Changes between Initial Version and Version 1 of Ticket #18761


Ignore:
Timestamp:
Sep 10, 2025, 12:53:15 PM (6 weeks ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #18761

    • Property Component Unassigned → Third Party
    • Property Owner set to Richard Scheltema
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → XMAS: color key deleted multiple times

  • Ticket #18761 – Description

    initial v1  
    24222422> #11,-0.047287,-0.19762,0.97914,47.757,0.3239,0.92424,0.20219,-66.044,-0.94491,0.3267,0.020305,232.25,#12,-0.047287,-0.19762,0.97914,47.757,0.3239,0.92424,0.20219,-66.044,-0.94491,0.3267,0.020305,232.25
    24232423
    2424 > view matrix models
    2425 > #11,-0.88887,-0.45801,0.011781,346.86,-0.23966,0.48671,0.84005,-8.5049,-0.39048,0.74387,-0.54239,168.45,#12,-0.88887,-0.45801,0.011781,346.86,-0.23966,0.48671,0.84005,-8.5049,-0.39048,0.74387,-0.54239,168.45
    2426 
    2427 > view matrix models
    2428 > #11,-0.19168,-0.96873,-0.15754,339.31,-0.75924,0.044642,0.64928,159.39,-0.62194,0.24407,-0.74406,302.98,#12,-0.19168,-0.96873,-0.15754,339.31,-0.75924,0.044642,0.64928,159.39,-0.62194,0.24407,-0.74406,302.98
    2429 
    2430 > fitmap #11 inMap #1
    2431 
    2432 Fit map
    2433 W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc in
    2434 map W20_J3623_consensus_structure_sharp.mrc using 42734 points 
    2435 correlation = 0.9154, correlation about mean = 0.4456, overlap = 5.735e+04 
    2436 steps = 104, shift = 9.56, angle = 10.3 degrees 
    2437  
    2438 Position of
    2439 W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc
    2440 (#11) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2441 Matrix rotation and translation 
    2442 -0.34146109 -0.91804101 -0.20150685 354.32329233 
    2443 -0.77726306 0.15526879 0.60971610 146.26157419 
    2444 -0.52845666 0.36481815 -0.76657763 277.10408311 
    2445 Axis -0.56679376 0.75669526 0.32581761 
    2446 Axis point 251.95105256 0.00000000 81.46580342 
    2447 Rotation angle (degrees) 167.52357003 
    2448 Shift along axis 0.13259978 
    2449  
    2450 
    2451 > fitmap #12 inMap #1
    2452 
    2453 Fit map
    2454 W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
    2455 in map W20_J3623_consensus_structure_sharp.mrc using 37926 points 
    2456 correlation = 0.9185, correlation about mean = 0.4316, overlap = 5.437e+04 
    2457 steps = 120, shift = 9.52, angle = 10.3 degrees 
    2458  
    2459 Position of
    2460 W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
    2461 (#12) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2462 Matrix rotation and translation 
    2463 -0.34132328 -0.91808135 -0.20155652 354.32310537 
    2464 -0.77719944 0.15505915 0.60985055 146.27901701 
    2465 -0.52863923 0.36480581 -0.76645762 277.14013363 
    2466 Axis -0.56684797 0.75662172 0.32589408 
    2467 Axis point 251.98254766 0.00000000 81.45327260 
    2468 Rotation angle (degrees) 167.51718440 
    2469 Shift along axis 0.14887713 
    2470  
    2471 
    2472 > select subtract #12
    2473 
    2474 2 models selected 
    2475 
    2476 > select subtract #11
    2477 
    2478 Nothing selected 
    2479 
    2480 > hide #!1 models
    2481 
    2482 > volume #11 level 1.414
    2483 
    2484 > hide #!11 models
    2485 
    2486 > hide #!12 models
    2487 
    2488 > show #!13 models
    2489 
    2490 > show #!1 models
    2491 
    2492 > show #!14 models
    2493 
    2494 > fitmap #13 inMap #1
    2495 
    2496 Fit map W20_J4021_005_volume_map_bprime_local.mrc in map
    2497 W20_J3623_consensus_structure_sharp.mrc using 138166 points 
    2498 correlation = 0.8362, correlation about mean = 0.2198, overlap = 1.935e+04 
    2499 steps = 64, shift = 0.521, angle = 0.419 degrees 
    2500  
    2501 Position of W20_J4021_005_volume_map_bprime_local.mrc (#13) relative to
    2502 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2503 Matrix rotation and translation 
    2504 0.99998250 0.00590533 0.00034832 -0.90323251 
    2505 -0.00590377 0.99997332 -0.00430079 1.11548441 
    2506 -0.00037371 0.00429865 0.99999069 -0.31823043 
    2507 Axis 0.58794667 0.04936530 -0.80739196 
    2508 Axis point 190.18082923 131.70665579 0.00000000 
    2509 Rotation angle (degrees) 0.41901428 
    2510 Shift along axis -0.21904963 
    2511  
    2512 
    2513 > fitmap #14 inMap #1
    2514 
    2515 Fit map W20_J4021_005_volume_map_sharp_bprime_local.mrc in map
    2516 W20_J3623_consensus_structure_sharp.mrc using 137893 points 
    2517 correlation = 0.8085, correlation about mean = 0.2734, overlap = 2.896e+04 
    2518 steps = 48, shift = 0.598, angle = 0.487 degrees 
    2519  
    2520 Position of W20_J4021_005_volume_map_sharp_bprime_local.mrc (#14) relative to
    2521 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2522 Matrix rotation and translation 
    2523 0.99997911 0.00638470 0.00100265 -1.04735728 
    2524 -0.00637907 0.99996444 -0.00551663 1.34954856 
    2525 -0.00103783 0.00551011 0.99998428 -0.33308547 
    2526 Axis 0.64900636 0.12009752 -0.75124386 
    2527 Axis point 215.82672874 137.56284372 -0.00000000 
    2528 Rotation angle (degrees) 0.48673885 
    2529 Shift along axis -0.26743568 
    2530  
    2531 
    2532 > hide #!14 models
    2533 
    2534 > hide #!13 models
    2535 
    2536 > show #!15 models
    2537 
    2538 > show #!16 models
    2539 
    2540 > fitmap #15 inMap #1
    2541 
    2542 Fit map W20_J4022_005_volume_map_bprime_local.mrc in map
    2543 W20_J3623_consensus_structure_sharp.mrc using 138200 points 
    2544 correlation = 0.8381, correlation about mean = 0.222, overlap = 1.906e+04 
    2545 steps = 40, shift = 0.303, angle = 0.34 degrees 
    2546  
    2547 Position of W20_J4022_005_volume_map_bprime_local.mrc (#15) relative to
    2548 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2549 Matrix rotation and translation 
    2550 0.99998447 0.00240641 0.00502780 -1.28358869 
    2551 -0.00241668 0.99999501 0.00203622 -0.22148190 
    2552 -0.00502288 -0.00204834 0.99998529 1.05482120 
    2553 Axis -0.34402829 0.84653419 -0.40623194 
    2554 Axis point 195.11366625 0.00000000 267.83446555 
    2555 Rotation angle (degrees) 0.34013109 
    2556 Shift along axis -0.17440325 
    2557  
    2558 
    2559 > fitmap #16 inMap #1
    2560 
    2561 Fit map W20_J4022_005_volume_map_sharp_bprime_local.mrc in map
    2562 W20_J3623_consensus_structure_sharp.mrc using 138084 points 
    2563 correlation = 0.8046, correlation about mean = 0.274, overlap = 2.955e+04 
    2564 steps = 48, shift = 0.324, angle = 0.293 degrees 
    2565  
    2566 Position of W20_J4022_005_volume_map_sharp_bprime_local.mrc (#16) relative to
    2567 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2568 Matrix rotation and translation 
    2569 0.99999153 0.00141184 0.00386537 -0.96250876 
    2570 -0.00142356 0.99999440 0.00302979 -0.53091994 
    2571 -0.00386107 -0.00303526 0.99998794 0.99298679 
    2572 Axis -0.59323978 0.75574456 -0.27733863 
    2573 Axis point 248.76134938 0.00000000 265.76556629 
    2574 Rotation angle (degrees) 0.29288616 
    2575 Shift along axis -0.10563498 
    2576  
    2577 
    2578 > hide #!16 models
    2579 
    2580 > hide #!15 models
    2581 
    2582 > show #!17 models
    2583 
    2584 > fitmap #17 inMap #1
    2585 
    2586 Fit map W20_J4023_003_volume_map_bprime_local.mrc in map
    2587 W20_J3623_consensus_structure_sharp.mrc using 138098 points 
    2588 correlation = 0.8373, correlation about mean = 0.2151, overlap = 1.874e+04 
    2589 steps = 68, shift = 0.363, angle = 0.333 degrees 
    2590  
    2591 Position of W20_J4023_003_volume_map_bprime_local.mrc (#17) relative to
    2592 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2593 Matrix rotation and translation 
    2594 0.99998345 0.00557936 0.00140325 -1.18658067 
    2595 -0.00557823 0.99998411 -0.00081217 0.60425107 
    2596 -0.00140776 0.00080432 0.99999869 0.20586820 
    2597 Axis 0.13912185 0.24192785 -0.96026873 
    2598 Axis point 117.12498270 207.62002695 0.00000000 
    2599 Rotation angle (degrees) 0.33286852 
    2600 Shift along axis -0.21658293 
    2601  
    2602 
    2603 > show #!18 models
    2604 
    2605 > fitmap #18 inMap #1
    2606 
    2607 Fit map W20_J4023_003_volume_map_sharp_bprime_local.mrc in map
    2608 W20_J3623_consensus_structure_sharp.mrc using 138171 points 
    2609 correlation = 0.7947, correlation about mean = 0.312, overlap = 3.526e+04 
    2610 steps = 68, shift = 0.461, angle = 0.264 degrees 
    2611  
    2612 Position of W20_J4023_003_volume_map_sharp_bprime_local.mrc (#18) relative to
    2613 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2614 Matrix rotation and translation 
    2615 0.99999048 0.00393326 0.00188760 -1.06407059 
    2616 -0.00393046 0.99999117 -0.00148458 0.41525484 
    2617 -0.00189342 0.00147715 0.99999712 0.25585356 
    2618 Axis 0.32142171 0.41033635 -0.85341207 
    2619 Axis point 145.82615217 239.01637261 0.00000000 
    2620 Rotation angle (degrees) 0.26397543 
    2621 Shift along axis -0.38996975 
    2622  
    2623 
    2624 > hide #!18 models
    2625 
    2626 > hide #!17 models
    2627 
    2628 > show #!19 models
    2629 
    2630 > fitmap #19 inMap #1
    2631 
    2632 Fit map W20_J4024_005_volume_map_bprime_local.mrc in map
    2633 W20_J3623_consensus_structure_sharp.mrc using 138193 points 
    2634 correlation = 0.8392, correlation about mean = 0.2773, overlap = 1.921e+04 
    2635 steps = 76, shift = 0.289, angle = 0.259 degrees 
    2636  
    2637 Position of W20_J4024_005_volume_map_bprime_local.mrc (#19) relative to
    2638 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2639 Matrix rotation and translation 
    2640 0.99999040 0.00368324 0.00237314 -0.77269801 
    2641 -0.00368586 0.99999260 0.00110036 0.16957827 
    2642 -0.00236907 -0.00110910 0.99999658 0.39066327 
    2643 Axis -0.24448082 0.52473318 -0.81540433 
    2644 Axis point 51.36886426 212.61995395 0.00000000 
    2645 Rotation angle (degrees) 0.25890214 
    2646 Shift along axis -0.04065533 
    2647  
    2648 
    2649 > fitmap #20 inMap #1
    2650 
    2651 Fit map W20_J4024_005_volume_map_sharp_bprime_local.mrc in map
    2652 W20_J3623_consensus_structure_sharp.mrc using 138123 points 
    2653 correlation = 0.8039, correlation about mean = 0.2975, overlap = 2.959e+04 
    2654 steps = 48, shift = 0.294, angle = 0.249 degrees 
    2655  
    2656 Position of W20_J4024_005_volume_map_sharp_bprime_local.mrc (#20) relative to
    2657 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2658 Matrix rotation and translation 
    2659 0.99999177 0.00343445 0.00216100 -0.68440650 
    2660 -0.00343784 0.99999286 0.00156920 0.06668376 
    2661 -0.00215559 -0.00157662 0.99999643 0.45265088 
    2662 Axis -0.36142806 0.49593828 -0.78956633 
    2663 Axis point 30.06869516 207.44842694 0.00000000 
    2664 Rotation angle (degrees) 0.24934854 
    2665 Shift along axis -0.07696315 
    2666  
    2667 
    2668 > hide #!19 models
    2669 
    2670 > show #!20 models
    2671 
    2672 > hide #!20 models
    2673 
    2674 > show #!21 models
    2675 
    2676 > fitmap #21 inMap #1
    2677 
    2678 Fit map W20_J4025_004_volume_map_bprime_local.mrc in map
    2679 W20_J3623_consensus_structure_sharp.mrc using 138084 points 
    2680 correlation = 0.8289, correlation about mean = 0.1891, overlap = 1.832e+04 
    2681 steps = 48, shift = 0.728, angle = 0.413 degrees 
    2682  
    2683 Position of W20_J4025_004_volume_map_bprime_local.mrc (#21) relative to
    2684 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2685 Matrix rotation and translation 
    2686 0.99998460 0.00544119 0.00108928 -0.83012202 
    2687 -0.00543611 0.99997458 -0.00461454 1.00696868 
    2688 -0.00111436 0.00460855 0.99998876 -0.07337997 
    2689 Axis 0.63914215 0.15270809 -0.75377553 
    2690 Axis point 193.72853355 115.34838902 0.00000000 
    2691 Rotation angle (degrees) 0.41340458 
    2692 Shift along axis -0.32148169 
    2693  
    2694 
    2695 > fitmap #22 inMap #1
    2696 
    2697 Fit map W20_J4025_004_volume_map_sharp_bprime_local.mrc in map
    2698 W20_J3623_consensus_structure_sharp.mrc using 137654 points 
    2699 correlation = 0.7511, correlation about mean = 0.2821, overlap = 3.85e+04 
    2700 steps = 52, shift = 0.819, angle = 0.498 degrees 
    2701  
    2702 Position of W20_J4025_004_volume_map_sharp_bprime_local.mrc (#22) relative to
    2703 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2704 Matrix rotation and translation 
    2705 0.99998155 0.00559478 0.00236633 -1.03081576 
    2706 -0.00557996 0.99996507 -0.00622345 1.34930492 
    2707 -0.00240107 0.00621013 0.99997783 -0.00730733 
    2708 Axis 0.71523902 0.27424352 -0.64282473 
    2709 Axis point 0.00000000 39.53456477 232.56399021 
    2710 Rotation angle (degrees) 0.49801542 
    2711 Shift along axis -0.36254420 
    2712  
    2713 
    2714 > show #!22 models
    2715 
    2716 > hide #!22 models
    2717 
    2718 > hide #!21 models
    2719 
    2720 > show #!23 models
    2721 
    2722 > show #!24 models
    2723 
    2724 > fitmap #23 inMap #1
    2725 
    2726 Fit map W20_J4026_004_volume_map_gammazeta_local.mrc in map
    2727 W20_J3623_consensus_structure_sharp.mrc using 138172 points 
    2728 correlation = 0.8607, correlation about mean = 0.3259, overlap = 2.201e+04 
    2729 steps = 52, shift = 0.541, angle = 0.494 degrees 
    2730  
    2731 Position of W20_J4026_004_volume_map_gammazeta_local.mrc (#23) relative to
    2732 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2733 Matrix rotation and translation 
    2734 0.99997866 -0.00017168 -0.00653102 0.57575571 
    2735 0.00020836 0.99998421 0.00561565 -0.37594588 
    2736 0.00652995 -0.00561689 0.99996290 0.02009032 
    2737 Axis -0.65188430 -0.75799762 0.02205601 
    2738 Axis point -2.93047519 0.00000000 79.19172412 
    2739 Rotation angle (degrees) 0.49363480 
    2740 Shift along axis -0.08991691 
    2741  
    2742 
    2743 > fitmap #24 inMap #1
    2744 
    2745 Fit map W20_J4026_004_volume_map_sharp_gammazeta_local.mrc in map
    2746 W20_J3623_consensus_structure_sharp.mrc using 138033 points 
    2747 correlation = 0.853, correlation about mean = 0.3795, overlap = 2.779e+04 
    2748 steps = 68, shift = 0.477, angle = 0.571 degrees 
    2749  
    2750 Position of W20_J4026_004_volume_map_sharp_gammazeta_local.mrc (#24) relative
    2751 to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2752 Matrix rotation and translation 
    2753 0.99996930 -0.00126227 -0.00773336 0.96231167 
    2754 0.00130980 0.99998026 0.00614469 -0.62594677 
    2755 0.00772545 -0.00615463 0.99995122 -0.10724743 
    2756 Axis -0.61739139 -0.77598860 0.12911066 
    2757 Axis point 12.56321001 0.00000000 114.62740380 
    2758 Rotation angle (degrees) 0.57071652 
    2759 Shift along axis -0.12224217 
    2760  
    2761 
    2762 > hide #!24 models
    2763 
    2764 > hide #!23 models
    2765 
    2766 > show #!25 models
    2767 
    2768 > show #!26 models
    2769 
    2770 > fitmap #25 inMap #1
    2771 
    2772 Fit map W20_J4027_005_volume_map_gammazeta_local.mrc in map
    2773 W20_J3623_consensus_structure_sharp.mrc using 138160 points 
    2774 correlation = 0.8845, correlation about mean = 0.4248, overlap = 2.208e+04 
    2775 steps = 48, shift = 0.937, angle = 0.528 degrees 
    2776  
    2777 Position of W20_J4027_005_volume_map_gammazeta_local.mrc (#25) relative to
    2778 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2779 Matrix rotation and translation 
    2780 0.99995803 -0.00131908 0.00906657 -1.56861951 
    2781 0.00131039 0.99999868 0.00096483 0.05951128 
    2782 -0.00906783 -0.00095291 0.99995843 2.12791102 
    2783 Axis -0.10408825 0.98427482 0.14271899 
    2784 Axis point 225.62409153 0.00000000 168.02231673 
    2785 Rotation angle (degrees) 0.52781987 
    2786 Shift along axis 0.52554363 
    2787  
    2788 
    2789 > fitmap #26 inMap #1
    2790 
    2791 Fit map W20_J4027_005_volume_map_sharp_gammazeta_local.mrc in map
    2792 W20_J3623_consensus_structure_sharp.mrc using 138211 points 
    2793 correlation = 0.8774, correlation about mean = 0.4648, overlap = 2.896e+04 
    2794 steps = 48, shift = 0.956, angle = 0.621 degrees 
    2795  
    2796 Position of W20_J4027_005_volume_map_sharp_gammazeta_local.mrc (#26) relative
    2797 to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2798 Matrix rotation and translation 
    2799 0.99994135 -0.00098967 0.01078522 -1.85651387 
    2800 0.00098601 0.99999945 0.00034465 0.18754839 
    2801 -0.01078555 -0.00033399 0.99994178 2.30481893 
    2802 Axis -0.03131444 0.99534338 0.09116443 
    2803 Axis point 208.92157622 0.00000000 171.95034602 
    2804 Rotation angle (degrees) 0.62086019 
    2805 Shift along axis 0.45492826 
    2806  
    2807 
    2808 > hide #!26 models
    2809 
    2810 > hide #!25 models
    2811 
    2812 > show #!27 models
    2813 
    2814 > fitmap #27 inMap #1
    2815 
    2816 Fit map W20_J4028_004_volume_map_gammazeta_local.mrc in map
    2817 W20_J3623_consensus_structure_sharp.mrc using 138218 points 
    2818 correlation = 0.8752, correlation about mean = 0.4062, overlap = 2.23e+04 
    2819 steps = 44, shift = 0.478, angle = 0.403 degrees 
    2820  
    2821 Position of W20_J4028_004_volume_map_gammazeta_local.mrc (#27) relative to
    2822 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2823 Matrix rotation and translation 
    2824 0.99997775 0.00042654 -0.00665697 0.77827945 
    2825 -0.00041158 0.99999739 0.00224763 0.14049133 
    2826 0.00665791 -0.00224484 0.99997532 -0.37918036 
    2827 Axis -0.31912872 -0.94583944 -0.05953667 
    2828 Axis point 60.52816960 0.00000000 99.51494449 
    2829 Rotation angle (degrees) 0.40328886 
    2830 Shift along axis -0.35867843 
    2831  
    2832 
    2833 > fitmap #28 inMap #1
    2834 
    2835 Fit map W20_J4028_004_volume_map_sharp_gammazeta_local.mrc in map
    2836 W20_J3623_consensus_structure_sharp.mrc using 137995 points 
    2837 correlation = 0.8679, correlation about mean = 0.4447, overlap = 2.897e+04 
    2838 steps = 48, shift = 0.432, angle = 0.487 degrees 
    2839  
    2840 Position of W20_J4028_004_volume_map_sharp_gammazeta_local.mrc (#28) relative
    2841 to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2842 Matrix rotation and translation 
    2843 0.99996809 -0.00001305 -0.00798826 1.06130917 
    2844 0.00003628 0.99999577 0.00290797 -0.02300922 
    2845 0.00798819 -0.00290817 0.99996387 -0.53329988 
    2846 Axis -0.34208068 -0.93966610 0.00290175 
    2847 Axis point 67.16980128 0.00000000 117.90291440 
    2848 Rotation angle (degrees) 0.48708480 
    2849 Shift along axis -0.34297988 
    2850  
    2851 
    2852 > show #!28 models
    2853 
    2854 > hide #!28 models
    2855 
    2856 > show #!28 models
    2857 
    2858 > hide #!28 models
    2859 
    2860 > hide #!27 models
    2861 
    2862 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    2863 > resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
    2864 
    2865 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    2866 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body001.mrc"
    2867 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    2868 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body002.mrc"
    2869 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    2870 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body003.mrc"
    2871 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    2872 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body004.mrc"
    2873 
    2874 Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
    2875 shown at level 0.00608, step 1, values float32 
    2876 Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
    2877 shown at level 0.00134, step 1, values float32 
    2878 Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
    2879 shown at level 0.000955, step 1, values float32 
    2880 Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
    2881 shown at level 0.000493, step 1, values float32 
    2882 
    2883 > select add #29
    2884 
    2885 9 models selected 
    2886 
    2887 > view matrix models
    2888 > #29,-0.47366,-0.87946,-0.046912,333.91,-0.83829,0.43388,0.33018,153.37,-0.27003,0.19572,-0.94275,297.34
    2889 
    2890 > ui mousemode right "translate selected models"
    2891 
    2892 > view matrix models
    2893 > #29,-0.47366,-0.87946,-0.046912,340.41,-0.83829,0.43388,0.33018,139.03,-0.27003,0.19572,-0.94275,298.38
    2894 
    2895 > fitmap #29 inMap #1
    2896 
    2897 Multiple maps for #29 
    2898 
    2899 > fitmap #29.1 inMap #1
    2900 
    2901 Fit map W20_J140_run_body001.mrc in map
    2902 W20_J3623_consensus_structure_sharp.mrc using 138225 points 
    2903 correlation = 0.9233, correlation about mean = 0.7294, overlap = 874.3 
    2904 steps = 156, shift = 14.4, angle = 22 degrees 
    2905  
    2906 Position of W20_J140_run_body001.mrc (#29.1) relative to
    2907 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2908 Matrix rotation and translation 
    2909 0.95200729 0.18684598 -0.24242669 1.82192845 
    2910 -0.12799492 0.96249869 0.23919359 -9.97975402 
    2911 0.27802773 -0.19668465 0.94022111 9.66133125 
    2912 Axis -0.58247333 -0.69549428 -0.42072857 
    2913 Axis point -33.51580829 0.00000000 18.51090823 
    2914 Rotation angle (degrees) 21.97250066 
    2915 Shift along axis 1.81483897 
    2916  
    2917 
    2918 > fitmap #29.2 inMap #1
    2919 
    2920 Fit map W20_J140_run_body002.mrc in map
    2921 W20_J3623_consensus_structure_sharp.mrc using 138046 points 
    2922 correlation = 0.8263, correlation about mean = 0.6371, overlap = 468.8 
    2923 steps = 280, shift = 31, angle = 21.8 degrees 
    2924  
    2925 Position of W20_J140_run_body002.mrc (#29.2) relative to
    2926 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2927 Matrix rotation and translation 
    2928 0.95172436 0.17711878 -0.25069840 4.25540621 
    2929 -0.11810903 0.96515525 0.23350719 -10.43311409 
    2930 0.28332138 -0.19262473 0.93948108 8.13777130 
    2931 Axis -0.57255681 -0.71751644 -0.39667222 
    2932 Axis point -25.70139502 0.00000000 26.08327898 
    2933 Rotation angle (degrees) 21.84708246 
    2934 Shift along axis 1.82144130 
    2935  
    2936 
    2937 > fitmap #29.3 inMap #1
    2938 
    2939 Fit map W20_J140_run_body003.mrc in map
    2940 W20_J3623_consensus_structure_sharp.mrc using 137660 points 
    2941 correlation = 0.5389, correlation about mean = 0.1615, overlap = 221.3 
    2942 steps = 180, shift = 25.4, angle = 11.9 degrees 
    2943  
    2944 Position of W20_J140_run_body003.mrc (#29.3) relative to
    2945 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2946 Matrix rotation and translation 
    2947 0.98378563 0.15518997 -0.08989941 -25.87512376 
    2948 -0.14501363 0.98324752 0.11043264 11.64818978 
    2949 0.10553141 -0.09560540 0.98980944 10.88183562 
    2950 Axis -0.49859202 -0.47292359 -0.72646353 
    2951 Axis point 58.49450968 174.49109696 0.00000000 
    2952 Rotation angle (degrees) 11.92434111 
    2953 Shift along axis -0.51283023 
    2954  
    2955 
    2956 > fitmap #29.4 inMap #1
    2957 
    2958 Fit map W20_J140_run_body004.mrc in map
    2959 W20_J3623_consensus_structure_sharp.mrc using 137970 points 
    2960 correlation = 0.7171, correlation about mean = 0.4553, overlap = 200.6 
    2961 steps = 192, shift = 16.7, angle = 21.7 degrees 
    2962  
    2963 Position of W20_J140_run_body004.mrc (#29.4) relative to
    2964 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    2965 Matrix rotation and translation 
    2966 0.95301433 0.19868762 -0.22866331 -0.93326951 
    2967 -0.14395018 0.96121397 0.23525740 -8.31020320 
    2968 0.26653710 -0.19128756 0.94465181 8.81821407 
    2969 Axis -0.57801628 -0.67105211 -0.46431266 
    2970 Axis point -34.90313676 0.00000000 8.20072337 
    2971 Rotation angle (degrees) 21.65230186 
    2972 Shift along axis 2.02161595 
    2973  
    2974 
    2975 > select subtract #29
    2976 
    2977 Nothing selected 
    2978 
    2979 > select add #29
    2980 
    2981 9 models selected 
    2982 
    2983 > select add #29.1
    2984 
    2985 9 models selected 
    2986 
    2987 > select subtract #29.1
    2988 
    2989 7 models selected 
    2990 
    2991 > select add #29.1
    2992 
    2993 9 models selected 
    2994 
    2995 > select subtract #29.1
    2996 
    2997 7 models selected 
    2998 
    2999 > color #29 darkgrey models
    3000 
    3001 > color #29 #a9a9a993 models
    3002 
    3003 > color #29 #a9a9a994 models
    3004 
    3005 > select add #29
    3006 
    3007 9 models selected 
    3008 
    3009 > select subtract #29
    3010 
    3011 Nothing selected 
    3012 
    3013 > hide #!29 models
    3014 
    3015 > rename #29 W20_J140_MB
    3016 
    3017 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3018 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body001.mrc"
    3019 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3020 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body002.mrc"
    3021 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3022 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body003.mrc"
    3023 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3024 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body004.mrc"
    3025 
    3026 Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
    3027 1.2, shown at level 0.00616, step 1, values float32 
    3028 Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
    3029 1.2, shown at level 0.00152, step 1, values float32 
    3030 Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
    3031 1.2, shown at level 0.000716, step 1, values float32 
    3032 Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
    3033 1.2, shown at level 0.000812, step 1, values float32 
    3034 
    3035 > select add #30
    3036 
    3037 9 models selected 
    3038 
    3039 > ui mousemode right "rotate selected models"
    3040 
    3041 > view matrix models
    3042 > #30,-0.35278,-0.9274,-0.12442,348.28,-0.78005,0.21805,0.5865,134.81,-0.51679,0.30396,-0.80034,301.49
    3043 
    3044 > ui mousemode right "translate selected models"
    3045 
    3046 > view matrix models
    3047 > #30,-0.35278,-0.9274,-0.12442,340.27,-0.78005,0.21805,0.5865,136.72,-0.51679,0.30396,-0.80034,288.45
    3048 
    3049 > fitmap #30.4 inMap #1
    3050 
    3051 Fit map W20_J145_run_ct8_body004.mrc in map
    3052 W20_J3623_consensus_structure_sharp.mrc using 137951 points 
    3053 correlation = 0.7282, correlation about mean = 0.4288, overlap = 228.8 
    3054 steps = 112, shift = 11.5, angle = 9.2 degrees 
    3055  
    3056 Position of W20_J145_run_ct8_body004.mrc (#30.4) relative to
    3057 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3058 Matrix rotation and translation 
    3059 0.98788522 -0.14632868 -0.05167889 26.91126566 
    3060 0.14822194 0.98833778 0.03490982 -21.95721425 
    3061 0.04596789 -0.04214685 0.99805340 -1.50223115 
    3062 Axis -0.24099906 -0.30539579 0.92122357 
    3063 Axis point 163.78780037 168.43265871 0.00000000 
    3064 Rotation angle (degrees) 9.19930630 
    3065 Shift along axis -1.16383962 
    3066  
    3067 
    3068 > fitmap #30.3 inMap #1
    3069 
    3070 Fit map W20_J145_run_ct8_body003.mrc in map
    3071 W20_J3623_consensus_structure_sharp.mrc using 137543 points 
    3072 correlation = 0.6493, correlation about mean = 0.3323, overlap = 237.6 
    3073 steps = 116, shift = 8.58, angle = 1.99 degrees 
    3074  
    3075 Position of W20_J145_run_ct8_body003.mrc (#30.3) relative to
    3076 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3077 Matrix rotation and translation 
    3078 0.99943608 -0.00513122 -0.03318412 -0.25293108 
    3079 0.00484442 0.99995027 -0.00871730 -4.33467984 
    3080 0.03322720 0.00855163 0.99941124 -5.67738477 
    3081 Axis 0.24904308 -0.95774784 0.14386320 
    3082 Axis point 184.40566041 0.00000000 -35.31005024 
    3083 Rotation angle (degrees) 1.98687515 
    3084 Shift along axis 3.27177278 
    3085  
    3086 
    3087 > fitmap #30.2 inMap #1
    3088 
    3089 Fit map W20_J145_run_ct8_body002.mrc in map
    3090 W20_J3623_consensus_structure_sharp.mrc using 137963 points 
    3091 correlation = 0.8212, correlation about mean = 0.6198, overlap = 468.2 
    3092 steps = 92, shift = 7.64, angle = 3.06 degrees 
    3093  
    3094 Position of W20_J145_run_ct8_body002.mrc (#30.2) relative to
    3095 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3096 Matrix rotation and translation 
    3097 0.99870570 0.02334084 -0.04519002 -1.99430024 
    3098 -0.02260011 0.99960285 0.01683358 -2.36740438 
    3099 0.04556498 -0.01579049 0.99883657 -3.32045770 
    3100 Axis -0.30540022 -0.84957484 -0.43006196 
    3101 Axis point 34.20968149 0.00000000 -17.75195541 
    3102 Rotation angle (degrees) 3.06173952 
    3103 Shift along axis 4.04834949 
    3104  
    3105 
    3106 > fitmap #30.1 inMap #1
    3107 
    3108 Fit map W20_J145_run_ct8_body001.mrc in map
    3109 W20_J3623_consensus_structure_sharp.mrc using 138203 points 
    3110 correlation = 0.9153, correlation about mean = 0.7173, overlap = 857.4 
    3111 steps = 84, shift = 6.27, angle = 2.89 degrees 
    3112  
    3113 Position of W20_J145_run_ct8_body001.mrc (#30.1) relative to
    3114 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3115 Matrix rotation and translation 
    3116 0.99917915 0.02581546 -0.03121838 -4.27539402 
    3117 -0.02486602 0.99922761 0.03042809 -4.63326697 
    3118 0.03197979 -0.02962683 0.99904932 0.16478454 
    3119 Axis -0.59553173 -0.62670160 -0.50258041 
    3120 Axis point -90.45500707 0.00000000 -32.19034476 
    3121 Rotation angle (degrees) 2.89015105 
    3122 Shift along axis 5.36699111 
    3123  
    3124 
    3125 > color #30 darkgrey models
    3126 
    3127 > color #30 #a9a9a980 models
    3128 
    3129 > select subtract #30
    3130 
    3131 Nothing selected 
    3132 
    3133 > hide #!30 models
    3134 
    3135 > rename #30 W20_J145_MB
    3136 
    3137 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3138 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body001.mrc"
    3139 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3140 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body002.mrc"
    3141 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3142 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body003.mrc"
    3143 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3144 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body004.mrc"
    3145 
    3146 Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
    3147 shown at level 0.0066, step 1, values float32 
    3148 Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
    3149 shown at level 0.0013, step 1, values float32 
    3150 Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
    3151 shown at level 0.000798, step 1, values float32 
    3152 Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
    3153 shown at level 0.000426, step 1, values float32 
    3154 
    3155 > select add #31
    3156 
    3157 9 models selected 
    3158 
    3159 > ui mousemode right "rotate selected models"
    3160 
    3161 > view matrix models
    3162 > #31,0.62778,0.15918,-0.76194,138.56,0.19756,0.91423,0.35377,-64.97,0.7529,-0.37262,0.54248,29.724
    3163 
    3164 > view matrix models
    3165 > #31,-0.3321,-0.94322,0.0062597,329.8,-0.75269,0.269,0.60092,127.95,-0.56848,0.19485,-0.79929,311.9
    3166 
    3167 > ui mousemode right "translate selected models"
    3168 
    3169 > view matrix models
    3170 > #31,-0.3321,-0.94322,0.0062597,332.22,-0.75269,0.269,0.60092,127.27,-0.56848,0.19485,-0.79929,317.96
    3171 
    3172 > fitmap #31.1 inMap #1
    3173 
    3174 Fit map W20_J150_run_body001.mrc in map
    3175 W20_J3623_consensus_structure_sharp.mrc using 138218 points 
    3176 correlation = 0.9172, correlation about mean = 0.7038, overlap = 893.5 
    3177 steps = 88, shift = 6.98, angle = 8.67 degrees 
    3178  
    3179 Position of W20_J150_run_body001.mrc (#31.1) relative to
    3180 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3181 Matrix rotation and translation 
    3182 0.99964242 -0.02165534 0.01568687 5.92000022 
    3183 0.01908723 0.98871756 0.14857073 -17.88200850 
    3184 -0.01872723 -0.14821819 0.98877736 29.33526708 
    3185 Axis -0.98423540 0.11412684 0.13511379 
    3186 Axis point 0.00000000 191.49090363 131.90319589 
    3187 Rotation angle (degrees) 8.67162751 
    3188 Shift along axis -3.90389179 
    3189  
    3190 
    3191 > fitmap #31.2 inMap #1
    3192 
    3193 Fit map W20_J150_run_body002.mrc in map
    3194 W20_J3623_consensus_structure_sharp.mrc using 138140 points 
    3195 correlation = 0.8053, correlation about mean = 0.5992, overlap = 456.9 
    3196 steps = 116, shift = 12.3, angle = 8.44 degrees 
    3197  
    3198 Position of W20_J150_run_body002.mrc (#31.2) relative to
    3199 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3200 Matrix rotation and translation 
    3201 0.99987004 -0.01303295 0.00948916 5.64171510 
    3202 0.01150966 0.98923255 0.14589889 -15.99717561 
    3203 -0.01128848 -0.14577072 0.98925400 27.73858221 
    3204 Axis -0.99397729 0.07080790 0.08363845 
    3205 Axis point 0.00000000 183.90016756 121.07225767 
    3206 Rotation angle (degrees) 8.43680332 
    3207 Shift along axis -4.42045109 
    3208  
    3209 
    3210 > fitmap #31.3 inMap #1
    3211 
    3212 Fit map W20_J150_run_body003.mrc in map
    3213 W20_J3623_consensus_structure_sharp.mrc using 137514 points 
    3214 correlation = 0.6146, correlation about mean = 0.266, overlap = 238.9 
    3215 steps = 124, shift = 9.37, angle = 6.56 degrees 
    3216  
    3217 Position of W20_J150_run_body003.mrc (#31.3) relative to
    3218 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3219 Matrix rotation and translation 
    3220 0.99927585 -0.03094085 0.02214582 5.52526341 
    3221 0.02837142 0.99372585 0.10818506 -14.70532330 
    3222 -0.02535421 -0.10747841 0.99388408 23.92950955 
    3223 Axis -0.94316639 0.20773307 0.25939184 
    3224 Axis point 0.00000000 219.38003792 144.69692071 
    3225 Rotation angle (degrees) 6.56495264 
    3226 Shift along axis -2.05890526 
    3227  
    3228 
    3229 > fitmap #31.4 inMap #1
    3230 
    3231 Fit map W20_J150_run_body004.mrc in map
    3232 W20_J3623_consensus_structure_sharp.mrc using 137710 points 
    3233 correlation = 0.7262, correlation about mean = 0.4714, overlap = 200 
    3234 steps = 100, shift = 8.31, angle = 7.56 degrees 
    3235  
    3236 Position of W20_J150_run_body004.mrc (#31.4) relative to
    3237 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3238 Matrix rotation and translation 
    3239 0.99968731 -0.01039845 0.02274087 4.61807189 
    3240 0.00737128 0.99156997 0.12936254 -14.95364310 
    3241 -0.02389433 -0.12915446 0.99133656 25.99366724 
    3242 Axis -0.98187156 0.17712480 0.06749108 
    3243 Axis point 0.00000000 195.98514242 120.93339845 
    3244 Rotation angle (degrees) 7.56466213 
    3245 Shift along axis -5.42867381 
    3246  
    3247 
    3248 > color #31 darkgrey models
    3249 
    3250 > color #31 #a9a9a980 models
    3251 
    3252 > select subtract #31
    3253 
    3254 Nothing selected 
    3255 
    3256 > hide #!31 models
    3257 
    3258 > rename #31 W20_J150_MB
    3259 
    3260 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3261 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body001.mrc"
    3262 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3263 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body002.mrc"
    3264 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3265 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body003.mrc"
    3266 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3267 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body004.mrc"
    3268 
    3269 Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
    3270 1.2, shown at level 0.0064, step 1, values float32 
    3271 Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
    3272 1.2, shown at level 0.00156, step 1, values float32 
    3273 Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
    3274 1.2, shown at level 0.000666, step 1, values float32 
    3275 Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
    3276 1.2, shown at level 0.000439, step 1, values float32 
    3277 
    3278 > select add #32
    3279 
    3280 9 models selected 
    3281 
    3282 > ui mousemode right "rotate selected models"
    3283 
    3284 > view matrix models
    3285 > #32,-0.094929,-0.99244,0.07775,390.6,-0.44492,0.11217,0.88852,96.076,-0.89053,0.049754,-0.45221,395
    3286 
    3287 > ui mousemode right "translate selected models"
    3288 
    3289 > view matrix models
    3290 > #32,-0.094929,-0.99244,0.07775,372.3,-0.44492,0.11217,0.88852,92.438,-0.89053,0.049754,-0.45221,335.63
    3291 
    3292 > ui mousemode right "translate selected models"
    3293 
    3294 > view matrix models
    3295 > #32,-0.094929,-0.99244,0.07775,368.31,-0.44492,0.11217,0.88852,91.761,-0.89053,0.049754,-0.45221,322.87
    3296 
    3297 > ui mousemode right "rotate selected models"
    3298 
    3299 > view matrix models
    3300 > #32,0.24986,-0.92724,-0.27892,355.61,-0.7966,-0.36061,0.48518,310.1,-0.55046,0.10096,-0.82874,322.22
    3301 
    3302 > ui mousemode right "translate selected models"
    3303 
    3304 > view matrix models
    3305 > #32,0.24986,-0.92724,-0.27892,326.75,-0.7966,-0.36061,0.48518,243.97,-0.55046,0.10096,-0.82874,318.12
    3306 
    3307 > ui mousemode right "rotate selected models"
    3308 
    3309 > view matrix models
    3310 > #32,0.049187,-0.95013,-0.30796,371.28,-0.76011,-0.23563,0.60556,193.56,-0.64792,0.2043,-0.7338,299.66
    3311 
    3312 > view matrix models
    3313 > #32,-0.38216,-0.71778,-0.58202,446.74,-0.57887,-0.30499,0.75623,147.95,-0.72032,0.62591,-0.29895,168.04
    3314 
    3315 > view matrix models
    3316 > #32,-0.12174,-0.98206,-0.14398,378.68,-0.79719,0.01032,0.60364,153.76,-0.59133,0.18827,-0.78414,308.73
    3317 
    3318 > ui mousemode right "translate selected models"
    3319 
    3320 > view matrix models
    3321 > #32,-0.12174,-0.98206,-0.14398,339.88,-0.79719,0.01032,0.60364,183.81,-0.59133,0.18827,-0.78414,311.67
    3322 
    3323 > view matrix models
    3324 > #32,-0.12174,-0.98206,-0.14398,341.73,-0.79719,0.01032,0.60364,179.24,-0.59133,0.18827,-0.78414,317.95
    3325 
    3326 > fitmap #32.4 inMap #1
    3327 
    3328 Fit map W20_J155_run_ct6_body004.mrc in map
    3329 W20_J3623_consensus_structure_sharp.mrc using 137851 points 
    3330 correlation = 0.7818, correlation about mean = 0.5257, overlap = 192.1 
    3331 steps = 124, shift = 4.21, angle = 14.8 degrees 
    3332  
    3333 Position of W20_J155_run_ct6_body004.mrc (#32.4) relative to
    3334 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3335 Matrix rotation and translation 
    3336 0.96755911 -0.24974155 0.03819070 46.04596253 
    3337 0.24817341 0.96782709 0.04148106 -19.98854272 
    3338 -0.04732154 -0.03065746 0.99840913 9.25104536 
    3339 Axis -0.14135691 0.16756298 0.97567457 
    3340 Axis point 102.10235956 170.64051821 0.00000000 
    3341 Rotation angle (degrees) 14.78333075 
    3342 Shift along axis -0.83224502 
    3343  
    3344 
    3345 > fitmap #32.3 inMap #1
    3346 
    3347 Fit map W20_J155_run_ct6_body003.mrc in map
    3348 W20_J3623_consensus_structure_sharp.mrc using 137790 points 
    3349 correlation = 0.5288, correlation about mean = 0.2458, overlap = 222.1 
    3350 steps = 212, shift = 24.3, angle = 25.3 degrees 
    3351  
    3352 Position of W20_J155_run_ct6_body003.mrc (#32.3) relative to
    3353 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3354 Matrix rotation and translation 
    3355 0.96236345 -0.02996556 0.27010858 -46.55042113 
    3356 -0.06370212 0.94133951 0.33139398 -51.24613942 
    3357 -0.26419429 -0.33612794 0.90400187 97.79261178 
    3358 Axis -0.78009899 0.62441264 -0.03942621 
    3359 Axis point 0.00000000 234.71472833 197.05127274 
    3360 Rotation angle (degrees) 25.33083616 
    3361 Shift along axis 0.45960726 
    3362  
    3363 
    3364 > fitmap #32.2 inMap #1
    3365 
    3366 Fit map W20_J155_run_ct6_body002.mrc in map
    3367 W20_J3623_consensus_structure_sharp.mrc using 138167 points 
    3368 correlation = 0.8427, correlation about mean = 0.6574, overlap = 508.2 
    3369 steps = 200, shift = 28.2, angle = 13.9 degrees 
    3370  
    3371 Position of W20_J155_run_ct6_body002.mrc (#32.2) relative to
    3372 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3373 Matrix rotation and translation 
    3374 0.97079416 -0.23981830 0.00677387 48.62036376 
    3375 0.23979745 0.97081570 0.00375114 -13.12837058 
    3376 -0.00747577 -0.00201723 0.99997002 1.33700507 
    3377 Axis -0.01202088 0.02969530 0.99948671 
    3378 Axis point 78.30820657 193.21986153 0.00000000 
    3379 Rotation angle (degrees) 13.88246944 
    3380 Shift along axis 0.36200848 
    3381  
    3382 
    3383 > fitmap #32.1 inMap #1
    3384 
    3385 Fit map W20_J155_run_ct6_body001.mrc in map
    3386 W20_J3623_consensus_structure_sharp.mrc using 138158 points 
    3387 correlation = 0.9152, correlation about mean = 0.7176, overlap = 887.9 
    3388 steps = 240, shift = 17.9, angle = 14.3 degrees 
    3389  
    3390 Position of W20_J155_run_ct6_body001.mrc (#32.1) relative to
    3391 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3392 Matrix rotation and translation 
    3393 0.96918769 -0.24592134 0.01406818 48.78106404 
    3394 0.24563656 0.96916974 0.01930526 -16.53168875 
    3395 -0.01838203 -0.01525477 0.99971466 4.87447888 
    3396 Axis -0.06998243 0.06571014 0.99538165 
    3397 Axis point 90.87557164 187.07445802 0.00000000 
    3398 Rotation angle (degrees) 14.29528730 
    3399 Shift along axis 0.35184982 
    3400  
    3401 
    3402 > select add #32.3
    3403 
    3404 9 models selected 
    3405 
    3406 > select subtract #32
    3407 
    3408 Nothing selected 
    3409 
    3410 > select subtract #32.3
    3411 
    3412 Nothing selected 
    3413 
    3414 > select add #32.3
    3415 
    3416 2 models selected 
    3417 
    3418 > view matrix models
    3419 > #32.3,0.96236,-0.029966,0.27011,-49.146,-0.063702,0.94134,0.33139,-16.537,-0.26419,-0.33613,0.904,117.55
    3420 
    3421 > fitmap #32.3 inMap #1
    3422 
    3423 Fit map W20_J155_run_ct6_body003.mrc in map
    3424 W20_J3623_consensus_structure_sharp.mrc using 137790 points 
    3425 correlation = 0.5773, correlation about mean = 0.2332, overlap = 255.7 
    3426 steps = 220, shift = 22.6, angle = 31.2 degrees 
    3427  
    3428 Position of W20_J155_run_ct6_body003.mrc (#32.3) relative to
    3429 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3430 Matrix rotation and translation 
    3431 0.93701301 -0.34494790 0.05493240 55.45886688 
    3432 0.34457856 0.93861493 0.01635939 -26.98464957 
    3433 -0.05720351 0.00359956 0.99835605 3.33562233 
    3434 Axis -0.01826220 0.16049183 0.98686821 
    3435 Axis point 102.63951914 141.92416208 0.00000000 
    3436 Rotation angle (degrees) 20.44761418 
    3437 Shift along axis -2.05179723 
    3438  
    3439 
    3440 > select subtract #32.3
    3441 
    3442 Nothing selected 
    3443 
    3444 > color #32 #929292ff models
    3445 
    3446 > color #32 #9292927d models
    3447 
    3448 > hide #!32 models
    3449 
    3450 > rename #32 W20_J155_MB
    3451 
    3452 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3453 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body001.mrc"
    3454 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3455 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body002.mrc"
    3456 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3457 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body003.mrc"
    3458 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3459 > resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body004.mrc"
    3460 
    3461 Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
    3462 1.2, shown at level 0.00725, step 1, values float32 
    3463 Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
    3464 1.2, shown at level 0.00154, step 1, values float32 
    3465 Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
    3466 1.2, shown at level 0.000864, step 1, values float32 
    3467 Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
    3468 1.2, shown at level 0.000379, step 1, values float32 
    3469 
    3470 > select add #33
    3471 
    3472 9 models selected 
    3473 
    3474 > ui mousemode right "rotate selected models"
    3475 
    3476 > view matrix models
    3477 > #33,0.31873,-0.82608,0.46476,171.28,-0.72157,0.10647,0.6841,150.82,-0.6146,-0.5534,-0.56214,456.98
    3478 
    3479 > view matrix models
    3480 > #33,-0.036679,-0.99898,-0.026385,337.23,-0.84584,0.016974,0.53317,211.08,-0.53218,0.041873,-0.8456,383.69
    3481 
    3482 > ui mousemode right "translate selected models"
    3483 
    3484 > view matrix models
    3485 > #33,-0.036679,-0.99898,-0.026385,334.88,-0.84584,0.016974,0.53317,195.64,-0.53218,0.041873,-0.8456,333.69
    3486 
    3487 > view matrix models
    3488 > #33,-0.036679,-0.99898,-0.026385,313.34,-0.84584,0.016974,0.53317,188.83,-0.53218,0.041873,-0.8456,328.42
    3489 
    3490 > view matrix models
    3491 > #33,-0.036679,-0.99898,-0.026385,311.41,-0.84584,0.016974,0.53317,189.7,-0.53218,0.041873,-0.8456,344.34
    3492 
    3493 > ui mousemode right "rotate selected models"
    3494 
    3495 > view matrix models
    3496 > #33,-0.35879,-0.93341,-0.0038469,340.33,-0.80584,0.30767,0.50593,135.86,-0.47106,0.18462,-0.86256,313.27
    3497 
    3498 > ui mousemode right "translate selected models"
    3499 
    3500 > view matrix models
    3501 > #33,-0.35879,-0.93341,-0.0038469,338.34,-0.80584,0.30767,0.50593,141.61,-0.47106,0.18462,-0.86256,318.7
    3502 
    3503 > fitmap #33.3 inMap #1
    3504 
    3505 Fit map W20_J160_run_ct6_body003.mrc in map
    3506 W20_J3623_consensus_structure_sharp.mrc using 137937 points 
    3507 correlation = 0.5867, correlation about mean = 0.2346, overlap = 250.3 
    3508 steps = 140, shift = 11.6, angle = 7.35 degrees 
    3509  
    3510 Position of W20_J160_run_ct6_body003.mrc (#33.3) relative to
    3511 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3512 Matrix rotation and translation 
    3513 0.99303756 0.05988139 0.10144267 -23.49545369 
    3514 -0.06488899 0.99679433 0.04680249 14.70011589 
    3515 -0.09831488 -0.05305914 0.99373986 28.54412294 
    3516 Axis -0.39036137 0.78085672 -0.48773024 
    3517 Axis point 309.26276930 0.00000000 226.94693512 
    3518 Rotation angle (degrees) 7.34879054 
    3519 Shift along axis 6.72856998 
    3520  
    3521 
    3522 > fitmap #33.2 inMap #1
    3523 
    3524 Fit map W20_J160_run_ct6_body002.mrc in map
    3525 W20_J3623_consensus_structure_sharp.mrc using 137991 points 
    3526 correlation = 0.819, correlation about mean = 0.6067, overlap = 480.4 
    3527 steps = 144, shift = 18.2, angle = 13.8 degrees 
    3528  
    3529 Position of W20_J160_run_ct6_body002.mrc (#33.2) relative to
    3530 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3531 Matrix rotation and translation 
    3532 0.99771963 -0.01489642 -0.06583042 17.27645423 
    3533 0.02956838 0.97323369 0.22790766 -26.83710836 
    3534 0.06067337 -0.22933444 0.97145481 35.68296509 
    3535 Axis -0.95958803 -0.26548631 0.09331575 
    3536 Axis point 0.00000000 140.48687556 141.38690851 
    3537 Rotation angle (degrees) 13.78322772 
    3538 Shift along axis -6.12361124 
    3539  
    3540 
    3541 > fitmap #33.1 inMap #1
    3542 
    3543 Fit map W20_J160_run_ct6_body001.mrc in map
    3544 W20_J3623_consensus_structure_sharp.mrc using 138219 points 
    3545 correlation = 0.9149, correlation about mean = 0.7061, overlap = 905.5 
    3546 steps = 240, shift = 9.92, angle = 13.4 degrees 
    3547  
    3548 Position of W20_J160_run_ct6_body001.mrc (#33.1) relative to
    3549 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3550 Matrix rotation and translation 
    3551 0.99744755 -0.02103927 -0.06823292 18.77482829 
    3552 0.03561801 0.97482901 0.22009032 -27.49182319 
    3553 0.06188489 -0.22195888 0.97309019 34.85093721 
    3554 Axis -0.95213476 -0.28026222 0.12203477 
    3555 Axis point 0.00000000 142.23926756 148.71521434 
    3556 Rotation angle (degrees) 13.42285005 
    3557 Shift along axis -5.91822131 
    3558  
    3559 
    3560 > fitmap #33.4 inMap #1
    3561 
    3562 Fit map W20_J160_run_ct6_body004.mrc in map
    3563 W20_J3623_consensus_structure_sharp.mrc using 137797 points 
    3564 correlation = 0.7345, correlation about mean = 0.436, overlap = 185.3 
    3565 steps = 144, shift = 10.1, angle = 13 degrees 
    3566  
    3567 Position of W20_J160_run_ct6_body004.mrc (#33.4) relative to
    3568 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    3569 Matrix rotation and translation 
    3570 0.99800988 0.00249027 -0.06300862 14.90861204 
    3571 0.01124609 0.97617108 0.21671073 -24.80457915 
    3572 0.06204686 -0.21698805 0.97420038 33.68609528 
    3573 Axis -0.96067232 -0.27700640 0.01939474 
    3574 Axis point 0.00000000 139.38706533 138.47533972 
    3575 Rotation angle (degrees) 13.04561440 
    3576 Shift along axis -6.79793059 
    3577  
    3578 
    3579 > select subtract #33
    3580 
    3581 Nothing selected 
    3582 
    3583 > color #33 #929292ff models
    3584 
    3585 > color #33 #92929280 models
    3586 
    3587 > hide #!33 models
    3588 
    3589 > rename #33 W20_J160_MB
    3590 
    3591 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    3592 > resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
    3593 
    3594 ——— End of log from Tue Jul 1 13:02:54 2025 ———
    3595 
    3596 opened ChimeraX session 
    3597 
    3598 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    3599 > files/alphafold/CopA-F8WHL2.pdb"
    3600 
    3601 CopA-F8WHL2.pdb title: 
    3602 Alphafold monomer V2.0 prediction for coatomer subunit α (F8WHL2) [more
    3603 info...] 
    3604  
    3605 Chain information for CopA-F8WHL2.pdb #34 
    3606 --- 
    3607 Chain | Description | UniProt 
    3608 A | coatomer subunit α | F8WHL2_MOUSE 1-1233 
    3609  
    3610 Computing secondary structure 
    3611 
    3612 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    3613 > files/alphafold/CopB_ Q9JIF7.pdb"
    3614 
    3615 CopB_ Q9JIF7.pdb title: 
    3616 Alphafold monomer V2.0 prediction for coatomer subunit β (Q9JIF7) [more
    3617 info...] 
    3618  
    3619 Chain information for CopB_ Q9JIF7.pdb #35 
    3620 --- 
    3621 Chain | Description | UniProt 
    3622 A | coatomer subunit β | COPB_MOUSE 1-953 
    3623  
    3624 Computing secondary structure 
    3625 
    3626 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    3627 > files/alphafold/CopBprime_O55029.pdb"
    3628 
    3629 CopBprime_O55029.pdb title: 
    3630 Alphafold monomer V2.0 prediction for coatomer subunit β' (O55029) [more
    3631 info...] 
    3632  
    3633 Chain information for CopBprime_O55029.pdb #36 
    3634 --- 
    3635 Chain | Description | UniProt 
    3636 A | coatomer subunit β' | COPB2_MOUSE 1-905 
    3637  
    3638 Computing secondary structure 
    3639 
    3640 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    3641 > files/alphafold/CopD_full_Q5XJY5.pdb"
    3642 
    3643 CopD_full_Q5XJY5.pdb title: 
    3644 Alphafold monomer V2.0 prediction for coatomer subunit δ (Q5XJY5) [more
    3645 info...] 
    3646  
    3647 Chain information for CopD_full_Q5XJY5.pdb #37 
    3648 --- 
    3649 Chain | Description | UniProt 
    3650 A | coatomer subunit δ | COPD_MOUSE 1-511 
    3651  
    3652 Computing secondary structure 
    3653 
    3654 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    3655 > files/alphafold/CopG1_ Q9QZE5.pdb"
    3656 
    3657 CopG1_ Q9QZE5.pdb title: 
    3658 Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
    3659 info...] 
    3660  
    3661 Chain information for CopG1_ Q9QZE5.pdb #38 
    3662 --- 
    3663 Chain | Description | UniProt 
    3664 A | coatomer subunit γ-1 | COPG1_MOUSE 1-874 
    3665  
    3666 Computing secondary structure 
    3667 
    3668 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    3669 > files/alphafold/CopG1_ Q9QZE5.pdb"
    3670 
    3671 CopG1_ Q9QZE5.pdb title: 
    3672 Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
    3673 info...] 
    3674  
    3675 Chain information for CopG1_ Q9QZE5.pdb #39 
    3676 --- 
    3677 Chain | Description | UniProt 
    3678 A | coatomer subunit γ-1 | COPG1_MOUSE 1-874 
    3679  
    3680 Computing secondary structure 
    3681 
    3682 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    3683 > files/alphafold/CopZ1_P61924.pdb"
    3684 
    3685 CopZ1_P61924.pdb title: 
    3686 Alphafold monomer V2.0 prediction for coatomer subunit ζ-1 (P61924) [more
    3687 info...] 
    3688  
    3689 Chain information for CopZ1_P61924.pdb #40 
    3690 --- 
    3691 Chain | Description | UniProt 
    3692 A | coatomer subunit ζ-1 | COPZ1_MOUSE 1-177 
    3693  
    3694 Computing secondary structure 
    3695 
    3696 > hide #40 models
    3697 
    3698 > hide #39 models
    3699 
    3700 > hide #38 models
    3701 
    3702 > hide #37 models
    3703 
    3704 > hide #36 models
    3705 
    3706 > hide #35 models
    3707 
    3708 > select add #34
    3709 
    3710 9810 atoms, 10032 bonds, 1233 residues, 1 model selected 
    3711 
    3712 > color list
    3713 
    3714 28 custom colors: alphav1
    3715 
    3716 , alphav2
    3717 
    3718 , alphav3
    3719 
    3720 , arf1v1
    3721 
    3722 , arf1v2
    3723 
    3724 , arf1v3
    3725 
    3726 , betapv1
    3727 
    3728 , betapv2
    3729 
    3730 , betapv3
    3731 
    3732 , betav1
    3733 
    3734 , betav2
    3735 
    3736 , betav3
    3737 
    3738 , deltav1
    3739 
    3740 , deltav2
    3741 
    3742 , deltav3
    3743 
    3744 , epsilonv1
    3745 
    3746 , epsilonv3
    3747 
    3748 , gammav1
    3749 
    3750 , gammav2
    3751 
    3752 , gammav3
    3753 
    3754 , label_purple
    3755 
    3756 , label_purple_v3
    3757 
    3758 , label_red
    3759 
    3760 , label_red_v3
    3761 
    3762 , lable_purple_v4
    3763 
    3764 , zetav1
    3765 
    3766 , zetav2
    3767 
    3768 , and zetav3
    3769 
    3770 . 
    3771 248 builtin colors: alice blue
    3772 
    3773 , aliceblue
    3774 
    3775 , antique white
    3776 
    3777 , antiquewhite
    3778 
    3779 , aqua
    3780 
    3781 , aquamarine
    3782 
    3783 , azure
    3784 
    3785 , beige
    3786 
    3787 , bisque
    3788 
    3789 , black
    3790 
    3791 , blanched almond
    3792 
    3793 , blanchedalmond
    3794 
    3795 , blue
    3796 
    3797 , blue violet
    3798 
    3799 , blueviolet
    3800 
    3801 , brown
    3802 
    3803 , burly wood
    3804 
    3805 , burlywood
    3806 
    3807 , cadet blue
    3808 
    3809 , cadetblue
    3810 
    3811 , chartreuse
    3812 
    3813 , chocolate
    3814 
    3815 , coral
    3816 
    3817 , cornflower blue
    3818 
    3819 , cornflowerblue
    3820 
    3821 , cornsilk
    3822 
    3823 , crimson
    3824 
    3825 , cyan
    3826 
    3827 , dark blue
    3828 
    3829 , dark cyan
    3830 
    3831 , dark goldenrod
    3832 
    3833 , dark gray
    3834 
    3835 , dark green
    3836 
    3837 , dark grey
    3838 
    3839 , dark khaki
    3840 
    3841 , dark magenta
    3842 
    3843 , dark olive green
    3844 
    3845 , dark orange
    3846 
    3847 , dark orchid
    3848 
    3849 , dark red
    3850 
    3851 , dark salmon
    3852 
    3853 , dark sea green
    3854 
    3855 , dark seagreen
    3856 
    3857 , dark slate blue
    3858 
    3859 , dark slate gray
    3860 
    3861 , dark slate grey
    3862 
    3863 , dark turquoise
    3864 
    3865 , dark violet
    3866 
    3867 , darkblue
    3868 
    3869 , darkcyan
    3870 
    3871 , darkgoldenrod
    3872 
    3873 , darkgray
    3874 
    3875 , darkgreen
    3876 
    3877 , darkgrey
    3878 
    3879 , darkkhaki
    3880 
    3881 , darkmagenta
    3882 
    3883 , darkolivegreen
    3884 
    3885 , darkorange
    3886 
    3887 , darkorchid
    3888 
    3889 , darkred
    3890 
    3891 , darksalmon
    3892 
    3893 , darkseagreen
    3894 
    3895 , darkslateblue
    3896 
    3897 , darkslategray
    3898 
    3899 , darkslategrey
    3900 
    3901 , darkturquoise
    3902 
    3903 , darkviolet
    3904 
    3905 , deep pink
    3906 
    3907 , deep sky blue
    3908 
    3909 , deep skyblue
    3910 
    3911 , deeppink
    3912 
    3913 , deepskyblue
    3914 
    3915 , dim gray
    3916 
    3917 , dim grey
    3918 
    3919 , dimgray
    3920 
    3921 , dimgrey
    3922 
    3923 , dodger blue
    3924 
    3925 , dodgerblue
    3926 
    3927 , fire brick
    3928 
    3929 , firebrick
    3930 
    3931 , floral white
    3932 
    3933 , floralwhite
    3934 
    3935 , forest green
    3936 
    3937 , forestgreen
    3938 
    3939 , fuchsia
    3940 
    3941 , gainsboro
    3942 
    3943 , ghost white
    3944 
    3945 , ghostwhite
    3946 
    3947 , gold
    3948 
    3949 , goldenrod
    3950 
    3951 , gray
    3952 
    3953 , green
    3954 
    3955 , green yellow
    3956 
    3957 , greenyellow
    3958 
    3959 , grey
    3960 
    3961 , honeydew
    3962 
    3963 , hot pink
    3964 
    3965 , hotpink
    3966 
    3967 , indian red
    3968 
    3969 , indianred
    3970 
    3971 , indigo
    3972 
    3973 , ivory
    3974 
    3975 , khaki
    3976 
    3977 , lavender
    3978 
    3979 , lavender blush
    3980 
    3981 , lavenderblush
    3982 
    3983 , lawn green
    3984 
    3985 , lawngreen
    3986 
    3987 , lemon chiffon
    3988 
    3989 , lemonchiffon
    3990 
    3991 , light blue
    3992 
    3993 , light coral
    3994 
    3995 , light cyan
    3996 
    3997 , light goldenrod yellow
    3998 
    3999 , light gray
    4000 
    4001 , light green
    4002 
    4003 , light grey
    4004 
    4005 , light pink
    4006 
    4007 , light salmon
    4008 
    4009 , light sea green
    4010 
    4011 , light seagreen
    4012 
    4013 , light sky blue
    4014 
    4015 , light skyblue
    4016 
    4017 , light slate gray
    4018 
    4019 , light slate grey
    4020 
    4021 , light steel blue
    4022 
    4023 , light yellow
    4024 
    4025 , lightblue
    4026 
    4027 , lightcoral
    4028 
    4029 , lightcyan
    4030 
    4031 , lightgoldenrodyellow
    4032 
    4033 , lightgray
    4034 
    4035 , lightgreen
    4036 
    4037 , lightgrey
    4038 
    4039 , lightpink
    4040 
    4041 , lightsalmon
    4042 
    4043 , lightseagreen
    4044 
    4045 , lightskyblue
    4046 
    4047 , lightslategray
    4048 
    4049 , lightslategrey
    4050 
    4051 , lightsteelblue
    4052 
    4053 , lightyellow
    4054 
    4055 , lime
    4056 
    4057 , lime green
    4058 
    4059 , limegreen
    4060 
    4061 , linen
    4062 
    4063 , magenta
    4064 
    4065 , maroon
    4066 
    4067 , medium aquamarine
    4068 
    4069 , medium blue
    4070 
    4071 , medium orchid
    4072 
    4073 , medium purple
    4074 
    4075 , medium sea green
    4076 
    4077 , medium seagreen
    4078 
    4079 , medium slate blue
    4080 
    4081 , medium spring green
    4082 
    4083 , medium turquoise
    4084 
    4085 , medium violet red
    4086 
    4087 , mediumaquamarine
    4088 
    4089 , mediumblue
    4090 
    4091 , mediumorchid
    4092 
    4093 , mediumpurple
    4094 
    4095 , mediumseagreen
    4096 
    4097 , mediumslateblue
    4098 
    4099 , mediumspringgreen
    4100 
    4101 , mediumturquoise
    4102 
    4103 , mediumvioletred
    4104 
    4105 , midnight blue
    4106 
    4107 , midnightblue
    4108 
    4109 , mint cream
    4110 
    4111 , mintcream
    4112 
    4113 , misty rose
    4114 
    4115 , mistyrose
    4116 
    4117 , moccasin
    4118 
    4119 , navajo white
    4120 
    4121 , navajowhite
    4122 
    4123 , navy
    4124 
    4125 , old lace
    4126 
    4127 , oldlace
    4128 
    4129 , olive
    4130 
    4131 , olive drab
    4132 
    4133 , olivedrab
    4134 
    4135 , orange
    4136 
    4137 , orange red
    4138 
    4139 , orangered
    4140 
    4141 , orchid
    4142 
    4143 , pale goldenrod
    4144 
    4145 , pale green
    4146 
    4147 , pale turquoise
    4148 
    4149 , pale violet red
    4150 
    4151 , palegoldenrod
    4152 
    4153 , palegreen
    4154 
    4155 , paleturquoise
    4156 
    4157 , palevioletred
    4158 
    4159 , papaya whip
    4160 
    4161 , papayawhip
    4162 
    4163 , peach puff
    4164 
    4165 , peachpuff
    4166 
    4167 , peru
    4168 
    4169 , pink
    4170 
    4171 , plum
    4172 
    4173 , powder blue
    4174 
    4175 , powderblue
    4176 
    4177 , purple
    4178 
    4179 , rebecca purple
    4180 
    4181 , rebeccapurple
    4182 
    4183 , red
    4184 
    4185 , rosy brown
    4186 
    4187 , rosybrown
    4188 
    4189 , royal blue
    4190 
    4191 , royalblue
    4192 
    4193 , saddle brown
    4194 
    4195 , saddlebrown
    4196 
    4197 , salmon
    4198 
    4199 , sandy brown
    4200 
    4201 , sandybrown
    4202 
    4203 , sea green
    4204 
    4205 , seagreen
    4206 
    4207 , seashell
    4208 
    4209 , sienna
    4210 
    4211 , silver
    4212 
    4213 , sky blue
    4214 
    4215 , skyblue
    4216 
    4217 , slate blue
    4218 
    4219 , slate gray
    4220 
    4221 , slate grey
    4222 
    4223 , slateblue
    4224 
    4225 , slategray
    4226 
    4227 , slategrey
    4228 
    4229 , snow
    4230 
    4231 , spring green
    4232 
    4233 , springgreen
    4234 
    4235 , steel blue
    4236 
    4237 , steelblue
    4238 
    4239 , tan
    4240 
    4241 , teal
    4242 
    4243 , thistle
    4244 
    4245 , tomato
    4246 
    4247 , transparent
    4248 
    4249 , turquoise
    4250 
    4251 , violet
    4252 
    4253 , wheat
    4254 
    4255 , white
    4256 
    4257 , white smoke
    4258 
    4259 , whitesmoke
    4260 
    4261 , yellow
    4262 
    4263 , yellow green
    4264 
    4265 , and yellowgreen
    4266 
    4267 . 
    4268 
    4269 > color sel navy
    4270 
    4271 > select subtract #34
    4272 
    4273 Nothing selected 
    4274 
    4275 > hide #34 models
    4276 
    4277 > show #35 models
    4278 
    4279 > select add #35
    4280 
    4281 7501 atoms, 7619 bonds, 953 residues, 1 model selected 
    4282 
    4283 > color sel betav1
    4284 
    4285 > select subtract #35
    4286 
    4287 Nothing selected 
    4288 
    4289 > hide #35 models
    4290 
    4291 > show #36 models
    4292 
    4293 > select add #36
    4294 
    4295 7214 atoms, 7373 bonds, 905 residues, 1 model selected 
    4296 
    4297 > color sel betapv2
    4298 
    4299 > color sel betapv3
    4300 
    4301 > select subtract #36
    4302 
    4303 Nothing selected 
    4304 
    4305 > hide #36 models
    4306 
    4307 > show #37 models
    4308 
    4309 > select add #37
    4310 
    4311 4014 atoms, 4083 bonds, 511 residues, 1 model selected 
    4312 
    4313 > color sel deltav3
    4314 
    4315 > select subtract #37
    4316 
    4317 Nothing selected 
    4318 
    4319 > hide #37 models
    4320 
    4321 > show #38 models
    4322 
    4323 > select add #38
    4324 
    4325 6830 atoms, 6947 bonds, 874 residues, 1 model selected 
    4326 
    4327 > close #39
    4328 
    4329 > close #40
    4330 
    4331 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    4332 > files/alphafold/CopZ1_P61924.pdb"
    4333 
    4334 CopZ1_P61924.pdb title: 
    4335 Alphafold monomer V2.0 prediction for coatomer subunit ζ-1 (P61924) [more
    4336 info...] 
