Changes between Initial Version and Version 1 of Ticket #17008


Ignore:
Timestamp:
Mar 4, 2025, 10:53:41 AM (8 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17008

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

  • Ticket #17008 – Description

    initial v1  
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    1652     "arch" : "arm64e",
    1653     "base" : 6598733824,
    1654     "size" : 32748,
    1655     "uuid" : "984d08b8-f85c-36f5-9e17-5bff7fc779a3",
    1656     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1657     "name" : "libsystem_platform.dylib"
    1658   },
    1659   {
    1660     "source" : "P",
    1661     "arch" : "arm64e",
    1662     "base" : 6661582848,
    1663     "CFBundleShortVersionString" : "6.9",
    1664     "CFBundleIdentifier" : "com.apple.AppKit",
    1665     "size" : 21221376,
    1666     "uuid" : "b88a44c1-d617-33dc-90ed-b6ab417c428e",
    1667     "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    1668     "name" : "AppKit",
    1669     "CFBundleVersion" : "2575.40.6"
    1670   },
    1671   {
    1672     "source" : "P",
    1673     "arch" : "arm64e",
    1674     "base" : 6695202816,
    1675     "CFBundleShortVersionString" : "1.600.0",
    1676     "CFBundleIdentifier" : "com.apple.SkyLight",
    1677     "size" : 5427200,
    1678     "uuid" : "f66e0c94-99b5-3fcd-b726-3e3cbca668a3",
    1679     "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    1680     "name" : "SkyLight"
    1681   },
    1682   {
    1683     "source" : "P",
    1684     "arch" : "arm64e",
    1685     "base" : 6596726784,
    1686     "size" : 290816,
    1687     "uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
    1688     "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1689     "name" : "libdispatch.dylib"
    1690   },
    1691   {
    1692     "source" : "P",
    1693     "arch" : "arm64e",
    1694     "base" : 6598963200,
    1695     "CFBundleShortVersionString" : "6.9",
    1696     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    1697     "size" : 5197824,
    1698     "uuid" : "190e6a36-fcaa-3ea3-94bb-7009c44653da",
    1699     "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    1700     "name" : "CoreFoundation",
    1701     "CFBundleVersion" : "3302.1.400"
    1702   },
    1703   {
    1704     "source" : "P",
    1705     "arch" : "arm64e",
    1706     "base" : 6788620288,
    1707     "CFBundleShortVersionString" : "2.1.1",
    1708     "CFBundleIdentifier" : "com.apple.HIToolbox",
    1709     "size" : 3178496,
    1710     "uuid" : "950f1236-acaf-379d-819f-6c6b0b5deabd",
    1711     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    1712     "name" : "HIToolbox"
    1713   },
    1714   {
    1715     "source" : "P",
    1716     "arch" : "arm64e",
    1717     "base" : 6594830336,
    1718     "size" : 532288,
    1719     "uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
    1720     "path" : "\/usr\/lib\/dyld",
    1721     "name" : "dyld"
    1722   },
    1723   {
    1724     "size" : 0,
    1725     "source" : "A",
    1726     "base" : 0,
    1727     "uuid" : "00000000-0000-0000-0000-000000000000"
    1728   },
    1729   {
    1730     "source" : "P",
    1731     "arch" : "arm64e",
    1732     "base" : 6617780224,
    1733     "CFBundleShortVersionString" : "6.9",
    1734     "CFBundleIdentifier" : "com.apple.Foundation",
    1735     "size" : 14974976,
    1736     "uuid" : "16d282d0-8b48-3e76-8036-fcb45dece518",
    1737     "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    1738     "name" : "Foundation",
    1739     "CFBundleVersion" : "3302.1.400"
    1740   },
    1741   {
    1742     "source" : "P",
    1743     "arch" : "arm64e",
    1744     "base" : 6660206592,
    1745     "CFBundleShortVersionString" : "2.0.2",
    1746     "CFBundleIdentifier" : "com.apple.framework.IOKit",
    1747     "size" : 921600,
    1748     "uuid" : "ffd74642-9d8e-31db-ad51-41eb5f08837b",
    1749     "path" : "\/System\/Library\/Frameworks\/IOKit.framework\/Versions\/A\/IOKit",
    1750     "name" : "IOKit"
    1751   },
    1752   {
    1753     "source" : "P",
    1754     "arch" : "arm64e",
    1755     "base" : 7152160768,
    1756     "CFBundleShortVersionString" : "104.1.2",
    1757     "CFBundleIdentifier" : "com.apple.IOGPU",
    1758     "size" : 270336,
    1759     "uuid" : "153b19ed-e98a-3714-89b3-e0a992f861b2",
    1760     "path" : "\/System\/Library\/PrivateFrameworks\/IOGPU.framework\/Versions\/A\/IOGPU",
    1761     "name" : "IOGPU",
    1762     "CFBundleVersion" : "104.1.2"
    1763   },
    1764   {
    1765     "source" : "P",
    1766     "arch" : "arm64e",
    1767     "base" : 6781698048,
    1768     "CFBundleShortVersionString" : "367.6",
    1769     "CFBundleIdentifier" : "com.apple.Metal",
    1770     "size" : 2596864,
    1771     "uuid" : "8e4d919e-aa4b-36c5-8621-dbc72ed287cd",
    1772     "path" : "\/System\/Library\/Frameworks\/Metal.framework\/Versions\/A\/Metal",
    1773     "name" : "Metal",
    1774     "CFBundleVersion" : "367.6"
    1775   }
     177[deleted to fit within ticket limits]
    1776178],
    1777179  "sharedCache" : {
    … …  
    2531933> show #!2 models
    2532934
    2533 > hide #!1 models
    2534 
    2535 > show #!1 models
    2536 
    2537 > volume #3 level 0.00154
    2538 
    2539 > volume #3 level 0.001765
    2540 
    2541 > volume #1 level 0.04849
    2542 
    2543 > volume #1 level 0.02544
    2544 
    2545 > volume #1 level 0.1144
    2546 
    2547 > volume #1 level 0.03861
    2548 
    2549 > volume #3 level 0.001202
    2550 
    2551 > surface dust #1 size 8.18
    2552 
    2553 > surface dust #2 size 8.18
    2554 
    2555 > hide #!4 models
    2556 
    2557 > show #!4 models
    2558 
    2559 > hide #!1 models
    2560 
    2561 > hide #!4 models
    2562 
    2563 > show #!1 models
    2564 
    2565 > show #!2 models
    2566 
    2567 > hide #!1 models
    2568 
    2569 > show #!3 models
    2570 
    2571 > hide #!2 models
    2572 
    2573 > show #!2 models
    2574 
    2575 > hide #!3 models
    2576 
    2577 > hide #!2 models
    2578 
    2579 > show #!2 models
    2580 
    2581 > hide #!2 models
    2582 
    2583 > show #!1 models
    2584 
    2585 > volume #3 level 0.001512
    2586 
    2587 > volume #3 level 0.002047
    2588 
    2589 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2590 > maps and masks/Head/Revised/J1187_head_sharpened.mrc"
    2591 
    2592 Opened J1187_head_sharpened.mrc as #5, grid size 540,540,540, pixel 0.818,
    2593 shown at level 0.000148, step 4, values float32 
    2594 
    2595 > volume #5 step 1
    2596 
    2597 > volume #5 level 0.06663
    2598 
    2599 > fitmap #5 inMap #1
    2600 
    2601 Fit map J1187_head_sharpened.mrc in map J1169_consensus_sharpened.mrc using
    2602 150205 points 
    2603 correlation = 0.47, correlation about mean = 0.1047, overlap = 6891 
    2604 steps = 80, shift = 1.61, angle = 1.79 degrees 
    2605  
    2606 Position of J1187_head_sharpened.mrc (#5) relative to
    2607 J1169_consensus_sharpened.mrc (#1) coordinates: 
    2608 Matrix rotation and translation 
    2609 0.99951322 0.02623089 -0.01688992 -2.79303153 
    2610 -0.02620120 0.99965474 0.00197655 4.79852728 
    2611 0.01693593 -0.00153305 0.99985540 -1.93261563 
    2612 Axis -0.05615814 -0.54125656 -0.83898010 
    2613 Axis point 164.75721743 111.28954436 0.00000000 
    2614 Rotation angle (degrees) 1.79064236 
    2615 Shift along axis -0.81895687 
    2616  
    2617 
    2618 > hide #!3 models
    2619 
    2620 > hide #!1 models
    2621 
    2622 > show #!2 models
    2623 
    2624 > volume #5 level 0.06663
    2625 
    2626 > volume #5 color #ffd479
    2627 
    2628 > volume #3 color #ff9300
    2629 
    2630 > show #!4 models
    2631 
    2632 > hide #!2 models
    2633 
    2634 > hide #!5 models
    2635 
    2636 Drag select of 9 residues 
    2637 
    2638 > select up
    2639 
    2640 1389 atoms, 1555 bonds, 68 residues, 1 model selected 
    2641 
    2642 > select up
    2643 
    2644 17030 atoms, 17621 bonds, 1912 residues, 1 model selected 
    2645 
    2646 > select down
    2647 
    2648 1389 atoms, 1555 bonds, 68 residues, 1 model selected 
    2649 
    2650 > ui tool show "Color Actions"
    2651 
    2652 > color sel orange
    2653 
    2654 > select clear
    2655 
    2656 Drag select of 3 residues 
    2657 
    2658 > select up
    2659 
    2660 930 atoms, 1046 bonds, 45 residues, 1 model selected 
    2661 
    2662 > color sel orange
    2663 
    2664 Drag select of 1 residues 
    2665 
    2666 > select up
    2667 
    2668 321 atoms, 357 bonds, 16 residues, 1 model selected 
    2669 
    2670 > color sel orange
    2671 
    2672 > select clear
    2673 
    2674 Drag select of 13 residues 
    2675 
    2676 > select up
    2677 
    2678 292 atoms, 298 bonds, 36 residues, 1 model selected 
    2679 
    2680 > select up
    2681 
    2682 4714 atoms, 4810 bonds, 591 residues, 1 model selected 
    2683 
    2684 > select up
    2685 
    2686 4741 atoms, 4836 bonds, 595 residues, 1 model selected 
    2687 
    2688 > select up
    2689 
    2690 6405 atoms, 6542 bonds, 802 residues, 1 model selected 
    2691 
    2692 > select up
    2693 
    2694 6458 atoms, 6594 bonds, 806 residues, 1 model selected 
    2695 
    2696 > select up
    2697 
    2698 17030 atoms, 17621 bonds, 1912 residues, 1 model selected 
    2699 
    2700 > select down
    2701 
    2702 6458 atoms, 6594 bonds, 806 residues, 1 model selected 
    2703 
    2704 > select up
    2705 
    2706 17030 atoms, 17621 bonds, 1912 residues, 1 model selected 
    2707 
    2708 > select down
    2709 
    2710 6458 atoms, 6594 bonds, 806 residues, 1 model selected 
    2711 
    2712 > color sel cornflower blue
    2713 
    2714 > color sel blue
    2715 
    2716 > color sel cornflower blue
    2717 
    2718 Drag select of 9 residues 
    2719 
    2720 > select up
    2721 
    2722 386 atoms, 391 bonds, 45 residues, 1 model selected 
    2723 
    2724 > select up
    2725 
    2726 4490 atoms, 4560 bonds, 552 residues, 1 model selected 
    2727 
    2728 > select up
    2729 
    2730 4535 atoms, 4604 bonds, 558 residues, 1 model selected 
    2731 
    2732 > select up
    2733 
    2734 5655 atoms, 5746 bonds, 693 residues, 1 model selected 
    2735 
    2736 > select up
    2737 
    2738 5674 atoms, 5764 bonds, 696 residues, 1 model selected 
    2739 
    2740 > select up
    2741 
    2742 5991 atoms, 6089 bonds, 733 residues, 1 model selected 
    2743 
    2744 > color sel lime
    2745 
    2746 > select clear
    2747 
    2748 Drag select of 2 residues 
    2749 
    2750 > select up
    2751 
    2752 1207 atoms, 1228 bonds, 153 residues, 1 model selected 
    2753 
    2754 > color sel magenta
    2755 
    2756 Drag select of 4 residues 
    2757 
    2758 > select up
    2759 
    2760 731 atoms, 752 bonds, 88 residues, 1 model selected 
    2761 
    2762 > color sel purple
    2763 
    2764 > select clear
    2765 
    2766 > volume #5 style mesh
    2767 
    2768 > volume #5 style surface
    2769 
    2770 > volume #5 level 0.05218
    2771 
    2772 > volume #5 level 0.06663
    2773 
    2774 > volume #5 style mesh
    2775 
    2776 > volume #5 level 0.08108
    2777 
    2778 > volume #5 level 0.2617
    2779 
    2780 > volume #5 level 0.03412
    2781 
    2782 > volume #5 style surface
    2783 
    2784 > volume #3 level 0.001509
    2785 
    2786 > volume #1 level 0.04881
    2787 
    2788 > hide #!4 models
    2789 
    2790 > volume #5 level 0.01245
    2791 
    2792 > surface dust #5 size 8.18
    2793 
    2794 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2795 > maps and masks/Consensus/223_consensus_locres.mrc"
    2796 
    2797 Opened 223_consensus_locres.mrc as #6, grid size 540,540,540, pixel 0.818,
    2798 shown at level 50, step 4, values float32 
    2799 
    2800 > ui tool show "Surface Color"
    2801 
    2802 > color sample #1.1 map #6 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
    2803 
    2804 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2805 
    2806 > color sample #1.1 map #6 palette
    2807 > 2.8,#0000ff:3.8,#00ffff:4.8,#00ff00:5.8,#ffff00:6.8,#ff0000
    2808 
    2809 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2810 
    2811 > color sample #1.1 map #6 palette
    2812 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:4.8,#ff0000
    2813 
    2814 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2815 
    2816 > color sample #1.1 map #6 palette
    2817 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000
    2818 
    2819 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2820 
    2821 > color sample #1.1 map #6 palette
    2822 > 2.8,#0000ff:3.1,#00ffff:3.4,#00ff00:3.7,#ffff00:6.8,#ff0000
    2823 
    2824 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2825 
    2826 > color sample #1.1 map #6 palette
    2827 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000
    2828 
    2829 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2830 
    2831 > color sample #1.1 map #6 palette
    2832 > 2.8,#ff0000:3.3,#ffff00:3.8,#00ff00:4.3,#00ffff:6.8,#0000ff
    2833 
    2834 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2835 
    2836 > color sample #1.1 map #6 palette
    2837 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000
    2838 
    2839 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2840 
    2841 > color single #1.1
    2842 
    2843 > color sample #1.1 map #6 palette
    2844 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000
    2845 
    2846 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2847 
    2848 > color single #1.1
    2849 
    2850 > color sample #1.1 map #6 palette
    2851 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000
    2852 
    2853 Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098 
    2854 
    2855 > color single #1.1
    2856 
    2857 > close #1-6
    2858 
    2859 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2860 > maps and masks/Consensus/J1169_consensus_sharpened.mrc"
    2861 
    2862 Opened J1169_consensus_sharpened.mrc as #1, grid size 540,540,540, pixel
    2863 0.818, shown at level 0.000199, step 4, values float32 
    2864 
    2865 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2866 > maps and masks/Consensus/J1031_consensus_mask.mrc"
    2867 
    2868 Opened J1031_consensus_mask.mrc as #2, grid size 540,540,540, pixel 0.818,
    2869 shown at level 1, step 4, values float32 
    2870 
    2871 > volume #2 step 1
    2872 
    2873 > volume #2 level 0.99
    2874 
    2875 > volume #1 step 1
    2876 
    2877 > volume #1 level 0.041
    2878 
    2879 > volume multiply #1-2
    2880 
