    6261  
    6262 Error processing trigger "new frame": 
    6263 IndexError: list index out of range 
    6264  
    6265 File
    6266 "/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/347285D8-B6DF-4FF1-9194-48E15CC67DD2/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    6267 packages/chimerax/model_panel/tool.py", line 203, in _fill_tree 
    6268 parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] 
    6269  
    6270 See log for complete Python traceback. 
    6271  
    6272 
    6273 > save image /Users/chunyan/2020/20200507-Figure5-B1.tif pixelSize 0.1
    6274 > supersample 4 transparentBackground true
    6275 
    6276 > lighting soft
    6277 
    6278 > fitmap #40 inMap #43
    6279 
    6280 Fit map gp8-asym-360-383-part-lp.mrc in map gp8-asym-lp.mrc using 26754 points 
    6281 correlation = 0.95, correlation about mean = 0.8047, overlap = 2.207 
    6282 steps = 60, shift = 0.465, angle = 0.272 degrees 
    6283  
    6284 Position of gp8-asym-360-383-part-lp.mrc (#40) relative to gp8-asym-lp.mrc
    6285 (#43) coordinates: 
    6286 Matrix rotation and translation 
    6287 0.99999867 -0.00116975 0.00113122 0.05528665 
    6288 0.00117189 0.99999751 -0.00189750 0.10726151 
    6289 -0.00112899 0.00189883 0.99999755 -0.00322989 
    6290 Axis 0.75920582 0.45200683 0.46829087 
    6291 Axis point 0.00000000 23.68192431 35.30910081 
    6292 Rotation angle (degrees) 0.14325100 
    6293 Shift along axis 0.08894435 
    6294  
    6295 
    6296 > volume #10 color #d2d2d268
    6297 
    6298 > volume #10 color #d2d2d274
    6299 
    6300 > volume #10 color #d2d2d277
    6301 
    6302 > volume #10 color #d2d2d27d
    6303 
    6304 > volume #10 color #d2d2d281
    6305 
    6306 > volume #10 color #d2d2d285
    6307 
    6308 > volume #10 color #d2d2d288
    6309 
    6310 > volume #10 color #d2d2d28d
    6311 
    6312 > volume #10 color #d2d2d28f
    6313 
    6314 > volume #10 color #d2d2d291
    6315 
    6316 > volume #10 color #d2d2d294
    6317 
    6318 > volume #10 color #d2d2d298
    6319 
    6320 > volume #10 color #d2d2d299
    6321 
    6322 > volume #10 color #d2d2d2a0
    6323 
    6324 > volume #10 color #d2d2d2b4
    6325 
    6326 > volume #10 color #d2d2d2b7
    6327 
    6328 > volume #10 color #d2d2d2ba
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    6330 > volume #10 color #d2d2d2c6
    6331 
    6332 > volume #10 color #d2d2d2d3
    6333 
    6334 > volume #10 color #d2d2d2d7
    6335 
    6336 > volume #10 color #d2d2d2da
    6337 
    6338 > volume #10 color #d2d2d2df
    6339 
    6340 > volume #10 color #d2d2d2eb
    6341 
    6342 > volume #10 color #d2d2d2ef
    6343 
    6344 > volume #10 color #d2d2d2
    6345 
    6346 > volume #10 color #d2d2d2f6
    6347 
    6348 > volume #10 color #d2d2d2ec
    6349 
    6350 > volume #10 color #d2d2d2d7
    6351 
    6352 > volume #10 color #d2d2d2c6
    6353 
    6354 > volume #10 color #d2d2d273
    6355 
    6356 > volume #10 color #d2d2d271
    6357 
    6358 > volume #10 color #d2d2d26f
    6359 
    6360 > volume #10 color #d2d2d25e
    6361 
    6362 > volume #10 color #d2d2d25c
    6363 
    6364 > volume #10 color #d2d2d25b
    6365 
    6366 > volume #10 color #d2d2d252
    6367 
    6368 > volume #10 color #d2d2d250
    6369 
    6370 > volume #10 color #d2d2d24d
    6371 
    6372 > volume #10 color #d2d2d247
    6373 
    6374 > volume #10 color #d2d2d246
    6375 
    6376 > volume #10 color #d2d2d244
    6377 
    6378 > volume #10 color #d2d2d243
    6379 
    6380 > volume #10 color #d2d2d240
    6381 
    6382 > volume #10 color #d2d2d23f
    6383 
    6384 > volume #10 color #d2d2d23e
    6385 
    6386 > volume #10 color #d2d2d23c
    6387 
    6388 > volume #10 color #d2d2d23b
    6389 
    6390 > volume #10 color #d2d2d23a
    6391 
    6392 > volume #10 color #d2d2d235
    6393 
    6394 > volume #10 color #d2d2d230
    6395 
    6396 > volume #10 color #d2d2d22a
    6397 
    6398 > volume #10 color #d2d2d227
    6399 
    6400 > volume #10 color #d2d2d228
    6401 
    6402 > volume #10 color #d2d2d233
    6403 
    6404 > volume #10 color #d2d2d24e
    6405 
    6406 > volume #10 color #d2d2d259
    6407 
    6408 > volume #10 color #d2d2d26f
    6409 
    6410 > volume #10 color #d2d2d271
    6411 
    6412 > volume #10 color #d2d2d276
    6413 
    6414 > volume #10 color #d2d2d279
    6415 
    6416 > volume #10 color #d2d2d27a
    6417 
    6418 > volume #10 color #d2d2d27d
    6419 
    6420 > volume #10 color #d2d2d280
    6421 
    6422 > volume #10 color #a2d2d280
     2418[had to reduce the Description length]
    64232419
    64242420> volume #10 color #a2a6d280