    4337  
    4338 Chain information for CopZ1_P61924.pdb #39 
    4339 --- 
    4340 Chain | Description | UniProt 
    4341 A | coatomer subunit ζ-1 | COPZ1_MOUSE 1-177 
    4342  
    4343 Computing secondary structure 
    4344 
    4345 > hide #39 models
    4346 
    4347 > color sel gammav3
    4348 
    4349 > select subtract #38
    4350 
    4351 Nothing selected 
    4352 
    4353 > hide #38 models
    4354 
    4355 > show #39 models
    4356 
    4357 > select add #39
    4358 
    4359 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    4360 
    4361 > zetav3
    4362 
    4363 Unknown command: zetav3 
    4364 
    4365 > color sel zetav3
    4366 
    4367 > select subtract #39
    4368 
    4369 Nothing selected 
    4370 
    4371 > hide #39 models
    4372 
    4373 > show #34 models
    4374 
    4375 > select add #34
    4376 
    4377 9810 atoms, 10032 bonds, 1233 residues, 1 model selected 
    4378 
    4379 > view matrix models #34,1,0,0,39.828,0,1,0,139.02,0,0,1,198.43
    4380 
    4381 > ui mousemode right "rotate selected models"
    4382 
    4383 > view matrix models
    4384 > #34,0.99004,0.0096002,0.14042,38.534,-0.012281,0.99976,0.018237,138.66,-0.14022,-0.01978,0.98992,196.08
    4385 
    4386 > view matrix models
    4387 > #34,0.13783,-0.38457,0.91275,20.074,-0.096945,0.91188,0.39884,134.94,-0.9857,-0.14346,0.088401,188.13
    4388 
    4389 > view matrix models
    4390 > #34,-0.34037,-0.83282,0.43653,18.135,0.30375,0.34197,0.88926,142.89,-0.88988,0.43527,0.13658,185.25
    4391 
    4392 > ui mousemode right "translate selected models"
    4393 
    4394 > view matrix models
    4395 > #34,-0.34037,-0.83282,0.43653,139.16,0.30375,0.34197,0.88926,104.42,-0.88988,0.43527,0.13658,153.4
    4396 
    4397 > view matrix models
    4398 > #34,-0.34037,-0.83282,0.43653,161.88,0.30375,0.34197,0.88926,148.44,-0.88988,0.43527,0.13658,135.72
    4399 
    4400 > ui mousemode right "rotate selected models"
    4401 
    4402 > view matrix models
    4403 > #34,-0.64868,-0.43267,-0.62611,161.12,0.47729,-0.87206,0.10814,166.41,-0.59279,-0.22869,0.7722,141.4
    4404 
    4405 > ui mousemode right "translate selected models"
    4406 
    4407 > view matrix models
    4408 > #34,-0.64868,-0.43267,-0.62611,149.78,0.47729,-0.87206,0.10814,138.8,-0.59279,-0.22869,0.7722,155.26
    4409 
    4410 > fitmap #34 inMap #1
    4411 
    4412 Fit molecule CopA-F8WHL2.pdb (#34) to map
    4413 W20_J3623_consensus_structure_sharp.mrc (#1) using 9810 atoms 
    4414 average map value = 0.1956, steps = 172 
    4415 shifted from previous position = 12.4 
    4416 rotated from previous position = 16.7 degrees 
    4417 atoms outside contour = 6664, contour level = 0.26383 
    4418  
    4419 Position of CopA-F8WHL2.pdb (#34) relative to
    4420 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4421 Matrix rotation and translation 
    4422 -0.40275740 -0.50265546 -0.76493398 155.53344658 
    4423 0.55537393 -0.79849851 0.23229283 137.87047167 
    4424 -0.72756189 -0.33126673 0.60076291 143.99545516 
    4425 Axis -0.46989046 -0.03116049 0.88217458 
    4426 Axis point 89.79461102 105.24732460 0.00000000 
    4427 Rotation angle (degrees) 143.15364698 
    4428 Shift along axis 49.64933605 
    4429  
    4430 
    4431 > view matrix models
    4432 > #34,-0.40276,-0.50266,-0.76493,152.08,0.55537,-0.7985,0.23229,129.79,-0.72756,-0.33127,0.60076,131.15
    4433 
    4434 > fitmap #34 inMap #1
    4435 
    4436 Fit molecule CopA-F8WHL2.pdb (#34) to map
    4437 W20_J3623_consensus_structure_sharp.mrc (#1) using 9810 atoms 
    4438 average map value = 0.3026, steps = 204 
    4439 shifted from previous position = 8.55 
    4440 rotated from previous position = 12.6 degrees 
    4441 atoms outside contour = 4835, contour level = 0.26383 
    4442  
    4443 Position of CopA-F8WHL2.pdb (#34) relative to
    4444 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4445 Matrix rotation and translation 
    4446 -0.54728967 -0.56189790 -0.62027800 158.57511981 
    4447 0.58976792 -0.78477262 0.19054069 127.65605082 
    4448 -0.59384159 -0.26153911 0.76088730 134.18075471 
    4449 Axis -0.36531666 -0.02136273 0.93063815 
    4450 Axis point 81.60160811 99.25852793 0.00000000 
    4451 Rotation angle (degrees) 141.77504660 
    4452 Shift along axis 64.21651520 
    4453  
    4454 
    4455 > select subtract #34
    4456 
    4457 Nothing selected 
    4458 
    4459 > hide #34 models
    4460 
    4461 > show #35 models
    4462 
    4463 > select add #35
    4464 
    4465 7501 atoms, 7619 bonds, 953 residues, 1 model selected 
    4466 
    4467 > view matrix models #35,1,0,0,116.88,0,1,0,-7.2403,0,0,1,111.96
    4468 
    4469 > view matrix models #35,1,0,0,112.47,0,1,0,89.143,0,0,1,196.06
    4470 
    4471 > ui mousemode right "rotate selected models"
    4472 
    4473 > view matrix models
    4474 > #35,0.0065824,0.90646,-0.42225,117.47,0.83324,-0.23843,-0.49886,91.055,-0.55287,-0.34855,-0.75686,209.75
    4475 
    4476 > ui mousemode right "translate selected models"
    4477 
    4478 > view matrix models
    4479 > #35,0.0065824,0.90646,-0.42225,96.987,0.83324,-0.23843,-0.49886,131.53,-0.55287,-0.34855,-0.75686,188.84
    4480 
    4481 > view matrix models
    4482 > #35,0.0065824,0.90646,-0.42225,132.29,0.83324,-0.23843,-0.49886,123.6,-0.55287,-0.34855,-0.75686,174.35
    4483 
    4484 > view matrix models
    4485 > #35,0.0065824,0.90646,-0.42225,129.73,0.83324,-0.23843,-0.49886,153.17,-0.55287,-0.34855,-0.75686,162.06
    4486 
    4487 > fitmap #35 inMap #1
    4488 
    4489 Fit molecule CopB_ Q9JIF7.pdb (#35) to map
    4490 W20_J3623_consensus_structure_sharp.mrc (#1) using 7501 atoms 
    4491 average map value = 0.272, steps = 140 
    4492 shifted from previous position = 13 
    4493 rotated from previous position = 19.4 degrees 
    4494 atoms outside contour = 4336, contour level = 0.26383 
    4495  
    4496 Position of CopB_ Q9JIF7.pdb (#35) relative to
    4497 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4498 Matrix rotation and translation 
    4499 0.29878946 0.85180997 -0.43028434 135.66407916 
    4500 0.69839777 -0.50244520 -0.50969537 144.97471611 
    4501 -0.65035790 -0.14821802 -0.74502752 155.00132184 
    4502 Axis 0.80301824 0.48889117 -0.34080365 
    4503 Axis point 0.00000000 17.11569470 112.17244297 
    4504 Rotation angle (degrees) 166.99275965 
    4505 Shift along axis 126.99257230 
    4506  
    4507 
    4508 > select subtract #35
    4509 
    4510 Nothing selected 
    4511 
    4512 > hide #35 models
    4513 
    4514 > show #36 models
    4515 
    4516 > select add #36
    4517 
    4518 7214 atoms, 7373 bonds, 905 residues, 1 model selected 
    4519 
    4520 > view matrix models #36,1,0,0,158.6,0,1,0,131.6,0,0,1,186.36
    4521 
    4522 > view matrix models #36,1,0,0,112.24,0,1,0,235.54,0,0,1,195.51
    4523 
    4524 > ui mousemode right "rotate selected models"
    4525 
    4526 > view matrix models
    4527 > #36,0.60674,-0.015574,0.79475,88.102,0.72366,0.42451,-0.54415,257.75,-0.3289,0.90529,0.26884,209.07
    4528 
    4529 > ui mousemode right "translate selected models"
    4530 
    4531 > view matrix models
    4532 > #36,0.60674,-0.015574,0.79475,110.55,0.72366,0.42451,-0.54415,182.27,-0.3289,0.90529,0.26884,183.11
    4533 
    4534 > view matrix models
    4535 > #36,0.60674,-0.015574,0.79475,107.23,0.72366,0.42451,-0.54415,189.41,-0.3289,0.90529,0.26884,154.84
    4536 
    4537 > view matrix models
    4538 > #36,0.60674,-0.015574,0.79475,127.45,0.72366,0.42451,-0.54415,196.73,-0.3289,0.90529,0.26884,180.58
    4539 
    4540 > fitmap #36 inMap #1
    4541 
    4542 Fit molecule CopBprime_O55029.pdb (#36) to map
    4543 W20_J3623_consensus_structure_sharp.mrc (#1) using 7214 atoms 
    4544 average map value = 0.2113, steps = 200 
    4545 shifted from previous position = 4.95 
    4546 rotated from previous position = 18 degrees 
    4547 atoms outside contour = 5449, contour level = 0.26383 
    4548  
    4549 Position of CopBprime_O55029.pdb (#36) relative to
    4550 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4551 Matrix rotation and translation 
    4552 0.50276875 0.12737660 0.85498467 126.31561890 
    4553 0.61912593 0.63718187 -0.45900148 191.39912628 
    4554 -0.60324678 0.76011477 0.24149298 177.83802946 
    4555 Axis 0.62095632 0.74274954 0.25047230 
    4556 Axis point 74.13696267 0.00000000 87.94186273 
    4557 Rotation angle (degrees) 79.00508960 
    4558 Shift along axis 265.14159471 
    4559  
    4560 
    4561 > select subtract #36
    4562 
    4563 Nothing selected 
    4564 
    4565 > hide #36 models
    4566 
    4567 > show #37 models
    4568 
    4569 > select add #37
    4570 
    4571 4014 atoms, 4083 bonds, 511 residues, 1 model selected 
    4572 
    4573 > view matrix models #37,1,0,0,30.593,0,1,0,199.33,0,0,1,198.85
    4574 
    4575 > view matrix models #37,1,0,0,157.99,0,1,0,204.81,0,0,1,141.3
    4576 
    4577 > ui mousemode right "rotate selected models"
    4578 
    4579 > view matrix models
    4580 > #37,0.43622,0.67922,-0.59023,141.13,-0.78114,-0.039782,-0.62309,191.16,-0.44669,0.73286,0.51321,126.99
    4581 
    4582 > ui mousemode right "translate selected models"
    4583 
    4584 > view matrix models
    4585 > #37,0.43622,0.67922,-0.59023,150.33,-0.78114,-0.039782,-0.62309,186.91,-0.44669,0.73286,0.51321,121.12
    4586 
    4587 > view matrix models
    4588 > #37,0.43622,0.67922,-0.59023,147.14,-0.78114,-0.039782,-0.62309,187.14,-0.44669,0.73286,0.51321,128.48
    4589 
    4590 > fitmap #37 inMap #1
    4591 
    4592 Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
    4593 W20_J3623_consensus_structure_sharp.mrc (#1) using 4014 atoms 
    4594 average map value = 0.1388, steps = 96 
    4595 shifted from previous position = 7.92 
    4596 rotated from previous position = 10.6 degrees 
    4597 atoms outside contour = 3125, contour level = 0.26383 
    4598  
    4599 Position of CopD_full_Q5XJY5.pdb (#37) relative to
    4600 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4601 Matrix rotation and translation 
    4602 0.41505472 0.79215751 -0.44745509 152.46783193 
    4603 -0.75869096 0.02993242 -0.65076269 180.94994695 
    4604 -0.50211314 0.60958226 0.61342633 132.05032423 
    4605 Axis 0.63044142 0.02734069 -0.77575518 
    4606 Axis point 250.00196774 -8.95488713 0.00000000 
    4607 Rotation angle (degrees) 88.32633929 
    4608 Shift along axis -1.36938916 
    4609  
    4610 
    4611 > view matrix models
    4612 > #37,0.41505,0.79216,-0.44746,143.76,-0.75869,0.029932,-0.65076,186.11,-0.50211,0.60958,0.61343,122.85
    4613 
    4614 > view matrix models
    4615 > #37,0.41505,0.79216,-0.44746,143.43,-0.75869,0.029932,-0.65076,185.75,-0.50211,0.60958,0.61343,122.85
    4616 
    4617 > view matrix models
    4618 > #37,0.41505,0.79216,-0.44746,142.4,-0.75869,0.029932,-0.65076,174.97,-0.50211,0.60958,0.61343,117.62
    4619 
    4620 > fitmap #37 inMap #1
    4621 
    4622 Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
    4623 W20_J3623_consensus_structure_sharp.mrc (#1) using 4014 atoms 
    4624 average map value = 0.1655, steps = 240 
    4625 shifted from previous position = 19.2 
    4626 rotated from previous position = 30 degrees 
    4627 atoms outside contour = 2918, contour level = 0.26383 
    4628  
    4629 Position of CopD_full_Q5XJY5.pdb (#37) relative to
    4630 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4631 Matrix rotation and translation 
    4632 0.54325309 0.50781797 -0.66857834 156.40844261 
    4633 -0.83919938 0.30481815 -0.45036685 164.83901629 
    4634 -0.02490957 0.80573371 0.59175392 110.35264351 
    4635 Axis 0.64381104 -0.32991074 -0.69041020 
    4636 Axis point 270.01565892 -103.01400891 0.00000000 
    4637 Rotation angle (degrees) 77.29610173 
    4638 Shift along axis -29.87327013 
    4639  
    4640 
    4641 > view matrix models
    4642 > #37,0.54325,0.50782,-0.66858,154.11,-0.8392,0.30482,-0.45037,160.13,-0.02491,0.80573,0.59175,113.09
    4643 
    4644 > view matrix models
    4645 > #37,0.54325,0.50782,-0.66858,152.8,-0.8392,0.30482,-0.45037,160.99,-0.02491,0.80573,0.59175,116.7
    4646 
    4647 > fitmap #37 inMap #1
    4648 
    4649 Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
    4650 W20_J3623_consensus_structure_sharp.mrc (#1) using 4014 atoms 
    4651 average map value = 0.1527, steps = 200 
    4652 shifted from previous position = 8.47 
    4653 rotated from previous position = 9.78 degrees 
    4654 atoms outside contour = 3000, contour level = 0.26383 
    4655  
    4656 Position of CopD_full_Q5XJY5.pdb (#37) relative to
    4657 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4658 Matrix rotation and translation 
    4659 0.52381084 0.45458159 -0.72040113 159.66823341 
    4660 -0.84399300 0.16247112 -0.51115453 164.46346911 
    4661 -0.11531706 0.87576179 0.46876781 118.49109089 
    4662 Axis 0.69555148 -0.30345531 -0.65124728 
    4663 Axis point 0.00000000 33.10752297 257.99354223 
    4664 Rotation angle (degrees) 85.55368957 
    4665 Shift along axis -16.01683616 
    4666  
    4667 
    4668 > select subtract #37
    4669 
    4670 Nothing selected 
    4671 
    4672 > hide #37 models
    4673 
    4674 > show #38 models
    4675 
    4676 > select add #38
    4677 
    4678 6830 atoms, 6947 bonds, 874 residues, 1 model selected 
    4679 
    4680 > view matrix models #38,1,0,0,4.9195,0,1,0,158.21,0,0,1,93.306
    4681 
    4682 > view matrix models #38,1,0,0,20.598,0,1,0,103.1,0,0,1,122.07
    4683 
    4684 > view matrix models #38,1,0,0,72.888,0,1,0,68.344,0,0,1,130.87
    4685 
    4686 > view matrix models #38,1,0,0,89.688,0,1,0,109.93,0,0,1,127.2
    4687 
    4688 > ui mousemode right "rotate selected models"
    4689 
    4690 > view matrix models
    4691 > #38,-0.10567,0.8283,0.55022,86.046,-0.72387,0.3153,-0.61367,108.49,-0.68179,-0.46314,0.56627,125.7
    4692 
    4693 > ui mousemode right "translate selected models"
    4694 
    4695 > view matrix models
    4696 > #38,-0.10567,0.8283,0.55022,94.304,-0.72387,0.3153,-0.61367,138.65,-0.68179,-0.46314,0.56627,138.14
    4697 
    4698 > view matrix models
    4699 > #38,-0.10567,0.8283,0.55022,112.86,-0.72387,0.3153,-0.61367,126.46,-0.68179,-0.46314,0.56627,130.13
    4700 
    4701 > fitmap #38 inMap #1
    4702 
    4703 Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
    4704 W20_J3623_consensus_structure_sharp.mrc (#1) using 6830 atoms 
    4705 average map value = 0.2013, steps = 104 
    4706 shifted from previous position = 5.21 
    4707 rotated from previous position = 10.3 degrees 
    4708 atoms outside contour = 4944, contour level = 0.26383 
    4709  
    4710 Position of CopG1_ Q9QZE5.pdb (#38) relative to
    4711 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4712 Matrix rotation and translation 
    4713 -0.18152050 0.89700589 0.40302697 113.56564500 
    4714 -0.70329404 0.16803702 -0.69075398 122.94853762 
    4715 -0.68733384 -0.40883247 0.60035673 126.40848670 
    4716 Axis 0.14406783 0.55719735 -0.81778700 
    4717 Axis point 133.98876902 46.90995141 0.00000000 
    4718 Rotation angle (degrees) 101.92103286 
    4719 Shift along axis -18.50746083 
    4720  
    4721 
    4722 > select subtract #38
    4723 
    4724 Nothing selected 
    4725 
    4726 > hide #38 models
    4727 
    4728 > show #39 models
    4729 
    4730 > select add #39
    4731 
    4732 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    4733 
    4734 > view matrix models #39,1,0,0,9.0898,0,1,0,160.45,0,0,1,-9.3444
    4735 
    4736 > view matrix models #39,1,0,0,60.276,0,1,0,127.59,0,0,1,121.27
    4737 
    4738 > view matrix models #39,1,0,0,127.7,0,1,0,116.45,0,0,1,94.356
    4739 
    4740 > view matrix models #39,1,0,0,126.09,0,1,0,140.04,0,0,1,103.22
    4741 
    4742 > ui mousemode right "rotate selected models"
    4743 
    4744 > view matrix models
    4745 > #39,0.77404,0.11317,-0.62294,121.61,-0.58601,0.50055,-0.63722,130.26,0.2397,0.85828,0.45376,105.69
    4746 
    4747 > fitmap #39 inMap #1
    4748 
    4749 Fit molecule CopZ1_P61924.pdb (#39) to map
    4750 W20_J3623_consensus_structure_sharp.mrc (#1) using 1420 atoms 
    4751 average map value = 0.2019, steps = 236 
    4752 shifted from previous position = 4.91 
    4753 rotated from previous position = 38.4 degrees 
    4754 atoms outside contour = 1084, contour level = 0.26383 
    4755  
    4756 Position of CopZ1_P61924.pdb (#39) relative to
    4757 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    4758 Matrix rotation and translation 
    4759 0.67082708 0.40413817 -0.62182263 120.91871935 
    4760 -0.65153203 -0.07936382 -0.75445836 130.14553587 
    4761 -0.35425563 0.91124845 0.21006956 98.85805425 
    4762 Axis 0.83698462 -0.13444710 -0.53045332 
    4763 Axis point 0.00000000 12.35504647 160.39862757 
    4764 Rotation angle (degrees) 95.69503877 
    4765 Shift along axis 31.26983397 
    4766  
    4767 
    4768 > select subtract #39
    4769 
    4770 Nothing selected 
    4771 
    4772 > hide #39 models
    4773 
    4774 > show #39 models
    4775 
    4776 > show #38 models
    4777 
    4778 > show #37 models
    4779 
    4780 > show #36 models
    4781 
    4782 > show #35 models
    4783 
    4784 > show #34 models
    4785 
    4786 > hide #!1 models
    4787 
    4788 > show #!3 models
    4789 
    4790 > fitmap #36 inMap #3
    4791 
    4792 Fit molecule CopBprime_O55029.pdb (#36) to map
    4793 W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
    4794 using 7214 atoms 
    4795 average map value = 0.2322, steps = 64 
    4796 shifted from previous position = 2.88 
    4797 rotated from previous position = 4.24 degrees 
    4798 atoms outside contour = 4591, contour level = 0.26875 
    4799  
    4800 Position of CopBprime_O55029.pdb (#36) relative to
    4801 W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
    4802 coordinates: 
    4803 Matrix rotation and translation 
    4804 -0.39263805 -0.91469425 -0.09575906 92.65990042 
    4805 -0.55910845 0.32006970 -0.76482228 179.90077864 
    4806 0.73022811 -0.24675864 -0.63708483 150.47739175 
    4807 Axis 0.49918086 -0.79588095 0.34262513 
    4808 Axis point 73.56777391 0.00000000 134.22819381 
    4809 Rotation angle (degrees) 148.74058258 
    4810 Shift along axis -45.36821860 
    4811  
    4812 
    4813 > fitmap #35 inMap #3
    4814 
    4815 Fit molecule CopB_ Q9JIF7.pdb (#35) to map
    4816 W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
    4817 using 7501 atoms 
    4818 average map value = 0.2689, steps = 112 
    4819 shifted from previous position = 7.58 
    4820 rotated from previous position = 7.06 degrees 
    4821 atoms outside contour = 3837, contour level = 0.26875 
    4822  
    4823 Position of CopB_ Q9JIF7.pdb (#35) relative to
    4824 W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
    4825 coordinates: 
    4826 Matrix rotation and translation 
    4827 -0.23385104 0.28135848 0.93067238 134.35318178 
    4828 -0.41876188 -0.89302545 0.16475441 150.63397364 
    4829 0.87746918 -0.35120213 0.32665714 138.57787474 
    4830 Axis -0.59215049 0.06105999 -0.80351072 
    4831 Axis point 39.18867412 76.76513978 0.00000000 
    4832 Rotation angle (degrees) 154.17248796 
    4833 Shift along axis -181.70840106 
    4834  
    4835 
    4836 > fitmap #34 inMap #3
    4837 
    4838 Fit molecule CopA-F8WHL2.pdb (#34) to map
    4839 W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
    4840 using 9810 atoms 
    4841 average map value = 0.2333, steps = 88 
    4842 shifted from previous position = 0.574 
    4843 rotated from previous position = 1.73 degrees 
    4844 atoms outside contour = 5294, contour level = 0.26875 
    4845  
    4846 Position of CopA-F8WHL2.pdb (#34) relative to
    4847 W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
    4848 coordinates: 
    4849 Matrix rotation and translation 
    4850 0.01921606 0.93572095 -0.35221737 156.63147150 
    4851 0.36634751 0.32119202 0.87328416 124.11551889 
    4852 0.93027967 -0.14581504 -0.33662699 137.77469414 
    4853 Axis -0.58763841 -0.73952029 -0.32831515 
    4854 Axis point 4.51722837 0.00000000 49.95590579 
    4855 Rotation angle (degrees) 119.87500102 
    4856 Shift along axis -229.06213308 
    4857  
    4858 
    4859 > hide #!3 models
    4860 
    4861 > show #!4 models
    4862 
    4863 > hide #!4 models
    4864 
    4865 > show #!5 models
    4866 
    4867 > hide #!5 models
    4868 
    4869 > show #!6 models
    4870 
    4871 > hide #!6 models
    4872 
    4873 > show #!7 models
    4874 
    4875 > hide #!7 models
    4876 
    4877 > show #!8 models
    4878 
    4879 > hide #!8 models
    4880 
    4881 > show #!9 models
    4882 
    4883 > fitmap #38 inMap #9
    4884 
    4885 Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
    4886 W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
    4887 (#9) using 6830 atoms 
    4888 average map value = 0.2056, steps = 112 
    4889 shifted from previous position = 3.87 
    4890 rotated from previous position = 8.6 degrees 
    4891 atoms outside contour = 4655, contour level = 0.28232 
    4892  
    4893 Position of CopG1_ Q9QZE5.pdb (#38) relative to
    4894 W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
    4895 (#9) coordinates: 
    4896 Matrix rotation and translation 
    4897 0.97147165 -0.22568138 0.07287489 181.98815327 
    4898 -0.21631778 -0.96919397 -0.11776953 160.81365369 
    4899 0.09720830 0.09864563 -0.99036336 147.52870008 
    4900 Axis 0.99282083 -0.11163133 0.04295621 
    4901 Axis point 0.00000000 86.77702657 74.77347983 
    4902 Rotation angle (degrees) 173.74290119 
    4903 Shift along axis 169.06706116 
    4904  
    4905 
    4906 > hide #!9 models
    4907 
    4908 > show #!10 models
    4909 
    4910 > hide #!10 models
    4911 
    4912 > show #!10 models
    4913 
    4914 > hide #!10 models
    4915 
    4916 > show #!10 models
    4917 
    4918 > hide #!10 models
    4919 
    4920 > show #!11 models
    4921 
    4922 > hide #!11 models
    4923 
    4924 > show #!23 models
    4925 
    4926 > fitmap #38 inMap #23
    4927 
    4928 Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
    4929 W20_J4026_004_volume_map_gammazeta_local.mrc (#23) using 6830 atoms 
    4930 average map value = 0.1938, steps = 88 
    4931 shifted from previous position = 1.48 
    4932 rotated from previous position = 1.93 degrees 
    4933 atoms outside contour = 4539, contour level = 0.26014 
    4934  
    4935 Position of CopG1_ Q9QZE5.pdb (#38) relative to
    4936 W20_J4026_004_volume_map_gammazeta_local.mrc (#23) coordinates: 
    4937 Matrix rotation and translation 
    4938 -0.15863519 0.95166183 0.26301070 116.52908933 
    4939 -0.70798986 0.07602756 -0.70211834 119.07331926 
    4940 -0.68817529 -0.29758959 0.66170629 125.26733072 
    4941 Axis 0.20689796 0.48648815 -0.84883597 
    4942 Axis point 135.80061352 37.60568602 0.00000000 
    4943 Rotation angle (degrees) 102.14876416 
    4944 Shift along axis -24.29402645 
    4945  
    4946 
    4947 > hide #!23 models
    4948 
    4949 > show #!25 models
    4950 
    4951 > fitmap #38 inMap #23
    4952 
    4953 Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
    4954 W20_J4026_004_volume_map_gammazeta_local.mrc (#23) using 6830 atoms 
    4955 average map value = 0.1938, steps = 48 
    4956 shifted from previous position = 0.0265 
    4957 rotated from previous position = 0.0358 degrees 
    4958 atoms outside contour = 4543, contour level = 0.26014 
    4959  
    4960 Position of CopG1_ Q9QZE5.pdb (#38) relative to
    4961 W20_J4026_004_volume_map_gammazeta_local.mrc (#23) coordinates: 
    4962 Matrix rotation and translation 
    4963 -0.15917554 0.95152929 0.26316374 116.52898909 
    4964 -0.70811196 0.07570421 -0.70203014 119.09089645 
    4965 -0.68792485 -0.29809542 0.66173902 125.28763210 
    4966 Axis 0.20661307 0.48648289 -0.84890838 
    4967 Axis point 135.76856788 37.64517816 0.00000000 
    4968 Rotation angle (degrees) 102.17311623 
    4969 Shift along axis -24.34562541 
    4970  
    4971 
    4972 > fitmap #38 inMap #25
    4973 
    4974 Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
    4975 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6830 atoms 
    4976 average map value = 0.2208, steps = 312 
    4977 shifted from previous position = 9.89 
    4978 rotated from previous position = 43.3 degrees 
    4979 atoms outside contour = 4003, contour level = 0.2532 
    4980  
    4981 Position of CopG1_ Q9QZE5.pdb (#38) relative to
    4982 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    4983 Matrix rotation and translation 
    4984 -0.51349164 0.78944189 0.33631509 107.60498851 
    4985 -0.18358145 0.28179025 -0.94174949 122.78040261 
    4986 -0.83822681 -0.54532170 0.00022995 120.22835474 
    4987 Axis 0.25155556 0.74531240 -0.61743762 
    4988 Axis point 81.37402006 0.00000000 79.41692880 
    4989 Rotation angle (degrees) 128.00539846 
    4990 Shift along axis 44.34488087 
    4991  
    4992 
    4993 > hide #!25 models
    4994 
    4995 > show #!25 models
    4996 
    4997 > color #25 #929292ff models
    4998 
    4999 > color #25 #92929297 models
    5000 
    5001 > select add #39
    5002 
    5003 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    5004 
    5005 > view matrix models
    5006 > #39,0.049821,0.95099,-0.30519,123.19,-0.98555,-0.0027194,-0.16936,132.83,-0.16189,0.30922,0.93711,101.07
    5007 
    5008 > ui mousemode right "translate selected models"
    5009 
    5010 > view matrix models
    5011 > #39,0.049821,0.95099,-0.30519,120.81,-0.98555,-0.0027194,-0.16936,149.13,-0.16189,0.30922,0.93711,88.072
    5012 
    5013 > view matrix models
    5014 > #39,0.049821,0.95099,-0.30519,127.16,-0.98555,-0.0027194,-0.16936,146.48,-0.16189,0.30922,0.93711,93.373
    5015 
    5016 > fitmap #39 inMap #25
    5017 
    5018 Fit molecule CopZ1_P61924.pdb (#39) to map
    5019 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms 
    5020 average map value = 0.2155, steps = 132 
    5021 shifted from previous position = 12.7 
    5022 rotated from previous position = 24.5 degrees 
    5023 atoms outside contour = 816, contour level = 0.2532 
    5024  
    5025 Position of CopZ1_P61924.pdb (#39) relative to
    5026 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5027 Matrix rotation and translation 
    5028 -0.02172282 0.87569029 -0.48238434 117.17569269 
    5029 -0.85704432 -0.26475204 -0.44201968 143.50099331 
    5030 -0.51478457 0.40382284 0.75625654 98.49893470 
    5031 Axis 0.43861563 0.01680130 -0.89851770 
    5032 Axis point 143.73837501 16.52006781 0.00000000 
    5033 Rotation angle (degrees) 105.37343878 
    5034 Shift along axis -34.69694324 
    5035  
    5036 
    5037 > select subtract #39
    5038 
    5039 Nothing selected 
    5040 
    5041 > hide #39 models
    5042 
    5043 > hide #38 models
    5044 
    5045 > hide #37 models
    5046 
    5047 > hide #36 models
    5048 
    5049 > hide #35 models
    5050 
    5051 > show #35 models
    5052 
    5053 > hide #35 models
    5054 
    5055 > hide #34 models
    5056 
    5057 > show #34 models
    5058 
    5059 > show #35 models
    5060 
    5061 > show #36 models
    5062 
    5063 > show #37 models
    5064 
    5065 > show #38 models
    5066 
    5067 > show #39 models
    5068 
    5069 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    5070 > predictions/fold_2025_01_17_alpha1_330gamma1_330zeta/fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif"
    5071 
    5072 Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif #40 
    5073 --- 
    5074 Chain | Description 
    5075 A | . 
    5076 B | . 
    5077 C | . 
    5078  
    5079 Computing secondary structure 
    5080 
    5081 > select add #40
    5082 
    5083 6676 atoms, 6817 bonds, 837 residues, 1 model selected 
    5084 
    5085 > ui tool show Matchmaker
    5086 
    5087 > matchmaker #40 to #34
    5088 
    5089 Computing secondary structure 
    5090 [Repeated 1 time(s)]  Parameters 
    5091 --- 
    5092 Chain pairing | bb 
    5093 Alignment algorithm | Needleman-Wunsch 
    5094 Similarity matrix | BLOSUM-62 
    5095 SS fraction | 0.3 
    5096 Gap open (HH/SS/other) | 18/18/6 
    5097 Gap extend | 1 
    5098 SS matrix |  |  | H | S | O 
    5099 ---|---|---|--- 
    5100 H | 6 | -9 | -6 
    5101 S |  | 6 | -6 
    5102 O |  |  | 4 
    5103 Iteration cutoff | 2 
    5104  
    5105 Matchmaker CopA-F8WHL2.pdb, chain A (#34) with
    5106 fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain B (#40), sequence
    5107 alignment score = 1723 
    5108 RMSD between 297 pruned atom pairs is 0.381 angstroms; (across all 330 pairs:
    5109 4.425) 
    5110  
    5111 
    5112 > select subtract #40
    5113 
    5114 Nothing selected 
    5115 
    5116 > fitmap #40 inMap #25
    5117 
    5118 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40) to map
    5119 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6676 atoms 
    5120 average map value = 0.2327, steps = 120 
    5121 shifted from previous position = 12.5 
    5122 rotated from previous position = 19.1 degrees 
    5123 atoms outside contour = 3778, contour level = 0.2532 
    5124  
    5125 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40)
    5126 relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5127 Matrix rotation and translation 
    5128 0.54165871 0.66183244 -0.51825058 133.50428914 
    5129 0.57871718 -0.74075578 -0.34112650 139.20476253 
    5130 -0.60966570 -0.11514637 -0.78425063 100.42690475 
    5131 Axis 0.87742311 0.35494156 -0.32271532 
    5132 Axis point 0.00000000 37.30416243 78.13952669 
    5133 Rotation angle (degrees) 172.60119629 
    5134 Shift along axis 134.14000391 
    5135  
    5136 
    5137 > ui tool show Matchmaker
    5138 
    5139 > matchmaker #39 to #40
    5140 
    5141 Computing secondary structure 
    5142 [Repeated 1 time(s)]  Parameters 
    5143 --- 
    5144 Chain pairing | bb 
    5145 Alignment algorithm | Needleman-Wunsch 
    5146 Similarity matrix | BLOSUM-62 
    5147 SS fraction | 0.3 
    5148 Gap open (HH/SS/other) | 18/18/6 
    5149 Gap extend | 1 
    5150 SS matrix |  |  | H | S | O 
    5151 ---|---|---|--- 
    5152 H | 6 | -9 | -6 
    5153 S |  | 6 | -6 
    5154 O |  |  | 4 
    5155 Iteration cutoff | 2 
    5156  
    5157 Matchmaker fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain C (#40)
    5158 with CopZ1_P61924.pdb, chain A (#39), sequence alignment score = 863.4 
    5159 RMSD between 141 pruned atom pairs is 0.407 angstroms; (across all 177 pairs:
    5160 16.666) 
    5161  
    5162 
    5163 > hide #40 models
    5164 
    5165 > fitmap #39 inMap #25
    5166 
    5167 Fit molecule CopZ1_P61924.pdb (#39) to map
    5168 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms 
    5169 average map value = 0.237, steps = 448 
    5170 shifted from previous position = 13.1 
    5171 rotated from previous position = 65.5 degrees 
    5172 atoms outside contour = 774, contour level = 0.2532 
    5173  
    5174 Position of CopZ1_P61924.pdb (#39) relative to
    5175 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5176 Matrix rotation and translation 
    5177 0.40316931 0.69456576 0.59584639 114.25318729 
    5178 -0.23944244 -0.54836159 0.80122836 139.81166245 
    5179 0.88324506 -0.46570160 -0.05477404 99.19539890 
    5180 Axis -0.79181872 -0.17962133 -0.58374591 
    5181 Axis point 0.00000000 56.29130506 -26.82207038 
    5182 Rotation angle (degrees) 126.86869176 
    5183 Shift along axis -173.48587819 
    5184  
    5185 
    5186 > undo
    5187 
    5188 > hide #39 models
    5189 
    5190 > hide #38 models
    5191 
    5192 > hide #37 models
    5193 
    5194 > hide #36 models
    5195 
    5196 > hide #35 models
    5197 
    5198 > hide #34 models
    5199 
    5200 > hide #!25 models
    5201 
    5202 > ui mousemode right select
    5203 
    5204 Drag select of 102 residues 
    5205 
    5206 > select up
    5207 
    5208 1089 atoms, 1111 bonds, 132 residues, 1 model selected 
    5209 
    5210 > select up
    5211 
    5212 2689 atoms, 2767 bonds, 330 residues, 1 model selected 
    5213 
    5214 > delete sel
    5215 
    5216 > fitmap #40 inMap #25
    5217 
    5218 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40) to map
    5219 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3987 atoms 
    5220 average map value = 0.2376, steps = 148 
    5221 shifted from previous position = 8.47 
    5222 rotated from previous position = 22.7 degrees 
    5223 atoms outside contour = 2154, contour level = 0.2532 
    5224  
    5225 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40)
    5226 relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5227 Matrix rotation and translation 
    5228 0.25729822 0.88581488 -0.38617305 122.95584280 
    5229 0.78223190 -0.42556216 -0.45498364 149.35405458 
    5230 -0.56737191 -0.18501039 -0.80240904 100.43354571 
    5231 Axis 0.79114243 0.53099377 -0.30354451 
    5232 Axis point 0.00000000 25.55099714 77.70315234 
    5233 Rotation angle (degrees) 170.17599112 
    5234 Shift along axis 146.09560633 
    5235  
    5236 
    5237 > show #!25 models
    5238 
    5239 > ui tool show Matchmaker
    5240 
    5241 > matchmaker #39 to #40
    5242 
    5243 Computing secondary structure 
    5244 [Repeated 1 time(s)]  Parameters 
    5245 --- 
    5246 Chain pairing | bb 
    5247 Alignment algorithm | Needleman-Wunsch 
    5248 Similarity matrix | BLOSUM-62 
    5249 SS fraction | 0.3 
    5250 Gap open (HH/SS/other) | 18/18/6 
    5251 Gap extend | 1 
    5252 SS matrix |  |  | H | S | O 
    5253 ---|---|---|--- 
    5254 H | 6 | -9 | -6 
    5255 S |  | 6 | -6 
    5256 O |  |  | 4 
    5257 Iteration cutoff | 2 
    5258  
    5259 Matchmaker fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain C (#40)
    5260 with CopZ1_P61924.pdb, chain A (#39), sequence alignment score = 863.4 
    5261 RMSD between 141 pruned atom pairs is 0.407 angstroms; (across all 177 pairs:
    5262 16.666) 
    5263  
    5264 
    5265 > show #39 models
    5266 
    5267 > hide #40 models
    5268 
    5269 > show #38 models
    5270 
    5271 > show #34 models
    5272 
    5273 > hide #39 models
    5274 
    5275 > hide #38 models
    5276 
    5277 > hide #!25 models
    5278 
    5279 Drag select of 84 residues 
    5280 
    5281 > select up
    5282 
    5283 956 atoms, 971 bonds, 118 residues, 1 model selected 
    5284 
    5285 > select up
    5286 
    5287 9810 atoms, 10032 bonds, 1233 residues, 1 model selected 
    5288 
    5289 > select down
    5290 
    5291 956 atoms, 971 bonds, 118 residues, 1 model selected 
    5292 Drag select of 309 residues 
    5293 
    5294 > delete sel
    5295 
    5296 > select clear
    5297 
    5298 [Repeated 2 time(s)]Drag select of 1 pseudobonds 
    5299 
    5300 > delete sel
    5301 
    5302 > select add #34
    5303 
    5304 7345 atoms, 7512 bonds, 2 pseudobonds, 924 residues, 2 models selected 
    5305 
    5306 > select subtract #34
    5307 
    5308 Nothing selected 
    5309 
    5310 > delete sel
    5311 
    5312 > close #34
    5313 
    5314 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    5315 > files/alphafold/CopA-F8WHL2.pdb"
    5316 
    5317 CopA-F8WHL2.pdb title: 
    5318 Alphafold monomer V2.0 prediction for coatomer subunit α (F8WHL2) [more
    5319 info...] 
    5320  
    5321 Chain information for CopA-F8WHL2.pdb #34 
    5322 --- 
    5323 Chain | Description | UniProt 
    5324 A | coatomer subunit α | F8WHL2_MOUSE 1-1233 
    5325  
    5326 Computing secondary structure 
    5327 
    5328 > show #!25 models
    5329 
    5330 > select add #34
    5331 
    5332 9810 atoms, 10032 bonds, 1233 residues, 1 model selected 
    5333 
    5334 > color sel navy
    5335 
    5336 > ui mousemode right "translate selected models"
    5337 
    5338 > view matrix models #34,1,0,0,139.38,0,1,0,77.792,0,0,1,174.15
    5339 
    5340 > view matrix models #34,1,0,0,143.17,0,1,0,116.78,0,0,1,157.74
    5341 
    5342 > ui mousemode right "rotate selected models"
    5343 
    5344 > view matrix models
    5345 > #34,-0.77292,0.46571,-0.43094,110.33,-0.63189,-0.50329,0.58942,111.94,0.057612,0.72788,0.68328,155.75
    5346 
    5347 > view matrix models
    5348 > #34,0.095488,0.54565,-0.83256,128.67,-0.72338,-0.53652,-0.43459,118.09,-0.68382,0.64375,0.34348,145.26
    5349 
    5350 > view matrix models
    5351 > #34,0.86645,-0.32341,0.38035,140.29,0.26177,0.943,0.20551,120.49,-0.42513,-0.078497,0.90172,151.23
    5352 
    5353 > view matrix models
    5354 > #34,-0.13249,-0.98099,-0.14179,130.68,-0.29114,-0.098228,0.95162,112.52,-0.94746,0.16737,-0.27259,148.51
    5355 
    5356 > view matrix models
    5357 > #34,-0.191,-0.9337,-0.30287,130.44,-0.10946,-0.28637,0.95185,117.25,-0.97547,0.21495,-0.047502,145.98
    5358 
    5359 > view matrix models
    5360 > #34,-0.60871,-0.63739,-0.47244,121.83,0.33431,-0.74608,0.57585,131.6,-0.71952,0.19258,0.66723,145.55
    5361 
    5362 > ui mousemode right "translate selected models"
    5363 
    5364 > view matrix models
    5365 > #34,-0.60871,-0.63739,-0.47244,153.15,0.33431,-0.74608,0.57585,151.65,-0.71952,0.19258,0.66723,153.4
    5366 
    5367 > view matrix models
    5368 > #34,-0.60871,-0.63739,-0.47244,154.56,0.33431,-0.74608,0.57585,133.83,-0.71952,0.19258,0.66723,140.34
    5369 
    5370 > ui mousemode right "rotate selected models"
    5371 
    5372 > view matrix models
    5373 > #34,-0.61566,-0.09401,-0.78238,152.7,0.38273,-0.90356,-0.1926,141.58,-0.68882,-0.41802,0.59227,145.99
    5374 
    5375 > ui mousemode right "translate selected models"
    5376 
    5377 > view matrix models
    5378 > #34,-0.61566,-0.09401,-0.78238,154.2,0.38273,-0.90356,-0.1926,117.01,-0.68882,-0.41802,0.59227,135.94
    5379 
    5380 > select up
    5381 
    5382 40776 atoms, 41545 bonds, 5160 residues, 68 models selected 
    5383 
    5384 > select down
    5385 
    5386 9810 atoms, 10032 bonds, 1233 residues, 1 model selected 
    5387 
    5388 > ui mousemode right select
    5389 
    5390 > select clear
    5391 
    5392 > fitmap #34 inMap #25
    5393 
    5394 Fit molecule CopA-F8WHL2.pdb (#34) to map
    5395 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 9810 atoms 
    5396 average map value = 0.2513, steps = 268 
    5397 shifted from previous position = 12.5 
    5398 rotated from previous position = 28.3 degrees 
    5399 atoms outside contour = 4976, contour level = 0.2532 
    5400  
    5401 Position of CopA-F8WHL2.pdb (#34) relative to
    5402 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5403 Matrix rotation and translation 
    5404 -0.53264139 -0.54606136 -0.64661437 159.40933932 
    5405 0.58383331 -0.79018975 0.18638357 127.28571811 
    5406 -0.61272491 -0.27823941 0.73969657 133.57411156 
    5407 Axis -0.38016417 -0.02772906 0.92450327 
    5408 Axis point 83.38396978 99.21518793 0.00000000 
    5409 Rotation angle (degrees) 142.33221845 
    5410 Shift along axis 59.35847140 
    5411  
    5412 
    5413 > hide #!25 models
    5414 
    5415 Drag select of 204 residues 
    5416 
    5417 > select up
    5418 
    5419 1872 atoms, 1904 bonds, 233 residues, 1 model selected 
    5420 
    5421 > delete sel
    5422 
    5423 Drag select of 67 residues, 2 pseudobonds 
    5424 Drag select of 44 residues, 3 pseudobonds 
    5425 
    5426 > select up
    5427 
    5428 515 atoms, 525 bonds, 3 pseudobonds, 65 residues, 2 models selected 
    5429 
    5430 > select up
    5431 
    5432 7938 atoms, 8122 bonds, 3 pseudobonds, 1000 residues, 2 models selected 
    5433 
    5434 > select down
    5435 
    5436 515 atoms, 525 bonds, 3 pseudobonds, 65 residues, 2 models selected 
    5437 Drag select of 62 residues, 3 pseudobonds 
    5438 
    5439 > select up
    5440 
    5441 597 atoms, 611 bonds, 3 pseudobonds, 76 residues, 2 models selected 
    5442 
    5443 > delete sel
    5444 
    5445 Drag select of 2 residues 
    5446 
    5447 > select up
    5448 
    5449 645 atoms, 657 bonds, 90 residues, 1 model selected 
    5450 
    5451 > delete sel
    5452 
    5453 > show #!25 models
    5454 
    5455 > fitmap #34 inMap #25
    5456 
    5457 Fit molecule CopA-F8WHL2.pdb (#34) to map
    5458 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6696 atoms 
    5459 average map value = 0.33, steps = 92 
    5460 shifted from previous position = 0.363 
    5461 rotated from previous position = 1.55 degrees 
    5462 atoms outside contour = 2309, contour level = 0.2532 
    5463  
    5464 Position of CopA-F8WHL2.pdb (#34) relative to
    5465 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5466 Matrix rotation and translation 
    5467 -0.55114104 -0.52745699 -0.64655447 159.68929082 
    5468 0.57420657 -0.80195943 0.16476617 126.61771889 
    5469 -0.60541752 -0.28044643 0.74486202 133.68887023 
    5470 Axis -0.37446301 -0.03459979 0.92659609 
    5471 Axis point 83.97786314 98.17305376 0.00000000 
    5472 Rotation angle (degrees) 143.52527944 
    5473 Shift along axis 59.69690535 
    5474  
    5475 
    5476 > hide #!34 models
    5477 
    5478 > show #35 models
    5479 
    5480 > fitmap #35 inMap #25
    5481 
    5482 Fit molecule CopB_ Q9JIF7.pdb (#35) to map
    5483 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 7501 atoms 
    5484 average map value = 0.2378, steps = 84 
    5485 shifted from previous position = 1.34 
    5486 rotated from previous position = 3.2 degrees 
    5487 atoms outside contour = 4024, contour level = 0.2532 
    5488  
    5489 Position of CopB_ Q9JIF7.pdb (#35) relative to
    5490 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5491 Matrix rotation and translation 
    5492 0.32064619 0.78921696 -0.52375815 142.21372577 
    5493 0.68088169 -0.57645114 -0.45177892 148.04005904 
    5494 -0.65847257 -0.21175615 -0.72220024 154.69062564 
    5495 Axis 0.81144623 0.45542974 -0.36624960 
    5496 Axis point 0.00000000 24.90601335 113.58992692 
    5497 Rotation angle (degrees) 171.49485982 
    5498 Shift along axis 126.16525710 
    5499  
    5500 
    5501 > fitmap #35 inMap #25
    5502 
    5503 Fit molecule CopB_ Q9JIF7.pdb (#35) to map
    5504 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 7501 atoms 
    5505 average map value = 0.2378, steps = 48 
    5506 shifted from previous position = 0.00712 
    5507 rotated from previous position = 0.00209 degrees 
    5508 atoms outside contour = 4022, contour level = 0.2532 
    5509  
    5510 Position of CopB_ Q9JIF7.pdb (#35) relative to
    5511 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5512 Matrix rotation and translation 
    5513 0.32064133 0.78920396 -0.52378071 142.21243830 
    5514 0.68089354 -0.57645720 -0.45175334 148.03333799 
    5515 -0.65846269 -0.21178811 -0.72219988 154.68860774 
    5516 Axis 0.81144528 0.45542871 -0.36625298 
    5517 Axis point 0.00000000 24.90541120 113.58774992 
    5518 Rotation angle (degrees) 171.49690419 
    5519 Shift along axis 126.16107988 
    5520  
    5521 
    5522 > hide #35 models
    5523 
    5524 > show #36 models
    5525 
    5526 > fitmap #36 inMap #25
    5527 
    5528 Fit molecule CopBprime_O55029.pdb (#36) to map
    5529 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 7214 atoms 
    5530 average map value = 0.1828, steps = 80 
    5531 shifted from previous position = 1.71 
    5532 rotated from previous position = 0.68 degrees 
    5533 atoms outside contour = 6397, contour level = 0.2532 
    5534  
    5535 Position of CopBprime_O55029.pdb (#36) relative to
    5536 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5537 Matrix rotation and translation 
    5538 0.50825278 0.05183494 0.85964658 125.87415961 
    5539 0.66191789 0.61506689 -0.42843603 193.30517521 
    5540 -0.55094811 0.78676926 0.27829898 176.59370632 
    5541 Axis 0.62023665 0.71996274 0.31138426 
    5542 Axis point 57.84080416 0.00000000 83.07791765 
    5543 Rotation angle (degrees) 78.41570987 
    5544 Shift along axis 272.23279077 
    5545  
    5546 
    5547 > hide #36 models
    5548 
    5549 > show #36 models
    5550 
    5551 > hide #36 models
    5552 
    5553 > show #37 models
    5554 
    5555 > hide #!25 models
    5556 
    5557 Drag select of 74 residues 
    5558 
    5559 > select up
    5560 
    5561 696 atoms, 711 bonds, 90 residues, 1 model selected 
    5562 
    5563 > delete sel
    5564 
    5565 > select clear
    5566 
    5567 Drag select of 39 residues 
    5568 
    5569 > select up
    5570 
    5571 652 atoms, 661 bonds, 80 residues, 1 model selected 
    5572 
    5573 > delete sel
    5574 
    5575 Drag select of 72 residues, 2 pseudobonds 
    5576 
    5577 > delete sel
    5578 
    5579 > show #!25 models
    5580 
    5581 > select add #25
    5582 
    5583 2 models selected 
    5584 
    5585 > select subtract #25
    5586 
    5587 Nothing selected 
    5588 
    5589 > select add #37
    5590 
    5591 2098 atoms, 2129 bonds, 269 residues, 1 model selected 
    5592 Drag select of 25 W20_J4027_005_volume_map_gammazeta_local.mrc , 10 residues 
    5593 
    5594 > select clear
    5595 
    5596 > select add #37
    5597 
    5598 2098 atoms, 2129 bonds, 269 residues, 1 model selected 
    5599 
    5600 > ui mousemode right "translate selected models"
    5601 
    5602 > view matrix models
    5603 > #37,0.52381,0.45458,-0.7204,159.74,-0.84399,0.16247,-0.51115,164.47,-0.11532,0.87576,0.46877,118.38
    5604 
    5605 > view matrix models
    5606 > #37,0.52381,0.45458,-0.7204,159.87,-0.84399,0.16247,-0.51115,160.32,-0.11532,0.87576,0.46877,115.66
    5607 
    5608 > ui mousemode right "rotate selected models"
    5609 
    5610 > view matrix models
    5611 > #37,-0.51843,-0.78578,-0.33732,156.47,0.64386,-0.0991,-0.7587,177.15,0.56274,-0.61052,0.55731,131.39
    5612 
    5613 > ui mousemode right "translate selected models"
    5614 
    5615 > view matrix models
    5616 > #37,-0.51843,-0.78578,-0.33732,156.82,0.64386,-0.0991,-0.7587,177.21,0.56274,-0.61052,0.55731,131.11
    5617 
    5618 > view matrix models
    5619 > #37,-0.51843,-0.78578,-0.33732,169.14,0.64386,-0.0991,-0.7587,188.43,0.56274,-0.61052,0.55731,154.61
    5620 
    5621 > view matrix models
    5622 > #37,-0.51843,-0.78578,-0.33732,168.55,0.64386,-0.0991,-0.7587,185.71,0.56274,-0.61052,0.55731,156.17
    5623 
    5624 > fitmap #37 inMap #25
    5625 
    5626 Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
    5627 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 2098 atoms 
    5628 average map value = 0.1523, steps = 264 
    5629 shifted from previous position = 11.8 
    5630 rotated from previous position = 42.5 degrees 
    5631 atoms outside contour = 1552, contour level = 0.2532 
    5632  
    5633 Position of CopD_full_Q5XJY5.pdb (#37) relative to
    5634 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5635 Matrix rotation and translation 
    5636 0.13421510 -0.97879473 -0.15474878 179.22768371 
    5637 0.80299796 0.19893091 -0.56180136 174.64912074 
    5638 0.58067252 -0.04886073 0.81266971 148.66115690 
    5639 Axis 0.25715468 -0.36869186 0.89327363 
    5640 Axis point -62.36776041 208.19731599 0.00000000 
    5641 Rotation angle (degrees) 85.81897760 
    5642 Shift along axis 114.49262034 
    5643  
    5644 
    5645 > ui mousemode right "rotate selected models"
    5646 
    5647 > view matrix models
    5648 > #37,0.17652,-0.98345,-0.040823,181.47,0.73295,0.15901,-0.66143,172.16,0.65698,0.086834,0.74889,148.4
    5649 
    5650 > view matrix models
    5651 > #37,0.4517,-0.88251,-0.13091,183.25,0.50738,0.3748,-0.77595,166,0.73385,0.28407,0.61707,146.24
    5652 
    5653 > view matrix models
    5654 > #37,0.19394,-0.76059,-0.61959,169.31,0.33983,0.64457,-0.68487,164.7,0.92028,-0.077732,0.38347,145.18
    5655 
    5656 > ui mousemode right "translate selected models"
    5657 
    5658 > ui mousemode right "rotate selected models"
    5659 
    5660 > view matrix models
    5661 > #37,0.13058,-0.95382,-0.27052,176.06,0.41699,0.30039,-0.85784,163.27,0.89948,-0.00078766,0.43696,145.75
    5662 
    5663 > ui mousemode right "translate selected models"
    5664 
    5665 > view matrix models
    5666 > #37,0.13058,-0.95382,-0.27052,175.12,0.41699,0.30039,-0.85784,169.65,0.89948,-0.00078766,0.43696,144.2
    5667 
    5668 > view matrix models
    5669 > #37,0.13058,-0.95382,-0.27052,176.92,0.41699,0.30039,-0.85784,173.28,0.89948,-0.00078766,0.43696,142.71
    5670 
    5671 > view matrix models
    5672 > #37,0.13058,-0.95382,-0.27052,176.07,0.41699,0.30039,-0.85784,171.32,0.89948,-0.00078766,0.43696,141.37
    5673 
    5674 > ui mousemode right "rotate selected models"
    5675 
    5676 > view matrix models
    5677 > #37,0.98025,0.13893,0.14075,193.31,0.13603,0.042901,-0.98977,165.4,-0.14355,0.98937,0.023155,115.29
    5678 
    5679 > view matrix models
    5680 > #37,-0.70422,-0.31127,-0.63811,154.89,0.39637,-0.91803,0.010376,192.21,-0.58904,-0.24562,0.76987,127.74
    5681 
    5682 > view matrix models
    5683 > #37,-0.068744,0.46239,-0.88401,156.66,-0.96301,-0.26218,-0.062249,169.55,-0.26056,0.84703,0.46331,123
    5684 
    5685 > ui mousemode right "translate selected models"
    5686 
    5687 > view matrix models
    5688 > #37,-0.068744,0.46239,-0.88401,155.46,-0.96301,-0.26218,-0.062249,163.71,-0.26056,0.84703,0.46331,114.14
    5689 
    5690 > view matrix models
    5691 > #37,-0.068744,0.46239,-0.88401,155.61,-0.96301,-0.26218,-0.062249,167.76,-0.26056,0.84703,0.46331,108.27
    5692 
    5693 > view matrix models
    5694 > #37,-0.068744,0.46239,-0.88401,151.7,-0.96301,-0.26218,-0.062249,167.34,-0.26056,0.84703,0.46331,109.96
    5695 
    5696 > view matrix models
    5697 > #37,-0.068744,0.46239,-0.88401,148.05,-0.96301,-0.26218,-0.062249,168.6,-0.26056,0.84703,0.46331,113.26
    5698 
    5699 > fitmap #37 inMap #25
    5700 
    5701 Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
    5702 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 2098 atoms 
    5703 average map value = 0.188, steps = 268 
    5704 shifted from previous position = 1.8 
    5705 rotated from previous position = 31.7 degrees 
    5706 atoms outside contour = 1411, contour level = 0.2532 
    5707  
    5708 Position of CopD_full_Q5XJY5.pdb (#37) relative to
    5709 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5710 Matrix rotation and translation 
    5711 -0.10900924 0.75139291 -0.65078850 146.28424526 
    5712 -0.97991274 0.02875802 0.19734233 168.20699465 
    5713 0.16699701 0.65922808 0.73316460 122.79115227 
    5714 Axis 0.23450114 -0.41519279 -0.87899042 
    5715 Axis point 141.38224991 -30.78701025 0.00000000 
    5716 Rotation angle (degrees) 99.99389905 
    5717 Shift along axis -143.46675599 
    5718  
    5719 
    5720 > select subtract #37
    5721 
    5722 Nothing selected 
    5723 
    5724 > hide #!37 models
    5725 
    5726 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    5727 > predictions/alphafold 3
    5728 > /fold_20240724_copbdg1z1_try2/fold_20240724_copbdg1z1_try2_model_0.cif"
    5729 
    5730 Chain information for fold_20240724_copbdg1z1_try2_model_0.cif #41 
    5731 --- 
    5732 Chain | Description 
    5733 A | . 
    5734 B | . 
    5735 C | . 
    5736 D | . 
    5737  
    5738 Computing secondary structure 
    5739 
    5740 > select add #41
    5741 
    5742 19765 atoms, 20090 bonds, 2515 residues, 1 model selected 
    5743 
    5744 > ui tool show Matchmaker
    5745 
    5746 > matchmaker #41 to #35
    5747 
    5748 Computing secondary structure 
    5749 [Repeated 1 time(s)]  Parameters 
    5750 --- 
    5751 Chain pairing | bb 
    5752 Alignment algorithm | Needleman-Wunsch 
    5753 Similarity matrix | BLOSUM-62 
    5754 SS fraction | 0.3 
    5755 Gap open (HH/SS/other) | 18/18/6 
    5756 Gap extend | 1 
    5757 SS matrix |  |  | H | S | O 
    5758 ---|---|---|--- 
    5759 H | 6 | -9 | -6 
    5760 S |  | 6 | -6 
    5761 O |  |  | 4 
    5762 Iteration cutoff | 2 
    5763  
    5764 Matchmaker CopB_ Q9JIF7.pdb, chain A (#35) with
    5765 fold_20240724_copbdg1z1_try2_model_0.cif, chain A (#41), sequence alignment
    5766 score = 4801.7 
    5767 RMSD between 351 pruned atom pairs is 0.825 angstroms; (across all 953 pairs:
    5768 12.162) 
    5769  
    5770 
    5771 > fitmap #41 inMap #25
    5772 
    5773 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
    5774 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 19765 atoms 
    5775 average map value = 0.1792, steps = 108 
    5776 shifted from previous position = 5.04 
    5777 rotated from previous position = 8.73 degrees 
    5778 atoms outside contour = 12927, contour level = 0.2532 
    5779  
    5780 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
    5781 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5782 Matrix rotation and translation 
    5783 0.76300462 0.02891891 -0.64574581 129.45795402 
    5784 0.59375195 -0.42623762 0.68248085 141.01253356 
    5785 -0.25550456 -0.90414887 -0.34239193 134.21937577 
    5786 Axis -0.91776836 -0.22573072 0.32672141 
    5787 Axis point 0.00000000 107.57830339 53.51898785 
    5788 Rotation angle (degrees) 120.18624651 
    5789 Shift along axis -106.79093220 
    5790  
    5791 
    5792 > hide #!25 models
    5793 
    5794 > view matrix models
    5795 > #41,0.75987,0.021282,-0.64972,128.96,0.5945,-0.42707,0.6813,141.3,-0.26298,-0.90397,-0.33717,134.98
    5796 
    5797 > ui mousemode right select
    5798 
    5799 > select clear
    5800 
    5801 > select #37/A
    5802 
    5803 2098 atoms, 2129 bonds, 269 residues, 1 model selected 
    5804 
    5805 > select #41/A
    5806 
    5807 7501 atoms, 7619 bonds, 953 residues, 1 model selected 
    5808 
    5809 > select #41/D
    5810 
    5811 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    5812 
    5813 > delete sel
    5814 
    5815 > select #41/C
    5816 
    5817 6830 atoms, 6947 bonds, 874 residues, 1 model selected 
    5818 
    5819 > delete sel
    5820 
    5821 > fitmap #41 inMap #25
    5822 
    5823 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
    5824 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 11515 atoms 
    5825 average map value = 0.1733, steps = 152 
    5826 shifted from previous position = 7.6 
    5827 rotated from previous position = 10.2 degrees 
    5828 atoms outside contour = 7595, contour level = 0.2532 
    5829  
    5830 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
    5831 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5832 Matrix rotation and translation 
    5833 0.72372649 0.02528009 -0.68962373 129.00641102 
    5834 0.66961476 -0.26733223 0.69292825 143.29008926 
    5835 -0.16684136 -0.96327275 -0.21040333 139.88692109 
    5836 Axis -0.89407287 -0.28221546 0.34783348 
    5837 Axis point 0.00000000 117.92026971 52.51002968 
    5838 Rotation angle (degrees) 112.14825963 
    5839 Shift along axis -107.12245762 
    5840  
    5841 
    5842 > show #!25 models
    5843 
    5844 > hide #!25 models
    5845 
    5846 Drag select of 19 residues 
    5847 
    5848 > select up
    5849 
    5850 374 atoms, 380 bonds, 50 residues, 1 model selected 
    5851 
    5852 > select up
    5853 
    5854 4014 atoms, 4083 bonds, 511 residues, 1 model selected 
    5855 
    5856 > select down
    5857 
    5858 374 atoms, 380 bonds, 50 residues, 1 model selected 
    5859 
    5860 > delete sel
    5861 
    5862 Drag select of 24 residues, 2 pseudobonds 
    5863 
    5864 > select up
    5865 
    5866 272 atoms, 278 bonds, 2 pseudobonds, 34 residues, 2 models selected 
    5867 
    5868 > delete sel
    5869 
    5870 Drag select of 46 residues, 2 pseudobonds 
    5871 
    5872 > select up
    5873 
    5874 840 atoms, 846 bonds, 2 pseudobonds, 103 residues, 2 models selected 
    5875 
    5876 > delete sel
    5877 
    5878 Drag select of 81 residues, 2 pseudobonds 
    5879 Drag select of 82 residues, 2 pseudobonds 
    5880 
    5881 > select clear
    5882 
    5883 Drag select of 53 residues 
    5884 
    5885 > select up
    5886 
    5887 483 atoms, 487 bonds, 61 residues, 1 model selected 
    5888 
    5889 > select clear
    5890 
    5891 Drag select of 82 residues, 2 pseudobonds 
    5892 
    5893 > select up
    5894 
    5895 844 atoms, 855 bonds, 2 pseudobonds, 108 residues, 2 models selected 
    5896 
    5897 > delete sel
    5898 
    5899 > fitmap #41 inMap #25
    5900 
    5901 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
    5902 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 9185 atoms 
    5903 average map value = 0.207, steps = 68 
    5904 shifted from previous position = 0.487 
    5905 rotated from previous position = 1.21 degrees 
    5906 atoms outside contour = 5435, contour level = 0.2532 
    5907  
    5908 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
    5909 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5910 Matrix rotation and translation 
    5911 0.71958143 0.04416992 -0.69300187 128.82756784 
    5912 0.67569054 -0.27468426 0.68409856 142.78127561 
    5913 -0.16014013 -0.96051943 -0.22750289 139.51471009 
    5914 Axis -0.89355970 -0.28951634 0.34312003 
    5915 Axis point 0.00000000 115.94606449 53.28137283 
    5916 Rotation angle (degrees) 113.03559189 
    5917 Shift along axis -108.58234297 
    5918  
    5919 
    5920 > show #!25 models
    5921 
    5922 > hide #!25 models
    5923 
    5924 Drag select of 248 residues 
    5925 
    5926 > select up
    5927 
    5928 2203 atoms, 2233 bonds, 279 residues, 1 model selected 
    5929 
    5930 > delete sel
    5931 
    5932 > fitmap #41 inMap #25
    5933 
    5934 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
    5935 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6982 atoms 
    5936 average map value = 0.2082, steps = 260 
    5937 shifted from previous position = 7.84 
    5938 rotated from previous position = 14 degrees 
    5939 atoms outside contour = 4267, contour level = 0.2532 
    5940  
    5941 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
    5942 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5943 Matrix rotation and translation 
    5944 0.60641983 0.19676174 -0.77041535 127.17385378 
    5945 0.79490418 -0.12618975 0.59346734 140.58903166 
    5946 0.01955314 -0.97229675 -0.23293070 138.75917394 
    5947 Axis -0.84500929 -0.42632905 0.32280465 
    5948 Axis point 0.00000000 109.24582338 58.49339501 
    5949 Rotation angle (degrees) 112.10779478 
    5950 Shift along axis -122.60816993 
    5951  
    5952 
    5953 > show #!25 models
    5954 
    5955 > hide #!25 models
    5956 
    5957 Drag select of 85 residues, 1 pseudobonds 
    5958 
    5959 > select up
    5960 
    5961 826 atoms, 836 bonds, 1 pseudobond, 108 residues, 2 models selected 
    5962 
    5963 > delete sel
    5964 
    5965 Drag select of 43 residues 
    5966 
    5967 > select clear
    5968 
    5969 Drag select of 67 residues 
    5970 
    5971 > select up
    5972 
    5973 711 atoms, 719 bonds, 95 residues, 1 model selected 
    5974 
    5975 > delete sel
    5976 
    5977 > fitmap #41 inMap #25
    5978 
    5979 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
    5980 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 5445 atoms 
    5981 average map value = 0.1782, steps = 88 
    5982 shifted from previous position = 2.03 
    5983 rotated from previous position = 3.11 degrees 
    5984 atoms outside contour = 3752, contour level = 0.2532 
    5985  
    5986 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
    5987 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    5988 Matrix rotation and translation 
    5989 0.60331496 0.23815668 -0.76111264 129.24175666 
    5990 0.79728988 -0.15805568 0.58253519 139.72739672 
    5991 0.01843647 -0.95827960 -0.28523727 137.10117129 
    5992 Axis -0.84890646 -0.42948982 0.30805246 
    5993 Axis point 0.00000000 103.56300999 60.01449132 
    5994 Rotation angle (degrees) 114.83389261 
    5995 Shift along axis -127.49130401 
    5996  
    5997 
    5998 > show #!25 models
    5999 
    6000 > select add #41
    6001 
    6002 5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected 
    6003 Drag select of 25 W20_J4027_005_volume_map_gammazeta_local.mrc , 43 residues 
    6004 
    6005 > select clear
    6006 
    6007 > select add #41
    6008 
    6009 5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected 
    6010 
    6011 > ui mousemode right "translate selected models"
    6012 
    6013 > view matrix models
    6014 > #41,0.60241,0.22967,-0.76444,137.4,0.7981,-0.15867,0.58126,145.75,0.012205,-0.96025,-0.27888,129.95
    6015 
    6016 > fitmap #41 inMap #25
    6017 
    6018 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
    6019 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 5445 atoms 
    6020 average map value = 0.203, steps = 116 
    6021 shifted from previous position = 3.37 
    6022 rotated from previous position = 14.2 degrees 
    6023 atoms outside contour = 3158, contour level = 0.2532 
    6024  
    6025 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
    6026 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    6027 Matrix rotation and translation 
    6028 0.52191157 0.05705493 -0.85108933 136.78168805 
    6029 0.85298460 -0.02899341 0.52113016 146.75941736 
    6030 0.00505707 -0.99794996 -0.06379897 132.92819195 
    6031 Axis -0.79251134 -0.44665565 0.41524030 
    6032 Axis point 0.00000000 120.55875518 58.21435828 
    6033 Rotation angle (degrees) 106.58517534 
    6034 Shift along axis -118.75481890 
    6035  
    6036 
    6037 > select subtract #41
    6038 
    6039 Nothing selected 
    6040 
    6041 > select add #41
    6042 
    6043 5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected 
    6044 
    6045 > select subtract #41
    6046 
    6047 Nothing selected 
    6048 
    6049 > select add #41
    6050 
    6051 5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected 
    6052 
    6053 > select subtract #41
    6054 
    6055 Nothing selected 
    6056 
    6057 > show #35 models
    6058 
    6059 > hide #35 models
    6060 
    6061 > ui tool show Matchmaker
    6062 
    6063 > matchmaker #!37 to #41
    6064 
    6065 Computing secondary structure 
    6066 [Repeated 1 time(s)]  Parameters 
    6067 --- 
    6068 Chain pairing | bb 
    6069 Alignment algorithm | Needleman-Wunsch 
    6070 Similarity matrix | BLOSUM-62 
    6071 SS fraction | 0.3 
    6072 Gap open (HH/SS/other) | 18/18/6 
    6073 Gap extend | 1 
    6074 SS matrix |  |  | H | S | O 
    6075 ---|---|---|--- 
    6076 H | 6 | -9 | -6 
    6077 S |  | 6 | -6 
    6078 O |  |  | 4 
    6079 Iteration cutoff | 2 
    6080  
    6081 Matchmaker fold_20240724_copbdg1z1_try2_model_0.cif, chain B (#41) with
    6082 CopD_full_Q5XJY5.pdb, chain A (#37), sequence alignment score = 2184.5 
    6083 RMSD between 114 pruned atom pairs is 0.700 angstroms; (across all 244 pairs:
    6084 25.738) 
    6085  
    6086 
    6087 > show #!37 models
    6088 
    6089 > show #35 models
    6090 
    6091 > hide #!41 models
    6092 
    6093 > hide #!25 models
    6094 
    6095 > ui mousemode right rotate
    6096 
    6097 > ui mousemode right select
    6098 
    6099 Drag select of 1 residues 
    6100 
    6101 > select up
    6102 
    6103 184 atoms, 186 bonds, 25 residues, 1 model selected 
    6104 
    6105 > delete sel
    6106 
    6107 > show #!25 models
    6108 
    6109 Drag select of 6 residues 
    6110 
    6111 > select up
    6112 
    6113 483 atoms, 491 bonds, 69 residues, 1 model selected 
    6114 
    6115 > delete sel
    6116 
    6117 > hide #!25 models
    6118 
    6119 > show #!25 models
    6120 
    6121 > show #!34 models
    6122 
    6123 > show #38 models
    6124 
    6125 > show #39 models
    6126 
    6127 > show #36 models
    6128 
    6129 > hide #39 models
    6130 
    6131 > hide #!37 models
    6132 
    6133 > hide #36 models
    6134 
    6135 > hide #35 models
    6136 
    6137 > hide #!34 models
    6138 
    6139 > hide #!25 models
    6140 
    6141 Drag select of 41 residues 
    6142 
    6143 > select up
    6144 
    6145 531 atoms, 541 bonds, 67 residues, 1 model selected 
    6146 
    6147 > delete sel
    6148 
    6149 Drag select of 26 residues, 1 pseudobonds 
    6150 
    6151 > select up
    6152 
    6153 494 atoms, 500 bonds, 1 pseudobond, 64 residues, 2 models selected 
    6154 
    6155 > delete sel
    6156 
    6157 Drag select of 3 residues 
    6158 
    6159 > select up
    6160 
    6161 215 atoms, 218 bonds, 30 residues, 1 model selected 
    6162 
    6163 > delete sel
    6164 
    6165 Drag select of 43 residues, 1 pseudobonds 
    6166 
    6167 > select up
    6168 
    6169 499 atoms, 507 bonds, 1 pseudobond, 62 residues, 2 models selected 
    6170 
    6171 > select clear
    6172 
    6173 Drag select of 23 residues 
    6174 
    6175 > select up
    6176 
    6177 296 atoms, 302 bonds, 36 residues, 1 model selected 
    6178 Drag select of 51 residues, 2 pseudobonds 
    6179 
    6180 > select clear
    6181 
    6182 Drag select of 19 residues, 3 pseudobonds 
    6183 
    6184 > select up
    6185 
    6186 167 atoms, 168 bonds, 3 pseudobonds, 20 residues, 2 models selected 
    6187 
    6188 > delete sel
    6189 
    6190 > show #!25 models
    6191 
    6192 > hide #!25 models
    6193 
    6194 Drag select of 33 residues 
    6195 
    6196 > select up
    6197 
    6198 594 atoms, 601 bonds, 75 residues, 1 model selected 
    6199 
    6200 > delete sel
    6201 
    6202 > show #!25 models
    6203 
    6204 > hide #!25 models
    6205 
    6206 Drag select of 65 residues, 3 pseudobonds 
    6207 
    6208 > select up
    6209 
    6210 603 atoms, 610 bonds, 3 pseudobonds, 79 residues, 2 models selected 
    6211 
    6212 > delete sel
    6213 
    6214 > show #!25 models
    6215 
    6216 > fitmap #38 inMap #25
    6217 
    6218 Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
    6219 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4226 atoms 
    6220 average map value = 0.2729, steps = 96 
    6221 shifted from previous position = 0.601 
    6222 rotated from previous position = 5.3 degrees 
    6223 atoms outside contour = 1993, contour level = 0.2532 
    6224  
    6225 Position of CopG1_ Q9QZE5.pdb (#38) relative to
    6226 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    6227 Matrix rotation and translation 
    6228 -0.43244711 0.82798862 0.35696546 106.28810019 
    6229 -0.18802207 0.30438532 -0.93380795 122.80007772 
    6230 -0.88183740 -0.47093993 0.02404958 119.35137932 
    6231 Axis 0.27755203 0.74283001 -0.60923595 
    6232 Axis point 83.94095393 0.00000000 76.41437643 
    6233 Rotation angle (degrees) 123.50474947 
    6234 Shift along axis 48.00691086 
    6235  
    6236 
    6237 > show #39 models
    6238 
    6239 > fitmap #39 inMap #25
    6240 
    6241 Fit molecule CopZ1_P61924.pdb (#39) to map
    6242 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms 
    6243 average map value = 0.2375, steps = 180 
    6244 shifted from previous position = 1.19 
    6245 rotated from previous position = 45.5 degrees 
    6246 atoms outside contour = 765, contour level = 0.2532 
    6247  
    6248 Position of CopZ1_P61924.pdb (#39) relative to
    6249 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    6250 Matrix rotation and translation 
    6251 0.15949015 0.95372824 0.25488301 116.12737830 
    6252 0.29301360 -0.29228658 0.91033598 142.77739950 
    6253 0.94271201 -0.07050544 -0.32607217 99.85061617 
    6254 Axis -0.71693601 -0.50276157 -0.48294261 
    6255 Axis point 0.00000000 31.13613117 -0.38312474 
    6256 Rotation angle (degrees) 136.83898997 
    6257 Shift along axis -203.26100587 
    6258  
    6259 
    6260 > undo
    6261 
    6262 > show #39 models
    6263 
    6264 > ui tool show Matchmaker
    6265 
    6266 > matchmaker #39 to #40
    6267 
    6268 Computing secondary structure 
    6269 [Repeated 1 time(s)]  Parameters 
    6270 --- 
    6271 Chain pairing | bb 
    6272 Alignment algorithm | Needleman-Wunsch 
    6273 Similarity matrix | BLOSUM-62 
    6274 SS fraction | 0.3 
    6275 Gap open (HH/SS/other) | 18/18/6 
    6276 Gap extend | 1 
    6277 SS matrix |  |  | H | S | O 
    6278 ---|---|---|--- 
    6279 H | 6 | -9 | -6 
    6280 S |  | 6 | -6 
    6281 O |  |  | 4 
    6282 Iteration cutoff | 2 
    6283  
    6284 Matchmaker fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain C (#40)
    6285 with CopZ1_P61924.pdb, chain A (#39), sequence alignment score = 863.4 
    6286 RMSD between 141 pruned atom pairs is 0.407 angstroms; (across all 177 pairs:
    6287 16.666) 
    6288  
    6289 
    6290 > select clear
    6291 
    6292 > show #!34 models
    6293 
    6294 > show #35 models
    6295 
    6296 > show #36 models
    6297 
    6298 > show #!37 models
    6299 
    6300 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    6301 > resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
    6302 
    6303 > hide #!25 models
    6304 
    6305 > show #!26 models
    6306 
    6307 > hide #!26 models
    6308 
    6309 > show #!27 models
    6310 
    6311 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    6312 > resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
    6313 
    6314 ——— End of log from Tue Jul 1 15:42:09 2025 ———
    6315 
    6316 > view name session-start
    6317 
    6318 opened ChimeraX session 
    6319 
    6320 > show #!1 models
    6321 
    6322 > hide #!1 models
    6323 
    6324 > hide #!27 models
    6325 
    6326 > show #!29 models
    6327 
    6328 > hide #!29 models
    6329 
    6330 > show #!29 models
    6331 
    6332 > volume #29.1 level 0.01218
    6333 
    6334 > volume #29.2 level 0.009354
    6335 
    6336 > volume #29.3 level 0.003817
    6337 
    6338 > volume #29.4 level 0.01012
    6339 
    6340 > hide #!29 models
    6341 
    6342 > show #!29 models
    6343 
    6344 > color #29 silver models
    6345 
    6346 > color #29 darkgrey models
    6347 
    6348 > color #29 #a9a9a9c7 models
    6349 
    6350 > color #29 darkgrey models
    6351 
    6352 > color #29 #929292ff models
    6353 
    6354 > color #29 darkgrey models
    6355 
    6356 > show #!30 models
    6357 
    6358 > volume #30.1 level 0.004859
    6359 
    6360 > hide #!29 models
    6361 
    6362 > color #30 #929292ff models
    6363 
    6364 > volume #30.1 level 0.01271
    6365 
    6366 > volume #30.2 level 0.00973
    6367 
    6368 > volume #30.3 level 0.008159
    6369 
    6370 > volume #30.4 level 0.01229
    6371 
    6372 > hide #!30 models
    6373 
    6374 > show #!31 models
    6375 
    6376 > volume #31.1 level 0.01583
    6377 
    6378 > color #31 #929292ff models
    6379 
    6380 > volume #31.2 level 0.0156
    6381 
    6382 > volume #31.3 level 0.008589
    6383 
    6384 > volume #31.4 level 0.01446
    6385 
    6386 > hide #!31 models
    6387 
    6388 > color #32 #929292ff models
    6389 
    6390 > show #!32 models
    6391 
    6392 > volume #32.1 level 0.01368
    6393 
    6394 > volume #32.3 level 0.01158
    6395 
    6396 > volume #32.4 level 0.01325
    6397 
    6398 > volume #32.2 level 0.01059
    6399 
    6400 > hide #!32 models
    6401 
    6402 > show #!33 models
    6403 
    6404 > volume #33.1 level 0.01263
    6405 
    6406 > color #33 #929292ff models
    6407 
    6408 > volume #33.1 level 0.01481
    6409 
    6410 > volume #33.2 level 0.01481
    6411 
    6412 > volume #33.3 level 0.01517
    6413 
    6414 > volume #33.4 level 0.01344
    6415 
    6416 > hide #!34 models
    6417 
    6418 > hide #35 models
    6419 
    6420 > hide #36 models
    6421 
    6422 > hide #!37 models
    6423 
    6424 > hide #!38 models
    6425 
    6426 > hide #39 models
    6427 
    6428 > show #!41 models
    6429 
    6430 > hide #!41 models
    6431 
    6432 > show #40 models
    6433 
    6434 > hide #40 models
    6435 
    6436 > show #!29 models
    6437 
    6438 > color #29 #8efa00ff models
    6439 
    6440 > color #29 #fffc79ff models
    6441 
    6442 > volume #29.1 level 0.01322
    6443 
    6444 > volume #29.2 level 0.0117
    6445 
    6446 > volume #29.3 level 0.01271
    6447 
    6448 > volume #29.4 level 0.01296
    6449 
    6450 > hide #!29 models
    6451 
    6452 > show #!29 models
    6453 
    6454 > hide #!33 models
    6455 
    6456 > show #!30 models
    6457 
    6458 > hide #!30 models
    6459 
    6460 > show #!31 models
    6461 
    6462 > hide #!31 models
    6463 
    6464 > show #!32 models
    6465 
    6466 > hide #!32 models
    6467 
    6468 > show #!33 models
    6469 
    6470 > show #!32 models
    6471 
    6472 > hide #!32 models
    6473 
    6474 > show #!32 models
    6475 
    6476 > hide #!32 models
    6477 
    6478 > show #!32 models
    6479 
    6480 > hide #!32 models
    6481 
    6482 > show #!32 models
    6483 
    6484 > hide #!33 models
    6485 
    6486 > show #!33 models
    6487 
    6488 > hide #!32 models
    6489 
    6490 > hide #!33 models
    6491 
    6492 > show #!30 models
    6493 
    6494 > hide #!29 models
    6495 
    6496 > volume maximum #30.1 #30.2 #30.3 #30.4
    6497 
    6498 Opened volume maximum as #42, grid size 285,281,252, pixel 1.2, shown at step
    6499 1, values float32 
    6500 
    6501 > rename #42 W20_J140_MB
    6502 
    6503 > hide #!42 models
    6504 
    6505 > show #!42 models
    6506 
    6507 > volume maximum #31.1 #31.2 #31.3 #31.4
    6508 
    6509 Opened volume maximum as #43, grid size 248,255,253, pixel 1.2, shown at step
    6510 1, values float32 
    6511 
    6512 > rename #43 W20_J145_MB
    6513 
    6514 > hide #!43 models
    6515 
    6516 > show #!43 models
    6517 
    6518 > volume maximum #32.1 #32.2 #32.3 #32.4
    6519 
    6520 Opened volume maximum as #44, grid size 275,269,255, pixel 1.2, shown at step
    6521 1, values float32 
    6522 
    6523 > rename #44 W20_J150_MB
    6524 
    6525 > hide #!44 models
    6526 
    6527 > show #!44 models
    6528 
    6529 > volume maximum #33.1 #33.2 #33.3 #33.4
    6530 
    6531 Opened volume maximum as #45, grid size 299,295,317, pixel 1.2, shown at step
    6532 1, values float32 
    6533 
    6534 > rename #45 W20_J155_MB
    6535 
    6536 > volume maximum #34.1 #34.2 #34.3 #34.4
    6537 
    6538 [Repeated 3 time(s)]
    6539 
    6540 > close #42
    6541 
    6542 > close #43
    6543 
    6544 > close #44
    6545 
    6546 > close #45
    6547 
    6548 > volume maximum #34.1 #34.2 #34.3 #34.4
    6549 
    6550 > volume maximum #29.1 #29.2 #29.3 #29.4
    6551 
    6552 Opened volume maximum as #42, grid size 281,271,305, pixel 1.2, shown at step
    6553 1, values float32 
    6554 
    6555 > volume maximum #30.1 #29.2 #29.3 #29.4
    6556 
    6557 Opened volume maximum as #43, grid size 324,314,331, pixel 1.2, shown at step
    6558 1, values float32 
    6559 
    6560 > close #43
    6561 
    6562 > volume maximum #30.1 #30.2 #30.3 #30.4
    6563 
    6564 Opened volume maximum as #43, grid size 285,281,252, pixel 1.2, shown at step
    6565 1, values float32 
    6566 
    6567 > volume maximum #31.1 #31.2 #31.3 #31.4
    6568 
    6569 Opened volume maximum as #44, grid size 248,255,253, pixel 1.2, shown at step
    6570 1, values float32 
    6571 
    6572 > volume maximum #32.1 #32.2 #32.3 #32.4
    6573 
    6574 Opened volume maximum as #45, grid size 275,269,255, pixel 1.2, shown at step
    6575 1, values float32 
    6576 
    6577 > volume maximum #33.1 #33.2 #33.3 #33.4
    6578 
    6579 Opened volume maximum as #46, grid size 299,295,317, pixel 1.2, shown at step
    6580 1, values float32 
    6581 
    6582 > rename #42 W20_J140_MB
    6583 
    6584 > rename #42 W20_J140_MB_joined
    6585 
    6586 > rename #43 W20_J145_MB_joined
    6587 
    6588 > rename #44 W20_J150_MB_joined
    6589 
    6590 > rename #45 W20_J155_MB_joined
    6591 
    6592 > rename #46 W20_J160_MB_joined
    6593 
    6594 > fitmap #42 inMap #1
    6595 
    6596 Fit map W20_J140_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    6597 using 130669 points 
    6598 correlation = 0.3924, correlation about mean = 0.006354, overlap = 259.4 
    6599 steps = 144, shift = 7.92, angle = 8.21 degrees 
    6600  
    6601 Position of W20_J140_MB_joined (#42) relative to
    6602 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    6603 Matrix rotation and translation 
    6604 0.91620955 0.25591004 -0.30833442 2.94589670 
    6605 -0.21484448 0.96327207 0.16108624 14.27677310 
    6606 0.33823352 -0.08134481 0.93753993 -22.28584079 
    6607 Axis -0.29008545 -0.77366308 -0.56329022 
    6608 Axis point 63.49232840 0.00000000 -7.08518329 
    6609 Rotation angle (degrees) 24.69964443 
    6610 Shift along axis 0.65342200 
    6611  
    6612 
    6613 > fitmap #43 inMap #1
    6614 
    6615 Fit map W20_J145_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    6616 using 142902 points 
    6617 correlation = 0.4199, correlation about mean = 0.04049, overlap = 303 
    6618 steps = 164, shift = 1.19, angle = 6.55 degrees 
    6619  
    6620 Position of W20_J145_MB_joined (#43) relative to
    6621 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    6622 Matrix rotation and translation 
    6623 0.99583148 0.04008635 0.08193132 -23.34504583 
    6624 -0.04315588 0.99841798 0.03604305 -2.05514686 
    6625 -0.08035687 -0.03942862 0.99598602 16.93949740 
    6626 Axis -0.38234856 0.82217147 -0.42171514 
    6627 Axis point 196.57839852 0.00000000 294.50364776 
    6628 Rotation angle (degrees) 5.66401964 
    6629 Shift along axis 0.09261895 
    6630  
    6631 
    6632 > fitmap #44 inMap #1
    6633 
    6634 Fit map W20_J150_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    6635 using 100519 points 
    6636 correlation = 0.4322, correlation about mean = -0.01831, overlap = 243.2 
    6637 steps = 80, shift = 5.66, angle = 2.97 degrees 
    6638  
    6639 Position of W20_J150_MB_joined (#44) relative to
    6640 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    6641 Matrix rotation and translation 
    6642 0.99916201 0.02809111 0.02976842 -4.49636094 
    6643 -0.03208054 0.98915209 0.14334916 -11.35419842 
    6644 -0.02541866 -0.14418402 0.98922437 24.23768179 
    6645 Axis -0.96196921 0.18463355 -0.20130992 
    6646 Axis point 0.00000000 157.84496089 87.73789734 
    6647 Rotation angle (degrees) 8.59507208 
    6648 Shift along axis -2.65029098 
    6649  
    6650 
    6651 > fitmap #45 inMap #1
    6652 
    6653 Fit map W20_J155_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    6654 using 138129 points 
    6655 correlation = 0.4135, correlation about mean = 0.03029, overlap = 293.3 
    6656 steps = 136, shift = 5.25, angle = 4.6 degrees 
    6657  
    6658 Position of W20_J155_MB_joined (#45) relative to
    6659 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    6660 Matrix rotation and translation 
    6661 0.97166385 -0.22776257 -0.06319474 54.87908166 
    6662 0.22867640 0.97347338 0.00752908 -17.23256599 
    6663 0.05980356 -0.02176688 0.99797281 -6.95123433 
    6664 Axis -0.06185438 -0.25969395 0.96370799 
    6665 Axis point 107.95346859 225.99227664 0.00000000 
    6666 Rotation angle (degrees) 13.69857239 
    6667 Shift along axis -5.61827826 
    6668  
    6669 
    6670 > fitmap #46 inMap #1
    6671 
    6672 Fit map W20_J160_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    6673 using 121938 points 
    6674 correlation = 0.4485, correlation about mean = 0.04548, overlap = 303.4 
    6675 steps = 176, shift = 10.8, angle = 12.9 degrees 
    6676  
    6677 Position of W20_J160_MB_joined (#46) relative to
    6678 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    6679 Matrix rotation and translation 
    6680 0.98515785 -0.09819617 0.14078890 -1.18436719 
    6681 0.06853050 0.97700616 0.20189734 -32.23116044 
    6682 -0.15737717 -0.18925241 0.96923472 51.60758570 
    6683 Axis -0.75318811 0.57414108 0.32104469 
    6684 Axis point 0.00000000 244.46953938 184.51242914 
    6685 Rotation angle (degrees) 15.05005024 
    6686 Shift along axis -1.04484054 
    6687  
    6688 
    6689 > show #!1 models
    6690 
    6691 > hide #!1 models
    6692 
    6693 > show #!2 models
    6694 
    6695 > hide #!2 models
    6696 
    6697 > hide #!42 models
    6698 
    6699 > hide #!43 models
    6700 
    6701 > hide #!44 models
    6702 
    6703 > hide #!45 models
    6704 
    6705 > hide #!46 models
    6706 
    6707 > show #!1 models
    6708 
    6709 > show #!2 models
    6710 
    6711 > hide #!2 models
    6712 
    6713 > show #!3 models
    6714 
    6715 > hide #!3 models
    6716 
    6717 > show #!4 models
    6718 
    6719 > hide #!4 models
    6720 
    6721 > show #!5 models
    6722 
    6723 > hide #!5 models
    6724 
    6725 > show #!6 models
    6726 
    6727 > hide #!6 models
    6728 
    6729 > show #!7 models
    6730 
    6731 > hide #!7 models
    6732 
    6733 > show #!8 models
    6734 
    6735 > hide #!8 models
    6736 
    6737 > show #!9 models
    6738 
    6739 > hide #!9 models
    6740 
    6741 > show #!10 models
    6742 
    6743 > hide #!10 models
    6744 
    6745 > show #!11 models
    6746 
    6747 > hide #!11 models
    6748 
    6749 > show #!12 models
    6750 
    6751 > hide #!12 models
    6752 
    6753 > show #!13 models
    6754 
    6755 > hide #!13 models
    6756 
    6757 > show #!14 models
    6758 
    6759 > hide #!14 models
    6760 
    6761 > show #!15 models
    6762 
    6763 > hide #!15 models
    6764 
    6765 > show #!16 models
    6766 
    6767 > hide #!16 models
    6768 
    6769 > show #!17 models
    6770 
    6771 > hide #!17 models
    6772 
    6773 > show #!18 models
    6774 
    6775 > hide #!18 models
    6776 
    6777 > show #!19 models
    6778 
    6779 > hide #!19 models
    6780 
    6781 > show #!20 models
    6782 
    6783 > hide #!20 models
    6784 
    6785 > show #!21 models
    6786 
    6787 > hide #!21 models
    6788 
    6789 > show #!22 models
    6790 
    6791 > hide #!22 models
    6792 
    6793 > show #!23 models
    6794 
    6795 > hide #!23 models
    6796 
    6797 > show #!24 models
    6798 
    6799 > hide #!24 models
    6800 
    6801 > show #!25 models
    6802 
    6803 > hide #!25 models
    6804 
    6805 > show #!25 models
    6806 
    6807 > color #25 silver models
    6808 
    6809 [Repeated 1 time(s)]
    6810 
    6811 > hide #!25 models
    6812 
    6813 > show #!26 models
    6814 
    6815 > hide #!26 models
    6816 
    6817 > show #!27 models
    6818 
    6819 > hide #!27 models
    6820 
    6821 > show #!28 models
    6822 
    6823 > hide #!28 models
    6824 
    6825 > show #!29 models
    6826 
    6827 > hide #!29 models
    6828 
    6829 > hide #!30 models
    6830 
    6831 > show #!30 models
    6832 
    6833 > hide #!30 models
    6834 
    6835 > show #!29 models
    6836 
    6837 > hide #!29 models
    6838 
    6839 > show #!30 models
    6840 
    6841 > hide #!30 models
    6842 
    6843 > show #!30.1 models
    6844 
    6845 > show #!30.2 models
    6846 
    6847 > show #!30.3 models
    6848 
    6849 > show #!30.4 models
    6850 
    6851 > show #!29 models
    6852 
    6853 > hide #!29 models
    6854 
    6855 > hide #!30 models
    6856 
    6857 > show #!30 models
    6858 
    6859 > hide #!30 models
    6860 
    6861 > show #!30 models
    6862 
    6863 > hide #!30 models
    6864 
    6865 > show #!30 models
    6866 
    6867 > hide #!30 models
    6868 
    6869 > show #!29.1 models
    6870 
    6871 > show #!29.2 models
    6872 
    6873 > show #!29.3 models
    6874 
    6875 > show #!29.4 models
    6876 
    6877 > hide #!29 models
    6878 
    6879 > show #!31 models
    6880 
    6881 > show #!31.1 models
    6882 
    6883 > show #!31.2 models
    6884 
    6885 > show #!31.3 models
    6886 
    6887 > show #!31.4 models
    6888 
    6889 > hide #!31 models
    6890 
    6891 > show #!31 models
    6892 
    6893 > hide #!31 models
    6894 
    6895 > show #!31 models
    6896 
    6897 > hide #!31 models
    6898 
    6899 > show #!32 models
    6900 
    6901 > show #!32.1 models
    6902 
    6903 > show #!32.2 models
    6904 
    6905 > show #!32.3 models
    6906 
    6907 > show #!32.4 models
    6908 
    6909 > hide #!32 models
    6910 
    6911 > select add #32
    6912 
    6913 9 models selected 
    6914 
    6915 > select subtract #32
    6916 
    6917 Nothing selected 
    6918 
    6919 > show #!32 models
    6920 
    6921 > hide #!32 models
    6922 
    6923 > show #!33 models
    6924 
    6925 > show #!33.1 models
    6926 
    6927 > show #!33.2 models
    6928 
    6929 > show #!33.3 models
    6930 
    6931 > show #!33.4 models
    6932 
    6933 > hide #!33 models
    6934 
    6935 > show #!32 models
    6936 
    6937 > hide #!32 models
    6938 
    6939 > show #!33 models
    6940 
    6941 > hide #!33 models
    6942 
    6943 > show #!42 models
    6944 
    6945 > hide #!42 models
    6946 
    6947 > show #!42 models
    6948 
    6949 > show #!43 models
    6950 
    6951 > hide #!43 models
    6952 
    6953 > select add #42
    6954 
    6955 2 models selected 
    6956 
    6957 > view matrix models
    6958 > #42,0.91621,0.25591,-0.30833,6.5795,-0.21484,0.96327,0.16109,11.618,0.33823,-0.081345,0.93754,-14.738
    6959 
    6960 > ui mousemode right "rotate selected models"
    6961 
    6962 > view matrix models
    6963 > #42,-0.20075,-0.93591,0.28944,250.09,-0.75521,0.33604,0.5628,121.07,-0.62399,-0.10561,-0.77426,360.31
    6964 
    6965 > ui mousemode right "translate selected models"
    6966 
    6967 > view matrix models
    6968 > #42,-0.20075,-0.93591,0.28944,258.45,-0.75521,0.33604,0.5628,111.09,-0.62399,-0.10561,-0.77426,373.71
    6969 
    6970 > ui mousemode right "rotate selected models"
    6971 
    6972 > view matrix models
    6973 > #42,-0.33018,-0.9414,-0.068949,327.26,-0.81305,0.24654,0.52742,137.15,-0.47951,0.2302,-0.8468,314.67
    6974 
    6975 > fitmap #42 inMap #1
    6976 
    6977 Fit map W20_J140_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    6978 using 130669 points 
    6979 correlation = 0.8803, correlation about mean = 0.3684, overlap = 1189 
    6980 steps = 172, shift = 19.9, angle = 7.77 degrees 
    6981  
    6982 Position of W20_J140_MB_joined (#42) relative to
    6983 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    6984 Matrix rotation and translation 
    6985 -0.35155267 -0.92578085 -0.13907028 347.82271473 
    6986 -0.76197836 0.19666262 0.61701928 136.35497869 
    6987 -0.54387471 0.32288331 -0.77456224 286.91060622 
    6988 Axis -0.55865111 0.76884323 0.31110933 
    6989 Axis point 248.45663259 0.00000000 85.56946066 
    6990 Rotation angle (degrees) 164.73667959 
    6991 Shift along axis -0.21537821 
    6992  
    6993 
    6994 > select subtract #42
    6995 
    6996 Nothing selected 
    6997 
    6998 > hide #!42 models
    6999 
    7000 > show #!43 models
    7001 
    7002 > select add #43
    7003 
    7004 2 models selected 
    7005 
    7006 > view matrix models
    7007 > #43,-0.71667,-0.59905,-0.3571,362.32,-0.66464,0.43155,0.60993,81.644,-0.21127,0.67446,-0.70744,174.56
    7008 
    7009 > view matrix models
    7010 > #43,-0.22267,-0.96408,0.14484,277.38,-0.843,0.26503,0.46809,150.16,-0.48966,-0.017866,-0.87173,336.37
    7011 
    7012 > ui mousemode right "translate selected models"
    7013 
    7014 > view matrix models
    7015 > #43,-0.22267,-0.96408,0.14484,278.5,-0.843,0.26503,0.46809,152.18,-0.48966,-0.017866,-0.87173,341.6
    7016 
    7017 > fitmap #43 inMap #1
    7018 
    7019 Fit map W20_J145_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    7020 using 142902 points 
    7021 correlation = 0.8839, correlation about mean = 0.3912, overlap = 1241 
    7022 steps = 176, shift = 16.1, angle = 20.5 degrees 
    7023  
    7024 Position of W20_J145_MB_joined (#43) relative to
    7025 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    7026 Matrix rotation and translation 
    7027 -0.33273365 -0.93244330 -0.14084678 345.90650730 
    7028 -0.76625576 0.18027360 0.61672809 139.19380919 
    7029 -0.54967302 0.31313085 -0.77447314 289.28503932 
    7030 Axis -0.56677541 0.76322385 0.31024988 
    7031 Axis point 250.48919740 0.00000000 85.44391549 
    7032 Rotation angle (degrees) 164.46490776 
    7033 Shift along axis -0.06461673 
    7034  
    7035 
    7036 > select subtract #43
    7037 
    7038 Nothing selected 
    7039 
    7040 > hide #!43 models
    7041 
    7042 > show #!44 models
    7043 
    7044 > select add #44
    7045 
    7046 2 models selected 
    7047 
    7048 > ui mousemode right "rotate selected models"
    7049 
    7050 > view matrix models
    7051 > #44,-0.64334,-0.25066,-0.72339,371.34,-0.44115,0.89362,0.082686,67.718,0.62571,0.37232,-0.68547,101.18
    7052 
    7053 > view matrix models
    7054 > #44,-0.33974,-0.91968,0.1969,294.7,-0.6214,0.37665,0.68702,81.003,-0.706,0.11106,-0.69945,324.73
    7055 
    7056 > view matrix models
    7057 > #44,-0.34685,-0.93744,0.029929,322.46,-0.77694,0.30504,0.55074,132.64,-0.52542,0.16777,-0.83414,311.06
    7058 
    7059 > ui mousemode right "translate selected models"
    7060 
    7061 > view matrix models
    7062 > #44,-0.34685,-0.93744,0.029929,328.6,-0.77694,0.30504,0.55074,126.41,-0.52542,0.16777,-0.83414,322.03
    7063 
    7064 > fitmap #44 inMap #1
    7065 
    7066 Fit map W20_J150_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    7067 using 100519 points 
    7068 correlation = 0.8806, correlation about mean = 0.2563, overlap = 1060 
    7069 steps = 104, shift = 9.91, angle = 11.1 degrees 
    7070  
    7071 Position of W20_J150_MB_joined (#44) relative to
    7072 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    7073 Matrix rotation and translation 
    7074 -0.34988200 -0.92650940 -0.13843016 347.22501351 
    7075 -0.75857847 0.19350448 0.62218544 135.60290867 
    7076 -0.54967381 0.32270162 -0.77053382 287.77852170 
    7077 Axis -0.55901416 0.76762419 0.31345858 
    7078 Axis point 248.55561653 0.00000000 85.33747140 
    7079 Rotation angle (degrees) 164.46257054 
    7080 Shift along axis 0.19501983 
    7081  
    7082 
    7083 > select subtract #44
    7084 
    7085 Nothing selected 
    7086 
    7087 > hide #!44 models
    7088 
    7089 > show #!45 models
    7090 
    7091 > ui mousemode right "rotate selected models"
    7092 
    7093 > select add #45
    7094 
    7095 2 models selected 
    7096 
    7097 > view matrix models
    7098 > #45,-0.93945,-0.28966,-0.18313,341.27,-0.33735,0.87568,0.34552,26.538,0.060286,0.38637,-0.92037,203.81
    7099 
    7100 > view matrix models
    7101 > #45,-0.39594,-0.91199,0.10724,318.12,-0.72625,0.38247,0.57121,120.46,-0.56195,0.14828,-0.81377,308.66
    7102 
    7103 > fitmap #45 inMap #1
    7104 
    7105 Fit map W20_J155_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    7106 using 138129 points 
    7107 correlation = 0.8776, correlation about mean = 0.3767, overlap = 1250 
    7108 steps = 140, shift = 15.4, angle = 15.9 degrees 
    7109  
    7110 Position of W20_J155_MB_joined (#45) relative to
    7111 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    7112 Matrix rotation and translation 
    7113 -0.35675611 -0.91947462 -0.16520144 351.40689174 
    7114 -0.78155048 0.19688467 0.59195886 143.25471986 
    7115 -0.51176551 0.34029820 -0.78885563 282.02499467 
    7116 Axis -0.55929726 0.77021311 0.30652624 
    7117 Axis point 248.57307844 0.00000000 86.50174383 
    7118 Rotation angle (degrees) 166.99833687 
    7119 Shift along axis 0.24381166 
    7120  
    7121 
    7122 > select subtract #45
    7123 
    7124 Nothing selected 
    7125 
    7126 > hide #!45 models
    7127 
    7128 > show #!46 models
    7129 
    7130 > select add #46
    7131 
    7132 2 models selected 
    7133 
    7134 > view matrix models
    7135 > #46,-0.25068,-0.94965,-0.18794,340.4,-0.93649,0.1887,0.29561,209.1,-0.24527,0.25011,-0.93664,265.98
    7136 
    7137 > view matrix models
    7138 > #46,-0.071284,-0.98257,0.17165,270.25,-0.5959,0.17996,0.78264,95.4,-0.79989,-0.046498,-0.59834,338.43
    7139 
    7140 > ui mousemode right "translate selected models"
    7141 
    7142 > view matrix models
    7143 > #46,-0.071284,-0.98257,0.17165,275.5,-0.5959,0.17996,0.78264,90.643,-0.79989,-0.046498,-0.59834,355.66
    7144 
    7145 > view matrix models
    7146 > #46,-0.071284,-0.98257,0.17165,285.03,-0.5959,0.17996,0.78264,91.932,-0.79989,-0.046498,-0.59834,362.22
    7147 
    7148 > fitmap #46 inMap #1
    7149 
    7150 Fit map W20_J160_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
    7151 using 121938 points 
    7152 correlation = 0.8667, correlation about mean = 0.3087, overlap = 1157 
    7153 steps = 208, shift = 18.2, angle = 31.4 degrees 
    7154  
    7155 Position of W20_J160_MB_joined (#46) relative to
    7156 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    7157 Matrix rotation and translation 
    7158 -0.39178850 -0.90130925 -0.18477932 357.17449457 
    7159 -0.76159854 0.20502417 0.61476235 135.64467847 
    7160 -0.51620677 0.38158448 -0.76676193 274.65181077 
    7161 Axis -0.54399036 0.77320089 0.32593693 
    7162 Axis point 245.55803639 0.00000000 83.69005707 
    7163 Rotation angle (degrees) 167.62426420 
    7164 Shift along axis 0.10027404 
    7165  
    7166 
    7167 > select subtract #46
    7168 
    7169 Nothing selected 
    7170 
    7171 > hide #!46 models
    7172 
    7173 > show #!46 models
    7174 
    7175 > hide #!46 models
    7176 
    7177 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    7178 > resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
    7179 
    7180 ——— End of log from Wed Jul 2 15:03:33 2025 ———
    7181 
    7182 > view name session-start
    7183 
    7184 opened ChimeraX session 
    7185 
    7186 > hide #!1 models
    7187 
    7188 > show #!46 models
    7189 
    7190 > show #!45 models
    7191 
    7192 > show #!25 models
    7193 
    7194 > color #25 #ff2600ff models
    7195 
    7196 > color #46 #ff9300ff models
    7197 
    7198 > color #45 #fffb00ff models
    7199 
    7200 > show #!9 models
    7201 
    7202 > color #9 #8efa00ff models
    7203 
    7204 > show #!27 models
    7205 
    7206 > color #27 #00fdffff models
    7207 
    7208 > show #!23 models
    7209 
    7210 > color #23 #0433ffff models
    7211 
    7212 > hide #!27 models
    7213 
    7214 > show #!27 models
    7215 
    7216 > hide #!27 models
    7217 
    7218 > hide #!25 models
    7219 
    7220 > hide #!23 models
    7221 
    7222 > hide #!9 models
    7223 
    7224 > hide #!45 models
    7225 
    7226 > hide #!46 models
    7227 
    7228 > show #!46 models
    7229 
    7230 > show #!23 models
    7231 
    7232 > hide #!46 models
    7233 
    7234 > hide #!23 models
    7235 
    7236 > show #!46 models
    7237 
    7238 > hide #!1 models
    7239 
    7240 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    7241 > resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
    7242 
    7243 ——— End of log from Wed Jul 2 17:43:06 2025 ———
    7244 
    7245 opened ChimeraX session 
    7246 
    7247 > color list
    7248 
    7249 28 custom colors: alphav1
    7250 
    7251 , alphav2
    7252 
    7253 , alphav3
    7254 
    7255 , arf1v1
    7256 
    7257 , arf1v2
    7258 
    7259 , arf1v3
    7260 
    7261 , betapv1
    7262 
    7263 , betapv2
    7264 
    7265 , betapv3
    7266 
    7267 , betav1
    7268 
    7269 , betav2
    7270 
    7271 , betav3
    7272 
    7273 , deltav1
    7274 
    7275 , deltav2
    7276 
    7277 , deltav3
    7278 
    7279 , epsilonv1
    7280 
    7281 , epsilonv3
    7282 
    7283 , gammav1
    7284 
    7285 , gammav2
    7286 
    7287 , gammav3
    7288 
    7289 , label_purple
    7290 
    7291 , label_purple_v3
    7292 
    7293 , label_red
    7294 
    7295 , label_red_v3
    7296 
    7297 , lable_purple_v4
    7298 
    7299 , zetav1
    7300 
    7301 , zetav2
    7302 
    7303 , and zetav3
    7304 
    7305 . 