    2881 Opened volume product as #3, grid size 540,540,540, pixel 0.818, shown at step
    2882 1, values float32 
    2883 
    2884 > volume #3 level 0.05077
    2885 
    2886 > hide #!3 models
    2887 
    2888 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2889 > maps and masks/Body/J1068_body_sharpened.mrc"
    2890 
    2891 Opened J1068_body_sharpened.mrc as #4, grid size 540,540,540, pixel 0.818,
    2892 shown at level 3.71e-05, step 4, values float32 
    2893 
    2894 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2895 > maps and masks/Body/J1033_body_mask.mrc"
    2896 
    2897 Opened J1033_body_mask.mrc as #5, grid size 540,540,540, pixel 0.818, shown at
    2898 level 0.336, step 4, values float32 
    2899 
    2900 > volume #5 step 1
    2901 
    2902 > volume #4 step 1
    2903 
    2904 > volume multiply #4-5
    2905 
    2906 Opened volume product as #6, grid size 540,540,540, pixel 0.818, shown at step
    2907 1, values float32 
    2908 
    2909 > volume #6 level 0.07179
    2910 
    2911 > volume #4 level 0.05983
    2912 
    2913 > hide #!6 models
    2914 
    2915 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2916 > maps and masks/Head/Revised/J1187_head_sharpened.mrc"
    2917 
    2918 Opened J1187_head_sharpened.mrc as #7, grid size 540,540,540, pixel 0.818,
    2919 shown at level 0.000148, step 4, values float32 
    2920 
    2921 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2922 > maps and masks/Head/J1032_head_mask.mrc"
    2923 
    2924 Opened J1032_head_mask.mrc as #8, grid size 540,540,540, pixel 0.818, shown at
    2925 level 0.997, step 4, values float32 
    2926 
    2927 > volume multiply #7-8
    2928 
    2929 Opened volume product as #9, grid size 540,540,540, pixel 0.818, shown at step
    2930 1, values float32 
    2931 
    2932 > volume #9 level 0.04106
    2933 
    2934 > volume #9 level 0.01502
    2935 
    2936 > open
    2937 > "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
    2938 > maps and masks/J1073_head_mask.mrc"
    2939 
    2940 Opened J1073_head_mask.mrc as #10, grid size 540,540,540, pixel 0.818, shown
    2941 at level 5e-05, step 4, values float32 
    2942 
    2943 > hide #!9 models
    2944 
    2945 > hide #!10 models
    2946 
    2947 > volume multiply #7,10
    2948 
    2949 Opened volume product as #11, grid size 540,540,540, pixel 0.818, shown at
    2950 step 1, values float32 
    2951 
    2952 > volume #11 level 0.0299
    2953 
    2954 > volume #11 level 0.02246
    2955 
    2956 > show #!9 models
    2957 
    2958 > hide #!9 models
    2959 
    2960 > show #!6 models
    2961 
    2962 > show #!3 models
    2963 
    2964 > show #!6 models
    2965 
    2966 > show #!9 models
    2967 
    2968 > hide #!9 models
    2969 
    2970 > show #!9 models
    2971 
    2972 > hide #!9 models
    2973 
    2974 > save "/Users/mulline1/Dropbox/FBH1/cryoEM_revised/Final maps and
    2975 > masks/Consensus/J1169_consensus_sharpened_masked.mrc" models #3
    2976 
    2977 > hide #!3 models
    2978 
    2979 > volume #6 level 0.05584
    2980 
    2981 > volume #11 level 0.05593
    2982 
    2983 > save "/Users/mulline1/Dropbox/FBH1/cryoEM_revised/Final maps and
    2984 > masks/Body/J1068_body_sharpened_masked.mrc" models #6
    2985 
    2986 > save "/Users/mulline1/Dropbox/FBH1/cryoEM_revised/Final maps and
    2987 > masks/Head/Revised/J1187_head_sharpened_masked.mrc" models #11
    2988 
    2989 > close #1-11
    2990 
    2991 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2992 > maps and masks/Consensus/J1169_consensus_sharpened_masked.mrc"
    2993 
    2994 Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
    2995 pixel 0.818, shown at level 2.26e-05, step 4, values float32 
    2996 
    2997 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    2998 > maps and masks/Head/Revised/J1187_head_sharpened_masked.mrc"
    2999 
    3000 Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
    3001 0.818, shown at level 0.000148, step 4, values float32 
    3002 
    3003 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3004 > maps and masks/Body/J1068_body_sharpened_masked.mrc"
    3005 
    3006 Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
    3007 0.818, shown at level 3.71e-05, step 4, values float32 
    3008 
    3009 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3010 > maps and masks/Substrate/237_substrate_sharpened_masked.mrc"
    3011 
    3012 Opened 237_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    3013 0.818, shown at level 8.06e-06, step 4, values float32 
    3014 
    3015 > volume #1 step 1
    3016 
    3017 > volume #2 step 1
    3018 
    3019 > volume #3 step 1
    3020 
    3021 > volume #4 step 1
    3022 
    3023 > volume #4 level 5.17e-05
    3024 
    3025 > volume #4 level 6.624e-05
    3026 
    3027 > volume #4 level 9.534e-05
    3028 
    3029 > volume #4 level 0.0001099
    3030 
    3031 > volume #4 level 0.0001244
    3032 
    3033 > volume #4 level 0.0001535
    3034 
    3035 > volume #4 level 0.0001826
    3036 
    3037 > volume #4 level 0.0001972
    3038 
    3039 > volume #4 level 0.0002553
    3040 
    3041 > volume #4 level 0.0002844
    3042 
    3043 > volume #4 level 0.0003135
    3044 
    3045 > volume #4 level 0.0003281
    3046 
    3047 > volume #4 level 0.0003426
    3048 
    3049 > volume #4 level 0.0003572
    3050 
    3051 > volume #4 level 0.0003717
    3052 
    3053 > volume #4 level 0.0003863
    3054 
    3055 > volume #4 level 0.0004153
    3056 
    3057 > volume #4 level 0.0004299
    3058 
    3059 > volume #4 level 0.0004444
    3060 
    3061 > volume #4 level 0.000459
    3062 
    3063 > volume #4 level 0.0004735
    3064 
    3065 > volume #4 level 0.0004881
    3066 
    3067 > volume #4 level 0.0005026
    3068 
    3069 > volume #4 level 0.0005172
    3070 
    3071 > volume #4 level 0.0005317
    3072 
    3073 > volume #4 level 0.0005463
    3074 
    3075 > close #4
    3076 
    3077 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3078 > maps and masks/Substrate/Revised/262_substrate_sharpened_masked.mrc"
    3079 
    3080 Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    3081 0.818, shown at level 1.48e-05, step 4, values float32 
    3082 
    3083 > volume #4 step 1
    3084 
    3085 > volume #4 level 0.0007471
    3086 
    3087 > volume #4 level 0.001241
    3088 
    3089 > volume #1 level 0.02042
    3090 
    3091 > volume #2 level 0.06516
    3092 
    3093 > volume #3 level 0.0465
    3094 
    3095 > volume #1 level 0.07142
    3096 
    3097 > volume #2 level 0.04349
    3098 
    3099 > volume #3 level 0.06973
    3100 
    3101 > volume #4 level 0.001686
    3102 
    3103 > ui tool show "Fit in Map"
    3104 
    3105 > fitmap #2 inMap #1
    3106 
    3107 Fit map J1187_head_sharpened_masked.mrc in map
    3108 J1169_consensus_sharpened_masked.mrc using 56800 points 
    3109 correlation = 0.5222, correlation about mean = 0.2802, overlap = 3254 
    3110 steps = 216, shift = 2.19, angle = 1.41 degrees 
    3111  
    3112 Position of J1187_head_sharpened_masked.mrc (#2) relative to
    3113 J1169_consensus_sharpened_masked.mrc (#1) coordinates: 
    3114 Matrix rotation and translation 
    3115 0.99969566 0.02370801 -0.00682039 -3.57433463 
    3116 -0.02370882 0.99971891 -0.00003754 4.43490885 
    3117 0.00681758 0.00019924 0.99997674 -0.19053019 
    3118 Axis 0.00479895 -0.27640972 -0.96102791 
    3119 Axis point 172.88925083 152.76969778 0.00000000 
    3120 Rotation angle (degrees) 1.41362159 
    3121 Shift along axis -1.05990014 
    3122  
    3123 
    3124 > fitmap #3 inMap #1
    3125 
    3126 Fit map J1068_body_sharpened_masked.mrc in map
    3127 J1169_consensus_sharpened_masked.mrc using 102847 points 
    3128 correlation = 0.9368, correlation about mean = 0.816, overlap = 2.303e+04 
    3129 steps = 68, shift = 0.361, angle = 1.21 degrees 
    3130  
    3131 Position of J1068_body_sharpened_masked.mrc (#3) relative to
    3132 J1169_consensus_sharpened_masked.mrc (#1) coordinates: 
    3133 Matrix rotation and translation 
    3134 0.99977978 0.02020549 -0.00566905 -2.71069053 
    3135 -0.02019621 0.99979461 0.00169013 4.30859413 
    3136 0.00570203 -0.00157527 0.99998250 -0.96829419 
    3137 Axis -0.07756628 -0.27010829 -0.95970047 
    3138 Axis point 211.62361753 136.55577568 0.00000000 
    3139 Rotation angle (degrees) 1.20611482 
    3140 Shift along axis -0.02425643 
    3141  
    3142 
    3143 > fitmap #4 inMap #1
    3144 
    3145 Fit map 262_substrate_sharpened_masked.mrc in map
    3146 J1169_consensus_sharpened_masked.mrc using 263331 points 
    3147 correlation = 0.455, correlation about mean = 0.1361, overlap = 80.48 
    3148 steps = 108, shift = 3.44, angle = 7.29 degrees 
    3149  
    3150 Position of 262_substrate_sharpened_masked.mrc (#4) relative to
    3151 J1169_consensus_sharpened_masked.mrc (#1) coordinates: 
    3152 Matrix rotation and translation 
    3153 0.99896011 0.01308895 0.04367363 -14.11352907 
    3154 -0.01817121 0.99283745 0.11808305 -24.51926830 
    3155 -0.04181523 -0.11875386 0.99204285 36.09570098 
    3156 Axis -0.93343294 0.33693280 -0.12320405 
    3157 Axis point 0.00000000 289.25896045 226.51819375 
    3158 Rotation angle (degrees) 7.28837631 
    3159 Shift along axis 0.46555048 
    3160  
    3161 
    3162 > volume #4 color #ff9300
    3163 
    3164 > volume #3 color #ffd479
    3165 
    3166 > volume #2 color #ffd479
    3167 
    3168 > volume #4 color #ffd479
    3169 
    3170 > volume #4 style mesh
    3171 
    3172 > volume #4 style surface
    3173 
    3174 > transparency #4.1 50
    3175 
    3176 > volume copy #4
    3177 
    3178 Opened 262_substrate_sharpened_masked.mrc copy as #5, grid size 540,540,540,
    3179 pixel 0.818, shown at step 1, values float32 
    3180 
    3181 > ui mousemode right "map eraser"
    3182 
    3183 > volume erase #5 center 213.96,203.15,200.62 radius 42.335
    3184 
    3185 > volume erase #5 center 210.56,205.11,217.9 radius 42.335
    3186 
    3187 > volume erase #5 center 205.41,245.35,235.44 radius 27.24
    3188 
    3189 > volume erase #5 center 236.82,246.12,244.23 radius 22.523
    3190 
    3191 > volume erase #5 center 240.14,220.11,243.41 radius 22.523
    3192 
    3193 > volume erase #5 center 261.83,234.17,236.36 radius 22.523
    3194 
    3195 > volume erase #5 center 223.52,236.05,190.19 radius 22.307
    3196 
    3197 > volume erase #5 center 228.71,237.61,237.79 radius 22.307
    3198 
    3199 > volume erase #5 center 228.99,247.93,242.84 radius 22.307
    3200 
    3201 > volume erase #5 center 227.76,213.75,238.14 radius 22.307
    3202 
    3203 > ui mousemode right translate
    3204 
    3205 > close #5
    3206 
    3207 > volume #4 style mesh
    3208 
    3209 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3210 > maps and masks/Head/Revised/260_head_locres.mrc"
    3211 
    3212 Opened 260_head_locres.mrc as #5, grid size 540,540,540, pixel 0.818, shown at
    3213 level 50, step 4, values float32 
    3214 
    3215 > ui tool show "Surface Color"
    3216 
    3217 > color sample #2.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
    3218 
    3219 Map values for surface "surface": minimum 3.589, mean 3.997, maximum 7.3 
    3220 
    3221 > color sample #2.1 map #5 palette
    3222 > 3.6,#0000ff:4.1,#00ffff:4.6,#00ff00:5.1,#ffff00:7.3,#ff0000
    3223 
    3224 Map values for surface "surface": minimum 3.589, mean 3.997, maximum 7.3 
    3225 
    3226 > volume #1 level 0.0657
    3227 
    3228 > volume #2 level 0.02528
    3229 
    3230 > volume #2 level 0.08598
    3231 
    3232 > volume #2 level 0.02528
    3233 
    3234 > color single #2.1
    3235 
    3236 > color sample #2.1 map #5 palette
    3237 > 3.6,#0000ff:4.1,#00ffff:4.6,#00ff00:5.1,#ffff00:7.3,#ff0000
    3238 
    3239 Map values for surface "surface": minimum 3.589, mean 4.018, maximum 7.701 
    3240 
    3241 > color single #2.1
    3242 
    3243 > close #5
    3244 
    3245 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3246 > maps and masks/Consensus/223_consensus_locres.mrc"
    3247 
    3248 Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
    3249 shown at level 50, step 4, values float32 
    3250 
    3251 > ui tool show "Surface Color"
    3252 
    3253 > color sample #1.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
    3254 
    3255 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    3256 
    3257 > color sample #1.1 map #5 palette
    3258 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000
    3259 
    3260 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    3261 
    3262 > color single #1.1
    3263 
    3264 > color sample #1.1 map #5 palette
    3265 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000
    3266 
    3267 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    3268 
    3269 > lighting full
    3270 
    3271 > lighting soft
    3272 
    3273 > set bgColor white
    3274 
    3275 > graphics silhouettes true
    3276 
    3277 > graphics silhouettes false
    3278 
    3279 > graphics silhouettes true
    3280 
    3281 > lighting shadows true intensity 0.5
    3282 
    3283 > lighting shadows false
    3284 
    3285 > lighting shadows true
    3286 
    3287 > lighting shadows false
    3288 
    3289 > lighting shadows true
    3290 
    3291 > lighting shadows false
    3292 
    3293 > lighting shadows true
    3294 
    3295 > lighting shadows false
    3296 
    3297 > lighting shadows true
    3298 
    3299 > lighting soft
    3300 
    3301 > lighting simple
    3302 
    3303 > lighting shadows true
    3304 
    3305 > lighting shadows false
    3306 
    3307 > lighting soft
    3308 
    3309 > lighting full
    3310 
    3311 > lighting shadows false
    3312 
    3313 > lighting soft
    3314 
    3315 > lighting simple
    3316 
    3317 > graphics silhouettes false
    3318 
    3319 > set bgColor black
    3320 
    3321 > set bgColor white
    3322 
    3323 > lighting soft
    3324 
    3325 > graphics silhouettes true
    3326 
    3327 > lighting flat
    3328 
    3329 > graphics silhouettes false
    3330 
    3331 > graphics silhouettes true
    3332 
    3333 > lighting soft
    3334 
    3335 > lighting flat
    3336 
    3337 > lighting soft
    3338 
    3339 > lighting shadows true intensity 0.5
    3340 
    3341 > lighting soft
    3342 
    3343 > graphics silhouettes false
    3344 
    3345 > color sample #1.1 map #5 palette
    3346 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000
    3347 
    3348 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    3349 
    3350 > graphics silhouettes true
    3351 
    3352 > graphics silhouettes false
    3353 
    3354 > graphics silhouettes true