    7306 248 builtin colors: alice blue
    7307 
    7308 , aliceblue
    7309 
    7310 , antique white
    7311 
    7312 , antiquewhite
    7313 
    7314 , aqua
    7315 
    7316 , aquamarine
    7317 
    7318 , azure
    7319 
    7320 , beige
    7321 
    7322 , bisque
    7323 
    7324 , black
    7325 
    7326 , blanched almond
    7327 
    7328 , blanchedalmond
    7329 
    7330 , blue
    7331 
    7332 , blue violet
    7333 
    7334 , blueviolet
    7335 
    7336 , brown
    7337 
    7338 , burly wood
    7339 
    7340 , burlywood
    7341 
    7342 , cadet blue
    7343 
    7344 , cadetblue
    7345 
    7346 , chartreuse
    7347 
    7348 , chocolate
    7349 
    7350 , coral
    7351 
    7352 , cornflower blue
    7353 
    7354 , cornflowerblue
    7355 
    7356 , cornsilk
    7357 
    7358 , crimson
    7359 
    7360 , cyan
    7361 
    7362 , dark blue
    7363 
    7364 , dark cyan
    7365 
    7366 , dark goldenrod
    7367 
    7368 , dark gray
    7369 
    7370 , dark green
    7371 
    7372 , dark grey
    7373 
    7374 , dark khaki
    7375 
    7376 , dark magenta
    7377 
    7378 , dark olive green
    7379 
    7380 , dark orange
    7381 
    7382 , dark orchid
    7383 
    7384 , dark red
    7385 
    7386 , dark salmon
    7387 
    7388 , dark sea green
    7389 
    7390 , dark seagreen
    7391 
    7392 , dark slate blue
    7393 
    7394 , dark slate gray
    7395 
    7396 , dark slate grey
    7397 
    7398 , dark turquoise
    7399 
    7400 , dark violet
    7401 
    7402 , darkblue
    7403 
    7404 , darkcyan
    7405 
    7406 , darkgoldenrod
    7407 
    7408 , darkgray
    7409 
    7410 , darkgreen
    7411 
    7412 , darkgrey
    7413 
    7414 , darkkhaki
    7415 
    7416 , darkmagenta
    7417 
    7418 , darkolivegreen
    7419 
    7420 , darkorange
    7421 
    7422 , darkorchid
    7423 
    7424 , darkred
    7425 
    7426 , darksalmon
    7427 
    7428 , darkseagreen
    7429 
    7430 , darkslateblue
    7431 
    7432 , darkslategray
    7433 
    7434 , darkslategrey
    7435 
    7436 , darkturquoise
    7437 
    7438 , darkviolet
    7439 
    7440 , deep pink
    7441 
    7442 , deep sky blue
    7443 
    7444 , deep skyblue
    7445 
    7446 , deeppink
    7447 
    7448 , deepskyblue
    7449 
    7450 , dim gray
    7451 
    7452 , dim grey
    7453 
    7454 , dimgray
    7455 
    7456 , dimgrey
    7457 
    7458 , dodger blue
    7459 
    7460 , dodgerblue
    7461 
    7462 , fire brick
    7463 
    7464 , firebrick
    7465 
    7466 , floral white
    7467 
    7468 , floralwhite
    7469 
    7470 , forest green
    7471 
    7472 , forestgreen
    7473 
    7474 , fuchsia
    7475 
    7476 , gainsboro
    7477 
    7478 , ghost white
    7479 
    7480 , ghostwhite
    7481 
    7482 , gold
    7483 
    7484 , goldenrod
    7485 
    7486 , gray
    7487 
    7488 , green
    7489 
    7490 , green yellow
    7491 
    7492 , greenyellow
    7493 
    7494 , grey
    7495 
    7496 , honeydew
    7497 
    7498 , hot pink
    7499 
    7500 , hotpink
    7501 
    7502 , indian red
    7503 
    7504 , indianred
    7505 
    7506 , indigo
    7507 
    7508 , ivory
    7509 
    7510 , khaki
    7511 
    7512 , lavender
    7513 
    7514 , lavender blush
    7515 
    7516 , lavenderblush
    7517 
    7518 , lawn green
    7519 
    7520 , lawngreen
    7521 
    7522 , lemon chiffon
    7523 
    7524 , lemonchiffon
    7525 
    7526 , light blue
    7527 
    7528 , light coral
    7529 
    7530 , light cyan
    7531 
    7532 , light goldenrod yellow
    7533 
    7534 , light gray
    7535 
    7536 , light green
    7537 
    7538 , light grey
    7539 
    7540 , light pink
    7541 
    7542 , light salmon
    7543 
    7544 , light sea green
    7545 
    7546 , light seagreen
    7547 
    7548 , light sky blue
    7549 
    7550 , light skyblue
    7551 
    7552 , light slate gray
    7553 
    7554 , light slate grey
    7555 
    7556 , light steel blue
    7557 
    7558 , light yellow
    7559 
    7560 , lightblue
    7561 
    7562 , lightcoral
    7563 
    7564 , lightcyan
    7565 
    7566 , lightgoldenrodyellow
    7567 
    7568 , lightgray
    7569 
    7570 , lightgreen
    7571 
    7572 , lightgrey
    7573 
    7574 , lightpink
    7575 
    7576 , lightsalmon
    7577 
    7578 , lightseagreen
    7579 
    7580 , lightskyblue
    7581 
    7582 , lightslategray
    7583 
    7584 , lightslategrey
    7585 
    7586 , lightsteelblue
    7587 
    7588 , lightyellow
    7589 
    7590 , lime
    7591 
    7592 , lime green
    7593 
    7594 , limegreen
    7595 
    7596 , linen
    7597 
    7598 , magenta
    7599 
    7600 , maroon
    7601 
    7602 , medium aquamarine
    7603 
    7604 , medium blue
    7605 
    7606 , medium orchid
    7607 
    7608 , medium purple
    7609 
    7610 , medium sea green
    7611 
    7612 , medium seagreen
    7613 
    7614 , medium slate blue
    7615 
    7616 , medium spring green
    7617 
    7618 , medium turquoise
    7619 
    7620 , medium violet red
    7621 
    7622 , mediumaquamarine
    7623 
    7624 , mediumblue
    7625 
    7626 , mediumorchid
    7627 
    7628 , mediumpurple
    7629 
    7630 , mediumseagreen
    7631 
    7632 , mediumslateblue
    7633 
    7634 , mediumspringgreen
    7635 
    7636 , mediumturquoise
    7637 
    7638 , mediumvioletred
    7639 
    7640 , midnight blue
    7641 
    7642 , midnightblue
    7643 
    7644 , mint cream
    7645 
    7646 , mintcream
    7647 
    7648 , misty rose
    7649 
    7650 , mistyrose
    7651 
    7652 , moccasin
    7653 
    7654 , navajo white
    7655 
    7656 , navajowhite
    7657 
    7658 , navy
    7659 
    7660 , old lace
    7661 
    7662 , oldlace
    7663 
    7664 , olive
    7665 
    7666 , olive drab
    7667 
    7668 , olivedrab
    7669 
    7670 , orange
    7671 
    7672 , orange red
    7673 
    7674 , orangered
    7675 
    7676 , orchid
    7677 
    7678 , pale goldenrod
    7679 
    7680 , pale green
    7681 
    7682 , pale turquoise
    7683 
    7684 , pale violet red
    7685 
    7686 , palegoldenrod
    7687 
    7688 , palegreen
    7689 
    7690 , paleturquoise
    7691 
    7692 , palevioletred
    7693 
    7694 , papaya whip
    7695 
    7696 , papayawhip
    7697 
    7698 , peach puff
    7699 
    7700 , peachpuff
    7701 
    7702 , peru
    7703 
    7704 , pink
    7705 
    7706 , plum
    7707 
    7708 , powder blue
    7709 
    7710 , powderblue
    7711 
    7712 , purple
    7713 
    7714 , rebecca purple
    7715 
    7716 , rebeccapurple
    7717 
    7718 , red
    7719 
    7720 , rosy brown
    7721 
    7722 , rosybrown
    7723 
    7724 , royal blue
    7725 
    7726 , royalblue
    7727 
    7728 , saddle brown
    7729 
    7730 , saddlebrown
    7731 
    7732 , salmon
    7733 
    7734 , sandy brown
    7735 
    7736 , sandybrown
    7737 
    7738 , sea green
    7739 
    7740 , seagreen
    7741 
    7742 , seashell
    7743 
    7744 , sienna
    7745 
    7746 , silver
    7747 
    7748 , sky blue
    7749 
    7750 , skyblue
    7751 
    7752 , slate blue
    7753 
    7754 , slate gray
    7755 
    7756 , slate grey
    7757 
    7758 , slateblue
    7759 
    7760 , slategray
    7761 
    7762 , slategrey
    7763 
    7764 , snow
    7765 
    7766 , spring green
    7767 
    7768 , springgreen
    7769 
    7770 , steel blue
    7771 
    7772 , steelblue
    7773 
    7774 , tan
    7775 
    7776 , teal
    7777 
    7778 , thistle
    7779 
    7780 , tomato
    7781 
    7782 , transparent
    7783 
    7784 , turquoise
    7785 
    7786 , violet
    7787 
    7788 , wheat
    7789 
    7790 , white
    7791 
    7792 , white smoke
    7793 
    7794 , whitesmoke
    7795 
    7796 , yellow
    7797 
    7798 , yellow green
    7799 
    7800 , and yellowgreen
    7801 
    7802 . 
    7803 
    7804 > color name gamma_1 #5EAF5A
    7805 
    7806 Color 'gamma_1' is opaque: rgb(36.9%, 68.6%, 35.3%) hex: #5eaf5a
    7807 
    7808  
    7809 
    7810 > color name gamma_2 #83CA6B
    7811 
    7812 Color 'gamma_2' is opaque: rgb(51.4%, 79.2%, 42%) hex: #83ca6b
    7813 
    7814  
    7815 
    7816 > color name gamma_3 #ADE57C
    7817 
    7818 Color 'gamma_3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c
    7819 
    7820  
    7821 
    7822 > color name gamma_4 #C9EA8C
    7823 
    7824 Color 'gamma_4' is opaque: rgb(78.8%, 91.8%, 54.9%) hex: #c9ea8c
    7825 
    7826  
    7827 
    7828 > color name gamma_5 #E1EF9C
    7829 
    7830 Color 'gamma_5' is opaque: rgb(88.2%, 93.7%, 61.2%) hex: #e1ef9c
    7831 
    7832  
    7833 
    7834 > color name gamma_6 #F3FIAD
    7835 
    7836 Missing or invalid "color" argument: expected hexadecimal digits after # 
    7837 
    7838 > color name gamma_6 #F3F1AD
    7839 
    7840 Color 'gamma_6' is opaque: rgb(95.3%, 94.5%, 67.8%) hex: #f3f1ad
    7841 
    7842  
    7843 
    7844 > show #!45 models
    7845 
    7846 > hide #!45 models
    7847 
    7848 > hide #!46 models
    7849 
    7850 > show #!46 models
    7851 
    7852 > show #!45 models
    7853 
    7854 > show #!25 models
    7855 
    7856 > hide #!46 models
    7857 
    7858 > hide #!45 models
    7859 
    7860 > show #!38 models
    7861 
    7862 > show #35 models
    7863 
    7864 > color #25 silver models
    7865 
    7866 > color #25 #c0c0c074 models
    7867 
    7868 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    7869 > resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/W20_C1_initial_model_v3.pdb"
    7870 
    7871 Chain information for W20_C1_initial_model_v3.pdb #47 
    7872 --- 
    7873 Chain | Description 
    7874 D E | No description available 
    7875 F | No description available 
    7876 G | No description available 
    7877 H | No description available 
    7878 I | No description available 
    7879 J | No description available 
    7880 K | No description available 
    7881 L | No description available 
    7882  
    7883 
    7884 > select add #47
    7885 
    7886 28705 atoms, 29239 bonds, 3 pseudobonds, 3615 residues, 2 models selected 
    7887 
    7888 > hide sel atoms
    7889 
    7890 > show sel cartoons
    7891 
    7892 > hide #!38 models
    7893 
    7894 > hide #35 models
    7895 
    7896 > view matrix models #47,1,0,0,-79.232,0,1,0,36.623,0,0,1,9.1376
    7897 
    7898 > view matrix models #47,1,0,0,-13.804,0,1,0,-20.445,0,0,1,10.191
    7899 
    7900 > view matrix models #47,1,0,0,0.72332,0,1,0,-4.6589,0,0,1,-2.6371
    7901 
    7902 > fitmap #47 inMap #1
    7903 
    7904 Fit molecule W20_C1_initial_model_v3.pdb (#47) to map
    7905 W20_J3623_consensus_structure_sharp.mrc (#1) using 28705 atoms 
    7906 average map value = 0.301, steps = 80 
    7907 shifted from previous position = 5.02 
    7908 rotated from previous position = 0.504 degrees 
    7909 atoms outside contour = 16132, contour level = 0.26383 
    7910  
    7911 Position of W20_C1_initial_model_v3.pdb (#47) relative to
    7912 W20_J3623_consensus_structure_sharp.mrc (#1) coordinates: 
    7913 Matrix rotation and translation 
    7914 0.99996809 -0.00526689 0.00600723 0.01730039 
    7915 0.00528904 0.99997925 -0.00367710 -0.57665128 
    7916 -0.00598774 0.00370875 0.99997520 0.14412341 
    7917 Axis 0.41958417 0.68142506 0.59967410 
    7918 Axis point 54.13790036 0.00000000 -23.49447330 
    7919 Rotation angle (degrees) 0.50428904 
    7920 Shift along axis -0.29925859 
    7921  
    7922 
    7923 > select subtract #47
    7924 
    7925 Nothing selected 
    7926 
    7927 > hide #!47 models
    7928 
    7929 > show #!47 models
    7930 
    7931 > split #47 chains
    7932 
    7933 Split W20_C1_initial_model_v3.pdb (#47) into 9 models 
    7934 Chain information for W20_C1_initial_model_v3.pdb D #47.1 
    7935 --- 
    7936 Chain | Description 
    7937 D | No description available 
    7938  
    7939 Chain information for W20_C1_initial_model_v3.pdb E #47.2 
    7940 --- 
    7941 Chain | Description 
    7942 E | No description available 
    7943  
    7944 Chain information for W20_C1_initial_model_v3.pdb F #47.3 
    7945 --- 
    7946 Chain | Description 
    7947 F | No description available 
    7948  
    7949 Chain information for W20_C1_initial_model_v3.pdb G #47.4 
    7950 --- 
    7951 Chain | Description 
    7952 G | No description available 
    7953  
    7954 Chain information for W20_C1_initial_model_v3.pdb H #47.5 
    7955 --- 
    7956 Chain | Description 
    7957 H | No description available 
    7958  
    7959 Chain information for W20_C1_initial_model_v3.pdb I #47.6 
    7960 --- 
    7961 Chain | Description 
    7962 I | No description available 
    7963  
    7964 Chain information for W20_C1_initial_model_v3.pdb J #47.7 
    7965 --- 
    7966 Chain | Description 
    7967 J | No description available 
    7968  
    7969 Chain information for W20_C1_initial_model_v3.pdb K #47.8 
    7970 --- 
    7971 Chain | Description 
    7972 K | No description available 
    7973  
    7974 Chain information for W20_C1_initial_model_v3.pdb L #47.9 
    7975 --- 
    7976 Chain | Description 
    7977 L | No description available 
    7978  
    7979 
    7980 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    7981 > resources/Processing/W20_MM_cyto_COPI/20250703_W20_COPI_cyto_alignments.cxs"
    7982 
    7983 ——— End of log from Thu Jul 3 17:41:19 2025 ———
    7984 
    7985 opened ChimeraX session 
    7986 
    7987 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    7988 > resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/FlexFit_W20_C1_initial_model_v3/W20_C1_initial_model_v3_no_wat_lig.pdb"
    7989 
    7990 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb #48 
    7991 --- 
    7992 Chain | Description 
    7993 D E | No description available 
    7994 F | No description available 
    7995 G | No description available 
    7996 H | No description available 
    7997 I | No description available 
    7998 J | No description available 
    7999 K | No description available 
    8000 L | No description available 
    8001  
    8002 
    8003 > hide #47.1-5,9#!48#!47.6-8 atoms
    8004 
    8005 > show #47.1-5,9#!48#!47.6-8 cartoons
    8006 
    8007 > hide #!47 models
    8008 
    8009 > hide #!48 models
    8010 
    8011 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    8012 > resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/RIBFIND_W20_C1_initial_model_v3/W20_C1_initial_model_v3_no_wat_lig.pdb"
    8013 
    8014 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb #49 
    8015 --- 
    8016 Chain | Description 
    8017 D E | No description available 
    8018 F | No description available 
    8019 G | No description available 
    8020 H | No description available 
    8021 I | No description available 
    8022 J | No description available 
    8023 K | No description available 
    8024 L | No description available 
    8025  
    8026 
    8027 > hide #!49 atoms
    8028 
    8029 > show #!49 cartoons
    8030 
    8031 > show #!48 models
    8032 
    8033 > hide #!48 models
    8034 
    8035 > show #!47 models
    8036 
    8037 > hide #!47 models
    8038 
    8039 > hide #!49 models
    8040 
    8041 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    8042 > resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/FlexFit_W20_C1_initial_model_TEMPyReff_flexfit/W20_C1_initial_model_no_wat_lig.pdb"
    8043 
    8044 Chain information for W20_C1_initial_model_no_wat_lig.pdb #50 
    8045 --- 
    8046 Chain | Description 
    8047 A0 | No description available 
    8048 A1 | No description available 
    8049 A2 | No description available 
    8050 A3 | No description available 
    8051 A4 | No description available 
    8052 A5 | No description available 
    8053 A6 | No description available 
    8054 A7 | No description available 
    8055 A8 | No description available 
    8056 A9 | No description available 
    8057 BA | No description available 
    8058  
    8059 
    8060 > hide #!50 atoms
    8061 
    8062 > show #!50 cartoons
    8063 
    8064 > select add #50
    8065 
    8066 25890 atoms, 26364 bonds, 22 pseudobonds, 3243 residues, 2 models selected 
    8067 
    8068 > select subtract #50
    8069 
    8070 Nothing selected 
    8071 
    8072 > ui tool show Matchmaker
    8073 
    8074 > matchmaker #!50 to #34
    8075 
    8076 Computing secondary structure 
    8077 Parameters 
    8078 --- 
    8079 Chain pairing | bb 
    8080 Alignment algorithm | Needleman-Wunsch 
    8081 Similarity matrix | BLOSUM-62 
    8082 SS fraction | 0.3 
    8083 Gap open (HH/SS/other) | 18/18/6 
    8084 Gap extend | 1 
    8085 SS matrix |  |  | H | S | O 
    8086 ---|---|---|--- 
    8087 H | 6 | -9 | -6 
    8088 S |  | 6 | -6 
    8089 O |  |  | 4 
    8090 Iteration cutoff | 2 
    8091  
    8092 Matchmaker CopA-F8WHL2.pdb, chain A (#34) with
    8093 W20_C1_initial_model_no_wat_lig.pdb, chain A2 (#50), sequence alignment score
    8094 = 2196.3 
    8095 RMSD between 303 pruned atom pairs is 0.597 angstroms; (across all 445 pairs:
    8096 4.918) 
    8097  
    8098 
    8099 > hide #!25 models
    8100 
    8101 > show #!7 models
    8102 
    8103 > hide #!7 models
    8104 
    8105 > show #!25 models
    8106 
    8107 > show #!7 models
    8108 
    8109 > hide #!7 models
    8110 
    8111 > show #!7 models
    8112 
    8113 > hide #!7 models
    8114 
    8115 > show #!7 models
    8116 
    8117 > hide #!7 models
    8118 
    8119 > show #!8 models
    8120 
    8121 > hide #!8 models
    8122 
    8123 > show #!7 models
    8124 
    8125 > hide #!7 models
    8126 
    8127 > open
    8128 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/A_fixed_model_2_A.pdb
    8129 
    8130 Summary of feedback from opening
    8131 /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/A_fixed_model_2_A.pdb 
    8132 --- 
    8133 warning | Ignored bad PDB record found on line 9748 
    8134  
    8135 Chain information for A_fixed_model_2_A.pdb #51 
    8136 --- 
    8137 Chain | Description 
    8138 A | No description available 
    8139  
    8140 Computing secondary structure 
    8141 
    8142 > open
    8143 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/B_fixed_model_2_B.pdb
    8144 
    8145 Summary of feedback from opening
    8146 /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/B_fixed_model_2_B.pdb 
    8147 --- 
    8148 warning | Ignored bad PDB record found on line 7507 
    8149  
    8150 Chain information for B_fixed_model_2_B.pdb #52 
    8151 --- 
    8152 Chain | Description 
    8153 B | No description available 
    8154  
    8155 Computing secondary structure 
    8156 
    8157 > open
    8158 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/C1_fixed_model_2_C1.pdb
    8159 
    8160 Summary of feedback from opening
    8161 /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/C1_fixed_model_2_C1.pdb 
    8162 --- 
    8163 warning | Ignored bad PDB record found on line 3967 
    8164  
    8165 Chain information for C1_fixed_model_2_C1.pdb #53 
    8166 --- 
    8167 Chain | Description 
    8168 C1 | No description available 
    8169  
    8170 Computing secondary structure 
    8171 
    8172 > open
    8173 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/D1_fixed_model_2_D1.pdb
    8174 
    8175 Summary of feedback from opening
    8176 /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/D1_fixed_model_2_D1.pdb 
    8177 --- 
    8178 warning | Ignored bad PDB record found on line 3307 
    8179  
    8180 Chain information for D1_fixed_model_2_D1.pdb #54 
    8181 --- 
    8182 Chain | Description 
    8183 D1 | No description available 
    8184  
    8185 Computing secondary structure 
    8186 
    8187 > open
    8188 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/E2_full_shifted_sm_1.pdb
    8189 
    8190 Summary of feedback from opening
    8191 /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/E2_full_shifted_sm_1.pdb 
    8192 --- 
    8193 warning | Ignored bad PDB record found on line 4486 
    8194  
    8195 Chain information for E2_full_shifted_sm_1.pdb #55 
    8196 --- 
    8197 Chain | Description 
    8198 E2 | No description available 
    8199  
    8200 Computing secondary structure 
    8201 
    8202 > open
    8203 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/F_fixed_model_2_F.pdb
    8204 
    8205 Summary of feedback from opening
    8206 /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/F_fixed_model_2_F.pdb 
    8207 --- 
    8208 warning | Ignored bad PDB record found on line 1426 
    8209  
    8210 Chain information for F_fixed_model_2_F.pdb #56 
    8211 --- 
    8212 Chain | Description 
    8213 F | No description available 
    8214  
    8215 Computing secondary structure 
    8216 
    8217 > hide #!25 models
    8218 
    8219 > show #!1 models
    8220 
    8221 > hide #56 models
    8222 
    8223 > hide #!55 models
    8224 
    8225 > hide #!54 models
    8226 
    8227 > hide #!53 models
    8228 
    8229 > hide #52 models
    8230 
    8231 > hide #51 models
    8232 
    8233 > hide #!1 models
    8234 
    8235 > show #!2 models
    8236 
    8237 > color #2 darkgrey models
    8238 
    8239 > color #2 #a9a9a980 models
    8240 
    8241 > hide #!50 models
    8242 
    8243 > show #!47 models
    8244 
    8245 > fitmap #47 inMap #2
    8246 
    8247 Fit molecules W20_C1_initial_model_v3.pdb D (#47.1),
    8248 W20_C1_initial_model_v3.pdb E (#47.2), W20_C1_initial_model_v3.pdb F (#47.3),
    8249 W20_C1_initial_model_v3.pdb G (#47.4), W20_C1_initial_model_v3.pdb H (#47.5),
    8250 W20_C1_initial_model_v3.pdb I (#47.6), W20_C1_initial_model_v3.pdb J (#47.7),
    8251 W20_C1_initial_model_v3.pdb K (#47.8), W20_C1_initial_model_v3.pdb L (#47.9)
    8252 to map W20_J3623_consensus_structure.mrc (#2) using 28705 atoms 
    8253 average map value = 0.26, steps = 44 
    8254 shifted from previous position = 0.0505 
    8255 rotated from previous position = 0.167 degrees 
    8256 atoms outside contour = 16402, contour level = 0.25746 
    8257  
    8258 Position of W20_C1_initial_model_v3.pdb D (#47.1) relative to
    8259 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8260 Matrix rotation and translation 
    8261 0.99995987 -0.00698720 0.00560699 0.30640707 
    8262 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8263 -0.00559747 0.00138070 0.99998338 0.47678248 
    8264 Axis 0.15020785 0.61824110 0.77150214 
    8265 Axis point 136.27032262 49.14800743 0.00000000 
    8266 Rotation angle (degrees) 0.51919628 
    8267 Shift along axis -0.28273161 
    8268  
    8269 Position of W20_C1_initial_model_v3.pdb E (#47.2) relative to
    8270 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8271 Matrix rotation and translation 
    8272 0.99995987 -0.00698720 0.00560699 0.30640707 
    8273 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8274 -0.00559747 0.00138070 0.99998338 0.47678248 
    8275 Axis 0.15020785 0.61824110 0.77150214 
    8276 Axis point 136.27032262 49.14800743 0.00000000 
    8277 Rotation angle (degrees) 0.51919628 
    8278 Shift along axis -0.28273161 
    8279  
    8280 Position of W20_C1_initial_model_v3.pdb F (#47.3) relative to
    8281 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8282 Matrix rotation and translation 
    8283 0.99995987 -0.00698720 0.00560699 0.30640707 
    8284 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8285 -0.00559747 0.00138070 0.99998338 0.47678248 
    8286 Axis 0.15020785 0.61824110 0.77150214 
    8287 Axis point 136.27032262 49.14800743 0.00000000 
    8288 Rotation angle (degrees) 0.51919628 
    8289 Shift along axis -0.28273161 
    8290  
    8291 Position of W20_C1_initial_model_v3.pdb G (#47.4) relative to
    8292 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8293 Matrix rotation and translation 
    8294 0.99995987 -0.00698720 0.00560699 0.30640707 
    8295 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8296 -0.00559747 0.00138070 0.99998338 0.47678248 
    8297 Axis 0.15020785 0.61824110 0.77150214 
    8298 Axis point 136.27032262 49.14800743 0.00000000 
    8299 Rotation angle (degrees) 0.51919628 
    8300 Shift along axis -0.28273161 
    8301  
    8302 Position of W20_C1_initial_model_v3.pdb H (#47.5) relative to
    8303 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8304 Matrix rotation and translation 
    8305 0.99995987 -0.00698720 0.00560699 0.30640707 
    8306 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8307 -0.00559747 0.00138070 0.99998338 0.47678248 
    8308 Axis 0.15020785 0.61824110 0.77150214 
    8309 Axis point 136.27032262 49.14800743 0.00000000 
    8310 Rotation angle (degrees) 0.51919628 
    8311 Shift along axis -0.28273161 
    8312  
    8313 Position of W20_C1_initial_model_v3.pdb I (#47.6) relative to
    8314 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8315 Matrix rotation and translation 
    8316 0.99995987 -0.00698720 0.00560699 0.30640707 
    8317 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8318 -0.00559747 0.00138070 0.99998338 0.47678248 
    8319 Axis 0.15020785 0.61824110 0.77150214 
    8320 Axis point 136.27032262 49.14800743 0.00000000 
    8321 Rotation angle (degrees) 0.51919628 
    8322 Shift along axis -0.28273161 
    8323  
    8324 Position of W20_C1_initial_model_v3.pdb J (#47.7) relative to
    8325 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8326 Matrix rotation and translation 
    8327 0.99995987 -0.00698720 0.00560699 0.30640707 
    8328 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8329 -0.00559747 0.00138070 0.99998338 0.47678248 
    8330 Axis 0.15020785 0.61824110 0.77150214 
    8331 Axis point 136.27032262 49.14800743 0.00000000 
    8332 Rotation angle (degrees) 0.51919628 
    8333 Shift along axis -0.28273161 
    8334  
    8335 Position of W20_C1_initial_model_v3.pdb K (#47.8) relative to
    8336 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8337 Matrix rotation and translation 
    8338 0.99995987 -0.00698720 0.00560699 0.30640707 
    8339 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8340 -0.00559747 0.00138070 0.99998338 0.47678248 
    8341 Axis 0.15020785 0.61824110 0.77150214 
    8342 Axis point 136.27032262 49.14800743 0.00000000 
    8343 Rotation angle (degrees) 0.51919628 
    8344 Shift along axis -0.28273161 
    8345  
    8346 Position of W20_C1_initial_model_v3.pdb L (#47.9) relative to
    8347 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8348 Matrix rotation and translation 
    8349 0.99995987 -0.00698720 0.00560699 0.30640707 
    8350 0.00699483 0.99997464 -0.00134153 -1.12673692 
    8351 -0.00559747 0.00138070 0.99998338 0.47678248 
    8352 Axis 0.15020785 0.61824110 0.77150214 
    8353 Axis point 136.27032262 49.14800743 0.00000000 
    8354 Rotation angle (degrees) 0.51919628 
    8355 Shift along axis -0.28273161 
    8356  
    8357 
    8358 > fitmap #47.1 inMap #2
    8359 
    8360 Fit molecule W20_C1_initial_model_v3.pdb D (#47.1) to map
    8361 W20_J3623_consensus_structure.mrc (#2) using 4763 atoms 
    8362 average map value = 0.3391, steps = 60 
    8363 shifted from previous position = 0.277 
    8364 rotated from previous position = 0.317 degrees 
    8365 atoms outside contour = 1269, contour level = 0.25746 
    8366  
    8367 Position of W20_C1_initial_model_v3.pdb D (#47.1) relative to
    8368 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8369 Matrix rotation and translation 
    8370 0.99993645 -0.00554192 0.00981798 -0.36993206 
    8371 0.00552327 0.99998289 0.00192574 -1.44337504 
    8372 -0.00982849 -0.00187139 0.99994995 1.45151156 
    8373 Axis -0.16606190 0.85921136 0.48392075 
    8374 Axis point 170.89777041 0.00000000 46.84174593 
    8375 Rotation angle (degrees) 0.65506824 
    8376 Shift along axis -0.47631604 
    8377  
    8378 
    8379 > fitmap #47.2 inMap #2
    8380 
    8381 Fit molecule W20_C1_initial_model_v3.pdb E (#47.2) to map
    8382 W20_J3623_consensus_structure.mrc (#2) using 1856 atoms 
    8383 average map value = 0.298, steps = 52 
    8384 shifted from previous position = 0.74 
    8385 rotated from previous position = 0.516 degrees 
    8386 atoms outside contour = 807, contour level = 0.25746 
    8387  
    8388 Position of W20_C1_initial_model_v3.pdb E (#47.2) relative to
    8389 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8390 Matrix rotation and translation 
    8391 0.99985158 -0.01068491 0.01351472 -0.71801951 
    8392 0.01073315 0.99993626 -0.00350238 -1.71551668 
    8393 -0.01347643 0.00364691 0.99990254 2.22722625 
    8394 Axis 0.20315994 0.76700206 0.60863280 
    8395 Axis point 169.67451772 0.00000000 53.39691400 
    8396 Rotation angle (degrees) 1.00818411 
    8397 Shift along axis -0.10611466 
    8398  
    8399 
    8400 > fitmap #47.3 inMap #2
    8401 
    8402 Fit molecule W20_C1_initial_model_v3.pdb F (#47.3) to map
    8403 W20_J3623_consensus_structure.mrc (#2) using 7214 atoms 
    8404 average map value = 0.1919, steps = 56 
    8405 shifted from previous position = 0.863 
    8406 rotated from previous position = 1.3 degrees 
    8407 atoms outside contour = 5840, contour level = 0.25746 
    8408  
    8409 Position of W20_C1_initial_model_v3.pdb F (#47.3) relative to
    8410 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8411 Matrix rotation and translation 
    8412 0.99983282 -0.01767194 -0.00469422 4.64975550 
    8413 0.01774465 0.99971568 0.01592750 -6.16380107 
    8414 0.00441141 -0.01600813 0.99986213 2.74940793 
    8415 Axis -0.65778440 -0.18755047 0.72948236 
    8416 Axis point 350.49529384 263.63816940 0.00000000 
    8417 Rotation angle (degrees) 1.39100037 
    8418 Shift along axis 0.10313173 
    8419  
    8420 
    8421 > fitmap #47.4 inMap #2
    8422 
    8423 Fit molecule W20_C1_initial_model_v3.pdb G (#47.4) to map
    8424 W20_J3623_consensus_structure.mrc (#2) using 1872 atoms 
    8425 average map value = 0.2684, steps = 48 
    8426 shifted from previous position = 0.694 
    8427 rotated from previous position = 1.52 degrees 
    8428 atoms outside contour = 902, contour level = 0.25746 
    8429  
    8430 Position of W20_C1_initial_model_v3.pdb G (#47.4) relative to
    8431 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8432 Matrix rotation and translation 
    8433 0.99999905 0.00004391 -0.00137935 0.08316312 
    8434 -0.00001180 0.99972908 0.02327568 -3.69665287 
    8435 0.00138000 -0.02327564 0.99972813 3.29847865 
    8436 Axis -0.99824711 -0.05917154 -0.00119461 
    8437 Axis point 0.00000000 139.85035535 160.11317726 
    8438 Rotation angle (degrees) 1.33605990 
    8439 Shift along axis 0.13177890 
    8440  
    8441 
    8442 > fitmap #47.5 inMap #2
    8443 
    8444 Fit molecule W20_C1_initial_model_v3.pdb H (#47.5) to map
    8445 W20_J3623_consensus_structure.mrc (#2) using 4752 atoms 
    8446 average map value = 0.2052, steps = 56 
    8447 shifted from previous position = 0.558 
    8448 rotated from previous position = 2.67 degrees 
    8449 atoms outside contour = 3635, contour level = 0.25746 
    8450  
    8451 Position of W20_C1_initial_model_v3.pdb H (#47.5) relative to
    8452 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8453 Matrix rotation and translation 
    8454 0.99873328 -0.02416117 0.04413700 -1.58450683 
    8455 0.02335616 0.99955296 0.01866451 -4.67495439 
    8456 -0.04456822 -0.01760999 0.99885112 6.98195313 
    8457 Axis -0.33911247 0.82926157 0.44421615 
    8458 Axis point 157.93980007 0.00000000 42.26069084 
    8459 Rotation angle (degrees) 3.06589704 
    8460 Shift along axis -0.23793767 
    8461  
    8462 
    8463 > fitmap #47.6 inMap #2
    8464 
    8465 Fit molecule W20_C1_initial_model_v3.pdb I (#47.6) to map
    8466 W20_J3623_consensus_structure.mrc (#2) using 2488 atoms 
    8467 average map value = 0.3942, steps = 48 
    8468 shifted from previous position = 0.0985 
    8469 rotated from previous position = 0.351 degrees 
    8470 atoms outside contour = 688, contour level = 0.25746 
    8471  
    8472 Position of W20_C1_initial_model_v3.pdb I (#47.6) relative to
    8473 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8474 Matrix rotation and translation 
    8475 0.99997623 -0.00687548 -0.00051167 1.19535071 
    8476 0.00687477 0.99997543 -0.00137176 -1.17275950 
    8477 0.00052109 0.00136821 0.99999893 -0.25085656 
    8478 Axis 0.19489694 -0.07346086 0.97806886 
    8479 Axis point 170.41255683 171.17704205 0.00000000 
    8480 Rotation angle (degrees) 0.40275148 
    8481 Shift along axis 0.07376713 
    8482  
    8483 
    8484 > fitmap #47.7 inMap #2
    8485 
    8486 Fit molecule W20_C1_initial_model_v3.pdb J (#47.7) to map
    8487 W20_J3623_consensus_structure.mrc (#2) using 2879 atoms 
    8488 average map value = 0.2974, steps = 40 
    8489 shifted from previous position = 0.0947 
    8490 rotated from previous position = 0.56 degrees 
    8491 atoms outside contour = 1205, contour level = 0.25746 
    8492  
    8493 Position of W20_C1_initial_model_v3.pdb J (#47.7) relative to
    8494 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8495 Matrix rotation and translation 
    8496 0.99998391 0.00266199 0.00500985 -1.32620675 
    8497 -0.00264770 0.99999241 -0.00285677 0.77420871 
    8498 -0.00501741 0.00284346 0.99998337 0.17173811 
    8499 Axis 0.44891807 0.78969202 -0.41816155 
    8500 Axis point 28.71795251 0.00000000 259.81340923 
    8501 Rotation angle (degrees) 0.36376436 
    8502 Shift along axis -0.05578601 
    8503  
    8504 
    8505 > fitmap #47.8 inMap #2
    8506 
    8507 Fit molecule W20_C1_initial_model_v3.pdb K (#47.8) to map
    8508 W20_J3623_consensus_structure.mrc (#2) using 1681 atoms 
    8509 average map value = 0.2582, steps = 2000 
    8510 shifted from previous position = 3.05 
    8511 rotated from previous position = 19.1 degrees 
    8512 atoms outside contour = 877, contour level = 0.25746 
    8513  
    8514 Position of W20_C1_initial_model_v3.pdb K (#47.8) relative to
    8515 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8516 Matrix rotation and translation 
    8517 0.94200137 -0.31946272 0.10284450 49.35608426 
    8518 0.31956519 0.94743045 0.01592570 -41.58693728 
    8519 -0.10252568 0.01786349 0.99456995 13.43084868 
    8520 Axis 0.00288696 0.30596518 0.95203833 
    8521 Axis point 151.23068995 127.03929522 0.00000000 
    8522 Rotation angle (degrees) 19.60965973 
    8523 Shift along axis 0.20501701 
    8524  
    8525 
    8526 > fitmap #47.9 inMap #2
    8527 
    8528 Fit molecule W20_C1_initial_model_v3.pdb L (#47.9) to map
    8529 W20_J3623_consensus_structure.mrc (#2) using 1200 atoms 
    8530 average map value = 0.225, steps = 104 
    8531 shifted from previous position = 7.72 
    8532 rotated from previous position = 16.8 degrees 
    8533 atoms outside contour = 923, contour level = 0.25746 
    8534  
    8535 Position of W20_C1_initial_model_v3.pdb L (#47.9) relative to
    8536 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8537 Matrix rotation and translation 
    8538 0.95622273 0.06913903 0.28435522 -32.79890580 
    8539 -0.07184973 0.99741506 -0.00090016 15.80706570 
    8540 -0.28368241 -0.01957009 0.95871857 38.27014130 
    8541 Axis -0.03188330 0.97005801 -0.24077150 
    8542 Axis point 121.59404774 0.00000000 133.26118376 
    8543 Rotation angle (degrees) 17.02478724 
    8544 Shift along axis 7.16514893 
    8545  
    8546 
    8547 > hide #!47 models
    8548 
    8549 > show #!48 models
    8550 
    8551 > split #48 chains
    8552 
    8553 Split W20_C1_initial_model_v3_no_wat_lig.pdb (#48) into 9 models 
    8554 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb D #48.1 
    8555 --- 
    8556 Chain | Description 
    8557 D | No description available 
    8558  
    8559 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb E #48.2 
    8560 --- 
    8561 Chain | Description 
    8562 E | No description available 
    8563  
    8564 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb F #48.3 
    8565 --- 
    8566 Chain | Description 
    8567 F | No description available 
    8568  
    8569 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb G #48.4 
    8570 --- 
    8571 Chain | Description 
    8572 G | No description available 
    8573  
    8574 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb H #48.5 
    8575 --- 
    8576 Chain | Description 
    8577 H | No description available 
    8578  
    8579 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb I #48.6 
    8580 --- 
    8581 Chain | Description 
    8582 I | No description available 
    8583  
    8584 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb J #48.7 
    8585 --- 
    8586 Chain | Description 
    8587 J | No description available 
    8588  
    8589 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb K #48.8 
    8590 --- 
    8591 Chain | Description 
    8592 K | No description available 
    8593  
    8594 Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb L #48.9 
    8595 --- 
    8596 Chain | Description 
    8597 L | No description available 
    8598  
    8599 
    8600 > fitmap #48.9 inMap #2
    8601 
    8602 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb L (#48.9) to map
    8603 W20_J3623_consensus_structure.mrc (#2) using 1200 atoms 
    8604 average map value = 0.225, steps = 104 
    8605 shifted from previous position = 7.35 
    8606 rotated from previous position = 17 degrees 
    8607 atoms outside contour = 923, contour level = 0.25746 
    8608  
    8609 Position of W20_C1_initial_model_v3_no_wat_lig.pdb L (#48.9) relative to
    8610 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8611 Matrix rotation and translation 
    8612 0.95618362 0.06935484 0.28443415 -32.83561380 
    8613 -0.07187151 0.99741263 -0.00159273 15.88500353 
    8614 -0.28380868 -0.01891977 0.95869426 38.21611444 
    8615 Axis -0.02957914 0.97005222 -0.24108871 
    8616 Axis point 121.32947981 0.00000000 133.38706461 
    8617 Rotation angle (degrees) 17.03122986 
    8618 Shift along axis 7.16705836 
    8619  
    8620 
    8621 > fitmap #48.8 inMap #2
    8622 
    8623 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb K (#48.8) to map
    8624 W20_J3623_consensus_structure.mrc (#2) using 1681 atoms 
    8625 average map value = 0.2582, steps = 2000 
    8626 shifted from previous position = 3 
    8627 rotated from previous position = 19.6 degrees 
    8628 atoms outside contour = 877, contour level = 0.25746 
    8629  
    8630 Position of W20_C1_initial_model_v3_no_wat_lig.pdb K (#48.8) relative to
    8631 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8632 Matrix rotation and translation 
    8633 0.94200226 -0.31945879 0.10284856 49.35474105 
    8634 0.31956109 0.94743180 0.01592780 -41.58682474 
    8635 -0.10253028 0.01786237 0.99456949 13.43178853 
    8636 Axis 0.00288219 0.30598035 0.95203347 
    8637 Axis point 151.23135956 127.03695546 0.00000000 
    8638 Rotation angle (degrees) 19.60950766 
    8639 Shift along axis 0.20501096 
    8640  
    8641 
    8642 > fitmap #48.7 inMap #2
    8643 
    8644 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb J (#48.7) to map
    8645 W20_J3623_consensus_structure.mrc (#2) using 2879 atoms 
    8646 average map value = 0.2974, steps = 60 
    8647 shifted from previous position = 0.232 
    8648 rotated from previous position = 0.38 degrees 
    8649 atoms outside contour = 1205, contour level = 0.25746 
    8650  
    8651 Position of W20_C1_initial_model_v3_no_wat_lig.pdb J (#48.7) relative to
    8652 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8653 Matrix rotation and translation 
    8654 0.99998287 0.00312090 0.00495157 -1.40345048 
    8655 -0.00310539 0.99999025 -0.00313821 0.88665991 
    8656 -0.00496131 0.00312278 0.99998282 0.10130440 
    8657 Axis 0.47162964 0.74671971 -0.46901508 
    8658 Axis point 14.97777640 0.00000000 278.97871593 
    8659 Rotation angle (degrees) 0.38031035 
    8660 Shift along axis -0.04733570 
    8661  
    8662 
    8663 > fitmap #48.6 inMap #2
    8664 
    8665 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb I (#48.6) to map
    8666 W20_J3623_consensus_structure.mrc (#2) using 2488 atoms 
    8667 average map value = 0.3942, steps = 68 
    8668 shifted from previous position = 0.638 
    8669 rotated from previous position = 0.407 degrees 
    8670 atoms outside contour = 688, contour level = 0.25746 
    8671  
    8672 Position of W20_C1_initial_model_v3_no_wat_lig.pdb I (#48.6) relative to
    8673 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8674 Matrix rotation and translation 
    8675 0.99997568 -0.00695350 -0.00053467 1.20906358 
    8676 0.00695275 0.99997488 -0.00137680 -1.17749870 
    8677 0.00054423 0.00137305 0.99999891 -0.25259458 
    8678 Axis 0.19342635 -0.07589115 0.97817523 
    8679 Axis point 169.14439112 171.16881708 0.00000000 
    8680 Rotation angle (degrees) 0.40727684 
    8681 Shift along axis 0.07614472 
    8682  
    8683 
    8684 > fitmap #48.5 inMap #2
    8685 
    8686 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb H (#48.5) to map
    8687 W20_J3623_consensus_structure.mrc (#2) using 4752 atoms 
    8688 average map value = 0.2052, steps = 56 
    8689 shifted from previous position = 0.398 
    8690 rotated from previous position = 3.04 degrees 
    8691 atoms outside contour = 3633, contour level = 0.25746 
    8692  
    8693 Position of W20_C1_initial_model_v3_no_wat_lig.pdb H (#48.5) relative to
    8694 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8695 Matrix rotation and translation 
    8696 0.99875256 -0.02376142 0.04391712 -1.59501966 
    8697 0.02297566 0.99956832 0.01831081 -4.59906082 
    8698 -0.04433325 -0.01727895 0.99886736 6.92788561 
    8699 Axis -0.33570594 0.83243532 0.44085481 
    8700 Axis point 157.55390321 0.00000000 42.61926354 
    8701 Rotation angle (degrees) 3.03852113 
    8702 Shift along axis -0.23877143 
    8703  
    8704 
    8705 > fitmap #48.4 inMap #2
    8706 
    8707 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb G (#48.4) to map
    8708 W20_J3623_consensus_structure.mrc (#2) using 1872 atoms 
    8709 average map value = 0.2684, steps = 52 
    8710 shifted from previous position = 0.66 
    8711 rotated from previous position = 1.34 degrees 
    8712 atoms outside contour = 904, contour level = 0.25746 
    8713  
    8714 Position of W20_C1_initial_model_v3_no_wat_lig.pdb G (#48.4) relative to
    8715 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8716 Matrix rotation and translation 
    8717 0.99999668 -0.00055774 -0.00251381 0.32378285 
    8718 0.00061619 0.99972807 0.02331118 -3.79263384 
    8719 0.00250012 -0.02331266 0.99972510 3.13991886 
    8720 Axis -0.99395584 -0.10688996 0.02502646 
    8721 Axis point 0.00000000 132.58526090 163.49903175 
    8722 Rotation angle (degrees) 1.34391993 
    8723 Shift along axis 0.16214970 
    8724  
    8725 
    8726 > fitmap #48.3 inMap #2
    8727 
    8728 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb F (#48.3) to map
    8729 W20_J3623_consensus_structure.mrc (#2) using 7214 atoms 
    8730 average map value = 0.1919, steps = 52 
    8731 shifted from previous position = 1.21 
    8732 rotated from previous position = 1.38 degrees 
    8733 atoms outside contour = 5841, contour level = 0.25746 
    8734  
    8735 Position of W20_C1_initial_model_v3_no_wat_lig.pdb F (#48.3) relative to
    8736 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8737 Matrix rotation and translation 
    8738 0.99983183 -0.01777810 -0.00449952 4.61473624 
    8739 0.01784647 0.99971839 0.01564141 -6.12537351 
    8740 0.00422018 -0.01571908 0.99986754 2.73144245 
    8741 Axis -0.64988004 -0.18069744 0.73824411 
    8742 Axis point 346.08368056 260.84380532 -0.00000000 
    8743 Rotation angle (degrees) 1.38256144 
    8744 Shift along axis 0.12428563 
    8745  
    8746 
    8747 > fitmap #48.2 inMap #2
    8748 
    8749 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb E (#48.2) to map
    8750 W20_J3623_consensus_structure.mrc (#2) using 1856 atoms 
    8751 average map value = 0.298, steps = 48 
    8752 shifted from previous position = 0.513 
    8753 rotated from previous position = 0.756 degrees 
    8754 atoms outside contour = 811, contour level = 0.25746 
    8755  
    8756 Position of W20_C1_initial_model_v3_no_wat_lig.pdb E (#48.2) relative to
    8757 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8758 Matrix rotation and translation 
    8759 0.99991922 -0.00558717 0.01141652 -1.06360279 
    8760 0.00562764 0.99997799 -0.00351551 -0.81089288 
    8761 -0.01139663 0.00357947 0.99992865 1.85466537 
    8762 Axis 0.26882817 0.86438839 0.42492838 
    8763 Axis point 169.58714833 0.00000000 89.68331202 
    8764 Rotation angle (degrees) 0.75610423 
    8765 Shift along axis -0.19875283 
    8766  
    8767 
    8768 > fitmap #48.1 inMap #2
    8769 
    8770 Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb D (#48.1) to map
    8771 W20_J3623_consensus_structure.mrc (#2) using 4763 atoms 
    8772 average map value = 0.3391, steps = 52 
    8773 shifted from previous position = 0.556 
    8774 rotated from previous position = 0.656 degrees 
    8775 atoms outside contour = 1271, contour level = 0.25746 
    8776  
    8777 Position of W20_C1_initial_model_v3_no_wat_lig.pdb D (#48.1) relative to
    8778 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8779 Matrix rotation and translation 
    8780 0.99993657 -0.00557361 0.00978726 -0.36204539 
    8781 0.00555366 0.99998245 0.00206434 -1.46156620 
    8782 -0.00979859 -0.00200985 0.99994997 1.46464333 
    8783 Axis -0.17797856 0.85559501 0.48608724 
    8784 Axis point 172.75674812 0.00000000 46.73299778 
    8785 Rotation angle (degrees) 0.65580741 
    8786 Shift along axis -0.47412801 
    8787  
    8788 
    8789 > hide #!48 models
    8790 
    8791 > show #!49 models
    8792 
    8793 > hide #!49 models
    8794 
    8795 > show #!50 models
    8796 
    8797 > fitmap #50 inMap #2
    8798 
    8799 Fit molecule W20_C1_initial_model_no_wat_lig.pdb (#50) to map
    8800 W20_J3623_consensus_structure.mrc (#2) using 25890 atoms 
    8801 average map value = 0.2892, steps = 92 
    8802 shifted from previous position = 6.37 
    8803 rotated from previous position = 6 degrees 
    8804 atoms outside contour = 13101, contour level = 0.25746 
    8805  
    8806 Position of W20_C1_initial_model_no_wat_lig.pdb (#50) relative to
    8807 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    8808 Matrix rotation and translation 
    8809 -0.92962183 0.23756050 -0.28172373 363.07149255 
    8810 -0.02176229 -0.79853926 -0.60154921 515.96615164 
    8811 -0.36787180 -0.55308232 0.74750939 166.87632524 
    8812 Axis 0.17464117 0.31041809 -0.93442018 
    8813 Axis point 215.59521690 272.59770300 0.00000000 
    8814 Rotation angle (degrees) 172.02382323 
    8815 Shift along axis 67.63985482 
    8816  
    8817 
    8818 > show #51 models
    8819 
    8820 > hide #51 models
    8821 
    8822 > hide #!50 models
    8823 
    8824 > show #!50 models
    8825 
    8826 > split #50 chains
    8827 
    8828 Split W20_C1_initial_model_no_wat_lig.pdb (#50) into 11 models 
    8829 Chain information for W20_C1_initial_model_no_wat_lig.pdb A0 #50.1 
    8830 --- 
    8831 Chain | Description 
    8832 A0 | No description available 
    8833  
    8834 Chain information for W20_C1_initial_model_no_wat_lig.pdb A1 #50.2 
    8835 --- 
    8836 Chain | Description 
    8837 A1 | No description available 
    8838  
    8839 Chain information for W20_C1_initial_model_no_wat_lig.pdb A2 #50.3 
    8840 --- 
    8841 Chain | Description 
    8842 A2 | No description available 
    8843  
    8844 Chain information for W20_C1_initial_model_no_wat_lig.pdb A3 #50.4 
    8845 --- 
    8846 Chain | Description 
    8847 A3 | No description available 
    8848  
    8849 Chain information for W20_C1_initial_model_no_wat_lig.pdb A4 #50.5 
    8850 --- 
    8851 Chain | Description 
    8852 A4 | No description available 
    8853  
    8854 Chain information for W20_C1_initial_model_no_wat_lig.pdb A5 #50.6 
    8855 --- 
    8856 Chain | Description 
    8857 A5 | No description available 
    8858  
    8859 Chain information for W20_C1_initial_model_no_wat_lig.pdb A6 #50.7 
    8860 --- 
    8861 Chain | Description 
    8862 A6 | No description available 
    8863  
    8864 Chain information for W20_C1_initial_model_no_wat_lig.pdb A7 #50.8 
    8865 --- 
    8866 Chain | Description 
    8867 A7 | No description available 
    8868  
    8869 Chain information for W20_C1_initial_model_no_wat_lig.pdb A8 #50.9 
    8870 --- 
    8871 Chain | Description 
    8872 A8 | No description available 
    8873  
    8874 Chain information for W20_C1_initial_model_no_wat_lig.pdb A9 #50.10 
    8875 --- 
    8876 Chain | Description 
    8877 A9 | No description available 
    8878  
    8879 Chain information for W20_C1_initial_model_no_wat_lig.pdb BA #50.11 
    8880 --- 
    8881 Chain | Description 
    8882 BA | No description available 
    8883  
    8884 
    8885 > hide #50.1 models
    8886 
    8887 > show #50.1 models
    8888 
    8889 > hide #50.1 models
    8890 
    8891 > show #50.1 models
    8892 
    8893 > hide #!50.2 models
    8894 
    8895 > show #!50.2 models
    8896 
    8897 > hide #!50.2 models
    8898 
    8899 > show #!50.2 models
    8900 
    8901 > hide #!50.3 models
    8902 
    8903 > show #!50.3 models
    8904 
    8905 > hide #!50.4 models
    8906 
    8907 > show #!50.4 models
    8908 
    8909 > hide #!50.3 models
    8910 
    8911 > show #!50.3 models
    8912 
    8913 > ui tool show Matchmaker
    8914 
    8915 > matchmaker #51 to #50.3
    8916 
    8917 Computing secondary structure 
    8918 Parameters 
    8919 --- 
    8920 Chain pairing | bb 
    8921 Alignment algorithm | Needleman-Wunsch 
    8922 Similarity matrix | BLOSUM-62 
    8923 SS fraction | 0.3 
    8924 Gap open (HH/SS/other) | 18/18/6 
    8925 Gap extend | 1 
    8926 SS matrix |  |  | H | S | O 
    8927 ---|---|---|--- 
    8928 H | 6 | -9 | -6 
    8929 S |  | 6 | -6 
    8930 O |  |  | 4 
    8931 Iteration cutoff | 2 
    8932  
    8933 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A2, chain A2 (#50.3) with
    8934 A_fixed_model_2_A.pdb, chain A (#51), sequence alignment score = 2192.7 
    8935 RMSD between 285 pruned atom pairs is 0.343 angstroms; (across all 445 pairs:
    8936 7.570) 
    8937  
    8938 
    8939 > show #51 models
    8940 
    8941 > hide #!50.7 models
    8942 
    8943 > show #!50.7 models
    8944 
    8945 > ui tool show Matchmaker
    8946 
    8947 > show #52 models
    8948 
    8949 > hide #52 models
    8950 
    8951 > show #!53 models
    8952 
    8953 > matchmaker #!53 to #50.7
    8954 
    8955 Computing secondary structure 
    8956 Parameters 
    8957 --- 
    8958 Chain pairing | bb 
    8959 Alignment algorithm | Needleman-Wunsch 
    8960 Similarity matrix | BLOSUM-62 
    8961 SS fraction | 0.3 
    8962 Gap open (HH/SS/other) | 18/18/6 
    8963 Gap extend | 1 
    8964 SS matrix |  |  | H | S | O 
    8965 ---|---|---|--- 
    8966 H | 6 | -9 | -6 
    8967 S |  | 6 | -6 
    8968 O |  |  | 4 
    8969 Iteration cutoff | 2 
    8970  
    8971 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A6, chain A6 (#50.7) with
    8972 C1_fixed_model_2_C1.pdb, chain C1 (#53), sequence alignment score = 1136.3 
    8973 RMSD between 188 pruned atom pairs is 0.567 angstroms; (across all 446 pairs:
    8974 42.070) 
    8975  
    8976 
    8977 > hide #!53 models
    8978 
    8979 > show #!54 models
    8980 
    8981 > hide #!50.8 models
    8982 
    8983 > show #!50.8 models
    8984 
    8985 > hide #!50.8 models
    8986 
    8987 > show #!50.8 models
    8988 
    8989 > ui tool show Matchmaker
    8990 
    8991 > hide #50.6 models
    8992 
    8993 > show #50.6 models
    8994 
    8995 > hide #!50.4 models
    8996 
    8997 > show #!50.4 models
    8998 
    8999 > matchmaker #52 to #50.4
    9000 
    9001 Computing secondary structure 
    9002 Parameters 
    9003 --- 
    9004 Chain pairing | bb 
    9005 Alignment algorithm | Needleman-Wunsch 
    9006 Similarity matrix | BLOSUM-62 
    9007 SS fraction | 0.3 
    9008 Gap open (HH/SS/other) | 18/18/6 
    9009 Gap extend | 1 
    9010 SS matrix |  |  | H | S | O 
    9011 ---|---|---|--- 
    9012 H | 6 | -9 | -6 
    9013 S |  | 6 | -6 
    9014 O |  |  | 4 
    9015 Iteration cutoff | 2 
    9016  
    9017 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A3, chain A3 (#50.4) with
    9018 B_fixed_model_2_B.pdb, chain B (#52), sequence alignment score = 2854.3 
    9019 RMSD between 172 pruned atom pairs is 0.254 angstroms; (across all 567 pairs:
    9020 4.295) 
    9021  
    9022 
    9023 > show #52 models
    9024 
    9025 > hide #52 models
    9026 
    9027 > ui tool show Matchmaker
    9028 
    9029 > matchmaker #!54 to #50.8
    9030 
    9031 Computing secondary structure 
    9032 Parameters 
    9033 --- 
    9034 Chain pairing | bb 
    9035 Alignment algorithm | Needleman-Wunsch 
    9036 Similarity matrix | BLOSUM-62 
    9037 SS fraction | 0.3 
    9038 Gap open (HH/SS/other) | 18/18/6 
    9039 Gap extend | 1 
    9040 SS matrix |  |  | H | S | O 
    9041 ---|---|---|--- 
    9042 H | 6 | -9 | -6 
    9043 S |  | 6 | -6 
    9044 O |  |  | 4 
    9045 Iteration cutoff | 2 
    9046  
    9047 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A7, chain A7 (#50.8) with
    9048 D1_fixed_model_2_D1.pdb, chain D1 (#54), sequence alignment score = 660 
    9049 RMSD between 129 pruned atom pairs is 0.312 angstroms; (across all 131 pairs:
    9050 0.453) 
    9051  
    9052 
    9053 > hide #!54 models
    9054 
    9055 > show #!55 models
    9056 
    9057 > hide #!55 models
    9058 
    9059 > show #!55 models
    9060 
    9061 > hide #!50.10 models
    9062 
    9063 > show #!50.10 models
    9064 
    9065 > hide #!50.10 models
    9066 
    9067 > show #!50.10 models
    9068 
    9069 > ui tool show Matchmaker
    9070 
    9071 > matchmaker #!55 to #50.10
    9072 
    9073 Computing secondary structure 
    9074 Parameters 
    9075 --- 
    9076 Chain pairing | bb 
    9077 Alignment algorithm | Needleman-Wunsch 
    9078 Similarity matrix | BLOSUM-62 
    9079 SS fraction | 0.3 
    9080 Gap open (HH/SS/other) | 18/18/6 
    9081 Gap extend | 1 
    9082 SS matrix |  |  | H | S | O 
    9083 ---|---|---|--- 
    9084 H | 6 | -9 | -6 
    9085 S |  | 6 | -6 
    9086 O |  |  | 4 
    9087 Iteration cutoff | 2 
    9088  
    9089 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A9, chain A9 (#50.10) with
    9090 E2_full_shifted_sm_1.pdb, chain E2 (#55), sequence alignment score = 1394.2 
    9091 RMSD between 277 pruned atom pairs is 0.670 angstroms; (across all 277 pairs:
    9092 0.670) 
    9093  
    9094 
    9095 > hide #!55 models
    9096 
    9097 > show #!55 models
    9098 
    9099 > hide #!55 models
    9100 
    9101 > show #!55 models
    9102 
    9103 > hide #!50.10 models
    9104 
    9105 > show #!50.10 models
    9106 
    9107 > hide #!55 models
    9108 
    9109 > show #56 models
    9110 
    9111 > hide #50.11 models
    9112 
    9113 > show #50.11 models
    9114 
    9115 > ui tool show Matchmaker
    9116 
    9117 > matchmaker #56 to #50.11
    9118 
    9119 Computing secondary structure 
    9120 Parameters 
    9121 --- 
    9122 Chain pairing | bb 
    9123 Alignment algorithm | Needleman-Wunsch 
    9124 Similarity matrix | BLOSUM-62 
    9125 SS fraction | 0.3 
    9126 Gap open (HH/SS/other) | 18/18/6 
    9127 Gap extend | 1 
    9128 SS matrix |  |  | H | S | O 
    9129 ---|---|---|--- 
    9130 H | 6 | -9 | -6 
    9131 S |  | 6 | -6 
    9132 O |  |  | 4 
    9133 Iteration cutoff | 2 
    9134  
    9135 Matchmaker W20_C1_initial_model_no_wat_lig.pdb BA, chain BA (#50.11) with
    9136 F_fixed_model_2_F.pdb, chain F (#56), sequence alignment score = 725 
    9137 RMSD between 144 pruned atom pairs is 0.244 angstroms; (across all 144 pairs:
    9138 0.244) 
    9139  
    9140 
    9141 > hide #56 models
    9142 
    9143 > hide #51 models
    9144 
    9145 > show #36 models
    9146 
    9147 > hide #36 models
    9148 
    9149 > show #36 models
    9150 
    9151 > hide #36 models
    9152 
    9153 > show #36 models
    9154 
    9155 > hide #36 models
    9156 
    9157 > show #35 models
    9158 
    9159 > hide #35 models
    9160 
    9161 > show #52 models
    9162 
    9163 > fitmap #52 inMap #2
    9164 
    9165 Fit molecule B_fixed_model_2_B.pdb (#52) to map
    9166 W20_J3623_consensus_structure.mrc (#2) using 7500 atoms 
    9167 average map value = 0.316, steps = 88 
    9168 shifted from previous position = 2.73 
    9169 rotated from previous position = 5.83 degrees 
    9170 atoms outside contour = 2940, contour level = 0.25746 
    9171  
    9172 Position of B_fixed_model_2_B.pdb (#52) relative to
    9173 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    9174 Matrix rotation and translation 
    9175 -0.33624269 -0.92088355 -0.19726715 276.34525406 
    9176 -0.77887628 0.15416253 0.60793557 158.89643495 
    9177 -0.52942667 0.35806060 -0.76909038 243.62727331 
    9178 Axis -0.56887772 0.75621078 0.32330079 
    9179 Axis point 214.85544208 0.00000000 65.79075689 
    9180 Rotation angle (degrees) 167.31322736 
    9181 Shift along axis 41.71742887 
    9182  
    9183 
    9184 > fitmap #50.112
    9185 
    9186 Missing required "in_map" argument 
    9187 
    9188 > fitmap #50.11 inMap #2
    9189 
    9190 Fit molecule W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) to map
    9191 W20_J3623_consensus_structure.mrc (#2) using 1158 atoms 
    9192 average map value = 0.2425, steps = 216 
    9193 shifted from previous position = 24 
    9194 rotated from previous position = 39.5 degrees 
    9195 atoms outside contour = 674, contour level = 0.25746 
    9196  
    9197 Position of W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) relative to
    9198 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    9199 Matrix rotation and translation 
    9200 -0.96490741 -0.23836579 -0.11016098 456.74587096 
    9201 0.21274833 -0.46373391 -0.86005174 403.93698444 
    9202 0.15392153 -0.85330687 0.49817221 176.52114975 
    9203 Axis 0.01290218 -0.50515953 0.86292954 
    9204 Axis point 197.70794601 288.88132577 0.00000000 
    9205 Rotation angle (degrees) 164.84772556 
    9206 Shift along axis -45.83428628 
    9207  
    9208 
    9209 > show #56 models
    9210 
    9211 > hide #56 models
    9212 
    9213 > show #56 models
    9214 
    9215 > hide #56 models
    9216 
    9217 > ui tool show Matchmaker
    9218 
    9219 > matchmaker #50.11 to #56
    9220 
    9221 Computing secondary structure 
    9222 Parameters 
    9223 --- 
    9224 Chain pairing | bb 
    9225 Alignment algorithm | Needleman-Wunsch 
    9226 Similarity matrix | BLOSUM-62 
    9227 SS fraction | 0.3 
    9228 Gap open (HH/SS/other) | 18/18/6 
    9229 Gap extend | 1 
    9230 SS matrix |  |  | H | S | O 
    9231 ---|---|---|--- 
    9232 H | 6 | -9 | -6 
    9233 S |  | 6 | -6 
    9234 O |  |  | 4 
    9235 Iteration cutoff | 2 
    9236  
    9237 Matchmaker F_fixed_model_2_F.pdb, chain F (#56) with
    9238 W20_C1_initial_model_no_wat_lig.pdb BA, chain BA (#50.11), sequence alignment
    9239 score = 725 
    9240 RMSD between 144 pruned atom pairs is 0.244 angstroms; (across all 144 pairs:
    9241 0.244) 
    9242  
    9243 
    9244 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    9245 > resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
    9246 
    9247 > hide #!2 models
    9248 
    9249 > hide #!50 models
    9250 
    9251 > show #!50 models
    9252 
    9253 > hide #52 models
    9254 
    9255 > show #!53 models
    9256 
    9257 > hide #!53 models
    9258 
    9259 > show #!54 models
    9260 
    9261 > hide #!54 models
    9262 
    9263 > show #!54 models
    9264 
    9265 > hide #!54 models
    9266 
    9267 > show #!55 models
    9268 
    9269 > hide #!55 models
    9270 
    9271 > show #52 models
    9272 
    9273 > show #!33 models
    9274 
    9275 > color #33 #b2b2b290 models
    9276 
    9277 > color #33 #b2b2b28f models
    9278 
    9279 > hide #52 models
    9280 
    9281 > show #52 models
    9282 
    9283 > hide #!50.8 models
    9284 
    9285 > show #!50.8 models
    9286 
    9287 > hide #50.6 models
    9288 
    9289 > show #50.6 models
    9290 
    9291 > hide #!50.4 models
    9292 
    9293 > hide #!50.8 models
    9294 
    9295 > show #!50.8 models
    9296 
    9297 > fitmap #50.8 inMap #2
    9298 
    9299 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) to map
    9300 W20_J3623_consensus_structure.mrc (#2) using 1057 atoms 
    9301 average map value = 0.2692, steps = 56 
    9302 shifted from previous position = 0.944 
    9303 rotated from previous position = 4.88 degrees 
    9304 atoms outside contour = 542, contour level = 0.25746 
    9305  
    9306 Position of W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) relative to
    9307 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    9308 Matrix rotation and translation 
    9309 -0.93105828 0.16643564 -0.32469934 390.48149308 
    9310 0.06181231 -0.80509185 -0.58992064 497.62568127 
    9311 -0.35959661 -0.56932091 0.73929966 170.58533102 
    9312 Axis 0.18360289 0.31103515 -0.93249510 
    9313 Axis point 219.20897097 271.57117220 0.00000000 
    9314 Rotation angle (degrees) 176.78409911 
    9315 Shift along axis 67.40262593 
    9316  
    9317 Must specify one map, got 4 
    9318 
    9319 > hide #!50.8 models
    9320 
    9321 > show #!50.8 models
    9322 
    9323 > hide #!33 models
    9324 
    9325 > show #!46 models
    9326 
    9327 > show #!33 models
    9328 
    9329 > hide #!46 models
    9330 
    9331 > hide #!33.4 models
    9332 
    9333 > show #!33.4 models
    9334 
    9335 > hide #!33.3 models
    9336 
    9337 > show #!33.3 models
    9338 
    9339 > hide #!33.2 models
    9340 
    9341 > show #!33.2 models
    9342 
    9343 > hide #!33.1 models
    9344 
    9345 > show #!33.1 models
    9346 
    9347 > fitmap #50.8 inMap #33.1
    9348 
    9349 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) to map
    9350 W20_J160_run_ct6_body001.mrc (#33.1) using 1057 atoms 
    9351 average map value = 0.01137, steps = 52 
    9352 shifted from previous position = 0.606 
    9353 rotated from previous position = 3.76 degrees 
    9354 atoms outside contour = 692, contour level = 0.014811 
    9355  
    9356 Position of W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) relative to
    9357 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    9358 Matrix rotation and translation 
    9359 -0.93056714 0.15394973 -0.33218109 390.44774590 
    9360 0.14816644 -0.67132819 -0.72619912 477.44064772 
    9361 -0.33480069 -0.72499513 0.60190577 233.60614941 
    9362 Axis 0.18631674 0.40538097 -0.89495941 
    9363 Axis point 219.95045580 291.28468198 0.00000000 
    9364 Rotation angle (degrees) 179.81487490 
    9365 Shift along axis 57.22428050 
    9366  
    9367 
    9368 > hide #!50.8 models
    9369 
    9370 > show #!50.8 models
    9371 
    9372 > hide #50.9 models
    9373 
    9374 > show #50.9 models
    9375 
    9376 > hide #!50.8 models
    9377 
    9378 > show #!50.8 models
    9379 
    9380 > select add #50.8
    9381 
    9382 1057 atoms, 1072 bonds, 1 pseudobond, 131 residues, 2 models selected 
    9383 
    9384 > view matrix models
    9385 > #50.8,-0.90846,0.21715,-0.35712,384.12,0.037606,-0.80851,-0.58728,501.46,-0.41627,-0.54695,0.72634,175.24
    9386 
    9387 > ui mousemode right "rotate selected models"
    9388 
    9389 > view matrix models
    9390 > #50.8,-0.98593,-0.16588,0.020652,396.52,0.059686,-0.46474,-0.88344,489.6,0.15614,-0.86977,0.4681,195.56
    9391 
    9392 > fitmap #50.8 inMap #33.1
    9393 
    9394 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) to map
    9395 W20_J160_run_ct6_body001.mrc (#33.1) using 1057 atoms 
    9396 average map value = 0.01486, steps = 88 
    9397 shifted from previous position = 2.12 
    9398 rotated from previous position = 17.4 degrees 
    9399 atoms outside contour = 497, contour level = 0.014811 
    9400  
    9401 Position of W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) relative to
    9402 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    9403 Matrix rotation and translation 
    9404 -0.98685430 0.03145837 0.15852120 311.01536433 
    9405 -0.16062302 -0.29929277 -0.94054457 509.24173521 
    9406 0.01785625 -0.95364260 0.30041129 284.21437212 
    9407 Axis -0.05493227 0.58993953 -0.80557668 
    9408 Axis point 163.53469015 347.02960176 0.00000000 
    9409 Rotation angle (degrees) 173.15292285 
    9410 Shift along axis 54.38058021 
    9411  
    9412 
    9413 > select subtract #50.8
    9414 
    9415 Nothing selected 
    9416 
    9417 > fitmap #50.7 inMap #33.1
    9418 
    9419 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) to map
    9420 W20_J160_run_ct6_body001.mrc (#33.1) using 4264 atoms 
    9421 average map value = 0.005768, steps = 160 
    9422 shifted from previous position = 2.43 
    9423 rotated from previous position = 3.77 degrees 
    9424 atoms outside contour = 3553, contour level = 0.014811 
    9425  
    9426 Position of W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) relative to
    9427 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    9428 Matrix rotation and translation 
    9429 -0.95014016 0.15038437 -0.27316336 382.66549579 
    9430 0.08966442 -0.70725915 -0.70124517 487.55197868 
    9431 -0.29865360 -0.69077423 0.65851119 202.15694868 
    9432 Axis 0.15703122 0.38227356 -0.91060865 
    9433 Axis point 213.00898151 282.79480162 0.00000000 
    9434 Rotation angle (degrees) 178.08938676 
    9435 Shift along axis 62.38279471 
    9436  
    9437 
    9438 > hide #50.11 models
    9439 
    9440 > show #50.11 models
    9441 
    9442 > fitmap #50.11inMap #33.3
    9443 
    9444 Missing or invalid "atomsOrMap" argument: only initial part "#50.11" of atom
    9445 specifier valid 
    9446 
    9447 > fitmap #50.11 inMap #33.3
    9448 
    9449 Fit molecule W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) to map
    9450 W20_J160_run_ct6_body003.mrc (#33.3) using 1158 atoms 
    9451 average map value = 0.0132, steps = 104 
    9452 shifted from previous position = 5.13 
    9453 rotated from previous position = 28.7 degrees 
    9454 atoms outside contour = 711, contour level = 0.015167 
    9455  
    9456 Position of W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) relative to
    9457 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    9458 Matrix rotation and translation 
    9459 -0.92321344 -0.13158780 -0.36105621 489.23124927 
    9460 0.28319718 -0.86806041 -0.40776278 396.62096334 
    9461 -0.25976200 -0.47870218 0.83867033 84.55689237 
    9462 Axis -0.16389770 -0.23402916 0.95831513 
    9463 Axis point 230.41567989 235.72565549 0.00000000 
    9464 Rotation angle (degrees) 167.50152307 
    9465 Shift along axis -91.97259645 
    9466  
    9467 
    9468 > hide #50.11 models
    9469 
    9470 > show #39 models
    9471 
    9472 > fitmap #39 inMap #33.3
    9473 
    9474 Fit molecule CopZ1_P61924.pdb (#39) to map W20_J160_run_ct6_body003.mrc
    9475 (#33.3) using 1420 atoms 
    9476 average map value = 0.01141, steps = 92 
    9477 shifted from previous position = 7.91 
    9478 rotated from previous position = 10.3 degrees 
    9479 atoms outside contour = 963, contour level = 0.015167 
    9480  
    9481 Position of CopZ1_P61924.pdb (#39) relative to W20_J160_run_ct6_body003.mrc
    9482 (#33.3) coordinates: 
    9483 Matrix rotation and translation 
    9484 -0.50106153 0.84740615 0.17561366 128.97282199 
    9485 -0.08865073 -0.25211715 0.96362752 130.68154277 
    9486 0.86085911 0.46726840 0.20144938 92.25448210 
    9487 Axis -0.39337422 -0.54307030 -0.74184323 
    9488 Axis point 46.59255051 18.60088904 0.00000000 
    9489 Rotation angle (degrees) 140.88349075 
    9490 Shift along axis -190.14221075 
    9491  
    9492 
    9493 > select add #39
    9494 
    9495 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    9496 
    9497 > view matrix models
    9498 > #39,-0.038392,0.25438,0.96634,124.66,0.50314,-0.8306,0.23864,135.53,0.86335,0.49537,-0.096103,99.479
    9499 
    9500 > fitmap #39 inMap #33.3
    9501 
    9502 Fit molecule CopZ1_P61924.pdb (#39) to map W20_J160_run_ct6_body003.mrc
    9503 (#33.3) using 1420 atoms 
    9504 average map value = 0.0138, steps = 140 
    9505 shifted from previous position = 3.19 
    9506 rotated from previous position = 29.8 degrees 
    9507 atoms outside contour = 768, contour level = 0.015167 
    9508  
    9509 Position of CopZ1_P61924.pdb (#39) relative to W20_J160_run_ct6_body003.mrc
    9510 (#33.3) coordinates: 
    9511 Matrix rotation and translation 
    9512 -0.59910220 0.35688559 0.71673513 128.54412804 
    9513 0.33901457 -0.69789676 0.63087974 127.78779026 
    9514 0.72535901 0.62094508 0.29712207 93.14122293 
    9515 Axis -0.44768773 -0.38862007 -0.80532611 
    9516 Axis point 38.57930905 41.25889004 0.00000000 
    9517 Rotation angle (degrees) 179.36426033 
    9518 Shift along axis -182.21758707 
    9519  
    9520 
    9521 > select subtract #39
    9522 
    9523 Nothing selected 
    9524 
    9525 > show #!34 models
    9526 
    9527 > hide #!34 models
    9528 
    9529 > show #!34 models
    9530 
    9531 > hide #!34 models
    9532 
    9533 > hide #39 models
    9534 
    9535 > hide #!50 models
    9536 
    9537 > show #!50 models
    9538 
    9539 > hide #!50 models
    9540 
    9541 > hide #50.1 models
    9542 
    9543 > show #!50 models
    9544 
    9545 > hide #!50 models
    9546 
    9547 > hide #52 models
    9548 
    9549 > show #!34 models
    9550 
    9551 > fitmap #33 inMap #33.3
    9552 
    9553 Multiple maps for #33 
    9554 
    9555 > fitmap #34 inMap #33.2
    9556 
    9557 Fit molecule CopA-F8WHL2.pdb (#34) to map W20_J160_run_ct6_body002.mrc (#33.2)
    9558 using 6696 atoms 
    9559 average map value = 0.01229, steps = 144 
    9560 shifted from previous position = 0.768 
    9561 rotated from previous position = 0.619 degrees 
    9562 atoms outside contour = 4035, contour level = 0.014809 
    9563  
    9564 Position of CopA-F8WHL2.pdb (#34) relative to W20_J160_run_ct6_body002.mrc
    9565 (#33.2) coordinates: 
    9566 Matrix rotation and translation 
    9567 -0.57247775 -0.57456895 -0.58492714 151.44699314 
    9568 0.70447239 -0.70969024 0.00764404 125.42515832 
    9569 -0.41950911 -0.40768897 0.81104982 121.20707602 
    9570 Axis -0.30653667 -0.12208683 0.94399686 
    9571 Axis point 68.14146734 105.20078411 -0.00000000 
    9572 Rotation angle (degrees) 137.35447863 
    9573 Shift along axis 52.68228363 
    9574  
    9575 
    9576 > show #50.1 models
    9577 
    9578 > hide #50.1 models
    9579 
    9580 > show #50.1 models
    9581 
    9582 > hide #!50 models
    9583 
    9584 > hide #50.1 models
    9585 
    9586 > show #!50 models
    9587 
    9588 > show #50.1 models
    9589 
    9590 > hide #!50.3 models
    9591 
    9592 > show #!50.3 models
    9593 
    9594 > hide #!50.5 models
    9595 
    9596 > hide #!50.2 models
    9597 
    9598 > hide #!50.3 models
    9599 
    9600 > hide #50.6 models
    9601 
    9602 > hide #!50.8 models
    9603 
    9604 > hide #50.9 models
    9605 
    9606 > hide #!50.7 models
    9607 
    9608 > hide #!50.10 models
    9609 
    9610 > hide #50.1 models
    9611 
    9612 > show #!50.2 models
    9613 
    9614 > show #!50.3 models
    9615 
    9616 > fitmap #50.2 inMap #33.2
    9617 
    9618 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A1 (#50.2) to map
    9619 W20_J160_run_ct6_body002.mrc (#33.2) using 2510 atoms 
    9620 average map value = 0.01804, steps = 44 
    9621 shifted from previous position = 0.476 
    9622 rotated from previous position = 0.223 degrees 
    9623 atoms outside contour = 1048, contour level = 0.014809 
    9624  
    9625 Position of W20_C1_initial_model_no_wat_lig.pdb A1 (#50.2) relative to
    9626 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    9627 Matrix rotation and translation 
    9628 -0.95004228 0.18207545 -0.25351172 368.13646707 
    9629 0.07472194 -0.65592625 -0.75111742 494.19899480 
    9630 -0.30304504 -0.73253620 0.60955264 227.59862474 
    9631 Axis 0.15525602 0.41387719 -0.89699567 
    9632 Axis point 211.61727753 293.61074195 0.00000000 
    9633 Rotation angle (degrees) 176.56933670 
    9634 Shift along axis 57.53811301 
    9635  
    9636 
    9637 > fitmap #50.3 inMap #33.2
    9638 
    9639 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) to map
    9640 W20_J160_run_ct6_body002.mrc (#33.2) using 3559 atoms 
    9641 average map value = 0.01022, steps = 184 
    9642 shifted from previous position = 2.7 
    9643 rotated from previous position = 7.42 degrees 
    9644 atoms outside contour = 2357, contour level = 0.014809 
    9645  
    9646 Position of W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) relative to
    9647 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    9648 Matrix rotation and translation 
    9649 -0.93274721 0.18386833 -0.31012106 379.03416947 
    9650 0.07603460 -0.74050966 -0.66773063 496.69481023 
    9651 -0.35242216 -0.64640381 0.67672796 193.41619316 
    9652 Axis 0.18107201 0.35915085 -0.91554552 
    9653 Axis point 216.23338293 280.38752423 0.00000000 
    9654 Rotation angle (degrees) 176.62387365 
    9655 Shift along axis 69.93951212 
    9656  
    9657 
    9658 > hide #!33 models
    9659 
    9660 > hide #!34 models
    9661 
    9662 > show #!34 models
    9663 
    9664 > hide #!50.2 models
    9665 
    9666 > show #!50.2 models
    9667 
    9668 > hide #!50.2 models
    9669 
    9670 > ui mousemode right select
    9671 
    9672 Drag select of 223 residues 
    9673 
    9674 > select up
    9675 
    9676 2109 atoms, 2166 bonds, 262 residues, 1 model selected 
    9677 
    9678 > select up
    9679 
    9680 6696 atoms, 6852 bonds, 834 residues, 1 model selected 
    9681 
    9682 > select down
    9683 
    9684 2109 atoms, 2166 bonds, 262 residues, 1 model selected 
    9685 
    9686 > select #34/A:127
    9687 
    9688 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9689 
    9690 > select clear
    9691 
    9692 Drag select of 1 residues 
    9693 
    9694 > select up
    9695 
    9696 6696 atoms, 6852 bonds, 834 residues, 1 model selected 
    9697 
    9698 > select down
    9699 
    9700 8 atoms, 1 residue, 1 model selected 
    9701 Drag select of 190 residues 
    9702 
    9703 > select up
    9704 
    9705 1664 atoms, 1710 bonds, 206 residues, 1 model selected 
    9706 
    9707 > select up
    9708 
    9709 6696 atoms, 6852 bonds, 834 residues, 1 model selected 
    9710 
    9711 > select down
    9712 
    9713 1664 atoms, 1710 bonds, 206 residues, 1 model selected 
    9714 
    9715 > delete sel
    9716 
    9717 Drag select of 63 residues, 2 pseudobonds 
    9718 
    9719 > select up
    9720 
    9721 788 atoms, 803 bonds, 2 pseudobonds, 96 residues, 2 models selected 
    9722 
    9723 > delete sel
    9724 
    9725 Drag select of 19 residues, 2 pseudobonds 
    9726 
    9727 > delete sel
    9728 
    9729 Drag select of 4 residues 
    9730 
    9731 > delete sel
    9732 
    9733 > show #!50.2 models
    9734 
    9735 > show #!33 models
    9736 
    9737 > fitmap #34 inMap #33.2
    9738 
    9739 Fit molecule CopA-F8WHL2.pdb (#34) to map W20_J160_run_ct6_body002.mrc (#33.2)
    9740 using 4046 atoms 
    9741 average map value = 0.009675, steps = 164 
    9742 shifted from previous position = 0.697 
    9743 rotated from previous position = 2.08 degrees 
    9744 atoms outside contour = 2782, contour level = 0.014809 
    9745  
    9746 Position of CopA-F8WHL2.pdb (#34) relative to W20_J160_run_ct6_body002.mrc
    9747 (#33.2) coordinates: 
    9748 Matrix rotation and translation 
    9749 -0.58668811 -0.55339986 -0.59122387 151.25489618 
    9750 0.67908972 -0.73393831 0.01310416 124.24263215 
    9751 -0.44117369 -0.39380599 0.80640103 120.81607944 
    9752 Axis -0.31143421 -0.11484294 0.94330262 
    9753 Axis point 69.89652487 102.51139715 0.00000000 
    9754 Rotation angle (degrees) 139.21031634 
    9755 Shift along axis 52.59178621 
    9756  
    9757 
    9758 > fitmap #50.3 inMap #33.2
    9759 
    9760 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) to map
    9761 W20_J160_run_ct6_body002.mrc (#33.2) using 3559 atoms 
    9762 average map value = 0.01022, steps = 160 
    9763 shifted from previous position = 0.0132 
    9764 rotated from previous position = 0.015 degrees 
    9765 atoms outside contour = 2353, contour level = 0.014809 
    9766  
    9767 Position of W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) relative to
    9768 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    9769 Matrix rotation and translation 
    9770 -0.93280742 0.18368258 -0.31005003 379.08438259 
    9771 0.07605879 -0.74062741 -0.66759726 496.69733667 
    9772 -0.35225754 -0.64632171 0.67689207 193.32199255 
    9773 Axis 0.18099805 0.35907301 -0.91559067 
    9774 Axis point 216.22488098 280.37147530 0.00000000 
    9775 Rotation angle (degrees) 176.63062081 
    9776 Shift along axis 69.96032790 
    9777  
    9778 
    9779 > combine #34
    9780 
    9781 > combine #50.3
    9782 
    9783 > hide #!50.3 models
    9784 
    9785 > hide #!34 models
    9786 
    9787 > hide #!33.4 models
    9788 
    9789 > show #!33.4 models
    9790 
    9791 > hide #!33 models
    9792 
    9793 > hide #!58 models
    9794 
    9795 > select clear
    9796 
    9797 > hide #!50.2 models
    9798 
    9799 Drag select of 243 residues 
    9800 
    9801 > select up
    9802 
    9803 2056 atoms, 2095 bonds, 259 residues, 1 model selected 
    9804 
    9805 > select up
    9806 
    9807 4046 atoms, 4125 bonds, 509 residues, 1 model selected 
    9808 
    9809 > select up
    9810 
    9811 101979 atoms, 103831 bonds, 12855 residues, 91 models selected 
    9812 
    9813 > select clear
    9814 
    9815 Drag select of 274 residues 
    9816 
    9817 > select up
    9818 
    9819 2192 atoms, 2235 bonds, 276 residues, 1 model selected 
    9820 
    9821 > delete sel
    9822 
    9823 Drag select of 2 residues, 1 pseudobonds 
    9824 
    9825 > delete sel
    9826 
    9827 > show #!33 models
    9828 
    9829 > fitmap #57 inMap #33.1
    9830 
    9831 Fit molecule copy of CopA-F8WHL2.pdb (#57) to map W20_J160_run_ct6_body001.mrc
    9832 (#33.1) using 1842 atoms 
    9833 average map value = 0.01399, steps = 76 
    9834 shifted from previous position = 7.58 
    9835 rotated from previous position = 11.9 degrees 
    9836 atoms outside contour = 1005, contour level = 0.014811 
    9837  
    9838 Position of copy of CopA-F8WHL2.pdb (#57) relative to
    9839 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    9840 Matrix rotation and translation 
    9841 -0.66070189 -0.61639558 -0.42840344 148.88789464 
    9842 0.70166098 -0.70992235 -0.06068050 124.32932168 
    9843 -0.26672999 -0.34068570 0.90154776 127.22528478 
    9844 Axis -0.20632088 -0.11912853 0.97120548 
    9845 Axis point 61.04505270 103.19655495 0.00000000 
    9846 Rotation angle (degrees) 137.26821223 
    9847 Shift along axis 78.03204323 
    9848  
    9849 
    9850 > hide #!57 models
    9851 
    9852 > hide #!33.4 models
    9853 
    9854 > show #!33.4 models
    9855 
    9856 > hide #!33 models
    9857 
    9858 > show #!58 models
    9859 
    9860 Drag select of 104 residues, 1 pseudobonds 
    9861 
    9862 > select clear
    9863 
    9864 Drag select of 282 residues, 6 pseudobonds 
    9865 
    9866 > delete sel
    9867 
    9868 > fitmap #87 inMap #33.1
    9869 
    9870 No atoms or maps for #87 
    9871 
    9872 > fitmap #58 inMap #33.1
    9873 
    9874 Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A2 (#58) to map
    9875 W20_J160_run_ct6_body001.mrc (#33.1) using 1297 atoms 
    9876 average map value = 0.01501, steps = 108 
    9877 shifted from previous position = 10.8 
    9878 rotated from previous position = 12.4 degrees 
    9879 atoms outside contour = 664, contour level = 0.014811 
    9880  
    9881 Position of copy of W20_C1_initial_model_no_wat_lig.pdb A2 (#58) relative to
    9882 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    9883 Matrix rotation and translation 
    9884 -0.95774575 0.09731996 -0.27065088 396.29244001 
    9885 0.15737130 -0.61033953 -0.77635039 474.71597461 
    9886 -0.24074332 -0.78613897 0.56923472 242.75449330 
    9887 Axis -0.14438058 -0.44113353 0.88575135 
    9888 Axis point 213.60576536 301.52927607 0.00000000 
    9889 Rotation angle (degrees) 178.05738481 
    9890 Shift along axis -51.60994703 
    9891  
    9892 
    9893 > show #!33 models
    9894 
    9895 > show #!57 models
    9896 
    9897 > hide #!58 models
    9898 
    9899 > show #!58 models
    9900 
    9901 > hide #!57 models
    9902 
    9903 > show #!57 models
    9904 
    9905 > hide #!33 models
    9906 
    9907 > show #!34 models
    9908 
    9909 > hide #!57 models
    9910 
    9911 > hide #!58 models
    9912 
    9913 > show #!58 models
    9914 
    9915 > hide #!58 models
    9916 
    9917 > show #!58 models
    9918 
    9919 > hide #!58 models
    9920 
    9921 Drag select of 144 residues 
    9922 
    9923 > select clear
    9924 
    9925 [Repeated 1 time(s)]
    9926 
    9927 > combine #34
    9928 
    9929 > hide #!34 models
    9930 
    9931 > show #!58 models
    9932 
    9933 > hide #!58 models
    9934 
    9935 > show #!58 models
    9936 
    9937 > hide #!58 models
    9938 
    9939 > show #!58 models
    9940 
    9941 > hide #!58 models
    9942 
    9943 > show #!58 models
    9944 
    9945 > hide #!58 models
    9946 
    9947 Drag select of 161 residues 
    9948 
    9949 > select up
    9950 
    9951 1359 atoms, 1382 bonds, 172 residues, 1 model selected 
    9952 
    9953 > show #!58 models
    9954 
    9955 > hide #!58 models
    9956 
    9957 > delete sel
    9958 
    9959 Drag select of 9 residues 
    9960 
    9961 > delete sel
    9962 
    9963 > fitmap #59 inMap #33.1
    9964 
    9965 Fit molecule copy of CopA-F8WHL2.pdb (#59) to map W20_J160_run_ct6_body001.mrc
    9966 (#33.1) using 2618 atoms 
    9967 average map value = 0.00517, steps = 108 
    9968 shifted from previous position = 1.61 
    9969 rotated from previous position = 4.74 degrees 
    9970 atoms outside contour = 2287, contour level = 0.014811 
    9971  
    9972 Position of copy of CopA-F8WHL2.pdb (#59) relative to
    9973 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    9974 Matrix rotation and translation 
    9975 -0.61097397 -0.53341027 -0.58496522 151.41100776 
    9976 0.68780030 -0.72352924 -0.05861913 123.94831007 
    9977 -0.39197139 -0.43815401 0.80893726 122.28836749 
    9978 Axis -0.29346029 -0.14922482 0.94425262 
    9979 Axis point 69.10859861 104.04335802 0.00000000 
    9980 Rotation angle (degrees) 139.71015631 
    9981 Shift along axis 52.54182884 
    9982  
    9983 
    9984 > fitmap #59 inMap #33.2
    9985 
    9986 Fit molecule copy of CopA-F8WHL2.pdb (#59) to map W20_J160_run_ct6_body002.mrc
    9987 (#33.2) using 2618 atoms 
    9988 average map value = 0.0148, steps = 72 
    9989 shifted from previous position = 1.57 
    9990 rotated from previous position = 4.66 degrees 
    9991 atoms outside contour = 1354, contour level = 0.014809 
    9992  
    9993 Position of copy of CopA-F8WHL2.pdb (#59) relative to
    9994 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    9995 Matrix rotation and translation 
    9996 -0.58463217 -0.55176650 -0.59477640 151.19300478 
    9997 0.68006639 -0.73305905 0.01158206 124.19731133 
    9998 -0.44239681 -0.39771619 0.80380775 120.82904766 
    9999 Axis -0.31316702 -0.11659043 0.94251424 
    10000 Axis point 69.96688260 102.62111999 0.00000000 
    10001 Rotation angle (degrees) 139.19532441 
    10002 Shift along axis 52.05421740 
    10003  
    10004 
    10005 > show #!33 models
    10006 
    10007 > show #!58 models
    10008 
    10009 > show #!50.2 models
    10010 
    10011 > hide #!33 models
    10012 
    10013 > show #!34 models
    10014 
    10015 > hide #!34 models
    10016 
    10017 > show #!34 models
    10018 
    10019 > hide #!34 models
    10020 
    10021 > show #!34 models
    10022 
    10023 > hide #!34 models
    10024 
    10025 > show #!34 models
    10026 
    10027 > hide #!50.2 models
    10028 
    10029 > show #!50.2 models
    10030 
    10031 > hide #!34 models
    10032 
    10033 > show #!34 models
    10034 
    10035 > hide #!34 models
    10036 
    10037 > show #!34 models
    10038 
    10039 > hide #!34 models
    10040 
    10041 > hide #!59 models
    10042 
    10043 > show #!59 models
    10044 
    10045 > show #!57 models
    10046 
    10047 > hide #!57 models
    10048 
    10049 > show #!57 models
    10050 
    10051 > hide #!57 models
    10052 
    10053 > hide #!59 models
    10054 
    10055 > show #!57 models
    10056 
    10057 > hide #!58 models
    10058 
    10059 > hide #!57 models
    10060 
    10061 > show #!33 models
    10062 
    10063 > show #!57 models
    10064 
    10065 > show #!58 models
    10066 
    10067 > hide #!58 models
    10068 
    10069 > show #!59 models
    10070 
    10071 > hide #!59 models
    10072 
    10073 > show #!59 models
    10074 
    10075 > hide #!57 models
    10076 
    10077 > show #!58 models
    10078 
    10079 > hide #!33 models
    10080 
    10081 > show #51 models
    10082 
    10083 > combine #51
    10084 
    10085 > hide #51 models
    10086 
    10087 > hide #!59 models
    10088 
    10089 > hide #!58 models
    10090 
    10091 > hide #!50.2 models
    10092 
    10093 Drag select of 667 residues 
    10094 
    10095 > select up
    10096 
    10097 6183 atoms, 6300 bonds, 784 residues, 1 model selected 
    10098 
    10099 > delete sel
    10100 
    10101 Drag select of 87 residues, 10 pseudobonds 
    10102 
    10103 > select clear
    10104 
    10105 Drag select of 61 residues, 5 pseudobonds 
    10106 
    10107 > select up
    10108 
    10109 758 atoms, 752 bonds, 5 pseudobonds, 95 residues, 2 models selected 
    10110 
    10111 > delete sel
    10112 
    10113 Drag select of 27 residues, 3 pseudobonds 
    10114 
    10115 > select up
    10116 
    10117 2800 atoms, 2874 bonds, 3 pseudobonds, 345 residues, 2 models selected 
    10118 
    10119 > select down
    10120 
    10121 210 atoms, 3 pseudobonds, 27 residues, 2 models selected 
    10122 
    10123 > delete sel
    10124 
    10125 > fitmap #60 inMap #33.2
    10126 
    10127 Fit molecule copy of A_fixed_model_2_A.pdb (#60) to map
    10128 W20_J160_run_ct6_body002.mrc (#33.2) using 2590 atoms 
    10129 average map value = 0.01604, steps = 212 
    10130 shifted from previous position = 8.36 
    10131 rotated from previous position = 37.7 degrees 
    10132 atoms outside contour = 1297, contour level = 0.014809 
    10133  
    10134 Position of copy of A_fixed_model_2_A.pdb (#60) relative to
    10135 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    10136 Matrix rotation and translation 
    10137 -0.12666898 -0.97960527 -0.15597590 240.27472629 
    10138 0.03811656 -0.16193319 0.98606530 35.82542257 
    10139 -0.99121244 0.11895862 0.05785109 200.76320490 
    10140 Axis -0.55003121 0.52981504 0.64557082 
    10141 Axis point 195.41347917 29.75172699 0.00000000 
    10142 Rotation angle (degrees) 127.97921254 
    10143 Shift along axis 16.42911600 
    10144  
    10145 
    10146 > show #!33 models
    10147 
    10148 > show #50.1 models
    10149 
    10150 > hide #50.1 models
    10151 
    10152 > show #!50.2 models
    10153 
    10154 > select add #60
    10155 
    10156 2590 atoms, 2665 bonds, 318 residues, 1 model selected 
    10157 
    10158 > ui mousemode right "rotate selected models"
    10159 
    10160 > view matrix models
    10161 > #60,-0.3575,-0.93077,-0.076565,262.87,-0.90319,0.36543,-0.22518,271.82,0.23757,-0.011349,-0.9713,201.17
    10162 
    10163 > ui tool show Matchmaker
    10164 
    10165 > matchmaker #!60 to #50.2
    10166 
    10167 Computing secondary structure 
    10168 Parameters 
    10169 --- 
    10170 Chain pairing | bb 
    10171 Alignment algorithm | Needleman-Wunsch 
    10172 Similarity matrix | BLOSUM-62 
    10173 SS fraction | 0.3 
    10174 Gap open (HH/SS/other) | 18/18/6 
    10175 Gap extend | 1 
    10176 SS matrix |  |  | H | S | O 
    10177 ---|---|---|--- 
    10178 H | 6 | -9 | -6 
    10179 S |  | 6 | -6 
    10180 O |  |  | 4 
    10181 Iteration cutoff | 2 
    10182  
    10183 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A1, chain A1 (#50.2) with copy
    10184 of A_fixed_model_2_A.pdb, chain A (#60), sequence alignment score = 1588.3 
    10185 RMSD between 296 pruned atom pairs is 0.254 angstroms; (across all 296 pairs:
    10186 0.254) 
    10187  
    10188 
    10189 > hide #!50.2 models
    10190 
    10191 > hide #!50 models
    10192 
    10193 > show #!50 models
    10194 
    10195 > hide #!50 models
    10196 
    10197 > select subtract #60
    10198 
    10199 Nothing selected 
    10200 
    10201 > show #!50.2 models
    10202 
    10203 > show #51 models
    10204 
    10205 > hide #51 models
    10206 
    10207 > show #51 models
    10208 
    10209 > hide #51 models
    10210 
    10211 > combine #51
    10212 
    10213 > hide #!33 models
    10214 
    10215 > hide #!50.2 models
    10216 
    10217 > hide #!60 models
    10218 
    10219 > ui mousemode right select
    10220 
    10221 Drag select of 103 residues 
    10222 
    10223 > select up
    10224 
    10225 1168 atoms, 1193 bonds, 145 residues, 1 model selected 
    10226 
    10227 > delete sel
    10228 
    10229 > hide #!61 models
    10230 
    10231 > show #!60 models
    10232 
    10233 > hide #!60 models
    10234 
    10235 > show #!61 models
    10236 
    10237 > select #61/A:318
    10238 
    10239 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10240 
    10241 > select up
    10242 
    10243 47 atoms, 47 bonds, 6 residues, 1 model selected 
    10244 
    10245 > select up
    10246 
    10247 7736 atoms, 7896 bonds, 978 residues, 1 model selected 
    10248 
    10249 > select down
    10250 
    10251 47 atoms, 47 bonds, 6 residues, 1 model selected 
    10252 
    10253 > delete sel
    10254 
    10255 Drag select of 100 residues, 3 pseudobonds 
    10256 
    10257 > select up
    10258 
    10259 1091 atoms, 1121 bonds, 3 pseudobonds, 134 residues, 2 models selected 
    10260 
    10261 > select down
    10262 
    10263 793 atoms, 3 pseudobonds, 100 residues, 2 models selected 
    10264 
    10265 > select clear
    10266 
    10267 > select #61/A:1
    10268 
    10269 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10270 
    10271 > select up
    10272 
    10273 533 atoms, 549 bonds, 64 residues, 1 model selected 
    10274 
    10275 > delete sel
    10276 
    10277 Drag select of 9 residues, 1 pseudobonds 
    10278 
    10279 > delete sel
    10280 
    10281 Drag select of 26 residues, 1 pseudobonds 
    10282 
    10283 > select up
    10284 
    10285 258 atoms, 264 bonds, 1 pseudobond, 33 residues, 2 models selected 
    10286 
    10287 > delete sel
    10288 
    10289 Drag select of 7 residues 
    10290 
    10291 > select clear
    10292 
    10293 [Repeated 1 time(s)]Drag select of 13 residues 
    10294 Drag select of 48 residues 
    10295 
    10296 > select up
    10297 
    10298 507 atoms, 517 bonds, 62 residues, 1 model selected 
    10299 
    10300 > select down
    10301 
    10302 384 atoms, 48 residues, 1 model selected 
    10303 
    10304 > select clear
    10305 
    10306 Drag select of 50 residues 
    10307 
    10308 > select up
    10309 
    10310 507 atoms, 517 bonds, 62 residues, 1 model selected 
    10311 
    10312 > select clear
    10313 
    10314 Drag select of 1 residues 
    10315 
    10316 > select up
    10317 
    10318 42 atoms, 42 bonds, 6 residues, 1 model selected 
    10319 
    10320 > delete sel
    10321 
    10322 > select #61/A:263
    10323 
    10324 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10325 
    10326 > select up
    10327 
    10328 44 atoms, 43 bonds, 6 residues, 1 model selected 
    10329 
    10330 > delete sel
    10331 
    10332 > select clear
    10333 
    10334 > select #61/A:258
    10335 
    10336 10 atoms, 10 bonds, 1 residue, 1 model selected 
    10337 
    10338 > select clear
    10339 
    10340 Drag select of 4 residues 
    10341 
    10342 > select clear
    10343 
    10344 Drag select of 4 residues 
    10345 
    10346 > select clear
    10347 
    10348 Drag select of 5 residues 
    10349 
    10350 > select up
    10351 
    10352 121 atoms, 122 bonds, 14 residues, 1 model selected 
    10353 
    10354 > delete sel
    10355 
    10356 > select clear
    10357 
    10358 > select #61/A:273
    10359 
    10360 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10361 
    10362 > select up
    10363 
    10364 54 atoms, 55 bonds, 6 residues, 1 model selected 
    10365 
    10366 > delete sel
    10367 
    10368 > select #61/A:278
    10369 
    10370 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10371 
    10372 > select clear
    10373 
    10374 Drag select of 1 residues 
    10375 Drag select of 6 residues 
    10376 
    10377 > select up
    10378 
    10379 90 atoms, 90 bonds, 11 residues, 1 model selected 
    10380 
    10381 > fitmap #60 inMap #33.2
    10382 
    10383 Fit molecule copy of A_fixed_model_2_A.pdb (#60) to map
    10384 W20_J160_run_ct6_body002.mrc (#33.2) using 2590 atoms 
    10385 average map value = 0.01743, steps = 48 
    10386 shifted from previous position = 0.0339 
    10387 rotated from previous position = 0.278 degrees 
    10388 atoms outside contour = 1142, contour level = 0.014809 
    10389  
    10390 Position of copy of A_fixed_model_2_A.pdb (#60) relative to
    10391 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    10392 Matrix rotation and translation 
    10393 -0.44176945 -0.87418787 -0.20158210 278.02704219 
    10394 -0.65633376 0.16174616 0.73692889 133.70992844 
    10395 -0.61160916 0.45785781 -0.64521352 224.98469771 
    10396 Axis -0.51515506 0.75689501 0.40215074 
    10397 Axis point 203.25110647 0.00000000 49.34812669 
    10398 Rotation angle (degrees) 164.28447736 
    10399 Shift along axis 48.45510328 
    10400  
    10401 
    10402 > delete sel
    10403 
    10404 Drag select of 16 residues, 1 pseudobonds 
    10405 
    10406 > select up
    10407 
    10408 205 atoms, 209 bonds, 1 pseudobond, 25 residues, 2 models selected 
    10409 
    10410 > select down
    10411 
    10412 126 atoms, 1 pseudobond, 16 residues, 2 models selected 
    10413 
    10414 > delete sel
    10415 
    10416 Drag select of 2 residues 
    10417 
    10418 > delete sel
    10419 
    10420 > show #!60 models
    10421 
    10422 > show #!33 models
    10423 
    10424 > fitmap #61 inMap #33.1
    10425 
    10426 Fit molecule copy of A_fixed_model_2_A.pdb (#61) to map
    10427 W20_J160_run_ct6_body001.mrc (#33.1) using 7151 atoms 
    10428 average map value = 0.004441, steps = 228 
    10429 shifted from previous position = 5.35 
    10430 rotated from previous position = 8.58 degrees 
    10431 atoms outside contour = 6297, contour level = 0.014811 
    10432  
    10433 Position of copy of A_fixed_model_2_A.pdb (#61) relative to
    10434 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    10435 Matrix rotation and translation 
    10436 -0.45222649 -0.82892764 -0.32919625 288.15586650 
    10437 -0.57376739 -0.01220253 0.81892739 121.44819917 
    10438 -0.68284858 0.55922273 -0.47009335 215.98047971 
    10439 Axis -0.51166679 0.69676128 0.50271344 
    10440 Axis point 206.53531672 0.00000000 35.33484489 
    10441 Rotation angle (degrees) 165.29851626 
    10442 Shift along axis 45.75690645 
    10443  
    10444 
    10445 > fitmap #61 inMap #33.2
    10446 
    10447 Fit molecule copy of A_fixed_model_2_A.pdb (#61) to map
    10448 W20_J160_run_ct6_body002.mrc (#33.2) using 7151 atoms 
    10449 average map value = 0.005548, steps = 2000 
    10450 shifted from previous position = 4.46 
    10451 rotated from previous position = 9.55 degrees 
    10452 atoms outside contour = 5855, contour level = 0.014809 
    10453  
    10454 Position of copy of A_fixed_model_2_A.pdb (#61) relative to
    10455 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    10456 Matrix rotation and translation 
    10457 -0.32348189 -0.90777241 -0.26703693 271.47554220 
    10458 -0.61054188 -0.01536719 0.79183487 128.17226278 
    10459 -0.72290946 0.41918147 -0.54926207 231.58959567 
    10460 Axis -0.56499205 0.69116330 0.45064096 
    10461 Axis point 214.35725794 0.00000000 37.95145878 
    10462 Rotation angle (degrees) 160.74418801 
    10463 Shift along axis 39.57019701 
    10464  
    10465 
    10466 > combine #61
    10467 
    10468 > hide #!61 models
    10469 
    10470 > hide #!60 models
    10471 
    10472 > hide #!50 models
    10473 
    10474 > show #!50 models
    10475 
    10476 > hide #!33 models
    10477 
    10478 Drag select of 1 residues 
    10479 
    10480 > select up
    10481 
    10482 7151 atoms, 7294 bonds, 906 residues, 1 model selected 
    10483 
    10484 > select clear
    10485 
    10486 Drag select of 169 residues 
    10487 
    10488 > select up
    10489 
    10490 1541 atoms, 1568 bonds, 193 residues, 1 model selected 
    10491 
    10492 > delete sel
    10493 
    10494 Drag select of 51 residues, 1 pseudobonds 
    10495 
    10496 > select up
    10497 
    10498 646 atoms, 657 bonds, 1 pseudobond, 82 residues, 2 models selected 
    10499 
    10500 > delete sel
    10501 
    10502 Drag select of 4 residues 
    10503 
    10504 > select clear
    10505 
    10506 Drag select of 3 residues 
    10507 
    10508 > select clear
    10509 
    10510 [Repeated 2 time(s)]Drag select of 20 residues, 2 pseudobonds 
    10511 
    10512 > select up
    10513 
    10514 796 atoms, 812 bonds, 2 pseudobonds, 108 residues, 2 models selected 
    10515 
    10516 > delete sel
    10517 
    10518 Drag select of 8 residues, 1 pseudobonds 
    10519 
    10520 > select clear
    10521 
    10522 Drag select of 15 residues 
    10523 
    10524 > delete sel
    10525 
    10526 > select clear
    10527 
    10528 > delete sel
    10529 
    10530 > select clear
    10531 
    10532 > delete sel
    10533 
    10534 > close #62
    10535 
    10536 > combine #61
    10537 
    10538 Drag select of 269 residues 
    10539 
    10540 > select up
    10541 
    10542 2282 atoms, 2326 bonds, 286 residues, 1 model selected 
    10543 
    10544 > delete sel
    10545 
    10546 Drag select of 37 residues, 2 pseudobonds 
    10547 
    10548 > select up
    10549 
    10550 738 atoms, 753 bonds, 2 pseudobonds, 101 residues, 2 models selected 
    10551 
    10552 > delete sel
    10553 
    10554 Drag select of 10 residues 
    10555 
    10556 > delete sel
    10557 
    10558 > close #62
    10559 
    10560 > combine #61
    10561 
    10562 > select clear
    10563 
    10564 [Repeated 1 time(s)]
    10565 
    10566 > select #62/A:873
    10567 
    10568 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10569 
    10570 > select clear
    10571 
    10572 Drag select of 1 residues 
    10573 
    10574 > select up
    10575 
    10576 645 atoms, 657 bonds, 90 residues, 1 model selected 
    10577 
    10578 > delete sel
    10579 
    10580 Drag select of 309 residues 
    10581 
    10582 > delete sel
    10583 
    10584 > fitmap #62 inMap #33.1
    10585 
    10586 Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
    10587 W20_J160_run_ct6_body001.mrc (#33.1) using 4038 atoms 
    10588 average map value = 0.007876, steps = 128 
    10589 shifted from previous position = 3.44 
    10590 rotated from previous position = 10.8 degrees 
    10591 atoms outside contour = 3167, contour level = 0.014811 
    10592  
    10593 Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
    10594 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    10595 Matrix rotation and translation 
    10596 -0.49233635 -0.83165726 -0.25680949 286.92215484 
    10597 -0.53267730 0.05454857 0.84455867 111.52201588 
    10598 -0.68837476 0.55260352 -0.46986119 217.04968179 
    10599 Axis -0.48600137 0.71840251 0.49769518 
    10600 Axis point 201.81367843 0.00000000 36.66306761 
    10601 Rotation angle (degrees) 162.52050103 
    10602 Shift along axis 48.69771641 
    10603  
    10604 
    10605 > show #!33 models
    10606 
    10607 > hide #!62 models
    10608 
    10609 > show #!62 models
    10610 
    10611 > hide #!62 models
    10612 
    10613 > show #!60 models
    10614 
    10615 > show #!61 models
    10616 
    10617 > hide #!61 models
    10618 
    10619 > show #!61 models
    10620 
    10621 > show #!62 models
    10622 
    10623 > hide #!62 models
    10624 
    10625 > show #!62 models
    10626 
    10627 > hide #!62 models
    10628 
    10629 > close #61
    10630 
    10631 > show #!62 models
    10632 
    10633 > combine #62
    10634 
    10635 > hide #!62 models
    10636 
    10637 > hide #!60 models
    10638 
    10639 > fitmap #61 inMap #33.2
    10640 
    10641 Fit molecule copy of copy of copy of A_fixed_model_2_A.pdb (#61) to map
    10642 W20_J160_run_ct6_body002.mrc (#33.2) using 4038 atoms 
    10643 average map value = 0.009974, steps = 196 
    10644 shifted from previous position = 3.26 
    10645 rotated from previous position = 10.9 degrees 
    10646 atoms outside contour = 2744, contour level = 0.014809 
    10647  
    10648 Position of copy of copy of copy of A_fixed_model_2_A.pdb (#61) relative to
    10649 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    10650 Matrix rotation and translation 
    10651 -0.32106500 -0.91005872 -0.26212669 270.65425094 
    10652 -0.60680985 -0.01482211 0.79470882 127.10234227 
    10653 -0.72711696 0.41421424 -0.54747373 232.51552841 
    10654 Axis -0.56535652 0.69090415 0.45058125 
    10655 Axis point 214.25644692 0.00000000 38.06080511 
    10656 Rotation angle (degrees) 160.33570313 
    10657 Shift along axis 39.56652768 
    10658  
    10659 
    10660 > hide #!33 models
    10661 
    10662 > show #!33 models
    10663 
    10664 > hide #!33 models
    10665 
    10666 Drag select of 10 residues 
    10667 
    10668 > select up
    10669 
    10670 388 atoms, 400 bonds, 50 residues, 1 model selected 
    10671 
    10672 > delete sel
    10673 
    10674 Drag select of 88 residues 
    10675 
    10676 > select clear
    10677 
    10678 Drag select of 57 residues 
    10679 
    10680 > select clear
    10681 
    10682 Drag select of 78 residues 
    10683 
    10684 > select up
    10685 
    10686 719 atoms, 728 bonds, 89 residues, 1 model selected 
    10687 
    10688 > delete sel
    10689 
    10690 Drag select of 3 residues 
    10691 
    10692 > select up
    10693 
    10694 125 atoms, 126 bonds, 16 residues, 1 model selected 
    10695 
    10696 > delete sel
    10697 
    10698 > select clear
    10699 
    10700 > select #61/A:670
    10701 
    10702 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10703 
    10704 > select clear
    10705 
    10706 Drag select of 2 residues 
    10707 
    10708 > select clear
    10709 
    10710 Drag select of 28 residues 
    10711 
    10712 > fitmap #62 inMap #33.1
    10713 
    10714 Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
    10715 W20_J160_run_ct6_body001.mrc (#33.1) using 4038 atoms 
    10716 average map value = 0.007876, steps = 40 
    10717 shifted from previous position = 0.0144 
    10718 rotated from previous position = 0.0178 degrees 
    10719 atoms outside contour = 3169, contour level = 0.014811 
    10720  
    10721 Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
    10722 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    10723 Matrix rotation and translation 
    10724 -0.49227524 -0.83177636 -0.25654079 286.90681543 
    10725 -0.53253090 0.05466159 0.84464368 111.49096886 
    10726 -0.68853172 0.55241307 -0.46985516 217.06478146 
    10727 Axis -0.48599732 0.71842724 0.49766344 
    10728 Axis point 201.81610476 0.00000000 36.65534481 
    10729 Rotation angle (degrees) 162.50332601 
    10730 Shift along axis 48.68741004 
    10731  
    10732 
    10733 > delete sel
    10734 
    10735 > select clear
    10736 
    10737 > fitmap #61 inMap #33.2
    10738 
    10739 Fit molecule copy of copy of copy of A_fixed_model_2_A.pdb (#61) to map
    10740 W20_J160_run_ct6_body002.mrc (#33.2) using 2593 atoms 
    10741 average map value = 0.01536, steps = 44 
    10742 shifted from previous position = 0.0309 
    10743 rotated from previous position = 0.286 degrees 
    10744 atoms outside contour = 1295, contour level = 0.014809 
    10745  
    10746 Position of copy of copy of copy of A_fixed_model_2_A.pdb (#61) relative to
    10747 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    10748 Matrix rotation and translation 
    10749 -0.31750805 -0.91177971 -0.26047341 270.11347052 
    10750 -0.60893731 -0.01451577 0.79308552 127.53984411 
    10751 -0.72690026 0.41042302 -0.55060781 232.93839308 
    10752 Axis -0.56686193 0.69094730 0.44861941 
    10753 Axis point 214.45195639 0.00000000 38.26217280 
    10754 Rotation angle (degrees) 160.27371795 
    10755 Shift along axis 39.50695274 
    10756  
    10757 
    10758 > show #!33 models
    10759 
    10760 > hide #!33 models
    10761 
    10762 > hide #!61 models
    10763 
    10764 > show #!61 models
    10765 
    10766 Drag select of 8 residues 
    10767 
    10768 > select up
    10769 
    10770 138 atoms, 140 bonds, 17 residues, 1 model selected 
    10771 
    10772 > select clear
    10773 
    10774 Drag select of 19 residues 
    10775 
    10776 > select up
    10777 
    10778 196 atoms, 200 bonds, 25 residues, 1 model selected 
    10779 
    10780 > select clear
    10781 
    10782 Drag select of 3 residues 
    10783 
    10784 > select up
    10785 
    10786 41 atoms, 42 bonds, 5 residues, 1 model selected 
    10787 
    10788 > delete sel
    10789 
    10790 > select #61/A:637
    10791 
    10792 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10793 
    10794 > delete sel
    10795 
    10796 Drag select of 2 residues 
    10797 
    10798 > delete sel
    10799 
    10800 Drag select of 9 residues 
    10801 
    10802 > delete sel
    10803 
    10804 > select #61/A:625
    10805 
    10806 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10807 
    10808 > delete sel
    10809 
    10810 > select #61/A:624
    10811 
    10812 6 atoms, 5 bonds, 1 residue, 1 model selected 
    10813 
    10814 > delete sel
    10815 
    10816 > select #61/A:623
    10817 
    10818 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10819 
    10820 > delete sel
    10821 
    10822 > select clear
    10823 
    10824 [Repeated 1 time(s)]
    10825 
    10826 > select #61/A:622
    10827 
    10828 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10829 
    10830 > delete sel
    10831 
    10832 > fitmap #61 inMap #33.2
    10833 
    10834 Fit molecule copy of copy of copy of A_fixed_model_2_A.pdb (#61) to map
    10835 W20_J160_run_ct6_body002.mrc (#33.2) using 2426 atoms 
    10836 average map value = 0.01573, steps = 64 
    10837 shifted from previous position = 0.0485 
    10838 rotated from previous position = 0.404 degrees 
    10839 atoms outside contour = 1173, contour level = 0.014809 
    10840  
    10841 Position of copy of copy of copy of A_fixed_model_2_A.pdb (#61) relative to
    10842 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    10843 Matrix rotation and translation 
    10844 -0.31268611 -0.91441000 -0.25706370 269.24111705 
    10845 -0.61103650 -0.01356040 0.79148626 127.91459578 
    10846 -0.72722884 0.40456206 -0.55449774 233.52795858 
    10847 Axis -0.56875957 0.69111966 0.44594414 
    10848 Axis point 214.64229202 0.00000000 38.50676211 
    10849 Rotation angle (degrees) 160.11414397 
    10850 Shift along axis 39.41125523 
    10851  
    10852 
    10853 > show #!33 models
    10854 
    10855 > show #!62 models
    10856 
    10857 > hide #!62 models
    10858 
    10859 > show #!60 models
    10860 
    10861 > hide #!61 models
    10862 
    10863 > hide #!60 models
    10864 
    10865 > show #!62 models
    10866 
    10867 > hide #!33 models
    10868 
    10869 Drag select of 2 residues 
    10870 
    10871 > select up
    10872 
    10873 60 atoms, 60 bonds, 7 residues, 1 model selected 
    10874 
    10875 > select up
    10876 
    10877 4038 atoms, 4115 bonds, 507 residues, 1 model selected 
    10878 
    10879 > select down
    10880 
    10881 60 atoms, 60 bonds, 7 residues, 1 model selected 
    10882 
    10883 > select clear
    10884 
    10885 Drag select of 245 residues 
    10886 
    10887 > select up
    10888 
    10889 2197 atoms, 2238 bonds, 276 residues, 1 model selected 
    10890 
    10891 > delete sel
    10892 
    10893 Drag select of 6 residues, 2 pseudobonds 
    10894 
    10895 > select clear
    10896 
    10897 Drag select of 4 residues 
    10898 
    10899 > select up
    10900 
    10901 1841 atoms, 1872 bonds, 231 residues, 1 model selected 
    10902 
    10903 > select down
    10904 
    10905 36 atoms, 4 residues, 1 model selected 
    10906 
    10907 > delete sel
    10908 
    10909 Drag select of 6 residues 
    10910 
    10911 > delete sel
    10912 
    10913 Drag select of 12 residues 
    10914 
    10915 > select up
    10916 
    10917 116 atoms, 117 bonds, 13 residues, 1 model selected 
    10918 
    10919 > delete sel
    10920 
    10921 > select clear
    10922 
    10923 [Repeated 2 time(s)]
    10924 
    10925 > select #62/A:618
    10926 
    10927 5 atoms, 4 bonds, 1 residue, 1 model selected 
    10928 
    10929 > delete sel
    10930 
    10931 > select clear
    10932 
    10933 > select #62/A:619
    10934 
    10935 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10936 
    10937 > delete sel
    10938 
    10939 > select clear
    10940 
    10941 > select #62/A:620
    10942 
    10943 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10944 
    10945 > delete sel
    10946 
    10947 > select #62/A:621
    10948 
    10949 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10950 
    10951 > delete sel
    10952 
    10953 > fitmap #62 inMap #33.1
    10954 
    10955 Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
    10956 W20_J160_run_ct6_body001.mrc (#33.1) using 1612 atoms 
    10957 average map value = 0.01422, steps = 100 
    10958 shifted from previous position = 1.05 
    10959 rotated from previous position = 7.03 degrees 
    10960 atoms outside contour = 871, contour level = 0.014811 
    10961  
    10962 Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
    10963 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    10964 Matrix rotation and translation 
    10965 -0.56465803 -0.76120461 -0.31894961 292.13379963 
    10966 -0.55687251 0.06616556 0.82795841 113.21112709 
    10967 -0.60914228 0.64512763 -0.46125484 203.93497656 
    10968 Axis -0.45795004 0.72686749 0.51180603 
    10969 Axis point 193.99705310 0.00000000 40.16949466 
    10970 Rotation angle (degrees) 168.48533814 
    10971 Shift along axis 52.88195186 
    10972  
    10973 
    10974 > show #!33 models
    10975 
    10976 > show #!61 models
    10977 
    10978 > show #!60 models
    10979 
    10980 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    10981 > resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
    10982 
    10983 ——— End of log from Fri Jul 4 09:53:55 2025 ———
    10984 
    10985 opened ChimeraX session 
    10986 
    10987 > hide #!33 models
    10988 
    10989 > show #!33 models
    10990 
    10991 > open
    10992 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_overall_best_map.ccp4
    10993 
    10994 Opened PredictAndBuild_1_overall_best_map.ccp4 as #63, grid size 138,147,182,
    10995 pixel 1.2, shown at level 0.422, step 1, values float32 
    10996 
    10997 > select add #63
    10998 
    10999 2 models selected 
    11000 
    11001 > select subtract #63
    11002 
    11003 Nothing selected 
    11004 
    11005 > hide #!33 models
    11006 
    11007 > volume #63 level 0.2752
    11008 
    11009 > toolshed show
    11010 
    11011 Downloading bundle ChimeraX_locscalesurfer-0.1.1-py3-none-any.whl 
    11012 Downloading bundle ChimeraX_ISOLDE-1.9-cp311-cp311-macosx_10_13_universal2.whl 
    11013 [Repeated 1 time(s)]
    11014 
    11015 > select add #63
    11016 
    11017 2 models selected 
    11018 
    11019 > show #!1 models
    11020 
    11021 > ui mousemode right "rotate selected models"
    11022 
    11023 > view matrix models
    11024 > #63,-0.58537,-0.79697,-0.1489,345.68,-0.68073,0.38338,0.6242,89.496,-0.44039,0.46675,-0.76694,243.81
    11025 
    11026 > fitmap #63 inMap #33.2
    11027 
    11028 Fit map PredictAndBuild_1_overall_best_map.ccp4 in map
    11029 W20_J160_run_ct6_body002.mrc using 134378 points 
    11030 correlation = 0.4, correlation about mean = 0.0294, overlap = 163.4 
    11031 steps = 156, shift = 19.7, angle = 10.1 degrees 
    11032  
    11033 Position of PredictAndBuild_1_overall_best_map.ccp4 (#63) relative to
    11034 W20_J160_run_ct6_body002.mrc (#33.2) coordinates: 
    11035 Matrix rotation and translation 
    11036 -0.49730946 -0.85158343 -0.16579799 356.32016493 
    11037 -0.56399341 0.17211906 0.80764255 80.81400003 
    11038 -0.65923801 0.49515725 -0.56588387 229.61138609 
    11039 Axis -0.47998711 0.75793917 0.44174720 
    11040 Axis point 229.49905252 0.00000000 52.36918700 
    11041 Rotation angle (degrees) 161.00326601 
    11042 Shift along axis -8.34680262 
    11043  
    11044 
    11045 > fitmap #63 inMap #2
    11046 
    11047 Fit map PredictAndBuild_1_overall_best_map.ccp4 in map
    11048 W20_J3623_consensus_structure.mrc using 134378 points 
    11049 correlation = 0.9819, correlation about mean = 0.7973, overlap = 2.007e+04 
    11050 steps = 112, shift = 10.7, angle = 7.31 degrees 
    11051  
    11052 Position of PredictAndBuild_1_overall_best_map.ccp4 (#63) relative to
    11053 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    11054 Matrix rotation and translation 
    11055 -0.34010494 -0.91904138 -0.19922745 353.84532994 
    11056 -0.77653019 0.15497541 0.61072375 146.03986464 
    11057 -0.53040504 0.36241629 -0.76637128 277.65026005 
    11058 Axis -0.56720681 0.75650641 0.32553722 
    11059 Axis point 251.99725576 0.00000000 81.48732765 
    11060 Rotation angle (degrees) 167.35637881 
    11061 Shift along axis 0.16210555 
    11062  
    11063 
    11064 > select subtract #63
    11065 
    11066 Nothing selected 
    11067 
    11068 > hide #!1 models
    11069 
    11070 > show #!11 models
    11071 
    11072 > hide #!11 models
    11073 
    11074 > show #!11 models
    11075 
    11076 > hide #!63 models
    11077 
    11078 > show #!63 models
    11079 
    11080 > hide #!11 models
    11081 
    11082 > show #!8 models
    11083 
    11084 > hide #!8 models
    11085 
    11086 > show #!7 models
    11087 
    11088 > hide #!63 models
    11089 
    11090 > show #!63 models
    11091 
    11092 > hide #!7 models
    11093 
    11094 > show #!7 models
    11095 
    11096 > hide #!7 models
    11097 
    11098 > show #!7 models
    11099 
    11100 > close #63
    11101 
    11102 > open
    11103 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_overall_best_superposed_predicted_models.pdb
    11104 
    11105 Chain information for
    11106 PredictAndBuild_1_overall_best_superposed_predicted_models.pdb #63 
    11107 --- 
    11108 Chain | Description 
    11109 A | No description available 
    11110 B | No description available 
    11111 F | No description available 
    11112  
    11113 Computing secondary structure 
    11114 
    11115 > open
    11116 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_overall_best.pdb
    11117 
    11118 Chain information for PredictAndBuild_1_overall_best.pdb #64 
    11119 --- 
    11120 Chain | Description 
    11121 A | No description available 
    11122 B | No description available 
    11123 C | No description available 
    11124 D | No description available 
    11125 F | No description available 
    11126  
    11127 
    11128 > open
    11129 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb
    11130 
    11131 Chain information for
    11132 PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb #65 
    11133 --- 
    11134 Chain | Description 
    11135 A | No description available 
    11136 B | No description available 
    11137 F | No description available 
    11138  
    11139 Computing secondary structure 
    11140 
    11141 > select add #63
    11142 
    11143 13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected 
    11144 
    11145 > select add #64
    11146 
    11147 34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected 
    11148 
    11149 > select add #65
    11150 
    11151 52865 atoms, 53866 bonds, 30 pseudobonds, 6628 residues, 5 models selected 
    11152 
    11153 > hide sel atoms
    11154 
    11155 > show sel cartoons
    11156 
    11157 Computing secondary structure 
    11158 
    11159 > select subtract #65
    11160 
    11161 34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected 
    11162 
    11163 > select subtract #64
    11164 
    11165 13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected 
    11166 
    11167 > select subtract #63
    11168 
    11169 Nothing selected 
    11170 
    11171 > select add #63
    11172 
    11173 13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected 
    11174 
    11175 > select add #64
    11176 
    11177 34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected 
    11178 
    11179 > select add #65
    11180 
    11181 52865 atoms, 53866 bonds, 30 pseudobonds, 6628 residues, 5 models selected 
    11182 
    11183 > view matrix models
    11184 > #63,-0.079462,-0.96928,-0.23276,330.08,-0.99279,0.055943,0.10597,250.15,-0.089693,0.2395,-0.96674,313.02,#64,-0.079462,-0.96928,-0.23276,330.08,-0.99279,0.055943,0.10597,250.15,-0.089693,0.2395,-0.96674,313.02,#65,-0.079462,-0.96928,-0.23276,330.08,-0.99279,0.055943,0.10597,250.15,-0.089693,0.2395,-0.96674,313.02
    11185 
    11186 > ui mousemode right "translate selected models"
    11187 
    11188 > view matrix models
    11189 > #63,-0.079462,-0.96928,-0.23276,336.58,-0.99279,0.055943,0.10597,275.32,-0.089693,0.2395,-0.96674,259.8,#64,-0.079462,-0.96928,-0.23276,336.58,-0.99279,0.055943,0.10597,275.32,-0.089693,0.2395,-0.96674,259.8,#65,-0.079462,-0.96928,-0.23276,336.58,-0.99279,0.055943,0.10597,275.32,-0.089693,0.2395,-0.96674,259.8
    11190 
    11191 > view matrix models
    11192 > #63,-0.079462,-0.96928,-0.23276,335,-0.99279,0.055943,0.10597,254.69,-0.089693,0.2395,-0.96674,251.24,#64,-0.079462,-0.96928,-0.23276,335,-0.99279,0.055943,0.10597,254.69,-0.089693,0.2395,-0.96674,251.24,#65,-0.079462,-0.96928,-0.23276,335,-0.99279,0.055943,0.10597,254.69,-0.089693,0.2395,-0.96674,251.24
    11193 
    11194 > ui mousemode right "rotate selected models"
    11195 
    11196 > view matrix models
    11197 > #63,-0.095152,-0.88164,0.46222,203.93,-0.95238,0.21575,0.21547,206.02,-0.28969,-0.41971,-0.86019,359.38,#64,-0.095152,-0.88164,0.46222,203.93,-0.95238,0.21575,0.21547,206.02,-0.28969,-0.41971,-0.86019,359.38,#65,-0.095152,-0.88164,0.46222,203.93,-0.95238,0.21575,0.21547,206.02,-0.28969,-0.41971,-0.86019,359.38
    11198 
    11199 > ui mousemode right "translate selected models"
    11200 
    11201 > view matrix models
    11202 > #63,-0.095152,-0.88164,0.46222,227.08,-0.95238,0.21575,0.21547,215.24,-0.28969,-0.41971,-0.86019,381.48,#64,-0.095152,-0.88164,0.46222,227.08,-0.95238,0.21575,0.21547,215.24,-0.28969,-0.41971,-0.86019,381.48,#65,-0.095152,-0.88164,0.46222,227.08,-0.95238,0.21575,0.21547,215.24,-0.28969,-0.41971,-0.86019,381.48
    11203 
    11204 > hide #!7 models
    11205 
    11206 > show #!33 models
    11207 
    11208 > select subtract #65
    11209 
    11210 34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected 
    11211 
    11212 > select subtract #64
    11213 
    11214 13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected 
    11215 
    11216 > select subtract #63
    11217 
    11218 Nothing selected 
    11219 
    11220 > hide #65 models
    11221 
    11222 > hide #!64 models
    11223 
    11224 > fitmap #63 inMap #2
    11225 
    11226 Fit molecule PredictAndBuild_1_overall_best_superposed_predicted_models.pdb
    11227 (#63) to map W20_J3623_consensus_structure.mrc (#2) using 13443 atoms 
    11228 average map value = 0.3311, steps = 268 
    11229 shifted from previous position = 24.1 
    11230 rotated from previous position = 48.9 degrees 
    11231 atoms outside contour = 4479, contour level = 0.25746 
    11232  
    11233 Position of PredictAndBuild_1_overall_best_superposed_predicted_models.pdb
    11234 (#63) relative to W20_J3623_consensus_structure.mrc (#2) coordinates: 
    11235 Matrix rotation and translation 
    11236 -0.33968216 -0.91923759 -0.19904344 353.65205126 
    11237 -0.77596080 0.15430364 0.61161690 145.90271071 
    11238 -0.53150812 0.36220526 -0.76570653 277.79017130 
    11239 Axis -0.56733253 0.75625188 0.32590934 
    11240 Axis point 251.98315191 0.00000000 81.43051773 
    11241 Rotation angle (degrees) 167.30207874 
    11242 Shift along axis 0.23529698 
    11243  
    11244 
    11245 > hide #!61 models
    11246 
    11247 > hide #!62 models
    11248 
    11249 > hide #!60 models
    11250 
    11251 > hide #!63 models
    11252 
    11253 > show #!63 models
    11254 
    11255 > hide #!63 models
    11256 
    11257 > show #!64 models
    11258 
    11259 > fitmap #64 inMap #2
    11260 
    11261 Fit molecule PredictAndBuild_1_overall_best.pdb (#64) to map
    11262 W20_J3623_consensus_structure.mrc (#2) using 20762 atoms 
    11263 average map value = 0.2661, steps = 552 
    11264 shifted from previous position = 15.4 
    11265 rotated from previous position = 48.8 degrees 
    11266 atoms outside contour = 10565, contour level = 0.25746 
    11267  
    11268 Position of PredictAndBuild_1_overall_best.pdb (#64) relative to
    11269 W20_J3623_consensus_structure.mrc (#2) coordinates: 
    11270 Matrix rotation and translation 
    11271 -0.33968228 -0.91946019 -0.19801243 353.57410808 
    11272 -0.77672233 0.15550766 0.61034400 145.97075470 
    11273 -0.53039456 0.36112372 -0.76698845 277.98078879 
    11274 Axis -0.56734428 0.75666030 0.32493947 
    11275 Axis point 251.92912923 0.00000000 81.66482425 
    11276 Rotation angle (degrees) 167.31225097 
    11277 Shift along axis 0.17895697 
    11278  
    11279 
    11280 > hide #!64 models
    11281 
    11282 > show #65 models
    11283 
    11284 > fitmap #65 inMap #2
    11285 
    11286 Fit molecule PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb
    11287 (#65) to map W20_J3623_consensus_structure.mrc (#2) using 18660 atoms 
    11288 average map value = 0.2436, steps = 340 
    11289 shifted from previous position = 22.1 
    11290 rotated from previous position = 48.8 degrees 
    11291 atoms outside contour = 9859, contour level = 0.25746 
    11292  
    11293 Position of PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb (#65)
    11294 relative to W20_J3623_consensus_structure.mrc (#2) coordinates: 
    11295 Matrix rotation and translation 
    11296 -0.34475277 -0.91893726 -0.19157204 353.38290459 
    11297 -0.77178767 0.16132165 0.61507653 143.76727401 
    11298 -0.53431202 0.35990227 -0.76484053 278.30475415 
    11299 Axis -0.56463658 0.75839755 0.32560511 
    11300 Axis point 251.20855212 0.00000000 81.61803612 
    11301 Rotation angle (degrees) 166.94047161 
    11302 Shift along axis 0.11728580 
    11303  
    11304 
    11305 > hide #65 models
    11306 
    11307 Downloading bundle ChimeraX_ISOLDE-1.9-cp311-cp311-macosx_10_13_universal2.whl 
    11308 
    11309 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    11310 > resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
    11311 
    11312 ——— End of log from Fri Jul 4 10:54:24 2025 ———
    11313 
    11314 opened ChimeraX session 
    11315 
    11316 > show #!46 models
    11317 
    11318 > hide #!46 models
    11319 
    11320 > hide #!50 models
    11321 
    11322 > show #!50 models
    11323 
    11324 > show #!60 models
    11325 
    11326 > hide #!60 models
    11327 
    11328 > show #!60 models
    11329 
    11330 > show #!61 models
    11331 
    11332 > hide #!61 models
    11333 
    11334 > show #!61 models
    11335 
    11336 > show #!62 models
    11337 
    11338 > color #60 #61 #62 navy
    11339 
    11340 > hide #!62 models
    11341 
    11342 > hide #!61 models
    11343 
    11344 > hide #!60 models
    11345 
    11346 > show #!60 models
    11347 
    11348 > show #!61 models
    11349 
    11350 > show #!62 models
    11351 
    11352 > close #57
    11353 
    11354 > close #58
    11355 
    11356 > close #59
    11357 
    11358 > show #51 models
    11359 
    11360 > hide #51 models
    11361 
    11362 > close #51
    11363 
    11364 > show #52 models
    11365 
    11366 > hide #!62 models
    11367 
    11368 > hide #!61 models
    11369 
    11370 > hide #!60 models
    11371 
    11372 > hide #!33 models
    11373 
    11374 > show #35 models
    11375 
    11376 > hide #35 models
    11377 
    11378 > combine #52
    11379 
    11380 > hide #52 models
    11381 
    11382 > ui mousemode right select
    11383 
    11384 > select clear
    11385 
    11386 > select #51/B:953
    11387 
    11388 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11389 
    11390 > select up
    11391 
    11392 54 atoms, 53 bonds, 7 residues, 1 model selected 
    11393 
    11394 > select up
    11395 
    11396 7500 atoms, 7618 bonds, 953 residues, 1 model selected 
    11397 
    11398 > select down
    11399 
    11400 54 atoms, 53 bonds, 7 residues, 1 model selected 
    11401 
    11402 > select clear
    11403 
    11404 Drag select of 76 residues 
    11405 
    11406 > select up
    11407 
    11408 756 atoms, 763 bonds, 99 residues, 1 model selected 
    11409 
    11410 > select clear
    11411 
    11412 Drag select of 58 residues 
    11413 
    11414 > select up
    11415 
    11416 773 atoms, 785 bonds, 99 residues, 1 model selected 
    11417 
    11418 > delete sel
    11419 