    3355 
    3356 > graphics silhouettes false
    3357 
    3358 > graphics silhouettes true
    3359 
    3360 > graphics silhouettes false
    3361 
    3362 > graphics silhouettes true
    3363 
    3364 > graphics silhouettes false
    3365 
    3366 > graphics silhouettes true
    3367 
    3368 > graphics silhouettes false
    3369 
    3370 > graphics silhouettes true
    3371 
    3372 > graphics silhouettes false
    3373 
    3374 > set bgColor gray
    3375 
    3376 > lighting simple
    3377 
    3378 > set bgColor black
    3379 
    3380 > lighting shadows true
    3381 
    3382 > lighting shadows false
    3383 
    3384 > lighting shadows true
    3385 
    3386 > lighting shadows false
    3387 
    3388 > lighting soft
    3389 
    3390 > lighting simple
    3391 
    3392 > lighting full
    3393 
    3394 > lighting flat
    3395 
    3396 > lighting simple
    3397 
    3398 > set bgColor white
    3399 
    3400 > color single #1.1
    3401 
    3402 > volume #1 color #919191
    3403 
    3404 > volume #1 color #797979
    3405 
    3406 > volume #1 color #919191
    3407 
    3408 > lighting soft
    3409 
    3410 > graphics silhouettes false
    3411 
    3412 > lighting simple
    3413 
    3414 > lighting full
    3415 
    3416 > lighting shadows false
    3417 
    3418 > color sample #1.1 map #5 palette
    3419 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000
    3420 
    3421 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    3422 
    3423 > lighting soft
    3424 
    3425 > graphics silhouettes true
    3426 
    3427 > graphics silhouettes false
    3428 
    3429 > graphics silhouettes true
    3430 
    3431 > graphics silhouettes false
    3432 
    3433 > graphics silhouettes true
    3434 
    3435 > graphics silhouettes false
    3436 
    3437 > graphics silhouettes true
    3438 
    3439 > graphics silhouettes false
    3440 
    3441 > graphics silhouettes true
    3442 
    3443 > view
    3444 
    3445 > view name side
    3446 
    3447 > select ~sel & ##selected
    3448 
    3449 Nothing selected 
    3450 
    3451 > select ~sel & ##selected
    3452 
    3453 Nothing selected 
    3454 
    3455 > select ~sel & ##selected
    3456 
    3457 Nothing selected 
    3458 
    3459 > view side
    3460 
    3461 > turn y 90
    3462 
    3463 > view side
    3464 
    3465 > turn y -90
    3466 
    3467 > view side
    3468 
    3469 > view name side
    3470 
    3471 > turn y -90
    3472 
    3473 > view side
    3474 
    3475 > turn y -110
    3476 
    3477 > view side
    3478 
    3479 > turn y -130
    3480 
    3481 > view side
    3482 
    3483 > turn y -145
    3484 
    3485 > view side
    3486 
    3487 > turn y -180
    3488 
    3489 > view side
    3490 
    3491 > turn y 90
    3492 
    3493 > view side
    3494 
    3495 > turn y 110
    3496 
    3497 > view side
    3498 
    3499 > turn y 145
    3500 
    3501 > view side
    3502 
    3503 > turn x 90
    3504 
    3505 > view side
    3506 
    3507 > turn x -90
    3508 
    3509 > view side
    3510 
    3511 > turn x -180
    3512 
    3513 > view side
    3514 
    3515 > turn y 180
    3516 
    3517 > view side
    3518 
    3519 > turn y -90
    3520 
    3521 > view side
    3522 
    3523 > turn y -90
    3524 
    3525 > view side
    3526 
    3527 > turn y 180
    3528 
    3529 > view side
    3530 
    3531 > turn y -90
    3532 
    3533 > view side
    3534 
    3535 > turn y -90
    3536 
    3537 > view side
    3538 
    3539 > turn y -90
    3540 
    3541 > view side
    3542 
    3543 > turn y 180
    3544 
    3545 > view side
    3546 
    3547 > turn y -90
    3548 
    3549 > view side
    3550 
    3551 > turn y 90
    3552 
    3553 > view side
    3554 
    3555 > turn y 180
    3556 
    3557 > view side
    3558 
    3559 > turn y 180
    3560 
    3561 > view side
    3562 
    3563 > turn y -90
    3564 
    3565 > view side
    3566 
    3567 > turn y -90
    3568 
    3569 > view side
    3570 
    3571 > turn y -90
    3572 
    3573 > view side
    3574 
    3575 > turn y -90
    3576 
    3577 > view side
    3578 
    3579 > turn y -90
    3580 
    3581 > view side
    3582 
    3583 > turn y -90
    3584 
    3585 > view side
    3586 
    3587 > turn y -90
    3588 
    3589 > view side
    3590 
    3591 > turn y -90
    3592 
    3593 > view side
    3594 
    3595 > turn y -90
    3596 
    3597 > view side
    3598 
    3599 > turn y -90
    3600 
    3601 > view side
    3602 
    3603 > turn y -180
    3604 
    3605 > view side
    3606 
    3607 > turn y -90
    3608 
    3609 > view side
    3610 
    3611 > turn y -90
    3612 
    3613 > view side
    3614 
    3615 > turn y -90
    3616 
    3617 > view side
    3618 
    3619 > color single #1.1
    3620 
    3621 > color sample #1.1 map #5 palette
    3622 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000
    3623 
    3624 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    3625 
    3626 > view side
    3627 
    3628 > turn y -90
    3629 
    3630 > turn x -90
    3631 
    3632 > view side
    3633 
    3634 > turn y -90
    3635 
    3636 > turn x 90
    3637 
    3638 > view side
    3639 
    3640 > turn x 90
    3641 
    3642 > view side
    3643 
    3644 > turn y -45
    3645 
    3646 > turn x 45
    3647 
    3648 > view side
    3649 
    3650 > turn y -75
    3651 
    3652 > turn x 75
    3653 
    3654 > view side
    3655 
    3656 > turn y -60
    3657 
    3658 > turn x 60
    3659 
    3660 > view side
    3661 
    3662 > turn y -180
    3663 
    3664 > view side
    3665 
    3666 > turn y -190
    3667 
    3668 > view side
    3669 
    3670 > turn y -90
    3671 
    3672 > view side
    3673 
    3674 > turn y -90
    3675 
    3676 > view side
    3677 
    3678 > turn y -110
    3679 
    3680 > view side
    3681 
    3682 > turn y -130
    3683 
    3684 > view side
    3685 
    3686 > turn y -110
    3687 
    3688 > view side
    3689 
    3690 > turn y -90
    3691 
    3692 > view side
    3693 
    3694 > turn y -180
    3695 
    3696 > view side
    3697 
    3698 > turn y -180
    3699 
    3700 > view side
    3701 
    3702 > turn y -180
    3703 
    3704 > view side
    3705 
    3706 > turn y -180
    3707 
    3708 > view side
    3709 
    3710 > turn y -180
    3711 
    3712 > view side
    3713 
    3714 > turn y -180
    3715 
    3716 > view side
    3717 
    3718 > turn y -190
    3719 
    3720 > view side
    3721 
    3722 > turn y -90
    3723 
    3724 > view side
    3725 
    3726 > turn y -90
    3727 
    3728 > view side
    3729 
    3730 > turn y -90
    3731 
    3732 > view side
    3733 
    3734 > turn y -90
    3735 
    3736 > view side
    3737 
    3738 > turn y -90
    3739 
    3740 > view side
    3741 
    3742 > turn y -90
    3743 
    3744 > view side
    3745 
    3746 > turn y -90
    3747 
    3748 > view side
    3749 
    3750 > turn y -90
    3751 
    3752 > view side
    3753 
    3754 > turn y -90
    3755 
    3756 > view side
    3757 
    3758 > turn y -90
    3759 
    3760 > view side
    3761 
    3762 > turn y -90
    3763 
    3764 > view side
    3765 
    3766 > turn y -90
    3767 
    3768 > view side
    3769 
    3770 > turn y -90
    3771 
    3772 > view side
    3773 
    3774 > turn y -90
    3775 
    3776 > view side
    3777 
    3778 > turn y -90
    3779 
    3780 > view side
    3781 
    3782 > turn y -90
    3783 
    3784 > view side
    3785 
    3786 > lighting simple
    3787 
    3788 > lighting soft
    3789 
    3790 > lighting full
    3791 
    3792 > lighting flat
    3793 
    3794 > turn y -90
    3795 
    3796 > view side
    3797 
    3798 > lighting simple
    3799 
    3800 > lighting soft
    3801 
    3802 > lighting full
    3803 
    3804 > lighting shadows false
    3805 
    3806 > lighting shadows true
    3807 
    3808 > lighting shadows false
    3809 
    3810 > lighting shadows true
    3811 
    3812 > lighting full
    3813 
    3814 > lighting simple
    3815 
    3816 > lighting shadows true
    3817 
    3818 > lighting shadows false
    3819 
    3820 > lighting soft
    3821 
    3822 > lighting full
    3823 
    3824 > lighting flat
    3825 
    3826 > lighting simple
    3827 
    3828 > lighting soft
    3829 
    3830 > view side
    3831 
    3832 > turn y -90
    3833 
    3834 > view side
    3835 
    3836 > turn y -90
    3837 
    3838 > view side
    3839 
    3840 > turn y -180
    3841 
    3842 > view side
    3843 
    3844 > turn y -180
    3845 
    3846 > view side
    3847 
    3848 > turn y -90
    3849 
    3850 > view side
    3851 
    3852 > close #1
    3853 
    3854 > close #2
    3855 
    3856 > close #3
    3857 
    3858 > close #4
    3859 
    3860 > close #5
    3861 
    3862 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3863 > maps and masks/Consensus/J1169_consensus_sharpened_masked.mrc"
    3864 
    3865 Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
    3866 pixel 0.818, shown at level 2.26e-05, step 4, values float32 
    3867 
    3868 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3869 > maps and masks/Head/Revised/J1187_head_sharpened_masked.mrc"
    3870 
    3871 Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
    3872 0.818, shown at level 0.000148, step 4, values float32 
    3873 
    3874 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3875 > maps and masks/Body/J1068_body_sharpened_masked.mrc"
    3876 
    3877 Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
    3878 0.818, shown at level 3.71e-05, step 4, values float32 
    3879 
    3880 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3881 > maps and masks/Substrate/237_substrate_sharpened_masked.mrc"
    3882 
    3883 Opened 237_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    3884 0.818, shown at level 8.06e-06, step 4, values float32 
    3885 
    3886 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3887 > maps and masks/Consensus/223_consensus_locres.mrc"
    3888 
    3889 Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
    3890 shown at level 50, step 4, values float32 
    3891 
    3892 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3893 > maps and masks/Head/Revised/260_head_locres.mrc"
    3894 
    3895 Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
    3896 level 50, step 4, values float32 
    3897 
    3898 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3899 > maps and masks/Body/220_body_locres.mrc"
    3900 
    3901 Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
    3902 level 50, step 4, values float32 
    3903 
    3904 > close #4
    3905 
    3906 > close #5
    3907 
    3908 > close #6
    3909 
    3910 > close #7
    3911 
    3912 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3913 > maps and masks/Substrate/Revised/262_substrate_sharpened_masked.mrc"
    3914 
    3915 Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    3916 0.818, shown at level 1.48e-05, step 4, values float32 
    3917 
    3918 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3919 > maps and masks/Consensus/223_consensus_locres.mrc"
    3920 
    3921 Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
    3922 shown at level 50, step 4, values float32 
    3923 
    3924 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3925 > maps and masks/Head/Revised/260_head_locres.mrc"
    3926 
    3927 Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
    3928 level 50, step 4, values float32 
    3929 
    3930 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    3931 > maps and masks/Body/220_body_locres.mrc"
    3932 
    3933 Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
    3934 level 50, step 4, values float32 
    3935 
    3936 > volume #1 step 1
    3937 
    3938 > volume #1 level 0.02068
    3939 
    3940 > volume #2 step 1
    3941 
    3942 > volume #2 level 0.02575
    3943 
    3944 > volume #3 step 1
    3945 
    3946 > volume #3 level 0.02748
    3947 
    3948 > volume #4 step 1
    3949 
    3950 > volume #4 level 0.0009821
    3951 
    3952 > volume #4 level 0.001305
    3953 
    3954 > volume #4 level 0.001401
    3955 
    3956 > volume #4 level 0.001595
    3957 
    3958 > volume #4 level 0.0017
    3959 
    3960 > volume #5 step 1
    3961 
    3962 > volume #6 step 1
    3963 
    3964 > volume #7 step 1
    3965 
    3966 > volume #1 level 0.06544
    3967 
    3968 > volume #2 level 0.05136
    3969 
    3970 > volume #3 level 0.07061
    3971 
    3972 > color sample #2.1 map #6 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
    3973 
    3974 Map values for surface "surface": minimum 3.588, mean 3.975, maximum 7.243 
    3975 
    3976 > color sample #2.1 map #6 palette
    3977 > 3.6,#0000ff:4.1,#00ffff:4.6,#00ff00:5.1,#ffff00:7.2,#ff0000
    3978 
    3979 Map values for surface "surface": minimum 3.588, mean 3.975, maximum 7.243 
    3980 
    3981 > view side
    3982 
    3983 > turn y -90
    3984 
    3985 > view side
    3986 
    3987 > turn y -90
    3988 
    3989 > ui tool show "Hide Dust"
    3990 
    3991 > surface dust #2 size 4.91
    3992 
    3993 > surface undust #2
    3994 
    3995 > surface dust #2 size 52.99
    3996 
    3997 > surface undust #2
    3998 
    3999 > surface dust #2 size 3.49
    4000 
    4001 > surface undust #2
    4002 
    4003 > surface dust #2 size 1.93
    4004 
    4005 > surface dust #2 size 1.9
    4006 
    4007 > surface dust #2 size 2.16
    4008 
    4009 > surface undust #2
    4010 
    4011 > surface dust #2 size 2.16
    4012 
    4013 > surface dust #2 size 2.09
    4014 
    4015 > surface dust #2 size 2.31
    4016 
    4017 > surface undust #2
    4018 
    4019 > surface dust #2 size 2.31
    4020 
    4021 > surface dust #2 size 2.35
    4022 
    4023 > surface dust #2 size 2.55
    4024 
    4025 > surface undust #2
    4026 
    4027 > surface dust #2 size 2.55
    4028 
    4029 > volume #2 level 0.08111
    4030 
    4031 > volume #2 level 0.06995
    4032 
    4033 > view side
    4034 
    4035 > surface undust #2
    4036 
    4037 > surface dust #2 size 2.55
    4038 
    4039 > turn y -90
    4040 
    4041 > view side
    4042 
    4043 > volume #2 level 0.0402
    4044 
    4045 > surface undust #2
    4046 
    4047 > surface dust #2 size 2.55
    4048 
    4049 > volume #2 level 0.06995
    4050 
    4051 > surface undust #2
    4052 
    4053 > volume #2 level 0.05136
    4054 
    4055 > surface dust #2 size 2.55
    4056 
    4057 > surface dust #2 size 2.47
    4058 
    4059 > surface dust #2 size 2.64
    4060 
    4061 > surface undust #2
    4062 
    4063 > surface dust #2 size 2.64
    4064 
    4065 > view side
    4066 
    4067 > turn y -90
    4068 