    11420 Drag select of 7 residues 
    11421 
    11422 > delete sel
    11423 
    11424 > select clear
    11425 
    11426 Drag select of 10 residues, 2 pseudobonds 
    11427 
    11428 > select up
    11429 
    11430 110 atoms, 109 bonds, 2 pseudobonds, 15 residues, 2 models selected 
    11431 
    11432 > delete sel
    11433 
    11434 Drag select of 62 residues 
    11435 
    11436 > select up
    11437 
    11438 883 atoms, 897 bonds, 115 residues, 1 model selected 
    11439 
    11440 > delete sel
    11441 
    11442 Drag select of 24 residues, 1 pseudobonds 
    11443 
    11444 > delete sel
    11445 
    11446 Drag select of 2 residues 
    11447 
    11448 > delete sel
    11449 
    11450 > show #!33 models
    11451 
    11452 > hide #!33 models
    11453 
    11454 Drag select of 13 residues 
    11455 
    11456 > select up
    11457 
    11458 126 atoms, 126 bonds, 17 residues, 1 model selected 
    11459 
    11460 > delete sel
    11461 
    11462 Drag select of 7 residues 
    11463 
    11464 > select up
    11465 
    11466 69 atoms, 69 bonds, 9 residues, 1 model selected 
    11467 
    11468 > delete sel
    11469 
    11470 > show #!33 models
    11471 
    11472 > select #51/B:664
    11473 
    11474 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11475 
    11476 > select up
    11477 
    11478 215 atoms, 217 bonds, 27 residues, 1 model selected 
    11479 
    11480 > delete sel
    11481 
    11482 > select clear
    11483 
    11484 > select #51/B:521
    11485 
    11486 12 atoms, 12 bonds, 1 residue, 1 model selected 
    11487 
    11488 > select up
    11489 
    11490 334 atoms, 338 bonds, 44 residues, 1 model selected 
    11491 
    11492 > delete sel
    11493 
    11494 > fitmap #51 inMap #33.1
    11495 
    11496 Fit molecule copy of B_fixed_model_2_B.pdb (#51) to map
    11497 W20_J160_run_ct6_body001.mrc (#33.1) using 4745 atoms 
    11498 average map value = 0.01558, steps = 60 
    11499 shifted from previous position = 0.386 
    11500 rotated from previous position = 0.444 degrees 
    11501 atoms outside contour = 2213, contour level = 0.014811 
    11502  
    11503 Position of copy of B_fixed_model_2_B.pdb (#51) relative to
    11504 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    11505 Matrix rotation and translation 
    11506 -0.39489665 -0.88949565 -0.22990026 277.26110723 
    11507 -0.63858809 0.08584769 0.76474533 131.14250865 
    11508 -0.66050124 0.44880693 -0.60192230 226.00577301 
    11509 Axis -0.53542046 0.72973902 0.42521276 
    11510 Axis point 208.19952618 0.00000000 43.73317487 
    11511 Rotation angle (degrees) 162.84020444 
    11512 Shift along axis 43.34907536 
    11513  
    11514 
    11515 > hide #!51 models
    11516 
    11517 > show #52 models
    11518 
    11519 > hide #!50 models
    11520 
    11521 > show #!50 models
    11522 
    11523 > hide #!33 models
    11524 
    11525 Drag select of 161 residues 
    11526 
    11527 > select up
    11528 
    11529 1472 atoms, 1497 bonds, 183 residues, 1 model selected 
    11530 
    11531 > delete sel
    11532 
    11533 Drag select of 68 residues, 3 pseudobonds 
    11534 
    11535 > select clear
    11536 
    11537 Drag select of 90 residues, 3 pseudobonds 
    11538 
    11539 > select up
    11540 
    11541 934 atoms, 946 bonds, 3 pseudobonds, 118 residues, 2 models selected 
    11542 
    11543 > delete sel
    11544 
    11545 Drag select of 208 residues 
    11546 
    11547 > select up
    11548 
    11549 2197 atoms, 2217 bonds, 276 residues, 1 model selected 
    11550 
    11551 > delete sel
    11552 
    11553 Drag select of 109 residues, 2 pseudobonds 
    11554 
    11555 > select clear
    11556 
    11557 Drag select of 98 residues, 2 pseudobonds 
    11558 
    11559 > select clear
    11560 
    11561 > select #52/B:624
    11562 
    11563 6 atoms, 5 bonds, 1 residue, 1 model selected 
    11564 Drag select of 109 residues, 2 pseudobonds 
    11565 
    11566 > select up
    11567 
    11568 854 atoms, 863 bonds, 2 pseudobonds, 110 residues, 2 models selected 
    11569 
    11570 > select down
    11571 
    11572 844 atoms, 2 pseudobonds, 109 residues, 2 models selected 
    11573 
    11574 > select clear
    11575 
    11576 Drag select of 109 residues, 2 pseudobonds 
    11577 
    11578 > select up
    11579 
    11580 854 atoms, 863 bonds, 2 pseudobonds, 110 residues, 2 models selected 
    11581 
    11582 > delete sel
    11583 
    11584 > show #!33 models
    11585 
    11586 > show #!37 models
    11587 
    11588 > hide #!37 models
    11589 
    11590 > show #!37 models
    11591 
    11592 > hide #!37 models
    11593 
    11594 > hide #!33 models
    11595 
    11596 Drag select of 3 residues 
    11597 
    11598 > select up
    11599 
    11600 69 atoms, 69 bonds, 9 residues, 1 model selected 
    11601 
    11602 > delete sel
    11603 
    11604 Drag select of 1 residues 
    11605 
    11606 > select clear
    11607 
    11608 [Repeated 1 time(s)]Drag select of 2 residues 
    11609 
    11610 > select up
    11611 
    11612 98 atoms, 98 bonds, 13 residues, 1 model selected 
    11613 
    11614 > select down
    11615 
    11616 12 atoms, 2 residues, 1 model selected 
    11617 
    11618 > select up
    11619 
    11620 98 atoms, 98 bonds, 13 residues, 1 model selected 
    11621 
    11622 > delete sel
    11623 
    11624 > show #!33 models
    11625 
    11626 > fitmap #62 inMap #33.1
    11627 
    11628 Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
    11629 W20_J160_run_ct6_body001.mrc (#33.1) using 1612 atoms 
    11630 average map value = 0.01422, steps = 44 
    11631 shifted from previous position = 0.0171 
    11632 rotated from previous position = 0.0202 degrees 
    11633 atoms outside contour = 870, contour level = 0.014811 
    11634  
    11635 Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
    11636 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    11637 Matrix rotation and translation 
    11638 -0.56449972 -0.76141548 -0.31872643 292.10636189 
    11639 -0.55678517 0.06618546 0.82801555 113.19196963 
    11640 -0.60936880 0.64487670 -0.46130652 203.97357809 
    11641 Axis -0.45800977 0.72686404 0.51175748 
    11642 Axis point 194.00483060 0.00000000 40.16620251 
    11643 Rotation angle (degrees) 168.46719367 
    11644 Shift along axis 52.87260780 
    11645  
    11646 
    11647 > fitmap #52 inMap #33.1
    11648 
    11649 Fit molecule B_fixed_model_2_B.pdb (#52) to map W20_J160_run_ct6_body001.mrc
    11650 (#33.1) using 1876 atoms 
    11651 average map value = 0.01465, steps = 68 
    11652 shifted from previous position = 1.95 
    11653 rotated from previous position = 6.84 degrees 
    11654 atoms outside contour = 924, contour level = 0.014811 
    11655  
    11656 Position of B_fixed_model_2_B.pdb (#52) relative to
    11657 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    11658 Matrix rotation and translation 
    11659 -0.32428809 -0.92759140 -0.18550319 265.85498427 
    11660 -0.58447784 0.04228657 0.81030704 122.87471915 
    11661 -0.74378954 0.37119543 -0.55586965 237.11232737 
    11662 Axis -0.55667228 0.70775295 0.43497325 
    11663 Axis point 213.01982007 0.00000000 38.79142480 
    11664 Rotation angle (degrees) 156.77096429 
    11665 Shift along axis 42.10836361 
    11666  
    11667 
    11668 > show #!51 models
    11669 
    11670 > show #!60 models
    11671 
    11672 > show #!61 models
    11673 
    11674 > show #!62 models
    11675 
    11676 > hide #!62 models
    11677 
    11678 > hide #!61 models
    11679 
    11680 > hide #!60 models
    11681 
    11682 > color #52 betav3
    11683 
    11684 > color #53 betav3
    11685 
    11686 > color #52 betav3
    11687 
    11688 > color #52 betav1
    11689 
    11690 > color #51 betav1
    11691 
    11692 > show #!62 models
    11693 
    11694 > show #!61 models
    11695 
    11696 > show #!60 models
    11697 
    11698 > hide #!52 models
    11699 
    11700 > hide #!51 models
    11701 
    11702 > show #!53 models
    11703 
    11704 > color #53 betapv3
    11705 
    11706 > hide #!53 models
    11707 
    11708 > show #50.1 models
    11709 
    11710 > hide #50.1 models
    11711 
    11712 > show #!50.2 models
    11713 
    11714 > hide #!50.2 models
    11715 
    11716 > show #!50.2 models
    11717 
    11718 > hide #!50.2 models
    11719 
    11720 > show #!50.3 models
    11721 
    11722 > hide #!50.3 models
    11723 
    11724 > show #!50.4 models
    11725 
    11726 > hide #!50.4 models
    11727 
    11728 > show #!50.5 models
    11729 
    11730 > hide #!50.5 models
    11731 
    11732 > show #50.6 models
    11733 
    11734 > show #!50.7 models
    11735 
    11736 > show #36 models
    11737 
    11738 > hide #36 models
    11739 
    11740 > show #36 models
    11741 
    11742 > ui tool show Matchmaker
    11743 
    11744 > matchmaker #50.6#!50.7 to #36
    11745 
    11746 Parameters 
    11747 --- 
    11748 Chain pairing | bb 
    11749 Alignment algorithm | Needleman-Wunsch 
    11750 Similarity matrix | BLOSUM-62 
    11751 SS fraction | 0.3 
    11752 Gap open (HH/SS/other) | 18/18/6 
    11753 Gap extend | 1 
    11754 SS matrix |  |  | H | S | O 
    11755 ---|---|---|--- 
    11756 H | 6 | -9 | -6 
    11757 S |  | 6 | -6 
    11758 O |  |  | 4 
    11759 Iteration cutoff | 2 
    11760  
    11761 Matchmaker CopBprime_O55029.pdb, chain A (#36) with
    11762 W20_C1_initial_model_no_wat_lig.pdb A5, chain A5 (#50.6), sequence alignment
    11763 score = 1599.3 
    11764 RMSD between 300 pruned atom pairs is 0.001 angstroms; (across all 300 pairs:
    11765 0.001) 
    11766  
    11767 Matchmaker CopBprime_O55029.pdb, chain A (#36) with
    11768 W20_C1_initial_model_no_wat_lig.pdb A6, chain A6 (#50.7), sequence alignment
    11769 score = 2777.6 
    11770 RMSD between 535 pruned atom pairs is 0.000 angstroms; (across all 535 pairs:
    11771 0.000) 
    11772  
    11773 
    11774 > hide #!60 models
    11775 
    11776 > hide #!61 models
    11777 
    11778 > hide #!62 models
    11779 
    11780 > hide #!33 models
    11781 
    11782 > show #!33 models
    11783 
    11784 > show #!29 models
    11785 
    11786 > hide #!33 models
    11787 
    11788 > hide #!29 models
    11789 
    11790 > show #!29 models
    11791 
    11792 > hide #!29 models
    11793 
    11794 > show #!7 models
    11795 
    11796 > hide #!7 models
    11797 
    11798 > show #!14 models
    11799 
    11800 > hide #!14 models
    11801 
    11802 > show #!15 models
    11803 
    11804 > hide #!15 models
    11805 
    11806 > show #!13 models
    11807 
    11808 > hide #!13 models
    11809 
    11810 > show #!29 models
    11811 
    11812 > hide #!29 models
    11813 
    11814 > show #!30 models
    11815 
    11816 > hide #!30 models
    11817 
    11818 > show #!31 models
    11819 
    11820 > hide #!31 models
    11821 
    11822 > show #!29 models
    11823 
    11824 > color #29 silver models
    11825 
    11826 > color #29 #c0c0c0bb models
    11827 
    11828 > fitmap #36 inMap #29.1
    11829 
    11830 Fit molecule CopBprime_O55029.pdb (#36) to map W20_J140_run_body001.mrc
    11831 (#29.1) using 7214 atoms 
    11832 average map value = 0.004094, steps = 196 
    11833 shifted from previous position = 6.85 
    11834 rotated from previous position = 8.52 degrees 
    11835 atoms outside contour = 6338, contour level = 0.01322 
    11836  
    11837 Position of CopBprime_O55029.pdb (#36) relative to W20_J140_run_body001.mrc
    11838 (#29.1) coordinates: 
    11839 Matrix rotation and translation 
    11840 0.34093560 0.24287995 0.90816972 145.36424309 
    11841 0.84442936 0.34545023 -0.40939370 186.54646641 
    11842 -0.41316096 0.90646206 -0.08731868 180.11258285 
    11843 Axis 0.67156017 0.67435435 0.30700677 
    11844 Axis point 37.00439488 0.00000000 72.89161043 
    11845 Rotation angle (degrees) 101.56423540 
    11846 Shift along axis 278.71503775 
    11847  
    11848 
    11849 > fitmap #50.7 inMap #29.1
    11850 
    11851 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) to map
    11852 W20_J140_run_body001.mrc (#29.1) using 4264 atoms 
    11853 average map value = 0.006635, steps = 664 
    11854 shifted from previous position = 6.45 
    11855 rotated from previous position = 16.7 degrees 
    11856 atoms outside contour = 3295, contour level = 0.01322 
    11857  
    11858 Position of W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) relative to
    11859 W20_J140_run_body001.mrc (#29.1) coordinates: 
    11860 Matrix rotation and translation 
    11861 -0.98916440 0.14663035 -0.00730224 336.07347063 
    11862 -0.09208236 -0.65838724 -0.74702549 537.00653368 
    11863 -0.11434431 -0.73825862 0.66475529 165.63484820 
    11864 Axis 0.03349195 0.40893115 -0.91195044 
    11865 Axis point 189.25291418 293.62591224 0.00000000 
    11866 Rotation angle (degrees) 172.47953493 
    11867 Shift along axis 79.80368535 
    11868  
    11869 
    11870 > fitmap #50.6 inMap #29.4
    11871 
    11872 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A5 (#50.6) to map
    11873 W20_J140_run_body004.mrc (#29.4) using 2406 atoms 
    11874 average map value = 0.01284, steps = 124 
    11875 shifted from previous position = 5.65 
    11876 rotated from previous position = 34.4 degrees 
    11877 atoms outside contour = 1273, contour level = 0.012962 
    11878  
    11879 Position of W20_C1_initial_model_no_wat_lig.pdb A5 (#50.6) relative to
    11880 W20_J140_run_body004.mrc (#29.4) coordinates: 
    11881 Matrix rotation and translation 
    11882 -0.88088930 -0.47324067 0.00879232 419.53745111 
    11883 0.15156939 -0.29963122 -0.94193835 456.11372933 
    11884 0.44839799 -0.82841077 0.33567073 130.22033922 
    11885 Axis 0.14698922 -0.56917708 0.80896948 
    11886 Axis point 147.85180587 327.64605342 0.00000000 
    11887 Rotation angle (degrees) 157.28319935 
    11888 Shift along axis -92.59771834 
    11889  
    11890 
    11891 > hide #36 models
    11892 
    11893 > show #36 models
    11894 
    11895 > hide #36 models
    11896 
    11897 > hide #50.6 models
    11898 
    11899 > show #50.6 models
    11900 
    11901 > hide #50.6 models
    11902 
    11903 > hide #!29 models
    11904 
    11905 > show #50.6 models
    11906 
    11907 > show #36 models
    11908 
    11909 > hide #!50.7 models
    11910 
    11911 > hide #36 models
    11912 
    11913 > show #36 models
    11914 
    11915 > show #!53 models
    11916 
    11917 > hide #!53 models
    11918 
    11919 > close #53
    11920 
    11921 > show #!63 models
    11922 
    11923 > hide #!63 models
    11924 
    11925 > close #63
    11926 
    11927 > close #64
    11928 
    11929 > close #65
    11930 
    11931 > show #!50.7 models
    11932 
    11933 > combine #36
    11934 
    11935 [Repeated 1 time(s)]
    11936 
    11937 > combine #50.7
    11938 
    11939 > hide #!58 models
    11940 
    11941 > hide #!50.7 models
    11942 
    11943 > hide #57 models
    11944 
    11945 > hide #53 models
    11946 
    11947 > hide #36 models
    11948 
    11949 > show #!50.7 models
    11950 
    11951 > show #!58 models
    11952 
    11953 > hide #!58 models
    11954 
    11955 > show #!58 models
    11956 
    11957 > hide #!50.7 models
    11958 
    11959 > hide #!58 models
    11960 
    11961 > show #!58 models
    11962 
    11963 > hide #!58 models
    11964 
    11965 > combine #50.7
    11966 
    11967 > hide #!59 models
    11968 
    11969 > show #!58 models
    11970 
    11971 > hide #50.6 models
    11972 
    11973 Drag select of 156 residues 
    11974 
    11975 > select up
    11976 
    11977 1543 atoms, 1574 bonds, 191 residues, 1 model selected 
    11978 
    11979 > delete sel
    11980 
    11981 Drag select of 37 residues, 1 pseudobonds 
    11982 
    11983 > select up
    11984 
    11985 516 atoms, 519 bonds, 1 pseudobond, 65 residues, 2 models selected 
    11986 
    11987 > delete sel
    11988 
    11989 Drag select of 7 residues, 1 pseudobonds 
    11990 
    11991 > select clear
    11992 
    11993 Drag select of 6 residues, 1 pseudobonds 
    11994 
    11995 > select up
    11996 
    11997 54 atoms, 51 bonds, 1 pseudobond, 9 residues, 2 models selected 
    11998 
    11999 > delete sel
    12000 
    12001 Drag select of 7 residues, 2 pseudobonds 
    12002 
    12003 > select up
    12004 
    12005 93 atoms, 93 bonds, 2 pseudobonds, 12 residues, 2 models selected 
    12006 
    12007 > delete sel
    12008 
    12009 Drag select of 4 residues 
    12010 
    12011 > delete sel
    12012 
    12013 > show #!29 models
    12014 
    12015 > fitmap #58 inMap #29.1
    12016 
    12017 Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#58) to map
    12018 W20_J140_run_body001.mrc (#29.1) using 2026 atoms 
    12019 average map value = 0.01347, steps = 40 
    12020 shifted from previous position = 0.0954 
    12021 rotated from previous position = 0.431 degrees 
    12022 atoms outside contour = 1055, contour level = 0.01322 
    12023  
    12024 Position of copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#58) relative to
    12025 W20_J140_run_body001.mrc (#29.1) coordinates: 
    12026 Matrix rotation and translation 
    12027 -0.98886569 0.14811277 -0.01439634 337.90273979 
    12028 -0.08759046 -0.65752799 -0.74832136 536.28441247 
    12029 -0.12030195 -0.73872833 0.66318013 167.31953501 
    12030 Axis 0.03709874 0.40956482 -0.91152638 
    12031 Axis point 190.29117406 293.80476850 0.00000000 
    12032 Rotation angle (degrees) 172.57141027 
    12033 Shift along axis 79.66282889 
    12034  
    12035 
    12036 > show #!60 models
    12037 
    12038 > show #!61 models
    12039 
    12040 > show #!62 models
    12041 
    12042 > hide #!62 models
    12043 
    12044 > hide #!61 models
    12045 
    12046 > hide #!60 models
    12047 
    12048 > hide #!58 models
    12049 
    12050 > hide #!29 models
    12051 
    12052 > show #!59 models
    12053 
    12054 Drag select of 143 residues, 1 pseudobonds 
    12055 
    12056 > select up
    12057 
    12058 1146 atoms, 1169 bonds, 1 pseudobond, 145 residues, 2 models selected 
    12059 
    12060 > delete sel
    12061 
    12062 > hide #!59 models
    12063 
    12064 > show #!58 models
    12065 
    12066 > hide #!58 models
    12067 
    12068 > show #!59 models
    12069 
    12070 Drag select of 51 residues 
    12071 
    12072 > select up
    12073 
    12074 444 atoms, 452 bonds, 55 residues, 1 model selected 
    12075 
    12076 > delete sel
    12077 
    12078 Drag select of 27 residues 
    12079 
    12080 > delete sel
    12081 
    12082 Drag select of 17 residues 
    12083 
    12084 > select up
    12085 
    12086 199 atoms, 201 bonds, 25 residues, 1 model selected 
    12087 
    12088 > delete sel
    12089 
    12090 > select #59/A6:588
    12091 
    12092 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12093 
    12094 > select #59/A6:588
    12095 
    12096 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12097 
    12098 > show #!58 models
    12099 
    12100 > show #!29 models
    12101 
    12102 > hide #!29 models
    12103 
    12104 > hide #!58 models
    12105 
    12106 > delete sel
    12107 
    12108 > select #59/A6:587
    12109 
    12110 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12111 
    12112 > delete sel
    12113 
    12114 > show #!58 models
    12115 
    12116 > fitmap #59 inMap #29.4
    12117 
    12118 Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#59) to map
    12119 W20_J140_run_body004.mrc (#29.4) using 2238 atoms 
    12120 average map value = 0.01488, steps = 128 
    12121 shifted from previous position = 9.04 
    12122 rotated from previous position = 24.7 degrees 
    12123 atoms outside contour = 1046, contour level = 0.012962 
    12124  
    12125 Position of copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#59) relative to
    12126 W20_J140_run_body004.mrc (#29.4) coordinates: 
    12127 Matrix rotation and translation 
    12128 -0.85413410 0.51616797 -0.06344729 245.49771496 
    12129 -0.20546679 -0.44701353 -0.87061031 558.08387697 
    12130 -0.47774295 -0.73058164 0.48786487 300.68201418 
    12131 Axis 0.16594922 0.49098549 -0.85521582 
    12132 Axis point 220.46254144 334.83017754 0.00000000 
    12133 Rotation angle (degrees) 155.04526429 
    12134 Shift along axis 57.60322791 
    12135  
    12136 
    12137 > show #!29 models
    12138 
    12139 > show #50.6 models
    12140 
    12141 > hide #!59 models
    12142 
    12143 > hide #!58 models
    12144 
    12145 > show #53 models
    12146 
    12147 > select #29.2
    12148 
    12149 2 models selected 
    12150 
    12151 > select #29.2
    12152 
    12153 2 models selected 
    12154 
    12155 > select clear
    12156 
    12157 [Repeated 1 time(s)]
    12158 
    12159 > select #53/A:876
    12160 
    12161 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12162 
    12163 > select up
    12164 
    12165 519 atoms, 525 bonds, 67 residues, 1 model selected 
    12166 
    12167 > delete sel
    12168 
    12169 > show #!58 models
    12170 
    12171 > hide #!58 models
    12172 
    12173 > select clear
    12174 
    12175 > select #53/A:640
    12176 
    12177 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12178 
    12179 > hide #!29 models
    12180 
    12181 Drag select of 184 residues 
    12182 
    12183 > select up
    12184 
    12185 1682 atoms, 1717 bonds, 208 residues, 1 model selected 
    12186 
    12187 > delete sel
    12188 
    12189 > hide #50.6 models
    12190 
    12191 Drag select of 419 residues, 4 pseudobonds 
    12192 
    12193 > select up
    12194 
    12195 3440 atoms, 3516 bonds, 4 pseudobonds, 432 residues, 2 models selected 
    12196 
    12197 > delete sel
    12198 
    12199 > fitmap #53 inMap #29.1
    12200 
    12201 Fit molecule copy of CopBprime_O55029.pdb (#53) to map
    12202 W20_J140_run_body001.mrc (#29.1) using 1573 atoms 
    12203 average map value = 0.0152, steps = 92 
    12204 shifted from previous position = 4.75 
    12205 rotated from previous position = 20.8 degrees 
    12206 atoms outside contour = 682, contour level = 0.01322 
    12207  
    12208 Position of copy of CopBprime_O55029.pdb (#53) relative to
    12209 W20_J140_run_body001.mrc (#29.1) coordinates: 
    12210 Matrix rotation and translation 
    12211 0.22399917 0.35238232 0.90865344 142.70226714 
    12212 0.67056970 0.62083889 -0.40607308 181.66322382 
    12213 -0.70722037 0.70027550 -0.09722951 169.81132058 
    12214 Axis 0.55763236 0.81444812 0.16037584 
    12215 Axis point 78.89411363 0.00000000 66.67498198 
    12216 Rotation angle (degrees) 97.24981271 
    12217 Shift along axis 254.76430584 
    12218  
    12219 
    12220 > show #!29 models
    12221 
    12222 > hide #!53 models
    12223 
    12224 > show #!53 models
    12225 
    12226 > show #!58 models
    12227 
    12228 > hide #!58 models
    12229 
    12230 > hide #!53 models
    12231 
    12232 > show #!53 models
    12233 
    12234 > hide #!53 models
    12235 
    12236 > show #!53 models
    12237 
    12238 > hide #!53 models
    12239 
    12240 > show #!53 models
    12241 
    12242 > show #57 models
    12243 
    12244 > hide #57 models
    12245 
    12246 > hide #!29 models
    12247 
    12248 > hide #!53 models
    12249 
    12250 > show #57 models
    12251 
    12252 Drag select of 6 residues 
    12253 
    12254 > select up
    12255 
    12256 519 atoms, 525 bonds, 67 residues, 1 model selected 
    12257 
    12258 > delete sel
    12259 
    12260 Drag select of 159 residues 
    12261 
    12262 > select up
    12263 
    12264 1356 atoms, 1383 bonds, 171 residues, 1 model selected 
    12265 
    12266 > delete sel
    12267 
    12268 Drag select of 13 residues, 1 pseudobonds 
    12269 
    12270 > select up
    12271 
    12272 109 atoms, 108 bonds, 1 pseudobond, 14 residues, 2 models selected 
    12273 
    12274 > delete sel
    12275 
    12276 Drag select of 5 residues 
    12277 
    12278 > select clear
    12279 
    12280 Drag select of 8 residues 
    12281 
    12282 > select up
    12283 
    12284 108 atoms, 110 bonds, 13 residues, 1 model selected 
    12285 
    12286 > delete sel
    12287 
    12288 > fitmap #57 inMap #29.4
    12289 
    12290 Fit molecule copy of CopBprime_O55029.pdb (#57) to map
    12291 W20_J140_run_body004.mrc (#29.4) using 5122 atoms 
    12292 average map value = 0.01184, steps = 144 
    12293 shifted from previous position = 8.94 
    12294 rotated from previous position = 13.8 degrees 
    12295 atoms outside contour = 3092, contour level = 0.012962 
    12296  
    12297 Position of copy of CopBprime_O55029.pdb (#57) relative to
    12298 W20_J140_run_body004.mrc (#29.4) coordinates: 
    12299 Matrix rotation and translation 
    12300 0.19336342 0.06063554 0.97925171 138.80893393 
    12301 0.87031534 0.45017771 -0.19972793 186.94884028 
    12302 -0.45294790 0.89087786 0.03427586 177.78973972 
    12303 Axis 0.55251909 0.72557622 0.41019729 
    12304 Axis point 33.82238390 0.00000000 47.06660425 
    12305 Rotation angle (degrees) 99.27025680 
    12306 Shift along axis 285.26908646 
    12307  
    12308 
    12309 > show #!29 models
    12310 
    12311 > ui tool show "Build Structure"
    12312 
    12313 > toolshed show
    12314 
    12315 > show #!53 models
    12316 
    12317 > hide #!53 models
    12318 
    12319 > fitmap #57 inMap #29.4
    12320 
    12321 Fit molecule copy of CopBprime_O55029.pdb (#57) to map
    12322 W20_J140_run_body004.mrc (#29.4) using 5122 atoms 
    12323 average map value = 0.01184, steps = 104 
    12324 shifted from previous position = 0.0162 
    12325 rotated from previous position = 0.0152 degrees 
    12326 atoms outside contour = 3088, contour level = 0.012962 
    12327  
    12328 Position of copy of CopBprime_O55029.pdb (#57) relative to
    12329 W20_J140_run_body004.mrc (#29.4) coordinates: 
    12330 Matrix rotation and translation 
    12331 0.19340630 0.06050533 0.97925130 138.80565926 
    12332 0.87021654 0.45038133 -0.19969933 186.94266371 
    12333 -0.45311938 0.89078379 0.03445385 177.80765427 
    12334 Axis 0.55243756 0.72563743 0.41019882 
    12335 Axis point 33.85424725 0.00000000 47.07180428 
    12336 Rotation angle (degrees) 99.25793540 
    12337 Shift along axis 285.27054234 
    12338  
    12339 
    12340 > combine #57
    12341 
    12342 > hide #!29 models
    12343 
    12344 > hide #!63 models
    12345 
    12346 Drag select of 2 residues 
    12347 
    12348 > select up
    12349 
    12350 50 atoms, 50 bonds, 6 residues, 1 model selected 
    12351 Drag select of 293 residues 
    12352 
    12353 > select up
    12354 
    12355 2400 atoms, 2461 bonds, 299 residues, 1 model selected 
    12356 
    12357 > delete sel
    12358 
    12359 > fitmap #57 inMap #29.4
    12360 
    12361 Fit molecule copy of CopBprime_O55029.pdb (#57) to map
    12362 W20_J140_run_body004.mrc (#29.4) using 2722 atoms 
    12363 average map value = 0.01488, steps = 60 
    12364 shifted from previous position = 0.588 
    12365 rotated from previous position = 4.72 degrees 
    12366 atoms outside contour = 1280, contour level = 0.012962 
    12367  
    12368 Position of copy of CopBprime_O55029.pdb (#57) relative to
    12369 W20_J140_run_body004.mrc (#29.4) coordinates: 
    12370 Matrix rotation and translation 
    12371 0.24483069 0.00098871 0.96956534 140.64125601 
    12372 0.85587662 0.46963714 -0.21660139 186.15669395 
    12373 -0.45555806 0.88285898 0.11413537 178.37372881 
    12374 Axis 0.55176004 0.71519280 0.42902227 
    12375 Axis point 33.88188669 0.00000000 44.81013344 
    12376 Rotation angle (degrees) 94.91618649 
    12377 Shift along axis 287.26445575 
    12378  
    12379 
    12380 > show #!29 models
    12381 
    12382 > select add #57
    12383 
    12384 2722 atoms, 2779 bonds, 341 residues, 1 model selected 
    12385 
    12386 > select clear
    12387 
    12388 > select add #57
    12389 
    12390 2722 atoms, 2779 bonds, 341 residues, 1 model selected 
    12391 
    12392 > ui mousemode right "translate selected models"
    12393 
    12394 > view matrix models
    12395 > #57,0.50755,-0.10762,0.85488,130.21,0.68026,0.65898,-0.32092,190.13,-0.52881,0.74442,0.40768,177.92
    12396 
    12397 > fitmap #57 inMap #29.4
    12398 
    12399 Fit molecule copy of CopBprime_O55029.pdb (#57) to map
    12400 W20_J140_run_body004.mrc (#29.4) using 2722 atoms 
    12401 average map value = 0.01488, steps = 64 
    12402 shifted from previous position = 2.72 
    12403 rotated from previous position = 0.042 degrees 
    12404 atoms outside contour = 1279, contour level = 0.012962 
    12405  
    12406 Position of copy of CopBprime_O55029.pdb (#57) relative to
    12407 W20_J140_run_body004.mrc (#29.4) coordinates: 
    12408 Matrix rotation and translation 
    12409 0.24476466 0.00100564 0.96958200 140.62777342 
    12410 0.85622153 0.46899298 -0.21663398 186.17961813 
    12411 -0.45494501 0.88320132 0.11393185 178.36605751 
    12412 Axis 0.55197003 0.71492178 0.42920384 
    12413 Axis point 33.76576678 0.00000000 44.80708945 
    12414 Rotation angle (degrees) 94.94245961 
    12415 Shift along axis 287.28157686 
    12416  
    12417 
    12418 > select subtract #57
    12419 
    12420 Nothing selected 
    12421 
    12422 > hide #!57 models
    12423 
    12424 > show #!63 models
    12425 
    12426 > hide #!29 models
    12427 
    12428 > ui mousemode right select
    12429 
    12430 Drag select of 285 residues 
    12431 
    12432 > select up
    12433 
    12434 2450 atoms, 2494 bonds, 306 residues, 1 model selected 
    12435 
    12436 > select up
    12437 
    12438 5122 atoms, 5241 bonds, 640 residues, 1 model selected 
    12439 
    12440 > select clear
    12441 
    12442 Drag select of 338 residues 
    12443 
    12444 > select up
    12445 
    12446 2722 atoms, 2779 bonds, 341 residues, 1 model selected 
    12447 
    12448 > select clear
    12449 
    12450 Drag select of 321 residues 
    12451 
    12452 > select up
    12453 
    12454 2643 atoms, 2694 bonds, 331 residues, 1 model selected 
    12455 
    12456 > select clear
    12457 
    12458 Drag select of 193 residues 
    12459 
    12460 > select up
    12461 
    12462 2186 atoms, 2221 bonds, 272 residues, 1 model selected 
    12463 
    12464 > delete sel
    12465 
    12466 > show #!57 models
    12467 
    12468 > hide #!63 models
    12469 
    12470 > hide #!57 models
    12471 
    12472 > show #!63 models
    12473 
    12474 > select #63/A:10
    12475 
    12476 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12477 
    12478 > select #63/A:577
    12479 
    12480 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12481 
    12482 > select up
    12483 
    12484 219 atoms, 213 bonds, 27 residues, 1 model selected 
    12485 
    12486 > delete sel
    12487 
    12488 > select clear
    12489 
    12490 > select #63/A:430
    12491 
    12492 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12493 Drag select of 14 residues, 1 pseudobonds 
    12494 
    12495 > select clear
    12496 
    12497 Drag select of 16 residues, 3 pseudobonds 
    12498 
    12499 > select up
    12500 
    12501 125 atoms, 125 bonds, 3 pseudobonds, 17 residues, 2 models selected 
    12502 
    12503 > delete sel
    12504 
    12505 Drag select of 3 residues 
    12506 
    12507 > delete sel
    12508 
    12509 Drag select of 3 residues 
    12510 
    12511 > select up
    12512 
    12513 42 atoms, 41 bonds, 6 residues, 1 model selected 
    12514 
    12515 > delete sel
    12516 
    12517 > select clear
    12518 
    12519 > select #63/A:353
    12520 
    12521 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12522 
    12523 > select up
    12524 
    12525 124 atoms, 124 bonds, 16 residues, 1 model selected 
    12526 
    12527 > select clear
    12528 
    12529 [Repeated 1 time(s)]Drag select of 1 residues 
    12530 
    12531 > select down
    12532 
    12533 4 atoms, 1 residue, 1 model selected 
    12534 
    12535 > select up
    12536 
    12537 124 atoms, 124 bonds, 16 residues, 1 model selected 
    12538 
    12539 > select clear
    12540 
    12541 > select #63/A:373
    12542 
    12543 4 atoms, 3 bonds, 1 residue, 1 model selected 
    12544 
    12545 > delete sel
    12546 
    12547 > select clear
    12548 
    12549 > select #63/A:354
    12550 
    12551 12 atoms, 12 bonds, 1 residue, 1 model selected 
    12552 
    12553 > delete sel
    12554 
    12555 > select clear
    12556 
    12557 > select #63/A:356
    12558 
    12559 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12560 
    12561 > \
    12562 
    12563 Unknown command: \ 
    12564 
    12565 > select clear
    12566 
    12567 > select #63/A:355
    12568 
    12569 7 atoms, 7 bonds, 1 residue, 1 model selected 
    12570 
    12571 > \
    12572 
    12573 Unknown command: \ 
    12574 
    12575 > delete sel
    12576 
    12577 > select clear
    12578 
    12579 [Repeated 1 time(s)]Drag select of 3 residues, 2 pseudobonds 
    12580 
    12581 > delete sel
    12582 
    12583 > select #63/A:320
    12584 
    12585 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12586 Drag select of 1 residues, 2 pseudobonds 
    12587 
    12588 > select up
    12589 
    12590 78 atoms, 76 bonds, 2 pseudobonds, 10 residues, 2 models selected 
    12591 
    12592 > close #63
    12593 
    12594 > combine #36
    12595 
    12596 Drag select of 280 residues 
    12597 
    12598 > select up
    12599 
    12600 3003 atoms, 3050 bonds, 379 residues, 1 model selected 
    12601 
    12602 > delete sel
    12603 
    12604 Drag select of 41 residues, 2 pseudobonds 
    12605 
    12606 > delete sel
    12607 
    12608 Drag select of 122 residues, 3 pseudobonds 
    12609 
    12610 > select up
    12611 
    12612 1221 atoms, 1239 bonds, 3 pseudobonds, 152 residues, 2 models selected 
    12613 
    12614 > delete sel
    12615 
    12616 Drag select of 9 residues, 2 pseudobonds 
    12617 
    12618 > select up
    12619 
    12620 91 atoms, 90 bonds, 2 pseudobonds, 12 residues, 2 models selected 
    12621 
    12622 > delete sel
    12623 
    12624 > select #63/A:373
    12625 
    12626 4 atoms, 3 bonds, 1 residue, 1 model selected 
    12627 
    12628 > delete sel
    12629 
    12630 > select #63/A:356
    12631 
    12632 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12633 
    12634 > delete sel
    12635 
    12636 > close #63
    12637 
    12638 > show #!53 models
    12639 
    12640 > hide #!53 models
    12641 
    12642 > show #!57 models
    12643 
    12644 > hide #!57 models
    12645 
    12646 > show #50.1 models
    12647 
    12648 > hide #50.1 models
    12649 
    12650 > show #!50.2 models
    12651 
    12652 > hide #!50.2 models
    12653 
    12654 > combine #36
    12655 
    12656 Drag select of 289 residues 
    12657 
    12658 > select up
    12659 
    12660 2306 atoms, 2348 bonds, 291 residues, 1 model selected 
    12661 
    12662 > delete sel
    12663 
    12664 Drag select of 218 residues 
    12665 
    12666 > select up
    12667 
    12668 1888 atoms, 1925 bonds, 237 residues, 1 model selected 
    12669 
    12670 > delete sel
    12671 
    12672 Drag select of 15 residues, 1 pseudobonds 
    12673 
    12674 > select up
    12675 
    12676 152 atoms, 153 bonds, 1 pseudobond, 18 residues, 2 models selected 
    12677 
    12678 > delete sel
    12679 
    12680 Drag select of 4 residues 
    12681 
    12682 > select up
    12683 
    12684 42 atoms, 41 bonds, 5 residues, 1 model selected 
    12685 
    12686 > delete sel
    12687 
    12688 Drag select of 29 residues, 2 pseudobonds 
    12689 
    12690 > select up
    12691 
    12692 302 atoms, 302 bonds, 2 pseudobonds, 39 residues, 2 models selected 
    12693 
    12694 > delete sel
    12695 
    12696 > select clear
    12697 
    12698 [Repeated 1 time(s)]
    12699 
    12700 > select #63/A:305
    12701 
    12702 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12703 
    12704 > delete sel
    12705 
    12706 > select clear
    12707 
    12708 Drag select of 8 residues, 1 pseudobonds 
    12709 
    12710 > select up
    12711 
    12712 119 atoms, 119 bonds, 1 pseudobond, 15 residues, 2 models selected 
    12713 
    12714 > show #!57 models
    12715 
    12716 > delete sel
    12717 
    12718 > fitmap #63 inMap #29.4
    12719 
    12720 Fit molecule copy of CopBprime_O55029.pdb (#63) to map
    12721 W20_J140_run_body004.mrc (#29.4) using 2400 atoms 
    12722 average map value = 0.01282, steps = 148 
    12723 shifted from previous position = 15.9 
    12724 rotated from previous position = 27.5 degrees 
    12725 atoms outside contour = 1275, contour level = 0.012962 
    12726  
    12727 Position of copy of CopBprime_O55029.pdb (#63) relative to
    12728 W20_J140_run_body004.mrc (#29.4) coordinates: 
    12729 Matrix rotation and translation 
    12730 0.53194142 0.55442248 0.64004222 123.33487031 
    12731 0.70035644 0.13679328 -0.70056295 183.98600531 
    12732 -0.47596132 0.82091614 -0.31552735 169.31259792 
    12733 Axis 0.80394040 0.58968956 0.07711063 
    12734 Axis point 0.00000000 -20.96531712 102.68367487 
    12735 Rotation angle (degrees) 108.86844509 
    12736 Shift along axis 220.70431310 
    12737  
    12738 
    12739 > show #!29 models
    12740 
    12741 > show #!53 models
    12742 
    12743 > show #!58 models
    12744 
    12745 > hide #!58 models
    12746 
    12747 > show #!58 models
    12748 
    12749 > hide #!53 models
    12750 
    12751 > show #!53 models
    12752 
    12753 > hide #!57 models
    12754 
    12755 > show #!57 models
    12756 
    12757 > hide #!57 models
    12758 
    12759 > show #!59 models
    12760 
    12761 > hide #!53 models
    12762 
    12763 > hide #!63 models
    12764 
    12765 > show #!63 models
    12766 
    12767 > hide #!63 models
    12768 
    12769 > show #!57 models
    12770 
    12771 > hide #!57 models
    12772 
    12773 > show #!57 models
    12774 
    12775 > hide #!57 models
    12776 
    12777 > show #!53 models
    12778 
    12779 > hide #!53 models
    12780 
    12781 > show #!53 models
    12782 
    12783 > hide #!53 models
    12784 
    12785 > show #!63 models
    12786 
    12787 > hide #!63 models
    12788 
    12789 > show #50.6 models
    12790 
    12791 > show #!63 models
    12792 
    12793 > hide #!63 models
    12794 
    12795 > show #!53 models
    12796 
    12797 > hide #!53 models
    12798 
    12799 > show #!53 models
    12800 
    12801 > hide #!53 models
    12802 
    12803 > show #!57 models
    12804 
    12805 > hide #!57 models
    12806 
    12807 > show #!57 models
    12808 
    12809 > hide #!57 models
    12810 
    12811 > combine #57
    12812 
    12813 > hide #!58 models
    12814 
    12815 > hide #!59 models
    12816 
    12817 > hide #50.6 models
    12818 
    12819 > show #!63 models
    12820 
    12821 > hide #!63 models
    12822 
    12823 > show #!63 models
    12824 
    12825 > hide #!63 models
    12826 
    12827 > show #!63 models
    12828 
    12829 > hide #!29 models
    12830 
    12831 > show #50.6 models
    12832 
    12833 > hide #50.6 models
    12834 
    12835 > hide #!63 models
    12836 
    12837 > show #!57 models
    12838 
    12839 > hide #!57 models
    12840 
    12841 > show #!57 models
    12842 
    12843 > hide #!57 models
    12844 
    12845 Drag select of 26 residues 
    12846 
    12847 > select up
    12848 
    12849 229 atoms, 232 bonds, 28 residues, 1 model selected 
    12850 
    12851 > delete sel
    12852 
    12853 Drag select of 9 residues 
    12854 
    12855 > select up
    12856 
    12857 76 atoms, 77 bonds, 10 residues, 1 model selected 
    12858 
    12859 > delete sel
    12860 
    12861 Drag select of 6 residues 
    12862 
    12863 > select clear
    12864 
    12865 Drag select of 10 residues 
    12866 
    12867 > select up
    12868 
    12869 115 atoms, 115 bonds, 14 residues, 1 model selected 
    12870 
    12871 > combine #57
    12872 
    12873 > select add #64
    12874 
    12875 2417 atoms, 2468 bonds, 303 residues, 1 model selected 
    12876 
    12877 > close #64
    12878 
    12879 > hide #!65 models
    12880 
    12881 > show #!65 models
    12882 
    12883 > show #!63 models
    12884 
    12885 > hide #!63 models
    12886 
    12887 > show #!63 models
    12888 
    12889 > hide #!63 models
    12890 
    12891 > show #!57 models
    12892 
    12893 > hide #!57 models
    12894 
    12895 > show #!57 models
    12896 
    12897 > hide #!65 models
    12898 
    12899 Drag select of 31 residues 
    12900 
    12901 > select up
    12902 
    12903 305 atoms, 310 bonds, 38 residues, 1 model selected 
    12904 
    12905 > delete sel
    12906 
    12907 Drag select of 13 residues 
    12908 
    12909 > select up
    12910 
    12911 115 atoms, 115 bonds, 14 residues, 1 model selected 
    12912 
    12913 > delete sel
    12914 
    12915 > hide #!57 models
    12916 
    12917 > show #!53 models
    12918 
    12919 > show #!57 models
    12920 
    12921 > fitmap #57 inMap #29.4
    12922 
    12923 Fit molecule copy of CopBprime_O55029.pdb (#57) to map
    12924 W20_J140_run_body004.mrc (#29.4) using 2302 atoms 
    12925 average map value = 0.01478, steps = 84 
    12926 shifted from previous position = 0.608 
    12927 rotated from previous position = 2.11 degrees 
    12928 atoms outside contour = 1083, contour level = 0.012962 
    12929  
    12930 Position of copy of CopBprime_O55029.pdb (#57) relative to
    12931 W20_J140_run_body004.mrc (#29.4) coordinates: 
    12932 Matrix rotation and translation 
    12933 0.26430656 -0.02399441 0.96414019 140.91312010 
    12934 0.84653335 0.48474763 -0.22000233 186.26213690 
    12935 -0.46208585 0.87432489 0.14843404 179.06445534 
    12936 Axis 0.54788377 0.71405160 0.43583676 
    12937 Axis point 34.54414646 0.00000000 44.00500794 
    12938 Rotation angle (degrees) 92.93803311 
    12939 Shift along axis 288.24766132 
    12940  
    12941 
    12942 > show #!63 models
    12943 
    12944 > show #!65 models
    12945 
    12946 > hide #!65 models
    12947 
    12948 > show #!65 models
    12949 
    12950 > hide #!65 models
    12951 
    12952 > show #!65 models
    12953 
    12954 > hide #!57 models
    12955 
    12956 > hide #!63 models
    12957 
    12958 Drag select of 243 residues 
    12959 
    12960 > select up
    12961 
    12962 2119 atoms, 2164 bonds, 266 residues, 1 model selected 
    12963 
    12964 > delete sel
    12965 
    12966 > hide #!65 models
    12967 
    12968 > show #!57 models
    12969 
    12970 > show #!63 models
    12971 
    12972 > hide #!63 models
    12973 
    12974 > hide #!57 models
    12975 
    12976 > show #!65 models
    12977 
    12978 Drag select of 17 residues, 1 pseudobonds 
    12979 
    12980 > select up
    12981 
    12982 159 atoms, 159 bonds, 1 pseudobond, 19 residues, 2 models selected 
    12983 Drag select of 22 residues, 2 pseudobonds 
    12984 
    12985 > delete sel
    12986 
    12987 > show #!57 models
    12988 
    12989 > select #57/A:547
    12990 
    12991 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12992 
    12993 > select clear
    12994 
    12995 > show #!29 models
    12996 
    12997 > hide #!29 models
    12998 
    12999 > hide #!57 models
    13000 
    13001 > select #65/A:588
    13002 
    13003 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13004 
    13005 > delete sel
    13006 
    13007 > show #!57 models
    13008 
    13009 > fitmap #64 inMap #29.4
    13010 
    13011 No atoms or maps for #64 
    13012 
    13013 > fitmap #65 inMap #29.4
    13014 
    13015 Fit molecule copy of copy of CopBprime_O55029.pdb (#65) to map
    13016 W20_J140_run_body004.mrc (#29.4) using 420 atoms 
    13017 average map value = 0.02083, steps = 56 
    13018 shifted from previous position = 2.51 
    13019 rotated from previous position = 13.6 degrees 
    13020 atoms outside contour = 145, contour level = 0.012962 
    13021  
    13022 Position of copy of copy of CopBprime_O55029.pdb (#65) relative to
    13023 W20_J140_run_body004.mrc (#29.4) coordinates: 
    13024 Matrix rotation and translation 
    13025 0.25505166 0.23428436 0.93811486 140.41746282 
    13026 0.81508493 0.46984578 -0.33894174 184.56399264 
    13027 -0.52017805 0.85109094 -0.07112670 178.31682392 
    13028 Axis 0.60413780 0.74032411 0.29485206 
    13029 Axis point 50.19505778 0.00000000 66.66205089 
    13030 Rotation angle (degrees) 99.96896003 
    13031 Shift along axis 274.04575231 
    13032  
    13033 
    13034 > show #!29 models
    13035 
    13036 > show #!63 models
    13037 
    13038 > show #!60 models
    13039 
    13040 > show #!61 models
    13041 
    13042 > show #!62 models
    13043 
    13044 > show #!51 models
    13045 
    13046 > show #!52 models
    13047 
    13048 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    13049 > resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
    13050 
    13051 ——— End of log from Fri Jul 4 14:29:17 2025 ———
    13052 
    13053 > view name session-start
    13054 
    13055 opened ChimeraX session 
    13056 
    13057 > hide #!65 models
    13058 
    13059 > hide #!63 models
    13060 
    13061 > show #!65 models
    13062 
    13063 > hide #!65 models
    13064 
    13065 > show #!63 models
    13066 
    13067 > show #!65 models
    13068 
    13069 > combine #60 #61 #62
    13070 
    13071 Remapping chain ID 'A' in copy of copy of copy of A_fixed_model_2_A.pdb #61 to
    13072 'B' 
    13073 Remapping chain ID 'A' in copy of copy of A_fixed_model_2_A.pdb #62 to 'C' 
    13074 
    13075 > rename #64 alpha-COPI
    13076 
    13077 > hide #!64 models
    13078 
    13079 > show #!64 models
    13080 
    13081 > hide #!64 models
    13082 
    13083 > show #!64 models
    13084 
    13085 > hide #!64 models
    13086 
    13087 > hide #!62 models
    13088 
    13089 > hide #!61 models
    13090 
    13091 > hide #!60 models
    13092 
    13093 > show #!64 models
    13094 
    13095 > combine #51 #52
    13096 
    13097 Remapping chain ID 'B' in B_fixed_model_2_B.pdb #52 to 'C' 
    13098 
    13099 > rename #66 beta-COPI
    13100 
    13101 > hide #!66 models
    13102 
    13103 > show #!66 models
    13104 
    13105 > hide #!66 models
    13106 
    13107 > show #!66 models
    13108 
    13109 > hide #!66 models
    13110 
    13111 > hide #!64 models
    13112 
    13113 > show #!64 models
    13114 
    13115 > hide #!52 models
    13116 
    13117 > hide #!51 models
    13118 
    13119 > hide #!65 models
    13120 
    13121 > hide #!63 models
    13122 
    13123 > hide #!57 models
    13124 
    13125 > hide #!53 models
    13126 
    13127 > show #!53 models
    13128 
    13129 > hide #!53 models
    13130 
    13131 > show #!65 models
    13132 
    13133 > hide #!65 models
    13134 
    13135 > show #!63 models
    13136 
    13137 > show #!53 models
    13138 
    13139 > hide #!53 models
    13140 
    13141 > show #!57 models
    13142 
    13143 > show #!53 models
    13144 
    13145 > hide #!53 models
    13146 
    13147 > show #!65 models
    13148 
    13149 > show #!53 models
    13150 
    13151 > combine #63 #57 #65 #53
    13152 
    13153 Remapping chain ID 'A' in copy of CopBprime_O55029.pdb #57 to 'B' 
    13154 Remapping chain ID 'A' in copy of copy of CopBprime_O55029.pdb #65 to 'C' 
    13155 Remapping chain ID 'A' in copy of CopBprime_O55029.pdb #53 to 'D' 
    13156 
    13157 > rename #67 betaprime-COPI
    13158 
    13159 > hide #!53 models
    13160 
    13161 > hide #!57 models
    13162 
    13163 > hide #!63 models
    13164 
    13165 > hide #!65 models
    13166 
    13167 > show #!66 models
    13168 
    13169 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    13170 > resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
    13171 
    13172 > show #!37 models
    13173 
    13174 > show #!38 models
    13175 
    13176 > hide #!38 models
    13177 
    13178 > hide #!37 models
    13179 
    13180 > show #!50.8 models
    13181 
    13182 > show #50.9 models
    13183 
    13184 > hide #!64 models
    13185 
    13186 > hide #!66 models
    13187 
    13188 > hide #!67 models
    13189 
    13190 > select add #50.9
    13191 
    13192 319 atoms, 320 bonds, 37 residues, 1 model selected 
    13193 
    13194 > fitmap #50.9 inMap #29.4
    13195 
    13196 Fit molecule W20_C1_initial_model_no_wat_lig.pdb A8 (#50.9) to map
    13197 W20_J140_run_body004.mrc (#29.4) using 319 atoms 
    13198 average map value = 0.01618, steps = 332 
    13199 shifted from previous position = 5.67 
    13200 rotated from previous position = 32.6 degrees 
    13201 atoms outside contour = 181, contour level = 0.012962 
    13202  
    13203 Position of W20_C1_initial_model_no_wat_lig.pdb A8 (#50.9) relative to
    13204 W20_J140_run_body004.mrc (#29.4) coordinates: 
    13205 Matrix rotation and translation 
    13206 -0.96507080 0.08189036 0.24886207 278.79886608 
    13207 -0.17377809 -0.91094231 -0.37414608 529.42927332 
    13208 0.19606003 -0.40432423 0.89335457 -19.89239692 
    13209 Axis -0.11483207 0.20091912 -0.97285410 
    13210 Axis point 157.88995888 252.84037243 0.00000000 
    13211 Rotation angle (degrees) 172.44942844 
    13212 Shift along axis 93.70981152 
    13213  
    13214 
    13215 > select subtract #50.9
    13216 
    13217 Nothing selected 
    13218 
    13219 > combine #37
    13220 
    13221 [Repeated 1 time(s)]
    13222 
    13223 > hide #!69 models
    13224 
    13225 > hide #50.9 models
    13226 
    13227 > hide #!29 models
    13228 
    13229 > ui mousemode right select
    13230 
    13231 Drag select of 11 residues 
    13232 
    13233 > select up
    13234 
    13235 319 atoms, 320 bonds, 37 residues, 1 model selected 
    13236 
    13237 > delete sel
    13238 
    13239 > fitmap #68 inMap #29.1
    13240 
    13241 Fit molecule copy of CopD_full_Q5XJY5.pdb (#68) to map
    13242 W20_J140_run_body001.mrc (#29.1) using 1112 atoms 
    13243 average map value = 0.01419, steps = 64 
    13244 shifted from previous position = 0.82 
    13245 rotated from previous position = 2.64 degrees 
    13246 atoms outside contour = 514, contour level = 0.01322 
    13247  
    13248 Position of copy of CopD_full_Q5XJY5.pdb (#68) relative to
    13249 W20_J140_run_body001.mrc (#29.1) coordinates: 
    13250 Matrix rotation and translation 
    13251 -0.11662970 -0.98563516 0.12215086 180.96364645 
    13252 -0.16309929 -0.10231295 -0.98129031 185.65988338 
    13253 0.97969185 -0.13437031 -0.14882367 140.80476056 
    13254 Axis 0.58040695 -0.58768567 0.56369614 
    13255 Axis point 145.90273812 0.00000000 210.04228211 
    13256 Rotation angle (degrees) 133.14783703 
    13257 Shift along axis 75.29400436 
    13258  
    13259 
    13260 > hide #!68 models
    13261 
    13262 > hide #!50.8 models
    13263 
    13264 > show #50.9 models
    13265 
    13266 > show #!69 models
    13267 
    13268 > ui tool show Matchmaker
    13269 
    13270 > matchmaker #!69 to #50.9
    13271 
    13272 Parameters 
    13273 --- 
    13274 Chain pairing | bb 
    13275 Alignment algorithm | Needleman-Wunsch 
    13276 Similarity matrix | BLOSUM-62 
    13277 SS fraction | 0.3 
    13278 Gap open (HH/SS/other) | 18/18/6 
    13279 Gap extend | 1 
    13280 SS matrix |  |  | H | S | O 
    13281 ---|---|---|--- 
    13282 H | 6 | -9 | -6 
    13283 S |  | 6 | -6 
    13284 O |  |  | 4 
    13285 Iteration cutoff | 2 
    13286  
    13287 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A8, chain A8 (#50.9) with copy
    13288 of CopD_full_Q5XJY5.pdb, chain A (#69), sequence alignment score = 189.1 
    13289 RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
    13290 0.000) 
    13291  
    13292 Drag select of 135 residues 
    13293 
    13294 > select up
    13295 
    13296 1112 atoms, 1129 bonds, 138 residues, 1 model selected 
    13297 
    13298 > delete sel
    13299 
    13300 > show #!68 models
    13301 
    13302 > hide #50.9 models
    13303 
    13304 > select clear
    13305 
    13306 [Repeated 1 time(s)]
    13307 
    13308 > select #68/A:138
    13309 
    13310 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13311 
    13312 > show sel atoms
    13313 
    13314 > style sel stick
    13315 
    13316 Changed 6 atom styles 
    13317 
    13318 > hide sel cartoons
    13319 
    13320 > color sel byhetero
    13321 
    13322 > select #69/A:139
    13323 
    13324 10 atoms, 10 bonds, 1 residue, 1 model selected 
    13325 
    13326 > show sel atoms
    13327 
    13328 > hide sel cartoons
    13329 
    13330 > color sel byhetero
    13331 
    13332 > select clear
    13333 
    13334 > ui tool show "Build Structure"
    13335 
    13336 > select #68/A:138@C
    13337 
    13338 1 atom, 1 residue, 1 model selected 
    13339 
    13340 > select add #69/A:139@N
    13341 
    13342 2 atoms, 2 residues, 2 models selected 
    13343 
    13344 > build join peptide sel length 1.33 omega 180 phi -120 move small
    13345 
    13346 > undo
    13347 
    13348 Undo failed, probably because structures have been modified. 
    13349 
    13350 > show #!29 models
    13351 
    13352 > build join peptide sel length 1.33 omega 90 phi -120 move small
    13353 
    13354 No chain-terminal carbons in atoms 
    13355 
    13356 > hide #!29 models
    13357 
    13358 Must select exactly 3 atoms in graphics window 
    13359 
    13360 > select #68/A:138@CA
    13361 
    13362 1 atom, 1 residue, 1 model selected 
    13363 
    13364 > select #68/A:138@C
    13365 
    13366 1 atom, 1 residue, 1 model selected 
    13367 
    13368 > select add #68/A:138@CA
    13369 
    13370 2 atoms, 1 residue, 1 model selected 
    13371 
    13372 > select add #68/A:139@N
    13373 
    13374 3 atoms, 2 residues, 1 model selected 
    13375 Cannot set the angle if the end atoms have a connection that does not pass
    13376 through the center atom 
    13377 
    13378 > select clear
    13379 
    13380 > select #68/A:138@CA
    13381 
    13382 1 atom, 1 residue, 1 model selected 
    13383 
    13384 > select add #68/A:138@C
    13385 
    13386 2 atoms, 1 residue, 1 model selected 
    13387 
    13388 > select add #68/A:139@N
    13389 
    13390 3 atoms, 2 residues, 1 model selected 
    13391 
    13392 > show #!29 models
    13393 
    13394 > angle #68:138@CA@C:139@N 137.7
    13395 
    13396 > angle #68:138@CA@C:139@N 91
    13397 
    13398 > angle #68:138@CA@C:139@N 67.2
    13399 
    13400 > angle #68:138@CA@C:139@N 110.2
    13401 
    13402 > select clear
    13403 
    13404 > select #68/A:152
    13405 
    13406 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13407 
    13408 > select up
    13409 
    13410 319 atoms, 320 bonds, 37 residues, 1 model selected 
    13411 
    13412 > ui mousemode right "translate selected atoms"
    13413 
    13414 > select add #68
    13415 
    13416 1431 atoms, 1450 bonds, 175 residues, 1 model selected 
    13417 
    13418 > select subtract #68
    13419 
    13420 Nothing selected 
    13421 
    13422 > ui mousemode right tug
    13423 
    13424 > ui mousemode right select
    13425 
    13426 > select #68/A:155
    13427 
    13428 5 atoms, 4 bonds, 1 residue, 1 model selected 
    13429 
    13430 > select up
    13431 
    13432 319 atoms, 320 bonds, 37 residues, 1 model selected 
    13433 
    13434 > ui mousemode right tug
    13435 
    13436 > ui mousemode right "bond rotation"
    13437 
    13438 > ui mousemode right select
    13439 
    13440 > ui mousemode right "play coordinates"
    13441 
    13442 > select add #68
    13443 
    13444 1431 atoms, 1450 bonds, 175 residues, 1 model selected 
    13445 
    13446 > select subtract #68
    13447 
    13448 Nothing selected 
    13449 
    13450 > hide #!68 models
    13451 
    13452 > close #68
    13453 
    13454 > combine 37
    13455 
    13456 Expected a keyword 
    13457 
    13458 > combine #37
    13459 
    13460 > delete sel
    13461 
    13462 > combine #37
    13463 
    13464 > hide #!69 models
    13465 
    13466 > hide #!29 models
    13467 
    13468 > ui mousemode right select
    13469 
    13470 Drag select of 7 residues 
    13471 
    13472 > select up
    13473 
    13474 319 atoms, 320 bonds, 37 residues, 1 model selected 
    13475 
    13476 > combine #37
    13477 
    13478 > delete sel
    13479 
    13480 > close #70
    13481 
    13482 > hide #!68 models
    13483 
    13484 > ui tool show Matchmaker
    13485 
    13486 > matchmaker #!69 to #50.9
    13487 
    13488 Parameters 
    13489 --- 
    13490 Chain pairing | bb 
    13491 Alignment algorithm | Needleman-Wunsch 
    13492 Similarity matrix | BLOSUM-62 
    13493 SS fraction | 0.3 
    13494 Gap open (HH/SS/other) | 18/18/6 
    13495 Gap extend | 1 
    13496 SS matrix |  |  | H | S | O 
    13497 ---|---|---|--- 
    13498 H | 6 | -9 | -6 
    13499 S |  | 6 | -6 
    13500 O |  |  | 4 
    13501 Iteration cutoff | 2 
    13502  
    13503 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A8, chain A8 (#50.9) with copy
    13504 of CopD_full_Q5XJY5.pdb, chain A (#69), sequence alignment score = 189.1 
    13505 RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
    13506 0.000) 
    13507  
    13508 
    13509 > show #!69 models
    13510 
    13511 Drag select of 103 residues 
    13512 
    13513 > select up
    13514 
    13515 936 atoms, 951 bonds, 116 residues, 1 model selected 
    13516 Drag select of 135 residues 
    13517 
    13518 > select up
    13519 
    13520 1112 atoms, 1129 bonds, 138 residues, 1 model selected 
    13521 
    13522 > delete sel
    13523 
    13524 > show #!29 models
    13525 
    13526 > show #!68 models
    13527 
    13528 > hide #!29 models
    13529 
    13530 > select #69/A:168
    13531 
    13532 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13533 
    13534 > select clear
    13535 
    13536 > select #69/A:165
    13537 
    13538 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13539 
    13540 > select clear
    13541 
    13542 > select #69/A:162
    13543 
    13544 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13545 
    13546 > show sel atoms
    13547 
    13548 > select #69/A:164
    13549 
    13550 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13551 
    13552 > show sel atoms
    13553 
    13554 > show #!29 models
    13555 
    13556 > hide #!29 models
    13557 
    13558 > show #!30 models
    13559 
    13560 > select #69/A:165
    13561 
    13562 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13563 
    13564 > show sel atoms
    13565 
    13566 > color #30.1 #92929280 models
    13567 
    13568 > color #30.4 #92929263 models
    13569 
    13570 > show #!67 models
    13571 
    13572 > select add #69
    13573 
    13574 319 atoms, 320 bonds, 37 residues, 1 model selected 
    13575 
    13576 > hide sel atoms
    13577 
    13578 > select subtract #69
    13579 
    13580 Nothing selected 
    13581 
    13582 > combine #68 #69
    13583 
    13584 Remapping chain ID 'A' in copy of CopD_full_Q5XJY5.pdb #69 to 'B' 
    13585 
    13586 > rename #70 delta-COPI
    13587 
    13588 > hide #!69 models
    13589 
    13590 > hide #!68 models
    13591 
    13592 > hide #!30.1 models
    13593 
    13594 > show #!30.1 models
    13595 
    13596 > hide #!30 models
    13597 
    13598 > show #!29 models
    13599 
    13600 > show #!66 models
    13601 
    13602 > show #!64 models
    13603 
    13604 > show #39 models
    13605 
    13606 > hide #!29 models
    13607 
    13608 > show #!33 models
    13609 
    13610 > hide #!33 models
    13611 
    13612 > show #!32 models
    13613 
    13614 > hide #!32 models
    13615 
    13616 > show #!33 models
    13617 
    13618 > fitmap #39 inMap #33.3
    13619 
    13620 Fit molecule CopZ1_P61924.pdb (#39) to map W20_J160_run_ct6_body003.mrc
    13621 (#33.3) using 1420 atoms 
    13622 average map value = 0.0138, steps = 80 
    13623 shifted from previous position = 0.00922 
    13624 rotated from previous position = 0.0243 degrees 
    13625 atoms outside contour = 767, contour level = 0.015167 
    13626  
    13627 Position of CopZ1_P61924.pdb (#39) relative to W20_J160_run_ct6_body003.mrc
    13628 (#33.3) coordinates: 
    13629 Matrix rotation and translation 
    13630 -0.59905768 0.35670401 0.71686272 128.55067540 
    13631 0.33940715 -0.69775395 0.63082663 127.78309606 
    13632 0.72521218 0.62120986 0.29692697 93.14263724 
    13633 Axis -0.44771433 -0.38871406 -0.80526596 
    13634 Axis point 38.57235221 41.25427436 0.00000000 
    13635 Rotation angle (degrees) 179.38464020 
    13636 Shift along axis -182.22965962 
    13637  
    13638 
    13639 > hide #39 models
    13640 
    13641 > show #39 models
    13642 
    13643 > combine #39
    13644 
    13645 > rename #71 zeta-COPI
    13646 
    13647 > show #56 models
    13648 
    13649 > hide #56 models
    13650 
    13651 > show #!55 models
    13652 
    13653 > hide #!55 models
    13654 
    13655 > show #!38 models
    13656 
    13657 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    13658 > resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
    13659 
    13660 > hide #!38 models
    13661 
    13662 > show #!50.4 models
    13663 
    13664 > hide #!50.4 models
    13665 
    13666 > show #!50.4 models
    13667 
    13668 > hide #!50.4 models
    13669 
    13670 > show #!50.4 models
    13671 
    13672 > hide #!50.4 models
    13673 
    13674 > show #50.1 models
    13675 
    13676 > show #!50.2 models
    13677 
    13678 > hide #!50.2 models
    13679 
    13680 > show #!50.3 models
    13681 
    13682 > hide #!50.3 models
    13683 
    13684 > show #!50.4 models
    13685 
    13686 > hide #!50.4 models
    13687 
    13688 > show #!50.5 models
    13689 
    13690 > hide #!50.5 models
    13691 
    13692 > show #50.6 models
    13693 
    13694 > hide #50.6 models
    13695 
    13696 > show #!50.7 models
    13697 
    13698 > hide #!50.7 models
    13699 
    13700 > show #!50.8 models
    13701 
    13702 > hide #!50.8 models
    13703 
    13704 > show #50.9 models
    13705 
    13706 > hide #50.9 models
    13707 
    13708 > show #!50.10 models
    13709 
    13710 > select add #50.10
    13711 
    13712 4143 atoms, 4205 bonds, 2 pseudobonds, 528 residues, 2 models selected 
    13713 Drag select of 33.3 W20_J160_run_ct6_body003.mrc , 4 residues 
    13714 
    13715 > select add #50.10
    13716 
    13717 4143 atoms, 4205 bonds, 2 pseudobonds, 528 residues, 4 models selected 
    13718 
    13719 > ui mousemode right "translate selected models"
    13720 
    13721 > view matrix models
    13722 > #33.3,0.99304,0.059881,0.10144,5.194,-0.064889,0.99679,0.046802,13.668,-0.098315,-0.053059,0.99374,40.329,#50.10,-0.92962,0.23756,-0.28172,353.7,-0.021762,-0.79854,-0.60155,498.49,-0.36787,-0.55308,0.74751,143.01
    13723 
    13724 > undo
    13725 
    13726 [Repeated 1 time(s)]
    13727 
    13728 > ui mousemode right select
    13729 
    13730 > select clear
    13731 
    13732 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    13733 > files/alphafold/CopG1_ Q9QZE5.pdb"
    13734 
    13735 CopG1_ Q9QZE5.pdb title: 
    13736 Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
    13737 info...] 