    4069 > volume #2 level 0.08111
    4070 
    4071 > surface undust #2
    4072 
    4073 > surface dust #2 size 2.64
    4074 
    4075 > view side
    4076 
    4077 > volume #4 color #ff0018
    4078 
    4079 > view side
    4080 
    4081 > turn y -90
    4082 
    4083 > view side
    4084 
    4085 > turn y -90
    4086 
    4087 > view side
    4088 
    4089 > color sample #1.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
    4090 
    4091 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    4092 
    4093 > color sample #1.1 map #5 palette
    4094 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000
    4095 
    4096 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    4097 
    4098 > surface dust #1 size 4.91
    4099 
    4100 > surface undust #1
    4101 
    4102 > surface dust #1 size 1.89
    4103 
    4104 > view side
    4105 
    4106 > color sample #3.1 map #7 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
    4107 
    4108 Map values for surface "surface": minimum 2.818, mean 3.082, maximum 4.439 
    4109 
    4110 > color sample #3.1 map #7 palette
    4111 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:4.4,#ff0000
    4112 
    4113 Map values for surface "surface": minimum 2.818, mean 3.082, maximum 4.439 
    4114 
    4115 > surface dust #3 size 4.91
    4116 
    4117 > color sample #3.1 map #7 palette
    4118 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000
    4119 
    4120 Map values for surface "surface": minimum 2.818, mean 3.082, maximum 4.439 
    4121 
    4122 > color sample #2.1 map #6 palette
    4123 > 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000
    4124 
    4125 Map values for surface "surface": minimum 3.588, mean 3.957, maximum 7.165 
    4126 
    4127 > view side
    4128 
    4129 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    4130 > maps and masks/Consensus/206_consensus_angdist.bild"
    4131 
    4132 Opened BILD data containing 12282 objects 
    4133 
    4134 > hide #8 models
    4135 
    4136 > hide #!1 models
    4137 
    4138 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    4139 > maps and masks/Head/Revised/067_head_angdist.bild"
    4140 
    4141 Opened BILD data containing 12270 objects 
    4142 
    4143 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    4144 > maps and masks/Body/055_body_angdist.bild"
    4145 
    4146 Opened BILD data containing 11692 objects 
    4147 
    4148 > hide #9 models
    4149 
    4150 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    4151 > maps and masks/Substrate/232_substrate_angdist.bild"
    4152 
    4153 Opened BILD data containing 766 objects 
    4154 
    4155 > hide #10 models
    4156 
    4157 > view side
    4158 
    4159 > show #10 models
    4160 
    4161 > show #9 models
    4162 
    4163 > show #8 models
    4164 
    4165 > view name side_ang
    4166 
    4167 > view side_ang
    4168 
    4169 > hide #11 models
    4170 
    4171 > hide #10 models
    4172 
    4173 > hide #9 models
    4174 
    4175 > show #9 models
    4176 
    4177 > hide #8 models
    4178 
    4179 > turn y -90
    4180 
    4181 > view side_ang
    4182 
    4183 > turn y -180
    4184 
    4185 > view side_ang
    4186 
    4187 > hide #9 models
    4188 
    4189 > show #10 models
    4190 
    4191 > show #9 models
    4192 
    4193 > hide #10 models
    4194 
    4195 > show #10 models
    4196 
    4197 > hide #9 models
    4198 
    4199 > show #9 models
    4200 
    4201 > hide #10 models
    4202 
    4203 > show #8 models
    4204 
    4205 > hide #9 models
    4206 
    4207 > show #10 models
    4208 
    4209 > hide #8 models
    4210 
    4211 > show #11 models
    4212 
    4213 > hide #10 models
    4214 
    4215 > turn y -90
    4216 
    4217 > view side_ang
    4218 
    4219 > turn y -90
    4220 
    4221 > view side_ang
    4222 
    4223 > turn y -180
    4224 
    4225 > view side_ang
    4226 
    4227 > view side
    4228 
    4229 > hide #11 models
    4230 
    4231 > show #!1 models
    4232 
    4233 > hide #!1 models
    4234 
    4235 > show #!2 models
    4236 
    4237 > turn y -180
    4238 
    4239 > view side
    4240 
    4241 > hide #!2 models
    4242 
    4243 > show #!3 models
    4244 
    4245 > hide #!3 models
    4246 
    4247 > show #!4 models
    4248 
    4249 > turn y -180
    4250 
    4251 > view side
    4252 
    4253 > turn y -90
    4254 
    4255 > hide #!4 models
    4256 
    4257 > show #!1 models
    4258 
    4259 > show #!2 models
    4260 
    4261 > hide #!1 models
    4262 
    4263 > show #!1 models
    4264 
    4265 > hide #!1 models
    4266 
    4267 > hide #!2 models
    4268 
    4269 > show #!3 models
    4270 
    4271 > show #!1 models
    4272 
    4273 > hide #!3 models
    4274 
    4275 > show #!3 models
    4276 
    4277 > hide #!1 models
    4278 
    4279 > show #!1 models
    4280 
    4281 > hide #!3 models
    4282 
    4283 > hide #!1 models
    4284 
    4285 > show #!3 models
    4286 
    4287 > hide #!3 models
    4288 
    4289 > show #!1 models
    4290 
    4291 > view side
    4292 
    4293 > lighting simple
    4294 
    4295 > lighting soft
    4296 
    4297 > lighting full
    4298 
    4299 > lighting flat
    4300 
    4301 > show #11 models
    4302 
    4303 > hide #11 models
    4304 
    4305 > lighting full
    4306 
    4307 > lighting soft
    4308 
    4309 > save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
    4310 
    4311 > turn y -90
    4312 
    4313 > volume #4 level 0.0015
    4314 
    4315 > volume #4 level 0.0013
    4316 
    4317 > volume #4 level 0.0015
    4318 
    4319 > view side
    4320 
    4321 > volume #4 level 0.0017
    4322 
    4323 > volume #4 level 0.0016
    4324 
    4325 > turn y -90
    4326 
    4327 > volume #4 level 0.0017
    4328 
    4329 > view side
    4330 
    4331 > key rainbow :2.8 :3.3 :3.8 :4.3 :8.0 showTool true
    4332 
    4333 > ui mousemode right "color key"
    4334 
    4335 > key pos 0.738154,0.0952705 size 0,0
    4336 
    4337 > key pos 0.72139,-0.037061 size 0.0132362,0.119166
    4338 
    4339 Key is partially or completely offscreen 
    4340 
    4341 > key pos 0.724228,0.0473076 size 0.0661502,0.621165
    4342 
    4343 > key pos 0.426843,0.195826 size 0.353538,0.0277699
    4344 
    4345 > key pos 0.608755,0.0507685
    4346 
    4347 > view side
    4348 
    4349 > key pos 0.613836,0.938746
    4350 
    4351 > view side
    4352 
    4353 > hide #!4 models
    4354 
    4355 > show #!1 models
    4356 
    4357 > show #!2 models
    4358 
    4359 > hide #!2 models
    4360 
    4361 > save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
    4362 
    4363 > hide #!1 models
    4364 
    4365 > show #!2 models
    4366 
    4367 > hide #!2 models
    4368 
    4369 > show #!3 models
    4370 
    4371 > hide #!3 models
    4372 
    4373 > show #!3 models
    4374 
    4375 > show #!2 models
    4376 
    4377 > hide #!2 models
    4378 
    4379 > show #!2 models
    4380 
    4381 > hide #!3 models
    4382 
    4383 > show #!3 models
    4384 
    4385 > hide #!3 models
    4386 
    4387 > show #!3 models
    4388 
    4389 > hide #!3 models
    4390 
    4391 > show #!3 models
    4392 
    4393 > hide #!2 models
    4394 
    4395 > show #!4 models
    4396 
    4397 > hide #!4 models
    4398 
    4399 > show #!4 models
    4400 
    4401 > show #!2 models
    4402 
    4403 > hide #!4 models
    4404 
    4405 > show #!4 models
    4406 
    4407 > hide #!4 models
    4408 
    4409 > show #!4 models
    4410 
    4411 > hide #!4 models
    4412 
    4413 > view side
    4414 
    4415 > turn y -90
    4416 
    4417 > view side
    4418 
    4419 > turn y -90
    4420 
    4421 > view side
    4422 
    4423 > hide #!2 models
    4424 
    4425 > show #!2 models
    4426 
    4427 > hide #!2 models
    4428 
    4429 > hide #!3 models
    4430 
    4431 > show #!1 models
    4432 
    4433 > view side
    4434 
    4435 > turn y -90
    4436 
    4437 > view side
    4438 
    4439 > hide #!3 models
    4440 
    4441 > hide #!2 models
    4442 
    4443 > show #8 models
    4444 
    4445 > view side_ang
    4446 
    4447 > hide #12 models
    4448 
    4449 > hide #8 models
    4450 
    4451 > show #9 models
    4452 
    4453 > hide #9 models
    4454 
    4455 > show #8 models
    4456 
    4457 > hide #8 models
    4458 
    4459 > show #9 models
    4460 
    4461 > hide #9 models
    4462 
    4463 > show #10 models
    4464 
    4465 > hide #10 models
    4466 
    4467 > show #11 models
    4468 
    4469 > view side_ang
    4470 
    4471 > view side
    4472 
    4473 > hide #11 models
    4474 
    4475 > show #12 models
    4476 
    4477 > show #!1 models
    4478 
    4479 > key ticks true
    4480 
    4481 > key ticks false
    4482 
    4483 > key border false
    4484 
    4485 > key border true
    4486 
    4487 > key border false
    4488 
    4489 > key border true
    4490 
    4491 > key colorTreatment distinct
    4492 
    4493 > key colorTreatment blended
    4494 
    4495 > key colorTreatment distinct
    4496 
    4497 > key colorTreatment blended
    4498 
    4499 > key colorTreatment distinct
    4500 
    4501 > key colorTreatment blended
    4502 
    4503 > ui mousemode right translate
    4504 
    4505 > hide #!1 models
    4506 
    4507 > show #!2 models
    4508 
    4509 > hide #!2 models
    4510 
    4511 > show #!3 models
    4512 
    4513 > hide #!3 models
    4514 
    4515 > show #!4 models
    4516 
    4517 > hide #!4 models
    4518 
    4519 > show #!3 models
    4520 
    4521 > hide #!3 models
    4522 
    4523 > show #!2 models
    4524 
    4525 > hide #!2 models
    4526 
    4527 > show #!1 models
    4528 
    4529 > hide #!1 models
    4530 
    4531 > show #!2 models
    4532 
    4533 > hide #!2 models
    4534 
    4535 > show #!2 models
    4536 
    4537 > hide #!2 models
    4538 
    4539 > show #!3 models
    4540 
    4541 > show #!1 models
    4542 
    4543 > hide #!1 models
    4544 
    4545 > hide #!3 models
    4546 
    4547 > show #!4 models
    4548 
    4549 > view side
    4550 
    4551 > turn y -90
    4552 
    4553 > view side
    4554 
    4555 > hide #!4 models
    4556 
    4557 > show #!3 models
    4558 
    4559 > hide #!3 models
    4560 
    4561 > show #!2 models
    4562 
    4563 > turn y -90
    4564 
    4565 > view side
    4566 
    4567 > show #!3 models
    4568 
    4569 > hide #!3 models
    4570 
    4571 > show #!3 models
    4572 
    4573 > hide #!2 models
    4574 
    4575 > show #!2 models
    4576 
    4577 > hide #!2 models
    4578 
    4579 > show #!2 models
    4580 
    4581 > hide #!2 models
    4582 
    4583 > show #!2 models
    4584 
    4585 > hide #!2 models
    4586 
    4587 > show #!2 models
    4588 
    4589 > hide #!2 models
    4590 
    4591 > show #!2 models
    4592 
    4593 > hide #!2 models
    4594 
    4595 > hide #!3 models
    4596 
    4597 > show #!1 models
    4598 
    4599 > show #!2 models
    4600 
    4601 > hide #!2 models
    4602 
    4603 > show #!2 models
    4604 
    4605 > hide #!2 models
    4606 
    4607 > show #!2 models
    4608 
    4609 > hide #!2 models
    4610 
    4611 > show #!2 models
    4612 
    4613 > hide #!2 models
    4614 
    4615 > show #!2 models
    4616 
    4617 > hide #!2 models
    4618 
    4619 > show #!2 models
    4620 
    4621 > hide #!2 models
    4622 
    4623 > show #!2 models
    4624 
    4625 > hide #!2 models
    4626 
    4627 > show #!2 models
    4628 
    4629 > hide #!2 models
    4630 
    4631 > show #!2 models
    4632 
    4633 > hide #!2 models
    4634 
    4635 > show #!2 models
    4636 
    4637 > view side
    4638 
    4639 > turn y -90
    4640 
    4641 > show #!1 models
    4642 
    4643 > hide #!2 models
    4644 
    4645 > show #!2 models
    4646 
    4647 > hide #!2 models
    4648 
    4649 > show #!2 models
    4650 
    4651 > hide #!2 models
    4652 
    4653 > show #!2 models
    4654 
    4655 > hide #!2 models
    4656 
    4657 > show #!2 models
    4658 
    4659 > hide #!2 models
    4660 
    4661 > show #!2 models
    4662 
    4663 > hide #!2 models
    4664 
    4665 > show #!2 models
    4666 
    4667 > hide #!2 models
    4668 
    4669 > show #!2 models
    4670 
    4671 > hide #!2 models
    4672 
    4673 > view side
    4674 
    4675 > save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
    4676 
    4677 > view side
    4678 
    4679 > show #!2 models
    4680 
    4681 > hide #!3 models
    4682 
    4683 > turn y -90
    4684 
    4685 > view side
    4686 
    4687 > turn y -90
    4688 
    4689 > view side
    4690 
    4691 > show #!1 models
    4692 
    4693 > hide #!2 models
    4694 
    4695 > view side
    4696 
    4697 > show #!2 models
    4698 
    4699 > hide #!4 models
    4700 
    4701 > volume #2 level 0.04392
    4702 
    4703 > surface dust #2 size 2.64
    4704 
    4705 > surface dust #2 size 2.47
    4706 
    4707 > surface dust #2 size 2.91
    4708 
    4709 > view side
    4710 
    4711 > turn y -90
    4712 
    4713 > volume #2 level 0.02161
    4714 
    4715 > surface dust #2 size 2.91
    4716 
    4717 > view side
    4718 
    4719 > turn y -90
    4720 
    4721 > view side
    4722 
    4723 > surface dust #2 size 2.91
    4724 
    4725 > surface dust #2 size 3.06
    4726 
    4727 > surface dust #2 size 3.38
    4728 
    4729 > surface dust #2 size 3.73
    4730 
    4731 > surface dust #2 size 3.06
    4732 
    4733 > surface dust #2 size 3.01
    4734 
    4735 > surface dust #2 size 3.85
    4736 
    4737 > view side
    4738 
    4739 > turn y -90
    4740 
    4741 > view side
    4742 
    4743 > volume #2 level 0.02905
    4744 
    4745 > volume #2 level 0.006734
    4746 
    4747 > volume #2 level 0.01417
    4748 
    4749 > view side
    4750 
    4751 > volume #2 level 0.015
    4752 
    4753 > surface undust #2
    4754 
    4755 > volume #2 level 0.018
    4756 
    4757 > volume #2 level 0.02
    4758 
    4759 > surface dust #2 size 3.85
    4760 
    4761 > volume #2 level 0.019
    4762 
    4763 > volume #2 level 0.022
    4764 
    4765 > view side
    4766 
    4767 > turn y -90
    4768 
    4769 > volume #2 level 0.05919
    4770 
    4771 > volume #2 level 0.022
    4772 
    4773 > view side
    4774 
    4775 > turn y -90
    4776 
    4777 > view side
    4778 
    4779 > save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
    4780 
    4781 > volume #4 color #ff2600
    4782 
    4783 > hide #!1 models
    4784 
    4785 > show #!2 models
    4786 
    4787 > hide #!2 models
    4788 
    4789 > show #!3 models
    4790 
    4791 > hide #!3 models
    4792 
    4793 > show #!4 models
    4794 