    13738  
    13739 Chain information for CopG1_ Q9QZE5.pdb #72 
    13740 --- 
    13741 Chain | Description | UniProt 
    13742 A | coatomer subunit γ-1 | COPG1_MOUSE 1-874 
    13743  
    13744 Computing secondary structure 
    13745 
    13746 > select add #72
    13747 
    13748 6830 atoms, 6947 bonds, 874 residues, 1 model selected 
    13749 
    13750 > ui tool show Matchmaker
    13751 
    13752 > matchmaker #72 to #50.10
    13753 
    13754 Parameters 
    13755 --- 
    13756 Chain pairing | bb 
    13757 Alignment algorithm | Needleman-Wunsch 
    13758 Similarity matrix | BLOSUM-62 
    13759 SS fraction | 0.3 
    13760 Gap open (HH/SS/other) | 18/18/6 
    13761 Gap extend | 1 
    13762 SS matrix |  |  | H | S | O 
    13763 ---|---|---|--- 
    13764 H | 6 | -9 | -6 
    13765 S |  | 6 | -6 
    13766 O |  |  | 4 
    13767 Iteration cutoff | 2 
    13768  
    13769 Matchmaker W20_C1_initial_model_no_wat_lig.pdb A9, chain A9 (#50.10) with
    13770 CopG1_ Q9QZE5.pdb, chain A (#72), sequence alignment score = 2728.3 
    13771 RMSD between 527 pruned atom pairs is 0.000 angstroms; (across all 528 pairs:
    13772 0.471) 
    13773  
    13774 
    13775 > select subtract #72
    13776 
    13777 Nothing selected 
    13778 
    13779 > hide #!64 models
    13780 
    13781 > hide #!66 models
    13782 
    13783 > hide #!67 models
    13784 
    13785 > hide #!70 models
    13786 
    13787 > hide #71 models
    13788 
    13789 > hide #39 models
    13790 
    13791 > color #72 gammav3
    13792 
    13793 > fitmap #72 inMap #33.3
    13794 
    13795 Fit molecule CopG1_ Q9QZE5.pdb (#72) to map W20_J160_run_ct6_body003.mrc
    13796 (#33.3) using 6830 atoms 
    13797 average map value = 0.008592, steps = 128 
    13798 shifted from previous position = 5.94 
    13799 rotated from previous position = 20.6 degrees 
    13800 atoms outside contour = 5149, contour level = 0.015167 
    13801  
    13802 Position of CopG1_ Q9QZE5.pdb (#72) relative to W20_J160_run_ct6_body003.mrc
    13803 (#33.3) coordinates: 
    13804 Matrix rotation and translation 
    13805 -0.21262269 0.89025762 0.40278153 115.23719127 
    13806 -0.39923844 0.29708069 -0.86738211 108.04417936 
    13807 -0.89185215 -0.34523099 0.29225897 114.80605117 
    13808 Axis 0.27475861 0.68124291 -0.67853946 
    13809 Axis point 106.74618671 0.00000000 53.93689380 
    13810 Rotation angle (degrees) 108.15818379 
    13811 Shift along axis 27.36630527 
    13812  
    13813 
    13814 > hide #!50.10 models
    13815 
    13816 > hide #50.1 models
    13817 
    13818 > hide #72 models
    13819 
    13820 > show #!41 models
    13821 
    13822 > show #40 models
    13823 
    13824 > hide #40 models
    13825 
    13826 > hide #!41 models
    13827 
    13828 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    13829 > predictions/alphafold 3
    13830 > /fold_20240724_copbdg1z1_try2/fold_20240724_copbdg1z1_try2_model_0.cif"
    13831 
    13832 Chain information for fold_20240724_copbdg1z1_try2_model_0.cif #73 
    13833 --- 
    13834 Chain | Description 
    13835 A | . 
    13836 B | . 
    13837 C | . 
    13838 D | . 
    13839  
    13840 Computing secondary structure 
    13841 
    13842 > ui tool show Matchmaker
    13843 
    13844 > matchmaker #73 to #72
    13845 
    13846 Parameters 
    13847 --- 
    13848 Chain pairing | bb 
    13849 Alignment algorithm | Needleman-Wunsch 
    13850 Similarity matrix | BLOSUM-62 
    13851 SS fraction | 0.3 
    13852 Gap open (HH/SS/other) | 18/18/6 
    13853 Gap extend | 1 
    13854 SS matrix |  |  | H | S | O 
    13855 ---|---|---|--- 
    13856 H | 6 | -9 | -6 
    13857 S |  | 6 | -6 
    13858 O |  |  | 4 
    13859 Iteration cutoff | 2 
    13860  
    13861 Matchmaker CopG1_ Q9QZE5.pdb, chain A (#72) with
    13862 fold_20240724_copbdg1z1_try2_model_0.cif, chain C (#73), sequence alignment
    13863 score = 4461 
    13864 RMSD between 219 pruned atom pairs is 1.225 angstroms; (across all 874 pairs:
    13865 21.353) 
    13866  
    13867 
    13868 > hide #!50 models
    13869 
    13870 > show #!50 models
    13871 
    13872 > hide #!33 models
    13873 
    13874 > select clear
    13875 
    13876 > select #73/B:154
    13877 
    13878 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13879 
    13880 > select up
    13881 
    13882 319 atoms, 320 bonds, 37 residues, 1 model selected 
    13883 
    13884 > select up
    13885 
    13886 4014 atoms, 4083 bonds, 511 residues, 1 model selected 
    13887 
    13888 > delete sel
    13889 
    13890 > select #73/A:242
    13891 
    13892 11 atoms, 10 bonds, 1 residue, 1 model selected 
    13893 
    13894 > select up
    13895 
    13896 49 atoms, 49 bonds, 6 residues, 1 model selected 
    13897 
    13898 > select up
    13899 
    13900 7501 atoms, 7619 bonds, 953 residues, 1 model selected 
    13901 
    13902 > delete sel
    13903 
    13904 > fitmap #73 inMap #33.3
    13905 
    13906 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#73) to map
    13907 W20_J160_run_ct6_body003.mrc (#33.3) using 8250 atoms 
    13908 average map value = 0.008274, steps = 184 
    13909 shifted from previous position = 16.4 
    13910 rotated from previous position = 27.6 degrees 
    13911 atoms outside contour = 6288, contour level = 0.015167 
    13912  
    13913 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#73) relative to
    13914 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    13915 Matrix rotation and translation 
    13916 0.89001705 -0.00769161 -0.45586235 140.75280440 
    13917 0.39379749 -0.49091643 0.77712585 125.72122596 
    13918 -0.22976767 -0.87117271 -0.43389506 123.79108229 
    13919 Axis -0.96307771 -0.13210395 0.23458445 
    13920 Axis point 0.00000000 97.90843398 46.99023466 
    13921 Rotation angle (degrees) 121.15782367 
    13922 Shift along axis -123.12469702 
    13923  
    13924 
    13925 > show #!33 models
    13926 
    13927 > show #71 models
    13928 
    13929 > hide #71 models
    13930 
    13931 > show #71 models
    13932 
    13933 > hide #71 models
    13934 
    13935 > show #71 models
    13936 
    13937 > hide #71 models
    13938 
    13939 > hide #!33 models
    13940 
    13941 > select #73/D:47
    13942 
    13943 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13944 
    13945 > select up
    13946 
    13947 128 atoms, 129 bonds, 15 residues, 1 model selected 
    13948 
    13949 > select up
    13950 
    13951 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    13952 
    13953 > delete sel
    13954 
    13955 > show #!33 models
    13956 
    13957 > fitmap #73 inMap #33.3
    13958 
    13959 Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#73) to map
    13960 W20_J160_run_ct6_body003.mrc (#33.3) using 6830 atoms 
    13961 average map value = 0.007849, steps = 80 
    13962 shifted from previous position = 1.21 
    13963 rotated from previous position = 2.15 degrees 
    13964 atoms outside contour = 5293, contour level = 0.015167 
    13965  
    13966 Position of fold_20240724_copbdg1z1_try2_model_0.cif (#73) relative to
    13967 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    13968 Matrix rotation and translation 
    13969 0.89436621 -0.03216667 -0.44617753 141.60252778 
    13970 0.36827977 -0.51322863 0.77522022 126.38957440 
    13971 -0.25392733 -0.85764892 -0.44716801 122.18980164 
    13972 Axis -0.96493218 -0.11360886 0.23664092 
    13973 Axis point 0.00000000 98.06597121 46.27860492 
    13974 Rotation angle (degrees) 122.20940815 
    13975 Shift along axis -122.08070325 
    13976  
    13977 
    13978 > show #35 models
    13979 
    13980 > close #73
    13981 
    13982 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    13983 > predictions/alphafold 3
    13984 > /fold_20240711_copi_golph3/fold_20240711_copi_golph3_model_0.cif"
    13985 
    13986 Chain information for fold_20240711_copi_golph3_model_0.cif #73 
    13987 --- 
    13988 Chain | Description 
    13989 A | . 
    13990 B C | . 
    13991 D | . 
    13992 E | . 
    13993 F | . 
    13994 G | . 
    13995 H | . 
    13996 I | . 
    13997  
    13998 
    13999 > ui tool show Matchmaker
    14000 
    14001 > matchmaker #73 to #72
    14002 
    14003 Computing secondary structure 
    14004 Parameters 
    14005 --- 
    14006 Chain pairing | bb 
    14007 Alignment algorithm | Needleman-Wunsch 
    14008 Similarity matrix | BLOSUM-62 
    14009 SS fraction | 0.3 
    14010 Gap open (HH/SS/other) | 18/18/6 
    14011 Gap extend | 1 
    14012 SS matrix |  |  | H | S | O 
    14013 ---|---|---|--- 
    14014 H | 6 | -9 | -6 
    14015 S |  | 6 | -6 
    14016 O |  |  | 4 
    14017 Iteration cutoff | 2 
    14018  
    14019 Matchmaker CopG1_ Q9QZE5.pdb, chain A (#72) with
    14020 fold_20240711_copi_golph3_model_0.cif, chain H (#73), sequence alignment score
    14021 = 3086.5 
    14022 RMSD between 216 pruned atom pairs is 1.190 angstroms; (across all 609 pairs:
    14023 15.751) 
    14024  
    14025 
    14026 > hide #35,73 atoms
    14027 
    14028 > hide #35,73 cartoons
    14029 
    14030 > show #35,73 cartoons
    14031 
    14032 > hide #35 models
    14033 
    14034 > hide #!33 models
    14035 
    14036 > select #73/C:142
    14037 
    14038 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14039 
    14040 > select up
    14041 
    14042 59 atoms, 58 bonds, 8 residues, 1 model selected 
    14043 
    14044 > select up
    14045 
    14046 1457 atoms, 1483 bonds, 181 residues, 1 model selected 
    14047 
    14048 > delete sel
    14049 
    14050 > split #73 chains
    14051 
    14052 Split fold_20240711_copi_golph3_model_0.cif (#73) into 8 models 
    14053 Chain information for fold_20240711_copi_golph3_model_0.cif A #73.1 
    14054 --- 
    14055 Chain | Description 
    14056 A | No description available 
    14057  
    14058 Chain information for fold_20240711_copi_golph3_model_0.cif B #73.2 
    14059 --- 
    14060 Chain | Description 
    14061 B | No description available 
    14062  
    14063 Chain information for fold_20240711_copi_golph3_model_0.cif D #73.3 
    14064 --- 
    14065 Chain | Description 
    14066 D | No description available 
    14067  
    14068 Chain information for fold_20240711_copi_golph3_model_0.cif E #73.4 
    14069 --- 
    14070 Chain | Description 
    14071 E | No description available 
    14072  
    14073 Chain information for fold_20240711_copi_golph3_model_0.cif F #73.5 
    14074 --- 
    14075 Chain | Description 
    14076 F | No description available 
    14077  
    14078 Chain information for fold_20240711_copi_golph3_model_0.cif G #73.6 
    14079 --- 
    14080 Chain | Description 
    14081 G | No description available 
    14082  
    14083 Chain information for fold_20240711_copi_golph3_model_0.cif H #73.7 
    14084 --- 
    14085 Chain | Description 
    14086 H | No description available 
    14087  
    14088 Chain information for fold_20240711_copi_golph3_model_0.cif I #73.8 
    14089 --- 
    14090 Chain | Description 
    14091 I | No description available 
    14092  
    14093 
    14094 > hide #73.1 models
    14095 
    14096 > show #73.1 models
    14097 
    14098 > close #73.1
    14099 
    14100 > hide #!73 models
    14101 
    14102 > show #!73 models
    14103 
    14104 > hide #73.2 models
    14105 
    14106 > show #73.2 models
    14107 
    14108 > close #73.2
    14109 
    14110 > hide #73.3 models
    14111 
    14112 > show #73.3 models
    14113 
    14114 > close #73.3
    14115 
    14116 > hide #73.4 models
    14117 
    14118 > show #73.4 models
    14119 
    14120 > hide #73.5 models
    14121 
    14122 > show #73.5 models
    14123 
    14124 > close #73.5
    14125 
    14126 > close #73.6
    14127 
    14128 > show #!33 models
    14129 
    14130 > close #73.4
    14131 
    14132 > show #!50.10 models
    14133 
    14134 > hide #!50.10 models
    14135 
    14136 > show #50.9 models
    14137 
    14138 > hide #50.9 models
    14139 
    14140 > show #50.9 models
    14141 
    14142 > hide #50.9 models
    14143 
    14144 > show #50.1 models
    14145 
    14146 > hide #50.1 models
    14147 
    14148 > show #71 models
    14149 
    14150 > close #73.8
    14151 
    14152 > combine #73.7
    14153 
    14154 > hide #73.7 models
    14155 
    14156 > hide #!73 models
    14157 
    14158 > hide #71 models
    14159 
    14160 > hide #!33 models
    14161 
    14162 > show #!33 models
    14163 
    14164 > select #74/H:609
    14165 
    14166 12 atoms, 11 bonds, 1 residue, 1 model selected 
    14167 
    14168 > select up
    14169 
    14170 227 atoms, 230 bonds, 31 residues, 1 model selected 
    14171 
    14172 > delete sel
    14173 
    14174 > select #74/H:564
    14175 
    14176 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14177 
    14178 > select up
    14179 
    14180 103 atoms, 104 bonds, 13 residues, 1 model selected 
    14181 
    14182 > select up
    14183 
    14184 4525 atoms, 4596 bonds, 578 residues, 1 model selected 
    14185 
    14186 > select clear
    14187 
    14188 > select #74/H:353
    14189 
    14190 6 atoms, 5 bonds, 1 residue, 1 model selected 
    14191 
    14192 > hide #!33 models
    14193 
    14194 Drag select of 109 residues 
    14195 
    14196 > select up
    14197 
    14198 939 atoms, 952 bonds, 119 residues, 1 model selected 
    14199 
    14200 > delete sel
    14201 
    14202 Drag select of 27 residues, 2 pseudobonds 
    14203 
    14204 > delete sel
    14205 
    14206 > fitmap #74 inMap #33.3
    14207 
    14208 Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#74) to map
    14209 W20_J160_run_ct6_body003.mrc (#33.3) using 3367 atoms 
    14210 average map value = 0.01504, steps = 104 
    14211 shifted from previous position = 1.23 
    14212 rotated from previous position = 8.87 degrees 
    14213 atoms outside contour = 1844, contour level = 0.015167 
    14214  
    14215 Position of copy of fold_20240711_copi_golph3_model_0.cif H (#74) relative to
    14216 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    14217 Matrix rotation and translation 
    14218 -0.99039171 0.12782412 -0.05277549 148.12639654 
    14219 0.13807487 0.93531006 -0.32577664 131.22576391 
    14220 0.00771933 -0.32993345 -0.94397263 135.30516062 
    14221 Axis -0.06759286 -0.98369069 0.16668480 
    14222 Axis point 68.34524384 0.00000000 79.86683576 
    14223 Rotation angle (degrees) 178.23793985 
    14224 Shift along axis -116.54453594 
    14225  
    14226 
    14227 > show #!33 models
    14228 
    14229 > hide #!33 models
    14230 
    14231 Drag select of 37 residues 
    14232 
    14233 > select up
    14234 
    14235 343 atoms, 348 bonds, 42 residues, 1 model selected 
    14236 
    14237 > delete sel
    14238 
    14239 > fitmap #74 inMap #33.3
    14240 
    14241 Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#74) to map
    14242 W20_J160_run_ct6_body003.mrc (#33.3) using 3024 atoms 
    14243 average map value = 0.01541, steps = 84 
    14244 shifted from previous position = 0.341 
    14245 rotated from previous position = 2.61 degrees 
    14246 atoms outside contour = 1604, contour level = 0.015167 
    14247  
    14248 Position of copy of fold_20240711_copi_golph3_model_0.cif H (#74) relative to
    14249 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    14250 Matrix rotation and translation 
    14251 -0.99016649 0.13961225 -0.00887325 145.93626541 
    14252 0.13499683 0.93694534 -0.32234963 131.14942473 
    14253 -0.03669021 -0.32037766 -0.94657909 136.23220850 
    14254 Axis 0.06976430 0.98410929 -0.16328456 
    14255 Axis point 68.87722497 0.00000000 78.50166031 
    14256 Rotation angle (degrees) 179.19020792 
    14257 Shift along axis 117.00189352 
    14258  
    14259 
    14260 > show #!33 models
    14261 
    14262 > hide #!33 models
    14263 
    14264 Drag select of 7 residues 
    14265 
    14266 > select up
    14267 
    14268 130 atoms, 130 bonds, 17 residues, 1 model selected 
    14269 Drag select of 5 residues 
    14270 
    14271 > select down
    14272 
    14273 44 atoms, 5 residues, 1 model selected 
    14274 
    14275 > select up
    14276 
    14277 142 atoms, 143 bonds, 18 residues, 1 model selected 
    14278 
    14279 > delete sel
    14280 
    14281 > fitmap #74 inMap #33.3
    14282 
    14283 Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#74) to map
    14284 W20_J160_run_ct6_body003.mrc (#33.3) using 2882 atoms 
    14285 average map value = 0.01543, steps = 60 
    14286 shifted from previous position = 0.199 
    14287 rotated from previous position = 0.43 degrees 
    14288 atoms outside contour = 1520, contour level = 0.015167 
    14289  
    14290 Position of copy of fold_20240711_copi_golph3_model_0.cif H (#74) relative to
    14291 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    14292 Matrix rotation and translation 
    14293 -0.99012237 0.14014794 -0.00403046 145.70159327 
    14294 0.13418777 0.93889954 -0.31695629 130.92767817 
    14295 -0.04063657 -0.31436635 -0.94843158 136.20145596 
    14296 Axis 0.06966230 0.98460506 -0.16031230 
    14297 Axis point 68.95076353 0.00000000 78.11025829 
    14298 Rotation angle (degrees) 178.93485378 
    14299 Shift along axis 117.22719466 
    14300  
    14301 
    14302 > show #!33 models
    14303 
    14304 > show #!50.10 models
    14305 
    14306 > hide #!50 models
    14307 
    14308 > show #!50 models
    14309 
    14310 > hide #!33 models
    14311 
    14312 > combine #50.10
    14313 
    14314 > hide #!50.10 models
    14315 
    14316 > hide #!74 models
    14317 
    14318 > show #!74 models
    14319 
    14320 > hide #!74 models
    14321 
    14322 Drag select of 113 residues 
    14323 
    14324 > select up
    14325 
    14326 1028 atoms, 1042 bonds, 130 residues, 1 model selected 
    14327 
    14328 > delete sel
    14329 
    14330 > fitmap #75 inMap #33.3
    14331 
    14332 Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A9 (#75) to map
    14333 W20_J160_run_ct6_body003.mrc (#33.3) using 3115 atoms 
    14334 average map value = 0.01389, steps = 132 
    14335 shifted from previous position = 1.68 
    14336 rotated from previous position = 15.8 degrees 
    14337 atoms outside contour = 1847, contour level = 0.015167 
    14338  
    14339 Position of copy of W20_C1_initial_model_no_wat_lig.pdb A9 (#75) relative to
    14340 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    14341 Matrix rotation and translation 
    14342 -0.96975860 0.09758407 -0.22370877 404.94223752 
    14343 0.05855198 -0.79680528 -0.60139256 482.79146988 
    14344 -0.23693866 -0.59630420 0.76699503 131.62487193 
    14345 Axis 0.12253380 0.31859145 -0.93993880 
    14346 Axis point 213.57688590 261.52023160 0.00000000 
    14347 Rotation angle (degrees) 178.81027642 
    14348 Shift along axis 79.71302152 
    14349  
    14350 
    14351 > show #!33 models
    14352 
    14353 > open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
    14354 > paper/Final maps and model/Model_files/20250328_COPI_GOLPH3_model_v2.cif"
    14355 
    14356 Chain information for 20250328_COPI_GOLPH3_model_v2.cif #76 
    14357 --- 
    14358 Chain | Description 
    14359 A | No description available 
    14360 B | No description available 
    14361 D | No description available 
    14362 E | No description available 
    14363 F | No description available 
    14364 G | No description available 
    14365 H | No description available 
    14366 I | No description available 
    14367 J | No description available 
    14368 K | No description available 
    14369 L | No description available 
    14370 M | No description available 
    14371 N | No description available 
    14372 O | No description available 
    14373 P | No description available 
    14374 R S T | No description available 
    14375  
    14376 
    14377 > hide #76#!75 atoms
    14378 
    14379 > show #76#!75 cartoons
    14380 
    14381 > ui tool show Matchmaker
    14382 
    14383 > matchmaker #76 to #66
    14384 
    14385 Parameters 
    14386 --- 
    14387 Chain pairing | bb 
    14388 Alignment algorithm | Needleman-Wunsch 
    14389 Similarity matrix | BLOSUM-62 
    14390 SS fraction | 0.3 
    14391 Gap open (HH/SS/other) | 18/18/6 
    14392 Gap extend | 1 
    14393 SS matrix |  |  | H | S | O 
    14394 ---|---|---|--- 
    14395 H | 6 | -9 | -6 
    14396 S |  | 6 | -6 
    14397 O |  |  | 4 
    14398 Iteration cutoff | 2 
    14399  
    14400 Matchmaker beta-COPI, chain B (#66) with 20250328_COPI_GOLPH3_model_v2.cif,
    14401 chain J (#76), sequence alignment score = 1591 
    14402 RMSD between 180 pruned atom pairs is 0.463 angstroms; (across all 289 pairs:
    14403 3.827) 
    14404  
    14405 
    14406 > show #!66 models
    14407 
    14408 > hide #!66 models
    14409 
    14410 > show #!66 models
    14411 
    14412 > hide #76 models
    14413 
    14414 > show #76 models
    14415 
    14416 > hide #76 models
    14417 
    14418 > show #76 models
    14419 
    14420 > select add #76
    14421 
    14422 17013 atoms, 16995 bonds, 4252 residues, 1 model selected 
    14423 
    14424 > select subtract #76
    14425 
    14426 Nothing selected 
    14427 
    14428 > hide #76 models
    14429 
    14430 > hide #!75 models
    14431 
    14432 > show #76 models
    14433 
    14434 > select add #76
    14435 
    14436 17013 atoms, 16995 bonds, 4252 residues, 1 model selected 
    14437 
    14438 > ui mousemode right "translate selected models"
    14439 
    14440 > view matrix models
    14441 > #76,-0.94328,0.33002,0.036298,249.11,-0.21754,-0.53176,-0.81848,562.73,-0.25081,-0.77995,0.57339,257.94
    14442 
    14443 > fitmap #76 inMap #33.1
    14444 
    14445 Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
    14446 W20_J160_run_ct6_body001.mrc (#33.1) using 17013 atoms 
    14447 average map value = 0.005784, steps = 248 
    14448 shifted from previous position = 23.7 
    14449 rotated from previous position = 25.1 degrees 
    14450 atoms outside contour = 13846, contour level = 0.014811 
    14451  
    14452 Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
    14453 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    14454 Matrix rotation and translation 
    14455 -0.95309148 0.15118983 -0.26221799 379.07308450 
    14456 0.09927921 -0.66223841 -0.74268696 486.62957335 
    14457 -0.28593754 -0.73388141 0.61616378 222.17176604 
    14458 Axis 0.15248160 0.41074018 -0.89891149 
    14459 Axis point 212.09731096 291.09961203 0.00000000 
    14460 Rotation angle (degrees) 178.34540300 
    14461 Shift along axis 57.96723338 
    14462  
    14463 
    14464 > select subtract #76
    14465 
    14466 Nothing selected 
    14467 
    14468 > ui tool show Matchmaker
    14469 
    14470 > matchmaker #76 to #66
    14471 
    14472 Parameters 
    14473 --- 
    14474 Chain pairing | bb 
    14475 Alignment algorithm | Needleman-Wunsch 
    14476 Similarity matrix | BLOSUM-62 
    14477 SS fraction | 0.3 
    14478 Gap open (HH/SS/other) | 18/18/6 
    14479 Gap extend | 1 
    14480 SS matrix |  |  | H | S | O 
    14481 ---|---|---|--- 
    14482 H | 6 | -9 | -6 
    14483 S |  | 6 | -6 
    14484 O |  |  | 4 
    14485 Iteration cutoff | 2 
    14486  
    14487 Matchmaker beta-COPI, chain B (#66) with 20250328_COPI_GOLPH3_model_v2.cif,
    14488 chain J (#76), sequence alignment score = 1591 
    14489 RMSD between 180 pruned atom pairs is 0.463 angstroms; (across all 289 pairs:
    14490 3.827) 
    14491  
    14492 
    14493 > undo
    14494 
    14495 > view matrix models
    14496 > #76,-0.94328,0.33002,0.036298,269.75,-0.21754,-0.53176,-0.81848,549.29,-0.25081,-0.77995,0.57339,234.77
    14497 
    14498 > select subtract #76
    14499 
    14500 Nothing selected 
    14501 
    14502 > select add #76
    14503 
    14504 17013 atoms, 16995 bonds, 4252 residues, 1 model selected 
    14505 
    14506 > view matrix models
    14507 > #76,-0.94328,0.33002,0.036298,244.4,-0.21754,-0.53176,-0.81848,557.07,-0.25081,-0.77995,0.57339,249.76
    14508 
    14509 > show #!51 models
    14510 
    14511 > hide #!51 models
    14512 
    14513 > show #!52 models
    14514 
    14515 > hide #!52 models
    14516 
    14517 > hide #!66 models
    14518 
    14519 > show #!52 models
    14520 
    14521 > hide #!52 models
    14522 
    14523 > show #!51 models
    14524 
    14525 > hide #!51 models
    14526 
    14527 > ui tool show Matchmaker
    14528 
    14529 > matchmaker #76 to #51
    14530 
    14531 Parameters 
    14532 --- 
    14533 Chain pairing | bb 
    14534 Alignment algorithm | Needleman-Wunsch 
    14535 Similarity matrix | BLOSUM-62 
    14536 SS fraction | 0.3 
    14537 Gap open (HH/SS/other) | 18/18/6 
    14538 Gap extend | 1 
    14539 SS matrix |  |  | H | S | O 
    14540 ---|---|---|--- 
    14541 H | 6 | -9 | -6 
    14542 S |  | 6 | -6 
    14543 O |  |  | 4 
    14544 Iteration cutoff | 2 
    14545  
    14546 Matchmaker copy of B_fixed_model_2_B.pdb, chain B (#51) with
    14547 20250328_COPI_GOLPH3_model_v2.cif, chain J (#76), sequence alignment score =
    14548 1591 
    14549 RMSD between 180 pruned atom pairs is 0.463 angstroms; (across all 289 pairs:
    14550 3.827) 
    14551  
    14552 
    14553 > view matrix models
    14554 > #76,-0.94328,0.33002,0.036298,250.65,-0.21754,-0.53176,-0.81848,564.67,-0.25081,-0.77995,0.57339,248.23
    14555 
    14556 > fitmap #76 inMap #33.1
    14557 
    14558 Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
    14559 W20_J160_run_ct6_body001.mrc (#33.1) using 17013 atoms 
    14560 average map value = 0.005784, steps = 256 
    14561 shifted from previous position = 20.4 
    14562 rotated from previous position = 25.2 degrees 
    14563 atoms outside contour = 13847, contour level = 0.014811 
    14564  
    14565 Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
    14566 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    14567 Matrix rotation and translation 
    14568 -0.95306184 0.15114897 -0.26234924 379.12122640 
    14569 0.09940762 -0.66223994 -0.74266842 486.60244827 
    14570 -0.28599171 -0.73388844 0.61613026 222.19665492 
    14571 Axis 0.15253453 0.41074061 -0.89890231 
    14572 Axis point 212.11797169 291.10158267 0.00000000 
    14573 Rotation angle (degrees) 178.35078282 
    14574 Shift along axis 57.96337940 
    14575  
    14576 
    14577 > select subtract #76
    14578 
    14579 Nothing selected 
    14580 
    14581 > hide #!50 models
    14582 
    14583 > show #!50 models
    14584 
    14585 > hide #!33 models
    14586 
    14587 > ui mousemode right select
    14588 
    14589 > select clear
    14590 
    14591 > select #76/F:486
    14592 
    14593 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14594 
    14595 > select up
    14596 
    14597 24 atoms, 23 bonds, 6 residues, 1 model selected 
    14598 
    14599 > select up
    14600 
    14601 2344 atoms, 2343 bonds, 586 residues, 1 model selected 
    14602 
    14603 > select up
    14604 
    14605 17013 atoms, 16995 bonds, 4252 residues, 1 model selected 
    14606 
    14607 > select down
    14608 
    14609 2344 atoms, 2343 bonds, 586 residues, 1 model selected 
    14610 
    14611 > delete sel
    14612 
    14613 > select #76/L:158
    14614 
    14615 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14616 
    14617 > select clear
    14618 
    14619 Drag select of 234 residues 
    14620 
    14621 > select clear
    14622 
    14623 Drag select of 67 residues 
    14624 
    14625 > select up
    14626 
    14627 544 atoms, 538 bonds, 136 residues, 1 model selected 
    14628 
    14629 > select up
    14630 
    14631 1940 atoms, 1938 bonds, 485 residues, 1 model selected 
    14632 
    14633 > delete sel
    14634 
    14635 > select #76/T:111
    14636 
    14637 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14638 
    14639 > select up
    14640 
    14641 48 atoms, 47 bonds, 12 residues, 1 model selected 
    14642 
    14643 > select up
    14644 
    14645 669 atoms, 668 bonds, 167 residues, 1 model selected 
    14646 
    14647 > delete sel
    14648 
    14649 > select clear
    14650 
    14651 [Repeated 1 time(s)]
    14652 
    14653 > select #76/L:243
    14654 
    14655 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14656 
    14657 > select up
    14658 
    14659 48 atoms, 47 bonds, 12 residues, 1 model selected 
    14660 
    14661 > select up
    14662 
    14663 804 atoms, 803 bonds, 201 residues, 1 model selected 
    14664 
    14665 > delete sel
    14666 
    14667 > select #76/K:689
    14668 
    14669 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14670 
    14671 > select up
    14672 
    14673 40 atoms, 39 bonds, 10 residues, 1 model selected 
    14674 
    14675 > select up
    14676 
    14677 204 atoms, 203 bonds, 51 residues, 1 model selected 
    14678 
    14679 > delete sel
    14680 
    14681 > select clear
    14682 
    14683 > select #76/J:133
    14684 
    14685 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14686 Drag select of 60 residues 
    14687 
    14688 > select clear
    14689 
    14690 Drag select of 34 residues 
    14691 
    14692 > select up
    14693 
    14694 204 atoms, 200 bonds, 51 residues, 1 model selected 
    14695 
    14696 > select up
    14697 
    14698 1244 atoms, 1243 bonds, 311 residues, 1 model selected 
    14699 
    14700 > delete sel
    14701 
    14702 > select clear
    14703 
    14704 > select #76/S:91
    14705 
    14706 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14707 
    14708 > select up
    14709 
    14710 28 atoms, 27 bonds, 7 residues, 1 model selected 
    14711 
    14712 > select up
    14713 
    14714 669 atoms, 668 bonds, 167 residues, 1 model selected 
    14715 
    14716 > delete sel
    14717 
    14718 > select #76/R:138
    14719 
    14720 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14721 
    14722 > select up
    14723 
    14724 32 atoms, 31 bonds, 8 residues, 1 model selected 
    14725 
    14726 > select up
    14727 
    14728 669 atoms, 668 bonds, 167 residues, 1 model selected 
    14729 
    14730 > delete sel
    14731 
    14732 > select clear
    14733 
    14734 > select #76/H:729
    14735 
    14736 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14737 
    14738 > select #76/H:727
    14739 
    14740 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14741 
    14742 > select clear
    14743 
    14744 Drag select of 12 residues 
    14745 
    14746 > select clear
    14747 
    14748 Drag select of 63 residues 
    14749 
    14750 > select up
    14751 
    14752 432 atoms, 427 bonds, 108 residues, 1 model selected 
    14753 
    14754 > select up
    14755 
    14756 3337 atoms, 3335 bonds, 834 residues, 1 model selected 
    14757 
    14758 > delete sel
    14759 
    14760 Drag select of 61 residues 
    14761 
    14762 > select up
    14763 
    14764 509 atoms, 503 bonds, 127 residues, 1 model selected 
    14765 
    14766 > select up
    14767 
    14768 977 atoms, 976 bonds, 244 residues, 1 model selected 
    14769 
    14770 > delete sel
    14771 
    14772 > show #!33 models
    14773 
    14774 > hide #76 models
    14775 
    14776 > show #76 models
    14777 
    14778 > show #!75 models
    14779 
    14780 > hide #!75 models
    14781 
    14782 > show #!74 models
    14783 
    14784 > hide #76 models
    14785 
    14786 > show #76 models
    14787 
    14788 > hide #!74 models
    14789 
    14790 > show #!74 models
    14791 
    14792 > hide #76 models
    14793 
    14794 > hide #!50 models
    14795 
    14796 > show #76 models
    14797 
    14798 > hide #!33 models
    14799 
    14800 > select clear
    14801 
    14802 > select #76/I:400
    14803 
    14804 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14805 
    14806 > select up
    14807 
    14808 64 atoms, 63 bonds, 16 residues, 1 model selected 
    14809 
    14810 > select up
    14811 
    14812 1252 atoms, 1251 bonds, 313 residues, 1 model selected 
    14813 
    14814 > delete sel
    14815 
    14816 > show #50.9 models
    14817 
    14818 > hide #50.9 models
    14819 
    14820 > show #!50.10 models
    14821 
    14822 > hide #!50.10 models
    14823 
    14824 > show #!50.10 models
    14825 
    14826 > hide #!50.10 models
    14827 
    14828 > show #50.9 models
    14829 
    14830 > hide #50.9 models
    14831 
    14832 > show #!50.8 models
    14833 
    14834 > hide #!50.8 models
    14835 
    14836 > show #72 models
    14837 
    14838 > hide #72 models
    14839 
    14840 > show #72 models
    14841 
    14842 > hide #72 models
    14843 
    14844 > show #!75 models
    14845 
    14846 > hide #!75 models
    14847 
    14848 > hide #76 models
    14849 
    14850 > show #76 models
    14851 
    14852 > hide #!74 models
    14853 
    14854 > show #!75 models
    14855 
    14856 > hide #!75 models
    14857 
    14858 > select #76/A:21
    14859 
    14860 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14861 
    14862 > select up
    14863 
    14864 36 atoms, 35 bonds, 9 residues, 1 model selected 
    14865 
    14866 > select up
    14867 
    14868 64 atoms, 63 bonds, 16 residues, 1 model selected 
    14869 
    14870 > delete sel
    14871 
    14872 Drag select of 15 residues 
    14873 
    14874 > select up
    14875 
    14876 116 atoms, 112 bonds, 29 residues, 1 model selected 
    14877 
    14878 > select up
    14879 
    14880 580 atoms, 579 bonds, 145 residues, 1 model selected 
    14881 
    14882 > delete sel
    14883 
    14884 > show #!75 models
    14885 
    14886 > hide #!75 models
    14887 
    14888 > show #!74 models
    14889 
    14890 > show #!33 models
    14891 
    14892 > select clear
    14893 
    14894 > select #76/O:107
    14895 
    14896 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14897 
    14898 > select up
    14899 
    14900 48 atoms, 47 bonds, 12 residues, 1 model selected 
    14901 
    14902 > select up
    14903 
    14904 1132 atoms, 1131 bonds, 283 residues, 1 model selected 
    14905 
    14906 > delete sel
    14907 
    14908 > hide #!33 models
    14909 
    14910 > hide #!74 models
    14911 
    14912 > show #!74 models
    14913 
    14914 > hide #76 models
    14915 
    14916 > hide #!74 models
    14917 
    14918 > show #76 models
    14919 
    14920 > select #76/M:371
    14921 
    14922 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14923 Drag select of 16 residues 
    14924 
    14925 > select up
    14926 
    14927 144 atoms, 142 bonds, 36 residues, 1 model selected 
    14928 Drag select of 48 residues 
    14929 
    14930 > select up
    14931 
    14932 216 atoms, 215 bonds, 54 residues, 1 model selected 
    14933 
    14934 > delete sel
    14935 
    14936 > show #!74 models
    14937 
    14938 > show #!33 models
    14939 
    14940 > show #!66 models
    14941 
    14942 > hide #76 models
    14943 
    14944 > hide #!66 models
    14945 
    14946 > show #76 models
    14947 
    14948 > hide #!33 models
    14949 
    14950 > show #!33 models
    14951 
    14952 > hide #!33 models
    14953 
    14954 > hide #76 models
    14955 
    14956 > show #!33 models
    14957 
    14958 > show #76 models
    14959 
    14960 > hide #!33 models
    14961 
    14962 > hide #!74 models
    14963 
    14964 > select #76/M:354
    14965 
    14966 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14967 
    14968 > select up
    14969 
    14970 12 atoms, 11 bonds, 3 residues, 1 model selected 
    14971 
    14972 > select up
    14973 
    14974 380 atoms, 379 bonds, 95 residues, 1 model selected 
    14975 
    14976 > select #76/M:363
    14977 
    14978 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14979 Drag select of 8 residues 
    14980 
    14981 > select up
    14982 
    14983 52 atoms, 51 bonds, 13 residues, 1 model selected 
    14984 
    14985 > delete sel
    14986 
    14987 Drag select of 4 residues 
    14988 
    14989 > select clear
    14990 
    14991 Drag select of 5 residues 
    14992 
    14993 > delete sel
    14994 
    14995 > show #!74 models
    14996 
    14997 > show #!33 models
    14998 
    14999 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    15000 > resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments_v2.cxs"
    15001 
    15002 [Repeated 1 time(s)]
    15003 
    15004 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    15005 > resources/Processing/W20_MM_cyto_COPI/20250705_W20_COPI_cyto_alignments.cxs"
    15006 
    15007 ——— End of log from Sat Jul 5 20:47:49 2025 ———
    15008 
    15009 > view name session-start
    15010 
    15011 opened ChimeraX session 
    15012 
    15013 > open
    15014 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_overall_best_superposed_predicted_models.pdb
    15015 
    15016 Chain information for
    15017 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb #77 
    15018 --- 
    15019 Chain | Description 
    15020 A | No description available 
    15021  
    15022 
    15023 > open
    15024 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_overall_best.pdb
    15025 
    15026 Chain information for PredictAndBuild_7_overall_best.pdb #78 
    15027 --- 
    15028 Chain | Description 
    15029 A | No description available 
    15030  
    15031 
    15032 > open
    15033 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb
    15034 
    15035 Chain information for
    15036 PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb #79 
    15037 --- 
    15038 Chain | Description 
    15039 A | No description available 
    15040  
    15041 
    15042 > open
    15043 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb
    15044 
    15045 Chain information for
    15046 PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb #80 
    15047 --- 
    15048 Chain | Description 
    15049 A | No description available 
    15050  
    15051 Computing secondary structure 
    15052 [Repeated 3 time(s)]
    15053 
    15054 > ui tool show Matchmaker
    15055 
    15056 > hide #!74 models
    15057 
    15058 > show #!74 models
    15059 
    15060 > hide #!74 models
    15061 
    15062 > show #!74 models
    15063 
    15064 > matchmaker #78-80#!77 to #74
    15065 
    15066 Parameters 
    15067 --- 
    15068 Chain pairing | bb 
    15069 Alignment algorithm | Needleman-Wunsch 
    15070 Similarity matrix | BLOSUM-62 
    15071 SS fraction | 0.3 
    15072 Gap open (HH/SS/other) | 18/18/6 
    15073 Gap extend | 1 
    15074 SS matrix |  |  | H | S | O 
    15075 ---|---|---|--- 
    15076 H | 6 | -9 | -6 
    15077 S |  | 6 | -6 
    15078 O |  |  | 4 
    15079 Iteration cutoff | 2 
    15080  
    15081 Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
    15082 PredictAndBuild_7_overall_best.pdb, chain A (#78), sequence alignment score =
    15083 2265.6 
    15084 RMSD between 256 pruned atom pairs is 1.119 angstroms; (across all 355 pairs:
    15085 2.263) 
    15086  
    15087 Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
    15088 PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb, chain A (#79),
    15089 sequence alignment score = 2735.5 
    15090 RMSD between 235 pruned atom pairs is 0.805 angstroms; (across all 372 pairs:
    15091 5.897) 
    15092  
    15093 Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
    15094 PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#80),
    15095 sequence alignment score = 2729.5 
    15096 RMSD between 327 pruned atom pairs is 0.888 angstroms; (across all 372 pairs:
    15097 4.838) 
    15098  
    15099 Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
    15100 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb, chain A (#77),
    15101 sequence alignment score = 2526.8 
    15102 RMSD between 255 pruned atom pairs is 0.833 angstroms; (across all 351 pairs:
    15103 2.256) 
    15104  
    15105 
    15106 > hide #!74 models
    15107 
    15108 > hide #76 models
    15109 
    15110 > hide #79 models
    15111 
    15112 > hide #80 models
    15113 
    15114 > hide #78 models
    15115 
    15116 > show #76 models
    15117 
    15118 > hide #76 models
    15119 
    15120 > show #76 models
    15121 
    15122 > hide #76 models
    15123 
    15124 > show #!74 models
    15125 
    15126 > hide #!74 models
    15127 
    15128 > show #!74 models
    15129 
    15130 > hide #!33 models
    15131 
    15132 > show #!33 models
    15133 
    15134 > show #!64 models
    15135 
    15136 > show #!66 models
    15137 
    15138 > color #77 gammav3
    15139 
    15140 > hide #!74 models
    15141 
    15142 > show #76 models
    15143 
    15144 > hide #76 models
    15145 
    15146 > show #76 models
    15147 
    15148 > hide #!77 models
    15149 
    15150 > show #!77 models
    15151 
    15152 > hide #!77 models
    15153 
    15154 > show #!77 models
    15155 
    15156 > hide #!77 models
    15157 
    15158 > show #!77 models
    15159 
    15160 > hide #!33 models
    15161 
    15162 > hide #!64 models
    15163 
    15164 > ui mousemode right select
    15165 
    15166 Drag select of 31 residues 
    15167 
    15168 > select up
    15169 
    15170 390 atoms, 396 bonds, 49 residues, 1 model selected 
    15171 
    15172 > select up
    15173 
    15174 2085 atoms, 2126 bonds, 265 residues, 1 model selected 
    15175 
    15176 > select down
    15177 
    15178 390 atoms, 396 bonds, 49 residues, 1 model selected 
    15179 
    15180 > select up
    15181 
    15182 2085 atoms, 2126 bonds, 265 residues, 1 model selected 
    15183 
    15184 > show #!33 models
    15185 
    15186 > delete sel
    15187 
    15188 > hide #!33 models
    15189 
    15190 > hide #!66 models
    15191 
    15192 > show #78 models
    15193 
    15194 > hide #78 models
    15195 
    15196 > combine #77
    15197 
    15198 [Repeated 1 time(s)]
    15199 
    15200 > hide #!77 models
    15201 
    15202 > hide #!82 models
    15203 
    15204 > hide #76 models
    15205 
    15206 > show #76 models
    15207 
    15208 > show #78 models
    15209 
    15210 > hide #!81 models
    15211 
    15212 > show #!82 models
    15213 
    15214 > hide #!82 models
    15215 
    15216 > show #80 models
    15217 
    15218 > hide #80 models
    15219 
    15220 > hide #78 models
    15221 
    15222 > show #78 models
    15223 
    15224 > hide #78 models
    15225 
    15226 > show #79 models
    15227 
    15228 > show #78 models
    15229 
    15230 > hide #78 models
    15231 
    15232 > hide #79 models
    15233 
    15234 > show #!81 models
    15235 
    15236 Drag select of 111 residues 
    15237 
    15238 > select up
    15239 
    15240 1038 atoms, 1052 bonds, 134 residues, 1 model selected 
    15241 
    15242 > delete sel
    15243 
    15244 Drag select of 57 residues, 2 pseudobonds 
    15245 
    15246 > select clear
    15247 
    15248 Drag select of 53 residues, 2 pseudobonds 
    15249 
    15250 > delete sel
    15251 
    15252 Drag select of 69 residues, 3 pseudobonds 
    15253 
    15254 > select up
    15255 
    15256 582 atoms, 590 bonds, 3 pseudobonds, 73 residues, 2 models selected 
    15257 
    15258 > delete sel
    15259 
    15260 > fitmap #81 inMap 33.3
    15261 
    15262 Invalid "inMap" argument: invalid density map specifier 
    15263 
    15264 > fitmap #81 inMap #33.3
    15265 
    15266 Fit molecule copy of
    15267 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
    15268 W20_J160_run_ct6_body003.mrc (#33.3) using 2348 atoms 
    15269 average map value = 0.0134, steps = 120 
    15270 shifted from previous position = 3.48 
    15271 rotated from previous position = 4.21 degrees 
    15272 atoms outside contour = 1408, contour level = 0.015167 
    15273  
    15274 Position of copy of
    15275 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
    15276 to W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    15277 Matrix rotation and translation 
    15278 -0.20129859 -0.97948015 -0.00987448 314.24082722 
    15279 -0.86511694 0.17304913 0.47077242 170.18293950 
    15280 -0.45940347 0.10330841 -0.88219942 322.78012223 
    15281 Axis -0.62096341 0.75964188 0.19325802 
    15282 Axis point 258.89532999 0.00000000 108.65698241 
    15283 Rotation angle (degrees) 162.78955563 
    15284 Shift along axis -3.47411885 
    15285  
    15286 
    15287 > show #!33 models
    15288 
    15289 > fitmap #81 inMap #33.1
    15290 
    15291 Fit molecule copy of
    15292 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
    15293 W20_J160_run_ct6_body001.mrc (#33.1) using 2348 atoms 
    15294 average map value = 0.01071, steps = 112 
    15295 shifted from previous position = 3.4 
    15296 rotated from previous position = 15.1 degrees 
    15297 atoms outside contour = 1585, contour level = 0.014811 
    15298  
    15299 Position of copy of
    15300 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
    15301 to W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    15302 Matrix rotation and translation 
    15303 -0.22739783 -0.93674263 -0.26608921 334.89658150 
    15304 -0.70727752 -0.02894807 0.70634306 146.59781389 
    15305 -0.66936442 0.34881979 -0.65595428 290.22146917 
    15306 Axis -0.61036394 0.68847171 0.39174298 
    15307 Axis point 263.55345573 -0.00000000 66.31084802 
    15308 Rotation angle (degrees) 162.96971650 
    15309 Shift along axis 10.21187265 
    15310  
    15311 
    15312 > hide #!33 models
    15313 
    15314 > select add #81
    15315 
    15316 2348 atoms, 2383 bonds, 301 residues, 1 model selected 
    15317 Drag select of 14 residues 
    15318 
    15319 > select add #81
    15320 
    15321 2384 atoms, 2383 bonds, 310 residues, 2 models selected 
    15322 
    15323 > select subtract #81
    15324 
    15325 36 atoms, 9 residues, 1 model selected 
    15326 
    15327 > select add #81
    15328 
    15329 2384 atoms, 2383 bonds, 310 residues, 2 models selected 
    15330 
    15331 > ui mousemode right "translate selected models"
    15332 
    15333 > view matrix models
    15334 > #76,-0.93321,0.21477,-0.28809,372.34,1.5257e-05,-0.80171,-0.59771,509.2,-0.35934,-0.5578,0.74816,166.22,#81,-0.16626,-0.95754,-0.23551,330.74,-0.84489,0.015188,0.53472,191.15,-0.50844,0.28789,-0.81155,305.14
    15335 
    15336 > view matrix models
    15337 > #76,-0.93321,0.21477,-0.28809,369.46,1.5257e-05,-0.80171,-0.59771,509.45,-0.35934,-0.5578,0.74816,167.85,#81,-0.16626,-0.95754,-0.23551,327.86,-0.84489,0.015188,0.53472,191.4,-0.50844,0.28789,-0.81155,306.78
    15338 
    15339 > view matrix models
    15340 > #76,-0.93321,0.21477,-0.28809,362.81,1.5257e-05,-0.80171,-0.59771,510.16,-0.35934,-0.5578,0.74816,162.77,#81,-0.16626,-0.95754,-0.23551,321.21,-0.84489,0.015188,0.53472,192.11,-0.50844,0.28789,-0.81155,301.69
    15341 
    15342 > select add #76
    15343 
    15344 3188 atoms, 3221 bonds, 511 residues, 2 models selected 
    15345 
    15346 > show #!33 models
    15347 
    15348 > view matrix models
    15349 > #76,-0.93321,0.21477,-0.28809,370.55,1.5257e-05,-0.80171,-0.59771,509.34,-0.35934,-0.5578,0.74816,168.09,#81,-0.16626,-0.95754,-0.23551,328.95,-0.84489,0.015188,0.53472,191.29,-0.50844,0.28789,-0.81155,307.01
    15350 
    15351 > select subtract #81
    15352 
    15353 840 atoms, 838 bonds, 210 residues, 1 model selected 
    15354 
    15355 > fitmap #76 inMap #33.1
    15356 
    15357 Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
    15358 W20_J160_run_ct6_body001.mrc (#33.1) using 840 atoms 
    15359 average map value = 0.02202, steps = 60 
    15360 shifted from previous position = 2.45 
    15361 rotated from previous position = 5.43 degrees 
    15362 atoms outside contour = 170, contour level = 0.014811 
    15363  
    15364 Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
    15365 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    15366 Matrix rotation and translation 
    15367 -0.96070020 0.05782811 -0.27149776 408.93422016 
    15368 0.16204598 -0.67727713 -0.71766064 466.60813032 
    15369 -0.22538019 -0.73345184 0.64128946 199.29795302 
    15370 Axis -0.13724964 -0.40083218 0.90581239 
    15371 Axis point 212.55034942 283.76140105 0.00000000 
    15372 Rotation angle (degrees) 176.70210838 
    15373 Shift along axis -62.63107629 
    15374  
    15375 
    15376 > fitmap #81 inMap #33.1
    15377 
    15378 Fit molecule copy of
    15379 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
    15380 W20_J160_run_ct6_body001.mrc (#33.1) using 2348 atoms 
    15381 average map value = 0.01071, steps = 56 
    15382 shifted from previous position = 1.86 
    15383 rotated from previous position = 0.0322 degrees 
    15384 atoms outside contour = 1584, contour level = 0.014811 
    15385  
    15386 Position of copy of
    15387 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
    15388 to W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    15389 Matrix rotation and translation 
    15390 -0.22745563 -0.93688214 -0.26554811 334.85796779 
    15391 -0.70718029 -0.02854799 0.70645669 146.50571825 
    15392 -0.66944752 0.34847794 -0.65605118 290.29252721 
    15393 Axis -0.61030750 0.68859628 0.39161196 
    15394 Axis point 263.52285147 0.00000000 66.35287841 
    15395 Rotation angle (degrees) 162.94573059 
    15396 Shift along axis 10.19898967 
    15397  
    15398 
    15399 > hide #!81 models
    15400 
    15401 > hide #76 models
    15402 
    15403 > show #!81 models
    15404 
    15405 > hide #!33 models
    15406 
    15407 > view matrix models
    15408 > #76,-0.94628,0.12198,-0.29946,442.05,0.074145,-0.8196,-0.56813,481.51,-0.31474,-0.55981,0.76652,186.98
    15409 
    15410 > ui mousemode right select
    15411 
    15412 Drag select of 123 residues 
    15413 
    15414 > select up
    15415 
    15416 983 atoms, 995 bonds, 129 residues, 1 model selected 
    15417 
    15418 > delete sel
    15419 
    15420 > show #!33 models
    15421 
    15422 > fitmap #81 inMap #33.1
    15423 
    15424 Fit molecule copy of
    15425 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
    15426 W20_J160_run_ct6_body001.mrc (#33.1) using 1365 atoms 
    15427 average map value = 0.01415, steps = 116 
    15428 shifted from previous position = 2.3 
    15429 rotated from previous position = 16.3 degrees 
    15430 atoms outside contour = 753, contour level = 0.014811 
    15431  
    15432 Position of copy of
    15433 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
    15434 to W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    15435 Matrix rotation and translation 
    15436 0.01747338 -0.99098181 -0.13285229 281.52273337 
    15437 -0.71306863 -0.10549261 0.69311214 162.28311421 
    15438 -0.70087645 0.08262179 -0.70848136 343.51081858 
    15439 Axis -0.69455315 0.64623949 0.31618104 
    15440 Axis point 0.00000000 268.41792558 210.72025848 
    15441 Rotation angle (degrees) 153.92902085 
    15442 Shift along axis 17.95286420 
    15443  
    15444 
    15445 > show #!74 models
    15446 
    15447 > hide #!74 models
    15448 
    15449 > show #!75 models
    15450 
    15451 > hide #!75 models
    15452 
    15453 > show #76 models
    15454 
    15455 > select add #76
    15456 
    15457 840 atoms, 838 bonds, 210 residues, 1 model selected 
    15458 Drag select of 33.1 W20_J160_run_ct6_body001.mrc , 2 residues 
    15459 
    15460 > select clear
    15461 
    15462 > select add #76
    15463 
    15464 840 atoms, 838 bonds, 210 residues, 1 model selected 
    15465 Drag select of 33.1 W20_J160_run_ct6_body001.mrc , 5 residues 
    15466 
    15467 > select add #76
    15468 
    15469 840 atoms, 838 bonds, 210 residues, 3 models selected 
    15470 
    15471 > select subtract #76
    15472 
    15473 2 models selected 
    15474 
    15475 > select clear
    15476 
    15477 > select add #76
    15478 
    15479 840 atoms, 838 bonds, 210 residues, 1 model selected 
    15480 
    15481 > ui mousemode right "translate selected models"
    15482 
    15483 > view matrix models
    15484 > #76,-0.94628,0.12198,-0.29946,406.27,0.074145,-0.8196,-0.56813,495.91,-0.31474,-0.55981,0.76652,151.84
    15485 
    15486 > fitmap #76 inMap #33.1
    15487 
    15488 Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
    15489 W20_J160_run_ct6_body001.mrc (#33.1) using 840 atoms 
    15490 average map value = 0.02201, steps = 112 
    15491 shifted from previous position = 10.6 
    15492 rotated from previous position = 0.0236 degrees 
    15493 atoms outside contour = 169, contour level = 0.014811 
    15494  
    15495 Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
    15496 W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    15497 Matrix rotation and translation 
    15498 -0.96080554 0.05790187 -0.27110898 408.84449350 
    15499 0.16172293 -0.67722645 -0.71778133 466.70494589 
    15500 -0.22516305 -0.73349282 0.64131886 199.25734435 
    15501 Axis -0.13708008 -0.40087044 0.90582114 
    15502 Axis point 212.50907521 283.77894704 0.00000000 
    15503 Rotation angle (degrees) 176.71471075 
    15504 Shift along axis -62.64113752 
    15505  
    15506 
    15507 > select subtract #76
    15508 
    15509 Nothing selected 
    15510 
    15511 > hide #76 models
    15512 
    15513 > hide #!33 models
    15514 
    15515 > ui mousemode right select
    15516 
    15517 Drag select of 66 residues 
    15518 
    15519 > select up
    15520 
    15521 1365 atoms, 1387 bonds, 172 residues, 1 model selected 
    15522 
    15523 > select down
    15524 
    15525 533 atoms, 66 residues, 1 model selected 
    15526 
    15527 > delete sel
    15528 
    15529 > fitmap #81 inMap #33.1
    15530 
    15531 Fit molecule copy of
    15532 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
    15533 W20_J160_run_ct6_body001.mrc (#33.1) using 832 atoms 
    15534 average map value = 0.01316, steps = 84 
    15535 shifted from previous position = 3.31 
    15536 rotated from previous position = 11.8 degrees 
    15537 atoms outside contour = 498, contour level = 0.014811 
    15538  
    15539 Position of copy of
    15540 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
    15541 to W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    15542 Matrix rotation and translation 
    15543 0.14691503 -0.96385323 -0.22226771 264.04905282 
    15544 -0.78499351 -0.25032946 0.56667482 218.34222261 
    15545 -0.60183151 0.09122566 -0.79339568 335.48317698 
    15546 Axis -0.74977491 0.59856539 0.28205861 
    15547 Axis point 0.00000000 250.13903908 195.48982431 
    15548 Rotation angle (degrees) 161.51470465 
    15549 Shift along axis 27.34066185 
    15550  
    15551 
    15552 > show #!33 models
    15553 
    15554 > show #76 models
    15555 
    15556 > hide #!33 models
    15557 
    15558 > hide #76 models
    15559 
    15560 Drag select of 75 residues 
    15561 
    15562 > delete sel
    15563 
    15564 > fitmap #81 inMap #33.1
    15565 
    15566 Fit molecule copy of
    15567 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
    15568 W20_J160_run_ct6_body001.mrc (#33.1) using 239 atoms 
    15569 average map value = 0.01661, steps = 68 
    15570 shifted from previous position = 0.894 
    15571 rotated from previous position = 22.1 degrees 
    15572 atoms outside contour = 87, contour level = 0.014811 
    15573  
    15574 Position of copy of
    15575 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
    15576 to W20_J160_run_ct6_body001.mrc (#33.1) coordinates: 
    15577 Matrix rotation and translation 
    15578 0.01560880 -0.84592101 -0.53307975 307.86268532 
    15579 -0.85667939 -0.28624403 0.42914424 255.66225987 
    15580 -0.51561303 0.44998001 -0.72915101 245.26898996 
    15581 Axis 0.71258549 -0.59736389 -0.36793789 
    15582 Axis point 0.00000000 255.65895561 203.35484992 
    15583 Rotation angle (degrees) 179.16231543 
    15584 Shift along axis -23.58867527 
    15585  
    15586 
    15587 > show #76 models
    15588 
    15589 > show #!33 models
    15590 
    15591 > hide #!33 models
    15592 
    15593 > show #!82 models
    15594 
    15595 > hide #76 models
    15596 
    15597 > hide #!81 models
    15598 
    15599 Drag select of 9 residues 
    15600 
    15601 > select add #82
    15602 
    15603 4394 atoms, 4464 bonds, 1 pseudobond, 561 residues, 2 models selected 
    15604 
    15605 > select subtract #82
    15606 
    15607 Nothing selected 
    15608 
    15609 > show #!81 models
    15610 
    15611 > hide #!82 models
    15612 
    15613 > hide #!81 models
    15614 
    15615 > show #!74 models
    15616 
    15617 > hide #!74 models
    15618 
    15619 > show #76 models
    15620 
    15621 > show #!77 models
    15622 
    15623 > hide #!77 models
    15624 
    15625 > show #78 models
    15626 
    15627 > show #!33 models
    15628 
    15629 > combine #78
    15630 
    15631 > hide #78 models
    15632 
    15633 > hide #!33 models
    15634 
    15635 > hide #76 models
    15636 
    15637 > show #76 models
    15638 
    15639 > hide #76 models
    15640 
    15641 > show #76 models
    15642 
    15643 > hide #76 models
    15644 
    15645 Drag select of 49 residues 
    15646 
    15647 > select up
    15648 
    15649 441 atoms, 448 bonds, 56 residues, 1 model selected 
    15650 
    15651 > delete sel
    15652 
    15653 > show #!74 models
    15654 
    15655 > hide #!74 models
    15656 
    15657 > show #76 models
    15658 
    15659 > fitmap #83 inMap #33.3
    15660 
    15661 Fit molecule copy of PredictAndBuild_7_overall_best.pdb (#83) to map
    15662 W20_J160_run_ct6_body003.mrc (#33.3) using 3367 atoms 
    15663 average map value = 0.01915, steps = 88 
    15664 shifted from previous position = 1.31 
    15665 rotated from previous position = 3.07 degrees 
    15666 atoms outside contour = 1342, contour level = 0.015167 
    15667  
    15668 Position of copy of PredictAndBuild_7_overall_best.pdb (#83) relative to
    15669 W20_J160_run_ct6_body003.mrc (#33.3) coordinates: 
    15670 Matrix rotation and translation 
    15671 -0.19901990 -0.97974509 -0.02215055 315.72725675 
    15672 -0.86258557 0.16440368 0.47845331 170.01428108 
    15673 -0.46512065 0.11432847 -0.87783357 321.74102683 
    15674 Axis -0.62215321 0.75687028 0.20018181 
    15675 Axis point 259.60135583 0.00000000 107.39223084 
    15676 Rotation angle (degrees) 162.98435754 
    15677 Shift along axis -3.34526606 
    15678  
    15679 
    15680 > show #!33 models
    15681 
    15682 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    15683 > resources/Processing/W20_MM_cyto_COPI/20250705_W20_COPI_cyto_alignments.cxs"
    15684 
    15685 > hide #!33 models
    15686 
    15687 > show #!9 models
    15688 
    15689 > hide #!9 models
    15690 
    15691 > show #!45 models
    15692 
    15693 > show #!46 models
    15694 
    15695 > hide #!46 models
    15696 
    15697 > hide #!45 models
    15698 
    15699 > show #!23 models
    15700 
    15701 > hide #!23 models
    15702 
    15703 > show #!25 models
    15704 
    15705 > fitmap #76 inMap #25
    15706 
    15707 Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
    15708 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 840 atoms 
    15709 average map value = 0.4915, steps = 56 
    15710 shifted from previous position = 1.01 
    15711 rotated from previous position = 4.93 degrees 
    15712 atoms outside contour = 19, contour level = 0.2532 
    15713  
    15714 Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
    15715 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    15716 Matrix rotation and translation 
    15717 -0.95361160 0.05892580 -0.29521631 421.68865993 
    15718 0.13475176 -0.79337176 -0.59363560 471.58547391 
    15719 -0.26919673 -0.60587871 0.74862815 156.24096699 
    15720 Axis -0.15097143 -0.32085083 0.93501999 
    15721 Axis point 218.58287062 267.06046758 0.00000000 
    15722 Rotation angle (degrees) 177.67614662 
    15723 Shift along axis -68.88310337 
    15724  
    15725 
    15726 > fitmap #77 inMap #25
    15727 
    15728 Fit molecule PredictAndBuild_7_overall_best_superposed_predicted_models.pdb
    15729 (#77) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4394
    15730 atoms 
    15731 average map value = 0.2705, steps = 120 
    15732 shifted from previous position = 6.58 
    15733 rotated from previous position = 13.2 degrees 
    15734 atoms outside contour = 2142, contour level = 0.2532 
    15735  
    15736 Position of PredictAndBuild_7_overall_best_superposed_predicted_models.pdb
    15737 (#77) relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25)
    15738 coordinates: 
    15739 Matrix rotation and translation 
    15740 -0.08911154 -0.97740547 -0.19167078 312.61104116 
    15741 -0.86513544 -0.01940313 0.50116283 207.38914458 
    15742 -0.49355830 0.21048058 -0.84385907 317.01597391 
    15743 Axis -0.66998680 0.69581356 0.25876858 
    15744 Axis point 280.81289084 0.00000000 94.39286792 
    15745 Rotation angle (degrees) 167.47114130 
    15746 Shift along axis 16.89268056 
    15747  
    15748 
    15749 > fitmap #78 inMap #25
    15750 
    15751 Fit molecule PredictAndBuild_7_overall_best.pdb (#78) to map
    15752 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3808 atoms 
    15753 average map value = 0.2752, steps = 92 
    15754 shifted from previous position = 5.3 
    15755 rotated from previous position = 5.46 degrees 
    15756 atoms outside contour = 1850, contour level = 0.2532 
    15757  
    15758 Position of PredictAndBuild_7_overall_best.pdb (#78) relative to
    15759 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    15760 Matrix rotation and translation 
    15761 -0.22705266 -0.96732791 -0.11279981 326.50448848 
    15762 -0.84045401 0.13610962 0.52451047 175.87350921 
    15763 -0.49202048 0.21389455 -0.84389867 316.29589561 
    15764 Axis -0.61344445 0.74893397 0.25056699 
    15765 Axis point 262.22373167 0.00000000 100.11436660 
    15766 Rotation angle (degrees) 165.33460884 
    15767 Shift along axis 10.67858762 
    15768  
    15769 
    15770 > fitmap #79 inMap #25
    15771 
    15772 Fit molecule PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb
    15773 (#79) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6818
    15774 atoms 
    15775 average map value = 0.2107, steps = 172 
    15776 shifted from previous position = 11.4 
    15777 rotated from previous position = 5.55 degrees 
    15778 atoms outside contour = 4196, contour level = 0.2532 
    15779  
    15780 Position of PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb (#79)
    15781 relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    15782 Matrix rotation and translation 
    15783 -0.68234026 -0.66974665 -0.29300373 396.66689712 
    15784 -0.70556204 0.49846977 0.50369643 102.82972208 
    15785 -0.19129550 0.55042467 -0.81267381 199.71422066 
    15786 Axis 0.39762109 -0.86545829 -0.30476124 
    15787 Axis point 218.52168169 0.00000000 88.43752525 
    15788 Rotation angle (degrees) 176.63137373 
    15789 Shift along axis 7.86313588 
    15790  
    15791 
    15792 > fitmap #80 inMap #25
    15793 
    15794 Fit molecule PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb
    15795 (#80) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6818
    15796 atoms 
    15797 average map value = 0.2002, steps = 128 
    15798 shifted from previous position = 3.93 
    15799 rotated from previous position = 13.2 degrees 
    15800 atoms outside contour = 4363, contour level = 0.2532 
    15801  
    15802 Position of PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb (#80)
    15803 relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    15804 Matrix rotation and translation 
    15805 -0.61808214 -0.74524170 -0.25017850 390.14177001 
    15806 -0.76859940 0.50608871 0.39131723 125.96407520 
    15807 -0.16501341 0.43415324 -0.88559671 224.77237006 
    15808 Axis 0.43643009 -0.86769550 -0.23797752 
    15809 Axis point 223.54405179 0.00000000 100.58607108 
    15810 Rotation angle (degrees) 177.18705406 
    15811 Shift along axis 7.48037378 
    15812  
    15813 
    15814 > fitmap #81 inMap #25
    15815 
    15816 Fit molecule copy of
    15817 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
    15818 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 239 atoms 
    15819 average map value = 0.2847, steps = 56 
    15820 shifted from previous position = 2.17 
    15821 rotated from previous position = 9.62 degrees 
    15822 atoms outside contour = 73, contour level = 0.2532 
    15823  
    15824 Position of copy of
    15825 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
    15826 to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    15827 Matrix rotation and translation 
    15828 -0.00169329 -0.79343761 -0.60864924 319.68781006 
    15829 -0.93882519 -0.20835191 0.27422025 280.49121917 
    15830 -0.34438989 0.57187957 -0.74454641 207.08413091 
    15831 Axis 0.70242609 -0.62360775 -0.34309032 
    15832 Axis point 0.00000000 266.91836814 201.99199878 
    15833 Rotation angle (degrees) 167.76748361 
    15834 Shift along axis -21.40799989 
    15835  
    15836 
    15837 > fitmap #82 inMap #25
    15838 
    15839 Fit molecule copy of
    15840 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#82) to map
    15841 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4394 atoms 
    15842 average map value = 0.2705, steps = 120 
    15843 shifted from previous position = 6.58 
    15844 rotated from previous position = 13.2 degrees 
    15845 atoms outside contour = 2142, contour level = 0.2532 
    15846  
    15847 Position of copy of
    15848 PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#82) relative
    15849 to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    15850 Matrix rotation and translation 
    15851 -0.08911154 -0.97740547 -0.19167078 312.61104116 
    15852 -0.86513544 -0.01940313 0.50116283 207.38914458 
    15853 -0.49355830 0.21048058 -0.84385907 317.01597391 
    15854 Axis -0.66998680 0.69581356 0.25876858 
    15855 Axis point 280.81289084 0.00000000 94.39286792 
    15856 Rotation angle (degrees) 167.47114130 
    15857 Shift along axis 16.89268056 
    15858  
    15859 
    15860 > fitmap #83 inMap #25
    15861 
    15862 Fit molecule copy of PredictAndBuild_7_overall_best.pdb (#83) to map
    15863 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3367 atoms 
    15864 average map value = 0.2736, steps = 104 
    15865 shifted from previous position = 4.19 
    15866 rotated from previous position = 7.76 degrees 
    15867 atoms outside contour = 1660, contour level = 0.2532 
    15868  
    15869 Position of copy of PredictAndBuild_7_overall_best.pdb (#83) relative to
    15870 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    15871 Matrix rotation and translation 
    15872 -0.20610544 -0.97397844 -0.09426847 320.31886481 
    15873 -0.84612639 0.12899838 0.51713592 179.53786545 
    15874 -0.49151875 0.18634757 -0.85069613 321.39018439 
    15875 Axis -0.62117839 0.74598543 0.24008987 
    15876 Axis point 263.85010261 0.00000000 102.01189567 
    15877 Rotation angle (degrees) 164.55823923 
    15878 Shift along axis 12.12000484 
    15879  
    15880 
    15881 > hide #83 models
    15882 
    15883 > hide #76 models
    15884 
    15885 > open
    15886 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best_superposed_predicted_models.pdb
    15887 
    15888 Chain information for
    15889 PredictAndBuild_4_overall_best_superposed_predicted_models.pdb #84 
    15890 --- 
    15891 Chain | Description 
    15892 A | No description available 
    15893  
    15894 
    15895 > open
    15896 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best.pdb
    15897 
    15898 Chain information for PredictAndBuild_4_overall_best.pdb #85 
    15899 --- 
    15900 Chain | Description 
    15901 A | No description available 
    15902  
    15903 
    15904 > open
    15905 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_superposed_predicted_untrimmed_cycle_1.pdb
    15906 
    15907 Chain information for
    15908 PredictAndBuild_4_superposed_predicted_untrimmed_cycle_1.pdb #86 
    15909 --- 
    15910 Chain | Description 
    15911 A | No description available 
    15912  
    15913 
    15914 > open
    15915 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_superposed_predicted_untrimmed_cycle_2.pdb
    15916 
    15917 Chain information for
    15918 PredictAndBuild_4_superposed_predicted_untrimmed_cycle_2.pdb #87 
    15919 --- 
    15920 Chain | Description 
    15921 A | No description available 
    15922  
    15923 
    15924 > open
    15925 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_superposed_predicted_untrimmed_cycle_3.pdb
    15926 
    15927 Chain information for
    15928 PredictAndBuild_4_superposed_predicted_untrimmed_cycle_3.pdb #88 
    15929 --- 
    15930 Chain | Description 
    15931 A | No description available 
    15932  
    15933 Computing secondary structure 
    15934 [Repeated 4 time(s)]
    15935 
    15936 > ui tool show Matchmaker
    15937 
    15938 > matchmaker #86-88#!84-85 to #83
    15939 
    15940 Parameters 
    15941 --- 
    15942 Chain pairing | bb 
    15943 Alignment algorithm | Needleman-Wunsch 
    15944 Similarity matrix | BLOSUM-62 
    15945 SS fraction | 0.3 
    15946 Gap open (HH/SS/other) | 18/18/6 
    15947 Gap extend | 1 
    15948 SS matrix |  |  | H | S | O 
    15949 ---|---|---|--- 
    15950 H | 6 | -9 | -6 
    15951 S |  | 6 | -6 
    15952 O |  |  | 4 
    15953 Iteration cutoff | 2 
    15954  
    15955 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    15956 PredictAndBuild_4_superposed_predicted_untrimmed_cycle_1.pdb, chain A (#86),
    15957 sequence alignment score = 2398.8 
    15958 RMSD between 245 pruned atom pairs is 0.859 angstroms; (across all 431 pairs:
    15959 6.247) 
    15960  
    15961 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    15962 PredictAndBuild_4_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#87),
    15963 sequence alignment score = 2398.8 
    15964 RMSD between 253 pruned atom pairs is 0.822 angstroms; (across all 431 pairs:
    15965 5.398) 
    15966  
    15967 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    15968 PredictAndBuild_4_superposed_predicted_untrimmed_cycle_3.pdb, chain A (#88),
    15969 sequence alignment score = 2398.8 
    15970 RMSD between 255 pruned atom pairs is 0.834 angstroms; (across all 431 pairs:
    15971 5.572) 
    15972  
    15973 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    15974 PredictAndBuild_4_overall_best_superposed_predicted_models.pdb, chain A (#84),
    15975 sequence alignment score = 2353 
    15976 RMSD between 261 pruned atom pairs is 0.933 angstroms; (across all 426 pairs:
    15977 5.270) 
    15978  
    15979 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    15980 PredictAndBuild_4_overall_best.pdb, chain A (#85), sequence alignment score =
    15981 2185.7 
    15982 RMSD between 274 pruned atom pairs is 0.698 angstroms; (across all 415 pairs:
    15983 4.042) 
    15984  
    15985 
    15986 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    15987 > predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_0.cif"
    15988 
    15989 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif #89 
    15990 --- 
    15991 Chain | Description 
    15992 A | . 
    15993 B | . 
    15994 C | . 
    15995 D | . 
    15996 E | . 
    15997 F | . 
    15998  
    15999 
    16000 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    16001 > predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_1.cif"
    16002 
    16003 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_1.cif #90 
    16004 --- 
    16005 Chain | Description 
    16006 A | . 
    16007 B | . 
    16008 C | . 
    16009 D | . 
    16010 E | . 
    16011 F | . 
    16012  
    16013 
    16014 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    16015 > predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_2.cif"
    16016 
    16017 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_2.cif #91 
    16018 --- 
    16019 Chain | Description 
    16020 A | . 
    16021 B | . 
    16022 C | . 
    16023 D | . 
    16024 E | . 
    16025 F | . 
    16026  
    16027 
    16028 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    16029 > predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_3.cif"
    16030 
    16031 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_3.cif #92 
    16032 --- 
    16033 Chain | Description 
    16034 A | . 
    16035 B | . 
    16036 C | . 
    16037 D | . 
    16038 E | . 
    16039 F | . 
    16040  
    16041 
    16042 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    16043 > predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_4.cif"