    4795 > turn y -90
    4796 
    4797 > hide #!4 models
    4798 
    4799 > show #!3 models
    4800 
    4801 > hide #!3 models
    4802 
    4803 > show #!2 models
    4804 
    4805 > hide #!2 models
    4806 
    4807 > show #!1 models
    4808 
    4809 > hide #!1 models
    4810 
    4811 > show #!2 models
    4812 
    4813 > show #!1 models
    4814 
    4815 > hide #!2 models
    4816 
    4817 > hide #!1 models
    4818 
    4819 > show #!2 models
    4820 
    4821 > hide #!2 models
    4822 
    4823 > show #!3 models
    4824 
    4825 > show #!2 models
    4826 
    4827 > hide #!3 models
    4828 
    4829 > hide #!2 models
    4830 
    4831 > show #!3 models
    4832 
    4833 > hide #!3 models
    4834 
    4835 > show #!4 models
    4836 
    4837 > view side
    4838 
    4839 > hide #!4 models
    4840 
    4841 > show #!3 models
    4842 
    4843 > show #!2 models
    4844 
    4845 > hide #!3 models
    4846 
    4847 > show #!1 models
    4848 
    4849 > hide #!2 models
    4850 
    4851 > show #!2 models
    4852 
    4853 > hide #!1 models
    4854 
    4855 > turn y -90
    4856 
    4857 > show #!1 models
    4858 
    4859 > hide #!2 models
    4860 
    4861 > show #!2 models
    4862 
    4863 > hide #!1 models
    4864 
    4865 > show #!3 models
    4866 
    4867 > hide #!2 models
    4868 
    4869 > show #!2 models
    4870 
    4871 > hide #!3 models
    4872 
    4873 > hide #!2 models
    4874 
    4875 > show #!1 models
    4876 
    4877 > show #!3 models
    4878 
    4879 > hide #!1 models
    4880 
    4881 > show #!1 models
    4882 
    4883 > hide #!3 models
    4884 
    4885 > show #!4 models
    4886 
    4887 > hide #!1 models
    4888 
    4889 > show #!3 models
    4890 
    4891 > show #!2 models
    4892 
    4893 > show #!1 models
    4894 
    4895 > view side
    4896 
    4897 > turn y -90
    4898 
    4899 > view side
    4900 
    4901 > turn y -90
    4902 
    4903 > view side
    4904 
    4905 > turn y -90
    4906 
    4907 > view side
    4908 
    4909 > hide #!4 models
    4910 
    4911 > hide #!3 models
    4912 
    4913 > hide #!2 models
    4914 
    4915 > show #!2 models
    4916 
    4917 > hide #!1 models
    4918 
    4919 > show #!3 models
    4920 
    4921 > volume #3 level 0.0467
    4922 
    4923 > volume #3 level 0.0706
    4924 
    4925 > view side
    4926 
    4927 > show #!4 models
    4928 
    4929 > view side
    4930 
    4931 > hide #!4 models
    4932 
    4933 > hide #!3 models
    4934 
    4935 > hide #!2 models
    4936 
    4937 > show #!1 models
    4938 
    4939 > show #!2 models
    4940 
    4941 > hide #!1 models
    4942 
    4943 > view side
    4944 
    4945 > hide #!2 models
    4946 
    4947 > show #!1 models
    4948 
    4949 > view side
    4950 
    4951 > show #!2 models
    4952 
    4953 > hide #!1 models
    4954 
    4955 > view side
    4956 
    4957 > show #!1 models
    4958 
    4959 > show #!3 models
    4960 
    4961 > show #!4 models
    4962 
    4963 > turn y -90
    4964 
    4965 > hide #!4 models
    4966 
    4967 > hide #!2 models
    4968 
    4969 > hide #!3 models
    4970 
    4971 > turn y -90
    4972 
    4973 > turn y 90
    4974 
    4975 > turn y -110
    4976 
    4977 > show #!4 models
    4978 
    4979 > hide #!4 models
    4980 
    4981 > turn y 110
    4982 
    4983 > show #!2 models
    4984 
    4985 > show #!3 models
    4986 
    4987 > show #!4 models
    4988 
    4989 > turn y -110
    4990 
    4991 > turn y 110
    4992 
    4993 > view side
    4994 
    4995 > turn y -90
    4996 
    4997 > view side
    4998 
    4999 > hide #!4 models
    5000 
    5001 > hide #!3 models
    5002 
    5003 > hide #!2 models
    5004 
    5005 > show #!2 models
    5006 
    5007 > hide #!1 models
    5008 
    5009 > hide #!2 models
    5010 
    5011 > show #!3 models
    5012 
    5013 > hide #!3 models
    5014 
    5015 > show #!4 models
    5016 
    5017 > show #!3 models
    5018 
    5019 > show #!2 models
    5020 
    5021 > show #!1 models
    5022 
    5023 > hide #!4 models
    5024 
    5025 > hide #!3 models
    5026 
    5027 > hide #!2 models
    5028 
    5029 > show #!4 models
    5030 
    5031 > show #!2 models
    5032 
    5033 > show #!3 models
    5034 
    5035 > view side
    5036 
    5037 > turn y -90
    5038 
    5039 > view side
    5040 
    5041 > turn y -90
    5042 
    5043 > view side
    5044 
    5045 > turn y -30
    5046 
    5047 > hide #!4 models
    5048 
    5049 > show #!4 models
    5050 
    5051 > hide #!2 models
    5052 
    5053 > hide #!3 models
    5054 
    5055 > hide #!4 models
    5056 
    5057 > show #!2 models
    5058 
    5059 > hide #!1 models
    5060 
    5061 > hide #!2 models
    5062 
    5063 > show #!3 models
    5064 
    5065 > show #!4 models
    5066 
    5067 > hide #!4 models
    5068 
    5069 > show #!4 models
    5070 
    5071 > hide #!4 models
    5072 
    5073 > show #!1 models
    5074 
    5075 > hide #!3 models
    5076 
    5077 > hide #!1 models
    5078 
    5079 > show #!2 models
    5080 
    5081 > hide #!2 models
    5082 
    5083 > show #!3 models
    5084 
    5085 > hide #!3 models
    5086 
    5087 > show #!4 models
    5088 
    5089 > hide #!4 models
    5090 
    5091 > show #!1 models
    5092 
    5093 > hide #!1 models
    5094 
    5095 > show #!2 models
    5096 
    5097 > show #!3 models
    5098 
    5099 > hide #!2 models
    5100 
    5101 > show #!1 models
    5102 
    5103 > hide #!3 models
    5104 
    5105 > show #!3 models
    5106 
    5107 > hide #!1 models
    5108 
    5109 > show #!4 models
    5110 
    5111 > hide #!3 models
    5112 
    5113 > hide #!4 models
    5114 
    5115 > show #!3 models
    5116 
    5117 > hide #!3 models
    5118 
    5119 > show #!2 models
    5120 
    5121 > hide #!2 models
    5122 
    5123 > show #!1 models
    5124 
    5125 > view side
    5126 
    5127 > show #!2 models
    5128 
    5129 > hide #!1 models
    5130 
    5131 > turn y -15
    5132 
    5133 > show #!3 models
    5134 
    5135 > hide #!2 models
    5136 
    5137 > hide #!3 models
    5138 
    5139 > show #!1 models
    5140 
    5141 > hide #!1 models
    5142 
    5143 > show #!4 models
    5144 
    5145 > turn y -5
    5146 
    5147 > hide #!4 models
    5148 
    5149 > show #!3 models
    5150 
    5151 > hide #!3 models
    5152 
    5153 > show #!2 models
    5154 
    5155 > hide #!2 models
    5156 
    5157 > show #!1 models
    5158 
    5159 > view side
    5160 
    5161 > show #!2 models
    5162 
    5163 > show #!3 models
    5164 
    5165 > show #!4 models
    5166 
    5167 > turn y -25
    5168 
    5169 > hide #!4 models
    5170 
    5171 > hide #!3 models
    5172 
    5173 > hide #!2 models
    5174 
    5175 > hide #!1 models
    5176 
    5177 > show #!2 models
    5178 
    5179 > show #!3 models
    5180 
    5181 > hide #!2 models
    5182 
    5183 > hide #!3 models
    5184 
    5185 > show #!4 models
    5186 
    5187 > view side
    5188 
    5189 > show #!1 models
    5190 
    5191 > hide #!4 models
    5192 
    5193 > hide #!1 models
    5194 
    5195 > show #!2 models
    5196 
    5197 > show #!3 models
    5198 
    5199 > view side
    5200 
    5201 > show #!1 models
    5202 
    5203 > show #!4 models
    5204 
    5205 > turn y -90
    5206 
    5207 > hide #!2 models
    5208 
    5209 > hide #!3 models
    5210 
    5211 > hide #!4 models
    5212 
    5213 > show #!2 models
    5214 
    5215 > hide #!1 models
    5216 
    5217 > hide #!2 models
    5218 
    5219 > show #!3 models
    5220 
    5221 > show #!4 models
    5222 
    5223 > hide #!3 models
    5224 
    5225 > view side
    5226 
    5227 > show #!3 models
    5228 
    5229 > show #!2 models
    5230 
    5231 > show #!1 models
    5232 
    5233 > turn y -25
    5234 
    5235 > hide #!3 models
    5236 
    5237 > hide #!2 models
    5238 
    5239 > hide #!1 models
    5240 
    5241 > show #!3 models
    5242 
    5243 > hide #!4 models
    5244 
    5245 > show #!2 models
    5246 
    5247 > hide #!3 models
    5248 
    5249 > hide #!2 models
    5250 
    5251 > show #!3 models
    5252 
    5253 > hide #!3 models
    5254 
    5255 > show #!4 models
    5256 
    5257 > view side
    5258 
    5259 > show #!1 models
    5260 
    5261 > show #!3 models
    5262 
    5263 > show #!2 models
    5264 
    5265 > turn y -15
    5266 
    5267 > turn y -5
    5268 
    5269 > hide #!3 models
    5270 
    5271 > hide #!2 models
    5272 
    5273 > hide #!1 models
    5274 
    5275 > show #!3 models
    5276 
    5277 > hide #!4 models
    5278 
    5279 > show #!2 models
    5280 
    5281 > hide #!3 models
    5282 
    5283 > show #!1 models
    5284 
    5285 > hide #!2 models
    5286 
    5287 > show #!2 models
    5288 
    5289 > hide #!1 models
    5290 
    5291 > view side
    5292 
    5293 > turn y -90
    5294 
    5295 > view side
    5296 
    5297 > close session
    5298 
    5299 > open
    5300 > "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
    5301 > maps and masks/J845_prepreconsensus_full.mrc"
    5302 
    5303 Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
    5304 shown at level 0.261, step 1, values float32 
    5305 
    5306 > open
    5307 > "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
    5308 > maps and masks/J918_preconsensus_full.mrc"
    5309 
    5310 Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
    5311 shown at level 0.00679, step 4, values float32 
    5312 
    5313 > volume #2 step 1
    5314 
    5315 > volume #2 level 0.1071
    5316 
    5317 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5318 > maps and masks/Consensus/206_consensus_full.mrc"
    5319 
    5320 Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
    5321 at level 0.000217, step 4, values float32 
    5322 
    5323 > volume #3 step 1
    5324 
    5325 > volume #3 level 0.002226
    5326 
    5327 > ui tool show "Fit in Map"
    5328 
    5329 > fitmap #1 inMap #2
    5330 
    5331 Fit map J845_prepreconsensus_full.mrc in map J918_preconsensus_full.mrc using
    5332 10000 points 
    5333 correlation = 0.3969, correlation about mean = 0.09316, overlap = 166.4 
    5334 steps = 700, shift = 62.5, angle = 19.7 degrees 
    5335  
    5336 Position of J845_prepreconsensus_full.mrc (#1) relative to
    5337 J918_preconsensus_full.mrc (#2) coordinates: 
    5338 Matrix rotation and translation 
    5339 0.98942181 0.14301702 -0.02430273 40.70976741 
    5340 -0.12864653 0.94244668 0.30861681 0.10306915 
    5341 0.06704148 -0.30222574 0.95087594 39.79727002 
    5342 Axis -0.90530123 -0.13537700 -0.40261987 
    5343 Axis point 0.00000000 55.81056270 33.27536695 
    5344 Rotation angle (degrees) 19.71670733 
    5345 Shift along axis -52.89172722 
    5346  
    5347 
    5348 > select add #1
    5349 
    5350 2 models selected 
    5351 
    5352 > ui mousemode right "translate selected models"
    5353 
    5354 > view matrix models
    5355 > #1,0.98942,0.14302,-0.024303,45.01,-0.12865,0.94245,0.30862,33.617,0.067041,-0.30223,0.95088,71.744
    5356 
    5357 > ui mousemode right "rotate selected models"
    5358 
    5359 > view matrix models
    5360 > #1,0.9852,0.16333,-0.052013,46.617,-0.16584,0.98497,-0.04828,88.765,0.043346,0.056191,0.99748,7.3339
    5361 
    5362 > ui mousemode right "translate selected models"
    5363 
    5364 > view matrix models
    5365 > #1,0.9852,0.16333,-0.052013,47.558,-0.16584,0.98497,-0.04828,96.957,0.043346,0.056191,0.99748,12.784
    5366 
    5367 > fitmap #1 inMap #2
    5368 
    5369 Fit map J845_prepreconsensus_full.mrc in map J918_preconsensus_full.mrc using
    5370 10000 points 
    5371 correlation = 0.8689, correlation about mean = 0.6293, overlap = 547.5 
    5372 steps = 144, shift = 7.21, angle = 11.2 degrees 
    5373  
    5374 Position of J845_prepreconsensus_full.mrc (#1) relative to
    5375 J918_preconsensus_full.mrc (#2) coordinates: 
    5376 Matrix rotation and translation 
    5377 0.99993739 -0.00856537 0.00720019 57.59147711 
    5378 0.00844916 0.99983602 0.01601703 53.94647800 
    5379 -0.00733620 -0.01595519 0.99984579 33.23887074 
    5380 Axis -0.81925571 0.37248012 0.43598009 
    5381 Axis point 0.00000000 2462.61126627 -3635.79739833 
    5382 Rotation angle (degrees) 1.11808154 
    5383 Shift along axis -12.59666952 
    5384  
    5385 
    5386 > ui mousemode right translate
    5387 
    5388 > select clear
    5389 
    5390 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5391 > maps and masks/Head/Revised/067_head_full.mrc"
    5392 
    5393 Opened 067_head_full.mrc as #4, grid size 540,540,540, pixel 0.818, shown at
    5394 level 0.000251, step 4, values float32 
    5395 
    5396 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5397 > maps and masks/Body/055_body_full.mrc"
    5398 
    5399 Opened 055_body_full.mrc as #5, grid size 540,540,540, pixel 0.818, shown at
    5400 level 0.000554, step 4, values float32 
    5401 
    5402 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5403 > maps and masks/Substrate/232_substrate_full.mrc"
    5404 
    5405 Opened 232_substrate_full.mrc as #6, grid size 540,540,540, pixel 0.818, shown
    5406 at level 0.000291, step 4, values float32 
    5407 
    5408 > close #4-6
    5409 
    5410 > hide #!1 models
    5411 
    5412 > hide #!2 models
    5413 
    5414 > show #!2 models
    5415 
    5416 > hide #!3 models
    5417 
    5418 > show #!3 models
    5419 
    5420 > hide #!3 models
    5421 
    5422 > show #!3 models
    5423 
    5424 > show #!1 models
    5425 
    5426 > hide #!1 models
    5427 
    5428 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5429 > classes/Head/058/run_it000_class001.mrc"
    5430 
    5431 Opened run_it000_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
    5432 at level 0.000143, step 4, values float32 
    5433 
    5434 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5435 > classes/Head/058/run_it000_class002.mrc"
    5436 
    5437 Opened run_it000_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
    5438 at level 0.000143, step 4, values float32 
    5439 
    5440 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5441 > classes/Head/058/run_it000_class003.mrc"
    5442 
    5443 Opened run_it000_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
    5444 at level 0.000143, step 4, values float32 
    5445 
    5446 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5447 > classes/Head/058/run_it000_class004.mrc"
    5448 
    5449 Opened run_it000_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
    5450 at level 0.000143, step 4, values float32 
    5451 
    5452 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5453 > classes/Head/058/run_it000_class005.mrc"
    5454 
    5455 Opened run_it000_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
    5456 at level 0.000143, step 4, values float32 
    5457 
    5458 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5459 > classes/Head/058/run_it000_class006.mrc"
    5460 
    5461 Opened run_it000_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
    5462 at level 0.000143, step 4, values float32 
    5463 
    5464 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5465 > maps and masks/Head/Revised/067_head_full.mrc"
    5466 
    5467 Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
    5468 level 0.000251, step 4, values float32 
    5469 
    5470 > volume #10 step 1
    5471 
    5472 > volume #10 level 0.0009942
    5473 
    5474 > volume #9 step 1
    5475 
    5476 > volume #9 level 0.0002468
    5477 
    5478 > volume #8 step 1
    5479 
    5480 > volume #8 level 0.0002562
    5481 
    5482 > volume #7 step 1
    5483 
    5484 > volume #7 level 0.0002562
    5485 
    5486 > volume #6 step 1
    5487 
    5488 > volume #6 level 0.0002468
    5489 
    5490 > volume #5 step 1
    5491 
    5492 > volume #5 level 0.0003318
    5493 
    5494 > volume #4 step 1
    5495 
    5496 > volume #4 level 0.0004831
    5497 
    5498 > hide #!2 models
    5499 
    5500 > hide #!3 models
    5501 
    5502 > hide #!10 models
    5503 
    5504 > hide #!9 models
    5505 
    5506 > hide #!8 models
    5507 
    5508 > hide #!7 models
    5509 
    5510 > hide #!6 models
    5511 
    5512 > hide #!5 models
    5513 
    5514 > close #4-10
    5515 
    5516 > show #!1 models
    5517 
    5518 > show #!2 models
    5519 
    5520 > hide #!1 models
    5521 
    5522 > volume #2 level 0.07096
    5523 
    5524 > show #!3 models
    5525 
    5526 > hide #!2 models
    5527 
    5528 > volume #3 level 0.002039
    5529 
    5530 > show #!2 models
    5531 
    5532 > hide #!3 models
    5533 
    5534 > show #!3 models
    5535 
    5536 > hide #!2 models
    5537 
    5538 > show #!2 models
    5539 
    5540 > hide #!2 models
    5541 
    5542 > show #!2 models
    5543 
    5544 > hide #!3 models
    5545 
    5546 > show #!3 models
    5547 
    5548 > hide #!2 models
    5549 
    5550 > show #!1 models
    5551 
    5552 > hide #!3 models
    5553 
    5554 > hide #!1 models
    5555 
    5556 > show #!2 models
    5557 
    5558 > show #!3 models
    5559 
    5560 > hide #!2 models
    5561 
    5562 > hide #!3 models
    5563 
    5564 > show #!1 models
    5565 
    5566 > hide #!1 models
    5567 
    5568 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5569 > classes/Head/058/run_it025_class001.mrc"
    5570 
    5571 Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
    5572 at level 5.87e-07, step 4, values float32 
    5573 
    5574 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5575 > classes/Head/058/run_it025_class002.mrc"
    5576 
    5577 Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
    5578 at level 6.93e-08, step 4, values float32 
    5579 
    5580 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5581 > classes/Head/058/run_it025_class003.mrc"
    5582 
    5583 Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
    5584 at level 4.3e-07, step 4, values float32 
    5585 
    5586 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5587 > classes/Head/058/run_it025_class004.mrc"
    5588 
    5589 Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
    5590 at level 5.13e-07, step 4, values float32 
    5591 
    5592 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5593 > classes/Head/058/run_it025_class005.mrc"
    5594 
    5595 Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
    5596 at level 5.47e-07, step 4, values float32 
    5597 
    5598 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5599 > classes/Head/058/run_it025_class006.mrc"
    5600 
    5601 Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
    5602 at level 3.57e-07, step 4, values float32 
    5603 
    5604 > show #!1 models
    5605 
    5606 > hide #!4 models
    5607 
    5608 > hide #!5 models
    5609 
    5610 > hide #!6 models
    5611 
    5612 > hide #!7 models
    5613 
    5614 > hide #!8 models
    5615 
    5616 > hide #!9 models
    5617 
    5618 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5619 > maps and masks/Head/Revised/067_head_full.mrc"
    5620 
    5621 Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
    5622 level 0.000251, step 4, values float32 
    5623 
    5624 > volume #10 step 1
    5625 
    5626 > volume #10 level 0.002525
    5627 
    5628 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5629 > classes/Body/045/run_it035_class001.mrc"
    5630 
    5631 Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
    5632 shown at level 1.24e-06, step 4, values float32 
    5633 
    5634 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5635 > classes/Body/045/run_it035_class002.mrc"
    5636 
    5637 Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
    5638 shown at level 1.4e-06, step 4, values float32 
    5639 
    5640 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5641 > classes/Body/045/run_it035_class003.mrc"
    5642 
    5643 Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
    5644 shown at level 7.73e-07, step 4, values float32 
    5645 
    5646 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5647 > classes/Body/045/run_it035_class004.mrc"
    5648 
    5649 Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
    5650 shown at level 9.89e-07, step 4, values float32 
    5651 
    5652 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5653 > classes/Body/045/run_it035_class005.mrc"
    5654 
    5655 Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
    5656 shown at level 3.7e-07, step 4, values float32 
    5657 
    5658 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5659 > classes/Body/045/run_it035_class006.mrc"
    5660 
    5661 Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
    5662 shown at level 1.67e-06, step 4, values float32 
    5663 
    5664 > hide #!11 models
    5665 
    5666 > hide #!12 models
    5667 
    5668 > hide #!13 models
    5669 
    5670 > hide #!14 models
    5671 
    5672 > hide #!15 models
    5673 
    5674 > hide #!16 models
    5675 
    5676 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5677 > maps and masks/Body/055_body_full.mrc"
    5678 
    5679 Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
    5680 level 0.000554, step 4, values float32 
    5681 
    5682 > volume #17 step 1
    5683 
    5684 > volume #17 level 0.002409
    5685 
    5686 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5687 > classes/Substrate/Round 1/124/run_it025_class001.mrc"
    5688 
    5689 Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
    5690 shown at level 1.21e-05, step 4, values float32 
    5691 
    5692 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5693 > classes/Substrate/Round 1/124/run_it025_class002.mrc"
    5694 
    5695 Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
    5696 shown at level 1.11e-05, step 4, values float32 
    5697 
    5698 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5699 > classes/Substrate/Round 1/124/run_it025_class003.mrc"
    5700 
    5701 Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
    5702 shown at level 2.68e-05, step 4, values float32 
    5703 
    5704 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5705 > classes/Substrate/Round 1/124/run_it025_class004.mrc"
    5706 
    5707 Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
    5708 shown at level 1.57e-05, step 4, values float32 
    5709 
    5710 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5711 > classes/Substrate/Round 1/124/run_it025_class005.mrc"
    5712 
    5713 Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
    5714 shown at level 1.87e-05, step 4, values float32 
    5715 
    5716 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5717 > classes/Substrate/Round 1/124/run_it025_class006.mrc"
    5718 
    5719 Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
    5720 shown at level 2.32e-05, step 4, values float32 
    5721 
    5722 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5723 > classes/Substrate/Round 1/124/run_it025_class007.mrc"
    5724 
    5725 Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
    5726 shown at level 1.39e-05, step 4, values float32 
    5727 
    5728 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5729 > classes/Substrate/Round 1/124/run_it025_class008.mrc"
    5730 
    5731 Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
    5732 shown at level 2.51e-05, step 4, values float32 
    5733 
    5734 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5735 > classes/Substrate/Round 1/124/run_it025_class009.mrc"
    5736 
    5737 Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
    5738 shown at level 2.3e-05, step 4, values float32 
    5739 
    5740 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5741 > classes/Substrate/Round 1/124/run_it025_class010.mrc"
    5742 
    5743 Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
    5744 shown at level 2.02e-05, step 4, values float32 
    5745 
    5746 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5747 > classes/Substrate/Round 1/124/run_it025_class011.mrc"
    5748 
    5749 Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
    5750 shown at level 1.7e-05, step 4, values float32 
    5751 
    5752 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5753 > classes/Substrate/Round 1/124/run_it025_class012.mrc"
    5754 
    5755 Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
    5756 shown at level 1.99e-05, step 4, values float32 
    5757 
    5758 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5759 > classes/Substrate/Round 2/159/run_it025_class001.mrc"
    5760 
    5761 Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
    5762 shown at level 2.03e-07, step 4, values float32 
    5763 
    5764 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5765 > classes/Substrate/Round 2/159/run_it025_class002.mrc"
    5766 
    5767 Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
    5768 shown at level 2.63e-07, step 4, values float32 
    5769 
    5770 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5771 > classes/Substrate/Round 2/159/run_it025_class003.mrc"
    5772 
    5773 Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
    5774 shown at level 6.38e-07, step 4, values float32 
    5775 
    5776 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
    5777 > classes/Substrate/Round 2/159/run_it025_class004.mrc"
    5778 
    5779 Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
    5780 shown at level 7.37e-07, step 4, values float32 
    5781 
    5782 > hide #!18 models
    5783 
    5784 > hide #!19 models
    5785 
    5786 > hide #!20 models
    5787 
    5788 > hide #!21 models
    5789 
    5790 > hide #!22 models
    5791 
    5792 > hide #!23 models
    5793 
    5794 > hide #!24 models
    5795 
    5796 > hide #!25 models
    5797 
    5798 > hide #!26 models
    5799 
    5800 > hide #!27 models
    5801 
    5802 > hide #!28 models
    5803 
    5804 > hide #!29 models
    5805 
    5806 > hide #!30 models
    5807 
    5808 > hide #!31 models
    5809 
    5810 > hide #!32 models
    5811 
    5812 > hide #!33 models
    5813 
    5814 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5815 > maps and masks/Substrate/232_substrate_full.mrc"
    5816 
    5817 Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
    5818 shown at level 0.000291, step 4, values float32 
    5819 
    5820 > volume #34 step 1
    5821 
    5822 > volume #34 level 0.0009319
    5823 
    5824 > fitmap #34 inMap #2
    5825 
    5826 Fit map 232_substrate_full.mrc in map J918_preconsensus_full.mrc using 818244
    5827 points 
    5828 correlation = 0.7032, correlation about mean = 0.2384, overlap = 107.4 
    5829 steps = 88, shift = 4.78, angle = 3.41 degrees 
    5830  
    5831 Position of 232_substrate_full.mrc (#34) relative to
    5832 J918_preconsensus_full.mrc (#2) coordinates: 
    5833 Matrix rotation and translation 
    5834 0.99994086 0.00092699 0.01083631 -4.32567070 
    5835 -0.00155919 0.99828742 0.05847901 -15.00632349 
    5836 -0.01076354 -0.05849245 0.99822982 13.69905736 
    5837 Axis -0.98315976 0.18154950 -0.02089670 
    5838 Axis point 0.00000000 226.56252672 267.10172357 
    5839 Rotation angle (degrees) 3.41039703 
    5840 Shift along axis 1.24216969 
    5841  
    5842 
    5843 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5844 > maps and masks/Consensus/J1031_consensus_mask.mrc"
    5845 
    5846 Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
    5847 shown at level 1, step 4, values float32 
    5848 
    5849 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5850 > maps and masks/Head/J1032_head_mask.mrc"
    5851 
    5852 Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
    5853 at level 0.997, step 4, values float32 
    5854 
    5855 > volume #35 step 1
    5856 
    5857 > volume #36 step 1
    5858 
    5859 > volume #35 level 0.99
    5860 
    5861 > volume #36 level 0.99
    5862 
    5863 > hide #!35 models
    5864 
    5865 > hide #!36 models
    5866 
    5867 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5868 > maps and masks/Body/J1033_body_mask.mrc"
    5869 
    5870 Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
    5871 at level 0.336, step 4, values float32 
    5872 
    5873 > volume #37 step 1
    5874 
    5875 > volume #37 level 0.99
    5876 
    5877 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5878 > maps and masks/Substrate/J1034_substrate_mask.mrc"
    5879 
    5880 Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
    5881 shown at level 1, step 4, values float32 
    5882 
    5883 > hide #!37 models
    5884 
    5885 > volume #38 step 1
    5886 
    5887 > volume #38 level 0.99
    5888 
    5889 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    5890 > maps and masks/Substrate/J1094_substrate_mask.mrc"
    5891 
    5892 Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
    5893 shown at level 1, step 4, values float32 
    5894 
    5895 > hide #!38 models
    5896 
    5897 > volume #39 step 1
    5898 
    5899 > volume #39 level 0.99
    5900 
    5901 > show #!38 models
    5902 
    5903 > hide #!38 models
    5904 
    5905 > hide #!39 models
    5906 
    5907 > hide #!34 models
    5908 
    5909 > hide #!10 models
    5910 
    5911 > hide #!17 models
    5912 
    5913 > select all
    5914 
    5915 78 models selected 
    5916 
    5917 > color all gray
    5918 
    5919 > ui tool show "Color Actions"