    16044 
    16045 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_4.cif #93 
    16046 --- 
    16047 Chain | Description 
    16048 A | . 
    16049 B | . 
    16050 C | . 
    16051 D | . 
    16052 E | . 
    16053 F | . 
    16054  
    16055 
    16056 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    16057 > files/COPI_soluble_job160_dhelix.pdb"
    16058 
    16059 Chain information for COPI_soluble_job160_dhelix.pdb #94 
    16060 --- 
    16061 Chain | Description 
    16062 D | No description available 
    16063 E | No description available 
    16064 F | No description available 
    16065 G | No description available 
    16066 H | No description available 
    16067 I | No description available 
    16068 J | No description available 
    16069 K | No description available 
    16070 L | No description available 
    16071 M | No description available 
    16072 N | No description available 
    16073 O | No description available 
    16074 P | No description available 
    16075 Q | No description available 
    16076  
    16077 
    16078 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    16079 > files/COPI_soluble_job155_dhelix.pdb"
    16080 
    16081 Chain information for COPI_soluble_job155_dhelix.pdb #95 
    16082 --- 
    16083 Chain | Description 
    16084 D | No description available 
    16085 E | No description available 
    16086 F | No description available 
    16087 G | No description available 
    16088 H | No description available 
    16089 I | No description available 
    16090 J | No description available 
    16091 K | No description available 
    16092 L | No description available 
    16093 M | No description available 
    16094 N | No description available 
    16095 O | No description available 
    16096 P | No description available 
    16097 Q | No description available 
    16098  
    16099 
    16100 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    16101 > files/COPI_soluble_job140_dhelix.pdb"
    16102 
    16103 Chain information for COPI_soluble_job140_dhelix.pdb #96 
    16104 --- 
    16105 Chain | Description 
    16106 D | No description available 
    16107 E | No description available 
    16108 F | No description available 
    16109 G | No description available 
    16110 H | No description available 
    16111 I | No description available 
    16112 J | No description available 
    16113 K | No description available 
    16114 L | No description available 
    16115 M | No description available 
    16116 N | No description available 
    16117 O | No description available 
    16118 P | No description available 
    16119 Q | No description available 
    16120  
    16121 
    16122 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    16123 > files/COPI_soluble_job150_dhelix.pdb"
    16124 
    16125 Chain information for COPI_soluble_job150_dhelix.pdb #97 
    16126 --- 
    16127 Chain | Description 
    16128 D | No description available 
    16129 E | No description available 
    16130 F | No description available 
    16131 G | No description available 
    16132 H | No description available 
    16133 I | No description available 
    16134 J | No description available 
    16135 K | No description available 
    16136 L | No description available 
    16137 M | No description available 
    16138 N | No description available 
    16139 O | No description available 
    16140 P | No description available 
    16141 Q | No description available 
    16142  
    16143 
    16144 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    16145 > files/COPI_soluble_job145_dhelix.pdb"
    16146 
    16147 Chain information for COPI_soluble_job145_dhelix.pdb #98 
    16148 --- 
    16149 Chain | Description 
    16150 D | No description available 
    16151 E | No description available 
    16152 F | No description available 
    16153 G | No description available 
    16154 H | No description available 
    16155 I | No description available 
    16156 J | No description available 
    16157 K | No description available 
    16158 L | No description available 
    16159 M | No description available 
    16160 N | No description available 
    16161 O | No description available 
    16162 P | No description available 
    16163 Q | No description available 
    16164  
    16165 
    16166 > ui tool show Matchmaker
    16167 
    16168 > matchmaker #89-93#!94-98 to #83
    16169 
    16170 Computing secondary structure 
    16171 [Repeated 4 time(s)]  Parameters 
    16172 --- 
    16173 Chain pairing | bb 
    16174 Alignment algorithm | Needleman-Wunsch 
    16175 Similarity matrix | BLOSUM-62 
    16176 SS fraction | 0.3 
    16177 Gap open (HH/SS/other) | 18/18/6 
    16178 Gap extend | 1 
    16179 SS matrix |  |  | H | S | O 
    16180 ---|---|---|--- 
    16181 H | 6 | -9 | -6 
    16182 S |  | 6 | -6 
    16183 O |  |  | 4 
    16184 Iteration cutoff | 2 
    16185  
    16186 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16187 fold_20250704_copi_abbprimedgz_trucadg_model_0.cif, chain E (#89), sequence
    16188 alignment score = 2394.6 
    16189 RMSD between 254 pruned atom pairs is 1.108 angstroms; (across all 431 pairs:
    16190 2.715) 
    16191  
    16192 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16193 fold_20250704_copi_abbprimedgz_trucadg_model_1.cif, chain E (#90), sequence
    16194 alignment score = 2394.6 
    16195 RMSD between 252 pruned atom pairs is 1.085 angstroms; (across all 431 pairs:
    16196 2.724) 
    16197  
    16198 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16199 fold_20250704_copi_abbprimedgz_trucadg_model_2.cif, chain E (#91), sequence
    16200 alignment score = 2391 
    16201 RMSD between 245 pruned atom pairs is 1.089 angstroms; (across all 431 pairs:
    16202 2.930) 
    16203  
    16204 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16205 fold_20250704_copi_abbprimedgz_trucadg_model_3.cif, chain E (#92), sequence
    16206 alignment score = 2401.8 
    16207 RMSD between 243 pruned atom pairs is 1.065 angstroms; (across all 431 pairs:
    16208 3.641) 
    16209  
    16210 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16211 fold_20250704_copi_abbprimedgz_trucadg_model_4.cif, chain E (#93), sequence
    16212 alignment score = 2401.8 
    16213 RMSD between 241 pruned atom pairs is 1.095 angstroms; (across all 431 pairs:
    16214 2.725) 
    16215  
    16216 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16217 COPI_soluble_job160_dhelix.pdb, chain M (#94), sequence alignment score =
    16218 1452.2 
    16219 RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
    16220 1.700) 
    16221  
    16222 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16223 COPI_soluble_job155_dhelix.pdb, chain M (#95), sequence alignment score =
    16224 1452.2 
    16225 RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
    16226 1.700) 
    16227  
    16228 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16229 COPI_soluble_job140_dhelix.pdb, chain M (#96), sequence alignment score =
    16230 1452.2 
    16231 RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
    16232 1.700) 
    16233  
    16234 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16235 COPI_soluble_job150_dhelix.pdb, chain M (#97), sequence alignment score =
    16236 1452.2 
    16237 RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
    16238 1.700) 
    16239  
    16240 Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
    16241 COPI_soluble_job145_dhelix.pdb, chain M (#98), sequence alignment score =
    16242 1452.2 
    16243 RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
    16244 1.700) 
    16245  
    16246 
    16247 > hide #86-93#!84-85,94-98 atoms
    16248 
    16249 > show #86-93#!84-85,94-98 cartoons
    16250 
    16251 > hide #93 models
    16252 
    16253 > hide #92 models
    16254 
    16255 > hide #91 models
    16256 
    16257 > hide #90 models
    16258 
    16259 > hide #89 models
    16260 
    16261 > hide #88 models
    16262 
    16263 > hide #87 models
    16264 
    16265 > hide #86 models
    16266 
    16267 > hide #!85 models
    16268 
    16269 > hide #!84 models
    16270 
    16271 > hide #!98 models
    16272 
    16273 > hide #!97 models
    16274 
    16275 > hide #!96 models
    16276 
    16277 > hide #!95 models
    16278 
    16279 > hide #!94 models
    16280 
    16281 > show #89 models
    16282 
    16283 > fitmap #89 inMap #25
    16284 
    16285 Fit molecule fold_20250704_copi_abbprimedgz_trucadg_model_0.cif (#89) to map
    16286 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 31307 atoms 
    16287 average map value = 0.1729, steps = 144 
    16288 shifted from previous position = 3.16 
    16289 rotated from previous position = 14.3 degrees 
    16290 atoms outside contour = 21652, contour level = 0.2532 
    16291  
    16292 Position of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif (#89) relative
    16293 to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16294 Matrix rotation and translation 
    16295 0.05328171 -0.76106194 -0.64648727 140.92255080 
    16296 0.28101753 0.63267016 -0.72163538 147.85576557 
    16297 0.95822242 -0.14322428 0.24758149 143.21536141 
    16298 Axis 0.28936539 -0.80279829 0.52132770 
    16299 Axis point 9.80405567 0.00000000 205.08316869 
    16300 Rotation angle (degrees) 91.90447951 
    16301 Shift along axis -3.25811224 
    16302  
    16303 
    16304 > hide #89 models
    16305 
    16306 > show #!94 models
    16307 
    16308 > fitmap #94 inMap #25
    16309 
    16310 Fit molecule COPI_soluble_job160_dhelix.pdb (#94) to map
    16311 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms 
    16312 average map value = 0.2718, steps = 204 
    16313 shifted from previous position = 15.7 
    16314 rotated from previous position = 16.6 degrees 
    16315 atoms outside contour = 14003, contour level = 0.2532 
    16316  
    16317 Position of COPI_soluble_job160_dhelix.pdb (#94) relative to
    16318 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16319 Matrix rotation and translation 
    16320 -0.94072620 0.21431989 -0.26287109 429.26780955 
    16321 0.04392373 -0.69153884 -0.72100259 611.48757588 
    16322 -0.33631076 -0.68981230 0.64113497 251.13731297 
    16323 Axis 0.16577200 0.39032157 -0.90563167 
    16324 Axis point 252.69703805 349.04589066 0.00000000 
    16325 Rotation angle (degrees) 174.60186768 
    16326 Shift along axis 82.39947160 
    16327  
    16328 
    16329 > fitmap #95 inMap #25
    16330 
    16331 Fit molecule COPI_soluble_job155_dhelix.pdb (#95) to map
    16332 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms 
    16333 average map value = 0.2423, steps = 164 
    16334 shifted from previous position = 15.2 
    16335 rotated from previous position = 11.8 degrees 
    16336 atoms outside contour = 15830, contour level = 0.2532 
    16337  
    16338 Position of COPI_soluble_job155_dhelix.pdb (#95) relative to
    16339 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16340 Matrix rotation and translation 
    16341 -0.93495608 0.23558445 -0.26524914 421.51639111 
    16342 0.02686846 -0.69850918 -0.71509651 616.29442709 
    16343 -0.35374457 -0.67571066 0.64674561 248.96083246 
    16344 Axis 0.17116994 0.38459904 -0.90707466 
    16345 Axis point 252.83551002 347.97043032 0.00000000 
    16346 Rotation angle (degrees) 173.39355126 
    16347 Shift along axis 83.35111726 
    16348  
    16349 
    16350 > fitmap #96 inMap #25
    16351 
    16352 Fit molecule COPI_soluble_job140_dhelix.pdb (#96) to map
    16353 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms 
    16354 average map value = 0.2622, steps = 256 
    16355 shifted from previous position = 18.3 
    16356 rotated from previous position = 12.3 degrees 
    16357 atoms outside contour = 14721, contour level = 0.2532 
    16358  
    16359 Position of COPI_soluble_job140_dhelix.pdb (#96) relative to
    16360 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16361 Matrix rotation and translation 
    16362 -0.93956714 0.21928330 -0.26292285 427.34338098 
    16363 0.03882046 -0.69477206 -0.71818156 612.97301969 
    16364 -0.34015668 -0.68498658 0.64427232 249.37443237 
    16365 Axis 0.16673989 0.38794901 -0.90647304 
    16366 Axis point 252.59063007 348.46957852 0.00000000 
    16367 Rotation angle (degrees) 174.28724830 
    16368 Shift along axis 83.00626481 
    16369  
    16370 
    16371 > fitmap #97 inMap #25
    16372 
    16373 Fit molecule COPI_soluble_job150_dhelix.pdb (#97) to map
    16374 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms 
    16375 average map value = 0.2628, steps = 212 
    16376 shifted from previous position = 21 
    16377 rotated from previous position = 15.7 degrees 
    16378 atoms outside contour = 14726, contour level = 0.2532 
    16379  
    16380 Position of COPI_soluble_job150_dhelix.pdb (#97) relative to
    16381 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16382 Matrix rotation and translation 
    16383 -0.94025104 0.21735184 -0.26208044 427.88998347 
    16384 0.04057084 -0.69272872 -0.72005619 612.48408539 
    16385 -0.33805619 -0.68766641 0.64252076 250.33040167 
    16386 Axis 0.16599686 0.38937389 -0.90599836 
    16387 Axis point 252.53671335 348.85846385 0.00000000 
    16388 Rotation angle (degrees) 174.40123581 
    16389 Shift along axis 82.71476836 
    16390  
    16391 
    16392 > fitmap #98 inMap #25
    16393 
    16394 Fit molecule COPI_soluble_job145_dhelix.pdb (#98) to map
    16395 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms 
    16396 average map value = 0.2587, steps = 272 
    16397 shifted from previous position = 18 
    16398 rotated from previous position = 11.9 degrees 
    16399 atoms outside contour = 15067, contour level = 0.2532 
    16400  
    16401 Position of COPI_soluble_job145_dhelix.pdb (#98) relative to
    16402 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16403 Matrix rotation and translation 
    16404 -0.93993457 0.21619613 -0.26416328 429.04174114 
    16405 0.04215368 -0.69443036 -0.71832412 612.05358105 
    16406 -0.33874190 -0.68631312 0.64360564 249.64587097 
    16407 Axis 0.16669352 0.38835946 -0.90630580 
    16408 Axis point 252.87215354 348.49166546 0.00000000 
    16409 Rotation angle (degrees) 174.49011360 
    16410 Shift along axis 82.95977526 
    16411  
    16412 
    16413 > hide #!94 models
    16414 
    16415 > show #!94 models
    16416 
    16417 > hide #!94 models
    16418 
    16419 > show #!95 models
    16420 
    16421 > hide #!95 models
    16422 
    16423 > show #!94 models
    16424 
    16425 > hide #!50 models
    16426 
    16427 > show #!33 models
    16428 
    16429 > hide #!25 models
    16430 
    16431 > hide #!33 models
    16432 
    16433 > show #!25 models
    16434 
    16435 > close #1
    16436 
    16437 > close #4
    16438 
    16439 > close #6
    16440 
    16441 > close #8
    16442 
    16443 > close #10
    16444 
    16445 > close #12
    16446 
    16447 > close #14
    16448 
    16449 > close #16
    16450 
    16451 > close #18
    16452 
    16453 > close #20
    16454 
    16455 > close #22
    16456 
    16457 > close #24
    16458 
    16459 > close #26
    16460 
    16461 > close #28
    16462 
    16463 > close #41
    16464 
    16465 > hide #!25 models
    16466 
    16467 > hide #!94 models
    16468 
    16469 > show #!96 models
    16470 
    16471 > show #!95 models
    16472 
    16473 > hide #!95 models
    16474 
    16475 > show #!94 models
    16476 
    16477 > hide #!94 models
    16478 
    16479 > show #!97 models
    16480 
    16481 > hide #!97 models
    16482 
    16483 > show #!98 models
    16484 
    16485 > hide #!98 models
    16486 
    16487 > hide #!96 models
    16488 
    16489 > show #!94 models
    16490 
    16491 > split #94 chains
    16492 
    16493 Split COPI_soluble_job160_dhelix.pdb (#94) into 14 models 
    16494 Chain information for COPI_soluble_job160_dhelix.pdb D #94.1 
    16495 --- 
    16496 Chain | Description 
    16497 D | No description available 
    16498  
    16499 Chain information for COPI_soluble_job160_dhelix.pdb E #94.2 
    16500 --- 
    16501 Chain | Description 
    16502 E | No description available 
    16503  
    16504 Chain information for COPI_soluble_job160_dhelix.pdb F #94.3 
    16505 --- 
    16506 Chain | Description 
    16507 F | No description available 
    16508  
    16509 Chain information for COPI_soluble_job160_dhelix.pdb G #94.4 
    16510 --- 
    16511 Chain | Description 
    16512 G | No description available 
    16513  
    16514 Chain information for COPI_soluble_job160_dhelix.pdb H #94.5 
    16515 --- 
    16516 Chain | Description 
    16517 H | No description available 
    16518  
    16519 Chain information for COPI_soluble_job160_dhelix.pdb I #94.6 
    16520 --- 
    16521 Chain | Description 
    16522 I | No description available 
    16523  
    16524 Chain information for COPI_soluble_job160_dhelix.pdb J #94.7 
    16525 --- 
    16526 Chain | Description 
    16527 J | No description available 
    16528  
    16529 Chain information for COPI_soluble_job160_dhelix.pdb K #94.8 
    16530 --- 
    16531 Chain | Description 
    16532 K | No description available 
    16533  
    16534 Chain information for COPI_soluble_job160_dhelix.pdb L #94.9 
    16535 --- 
    16536 Chain | Description 
    16537 L | No description available 
    16538  
    16539 Chain information for COPI_soluble_job160_dhelix.pdb M #94.10 
    16540 --- 
    16541 Chain | Description 
    16542 M | No description available 
    16543  
    16544 Chain information for COPI_soluble_job160_dhelix.pdb N #94.11 
    16545 --- 
    16546 Chain | Description 
    16547 N | No description available 
    16548  
    16549 Chain information for COPI_soluble_job160_dhelix.pdb O #94.12 
    16550 --- 
    16551 Chain | Description 
    16552 O | No description available 
    16553  
    16554 Chain information for COPI_soluble_job160_dhelix.pdb P #94.13 
    16555 --- 
    16556 Chain | Description 
    16557 P | No description available 
    16558  
    16559 Chain information for COPI_soluble_job160_dhelix.pdb Q #94.14 
    16560 --- 
    16561 Chain | Description 
    16562 Q | No description available 
    16563  
    16564 
    16565 > show #!95 models
    16566 
    16567 > hide #!95 models
    16568 
    16569 > close #95
    16570 
    16571 > close #96
    16572 
    16573 > close #97
    16574 
    16575 > close #98
    16576 
    16577 > hide #94.1 models
    16578 
    16579 > hide #94.2 models
    16580 
    16581 > hide #94.3 models
    16582 
    16583 > hide #94.4 models
    16584 
    16585 > hide #94.5 models
    16586 
    16587 > hide #!94.6 models
    16588 
    16589 > hide #!94.7 models
    16590 
    16591 > hide #94.8 models
    16592 
    16593 > show #94.8 models
    16594 
    16595 > hide #94.8 models
    16596 
    16597 > hide #94.12 models
    16598 
    16599 > hide #!94.13 models
    16600 
    16601 > hide #!94.14 models
    16602 
    16603 > show #89 models
    16604 
    16605 > show #!25 models
    16606 
    16607 > hide #89 models
    16608 
    16609 > show #90 models
    16610 
    16611 > show #89 models
    16612 
    16613 > hide #89 models
    16614 
    16615 > hide #90 models
    16616 
    16617 > show #91 models
    16618 
    16619 > hide #91 models
    16620 
    16621 > show #92 models
    16622 
    16623 > hide #92 models
    16624 
    16625 > show #93 models
    16626 
    16627 > hide #93 models
    16628 
    16629 > show #88 models
    16630 
    16631 > hide #88 models
    16632 
    16633 > show #78 models
    16634 
    16635 > hide #78 models
    16636 
    16637 > show #!81 models
    16638 
    16639 > hide #!81 models
    16640 
    16641 > show #!81 models
    16642 
    16643 > hide #!81 models
    16644 
    16645 > show #!82 models
    16646 
    16647 > hide #!82 models
    16648 
    16649 > show #79 models
    16650 
    16651 > hide #79 models
    16652 
    16653 > show #80 models
    16654 
    16655 > fitmap #80 inMap #25
    16656 
    16657 Fit molecule PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb
    16658 (#80) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6818
    16659 atoms 
    16660 average map value = 0.2002, steps = 28 
    16661 shifted from previous position = 0.0204 
    16662 rotated from previous position = 0.023 degrees 
    16663 atoms outside contour = 4363, contour level = 0.2532 
    16664  
    16665 Position of PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb (#80)
    16666 relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16667 Matrix rotation and translation 
    16668 -0.61827994 -0.74501686 -0.25035934 390.17808029 
    16669 -0.76844646 0.50614879 0.39153982 125.89539509 
    16670 -0.16498469 0.43446897 -0.88544721 224.70859005 
    16671 Axis 0.43631396 -0.86771240 -0.23812878 
    16672 Axis point 223.52898003 0.00000000 100.56670382 
    16673 Rotation angle (degrees) 177.18018194 
    16674 Shift along axis 7.48956636 
    16675  
    16676 
    16677 > ui tool show Matchmaker
    16678 
    16679 > matchmaker #80 to #94.9
    16680 
    16681 Parameters 
    16682 --- 
    16683 Chain pairing | bb 
    16684 Alignment algorithm | Needleman-Wunsch 
    16685 Similarity matrix | BLOSUM-62 
    16686 SS fraction | 0.3 
    16687 Gap open (HH/SS/other) | 18/18/6 
    16688 Gap extend | 1 
    16689 SS matrix |  |  | H | S | O 
    16690 ---|---|---|--- 
    16691 H | 6 | -9 | -6 
    16692 S |  | 6 | -6 
    16693 O |  |  | 4 
    16694 Iteration cutoff | 2 
    16695  
    16696 Matchmaker COPI_soluble_job160_dhelix.pdb L, chain L (#94.9) with
    16697 PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#80),
    16698 sequence alignment score = 751 
    16699 RMSD between 111 pruned atom pairs is 0.761 angstroms; (across all 149 pairs:
    16700 2.111) 
    16701  
    16702 
    16703 > ui tool show Matchmaker
    16704 
    16705 > matchmaker #80 to #94.10
    16706 
    16707 Parameters 
    16708 --- 
    16709 Chain pairing | bb 
    16710 Alignment algorithm | Needleman-Wunsch 
    16711 Similarity matrix | BLOSUM-62 
    16712 SS fraction | 0.3 
    16713 Gap open (HH/SS/other) | 18/18/6 
    16714 Gap extend | 1 
    16715 SS matrix |  |  | H | S | O 
    16716 ---|---|---|--- 
    16717 H | 6 | -9 | -6 
    16718 S |  | 6 | -6 
    16719 O |  |  | 4 
    16720 Iteration cutoff | 2 
    16721  
    16722 Matchmaker COPI_soluble_job160_dhelix.pdb M, chain M (#94.10) with
    16723 PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#80),
    16724 sequence alignment score = 1461.2 
    16725 RMSD between 282 pruned atom pairs is 0.718 angstroms; (across all 283 pairs:
    16726 0.728) 
    16727  
    16728 
    16729 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    16730 > resources/Processing/W20_MM_cyto_COPI/20250706_W20_COPI_cyto_alignments.cxs"
    16731 
    16732 > show #89 models
    16733 
    16734 > split #89 chains
    16735 
    16736 Split fold_20250704_copi_abbprimedgz_trucadg_model_0.cif (#89) into 6 models 
    16737 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif A
    16738 #89.1 
    16739 --- 
    16740 Chain | Description 
    16741 A | No description available 
    16742  
    16743 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif B
    16744 #89.2 
    16745 --- 
    16746 Chain | Description 
    16747 B | No description available 
    16748  
    16749 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif C
    16750 #89.3 
    16751 --- 
    16752 Chain | Description 
    16753 C | No description available 
    16754  
    16755 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif D
    16756 #89.4 
    16757 --- 
    16758 Chain | Description 
    16759 D | No description available 
    16760  
    16761 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E
    16762 #89.5 
    16763 --- 
    16764 Chain | Description 
    16765 E | No description available 
    16766  
    16767 Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif F
    16768 #89.6 
    16769 --- 
    16770 Chain | Description 
    16771 F | No description available 
    16772  
    16773 
    16774 > show #90 models
    16775 
    16776 > hide #90 models
    16777 
    16778 > close #90
    16779 
    16780 > close #91-93
    16781 
    16782 > hide #89.1 models
    16783 
    16784 > hide #89.2 models
    16785 
    16786 > show #89.2 models
    16787 
    16788 > hide #89.3 models
    16789 
    16790 > hide #89.4 models
    16791 
    16792 > hide #89.6 models
    16793 
    16794 > hide #80 models
    16795 
    16796 > hide #89.2 models
    16797 
    16798 > hide #!94 models
    16799 
    16800 > show #!94 models
    16801 
    16802 > hide #!94 models
    16803 
    16804 > show #!94 models
    16805 
    16806 > hide #!94 models
    16807 
    16808 > show #!94 models
    16809 
    16810 > hide #!94 models
    16811 
    16812 > combine #89.5
    16813 
    16814 [Repeated 1 time(s)]
    16815 
    16816 > hide #!89 models
    16817 
    16818 > hide #!25 models
    16819 
    16820 > hide #4 models
    16821 
    16822 Drag select of 2 residues 
    16823 
    16824 > select up
    16825 
    16826 41 atoms, 40 bonds, 5 residues, 1 model selected 
    16827 
    16828 > delete sel
    16829 
    16830 Drag select of 23 residues 
    16831 
    16832 > select up
    16833 
    16834 293 atoms, 299 bonds, 37 residues, 1 model selected 
    16835 
    16836 > delete sel
    16837 
    16838 Drag select of 11 residues, 1 pseudobonds 
    16839 
    16840 > delete sel
    16841 
    16842 > show #!94 models
    16843 
    16844 > hide #!94 models
    16845 
    16846 > show #!94 models
    16847 
    16848 Drag select of 14 residues 
    16849 
    16850 > select up
    16851 
    16852 308 atoms, 312 bonds, 41 residues, 1 model selected 
    16853 
    16854 > delete sel
    16855 
    16856 > hide #!94 models
    16857 
    16858 > show #!94 models
    16859 
    16860 > hide #!94 models
    16861 
    16862 Drag select of 113 residues 
    16863 
    16864 > select up
    16865 
    16866 1028 atoms, 1043 bonds, 131 residues, 1 model selected 
    16867 
    16868 > delete sel
    16869 
    16870 > fitmap #1 inMap #25
    16871 
    16872 Fit molecule copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#1)
    16873 to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3497 atoms 
    16874 average map value = 0.3397, steps = 120 
    16875 shifted from previous position = 9.43 
    16876 rotated from previous position = 15.4 degrees 
    16877 atoms outside contour = 1097, contour level = 0.2532 
    16878  
    16879 Position of copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#1)
    16880 relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16881 Matrix rotation and translation 
    16882 0.28192072 -0.63906244 -0.71562553 141.48853049 
    16883 0.25178912 0.76901734 -0.58754964 138.75926341 
    16884 0.92580935 -0.01454430 0.37771089 139.40543708 
    16885 Axis 0.29331865 -0.84024256 0.45602259 
    16886 Axis point -12.05331597 0.00000000 214.52876942 
    16887 Rotation angle (degrees) 77.62410125 
    16888 Shift along axis -11.51818437 
    16889  
    16890 
    16891 > show #!25 models
    16892 
    16893 > hide #!1 models
    16894 
    16895 > show #!1 models
    16896 
    16897 > hide #!1 models
    16898 
    16899 > show #4 models
    16900 
    16901 > hide #!25 models
    16902 
    16903 > hide #4 models
    16904 
    16905 > show #!1 models
    16906 
    16907 > show #4 models
    16908 
    16909 > show #!25 models
    16910 
    16911 > hide #!1 models
    16912 
    16913 > hide #!25 models
    16914 
    16915 > show #!1 models
    16916 
    16917 > hide #!1 models
    16918 
    16919 > show #!1 models
    16920 
    16921 > hide #!1 models
    16922 
    16923 > hide #4 models
    16924 
    16925 > show #!1 models
    16926 
    16927 > hide #!1 models
    16928 
    16929 > show #4 models
    16930 
    16931 Drag select of 17 residues 
    16932 
    16933 > select up
    16934 
    16935 334 atoms, 340 bonds, 42 residues, 1 model selected 
    16936 
    16937 > delete sel
    16938 
    16939 Drag select of 9 residues 
    16940 
    16941 > select up
    16942 
    16943 183 atoms, 186 bonds, 22 residues, 1 model selected 
    16944 
    16945 > delete sel
    16946 
    16947 Drag select of 19 residues 
    16948 
    16949 > select up
    16950 
    16951 215 atoms, 218 bonds, 30 residues, 1 model selected 
    16952 
    16953 > select clear
    16954 
    16955 Drag select of 9 residues 
    16956 
    16957 > delete sel
    16958 
    16959 Drag select of 7 residues 
    16960 
    16961 > select clear
    16962 
    16963 Drag select of 13 residues 
    16964 
    16965 > select clear
    16966 
    16967 Drag select of 15 residues 
    16968 
    16969 > delete sel
    16970 
    16971 > show #!25 models
    16972 
    16973 > fitmap #4 inMap #25
    16974 
    16975 Fit molecule copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#4)
    16976 to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4566 atoms 
    16977 average map value = 0.3172, steps = 112 
    16978 shifted from previous position = 8.14 
    16979 rotated from previous position = 15.5 degrees 
    16980 atoms outside contour = 1647, contour level = 0.2532 
    16981  
    16982 Position of copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#4)
    16983 relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    16984 Matrix rotation and translation 
    16985 0.28339787 -0.63805488 -0.71594107 141.54232791 
    16986 0.25944422 0.76971940 -0.58328444 139.21027357 
    16987 0.92324122 -0.02044520 0.38367649 139.06277017 
    16988 Axis 0.28838113 -0.83986547 0.45985032 
    16989 Axis point -12.84705545 0.00000000 215.45471328 
    16990 Rotation angle (degrees) 77.38510832 
    16991 Shift along axis -12.15170567 
    16992  
    16993 
    16994 > select #4/E:584
    16995 
    16996 7 atoms, 6 bonds, 1 residue, 1 model selected 
    16997 
    16998 > delete sel
    16999 
    17000 > select #4/E:583
    17001 
    17002 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17003 
    17004 > delete sel
    17005 
    17006 > hide #!4 models
    17007 
    17008 > show #!4 models
    17009 
    17010 > combine #4
    17011 
    17012 > hide #!4 models
    17013 
    17014 > rename #4 gamma-COPI_v1
    17015 
    17016 > combine #64 #66 #67 #70 #71 #4
    17017 
    17018 Remapping chain ID 'B' in beta-COPI #66 to 'D' 
    17019 Remapping chain ID 'C' in beta-COPI #66 to 'E' 
    17020 Remapping chain ID 'A' in betaprime-COPI #67 to 'F' 
    17021 Remapping chain ID 'B' in betaprime-COPI #67 to 'G' 
    17022 Remapping chain ID 'C' in betaprime-COPI #67 to 'H' 
    17023 Remapping chain ID 'D' in betaprime-COPI #67 to 'I' 
    17024 Remapping chain ID 'A' in delta-COPI #70 to 'J' 
    17025 Remapping chain ID 'B' in delta-COPI #70 to 'K' 
    17026 Remapping chain ID 'A' in zeta-COPI #71 to 'L' 
    17027 Remapping chain ID 'E' in gamma-COPI_v1 #4 to 'M' 
    17028 
    17029 > hide #!6 models
    17030 
    17031 > fitmap #4 inMap #25
    17032 
    17033 Fit molecule gamma-COPI_v1 (#4) to map
    17034 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4552 atoms 
    17035 average map value = 0.3176, steps = 40 
    17036 shifted from previous position = 0.0254 
    17037 rotated from previous position = 0.0198 degrees 
    17038 atoms outside contour = 1637, contour level = 0.2532 
    17039  
    17040 Position of gamma-COPI_v1 (#4) relative to
    17041 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    17042 Matrix rotation and translation 
    17043 0.28348444 -0.63781373 -0.71612165 141.56919510 
    17044 0.25922020 0.76992233 -0.58311620 139.19563791 
    17045 0.92327756 -0.02032883 0.38359520 139.07316286 
    17046 Axis 0.28836144 -0.83999668 0.45962296 
    17047 Axis point -12.85164212 0.00000000 215.45181715 
    17048 Rotation angle (degrees) 77.37899637 
    17049 Shift along axis -12.17955787 
    17050  
    17051 
    17052 > fitmap #4 inMap #25
    17053 
    17054 Fit molecule gamma-COPI_v1 (#4) to map
    17055 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4552 atoms 
    17056 average map value = 0.3176, steps = 40 
    17057 shifted from previous position = 0.0216 
    17058 rotated from previous position = 0.0256 degrees 
    17059 atoms outside contour = 1634, contour level = 0.2532 
    17060  
    17061 Position of gamma-COPI_v1 (#4) relative to
    17062 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    17063 Matrix rotation and translation 
    17064 0.28351557 -0.63806429 -0.71588608 141.55271505 
    17065 0.25957296 0.76971101 -0.58323823 139.22244867 
    17066 0.92316889 -0.02046756 0.38384929 139.05660502 
    17067 Axis 0.28835533 -0.83982741 0.45993599 
    17068 Axis point -12.85662194 0.00000000 215.49138830 
    17069 Rotation angle (degrees) 77.37682658 
    17070 Shift along axis -12.14821127 
    17071  
    17072 
    17073 > fitmap #64 inMap #25
    17074 
    17075 Fit molecule alpha-COPI (#64) to map
    17076 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6628 atoms 
    17077 average map value = 0.3537, steps = 72 
    17078 shifted from previous position = 0.413 
    17079 rotated from previous position = 1.38 degrees 
    17080 atoms outside contour = 1857, contour level = 0.2532 
    17081  
    17082 Position of alpha-COPI (#64) relative to
    17083 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    17084 Matrix rotation and translation 
    17085 -0.36586447 -0.91732918 -0.15700440 275.35878138 
    17086 -0.79670780 0.22151549 0.56230559 163.87536925 
    17087 -0.48104042 0.33081427 -0.81188796 242.97769193 
    17088 Axis -0.55633921 0.77875030 0.28988732 
    17089 Axis point 211.74531088 0.00000000 70.70797620 
    17090 Rotation angle (degrees) 167.99197292 
    17091 Shift along axis 44.86125869 
    17092  
    17093 
    17094 > fitmap #66 inMap #25
    17095 
    17096 Fit molecule beta-COPI (#66) to map
    17097 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6621 atoms 
    17098 average map value = 0.2922, steps = 64 
    17099 shifted from previous position = 0.113 
    17100 rotated from previous position = 1.01 degrees 
    17101 atoms outside contour = 2335, contour level = 0.2532 
    17102  
    17103 Position of beta-COPI (#66) relative to
    17104 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    17105 Matrix rotation and translation 
    17106 -0.33217082 -0.91999498 -0.20801872 277.50726921 
    17107 -0.77605969 0.14122581 0.61464349 158.87975673 
    17108 -0.53609132 0.36560157 -0.76088211 242.10904879 
    17109 Axis -0.57078454 0.75191666 0.32988838 
    17110 Axis point 215.84062714 0.00000000 64.11235965 
    17111 Rotation angle (degrees) 167.39915972 
    17112 Shift along axis 40.93643893 
    17113  
    17114 
    17115 > fitmap #70 inMap #25
    17116 
    17117 Fit molecule delta-COPI (#70) to map
    17118 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1431 atoms 
    17119 average map value = 0.2517, steps = 140 
    17120 shifted from previous position = 0.914 
    17121 rotated from previous position = 5.42 degrees 
    17122 atoms outside contour = 770, contour level = 0.2532 
    17123  
    17124 Position of delta-COPI (#70) relative to
    17125 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    17126 Matrix rotation and translation 
    17127 -0.34798043 -0.93749415 -0.00378617 175.64116001 
    17128 0.05522224 -0.01646557 -0.99833831 178.10409974 
    17129 0.93587399 -0.34761128 0.05750022 154.89993905 
    17130 Axis 0.42983493 -0.62068846 0.65573452 
    17131 Axis point -39.53177108 213.69242364 0.00000000 
    17132 Rotation angle (degrees) 130.80395777 
    17133 Shift along axis 66.52278419 
    17134  
    17135 
    17136 > fitmap #71 inMap #25
    17137 
    17138 Fit molecule zeta-COPI (#71) to map
    17139 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms 
    17140 average map value = 0.2522, steps = 180 
    17141 shifted from previous position = 10.5 
    17142 rotated from previous position = 19.5 degrees 
    17143 atoms outside contour = 661, contour level = 0.2532 
    17144  
    17145 Position of zeta-COPI (#71) relative to
    17146 W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates: 
    17147 Matrix rotation and translation 
    17148 -0.32469740 0.40326773 0.85553887 117.00818860 
    17149 0.20978479 -0.85131177 0.48089357 145.18762928 
    17150 0.92225916 0.33562393 0.19181929 99.65953140 
    17151 Axis -0.57881168 -0.26584003 -0.77091253 
    17152 Axis point 25.03383553 54.96126454 0.00000000 
    17153 Rotation angle (degrees) 172.79097233 
    17154 Shift along axis -183.15117020 
    17155  
    17156 
    17157 > show #71 models
    17158 
    17159 > hide #71 models
    17160 
    17161 > show #71 models
    17162 
    17163 > hide #71 models
    17164 
    17165 > close #8
    17166 
    17167 > combine #64 #66 #67 #70 #71 #4
    17168 
    17169 Remapping chain ID 'B' in beta-COPI #66 to 'D' 
    17170 Remapping chain ID 'C' in beta-COPI #66 to 'E' 
    17171 Remapping chain ID 'A' in betaprime-COPI #67 to 'F' 
    17172 Remapping chain ID 'B' in betaprime-COPI #67 to 'G' 
    17173 Remapping chain ID 'C' in betaprime-COPI #67 to 'H' 
    17174 Remapping chain ID 'D' in betaprime-COPI #67 to 'I' 
    17175 Remapping chain ID 'A' in delta-COPI #70 to 'J' 
    17176 Remapping chain ID 'B' in delta-COPI #70 to 'K' 
    17177 Remapping chain ID 'A' in zeta-COPI #71 to 'L' 
    17178 Remapping chain ID 'E' in gamma-COPI_v1 #4 to 'M' 
    17179 
    17180 > rename #8 COPI_cyto_for_J4027_v1
    17181 
    17182 > cd "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17183 > resources/Processing/W20_MM_cyto_COPI"
    17184 
    17185 Current working directory is: /Users/becca/Desktop/Postdoc/COPI notebooks and
    17186 resources/Processing/W20_MM_cyto_COPI 
    17187 
    17188 > save COPI_cyto_for_J4027_v1.pdb #8
    17189 
    17190 > open
    17191 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/cc_map.ccp4
    17192 
    17193 Opened cc_map.ccp4 as #10, grid size 240,240,240, pixel 1.19, shown at level
    17194 0.697, step 1, values float32 
    17195 
    17196 > open
    17197 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/composite_map.ccp4
    17198 
    17199 Opened composite_map.ccp4 as #12, grid size 240,240,240, pixel 1.19, shown at
    17200 level 5.35, step 1, values float32 
    17201 
    17202 > open
    17203 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/composite_map.pdb
    17204 
    17205 Summary of feedback from opening
    17206 /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/composite_map.pdb 
    17207 --- 
    17208 warning | Ignored bad PDB record found on line 27366 
    17209  
    17210 Chain information for composite_map.pdb #14 
    17211 --- 
    17212 Chain | Description 
    17213 A | No description available 
    17214 B | No description available 
    17215 C | No description available 
    17216 D | No description available 
    17217 E | No description available 
    17218 F | No description available 
    17219 G | No description available 
    17220 H | No description available 
    17221 I | No description available 
    17222 J | No description available 
    17223 K | No description available 
    17224 L | No description available 
    17225 M | No description available 
    17226  
    17227 
    17228 > open
    17229 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/contribution_map_1.ccp4
    17230 
    17231 Opened contribution_map_1.ccp4 as #16, grid size 240,240,240, pixel 1.19,
    17232 shown at level 1, step 1, values float32 
    17233 
    17234 > open
    17235 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/contribution_map_2.ccp4
    17236 
    17237 Opened contribution_map_2.ccp4 as #18, grid size 240,240,240, pixel 1.19,
    17238 shown at level 0.47, step 1, values float32 
    17239 
    17240 > hide #!8 models
    17241 
    17242 > hide #!10 models
    17243 
    17244 > hide #!12 models
    17245 
    17246 > hide #!14 models
    17247 
    17248 > hide #!16 models
    17249 
    17250 > hide #!18 models
    17251 
    17252 > hide #!25 models
    17253 
    17254 > show #!10 models
    17255 
    17256 > show #!12 models
    17257 
    17258 > show #!14 models
    17259 
    17260 > show #!16 models
    17261 
    17262 > show #!18 models
    17263 
    17264 > close #18
    17265 
    17266 > hide #!14 models
    17267 
    17268 > close #10
    17269 
    17270 > close #12
    17271 
    17272 > show #!14 models
    17273 
    17274 > hide #!14 models
    17275 
    17276 > hide #!16 models
    17277 
    17278 > show #!16 models
    17279 
    17280 > close #16
    17281 
    17282 > close #14
    17283 
    17284 > show #!4 models
    17285 
    17286 > show #!25 models
    17287 
    17288 > hide #!25 models
    17289 
    17290 > show #!23 models
    17291 
    17292 > show #!27 models
    17293 
    17294 > show #!25 models
    17295 
    17296 > hide #!27 models
    17297 
    17298 > show #!32 models
    17299 
    17300 > hide #!32 models
    17301 
    17302 > show #!33 models
    17303 
    17304 > hide #!25 models
    17305 
    17306 > hide #!23 models
    17307 
    17308 > hide #!33 models
    17309 
    17310 > show #!2 models
    17311 
    17312 > hide #!2 models
    17313 
    17314 > show #!3 models
    17315 
    17316 > close #3
    17317 
    17318 > show #!5 models
    17319 
    17320 > close #5
    17321 
    17322 > show #!7 models
    17323 
    17324 > hide #!7 models
    17325 
    17326 > show #!9 models
    17327 
    17328 > show #!23 models
    17329 
    17330 > show #!25 models
    17331 
    17332 > show #!27 models
    17333 
    17334 > hide #!9 models
    17335 
    17336 > show #!9 models
    17337 
    17338 > hide #!9 models
    17339 
    17340 > hide #!23 models
    17341 
    17342 > hide #!27 models
    17343 
    17344 > hide #!25 models
    17345 
    17346 > show #!7 models
    17347 
    17348 > hide #!7 models
    17349 
    17350 > show #!9 models
    17351 
    17352 > hide #!9 models
    17353 
    17354 > show #!11 models
    17355 
    17356 > close #11
    17357 
    17358 > show #!13 models
    17359 
    17360 > show #!15 models
    17361 
    17362 > hide #!15 models
    17363 
    17364 > show #!17 models
    17365 
    17366 > hide #!17 models
    17367 
    17368 > show #!19 models
    17369 
    17370 > show #!17 models
    17371 
    17372 > show #!15 models
    17373 
    17374 > show #!21 models
    17375 
    17376 > hide #!21 models
    17377 
    17378 > hide #!19 models
    17379 
    17380 > hide #!17 models
    17381 
    17382 > hide #!15 models
    17383 
    17384 > hide #!13 models
    17385 
    17386 > show #!29 models
    17387 
    17388 > hide #!29 models
    17389 
    17390 > show #!30 models
    17391 
    17392 > show #!29 models
    17393 
    17394 > show #!31 models
    17395 
    17396 > hide #!31 models
    17397 
    17398 > hide #!30 models
    17399 
    17400 > hide #!29 models
    17401 
    17402 > show #!32 models
    17403 
    17404 > hide #!4 models
    17405 
    17406 > hide #!32 models
    17407 
    17408 > show #!13 models
    17409 
    17410 > show #!15 models
    17411 
    17412 > hide #!15 models
    17413 
    17414 > show #!17 models
    17415 
    17416 > hide #!17 models
    17417 
    17418 > show #!19 models
    17419 
    17420 > show #!21 models
    17421 
    17422 > hide #!21 models
    17423 
    17424 > hide #!19 models
    17425 
    17426 > hide #!13 models
    17427 
    17428 > hide #!2 models
    17429 
    17430 > show #!2 models
    17431 
    17432 > hide #!2 models
    17433 
    17434 > show #!1 models
    17435 
    17436 > hide #!1 models
    17437 
    17438 > show #!4 models
    17439 
    17440 > show #!7 models
    17441 
    17442 > hide #!7 models
    17443 
    17444 > close #1
    17445 
    17446 > hide #!4 models
    17447 
    17448 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17449 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_A.mrc"
    17450 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17451 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_B.mrc"
    17452 
    17453 Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #1.1, grid size
    17454 240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32 
    17455 Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #1.2, grid size
    17456 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    17457 
    17458 > hide #!1.1 models
    17459 
    17460 > show #!1.1 models
    17461 
    17462 > hide #!1.2 models
    17463 
    17464 > show #!1.2 models
    17465 
    17466 > show #!2 models
    17467 
    17468 > hide #!2 models
    17469 
    17470 > show #!2 models
    17471 
    17472 > volume #1.1 level 0.2608
    17473 
    17474 > volume #1.2 level 0.2582
    17475 
    17476 > hide #!1 models
    17477 
    17478 > close #1
    17479 
    17480 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17481 > resources/Processing/W20_MM_cyto_COPI/J3623_auto_sharpened_map.ccp4"
    17482 
    17483 Opened J3623_auto_sharpened_map.ccp4 as #1, grid size 240,240,240, pixel 1.19,
    17484 shown at level 3.17, step 1, values float32 
    17485 
    17486 > hide #!2 models
    17487 
    17488 > volume #1 level 2.641
    17489 
    17490 > hide #!1 models
    17491 
    17492 > show #!1 models
    17493 
    17494 > show #!2 models
    17495 
    17496 > hide #!1 models
    17497 
    17498 > show #!1 models
    17499 
    17500 > open
    17501 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_22/denmod_resolution_map.ccp4
    17502 
    17503 Opened denmod_resolution_map.ccp4 as #3, grid size 104,126,128, pixel 1.19,
    17504 shown at level 11.3, step 1, values float32 
    17505 
    17506 > hide #!3 models
    17507 
    17508 > show #!3 models
    17509 
    17510 > hide #!2 models
    17511 
    17512 > hide #!1 models
    17513 
    17514 > hide #!3 models
    17515 
    17516 > close #3
    17517 
    17518 > open
    17519 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_22/J3623_denmod_map.ccp4
    17520 
    17521 Opened J3623_denmod_map.ccp4 as #3, grid size 104,126,128, pixel 1.19, shown
    17522 at level 0.531, step 1, values float32 
    17523 
    17524 > volume #3 level 0.2174
    17525 
    17526 > show #!66 models
    17527 
    17528 > show #!64 models
    17529 
    17530 > hide #!64 models
    17531 
    17532 > show #!64 models
    17533 
    17534 > hide #!66 models
    17535 
    17536 > hide #!64 models
    17537 
    17538 > show #!70 models
    17539 
    17540 > volume #3 level 0.1325
    17541 
    17542 > volume #3 level 0.25
    17543 
    17544 > show #!66 models
    17545 
    17546 > color #5 gammav3
    17547 
    17548 > color #4 gammav3
    17549 
    17550 > hide #!3 models
    17551 
    17552 > close #3
    17553 
    17554 > close #2
    17555 
    17556 > close #1
    17557 
    17558 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17559 > resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure.mrc"
    17560 
    17561 Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
    17562 1.19, shown at level 0.257, step 1, values float32 
    17563 
    17564 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17565 > resources/Processing/W20_MM_cyto_COPI/J3623_auto_sharpened_map.ccp4"
    17566 
    17567 Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
    17568 shown at level 3.17, step 1, values float32 
    17569 
    17570 > hide #!70 models
    17571 
    17572 > hide #!66 models
    17573 
    17574 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17575 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_A.mrc"
    17576 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17577 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_B.mrc"
    17578 
    17579 Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
    17580 240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32 
    17581 Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
    17582 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    17583 
    17584 > rename #3 J3623_half_maps
    17585 
    17586 > combine #4
    17587 
    17588 > close #4
    17589 
    17590 > combine #5
    17591 
    17592 [Repeated 1 time(s)]
    17593 
    17594 > close #4
    17595 
    17596 > close #5
    17597 
    17598 > show #!6 models
    17599 
    17600 > hide #!6 models
    17601 
    17602 > close #6
    17603 
    17604 > show #!7 models
    17605 
    17606 > hide #!7 models
    17607 
    17608 > close #7
    17609 
    17610 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17611 > resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc"
    17612 
    17613 Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
    17614 as #4, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
    17615 float32 
    17616 
    17617 > select add #4
    17618 
    17619 2 models selected 
    17620 
    17621 > ui mousemode right "rotate selected models"
    17622 
    17623 > view matrix models
    17624 > #4,-0.25307,-0.96623,-0.048581,315.98,-0.86086,0.202,0.46702,167.97,-0.44144,0.16001,-0.88291,294.43
    17625 
    17626 > view matrix models
    17627 > #4,-0.14459,-0.98817,-0.051169,305.09,-0.67606,0.060895,0.73433,127.29,-0.72252,0.14077,-0.67686,306.41
    17628 
    17629 > ui mousemode right "translate selected models"
    17630 
    17631 > view matrix models
    17632 > #4,-0.14459,-0.98817,-0.051169,320.79,-0.67606,0.060895,0.73433,129.24,-0.72252,0.14077,-0.67686,326.78
    17633 
    17634 > fitmap #4 inMap #1
    17635 
    17636 Fit map
    17637 W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc in map
    17638 W20_J3623_consensus_structure.mrc using 138206 points 
    17639 correlation = 0.982, correlation about mean = 0.7994, overlap = 2.043e+04 
    17640 steps = 156, shift = 6.09, angle = 17.9 degrees 
    17641  
    17642 Position of
    17643 W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc (#4)
    17644 relative to W20_J3623_consensus_structure.mrc (#1) coordinates: 
    17645 Matrix rotation and translation 
    17646 -0.33998516 -0.91904572 -0.19941175 353.84995809 
    17647 -0.77678119 0.15490951 0.61042118 146.12290386 
    17648 -0.53011420 0.36243344 -0.76656437 277.61520820 
    17649 Axis -0.56728131 0.75649433 0.32543548 
    17650 Axis point 252.00716027 0.00000000 81.49850043 
    17651 Rotation angle (degrees) 167.37461303 
    17652 Shift along axis 0.15451903 
    17653  
    17654 
    17655 > volume resample #4 onGrid #1
    17656 
    17657 Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
    17658 resampled as #5, grid size 240,240,240, pixel 1.19, shown at step 1, values
    17659 float32 
    17660 
    17661 > select subtract #4
    17662 
    17663 Nothing selected 
    17664 
    17665 > close #4
    17666 
    17667 > cd "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17668 > resources/Processing/W20_MM_cyto_COPI"
    17669 
    17670 Current working directory is: /Users/becca/Desktop/Postdoc/COPI notebooks and
    17671 resources/Processing/W20_MM_cyto_COPI 
    17672 
    17673 > save W20_J3987_consensus_resampled.mrc #5
    17674 
    17675 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17676 > resources/Processing/W20_MM_cyto_COPI/W20_J3987_consensus_resampled.mrc"
    17677 
    17678 Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
    17679 1.19, shown at level 0.277, step 1, values float32 
    17680 
    17681 > hide #!5 models
    17682 
    17683 > fitmap #4 inMap #1
    17684 
    17685 Fit map W20_J3987_consensus_resampled.mrc in map
    17686 W20_J3623_consensus_structure.mrc using 138117 points 
    17687 correlation = 0.9803, correlation about mean = 0.7915, overlap = 2.075e+04 
    17688 steps = 28, shift = 0.021, angle = 0.00696 degrees 
    17689  
    17690 Position of W20_J3987_consensus_resampled.mrc (#4) relative to
    17691 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    17692 Matrix rotation and translation 
    17693 1.00000000 0.00006999 -0.00003626 -0.00018519 
    17694 -0.00006999 0.99999999 -0.00009239 0.04429622 
    17695 0.00003626 0.00009240 1.00000000 -0.01684920 
    17696 Axis 0.76076686 -0.29856000 -0.57627746 
    17697 Axis point 0.00000000 205.18615312 467.59873778 
    17698 Rotation angle (degrees) 0.00695857 
    17699 Shift along axis -0.00365615 
    17700  
    17701 
    17702 > close #5
    17703 
    17704 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17705 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3987_004_volume_map_half_B.mrc"
    17706 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17707 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3987_004_volume_map_half_A.mrc"
    17708 
    17709 Opened cryosparc_P126_J3987_004_volume_map_half_B.mrc as #5.1, grid size
    17710 240,240,240, pixel 1.2, shown at level 0.274, step 1, values float32 
    17711 Opened cryosparc_P126_J3987_004_volume_map_half_A.mrc as #5.2, grid size
    17712 240,240,240, pixel 1.2, shown at level 0.274, step 1, values float32 
    17713 
    17714 > select add #5.1
    17715 
    17716 2 models selected 
    17717 
    17718 > select add #5.2
    17719 
    17720 4 models selected 
    17721 
    17722 > ui mousemode right "rotate selected models"
    17723 
    17724 > view matrix models
    17725 > #5.1,-0.38208,-0.71776,-0.5821,371.56,-0.90525,0.41738,0.079546,196.1,0.18586,0.55733,-0.80922,143.66,#5.2,-0.38208,-0.71776,-0.5821,371.56,-0.90525,0.41738,0.079546,196.1,0.18586,0.55733,-0.80922,143.66
    17726 
    17727 > view matrix models
    17728 > #5.1,-0.42487,-0.88152,-0.20596,349.25,-0.72637,0.19619,0.6587,124.33,-0.54025,0.42946,-0.72366,248.21,#5.2,-0.42487,-0.88152,-0.20596,349.25,-0.72637,0.19619,0.6587,124.33,-0.54025,0.42946,-0.72366,248.21
    17729 
    17730 > ui mousemode right "translate selected models"
    17731 
    17732 > view matrix models
    17733 > #5.1,-0.42487,-0.88152,-0.20596,359.35,-0.72637,0.19619,0.6587,126.62,-0.54025,0.42946,-0.72366,262.21,#5.2,-0.42487,-0.88152,-0.20596,359.35,-0.72637,0.19619,0.6587,126.62,-0.54025,0.42946,-0.72366,262.21
    17734 
    17735 > fitmap #5.1 inMap #1
    17736 
    17737 Fit map cryosparc_P126_J3987_004_volume_map_half_B.mrc in map
    17738 W20_J3623_consensus_structure.mrc using 138219 points 
    17739 correlation = 0.9769, correlation about mean = 0.7541, overlap = 2.056e+04 
    17740 steps = 80, shift = 1.82, angle = 5.92 degrees 
    17741  
    17742 Position of cryosparc_P126_J3987_004_volume_map_half_B.mrc (#5.1) relative to
    17743 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    17744 Matrix rotation and translation 
    17745 -0.34088191 -0.91883476 -0.19885219 353.85897435 
    17746 -0.77626012 0.15578649 0.61086069 145.85323816 
    17747 -0.53030155 0.36259239 -0.76635958 277.59067344 
    17748 Axis -0.56685311 0.75677442 0.32553039 
    17749 Axis point 251.87895379 0.00000000 81.50551240 
    17750 Rotation angle (degrees) 167.35038692 
    17751 Shift along axis 0.15614218 
    17752  
    17753 
    17754 > fitmap #5.2 inMap #1
    17755 
    17756 Fit map cryosparc_P126_J3987_004_volume_map_half_A.mrc in map
    17757 W20_J3623_consensus_structure.mrc using 138231 points 
    17758 correlation = 0.9769, correlation about mean = 0.7539, overlap = 2.061e+04 
    17759 steps = 80, shift = 1.81, angle = 6.04 degrees 
    17760  
    17761 Position of cryosparc_P126_J3987_004_volume_map_half_A.mrc (#5.2) relative to
    17762 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    17763 Matrix rotation and translation 
    17764 -0.33893365 -0.91937774 -0.19967107 353.79911788 
    17765 -0.77742964 0.15417077 0.60978235 146.41544867 
    17766 -0.52983688 0.36190597 -0.76700517 277.70182392 
    17767 Axis -0.56776952 0.75625634 0.32513709 
    17768 Axis point 252.14174450 0.00000000 81.52863602 
    17769 Rotation angle (degrees) 167.39140634 
    17770 Shift along axis 0.14242009 
    17771  
    17772 
    17773 > select subtract #5.2
    17774 
    17775 2 models selected 
    17776 
    17777 > select subtract #5.1
    17778 
    17779 Nothing selected 
    17780 
    17781 > volume resample #5.1 #5.2 onGrid #1
    17782 
    17783 Opened cryosparc_P126_J3987_004_volume_map_half_B.mrc resampled as #6, grid
    17784 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    17785 Opened cryosparc_P126_J3987_004_volume_map_half_A.mrc resampled as #7, grid
    17786 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    17787 
    17788 > save W20_J3987_halfA_consensus_resampled.mrc #7
    17789 
    17790 > save W20_J3987_halfB_consensus_resampled.mrc #6
    17791 
    17792 > close #5-7#5.1-2
    17793 
    17794 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17795 > resources/Processing/W20_MM_cyto_COPI/W20_J3987_halfA_consensus_resampled.mrc"
    17796 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17797 > resources/Processing/W20_MM_cyto_COPI/W20_J3987_halfB_consensus_resampled.mrc"
    17798 
    17799 Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
    17800 pixel 1.19, shown at level 0.276, step 1, values float32 
    17801 Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
    17802 pixel 1.19, shown at level 0.276, step 1, values float32 
    17803 
    17804 > rename #5 J3987_half_maps
    17805 
    17806 > show #!8 models
    17807 
    17808 > hide #!8 models
    17809 
    17810 > combine #8
    17811 
    17812 [Repeated 2 time(s)]
    17813 
    17814 > close #6-8
    17815 
    17816 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17817 > resources/Processing/W20_MM_cyto_COPI/W20_J4021_005_volume_map_bprime_local.mrc"
    17818 
    17819 Opened W20_J4021_005_volume_map_bprime_local.mrc as #6, grid size 240,240,240,
    17820 pixel 1.19, shown at level 0.26, step 1, values float32 
    17821 
    17822 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17823 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4021_005_volume_map_half_B.mrc"
    17824 
    17825 Opened cryosparc_P126_J4021_005_volume_map_half_B.mrc as #7, grid size
    17826 240,240,240, pixel 1.19, shown at level 0.263, step 1, values float32 
    17827 
    17828 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17829 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4021_005_volume_map_half_A.mrc"
    17830 
    17831 Opened cryosparc_P126_J4021_005_volume_map_half_A.mrc as #8, grid size
    17832 240,240,240, pixel 1.19, shown at level 0.262, step 1, values float32 
    17833 
    17834 > volume resample #6 #7 #8 onGrid #1
    17835 
    17836 Opened W20_J4021_005_volume_map_bprime_local.mrc resampled as #12, grid size
    17837 240,240,240, pixel 1.19, shown at step 1, values float32 
    17838 Opened cryosparc_P126_J4021_005_volume_map_half_B.mrc resampled as #14, grid
    17839 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    17840 Opened cryosparc_P126_J4021_005_volume_map_half_A.mrc resampled as #16, grid
    17841 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    17842 
    17843 > hide #!16 models
    17844 
    17845 > show #!16 models
    17846 
    17847 > hide #!16 models
    17848 
    17849 > show #!16 models
    17850 
    17851 > hide #!16 models
    17852 
    17853 > show #!16 models
    17854 
    17855 > close #16
    17856 
    17857 > close #14
    17858 
    17859 > close #12
    17860 
    17861 > hide #!5 models
    17862 
    17863 > hide #!4 models
    17864 
    17865 > hide #!3 models
    17866 
    17867 > hide #!2 models
    17868 
    17869 > fitmap #6 #7 #8 inMap #1
    17870 
    17871 Multiple maps for #6#7#8 
    17872 
    17873 > show #!6 models
    17874 
    17875 > show #!7 models
    17876 
    17877 > show #!8 models
    17878 
    17879 > fitmap #6 inMap #1
    17880 
    17881 Fit map W20_J4021_005_volume_map_bprime_local.mrc in map
    17882 W20_J3623_consensus_structure.mrc using 138166 points 
    17883 correlation = 0.9132, correlation about mean = 0.2137, overlap = 1.684e+04 
    17884 steps = 52, shift = 0.553, angle = 0.278 degrees 
    17885  
    17886 Position of W20_J4021_005_volume_map_bprime_local.mrc (#6) relative to
    17887 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    17888 Matrix rotation and translation 
    17889 0.99999230 0.00368913 -0.00133441 -0.32621193 
    17890 -0.00369294 0.99998910 -0.00285852 0.49731748 
    17891 0.00132385 0.00286342 0.99999502 -0.37762592 
    17892 Axis 0.58922795 -0.27373864 -0.76018260 
    17893 Axis point 131.36464990 82.10529237 0.00000000 
    17894 Rotation angle (degrees) 0.27819836 
    17895 Shift along axis -0.04128355 
    17896  
    17897 
    17898 > fitmap #7 inMap #1
    17899 
    17900 Fit map cryosparc_P126_J4021_005_volume_map_half_B.mrc in map
    17901 W20_J3623_consensus_structure.mrc using 138066 points 
    17902 correlation = 0.907, correlation about mean = 0.2359, overlap = 1.707e+04 
    17903 steps = 68, shift = 0.546, angle = 0.314 degrees 
    17904  
    17905 Position of cryosparc_P126_J4021_005_volume_map_half_B.mrc (#7) relative to
    17906 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    17907 Matrix rotation and translation 
    17908 0.99999065 0.00386110 -0.00194507 -0.25775142 
    17909 -0.00386765 0.99998683 -0.00337455 0.61622992 
    17910 0.00193201 0.00338205 0.99999241 -0.53165616 
    17911 Axis 0.61572178 -0.35331456 -0.70431208 
    17912 Axis point 158.92151900 66.82584882 0.00000000 
    17913 Rotation angle (degrees) 0.31436809 
    17914 Shift along axis -0.00197431 
    17915  
    17916 
    17917 > fitmap #8 inMap #1
    17918 
    17919 Fit map cryosparc_P126_J4021_005_volume_map_half_A.mrc in map
    17920 W20_J3623_consensus_structure.mrc using 138185 points 
    17921 correlation = 0.9063, correlation about mean = 0.2362, overlap = 1.703e+04 
    17922 steps = 44, shift = 0.534, angle = 0.288 degrees 
    17923  
    17924 Position of cryosparc_P126_J4021_005_volume_map_half_A.mrc (#8) relative to
    17925 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    17926 Matrix rotation and translation 
    17927 0.99999293 0.00344362 -0.00151137 -0.26561114 
    17928 -0.00344864 0.99998850 -0.00333361 0.55833592 
    17929 0.00149988 0.00333880 0.99999330 -0.46926499 
    17930 Axis 0.66362765 -0.29949438 -0.68549359 
    17931 Axis point 159.76195443 73.25690596 0.00000000 
    17932 Rotation angle (degrees) 0.28804014 
    17933 Shift along axis -0.02180722 
    17934  
    17935 
    17936 > volume resample #6 #7 #8 onGrid #1
    17937 
    17938 Opened W20_J4021_005_volume_map_bprime_local.mrc resampled as #12, grid size
    17939 240,240,240, pixel 1.19, shown at step 1, values float32 
    17940 Opened cryosparc_P126_J4021_005_volume_map_half_B.mrc resampled as #14, grid
    17941 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    17942 Opened cryosparc_P126_J4021_005_volume_map_half_A.mrc resampled as #16, grid
    17943 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    17944 
    17945 > hide #!10 models
    17946 
    17947 > hide #!11 models
    17948 
    17949 > close #13
    17950 
    17951 > save W20_J4021_halfA_consensus_resampled.mrc #16
    17952 
    17953 > save W20_J4021_halfB_consensus_resampled.mrc #14
    17954 
    17955 > save W20_J4021_consensus_resampled.mrc #12
    17956 
    17957 > close #6-8
    17958 
    17959 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17960 > resources/Processing/W20_MM_cyto_COPI/W20_J4021_consensus_resampled.mrc"
    17961 
    17962 Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
    17963 1.19, shown at level 0.259, step 1, values float32 
    17964 
    17965 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17966 > resources/Processing/W20_MM_cyto_COPI/W20_J4021_halfA_consensus_resampled.mrc"
    17967 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    17968 > resources/Processing/W20_MM_cyto_COPI/W20_J4021_halfB_consensus_resampled.mrc"
    17969 
    17970 Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
    17971 pixel 1.19, shown at level 0.26, step 1, values float32 
    17972 Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
    17973 pixel 1.19, shown at level 0.261, step 1, values float32 
    17974 
    17975 > rename #7 J4021_half_maps
    17976 
    17977 > combine #10
    17978 
    17979 [Repeated 1 time(s)]
    17980 
    17981 > combine #11
    17982 
    17983 > close #8
    17984 
    17985 > close #9
    17986 
    17987 > hide #!18 models
    17988 
    17989 > hide #!16 models
    17990 
    17991 > hide #!14 models
    17992 
    17993 > hide #!13 models
    17994 
    17995 > hide #!12 models
    17996 
    17997 > hide #!7 models
    17998 
    17999 > hide #!6 models
    18000 
    18001 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18002 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_bprime_local.mrc"
    18003 
    18004 Opened W20_J4022_005_volume_map_bprime_local.mrc as #8, grid size 240,240,240,
    18005 pixel 1.19, shown at level 0.256, step 1, values float32 
    18006 
    18007 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18008 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_A.mrc"
    18009 
    18010 Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc as #9, grid size
    18011 240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32 
    18012 
    18013 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18014 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"
    18015 
    18016 Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #20, grid size
    18017 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    18018 
    18019 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18020 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"
    18021 
    18022 Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #22, grid size
    18023 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    18024 
    18025 > close #22
    18026 
    18027 > close #20
    18028 
    18029 > close #10
    18030 
    18031 > close #11
    18032 
    18033 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18034 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"
    18035 
    18036 Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #10, grid size
    18037 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    18038 
    18039 > fitmap #8 inMap #1
    18040 
    18041 Fit map W20_J4022_005_volume_map_bprime_local.mrc in map
    18042 W20_J3623_consensus_structure.mrc using 138200 points 
    18043 correlation = 0.9195, correlation about mean = 0.2263, overlap = 1.667e+04 
    18044 steps = 64, shift = 0.329, angle = 0.376 degrees 
    18045  
    18046 Position of W20_J4022_005_volume_map_bprime_local.mrc (#8) relative to
    18047 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18048 Matrix rotation and translation 
    18049 0.99997966 0.00237299 0.00592048 -1.40324868 
    18050 -0.00238223 0.99999595 0.00155423 -0.17561136 
    18051 -0.00591677 -0.00156830 0.99998127 1.18884605 
    18052 Axis -0.23775685 0.90131776 -0.36207456 
    18053 Axis point 184.53246236 0.00000000 247.89429522 
    18054 Rotation angle (degrees) 0.37624341 
    18055 Shift along axis -0.25510056 
    18056  
    18057 
    18058 > fitmap #9 inMap #1
    18059 
    18060 Fit map cryosparc_P126_J4022_005_volume_map_half_A.mrc in map
    18061 W20_J3623_consensus_structure.mrc using 138165 points 
    18062 correlation = 0.9121, correlation about mean = 0.2433, overlap = 1.687e+04 
    18063 steps = 52, shift = 0.339, angle = 0.357 degrees 
    18064  
    18065 Position of cryosparc_P126_J4022_005_volume_map_half_A.mrc (#9) relative to
    18066 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18067 Matrix rotation and translation 
    18068 0.99998304 0.00160770 0.00559706 -1.23594018 
    18069 -0.00161999 0.99999628 0.00219278 -0.39387001 
    18070 -0.00559351 -0.00220181 0.99998193 1.22871953 
    18071 Axis -0.35302911 0.89896616 -0.25928803 
    18072 Axis point 207.94947596 0.00000000 236.35689026 
    18073 Rotation angle (degrees) 0.35661877 
    18074 Shift along axis -0.23634521 
    18075  
    18076 
    18077 > fitmap #10 inMap #1
    18078 
    18079 Fit map cryosparc_P126_J4022_005_volume_map_half_B.mrc in map
    18080 W20_J3623_consensus_structure.mrc using 138076 points 
    18081 correlation = 0.9128, correlation about mean = 0.2508, overlap = 1.688e+04 
    18082 steps = 64, shift = 0.335, angle = 0.335 degrees 
    18083  
    18084 Position of cryosparc_P126_J4022_005_volume_map_half_B.mrc (#10) relative to
    18085 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18086 Matrix rotation and translation 
    18087 0.99998354 0.00229208 0.00525924 -1.29178101 
    18088 -0.00229810 0.99999671 0.00113989 -0.13676617 
    18089 -0.00525661 -0.00115196 0.99998552 0.99455043 
    18090 Axis -0.19587427 0.89873969 -0.39230121 
    18091 Axis point 169.08755660 -0.00000000 255.83594172 
    18092 Rotation angle (degrees) 0.33520093 
    18093 Shift along axis -0.26005386 
    18094  
    18095 
    18096 > volume resample #8 #9 #10 onGrid #1
    18097 
    18098 Opened W20_J4022_005_volume_map_bprime_local.mrc resampled as #11, grid size
    18099 240,240,240, pixel 1.19, shown at step 1, values float32 
    18100 Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc resampled as #20, grid
    18101 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18102 Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc resampled as #22, grid
    18103 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18104 
    18105 > save W20_J4022_halfB_consensus_resampled.mrc #22
    18106 
    18107 > save W20_J4022_half1_consensus_resampled.mrc #20
    18108 
    18109 > save W20_J4022_halfA_consensus_resampled.mrc #20
    18110 
    18111 > save W20_J4022_consensus_resampled.mrc #11
    18112 
    18113 > close #8-10
    18114 
    18115 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18116 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_consensus_resampled.mrc"
    18117 
    18118 Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
    18119 1.19, shown at level 0.256, step 1, values float32 
    18120 
    18121 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18122 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfA_consensus_resampled.mrc"
    18123 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18124 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfB_consensus_resampled.mrc"
    18125 
    18126 Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
    18127 pixel 1.19, shown at level 0.257, step 1, values float32 
    18128 Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
    18129 pixel 1.19, shown at level 0.255, step 1, values float32 
    18130 
    18131 > rename #9 J4022_half_maps
    18132 
    18133 > combine #13
    18134 
    18135 [Repeated 1 time(s)]
    18136 
    18137 > combine #18
    18138 
    18139 > hide #!10 models
    18140 
    18141 > close #10-17
    18142 
    18143 > hide #!9 models
    18144 
    18145 > hide #!8 models
    18146 
    18147 > show #!25 models
    18148 
    18149 > hide #!24 models
    18150 
    18151 > hide #!26 models
    18152 
    18153 > hide #!25 models
    18154 
    18155 > hide #!22 models
    18156 
    18157 > hide #!20 models
    18158 
    18159 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18160 > resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_bprime_local.mrc"
    18161 
    18162 Opened W20_J4023_003_volume_map_bprime_local.mrc as #10, grid size
    18163 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18164 
    18165 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18166 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_A.mrc"
    18167 
    18168 Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc as #11, grid size
    18169 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18170 
    18171 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18172 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_B.mrc"
    18173 
    18174 Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc as #12, grid size
    18175 240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32 
    18176 
    18177 > fitmap #10 inMap #1
    18178 
    18179 Fit map W20_J4023_003_volume_map_bprime_local.mrc in map
    18180 W20_J3623_consensus_structure.mrc using 138098 points 
    18181 correlation = 0.9217, correlation about mean = 0.2228, overlap = 1.65e+04 
    18182 steps = 52, shift = 0.377, angle = 0.32 degrees 
    18183  
    18184 Position of W20_J4023_003_volume_map_bprime_local.mrc (#10) relative to
    18185 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18186 Matrix rotation and translation 
    18187 0.99998445 0.00551741 0.00081396 -1.06075152 
    18188 -0.00551761 0.99998475 0.00023719 0.41218042 
    18189 -0.00081264 -0.00024168 0.99999964 0.27797318 
    18190 Axis -0.04289152 0.14569399 -0.98839950 
    18191 Axis point 78.63485140 193.79218176 0.00000000 
    18192 Rotation angle (degrees) 0.31984208 
    18193 Shift along axis -0.16919909 
    18194  
    18195 
    18196 > fitmap #11 inMap #1
    18197 
    18198 Fit map cryosparc_P126_J4023_003_volume_map_half_A.mrc in map
    18199 W20_J3623_consensus_structure.mrc using 138113 points 
    18200 correlation = 0.9179, correlation about mean = 0.2457, overlap = 1.663e+04 
    18201 steps = 52, shift = 0.377, angle = 0.301 degrees 
    18202  
    18203 Position of cryosparc_P126_J4023_003_volume_map_half_A.mrc (#11) relative to
    18204 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18205 Matrix rotation and translation 
    18206 0.99998625 0.00523529 0.00031389 -0.97109463 
    18207 -0.00523523 0.99998627 -0.00021220 0.44237207 
    18208 -0.00031500 0.00021056 0.99999993 0.12645487 
    18209 Axis 0.04027075 0.05990654 -0.99739133 
    18210 Axis point 85.60249694 184.64779847 0.00000000 
    18211 Rotation angle (degrees) 0.30074416 
    18212 Shift along axis -0.13873071 
    18213  
    18214 
    18215 > fitmap #11 inMap #1
    18216 
    18217 Fit map cryosparc_P126_J4023_003_volume_map_half_A.mrc in map
    18218 W20_J3623_consensus_structure.mrc using 138113 points 
    18219 correlation = 0.9179, correlation about mean = 0.2458, overlap = 1.664e+04 
    18220 steps = 28, shift = 0.0171, angle = 0.0164 degrees 
    18221  
    18222 Position of cryosparc_P126_J4023_003_volume_map_half_A.mrc (#11) relative to
    18223 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18224 Matrix rotation and translation 
    18225 0.99998502 0.00545441 0.00046410 -1.02505042 
    18226 -0.00545426 0.99998508 -0.00031696 0.50618634 
    18227 -0.00046583 0.00031443 0.99999984 0.13601178 
    18228 Axis 0.05757496 0.08479798 -0.99473334 
    18229 Axis point 94.64872752 186.59259606 0.00000000 
    18230 Rotation angle (degrees) 0.31416658 
    18231 Shift along axis -0.15138911 
    18232  
    18233 
    18234 > volume resample #11 #12 #10 onGrid #1
    18235 
    18236 Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc resampled as #13, grid
    18237 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18238 Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc resampled as #14, grid
    18239 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18240 Opened W20_J4023_003_volume_map_bprime_local.mrc resampled as #15, grid size
    18241 240,240,240, pixel 1.19, shown at step 1, values float32 
    18242 
    18243 > save W20_J4022_halfA_consensus_resampled.mrc #13
    18244 
    18245 > save W20_J4022_halfB_consensus_resampled.mrc #14
    18246 
    18247 > save W20_J4022_consensus_resampled.mrc #15
    18248 
    18249 > close #10-15
    18250 
    18251 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18252 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_consensus_resampled.mrc"
    18253 
    18254 Opened W20_J4022_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
    18255 1.19, shown at level 0.256, step 1, values float32 
    18256 
    18257 > show #!8 models
    18258 
    18259 > hide #!10 models
    18260 
    18261 > show #!10 models
    18262 
    18263 > hide #!10 models
    18264 
    18265 > show #!10 models
    18266 
    18267 > hide #!10 models
    18268 
    18269 > show #!10 models
    18270 
    18271 > hide #!10 models
    18272 
    18273 > show #!10 models
    18274 
    18275 > hide #!10 models
    18276 
    18277 > close #8-10
    18278 
    18279 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18280 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_bprime_local.mrc"
    18281 
    18282 Opened W20_J4022_005_volume_map_bprime_local.mrc as #8, grid size 240,240,240,
    18283 pixel 1.19, shown at level 0.256, step 1, values float32 
    18284 
    18285 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18286 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_A.mrc"
    18287 
    18288 Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc as #9, grid size
    18289 240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32 
    18290 
    18291 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18292 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"
    18293 
    18294 Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #10, grid size
    18295 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    18296 
    18297 > fitmap #8 inMap #1
    18298 
    18299 Fit map W20_J4022_005_volume_map_bprime_local.mrc in map
    18300 W20_J3623_consensus_structure.mrc using 138200 points 
    18301 correlation = 0.9195, correlation about mean = 0.2263, overlap = 1.667e+04 
    18302 steps = 64, shift = 0.329, angle = 0.376 degrees 
    18303  
    18304 Position of W20_J4022_005_volume_map_bprime_local.mrc (#8) relative to
    18305 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18306 Matrix rotation and translation 
    18307 0.99997966 0.00237299 0.00592048 -1.40324868 
    18308 -0.00238223 0.99999595 0.00155423 -0.17561136 
    18309 -0.00591677 -0.00156830 0.99998127 1.18884605 
    18310 Axis -0.23775685 0.90131776 -0.36207456 
    18311 Axis point 184.53246236 0.00000000 247.89429522 
    18312 Rotation angle (degrees) 0.37624341 
    18313 Shift along axis -0.25510056 
    18314  
    18315 
    18316 > fitmap #9 inMap #1
    18317 
    18318 Fit map cryosparc_P126_J4022_005_volume_map_half_A.mrc in map
    18319 W20_J3623_consensus_structure.mrc using 138165 points 
    18320 correlation = 0.9121, correlation about mean = 0.2433, overlap = 1.687e+04 
    18321 steps = 52, shift = 0.339, angle = 0.357 degrees 
    18322  
    18323 Position of cryosparc_P126_J4022_005_volume_map_half_A.mrc (#9) relative to
    18324 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18325 Matrix rotation and translation 
    18326 0.99998304 0.00160770 0.00559706 -1.23594018 
    18327 -0.00161999 0.99999628 0.00219278 -0.39387001 
    18328 -0.00559351 -0.00220181 0.99998193 1.22871953 
    18329 Axis -0.35302911 0.89896616 -0.25928803 
    18330 Axis point 207.94947596 0.00000000 236.35689026 
    18331 Rotation angle (degrees) 0.35661877 
    18332 Shift along axis -0.23634521 
    18333  
    18334 
    18335 > fitmap #10 inMap #1
    18336 
    18337 Fit map cryosparc_P126_J4022_005_volume_map_half_B.mrc in map
    18338 W20_J3623_consensus_structure.mrc using 138076 points 
    18339 correlation = 0.9128, correlation about mean = 0.2508, overlap = 1.688e+04 
    18340 steps = 64, shift = 0.335, angle = 0.335 degrees 
    18341  
    18342 Position of cryosparc_P126_J4022_005_volume_map_half_B.mrc (#10) relative to
    18343 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18344 Matrix rotation and translation 
    18345 0.99998354 0.00229208 0.00525924 -1.29178101 
    18346 -0.00229810 0.99999671 0.00113989 -0.13676617 
    18347 -0.00525661 -0.00115196 0.99998552 0.99455043 