    5920 
    5921 > color sel dark gray
    5922 
    5923 > color sel light gray
    5924 
    5925 > color sel dark gray
    5926 
    5927 > color sel dim gray
    5928 
    5929 > color sel gray
    5930 
    5931 > color sel dark gray
    5932 
    5933 > color sel silver
    5934 
    5935 > color sel light gray
    5936 
    5937 > color sel gray
    5938 
    5939 > color sel dark gray
    5940 
    5941 > lighting simple
    5942 
    5943 > lighting soft
    5944 
    5945 > lighting full
    5946 
    5947 > lighting simple
    5948 
    5949 > color sel gray
    5950 
    5951 > color sel dim gray
    5952 
    5953 > color sel gray
    5954 
    5955 > hide #!1 models
    5956 
    5957 > show #!2 models
    5958 
    5959 > graphics silhouettes false
    5960 
    5961 > select clear
    5962 
    5963 > show #!35 models
    5964 
    5965 > show #!36 models
    5966 
    5967 > show #!37 models
    5968 
    5969 > show #!38 models
    5970 
    5971 > show #!39 models
    5972 
    5973 > color orange
    5974 
    5975 > transparency #35-39 50
    5976 
    5977 > hide #!36 models
    5978 
    5979 > hide #!37 models
    5980 
    5981 > hide #!38 models
    5982 
    5983 > hide #!39 models
    5984 
    5985 > transparency #35-39 70
    5986 
    5987 > hide #!35 models
    5988 
    5989 > show #!35 models
    5990 
    5991 > hide #!35 models
    5992 
    5993 > show #!35 models
    5994 
    5995 > hide #!35 models
    5996 
    5997 > hide #!2 models
    5998 
    5999 > show #!2 models
    6000 
    6001 > color all gray
    6002 
    6003 > color gray
    6004 
    6005 > color dim gray
    6006 
    6007 > color gray
    6008 
    6009 > hide #!2 models
    6010 
    6011 > show #!2 models
    6012 
    6013 > hide #!2 models
    6014 
    6015 > show #!35 models
    6016 
    6017 > show #!36 models
    6018 
    6019 > show #!37 models
    6020 
    6021 > show #!38 models
    6022 
    6023 > show #!39 models
    6024 
    6025 > color orange
    6026 
    6027 > hide #!39 models
    6028 
    6029 > hide #!38 models
    6030 
    6031 > hide #!37 models
    6032 
    6033 > hide #!36 models
    6034 
    6035 > hide #!35 models
    6036 
    6037 > show #!34 models
    6038 
    6039 > hide #!34 models
    6040 
    6041 > color #1-34 gray
    6042 
    6043 > show #!34 models
    6044 
    6045 > hide #!34 models
    6046 
    6047 > show #!33 models
    6048 
    6049 > hide #!33 models
    6050 
    6051 > show #!2 models
    6052 
    6053 > show #!35 models
    6054 
    6055 > transparency #35-39 80
    6056 
    6057 > transparency #35-39 70
    6058 
    6059 > hide #!35 models
    6060 
    6061 > show #!36 models
    6062 
    6063 > hide #!36 models
    6064 
    6065 > show #!37 models
    6066 
    6067 > hide #!37 models
    6068 
    6069 > show #!38 models
    6070 
    6071 > hide #!38 models
    6072 
    6073 > show #!39 models
    6074 
    6075 > hide #!39 models
    6076 
    6077 > hide #!2 models
    6078 
    6079 > show #!3 models
    6080 
    6081 > show #!36 models
    6082 
    6083 > hide #!36 models
    6084 
    6085 > show #!37 models
    6086 
    6087 > save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
    6088 
    6089 > view list
    6090 
    6091 No named views. 
    6092 
    6093 > hide #!37 models
    6094 
    6095 > show #!39 models
    6096 
    6097 > hide #!39 models
    6098 
    6099 > show #!38 models
    6100 
    6101 > hide #!38 models
    6102 
    6103 > show #!37 models
    6104 
    6105 > hide #!37 models
    6106 
    6107 > show #!36 models
    6108 
    6109 > hide #!36 models
    6110 
    6111 > show #!35 models
    6112 
    6113 > hide #!35 models
    6114 
    6115 > hide #!3 models
    6116 
    6117 > show #!1 models
    6118 
    6119 > volume all level 1
    6120 
    6121 > volume all level 0.99
    6122 
    6123 > volume all step 1 level 0.99
    6124 
    6125 > volume #1 level 0.2042
    6126 
    6127 > volume #1 level 0.1125
    6128 
    6129 > volume #1 level 0.1404
    6130 
    6131 > volume #1 level 0.1205
    6132 
    6133 > show #!2 models
    6134 
    6135 > hide #!1 models
    6136 
    6137 > hide #!2 models
    6138 
    6139 > show #!2 models
    6140 
    6141 > volume #2 level 0.07969
    6142 
    6143 > volume #3 level 0.002132
    6144 
    6145 > volume #3 level 0.002179
    6146 
    6147 > volume #2 level 0.0728
    6148 
    6149 > show #!4 models
    6150 
    6151 > hide #!3 models
    6152 
    6153 > volume #4 level 0.001121
    6154 
    6155 > hide #!4 models
    6156 
    6157 > show #!8 models
    6158 
    6159 > volume #8 level 0.001456
    6160 
    6161 > volume #8 level 0.0015
    6162 
    6163 > volume #4-9 step 1 level 0.0015
    6164 
    6165 > hide #!8 models
    6166 
    6167 > show #!4 models
    6168 
    6169 > hide #!4 models
    6170 
    6171 > show #!5 models
    6172 
    6173 > hide #!5 models
    6174 
    6175 > show #!6 models
    6176 
    6177 > hide #!6 models
    6178 
    6179 > show #!7 models
    6180 
    6181 > hide #!7 models
    6182 
    6183 > show #!8 models
    6184 
    6185 > hide #!8 models
    6186 
    6187 > show #!9 models
    6188 
    6189 > hide #!9 models
    6190 
    6191 > show #!10 models
    6192 
    6193 > volume #10 level 0.002452
    6194 
    6195 > volume #10 level 0.002627
    6196 
    6197 > volume #10 level 0.002364
    6198 
    6199 > hide #!10 models
    6200 
    6201 > show #!11 models
    6202 
    6203 > hide #!11 models
    6204 
    6205 > show #!1 models
    6206 
    6207 > hide #!1 models
    6208 
    6209 > show #!2 models
    6210 
    6211 > hide #!2 models
    6212 
    6213 > show #!3 models
    6214 
    6215 > hide #!3 models
    6216 
    6217 > show #!4 models
    6218 
    6219 > hide #!4 models
    6220 
    6221 > show #!8 models
    6222 
    6223 > hide #!8 models
    6224 
    6225 > show #!10 models
    6226 
    6227 > hide #!10 models
    6228 
    6229 > show #!11 models
    6230 
    6231 > hide #!11 models
    6232 
    6233 > show #!16 models
    6234 
    6235 > volume #16 level 0.003266
    6236 
    6237 > volume #16 level 0.002857
    6238 
    6239 > volume #16 level 0.003215
    6240 
    6241 > volume #11-16 step 1 level 0.003
    6242 
    6243 > hide #!16 models
    6244 
    6245 > show #!15 models
    6246 
    6247 > hide #!15 models
    6248 
    6249 > show #!14 models
    6250 
    6251 > hide #!14 models
    6252 
    6253 > show #!13 models
    6254 
    6255 > hide #!13 models
    6256 
    6257 > show #!12 models
    6258 
    6259 > hide #!12 models
    6260 
    6261 > show #!11 models
    6262 
    6263 > hide #!11 models
    6264 
    6265 > show #!16 models
    6266 
    6267 > volume #11-16 step 1 level 0.0025
    6268 
    6269 > volume #11-16 step 1 level 0.0027
    6270 
    6271 > hide #!16 models
    6272 
    6273 > show #!15 models
    6274 
    6275 > hide #!15 models
    6276 
    6277 > show #!14 models
    6278 
    6279 > hide #!14 models
    6280 
    6281 > show #!13 models
    6282 
    6283 > hide #!13 models
    6284 
    6285 > show #!12 models
    6286 
    6287 > hide #!12 models
    6288 
    6289 > show #!11 models
    6290 
    6291 > show #!16 models
    6292 
    6293 > hide #!11 models
    6294 
    6295 > volume #11-16 step 1 level 0.003
    6296 
    6297 > volume #11-16 step 1 level 0.0027
    6298 
    6299 > volume #11-16 step 1 level 0.0028
    6300 
    6301 > show #!3 models
    6302 
    6303 > hide #!16 models
    6304 
    6305 > show #!16 models
    6306 
    6307 > hide #!3 models
    6308 
    6309 > show #!17 models
    6310 
    6311 > hide #!16 models
    6312 
    6313 > volume #17 level 0.003578
    6314 
    6315 > volume #17 level 0.002898
    6316 
    6317 > show #!3 models
    6318 
    6319 > hide #!17 models
    6320 
    6321 > show #!17 models
    6322 
    6323 > hide #!3 models
    6324 
    6325 > show #!3 models
    6326 
    6327 > hide #!3 models
    6328 
    6329 > show #!3 models
    6330 
    6331 > hide #!3 models
    6332 
    6333 > show #!3 models
    6334 
    6335 > hide #!3 models
    6336 
    6337 > show #!3 models
    6338 
    6339 > hide #!17 models
    6340 
    6341 > show #!17 models
    6342 
    6343 > hide #!17 models
    6344 
    6345 > show #!17 models
    6346 
    6347 > hide #!3 models
    6348 
    6349 > volume #17 level 0.003331
    6350 
    6351 > show #!3 models
    6352 
    6353 > hide #!17 models
    6354 
    6355 > show #!17 models
    6356 
    6357 > hide #!3 models
    6358 
    6359 > show #!10 models
    6360 
    6361 > hide #!10 models
    6362 
    6363 > volume #17 level 0.003022
    6364 
    6365 > show #!10 models
    6366 
    6367 > hide #!10 models
    6368 
    6369 > show #!10 models
    6370 
    6371 > hide #!10 models
    6372 
    6373 > hide #!17 models
    6374 
    6375 > show #!17 models
    6376 
    6377 > hide #!17 models
    6378 
    6379 > show #!18 models
    6380 
    6381 > volume #18 level 0.001598
    6382 
    6383 > volume #18 level 0.001057
    6384 
    6385 > volume #18 level 0.001566
    6386 
    6387 > volume #18 level 0.0015
    6388 
    6389 > volume #18-33 step 1 level 0.0015
    6390 
    6391 > show #!30 models
    6392 
    6393 > hide #!18 models
    6394 
    6395 > show #!18 models
    6396 
    6397 > hide #!30 models
    6398 
    6399 > show #!30 models
    6400 
    6401 > hide #!18 models
    6402 
    6403 > show #!34 models
    6404 
    6405 > hide #!30 models
    6406 
    6407 > volume #34 level 0.001624
    6408 
    6409 > volume #34 level 0.001805
    6410 
    6411 > show #!30 models
    6412 
    6413 > hide #!34 models
    6414 
    6415 > show #!34 models
    6416 
    6417 > hide #!34 models
    6418 
    6419 > show #!34 models
    6420 
    6421 > hide #!30 models
    6422 
    6423 > hide #!34 models
    6424 
    6425 > show #!30 models
    6426 
    6427 > hide #!30 models
    6428 
    6429 > show #!18 models
    6430 
    6431 > show #!34 models
    6432 
    6433 > hide #!18 models
    6434 
    6435 > hide #!34 models
    6436 
    6437 > hide #!39 models
    6438 
    6439 > show #!1 models
    6440 
    6441 > save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
    6442 
    6443 > close session
    6444 
    6445 > open /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs format
    6446 > session
    6447 
    6448 Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
    6449 pixel 0.818, shown at level 0.0654, step 1, values float32 
    6450 Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
    6451 0.818, shown at level 0.022, step 1, values float32 
    6452 Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
    6453 0.818, shown at level 0.0706, step 1, values float32 
    6454 Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    6455 0.818, shown at level 0.0017, step 1, values float32 
    6456 Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
    6457 shown at level 50, step 1, values float32 
    6458 Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
    6459 level 50, step 1, values float32 
    6460 Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
    6461 level 50, step 1, values float32 
    6462 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    6463 opened ChimeraX session 
    6464 
    6465 > view matrix camera
    6466 
    6467 Missing "camera" keyword's argument 
    6468 
    6469 > view matrix
    6470 
    6471 view matrix camera
    6472 -0.021492,0.035484,-0.99914,-403.95,0.70539,0.70875,0.0099977,247.22,0.70849,-0.70457,-0.040263,168.98 
    6473 view matrix models
    6474 #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#11,1,0,0,0,0,1,0,0,0,0,1,0 
    6475  
    6476 
    6477 > view matrix camera
    6478 > -0.021492,0.035484,-0.99914,-403.95,0.70539,0.70875,0.0099977,247.22,0.70849,-0.70457,-0.040263,168.98
    6479 
    6480 > close session
    6481 
    6482 > open /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs format
    6483 > session
    6484 
    6485 restore_snapshot for "Volume" returned None 
    6486 
    6487 restore_snapshot for "VolumeSurface" returned None 
    6488 
    6489 Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
    6490 shown at level 0.12, step 1, values float32 
    6491 Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
    6492 shown at level 0.0728, step 1, values float32 
    6493 Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
    6494 at level 0.00218, step 1, values float32 
    6495 Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
    6496 at level 0.0015, step 1, values float32 
    6497 Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
    6498 at level 0.0015, step 1, values float32 
    6499 Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
    6500 at level 0.0015, step 1, values float32 
    6501 Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
    6502 at level 0.0015, step 1, values float32 
    6503 Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
    6504 at level 0.0015, step 1, values float32 
    6505 Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
    6506 at level 0.0015, step 1, values float32 
    6507 Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
    6508 level 0.00236, step 1, values float32 
    6509 Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
    6510 shown at level 0.0028, step 1, values float32 
    6511 Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
    6512 shown at level 0.0028, step 1, values float32 
    6513 Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
    6514 shown at level 0.0028, step 1, values float32 
    6515 Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
    6516 shown at level 0.0028, step 1, values float32 
    6517 Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
    6518 shown at level 0.0028, step 1, values float32 
    6519 Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
    6520 shown at level 0.0028, step 1, values float32 
    6521 Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
    6522 level 0.00302, step 1, values float32 
    6523 Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
    6524 shown at level 0.0015, step 1, values float32 
    6525 Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
    6526 shown at level 0.0015, step 1, values float32 
    6527 Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
    6528 shown at level 0.0015, step 1, values float32 
    6529 Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
    6530 shown at level 0.0015, step 1, values float32 
    6531 Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
    6532 shown at level 0.0015, step 1, values float32 
    6533 Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
    6534 shown at level 0.0015, step 1, values float32 
    6535 Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
    6536 shown at level 0.0015, step 1, values float32 
    6537 Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
    6538 shown at level 0.0015, step 1, values float32 
    6539 Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
    6540 shown at level 0.0015, step 1, values float32 
    6541 Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
    6542 shown at level 0.0015, step 1, values float32 
    6543 Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
    6544 shown at level 0.0015, step 1, values float32 
    6545 Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
    6546 shown at level 0.0015, step 1, values float32 
    6547 Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
    6548 shown at level 0.0015, step 1, values float32 
    6549 Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
    6550 shown at level 0.0015, step 1, values float32 
    6551 Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
    6552 shown at level 0.0015, step 1, values float32 
    6553 Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
    6554 shown at level 0.0015, step 1, values float32 
    6555 Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
    6556 shown at level 0.0018, step 1, values float32 
    6557 Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
    6558 shown at level 0.99, step 1, values float32 
    6559 Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
    6560 at level 0.99, step 1, values float32 
    6561 Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
    6562 at level 0.99, step 1, values float32 
    6563 Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
    6564 shown at level 0.99, step 1, values float32 
    6565 opened ChimeraX session 
    6566 
    6567 > hide #!1 models
    6568 
    6569 > show #!2 models
    6570 
    6571 > hide #!2 models
    6572 
    6573 > view matrix camera
    6574 > -0.021492,0.035484,-0.99914,-403.95,0.70539,0.70875,0.0099977,247.22,0.70849,-0.70457,-0.040263,168.98
    6575 
    6576 > show #!1 models
    6577 
    6578 > hide #!1 models
    6579 
    6580 > show #!2 models
    6581 
    6582 > hide #!2 models
    6583 
    6584 > show #!3 models
    6585 
    6586 > hide #!3 models
    6587 
    6588 > show #!35 models
    6589 
    6590 > view name side
    6591 
    6592 > show #!2 models
    6593 
    6594 > hide #!2 models
    6595 
    6596 > show #!3 models
    6597 
    6598 > hide #!3 models
    6599 
    6600 > show #!1 models
    6601 
    6602 > hide #!1 models
    6603 
    6604 > show #!2 models
    6605 
    6606 > hide #!2 models
    6607 
    6608 > show #!3 models
    6609 
    6610 > hide #!3 models
    6611 
    6612 > show #!4 models
    6613 
    6614 > hide #!4 models
    6615 
    6616 > hide #!35 models
    6617 
    6618 > show #!36 models
    6619 
    6620 > hide #!36 models
    6621 
    6622 > show #!37 models
    6623 
    6624 > hide #!37 models
    6625 
    6626 > show #!39 models
    6627 
    6628 > hide #!39 models
    6629 
    6630 > show #!39 models
    6631 
    6632 > hide #!39 models
    6633 
    6634 > show #!39 models
    6635 
    6636 > hide #!39 models
    6637 
    6638 > show #!16 models
    6639 
    6640 > hide #!16 models
    6641 
    6642 > show #!16 models
    6643 
    6644 > show #!15 models
    6645 
    6646 > show #!17 models
    6647 
    6648 > hide #!16 models
    6649 
    6650 > hide #!15 models
    6651 
    6652 > hide #!17 models
    6653 
    6654 > show #!16 models
    6655 
    6656 > hide #!16 models
    6657 
    6658 > show #!15 models
    6659 
    6660 > hide #!15 models
    6661 
    6662 > show #!14 models
    6663 
    6664 > hide #!14 models
    6665 
    6666 > show #!3 models
    6667 
    6668 > hide #!3 models
    6669 
    6670 > show #!4 models
    6671 
    6672 > hide #!4 models
    6673 
    6674 > show #!5 models
    6675 
    6676 > hide #!5 models
    6677 
    6678 > show #!6 models
    6679 
    6680 > hide #!6 models
    6681 
    6682 > show #!7 models
    6683 
    6684 > hide #!7 models
    6685 
    6686 > show #!8 models
    6687 
    6688 > hide #!8 models
    6689 
    6690 > show #!35 models
    6691 
    6692 > hide #!35 models
    6693 
    6694 > show #!36 models
    6695 
    6696 > hide #!36 models
    6697 
    6698 > show #!37 models
    6699 
    6700 > hide #!37 models
    6701 
    6702 > show #!39 models
    6703 
    6704 > hide #!39 models
    6705 
    6706 > close #39
    6707 
    6708 > open
    6709 > "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
    6710 > maps and masks/J1034_substrate_mask.mrc"
    6711 
    6712 Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
    6713 shown at level 1, step 4, values float32 
    6714 
    6715 > open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
    6716 > maps and masks/Substrate/J1094_substrate_mask.mrc"
    6717 
    6718 Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
    6719 shown at level 1, step 4, values float32 
    6720 
    6721 > color #38-39 orange
    6722 
    6723 > hide #!38 models
    6724 
    6725 > show #!38 models
    6726 
    6727 > hide #!39 models
    6728 
    6729 > show #!39 models
    6730 
    6731 > volume #38 step 1
    6732 
    6733 > volume #39 step 1
    6734 
    6735 > volume #38 level 0.99
    6736 
    6737 > volume #39 level 0.99
    6738 
    6739 > transparency #38-39 70
    6740 
    6741 > hide #!39 models
    6742 
    6743 > hide #!38 models
    6744 
    6745 > show #!37 models
    6746 
    6747 > hide #!37 models
    6748 
    6749 > show #!39 models
    6750 
    6751 > hide #!39 models
    6752 
    6753 > show #!2 models
    6754 
    6755 > show #!35 models
    6756 
    6757 > view side
    6758 
    6759 > turn y -30
    6760 
    6761 > hide #!35 models
    6762 
    6763 > show #!34 models
    6764 
    6765 > show #!39 models
    6766 
    6767 > hide #!39 models
    6768 
    6769 > hide #!34 models
    6770 
    6771 > view side
    6772 
    6773 > turn y -30
    6774 
    6775 > show #!39 models
    6776 
    6777 > hide #!39 models
    6778 
    6779 > show #!38 models
    6780 
    6781 > hide #!38 models
    6782 
    6783 > show #!35 models
    6784 
    6785 > view side
    6786 
    6787 > view name side
    6788 
    6789 > turn y -30
    6790 
    6791 > hide #!35 models
    6792 
    6793 > hide #!2 models
    6794 
    6795 > show #!4 models
    6796 
    6797 > hide #!4 models
    6798 
    6799 > show #!5 models
    6800 
    6801 > hide #!5 models
    6802 
    6803 > show #!6 models
    6804 
    6805 > hide #!6 models
    6806 
    6807 > show #!7 models
    6808 
    6809 > hide #!7 models
    6810 
    6811 > show #!8 models
    6812 
    6813 > hide #!8 models
    6814 
    6815 > show #!9 models
    6816 
    6817 > show #!8 models
    6818 
    6819 > hide #!9 models
    6820 
    6821 > view side
    6822 
    6823 > hide #!8 models
    6824 
    6825 > show #!9 models
    6826 
    6827 > hide #!9 models
    6828 
    6829 > show #!10 models
    6830 
    6831 > turn y -25
    6832 
    6833 > view side
    6834 
    6835 > hide #!10 models
    6836 
    6837 > show #!1 models
    6838 
    6839 > save
    6840 > /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
    6841 
    6842 > hide #!1 models
    6843 
    6844 > show #!3 models
    6845 
    6846 > show #!35 models
    6847 
    6848 > hide #!35 models
    6849 
    6850 > show #!36 models
    6851 
    6852 > hide #!36 models
    6853 
    6854 > show #!37 models
    6855 
    6856 > show #!36 models
    6857 
    6858 > hide #!36 models
    6859 
    6860 > hide #!37 models
    6861 
    6862 > show #!38 models
    6863 
    6864 > hide #!38 models
    6865 
    6866 > show #!39 models
    6867 
    6868 > hide #!39 models
    6869 
    6870 > close session
    6871 
    6872 > open
    6873 > /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
    6874 
    6875 Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
    6876 pixel 0.818, shown at level 0.0654, step 1, values float32 
    6877 Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
    6878 0.818, shown at level 0.022, step 1, values float32 
    6879 Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
    6880 0.818, shown at level 0.0706, step 1, values float32 
    6881 Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    6882 0.818, shown at level 0.0017, step 1, values float32 
    6883 Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
    6884 shown at level 50, step 1, values float32 
    6885 Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
    6886 level 50, step 1, values float32 
    6887 Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
    6888 level 50, step 1, values float32 
    6889 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    6890 opened ChimeraX session 
    6891 
    6892 > close session
    6893 
    6894 > open
    6895 > /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
    6896 
    6897 Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
    6898 shown at level 0.12, step 1, values float32 
    6899 Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
    6900 shown at level 0.0728, step 1, values float32 
    6901 Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
    6902 at level 0.00218, step 1, values float32 
    6903 Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
    6904 at level 0.0015, step 1, values float32 
    6905 Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
    6906 at level 0.0015, step 1, values float32 
    6907 Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
    6908 at level 0.0015, step 1, values float32 
    6909 Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
    6910 at level 0.0015, step 1, values float32 
    6911 Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
    6912 at level 0.0015, step 1, values float32 
    6913 Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
    6914 at level 0.0015, step 1, values float32 
    6915 Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
    6916 level 0.00236, step 1, values float32 
    6917 Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
    6918 shown at level 0.0028, step 1, values float32 
    6919 Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
    6920 shown at level 0.0028, step 1, values float32 
    6921 Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
    6922 shown at level 0.0028, step 1, values float32 
    6923 Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
    6924 shown at level 0.0028, step 1, values float32 
    6925 Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
    6926 shown at level 0.0028, step 1, values float32 
    6927 Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
    6928 shown at level 0.0028, step 1, values float32 
    6929 Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
    6930 level 0.00302, step 1, values float32 
    6931 Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
    6932 shown at level 0.0015, step 1, values float32 
    6933 Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
    6934 shown at level 0.0015, step 1, values float32 
    6935 Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
    6936 shown at level 0.0015, step 1, values float32 
    6937 Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
    6938 shown at level 0.0015, step 1, values float32 
    6939 Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
    6940 shown at level 0.0015, step 1, values float32 
    6941 Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
    6942 shown at level 0.0015, step 1, values float32 
    6943 Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
    6944 shown at level 0.0015, step 1, values float32 
    6945 Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
    6946 shown at level 0.0015, step 1, values float32 
    6947 Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
    6948 shown at level 0.0015, step 1, values float32 
    6949 Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
    6950 shown at level 0.0015, step 1, values float32 
    6951 Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
    6952 shown at level 0.0015, step 1, values float32 
    6953 Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
    6954 shown at level 0.0015, step 1, values float32 
    6955 Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
    6956 shown at level 0.0015, step 1, values float32 
    6957 Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
    6958 shown at level 0.0015, step 1, values float32 
    6959 Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
    6960 shown at level 0.0015, step 1, values float32 
    6961 Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
    6962 shown at level 0.0015, step 1, values float32 
    6963 Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
    6964 shown at level 0.0018, step 1, values float32 
    6965 Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
    6966 shown at level 0.99, step 1, values float32 
    6967 Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
    6968 at level 0.99, step 1, values float32 
    6969 Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
    6970 at level 0.99, step 1, values float32 
    6971 Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
    6972 shown at level 0.99, step 1, values float32 
    6973 Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
    6974 shown at level 0.99, step 1, values float32 
    6975 opened ChimeraX session 
    6976 
    6977 > close session
    6978 
    6979 > open
    6980 > /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
    6981 
    6982 Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
    6983 pixel 0.818, shown at level 0.0654, step 1, values float32 
    6984 Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
    6985 0.818, shown at level 0.022, step 1, values float32 
    6986 Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
    6987 0.818, shown at level 0.0706, step 1, values float32 
    6988 Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    6989 0.818, shown at level 0.0017, step 1, values float32 
    6990 Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
    6991 shown at level 50, step 1, values float32 
    6992 Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
    6993 level 50, step 1, values float32 
    6994 Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
    6995 level 50, step 1, values float32 
    6996 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    6997 opened ChimeraX session 
    6998 
    6999 > hide #!1 models
    7000 
    7001 > show #!2 models
    7002 
    7003 > hide #!2 models
    7004 
    7005 > show #!2 models
    7006 
    7007 > hide #!2 models
    7008 
    7009 > show #!3 models
    7010 
    7011 > hide #!3 models
    7012 
    7013 > show #!4 models
    7014 
    7015 > hide #!4 models
    7016 
    7017 > show #!1 models
    7018 
    7019 > show #!2 models
    7020 
    7021 > hide #!1 models
    7022 
    7023 > show #!1 models
    7024 
    7025 > hide #!2 models
    7026 
    7027 > hide #!1 models
    7028 
    7029 > show #!2 models
    7030 
    7031 > hide #!2 models
    7032 
    7033 > show #!3 models
    7034 
    7035 > hide #!3 models
    7036 
    7037 > show #!5 models
    7038 
    7039 > hide #!5 models
    7040 
    7041 > show #!4 models
    7042 
    7043 > hide #!4 models
    7044 
    7045 > show #!1 models
    7046 
    7047 > hide #!1 models
    7048 
    7049 > show #!2 models
    7050 
    7051 > turn y -25
    7052 
    7053 > view side
    7054 
    7055 > hide #!2 models
    7056 
    7057 > show #!1 models
    7058 
    7059 > show #!2 models
    7060 
    7061 > show #!3 models
    7062 
    7063 > show #!4 models
    7064 
    7065 > turn y -25
    7066 
    7067 > hide #!4 models
    7068 
    7069 > hide #!3 models
    7070 
    7071 > hide #!2 models
    7072 
    7073 > view side
    7074 
    7075 > close session
    7076 
    7077 > open
    7078 > /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
    7079 
    7080 Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
    7081 pixel 0.818, shown at level 0.0654, step 1, values float32 
    7082 Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
    7083 0.818, shown at level 0.022, step 1, values float32 
    7084 Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
    7085 0.818, shown at level 0.0706, step 1, values float32 
    7086 Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
    7087 0.818, shown at level 0.0017, step 1, values float32 
    7088 Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
    7089 shown at level 50, step 1, values float32 
    7090 Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
    7091 level 50, step 1, values float32 
    7092 Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
    7093 level 50, step 1, values float32 
    7094 Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077 
    7095 opened ChimeraX session 
    7096 
    7097 > view side
    7098 
    7099 > turn y -25
    7100 
    7101 > turn y 25
    7102 
    7103 > view list
    7104 
    7105 Named views: side, side_ang 
    7106 
    7107 > view side_ang
    7108 
    7109 > hide #!1 models
    7110 
    7111 > show #!7 models
    7112 
    7113 > hide #!7 models
    7114 
    7115 > show #8 models
    7116 
    7117 > show #!1 models
    7118 
    7119 > view side
    7120 
    7121 > hide #8 models
    7122 
    7123 > turn y -25
    7124 
    7125 > hide #!1 models
    7126 
    7127 > show #!2 models
    7128 
    7129 > view side
     935[deleted to fit within ticket limits]
    7130936
    7131937> turn y -25