    18348 Axis -0.19587427 0.89873969 -0.39230121 
    18349 Axis point 169.08755660 -0.00000000 255.83594172 
    18350 Rotation angle (degrees) 0.33520093 
    18351 Shift along axis -0.26005386 
    18352  
    18353 
    18354 > volume resample #8 #9 #10 onGrid #1
    18355 
    18356 Opened W20_J4022_005_volume_map_bprime_local.mrc resampled as #11, grid size
    18357 240,240,240, pixel 1.19, shown at step 1, values float32 
    18358 Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc resampled as #12, grid
    18359 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18360 Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc resampled as #13, grid
    18361 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18362 
    18363 > save W20_J4022_halfA_consensus_resampled.mrc #12
    18364 
    18365 > save W20_J4022_halfb_consensus_resampled.mrc #12
    18366 
    18367 > save W20_J4022_halfB_consensus_resampled.mrc #12
    18368 
    18369 > save W20_J4022_halfB_consensus_resampled.mrc #13
    18370 
    18371 > save W20_J4022_halfA_consensus_resampled.mrc #12
    18372 
    18373 > save W20_J4022_consensus_resampled.mrc #11
    18374 
    18375 > close #8-10
    18376 
    18377 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18378 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_consensus_resampled.mrc"
    18379 
    18380 Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
    18381 1.19, shown at level 0.256, step 1, values float32 
    18382 
    18383 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18384 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfA_consensus_resampled.mrc"
    18385 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18386 > resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfB_consensus_resampled.mrc"
    18387 
    18388 Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
    18389 pixel 1.19, shown at level 0.257, step 1, values float32 
    18390 Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
    18391 pixel 1.19, shown at level 0.255, step 1, values float32 
    18392 
    18393 > rename #9 J4022_half_maps
    18394 
    18395 > close #11-13
    18396 
    18397 > hide #!9 models
    18398 
    18399 > hide #!8 models
    18400 
    18401 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18402 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_A.mrc"
    18403 
    18404 Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc as #10, grid size
    18405 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18406 
    18407 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18408 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_B.mrc"
    18409 
    18410 Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc as #11, grid size
    18411 240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32 
    18412 
    18413 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18414 > resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_bprime_local.mrc"
    18415 
    18416 Opened W20_J4023_003_volume_map_bprime_local.mrc as #12, grid size
    18417 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18418 
    18419 > fitmap #10 inMap #1
    18420 
    18421 Fit map cryosparc_P126_J4023_003_volume_map_half_A.mrc in map
    18422 W20_J3623_consensus_structure.mrc using 138113 points 
    18423 correlation = 0.9179, correlation about mean = 0.2457, overlap = 1.663e+04 
    18424 steps = 52, shift = 0.377, angle = 0.301 degrees 
    18425  
    18426 Position of cryosparc_P126_J4023_003_volume_map_half_A.mrc (#10) relative to
    18427 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18428 Matrix rotation and translation 
    18429 0.99998625 0.00523529 0.00031389 -0.97109463 
    18430 -0.00523523 0.99998627 -0.00021220 0.44237207 
    18431 -0.00031500 0.00021056 0.99999993 0.12645487 
    18432 Axis 0.04027075 0.05990654 -0.99739133 
    18433 Axis point 85.60249694 184.64779847 0.00000000 
    18434 Rotation angle (degrees) 0.30074416 
    18435 Shift along axis -0.13873071 
    18436  
    18437 
    18438 > fitmap #11 inMap #1
    18439 
    18440 Fit map cryosparc_P126_J4023_003_volume_map_half_B.mrc in map
    18441 W20_J3623_consensus_structure.mrc using 138029 points 
    18442 correlation = 0.9185, correlation about mean = 0.2483, overlap = 1.668e+04 
    18443 steps = 68, shift = 0.416, angle = 0.319 degrees 
    18444  
    18445 Position of cryosparc_P126_J4023_003_volume_map_half_B.mrc (#11) relative to
    18446 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18447 Matrix rotation and translation 
    18448 0.99998492 0.00536357 0.00117882 -1.09568335 
    18449 -0.00536466 0.99998519 0.00091977 0.25675329 
    18450 -0.00117387 -0.00092608 0.99999888 0.47324489 
    18451 Axis -0.16573766 0.21124575 -0.96327891 
    18452 Axis point 55.94119463 211.23890617 0.00000000 
    18453 Rotation angle (degrees) 0.31905878 
    18454 Shift along axis -0.22003278 
    18455  
    18456 
    18457 > fitmap #12 inMap #1
    18458 
    18459 Fit map W20_J4023_003_volume_map_bprime_local.mrc in map
    18460 W20_J3623_consensus_structure.mrc using 138098 points 
    18461 correlation = 0.9217, correlation about mean = 0.2228, overlap = 1.65e+04 
    18462 steps = 52, shift = 0.377, angle = 0.32 degrees 
    18463  
    18464 Position of W20_J4023_003_volume_map_bprime_local.mrc (#12) relative to
    18465 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18466 Matrix rotation and translation 
    18467 0.99998445 0.00551741 0.00081396 -1.06075152 
    18468 -0.00551761 0.99998475 0.00023719 0.41218042 
    18469 -0.00081264 -0.00024168 0.99999964 0.27797318 
    18470 Axis -0.04289152 0.14569399 -0.98839950 
    18471 Axis point 78.63485140 193.79218176 0.00000000 
    18472 Rotation angle (degrees) 0.31984208 
    18473 Shift along axis -0.16919909 
    18474  
    18475 
    18476 > volume resample #11 #12 #10 onGrid #1
    18477 
    18478 Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc resampled as #13, grid
    18479 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18480 Opened W20_J4023_003_volume_map_bprime_local.mrc resampled as #14, grid size
    18481 240,240,240, pixel 1.19, shown at step 1, values float32 
    18482 Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc resampled as #15, grid
    18483 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18484 
    18485 > save W20_J4023_halfA_consensus_resampled.mrc #15
    18486 
    18487 > save W20_J4023_halfB_consensus_resampled.mrc #13
    18488 
    18489 > save W20_J4023_consensus_resampled.mrc #14
    18490 
    18491 > close #10-12
    18492 
    18493 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18494 > resources/Processing/W20_MM_cyto_COPI/W20_J4023_consensus_resampled.mrc"
    18495 
    18496 Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
    18497 1.19, shown at level 0.259, step 1, values float32 
    18498 
    18499 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18500 > resources/Processing/W20_MM_cyto_COPI/W20_J4023_halfA_consensus_resampled.mrc"
    18501 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18502 > resources/Processing/W20_MM_cyto_COPI/W20_J4023_halfB_consensus_resampled.mrc"
    18503 
    18504 Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
    18505 240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32 
    18506 Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
    18507 240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32 
    18508 
    18509 > rename #11 J4023_half_maps
    18510 
    18511 > close #13-15
    18512 
    18513 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18514 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4024_005_volume_map_half_B.mrc"
    18515 
    18516 Opened cryosparc_P126_J4024_005_volume_map_half_B.mrc as #12, grid size
    18517 240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32 
    18518 
    18519 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18520 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4024_005_volume_map_half_A.mrc"
    18521 
    18522 Opened cryosparc_P126_J4024_005_volume_map_half_A.mrc as #13, grid size
    18523 240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32 
    18524 
    18525 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18526 > resources/Processing/W20_MM_cyto_COPI/W20_J4024_005_volume_map_bprime_local.mrc"
    18527 
    18528 Opened W20_J4024_005_volume_map_bprime_local.mrc as #14, grid size
    18529 240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32 
    18530 
    18531 > hide #!10 models
    18532 
    18533 > hide #!11 models
    18534 
    18535 > fitmap #12 inMap #1
    18536 
    18537 Fit map cryosparc_P126_J4024_005_volume_map_half_B.mrc in map
    18538 W20_J3623_consensus_structure.mrc using 138074 points 
    18539 correlation = 0.9152, correlation about mean = 0.3069, overlap = 1.694e+04 
    18540 steps = 48, shift = 0.275, angle = 0.182 degrees 
    18541  
    18542 Position of cryosparc_P126_J4024_005_volume_map_half_B.mrc (#12) relative to
    18543 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18544 Matrix rotation and translation 
    18545 0.99999497 0.00227004 0.00221345 -0.56219185 
    18546 -0.00226948 0.99999739 -0.00025704 0.14204421 
    18547 -0.00221402 0.00025201 0.99999752 0.19043665 
    18548 Axis 0.08002006 0.69597786 -0.71359065 
    18549 Axis point 87.46071279 244.95972740 0.00000000 
    18550 Rotation angle (degrees) 0.18224416 
    18551 Shift along axis -0.08202081 
    18552  
    18553 
    18554 > fitmap #13 inMap #1
    18555 
    18556 Fit map cryosparc_P126_J4024_005_volume_map_half_A.mrc in map
    18557 W20_J3623_consensus_structure.mrc using 138160 points 
    18558 correlation = 0.9177, correlation about mean = 0.3098, overlap = 1.706e+04 
    18559 steps = 52, shift = 0.291, angle = 0.229 degrees 
    18560  
    18561 Position of cryosparc_P126_J4024_005_volume_map_half_A.mrc (#13) relative to
    18562 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18563 Matrix rotation and translation 
    18564 0.99999333 0.00148868 0.00333575 -0.58679763 
    18565 -0.00149415 0.99999754 0.00163794 -0.27610320 
    18566 -0.00333331 -0.00164291 0.99999309 0.70324776 
    18567 Axis -0.40966600 0.83273727 -0.37245458 
    18568 Axis point 182.44969494 0.00000000 207.15832332 
    18569 Rotation angle (degrees) 0.22943002 
    18570 Shift along axis -0.25145824 
    18571  
    18572 
    18573 > fitmap #14 inMap #1
    18574 
    18575 Fit map W20_J4024_005_volume_map_bprime_local.mrc in map
    18576 W20_J3623_consensus_structure.mrc using 138193 points 
    18577 correlation = 0.9249, correlation about mean = 0.3066, overlap = 1.679e+04 
    18578 steps = 64, shift = 0.289, angle = 0.207 degrees 
    18579  
    18580 Position of W20_J4024_005_volume_map_bprime_local.mrc (#14) relative to
    18581 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18582 Matrix rotation and translation 
    18583 0.99999384 0.00210499 0.00280839 -0.61107104 
    18584 -0.00210740 0.99999741 0.00085537 -0.06363233 
    18585 -0.00280658 -0.00086128 0.99999569 0.47576775 
    18586 Axis -0.23755676 0.77702082 -0.58292833 
    18587 Axis point 131.43847496 0.00000000 233.23904124 
    18588 Rotation angle (degrees) 0.20701789 
    18589 Shift along axis -0.18161809 
    18590  
    18591 
    18592 > volume resample #13 #12 #14 onGrid #1
    18593 
    18594 Opened cryosparc_P126_J4024_005_volume_map_half_A.mrc resampled as #15, grid
    18595 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18596 Opened cryosparc_P126_J4024_005_volume_map_half_B.mrc resampled as #16, grid
    18597 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18598 Opened W20_J4024_005_volume_map_bprime_local.mrc resampled as #17, grid size
    18599 240,240,240, pixel 1.19, shown at step 1, values float32 
    18600 
    18601 > save W20_J4024_halfA_consensus_resampled.mrc #15
    18602 
    18603 > save W20_J4024_halfB_consensus_resampled.mrc #16
    18604 
    18605 > save W20_J4024_consensus_resampled.mrc #17
    18606 
    18607 > combine #18
    18608 
    18609 > hide #!28 models
    18610 
    18611 > close #12-14
    18612 
    18613 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18614 > resources/Processing/W20_MM_cyto_COPI/W20_J4024_consensus_resampled.mrc"
    18615 
    18616 Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
    18617 1.19, shown at level 0.256, step 1, values float32 
    18618 
    18619 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18620 > resources/Processing/W20_MM_cyto_COPI/W20_J4024_halfA_consensus_resampled.mrc"
    18621 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18622 > resources/Processing/W20_MM_cyto_COPI/W20_J4024_halfB_consensus_resampled.mrc"
    18623 
    18624 Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
    18625 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    18626 Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
    18627 240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32 
    18628 
    18629 > rename #13 J4024_half_maps
    18630 
    18631 > hide #!13 models
    18632 
    18633 > hide #!12 models
    18634 
    18635 > close #15-17
    18636 
    18637 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18638 > resources/Processing/W20_MM_cyto_COPI/W20_J4025_004_volume_map_bprime_local.mrc"
    18639 
    18640 Opened W20_J4025_004_volume_map_bprime_local.mrc as #14, grid size
    18641 240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32 
    18642 
    18643 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18644 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4025_004_volume_map_half_A.mrc"
    18645 
    18646 Opened cryosparc_P126_J4025_004_volume_map_half_A.mrc as #15, grid size
    18647 240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32 
    18648 
    18649 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18650 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4025_004_volume_map_half_B.mrc"
    18651 
    18652 Opened cryosparc_P126_J4025_004_volume_map_half_B.mrc as #16, grid size
    18653 240,240,240, pixel 1.19, shown at level 0.262, step 1, values float32 
    18654 
    18655 > fitmap #14 inMap #1
    18656 
    18657 Fit map W20_J4025_004_volume_map_bprime_local.mrc in map
    18658 W20_J3623_consensus_structure.mrc using 138084 points 
    18659 correlation = 0.9112, correlation about mean = 0.1801, overlap = 1.617e+04 
    18660 steps = 56, shift = 0.729, angle = 0.309 degrees 
    18661  
    18662 Position of W20_J4025_004_volume_map_bprime_local.mrc (#14) relative to
    18663 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18664 Matrix rotation and translation 
    18665 0.99999126 0.00417664 -0.00019252 -0.45232897 
    18666 -0.00417727 0.99998545 -0.00341415 0.60739960 
    18667 0.00017826 0.00341492 0.99999415 -0.09374688 
    18668 Axis 0.63253451 -0.03434313 -0.77377041 
    18669 Axis point 143.22381791 73.09529688 0.00000000 
    18670 Rotation angle (degrees) 0.30929457 
    18671 Shift along axis -0.23443512 
    18672  
    18673 
    18674 > fitmap #15 inMap #1
    18675 
    18676 Fit map cryosparc_P126_J4025_004_volume_map_half_A.mrc in map
    18677 W20_J3623_consensus_structure.mrc using 138098 points 
    18678 correlation = 0.9052, correlation about mean = 0.2004, overlap = 1.632e+04 
    18679 steps = 56, shift = 0.719, angle = 0.323 degrees 
    18680  
    18681 Position of cryosparc_P126_J4025_004_volume_map_half_A.mrc (#15) relative to
    18682 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18683 Matrix rotation and translation 
    18684 0.99998806 0.00478731 -0.00097621 -0.44930386 
    18685 -0.00479005 0.99998454 -0.00282388 0.63846920 
    18686 0.00096268 0.00282852 0.99999554 -0.08426557 
    18687 Axis 0.50071333 -0.17175476 -0.84840230 
    18688 Axis point 123.64037299 66.63895829 0.00000000 
    18689 Rotation angle (degrees) 0.32339898 
    18690 Shift along axis -0.26314146 
    18691  
    18692 
    18693 > fitmap #16 inMap #1
    18694 
    18695 Fit map cryosparc_P126_J4025_004_volume_map_half_B.mrc in map
    18696 W20_J3623_consensus_structure.mrc using 138173 points 
    18697 correlation = 0.9079, correlation about mean = 0.2131, overlap = 1.642e+04 
    18698 steps = 52, shift = 0.742, angle = 0.262 degrees 
    18699  
    18700 Position of cryosparc_P126_J4025_004_volume_map_half_B.mrc (#16) relative to
    18701 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18702 Matrix rotation and translation 
    18703 0.99999486 0.00315412 0.00057190 -0.38968890 
    18704 -0.00315224 0.99998971 -0.00326115 0.40412911 
    18705 -0.00058218 0.00325933 0.99999452 0.02235804 
    18706 Axis 0.71306302 0.12620638 -0.68964707 
    18707 Axis point 0.00000000 44.63041208 133.15812471 
    18708 Rotation angle (degrees) 0.26196640 
    18709 Shift along axis -0.24228822 
    18710  
    18711 
    18712 > volume resample #15 #16 #14 onGrid #1
    18713 
    18714 Opened cryosparc_P126_J4025_004_volume_map_half_A.mrc resampled as #17, grid
    18715 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18716 Opened cryosparc_P126_J4025_004_volume_map_half_B.mrc resampled as #41, grid
    18717 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18718 Opened W20_J4025_004_volume_map_bprime_local.mrc resampled as #90, grid size
    18719 240,240,240, pixel 1.19, shown at step 1, values float32 
    18720 
    18721 > save W20_J4024_halfA_consensus_resampled.mrc #17
    18722 
    18723 > hide #!13.2 models
    18724 
    18725 > hide #!13.1 models
    18726 
    18727 > show #!13.1 models
    18728 
    18729 > hide #!13.1 models
    18730 
    18731 > hide #!13 models
    18732 
    18733 > hide #!41 models
    18734 
    18735 > hide #!90 models
    18736 
    18737 > show #!13.1 models
    18738 
    18739 > hide #!13.1 models
    18740 
    18741 > show #!13.1 models
    18742 
    18743 > hide #!13.1 models
    18744 
    18745 > show #!13.1 models
    18746 
    18747 > hide #!13.1 models
    18748 
    18749 > show #!13.2 models
    18750 
    18751 > show #!13.1 models
    18752 
    18753 > hide #!13.1 models
    18754 
    18755 > hide #!13.2 models
    18756 
    18757 > save W20_J4024_halfA_consensus_resampled.mrc #13.1
    18758 
    18759 > save W20_J4025_halfA_consensus_resampled.mrc #17
    18760 
    18761 > rename #17 W20_J4025_halfA_consensus_resampled.mrc
    18762 
    18763 > show #!90 models
    18764 
    18765 > show #!41 models
    18766 
    18767 > save W20_J4025_halfB_consensus_resampled.mrc #41
    18768 
    18769 > save W20_J4025_consensus_resampled.mrc #90
    18770 
    18771 > hide #!13 models
    18772 
    18773 > close #14-16
    18774 
    18775 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18776 > resources/Processing/W20_MM_cyto_COPI/W20_J4025_consensus_resampled.mrc"
    18777 
    18778 Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
    18779 1.19, shown at level 0.26, step 1, values float32 
    18780 
    18781 > hide #!17 models
    18782 
    18783 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18784 > resources/Processing/W20_MM_cyto_COPI/W20_J4025_halfA_consensus_resampled.mrc"
    18785 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18786 > resources/Processing/W20_MM_cyto_COPI/W20_J4025_halfB_consensus_resampled.mrc"
    18787 
    18788 Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
    18789 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18790 Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
    18791 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18792 
    18793 > save W20_J4024_halfA_consensus_resampled.mrc #13.1
    18794 
    18795 > rename #15 J4025_half_maps
    18796 
    18797 > hide #!15 models
    18798 
    18799 > hide #!14 models
    18800 
    18801 > close #17
    18802 
    18803 > close #18
    18804 
    18805 > close #19
    18806 
    18807 > close #20
    18808 
    18809 > close #21
    18810 
    18811 > close #22
    18812 
    18813 > close #23
    18814 
    18815 > hide #!1 models
    18816 
    18817 > show #!1 models
    18818 
    18819 > hide #!1 models
    18820 
    18821 > show #!1 models
    18822 
    18823 > hide #!1 models
    18824 
    18825 > show #!2 models
    18826 
    18827 > hide #!2 models
    18828 
    18829 > show #!2 models
    18830 
    18831 > hide #!2 models
    18832 
    18833 > show #!3 models
    18834 
    18835 > hide #!3 models
    18836 
    18837 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18838 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4026_004_volume_map_half_A.mrc"
    18839 
    18840 Opened cryosparc_P126_J4026_004_volume_map_half_A.mrc as #16, grid size
    18841 240,240,240, pixel 1.19, shown at level 0.266, step 1, values float32 
    18842 
    18843 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18844 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4026_004_volume_map_half_B.mrc"
    18845 
    18846 Opened cryosparc_P126_J4026_004_volume_map_half_B.mrc as #17, grid size
    18847 240,240,240, pixel 1.19, shown at level 0.265, step 1, values float32 
    18848 
    18849 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18850 > resources/Processing/W20_MM_cyto_COPI/W20_J4026_004_volume_map_gammazeta_local.mrc"
    18851 
    18852 Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #18, grid size
    18853 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18854 
    18855 > hide #!17 models
    18856 
    18857 > show #!17 models
    18858 
    18859 > hide #!17 models
    18860 
    18861 > show #!17 models
    18862 
    18863 > hide #!18 models
    18864 
    18865 > hide #!41 models
    18866 
    18867 > hide #!90 models
    18868 
    18869 > hide #!17 models
    18870 
    18871 > show #!17 models
    18872 
    18873 > hide #!17 models
    18874 
    18875 > hide #!16 models
    18876 
    18877 > show #!18 models
    18878 
    18879 > hide #!18 models
    18880 
    18881 > show #!18 models
    18882 
    18883 > show #!17 models
    18884 
    18885 > hide #!17 models
    18886 
    18887 > show #!16 models
    18888 
    18889 > hide #!16 models
    18890 
    18891 > show #!16 models
    18892 
    18893 > show #!17 models
    18894 
    18895 > hide #!16 models
    18896 
    18897 > show #!16 models
    18898 
    18899 > hide #!17 models
    18900 
    18901 > show #!17 models
    18902 
    18903 > fitmap #16 inMap #1
    18904 
    18905 Fit map cryosparc_P126_J4026_004_volume_map_half_A.mrc in map
    18906 W20_J3623_consensus_structure.mrc using 138044 points 
    18907 correlation = 0.9061, correlation about mean = 0.2969, overlap = 1.877e+04 
    18908 steps = 52, shift = 0.633, angle = 0.336 degrees 
    18909  
    18910 Position of cryosparc_P126_J4026_004_volume_map_half_A.mrc (#16) relative to
    18911 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18912 Matrix rotation and translation 
    18913 0.99999262 0.00086300 -0.00374493 -0.00440355 
    18914 -0.00084638 0.99998980 0.00443601 -0.04656357 
    18915 0.00374872 -0.00443280 0.99998315 0.35139305 
    18916 Axis -0.75569566 -0.63852116 -0.14565300 
    18917 Axis point 0.00000000 78.62510597 13.28594619 
    18918 Rotation angle (degrees) 0.33621225 
    18919 Shift along axis -0.01812188 
    18920  
    18921 
    18922 > fitmap #17 inMap #1
    18923 
    18924 Fit map cryosparc_P126_J4026_004_volume_map_half_B.mrc in map
    18925 W20_J3623_consensus_structure.mrc using 138078 points 
    18926 correlation = 0.906, correlation about mean = 0.2947, overlap = 1.874e+04 
    18927 steps = 56, shift = 0.632, angle = 0.326 degrees 
    18928  
    18929 Position of cryosparc_P126_J4026_004_volume_map_half_B.mrc (#17) relative to
    18930 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18931 Matrix rotation and translation 
    18932 0.99999516 0.00097527 -0.00295606 -0.10060790 
    18933 -0.00096120 0.99998823 0.00475526 -0.05419298 
    18934 0.00296066 -0.00475240 0.99998432 0.51671634 
    18935 Axis -0.83660673 -0.52062903 -0.17039538 
    18936 Axis point 0.00000000 109.57038951 9.00298594 
    18937 Rotation angle (degrees) 0.32557225 
    18938 Shift along axis 0.02433761 
    18939  
    18940 
    18941 > fitmap #18 inMap #1
    18942 
    18943 Fit map W20_J4026_004_volume_map_gammazeta_local.mrc in map
    18944 W20_J3623_consensus_structure.mrc using 138172 points 
    18945 correlation = 0.917, correlation about mean = 0.2905, overlap = 1.854e+04 
    18946 steps = 52, shift = 0.635, angle = 0.343 degrees 
    18947  
    18948 Position of W20_J4026_004_volume_map_gammazeta_local.mrc (#18) relative to
    18949 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    18950 Matrix rotation and translation 
    18951 0.99999273 0.00094755 -0.00369338 -0.01379933 
    18952 -0.00093047 0.99998888 0.00462325 -0.05119869 
    18953 0.00369772 -0.00461978 0.99998249 0.38867466 
    18954 Axis -0.77135465 -0.61680564 -0.15672526 
    18955 Axis point 0.00000000 83.44645675 13.76857176 
    18956 Rotation angle (degrees) 0.34328547 
    18957 Shift along axis -0.01869132 
    18958  
    18959 
    18960 > volume resample #17 #16 #18 onGrid #1
    18961 
    18962 Opened cryosparc_P126_J4026_004_volume_map_half_B.mrc resampled as #19, grid
    18963 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18964 Opened cryosparc_P126_J4026_004_volume_map_half_A.mrc resampled as #20, grid
    18965 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18966 Opened W20_J4026_004_volume_map_gammazeta_local.mrc resampled as #21, grid
    18967 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    18968 
    18969 > save W20_J4026_halfA_consensus_resampled.mrc #20
    18970 
    18971 > save W20_J4026_halfB_consensus_resampled.mrc #19
    18972 
    18973 > save W20_J4026_consensus_resampled.mrc #21
    18974 
    18975 > close #16-18
    18976 
    18977 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18978 > resources/Processing/W20_MM_cyto_COPI/W20_J4026_consensus_resampled.mrc"
    18979 
    18980 Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
    18981 1.19, shown at level 0.26, step 1, values float32 
    18982 
    18983 > hide #!21 models
    18984 
    18985 > hide #!20 models
    18986 
    18987 > hide #!19 models
    18988 
    18989 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18990 > resources/Processing/W20_MM_cyto_COPI/W20_J4026_halfA_consensus_resampled.mrc"
    18991 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    18992 > resources/Processing/W20_MM_cyto_COPI/W20_J4026_halfB_consensus_resampled.mrc"
    18993 
    18994 Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
    18995 240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32 
    18996 Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
    18997 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    18998 
    18999 > rename #17 J4026_half_maps
    19000 
    19001 > close #19-21
    19002 
    19003 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19004 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4027_005_volume_map_half_A.mrc"
    19005 
    19006 Opened cryosparc_P126_J4027_005_volume_map_half_A.mrc as #18, grid size
    19007 240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32 
    19008 
    19009 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19010 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4027_005_volume_map_half_B.mrc"
    19011 
    19012 Opened cryosparc_P126_J4027_005_volume_map_half_B.mrc as #19, grid size
    19013 240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32 
    19014 
    19015 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19016 > resources/Processing/W20_MM_cyto_COPI/W20_J4027_005_volume_map_gammazeta_local.mrc"
    19017 
    19018 Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #20, grid size
    19019 240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32 
    19020 
    19021 > hide #!17 models
    19022 
    19023 > hide #!16 models
    19024 
    19025 > fitmap #18 inMap #1
    19026 
    19027 Fit map cryosparc_P126_J4027_005_volume_map_half_A.mrc in map
    19028 W20_J3623_consensus_structure.mrc using 138063 points 
    19029 correlation = 0.9242, correlation about mean = 0.4068, overlap = 1.895e+04 
    19030 steps = 64, shift = 0.865, angle = 0.418 degrees 
    19031  
    19032 Position of cryosparc_P126_J4027_005_volume_map_half_A.mrc (#18) relative to
    19033 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19034 Matrix rotation and translation 
    19035 0.99997669 -0.00229559 0.00643030 -1.04477946 
    19036 0.00227893 0.99999403 0.00259782 -0.33276084 
    19037 -0.00643622 -0.00258311 0.99997595 1.91301880 
    19038 Axis -0.35472898 0.88094699 0.31320880 
    19039 Axis point 263.82795379 0.00000000 126.10679381 
    19040 Rotation angle (degrees) 0.41841556 
    19041 Shift along axis 0.67664322 
    19042  
    19043 
    19044 > fitmap #19 inMap #1
    19045 
    19046 Fit map cryosparc_P126_J4027_005_volume_map_half_B.mrc in map
    19047 W20_J3623_consensus_structure.mrc using 138195 points 
    19048 correlation = 0.9253, correlation about mean = 0.4118, overlap = 1.9e+04 
    19049 steps = 68, shift = 0.852, angle = 0.431 degrees 
    19050  
    19051 Position of cryosparc_P126_J4027_005_volume_map_half_B.mrc (#19) relative to
    19052 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19053 Matrix rotation and translation 
    19054 0.99997498 -0.00277336 0.00650725 -0.98066980 
    19055 0.00275654 0.99999284 0.00259285 -0.39125472 
    19056 -0.00651439 -0.00257484 0.99997547 1.90493875 
    19057 Axis -0.34310644 0.86456626 0.36715549 
    19058 Axis point 252.66913251 0.00000000 114.89251767 
    19059 Rotation angle (degrees) 0.43148350 
    19060 Shift along axis 0.69761723 
    19061  
    19062 
    19063 > fitmap #20 inMap #1
    19064 
    19065 Fit map W20_J4027_005_volume_map_gammazeta_local.mrc in map
    19066 W20_J3623_consensus_structure.mrc using 138160 points 
    19067 correlation = 0.9373, correlation about mean = 0.4299, overlap = 1.864e+04 
    19068 steps = 64, shift = 0.871, angle = 0.411 degrees 
    19069  
    19070 Position of W20_J4027_005_volume_map_gammazeta_local.mrc (#20) relative to
    19071 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19072 Matrix rotation and translation 
    19073 0.99997680 -0.00234496 0.00639584 -1.04246365 
    19074 0.00233059 0.99999474 0.00225441 -0.28336984 
    19075 -0.00640109 -0.00223945 0.99997701 1.85486702 
    19076 Axis -0.31324184 0.89200052 0.32590584 
    19077 Axis point 254.76967129 0.00000000 130.69543046 
    19078 Rotation angle (degrees) 0.41099531 
    19079 Shift along axis 0.67828918 
    19080  
    19081 
    19082 > volume resample #19 #20 #18 onGrid #1
    19083 
    19084 Opened cryosparc_P126_J4027_005_volume_map_half_B.mrc resampled as #21, grid
    19085 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19086 Opened W20_J4027_005_volume_map_gammazeta_local.mrc resampled as #22, grid
    19087 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19088 Opened cryosparc_P126_J4027_005_volume_map_half_A.mrc resampled as #23, grid
    19089 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19090 
    19091 > save W20_J4027_halfB_consensus_resampled.mrc #21
    19092 
    19093 > save W20_J4027_halfA_consensus_resampled.mrc #23
    19094 
    19095 > save W20_J4027_consensus_resampled.mrc #22
    19096 
    19097 > close #18-20
    19098 
    19099 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19100 > resources/Processing/W20_MM_cyto_COPI/W20_J4027_consensus_resampled.mrc"
    19101 
    19102 Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
    19103 1.19, shown at level 0.253, step 1, values float32 
    19104 
    19105 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19106 > resources/Processing/W20_MM_cyto_COPI/W20_J4027_halfA_consensus_resampled.mrc"
    19107 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19108 > resources/Processing/W20_MM_cyto_COPI/W20_J4027_halfB_consensus_resampled.mrc"
    19109 
    19110 Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
    19111 240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32 
    19112 Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
    19113 240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32 
    19114 
    19115 > rename #19 J4017_half_maps
    19116 
    19117 > rename #19 J4027_half_maps
    19118 
    19119 > close #21-23
    19120 
    19121 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19122 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4028_004_volume_map_half_A.mrc"
    19123 
    19124 Opened cryosparc_P126_J4028_004_volume_map_half_A.mrc as #20, grid size
    19125 240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32 
    19126 
    19127 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19128 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4028_004_volume_map_half_B.mrc"
    19129 
    19130 Opened cryosparc_P126_J4028_004_volume_map_half_B.mrc as #21, grid size
    19131 240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32 
    19132 
    19133 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19134 > resources/Processing/W20_MM_cyto_COPI/W20_J4028_004_volume_map_gammazeta_local.mrc"
    19135 
    19136 Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #22, grid size
    19137 240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32 
    19138 
    19139 > hide #!19 models
    19140 
    19141 > hide #!18 models
    19142 
    19143 > fitmap #20 inMap #1
    19144 
    19145 Fit map cryosparc_P126_J4028_004_volume_map_half_A.mrc in map
    19146 W20_J3623_consensus_structure.mrc using 138211 points 
    19147 correlation = 0.9192, correlation about mean = 0.3816, overlap = 1.899e+04 
    19148 steps = 52, shift = 0.522, angle = 0.296 degrees 
    19149  
    19150 Position of cryosparc_P126_J4028_004_volume_map_half_A.mrc (#20) relative to
    19151 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19152 Matrix rotation and translation 
    19153 0.99998706 0.00198963 -0.00468116 0.25998221 
    19154 -0.00198544 0.99999762 0.00090051 0.55733772 
    19155 0.00468294 -0.00089120 0.99998864 -0.22070790 
    19156 Axis -0.17345663 -0.90654298 -0.38482804 
    19157 Axis point 85.46846238 0.00000000 38.05634596 
    19158 Rotation angle (degrees) 0.29591860 
    19159 Shift along axis -0.46541164 
    19160  
    19161 
    19162 > fitmap #21 inMap #1
    19163 
    19164 Fit map cryosparc_P126_J4028_004_volume_map_half_B.mrc in map
    19165 W20_J3623_consensus_structure.mrc using 138125 points 
    19166 correlation = 0.9186, correlation about mean = 0.3805, overlap = 1.898e+04 
    19167 steps = 48, shift = 0.516, angle = 0.21 degrees 
    19168  
    19169 Position of cryosparc_P126_J4028_004_volume_map_half_B.mrc (#21) relative to
    19170 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19171 Matrix rotation and translation 
    19172 0.99999365 0.00064252 -0.00350470 0.30153938 
    19173 -0.00063949 0.99999942 0.00086460 0.34856397 
    19174 0.00350526 -0.00086235 0.99999348 -0.04103359 
    19175 Axis -0.23552090 -0.95601319 -0.17483906 
    19176 Axis point 31.62231369 0.00000000 59.29711678 
    19177 Rotation angle (degrees) 0.21006100 
    19178 Shift along axis -0.39707630 
    19179  
    19180 
    19181 > fitmap #22 inMap #1
    19182 
    19183 Fit map W20_J4028_004_volume_map_gammazeta_local.mrc in map
    19184 W20_J3623_consensus_structure.mrc using 138218 points 
    19185 correlation = 0.9302, correlation about mean = 0.3927, overlap = 1.873e+04 
    19186 steps = 52, shift = 0.535, angle = 0.265 degrees 
    19187  
    19188 Position of W20_J4028_004_volume_map_gammazeta_local.mrc (#22) relative to
    19189 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19190 Matrix rotation and translation 
    19191 0.99998992 0.00112578 -0.00434648 0.33637900 
    19192 -0.00112111 0.99999879 0.00107657 0.40418343 
    19193 0.00434769 -0.00107168 0.99998997 -0.12603288 
    19194 Axis -0.23266548 -0.94161994 -0.24334886 
    19195 Axis point 53.07995958 0.00000000 54.34764883 
    19196 Rotation angle (degrees) 0.26451275 
    19197 Shift along axis -0.42818100 
    19198  
    19199 
    19200 > volume resample #21 #20 #22 onGrid #1
    19201 
    19202 Opened cryosparc_P126_J4028_004_volume_map_half_B.mrc resampled as #23, grid
    19203 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19204 Opened cryosparc_P126_J4028_004_volume_map_half_A.mrc resampled as #91, grid
    19205 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19206 Opened W20_J4028_004_volume_map_gammazeta_local.mrc resampled as #92, grid
    19207 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19208 
    19209 > save W20_J4028_halfA_consensus_resampled.mrc #91
    19210 
    19211 > save W20_J4028_halfB_consensus_resampled.mrc #23
    19212 
    19213 > save W20_J4028_consensus_resampled.mrc #92
    19214 
    19215 > close #20-22
    19216 
    19217 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19218 > resources/Processing/W20_MM_cyto_COPI/W20_J4028_consensus_resampled.mrc"
    19219 
    19220 Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
    19221 1.19, shown at level 0.255, step 1, values float32 
    19222 
    19223 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19224 > resources/Processing/W20_MM_cyto_COPI/W20_J4028_halfA_consensus_resampled.mrc"
    19225 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19226 > resources/Processing/W20_MM_cyto_COPI/W20_J4028_halfB_consensus_resampled.mrc"
    19227 
    19228 Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
    19229 240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32 
    19230 Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
    19231 240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32 
    19232 
    19233 > rename #21 J4028_half_maps
    19234 
    19235 > combine #24
    19236 
    19237 [Repeated 1 time(s)]
    19238 
    19239 > close #22-24
    19240 
    19241 > close #25
    19242 
    19243 > close #26
    19244 
    19245 > close #27
    19246 
    19247 > hide #!93 models
    19248 
    19249 > hide #!92 models
    19250 
    19251 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19252 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3988_003_volume_map_half_A.mrc"
    19253 
    19254 Opened cryosparc_P126_J3988_003_volume_map_half_A.mrc as #22, grid size
    19255 240,240,240, pixel 1.2, shown at level 0.291, step 1, values float32 
    19256 
    19257 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19258 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3988_003_volume_map_half_B.mrc"
    19259 
    19260 Opened cryosparc_P126_J3988_003_volume_map_half_B.mrc as #23, grid size
    19261 240,240,240, pixel 1.2, shown at level 0.291, step 1, values float32 
    19262 
    19263 > select add #22
    19264 
    19265 2 models selected 
    19266 
    19267 > select add #23
    19268 
    19269 4 models selected 
    19270 
    19271 > hide #!21 models
    19272 
    19273 > hide #!20 models
    19274 
    19275 > ui mousemode right "rotate selected models"
    19276 
    19277 > view matrix models
    19278 > #22,-0.85576,-0.11016,-0.5055,355.25,-0.33846,0.85818,0.38596,14.029,0.3913,0.50138,-0.77169,124.47,#23,-0.85576,-0.11016,-0.5055,355.25,-0.33846,0.85818,0.38596,14.029,0.3913,0.50138,-0.77169,124.47
    19279 
    19280 > view matrix models
    19281 > #22,-0.53192,-0.84561,0.044824,336.27,-0.68771,0.46227,0.55979,96.534,-0.49408,0.26694,-0.82742,293.75,#23,-0.53192,-0.84561,0.044824,336.27,-0.68771,0.46227,0.55979,96.534,-0.49408,0.26694,-0.82742,293.75
    19282 
    19283 > ui mousemode right "translate selected models"
    19284 
    19285 > view matrix models
    19286 > #22,-0.53192,-0.84561,0.044824,335.35,-0.68771,0.46227,0.55979,94.798,-0.49408,0.26694,-0.82742,289.5,#23,-0.53192,-0.84561,0.044824,335.35,-0.68771,0.46227,0.55979,94.798,-0.49408,0.26694,-0.82742,289.5
    19287 
    19288 > view matrix models
    19289 > #22,-0.53192,-0.84561,0.044824,337.81,-0.68771,0.46227,0.55979,89.918,-0.49408,0.26694,-0.82742,289.61,#23,-0.53192,-0.84561,0.044824,337.81,-0.68771,0.46227,0.55979,89.918,-0.49408,0.26694,-0.82742,289.61
    19290 
    19291 > hide #!91 models
    19292 
    19293 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19294 > resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc"
    19295 
    19296 Opened
    19297 W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
    19298 #24, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
    19299 float32 
    19300 
    19301 > select add #24
    19302 
    19303 6 models selected 
    19304 
    19305 > select subtract #23
    19306 
    19307 4 models selected 
    19308 
    19309 > select subtract #22
    19310 
    19311 2 models selected 
    19312 
    19313 > view matrix models #24,1,0,0,4.4068,0,1,0,-1.5627,0,0,1,7.0623
    19314 
    19315 > show #!1 models
    19316 
    19317 > ui mousemode right "rotate selected models"
    19318 
    19319 > view matrix models
    19320 > #24,-0.59721,0.29169,0.74717,82.383,0.43729,-0.66251,0.60816,89.121,0.6724,0.68993,0.2681,-83.296
    19321 
    19322 > view matrix models
    19323 > #24,0.58998,-0.6462,-0.4841,224.91,-0.8066,-0.49879,-0.31719,374.29,-0.036497,0.57761,-0.8155,188.31
    19324 
    19325 > view matrix models
    19326 > #24,-0.46477,-0.87473,-0.13728,358.04,-0.68335,0.25576,0.68383,105.04,-0.56305,0.41163,-0.71661,272.86
    19327 
    19328 > fitmap #22 inMap #1
    19329 
    19330 Fit map cryosparc_P126_J3988_003_volume_map_half_A.mrc in map
    19331 W20_J3623_consensus_structure.mrc using 138175 points 
    19332 correlation = 0.9519, correlation about mean = 0.5985, overlap = 2.143e+04 
    19333 steps = 320, shift = 8.89, angle = 19.2 degrees 
    19334  
    19335 Position of cryosparc_P126_J3988_003_volume_map_half_A.mrc (#22) relative to
    19336 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19337 Matrix rotation and translation 
    19338 -0.33642694 -0.92057260 -0.19840110 353.49844057 
    19339 -0.77937135 0.15392648 0.60736063 147.09880294 
    19340 -0.52858037 0.35896062 -0.76925292 278.05341217 
    19341 Axis -0.56888343 0.75617354 0.32337782 
    19342 Axis point 252.39557005 0.00000000 81.74420969 
    19343 Rotation angle (degrees) 167.38948043 
    19344 Shift along axis 0.04912198 
    19345  
    19346 
    19347 > fitmap #23 inMap #1
    19348 
    19349 Fit map cryosparc_P126_J3988_003_volume_map_half_B.mrc in map
    19350 W20_J3623_consensus_structure.mrc using 138208 points 
    19351 correlation = 0.9526, correlation about mean = 0.6, overlap = 2.142e+04 
    19352 steps = 324, shift = 8.99, angle = 19.2 degrees 
    19353  
    19354 Position of cryosparc_P126_J3988_003_volume_map_half_B.mrc (#23) relative to
    19355 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19356 Matrix rotation and translation 
    19357 -0.33657596 -0.92064163 -0.19782722 353.45179614 
    19358 -0.77865335 0.15396136 0.60827203 146.98371640 
    19359 -0.52954280 0.35876857 -0.76868038 278.15909277 
    19360 Axis -0.56874816 0.75615237 0.32366516 
    19361 Axis point 252.42080897 0.00000000 81.66752530 
    19362 Rotation angle (degrees) 167.32947007 
    19363 Shift along axis 0.14743379 
    19364  
    19365 
    19366 > fitmap #24 inMap #1
    19367 
    19368 Fit map
    19369 W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc in
    19370 map W20_J3623_consensus_structure.mrc using 138204 points 
    19371 correlation = 0.9643, correlation about mean = 0.6577, overlap = 2.107e+04 
    19372 steps = 104, shift = 5.31, angle = 9.46 degrees 
    19373  
    19374 Position of
    19375 W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
    19376 (#24) relative to W20_J3623_consensus_structure.mrc (#1) coordinates: 
    19377 Matrix rotation and translation 
    19378 -0.33645113 -0.92061038 -0.19818457 353.46943026 
    19379 -0.77924371 0.15400594 0.60750421 147.10114448 
    19380 -0.52875310 0.35882956 -0.76919534 278.08170115 
    19381 Axis -0.56885571 0.75619205 0.32338333 
    19382 Axis point 252.40251661 0.00000000 81.72856043 
    19383 Rotation angle (degrees) 167.37468234 
    19384 Shift along axis 0.09059859 
    19385  
    19386 
    19387 > select subtract #24
    19388 
    19389 Nothing selected 
    19390 
    19391 > volume resample #24 #23 #22 onGrid #1
    19392 
    19393 Opened
    19394 W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
    19395 resampled as #25, grid size 240,240,240, pixel 1.19, shown at step 1, values
    19396 float32 
    19397 Opened cryosparc_P126_J3988_003_volume_map_half_B.mrc resampled as #26, grid
    19398 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19399 Opened cryosparc_P126_J3988_003_volume_map_half_A.mrc resampled as #27, grid
    19400 size 240,240,240, pixel 1.19, shown at step 1, values float32 
    19401 
    19402 > save W20_J3988_halfB_consensus_resampled.mrc #26
    19403 
    19404 > save W20_J3988_halfA_consensus_resampled.mrc #27
    19405 
    19406 > save W20_J3988_consensus_resampled.mrc #25
    19407 
    19408 > close #22-24
    19409 
    19410 > hide #!25 models
    19411 
    19412 > hide #!26 models
    19413 
    19414 > hide #!27 models
    19415 
    19416 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19417 > resources/Processing/W20_MM_cyto_COPI/W20_J3988_consensus_resampled.mrc"
    19418 
    19419 Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
    19420 1.19, shown at level 0.286, step 1, values float32 
    19421 
    19422 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19423 > resources/Processing/W20_MM_cyto_COPI/W20_J3988_halfA_consensus_resampled.mrc"
    19424 > "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19425 > resources/Processing/W20_MM_cyto_COPI/W20_J3988_halfB_consensus_resampled.mrc"
    19426 
    19427 Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
    19428 240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32 
    19429 Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
    19430 240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32 
    19431 
    19432 > rename #23 J3988_half_maps
    19433 
    19434 > close #25-27
    19435 
    19436 > show #!28 models
    19437 
    19438 > hide #!28 models
    19439 
    19440 > rename #28 COPI_cyto_for_J4027_v1
    19441 
    19442 > hide #!23 models
    19443 
    19444 > hide #!22 models
    19445 
    19446 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19447 > resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
    19448 
    19449 > open
    19450 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/LocalResolution_21/W20_J3623_consensus_structure_full.ccp4
    19451 
    19452 Opened W20_J3623_consensus_structure_full.ccp4 as #24, grid size 240,240,240,
    19453 pixel 1.19, shown at level 0.257, step 1, values float32 
    19454 
    19455 > open
    19456 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/LocalResolution_21/W20_J3623_consensus_structure_local_resolution.ccp4
    19457 
    19458 Opened W20_J3623_consensus_structure_local_resolution.ccp4 as #25, grid size
    19459 240,240,240, pixel 1.19, shown at level 14, step 1, values float32 
    19460 
    19461 > hide #!25 models
    19462 
    19463 > show #!25 models
    19464 
    19465 > hide #!25 models
    19466 
    19467 > hide #!24 models
    19468 
    19469 > show #!24 models
    19470 
    19471 > hide #!1 models
    19472 
    19473 > color sample #24 map #2 palette
    19474 > 2.0,purple:2.3,indigo:2.5,blue:2.8,cyan:3.0,lime:3.2, yellow:3.5,
    19475 > red:4.0,salmon:5.0,pink
    19476 
    19477 Invalid "palette" argument: Missing color name or specifier 
    19478 
    19479 > color sample #24 map #2
    19480 
    19481 Map values for surface "surface": minimum -19.22, mean 2.61, maximum 22.06 
    19482 
    19483 > close #24-25
    19484 
    19485 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    19486 > resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
    19487 
    19488 > combine #27
    19489 
    19490 No structures specified 
    19491 
    19492 > combine #29
    19493 
    19494 No structures specified 
    19495 
    19496 > combine #28
    19497 
    19498 > rename #24 COPI_cyto_for_J4027_v1
    19499 
    19500 > split #24 chains
    19501 
    19502 Split COPI_cyto_for_J4027_v1 (#24) into 13 models 
    19503 Chain information for COPI_cyto_for_J4027_v1 A #24.1 
    19504 --- 
    19505 Chain | Description 
    19506 A | No description available 
    19507  
    19508 Chain information for COPI_cyto_for_J4027_v1 B #24.2 
    19509 --- 
    19510 Chain | Description 
    19511 B | No description available 
    19512  
    19513 Chain information for COPI_cyto_for_J4027_v1 C #24.3 
    19514 --- 
    19515 Chain | Description 
    19516 C | No description available 
    19517  
    19518 Chain information for COPI_cyto_for_J4027_v1 D #24.4 
    19519 --- 
    19520 Chain | Description 
    19521 D | No description available 
    19522  
    19523 Chain information for COPI_cyto_for_J4027_v1 E #24.5 
    19524 --- 
    19525 Chain | Description 
    19526 E | No description available 
    19527  
    19528 Chain information for COPI_cyto_for_J4027_v1 F #24.6 
    19529 --- 
    19530 Chain | Description 
    19531 F | No description available 
    19532  
    19533 Chain information for COPI_cyto_for_J4027_v1 G #24.7 
    19534 --- 
    19535 Chain | Description 
    19536 G | No description available 
    19537  
    19538 Chain information for COPI_cyto_for_J4027_v1 H #24.8 
    19539 --- 
    19540 Chain | Description 
    19541 H | No description available 
    19542  
    19543 Chain information for COPI_cyto_for_J4027_v1 I #24.9 
    19544 --- 
    19545 Chain | Description 
    19546 I | No description available 
    19547  
    19548 Chain information for COPI_cyto_for_J4027_v1 J #24.10 
    19549 --- 
    19550 Chain | Description 
    19551 J | No description available 
    19552  
    19553 Chain information for COPI_cyto_for_J4027_v1 K #24.11 
    19554 --- 
    19555 Chain | Description 
    19556 K | No description available 
    19557  
    19558 Chain information for COPI_cyto_for_J4027_v1 L #24.12 
    19559 --- 
    19560 Chain | Description 
    19561 L | No description available 
    19562  
    19563 Chain information for COPI_cyto_for_J4027_v1 M #24.13 
    19564 --- 
    19565 Chain | Description 
    19566 M | No description available 
    19567  
    19568 
    19569 > show #!1 models
    19570 
    19571 > color #1 darkgrey models
    19572 
    19573 > color #1 #a9a9a9c0 models
    19574 
    19575 > rename #24 COPI_cyto_J3623_model
    19576 
    19577 > hide #!24 models
    19578 
    19579 > show #!24 models
    19580 
    19581 > hide #!1 models
    19582 
    19583 > hide #!24 models
    19584 
    19585 > combine #28
    19586 
    19587 > split #25 chains
    19588 
    19589 Split copy of COPI_cyto_for_J4027_v1 (#25) into 13 models 
    19590 Chain information for copy of COPI_cyto_for_J4027_v1 A #25.1 
    19591 --- 
    19592 Chain | Description 
    19593 A | No description available 
    19594  
    19595 Chain information for copy of COPI_cyto_for_J4027_v1 B #25.2 
    19596 --- 
    19597 Chain | Description 
    19598 B | No description available 
    19599  
    19600 Chain information for copy of COPI_cyto_for_J4027_v1 C #25.3 
    19601 --- 
    19602 Chain | Description 
    19603 C | No description available 
    19604  
    19605 Chain information for copy of COPI_cyto_for_J4027_v1 D #25.4 
    19606 --- 
    19607 Chain | Description 
    19608 D | No description available 
    19609  
    19610 Chain information for copy of COPI_cyto_for_J4027_v1 E #25.5 
    19611 --- 
    19612 Chain | Description 
    19613 E | No description available 
    19614  
    19615 Chain information for copy of COPI_cyto_for_J4027_v1 F #25.6 
    19616 --- 
    19617 Chain | Description 
    19618 F | No description available 
    19619  
    19620 Chain information for copy of COPI_cyto_for_J4027_v1 G #25.7 
    19621 --- 
    19622 Chain | Description 
    19623 G | No description available 
    19624  
    19625 Chain information for copy of COPI_cyto_for_J4027_v1 H #25.8 
    19626 --- 
    19627 Chain | Description 
    19628 H | No description available 
    19629  
    19630 Chain information for copy of COPI_cyto_for_J4027_v1 I #25.9 
    19631 --- 
    19632 Chain | Description 
    19633 I | No description available 
    19634  
    19635 Chain information for copy of COPI_cyto_for_J4027_v1 J #25.10 
    19636 --- 
    19637 Chain | Description 
    19638 J | No description available 
    19639  
    19640 Chain information for copy of COPI_cyto_for_J4027_v1 K #25.11 
    19641 --- 
    19642 Chain | Description 
    19643 K | No description available 
    19644  
    19645 Chain information for copy of COPI_cyto_for_J4027_v1 L #25.12 
    19646 --- 
    19647 Chain | Description 
    19648 L | No description available 
    19649  
    19650 Chain information for copy of COPI_cyto_for_J4027_v1 M #25.13 
    19651 --- 
    19652 Chain | Description 
    19653 M | No description available 
    19654  
    19655 
    19656 > show #!4 models
    19657 
    19658 > rename #25 COPI_cyto_for_J4027_v1
    19659 
    19660 > rename #25 COPI_cyto_J3987_model
    19661 
    19662 > fitmap #25.1 inMap #4
    19663 
    19664 Fit molecule copy of COPI_cyto_for_J4027_v1 A (#25.1) to map
    19665 W20_J3987_consensus_resampled.mrc (#4) using 2590 atoms 
    19666 average map value = 0.3221, steps = 104 
    19667 shifted from previous position = 0.721 
    19668 rotated from previous position = 1.24 degrees 
    19669 atoms outside contour = 795, contour level = 0.27665 
    19670  
    19671 Position of copy of COPI_cyto_for_J4027_v1 A (#25.1) relative to
    19672 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19673 Matrix rotation and translation 
    19674 -0.38689637 -0.90569538 -0.17328327 278.18188435 
    19675 -0.79467842 0.23216071 0.56088111 163.52034472 
    19676 -0.46775786 0.35470734 -0.80955871 239.74100561 
    19677 Axis -0.54800188 0.78270203 0.29507876 
    19678 Axis point 210.04111237 0.00000000 70.64408205 
    19679 Rotation angle (degrees) 169.15725379 
    19680 Shift along axis 46.28598736 
    19681  
    19682 
    19683 > fitmap #25.2 inMap #4
    19684 
    19685 Fit molecule copy of COPI_cyto_for_J4027_v1 B (#25.2) to map
    19686 W20_J3987_consensus_resampled.mrc (#4) using 2426 atoms 
    19687 average map value = 0.3153, steps = 72 
    19688 shifted from previous position = 0.757 
    19689 rotated from previous position = 2.26 degrees 
    19690 atoms outside contour = 839, contour level = 0.27665 
    19691  
    19692 Position of copy of COPI_cyto_for_J4027_v1 B (#25.2) relative to
    19693 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19694 Matrix rotation and translation 
    19695 -0.39471401 -0.89888974 -0.19025799 280.36384015 
    19696 -0.79142130 0.22743083 0.56738660 162.69216971 
    19697 -0.46674746 0.37452966 -0.80117062 238.28935068 
    19698 Axis -0.54506838 0.78143761 0.30373627 
    19699 Axis point 209.70723896 0.00000000 70.08028018 
    19700 Rotation angle (degrees) 169.81012722 
    19701 Shift along axis 46.69343412 
    19702  
    19703 
    19704 > fitmap #25.3 inMap #4
    19705 
    19706 Fit molecule copy of COPI_cyto_for_J4027_v1 C (#25.3) to map
    19707 W20_J3987_consensus_resampled.mrc (#4) using 1612 atoms 
    19708 average map value = 0.3176, steps = 56 
    19709 shifted from previous position = 0.728 
    19710 rotated from previous position = 2.04 degrees 
    19711 atoms outside contour = 641, contour level = 0.27665 
    19712  
    19713 Position of copy of COPI_cyto_for_J4027_v1 C (#25.3) relative to
    19714 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19715 Matrix rotation and translation 
    19716 -0.39605343 -0.89988782 -0.18260232 278.68660008 
    19717 -0.79444663 0.23610267 0.55956242 163.22266002 
    19718 -0.46043050 0.36668441 -0.80842211 238.93411170 
    19719 Axis -0.54443563 0.78422400 0.29762824 
    19720 Axis point 208.79769571 0.00000000 71.16300785 
    19721 Rotation angle (degrees) 169.79703161 
    19722 Shift along axis 47.38975067 
    19723  
    19724 
    19725 > fitmap #25.4 inMap #4
    19726 
    19727 Fit molecule copy of COPI_cyto_for_J4027_v1 D (#25.4) to map
    19728 W20_J3987_consensus_resampled.mrc (#4) using 4745 atoms 
    19729 average map value = 0.3393, steps = 64 
    19730 shifted from previous position = 0.197 
    19731 rotated from previous position = 0.999 degrees 
    19732 atoms outside contour = 1721, contour level = 0.27665 
    19733  
    19734 Position of copy of COPI_cyto_for_J4027_v1 D (#25.4) relative to
    19735 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19736 Matrix rotation and translation 
    19737 -0.36755215 -0.91697806 -0.15510211 274.92468941 
    19738 -0.80291601 0.22872446 0.55046437 165.41983596 
    19739 -0.46928810 0.32685833 -0.82032452 243.67714165 
    19740 Axis -0.55602986 0.78127043 0.28363236 
    19741 Axis point 211.32871948 0.00000000 72.29578138 
    19742 Rotation angle (degrees) 168.40024254 
    19743 Shift along axis 45.48601304 
    19744  
    19745 
    19746 > fitmap #25.5 inMap #4
    19747 
    19748 Fit molecule copy of COPI_cyto_for_J4027_v1 E (#25.5) to map
    19749 W20_J3987_consensus_resampled.mrc (#4) using 1876 atoms 
    19750 average map value = 0.3141, steps = 48 
    19751 shifted from previous position = 0.53 
    19752 rotated from previous position = 0.888 degrees 
    19753 atoms outside contour = 674, contour level = 0.27665 
    19754  
    19755 Position of copy of COPI_cyto_for_J4027_v1 E (#25.5) relative to
    19756 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19757 Matrix rotation and translation 
    19758 -0.38334136 -0.90913799 -0.16284208 277.17803202 
    19759 -0.79171318 0.23265338 0.56485632 162.82482750 
    19760 -0.47564657 0.34545700 -0.80896218 242.10131222 
    19761 Axis -0.54889072 0.78257074 0.29377205 
    19762 Axis point 210.42677765 0.00000000 70.96904172 
    19763 Rotation angle (degrees) 168.47140268 
    19764 Shift along axis 46.40409379 
    19765  
    19766 
    19767 > fitmap #25.6 inMap #4
    19768 
    19769 Fit molecule copy of COPI_cyto_for_J4027_v1 F (#25.6) to map
    19770 W20_J3987_consensus_resampled.mrc (#4) using 2400 atoms 
    19771 average map value = 0.2626, steps = 84 
    19772 shifted from previous position = 2.71 
    19773 rotated from previous position = 2.99 degrees 
    19774 atoms outside contour = 1310, contour level = 0.27665 
    19775  
    19776 Position of copy of COPI_cyto_for_J4027_v1 F (#25.6) relative to
    19777 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19778 Matrix rotation and translation 
    19779 -0.40199255 -0.90304968 -0.15133829 274.52161881 
    19780 -0.76596507 0.24109454 0.59596221 157.65702153 
    19781 -0.50169664 0.35549220 -0.78862272 240.80158217 
    19782 Axis -0.53855753 0.78466390 0.30701522 
    19783 Axis point 207.61107533 0.00000000 67.84938526 
    19784 Rotation angle (degrees) 167.09978512 
    19785 Shift along axis 49.79183984 
    19786  
    19787 
    19788 > fitmap #25.7 inMap #4
    19789 
    19790 Fit molecule copy of COPI_cyto_for_J4027_v1 G (#25.7) to map
    19791 W20_J3987_consensus_resampled.mrc (#4) using 2302 atoms 
    19792 average map value = 0.2759, steps = 60 
    19793 shifted from previous position = 1.78 
    19794 rotated from previous position = 1.99 degrees 
    19795 atoms outside contour = 1124, contour level = 0.27665 
    19796  
    19797 Position of copy of COPI_cyto_for_J4027_v1 G (#25.7) relative to
    19798 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19799 Matrix rotation and translation 
    19800 -0.37472415 -0.90717861 -0.19133425 277.62448174 
    19801 -0.79104565 0.20520230 0.57631485 166.08473990 
    19802 -0.48355827 0.36731321 -0.79451395 238.83413932 
    19803 Axis -0.55353568 0.77394812 0.30757528 
    19804 Axis point 211.98709934 0.00000000 67.68536340 
    19805 Rotation angle (degrees) 169.11794633 
    19806 Shift along axis 48.32539250 
    19807  
    19808 
    19809 > fitmap #25.8 inMap #4
    19810 
    19811 Fit molecule copy of COPI_cyto_for_J4027_v1 H (#25.8) to map
    19812 W20_J3987_consensus_resampled.mrc (#4) using 420 atoms 
    19813 average map value = 0.339, steps = 56 
    19814 shifted from previous position = 1.73 
    19815 rotated from previous position = 4.37 degrees 
    19816 atoms outside contour = 139, contour level = 0.27665 
    19817  
    19818 Position of copy of COPI_cyto_for_J4027_v1 H (#25.8) relative to
    19819 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19820 Matrix rotation and translation 
    19821 -0.30262332 -0.93808653 -0.16856100 274.79297984 
    19822 -0.83162161 0.17348487 0.52754953 176.28282750 
    19823 -0.46564432 0.29982776 -0.83263359 248.60795718 
    19824 Axis -0.58515271 0.76338380 0.27357170 
    19825 Axis point 220.21870033 0.00000000 73.46391590 
    19826 Rotation angle (degrees) 168.77962388 
    19827 Shift along axis 41.78769794 
    19828  
    19829 
    19830 > fitmap #25.9 inMap #4
    19831 
    19832 Fit molecule copy of COPI_cyto_for_J4027_v1 I (#25.9) to map
    19833 W20_J3987_consensus_resampled.mrc (#4) using 1573 atoms 
    19834 average map value = 0.3297, steps = 60 
    19835 shifted from previous position = 0.384 
    19836 rotated from previous position = 0.597 degrees 
    19837 atoms outside contour = 540, contour level = 0.27665 
    19838  
    19839 Position of copy of COPI_cyto_for_J4027_v1 I (#25.9) relative to
    19840 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19841 Matrix rotation and translation 
    19842 -0.37451788 -0.91088738 -0.17326443 276.29637371 
    19843 -0.79727848 0.22096017 0.56171491 164.46884657 
    19844 -0.47337448 0.34851227 -0.80898443 241.62397254 
    19845 Axis -0.55339354 0.77897237 0.29488579 
    19846 Axis point 210.79260550 0.00000000 70.83395311 
    19847 Rotation angle (degrees) 168.89357390 
    19848 Shift along axis 46.46753453 
    19849  
    19850 
    19851 > fitmap #25.10 inMap #4
    19852 
    19853 Fit molecule copy of COPI_cyto_for_J4027_v1 J (#25.10) to map
    19854 W20_J3987_consensus_resampled.mrc (#4) using 1112 atoms 
    19855 average map value = 0.3174, steps = 56 
    19856 shifted from previous position = 0.808 
    19857 rotated from previous position = 4.24 degrees 
    19858 atoms outside contour = 445, contour level = 0.27665 
    19859  
    19860 Position of copy of COPI_cyto_for_J4027_v1 J (#25.10) relative to
    19861 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19862 Matrix rotation and translation 
    19863 -0.37184146 -0.92295368 -0.09945074 269.60235343 
    19864 -0.79986239 0.26418072 0.53891439 164.53018199 
    19865 -0.47112005 0.27993762 -0.83646927 249.12759996 
    19866 Axis -0.55169100 0.79175677 0.26221794 
    19867 Axis point 209.92414105 0.00000000 75.11235729 
    19868 Rotation angle (degrees) 166.42536541 
    19869 Shift along axis 46.85641909 
    19870  
    19871 
    19872 > fitmap #25.11 inMap #4
    19873 
    19874 Fit molecule copy of COPI_cyto_for_J4027_v1 K (#25.11) to map
    19875 W20_J3987_consensus_resampled.mrc (#4) using 319 atoms 
    19876 average map value = 0.3247, steps = 356 
    19877 shifted from previous position = 18 
    19878 rotated from previous position = 29.8 degrees 
    19879 atoms outside contour = 122, contour level = 0.27665 
    19880  
    19881 Position of copy of COPI_cyto_for_J4027_v1 K (#25.11) relative to
    19882 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19883 Matrix rotation and translation 
    19884 -0.11497818 -0.99056474 0.07457564 250.16493380 
    19885 -0.55287660 0.12618381 0.82365352 113.16758699 
    19886 -0.82529237 0.05347106 -0.56216845 259.79352847 
    19887 Axis -0.60992918 0.71263081 0.34661756 
    19888 Axis point 236.76411941 0.00000000 37.20193482 
    19889 Rotation angle (degrees) 140.84869902 
    19890 Shift along axis 18.11281583 
    19891  
    19892 
    19893 > fitmap #25.12 inMap #4
    19894 
    19895 Fit molecule copy of COPI_cyto_for_J4027_v1 L (#25.12) to map
    19896 W20_J3987_consensus_resampled.mrc (#4) using 1420 atoms 
    19897 average map value = 0.2216, steps = 244 
    19898 shifted from previous position = 20 
    19899 rotated from previous position = 43.1 degrees 
    19900 atoms outside contour = 1209, contour level = 0.27665 
    19901  
    19902 Position of copy of COPI_cyto_for_J4027_v1 L (#25.12) relative to
    19903 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19904 Matrix rotation and translation 
    19905 -0.33704271 -0.93889900 0.06979181 244.25606438 
    19906 -0.21172527 0.14781713 0.96608619 12.69558044 
    19907 -0.91737377 0.31083561 -0.24860932 233.11919004 
    19908 Axis -0.47133855 0.71009352 0.52307472 
    19909 Axis point 190.36197930 0.00000000 40.21086330 
    19910 Rotation angle (degrees) 135.96517505 
    19911 Shift along axis 15.82650607 
    19912  
    19913 
    19914 > close #25
    19915 
    19916 > combine #28
    19917 
    19918 > color #4 darkgrey models
    19919 
    19920 > color #4 #a9a9a9bf models
    19921 
    19922 > rename #25 COPI_cyto_J3987_model
    19923 
    19924 > fitmap #25 inMap #4
    19925 
    19926 Fit molecule COPI_cyto_J3987_model (#25) to map
    19927 W20_J3987_consensus_resampled.mrc (#4) using 27347 atoms 
    19928 average map value = 0.2864, steps = 40 
    19929 shifted from previous position = 0.228 
    19930 rotated from previous position = 0.219 degrees 
    19931 atoms outside contour = 13455, contour level = 0.27665 
    19932  
    19933 Position of COPI_cyto_J3987_model (#25) relative to
    19934 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    19935 Matrix rotation and translation 
    19936 -0.37179442 -0.91394156 -0.16272598 275.88087564 
    19937 -0.79687792 0.22429417 0.56096143 164.32455600 
    19938 -0.47618747 0.33823507 -0.81169116 242.44716299 
    19939 Axis -0.55410562 0.77983932 0.29123460 
    19940 Axis point 211.23166983 0.00000000 70.92651391 
    19941 Rotation angle (degrees) 168.40582967 
    19942 Shift along axis 45.88860967 
    19943  
    19944 
    19945 > hide #!25 models
    19946 
    19947 > show #!24 models
    19948 
    19949 > combine #28
    19950 
    19951 > hide #!4 models
    19952 
    19953 > show #!6 models
    19954 
    19955 > color #6 darkgrey models
    19956 
    19957 > color #6 #a9a9a9bf models
    19958 
    19959 > fitmap #26 inMap #6
    19960 
    19961 Fit molecule copy of COPI_cyto_for_J4027_v1 (#26) to map
    19962 W20_J4021_consensus_resampled.mrc (#6) using 27347 atoms 
    19963 average map value = 0.2574, steps = 88 
    19964 shifted from previous position = 0.804 
    19965 rotated from previous position = 1.33 degrees 
    19966 atoms outside contour = 13999, contour level = 0.25941 
    19967  
    19968 Position of copy of COPI_cyto_for_J4027_v1 (#26) relative to
    19969 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    19970 Matrix rotation and translation 
    19971 -0.39044300 -0.90597356 -0.16360374 277.32294036 
    19972 -0.78887242 0.23762979 0.56675603 162.18357201 
    19973 -0.47458885 0.35034840 -0.80747844 241.34338581 
    19974 Axis -0.54571767 0.78421483 0.29529532 
    19975 Axis point 209.61127190 0.00000000 70.79010036 
    19976 Rotation angle (degrees) 168.56372015 
    19977 Shift along axis 47.11430470 
    19978  
    19979 
    19980 > rename #26 COPI_cyto_J4021_model
    19981 
    19982 > hide #!26 models
    19983 
    19984 > combine #28
    19985 
    19986 > close #29-33
    19987 
    19988 > rename #27 COPI_cyto_J4022_model
    19989 
    19990 > rename #28 COPI_cyto_J4023_model
    19991 
    19992 > combine #28
    19993 
    19994 > hide #!27 models
    19995 
    19996 > hide #!24 models
    19997 
    19998 > rename #29 COPI_cyto_J4024_model
    19999 
    20000 > combine #29
    20001 
    20002 [Repeated 1 time(s)]
    20003 
    20004 > rename #30 COPI_cyto_J4025_model
    20005 
    20006 > rename #31 COPI_cyto_J4026_model
    20007 
    20008 > combine #29
    20009 
    20010 > rename #32 COPI_cyto_J4027_model
    20011 
    20012 > combine #29
    20013 
    20014 > rename #33 COPI_cyto_J4028_model
    20015 
    20016 > hide #!29 models
    20017 
    20018 > hide #!30 models
    20019 
    20020 > hide #!31 models
    20021 
    20022 > hide #!32 models
    20023 
    20024 > hide #!33 models
    20025 
    20026 > combine #29
    20027 
    20028 > close #35-36,39#34,37-38
    20029 
    20030 > combine #29
    20031 
    20032 > rename #34 COPI_cyto_J3988_model
    20033 
    20034 > hide #!34 models
    20035 
    20036 > close #40
    20037 
    20038 > close #41
    20039 
    20040 > close #42-46
    20041 
    20042 > hide #!6 models
    20043 
    20044 > show #!6 models
    20045 
    20046 > hide #!6 models
    20047 
    20048 > show #!1 models
    20049 
    20050 > fitmap #24.1 inMap #1
    20051 
    20052 Fit molecule COPI_cyto_for_J4027_v1 A (#24.1) to map
    20053 W20_J3623_consensus_structure.mrc (#1) using 2590 atoms 
    20054 average map value = 0.3549, steps = 116 
    20055 shifted from previous position = 0.529 
    20056 rotated from previous position = 1.66 degrees 
    20057 atoms outside contour = 606, contour level = 0.25746 
    20058  
    20059 Position of COPI_cyto_for_J4027_v1 A (#24.1) relative to
    20060 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20061 Matrix rotation and translation 
    20062 -0.39542896 -0.90304867 -0.16774700 278.17983361 
    20063 -0.78821131 0.23986960 0.56673233 161.55778287 
    20064 -0.47154946 0.35632245 -0.80664455 240.52362588 
    20065 Axis -0.54371860 0.78505369 0.29675038 
    20066 Axis point 209.13140963 0.00000000 70.83505847 
    20067 Rotation angle (degrees) 168.84338449 
    20068 Shift along axis 46.95546224 
    20069  
    20070 
    20071 > fitmap #24.2 inMap #1
    20072 
    20073 Fit molecule COPI_cyto_for_J4027_v1 B (#24.2) to map
    20074 W20_J3623_consensus_structure.mrc (#1) using 2426 atoms 
    20075 average map value = 0.3443, steps = 84 
    20076 shifted from previous position = 1.05 
    20077 rotated from previous position = 2.23 degrees 
    20078 atoms outside contour = 613, contour level = 0.25746 
    20079  
    20080 Position of COPI_cyto_for_J4027_v1 B (#24.2) relative to
    20081 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20082 Matrix rotation and translation 
    20083 -0.39499091 -0.89904452 -0.18894748 279.87559115 
    20084 -0.79097752 0.22820260 0.56769548 163.08646468 
    20085 -0.46726520 0.37368776 -0.80126194 238.60471247 
    20086 Axis -0.54487475 0.78166114 0.30350844 
    20087 Axis point 209.64905720 0.00000000 70.09351394 
    20088 Rotation angle (degrees) 169.74498652 
    20089 Shift along axis 47.39975428 
    20090  
    20091 
    20092 > fitmap #24.3 inMap #1
    20093 
    20094 Fit molecule COPI_cyto_for_J4027_v1 C (#24.3) to map
    20095 W20_J3623_consensus_structure.mrc (#1) using 1612 atoms 
    20096 average map value = 0.3398, steps = 68 
    20097 shifted from previous position = 0.582 
    20098 rotated from previous position = 1.57 degrees 
    20099 atoms outside contour = 545, contour level = 0.25746 
    20100  
    20101 Position of COPI_cyto_for_J4027_v1 C (#24.3) relative to
    20102 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20103 Matrix rotation and translation 
    20104 -0.38289473 -0.90536973 -0.18356823 277.48749747 
    20105 -0.80205073 0.22720768 0.55235071 164.98384273 
    20106 -0.45837350 0.35872321 -0.81314907 239.04481293 
    20107 Axis -0.55056634 0.78138966 0.29378038 
    20108 Axis point 209.64934014 0.00000000 71.32622789 
    20109 Rotation angle (degrees) 169.87222630 
    20110 Shift along axis 46.36806823 
    20111  
    20112 
    20113 > fitmap #24.4 inMap #1
    20114 
    20115 Fit molecule COPI_cyto_for_J4027_v1 D (#24.4) to map
    20116 W20_J3623_consensus_structure.mrc (#1) using 4745 atoms 
    20117 average map value = 0.3686, steps = 104 
    20118 shifted from previous position = 0.253 
    20119 rotated from previous position = 1.26 degrees 
    20120 atoms outside contour = 1389, contour level = 0.25746 
    20121  
    20122 Position of COPI_cyto_for_J4027_v1 D (#24.4) relative to
    20123 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20124 Matrix rotation and translation 
    20125 -0.36437524 -0.91895662 -0.15082912 274.51036554 
    20126 -0.80384056 0.22859535 0.54916713 165.68273324 
    20127 -0.47018193 0.32134547 -0.82198909 244.27756191 
    20128 Axis -0.55725502 0.78114152 0.28157552 
    20129 Axis point 211.66245571 0.00000000 72.46008698 
    20130 Rotation angle (degrees) 168.20479189 
    20131 Shift along axis 45.23196284 
    20132  
    20133 
    20134 > fitmap #24.5 inMap #1
    20135 
    20136 Fit molecule COPI_cyto_for_J4027_v1 E (#24.5) to map
    20137 W20_J3623_consensus_structure.mrc (#1) using 1876 atoms 
    20138 average map value = 0.352, steps = 52 
    20139 shifted from previous position = 0.551 
    20140 rotated from previous position = 2.49 degrees 
    20141 atoms outside contour = 518, contour level = 0.25746 
    20142  
    20143 Position of COPI_cyto_for_J4027_v1 E (#24.5) relative to
    20144 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20145 Matrix rotation and translation 
    20146 -0.40106793 -0.89989636 -0.17126318 279.30609803 
    20147 -0.77603258 0.23443438 0.58550318 159.37835572 
    20148 -0.48674220 0.36773235 -0.79237300 240.44712243 
    20149 Axis -0.54056671 0.78310515 0.30746375 
    20150 Axis point 209.32932986 0.00000000 69.11212793 
    20151 Rotation angle (degrees) 168.37950772 
    20152 Shift along axis 47.75520439 
    20153  
    20154 
    20155 > fitmap #24.6 inMap #1
    20156 
    20157 Fit molecule COPI_cyto_for_J4027_v1 F (#24.6) to map
    20158 W20_J3623_consensus_structure.mrc (#1) using 2400 atoms 
    20159 average map value = 0.1995, steps = 32 
    20160 shifted from previous position = 0.88 
    20161 rotated from previous position = 2.72 degrees 
    20162 atoms outside contour = 2236, contour level = 0.25746 
    20163  
    20164 Position of COPI_cyto_for_J4027_v1 F (#24.6) relative to
    20165 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20166 Matrix rotation and translation 
    20167 -0.34705513 -0.92807037 -0.13504869 272.53895474 
    20168 -0.78593629 0.20923862 0.58182761 162.32498204 
    20169 -0.51171956 0.30806592 -0.80202151 247.95535590 
    20170 Axis -0.56230557 0.77368067 0.29194291 
    20171 Axis point 214.01677259 0.00000000 69.57811076 
    20172 Rotation angle (degrees) 165.91105545 
    20173 Shift along axis 44.72633565 
    20174  
    20175 
    20176 > fitmap #24.7 inMap #1
    20177 
    20178 Fit molecule COPI_cyto_for_J4027_v1 G (#24.7) to map
    20179 W20_J3623_consensus_structure.mrc (#1) using 2302 atoms 
    20180 average map value = 0.2042, steps = 56 
    20181 shifted from previous position = 0.732 
    20182 rotated from previous position = 2.42 degrees 
    20183 atoms outside contour = 1956, contour level = 0.25746 
    20184  
    20185 Position of COPI_cyto_for_J4027_v1 G (#24.7) relative to
    20186 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20187 Matrix rotation and translation 
    20188 -0.40089736 -0.90460310 -0.14482596 274.53357578 
    20189 -0.79035024 0.26156664 0.55401210 159.12795064 
    20190 -0.46327942 0.33656522 -0.81981464 242.17863151 
    20191 Axis -0.54066936 0.79181649 0.28408325 
    20192 Axis point 206.28449602 0.00000000 73.32567888 
    20193 Rotation angle (degrees) 168.39926749 
    20194 Shift along axis 46.36713644 
    20195  
    20196 
    20197 > fitmap #24.8 inMap #1
    20198 
    20199 Fit molecule COPI_cyto_for_J4027_v1 H (#24.8) to map
    20200 W20_J3623_consensus_structure.mrc (#1) using 420 atoms 
    20201 average map value = 0.2665, steps = 72 
    20202 shifted from previous position = 1.63 
    20203 rotated from previous position = 6.63 degrees 
    20204 atoms outside contour = 172, contour level = 0.25746 
    20205  
    20206 Position of COPI_cyto_for_J4027_v1 H (#24.8) relative to
    20207 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20208 Matrix rotation and translation 
    20209 -0.32134690 -0.93539737 -0.14753964 274.57265625 
    20210 -0.85481390 0.21949425 0.47022919 174.99288921 
    20211 -0.40746704 0.27722563 -0.87012446 247.94129870 
    20212 Axis -0.57850272 0.77909809 0.24153833 
    20213 Axis point 215.13355776 0.00000000 80.87806975 
    20214 Rotation angle (degrees) 170.39742774 
    20215 Shift along axis 37.38292387 
    20216  
    20217 
    20218 > fitmap #24.9 inMap #1
    20219 
    20220 Fit molecule COPI_cyto_for_J4027_v1 I (#24.9) to map
    20221 W20_J3623_consensus_structure.mrc (#1) using 1573 atoms 
    20222 average map value = 0.3464, steps = 64 
    20223 shifted from previous position = 0.478 
    20224 rotated from previous position = 0.943 degrees 
    20225 atoms outside contour = 463, contour level = 0.25746 
    20226  
    20227 Position of COPI_cyto_for_J4027_v1 I (#24.9) relative to
    20228 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20229 Matrix rotation and translation 
    20230 -0.36293127 -0.91488242 -0.17683625 275.64058476 
    20231 -0.80647349 0.21333854 0.55144102 166.30863857 
    20232 -0.46677771 0.34274894 -0.81525564 240.90103613 
    20233 Axis -0.55901039 0.77664797 0.29038821 
    20234 Axis point 211.48290973 0.00000000 71.12426755 
    20235 Rotation angle (degrees) 169.24194914 
    20236 Shift along axis 45.03213770 
    20237  
    20238 
    20239 > fitmap #24.10 inMap #1
    20240 
    20241 Fit molecule COPI_cyto_for_J4027_v1 J (#24.10) to map
    20242 W20_J3623_consensus_structure.mrc (#1) using 1112 atoms 
    20243 average map value = 0.3459, steps = 52 
    20244 shifted from previous position = 0.38 
    20245 rotated from previous position = 3.4 degrees 
    20246 atoms outside contour = 351, contour level = 0.25746 
    20247  
    20248 Position of COPI_cyto_for_J4027_v1 J (#24.10) relative to
    20249 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20250 Matrix rotation and translation 
    20251 -0.36982106 -0.92265040 -0.10930983 270.39934908 
    20252 -0.79564879 0.25374928 0.55004938 163.22079540 
    20253 -0.47976598 0.29039208 -0.82794750 248.56734521 
    20254 Axis -0.55260110 0.78840254 0.27028405 
    20255 Axis point 210.23381150 0.00000000 73.93598950 
    20256 Rotation angle (degrees) 166.41185550 
    20257 Shift along axis 46.44450154 
    20258  
    20259 
    20260 > fitmap #24.11 inMap #1
    20261 
    20262 Fit molecule COPI_cyto_for_J4027_v1 K (#24.11) to map
    20263 W20_J3623_consensus_structure.mrc (#1) using 319 atoms 
    20264 average map value = 0.2981, steps = 324 
    20265 shifted from previous position = 19.5 
    20266 rotated from previous position = 32.5 degrees 
    20267 atoms outside contour = 138, contour level = 0.25746 
    20268  
    20269 Position of COPI_cyto_for_J4027_v1 K (#24.11) relative to
    20270 W20_J3623_consensus_structure.mrc (#1) coordinates: 
    20271 Matrix rotation and translation 
    20272 -0.06351642 -0.99614584 0.06049082 250.07246282 
    20273 -0.53379297 0.08512482 0.84131971 112.08368631 
    20274 -0.84322639 0.02114804 -0.53714247 260.93738590 
    20275 Axis -0.62845977 0.69247687 0.35427971 
    20276 Axis point 244.61405927 0.00000000 32.59441219 
    20277 Rotation angle (degrees) 139.26773764 
    20278 Shift along axis 12.89969989 
    20279  
    20280 
    20281 > split #25 chains
    20282 
    20283 Split COPI_cyto_J3987_model (#25) into 13 models 
    20284 Chain information for COPI_cyto_J3987_model A #25.1 
    20285 --- 
    20286 Chain | Description 
    20287 A | No description available 
    20288  
    20289 Chain information for COPI_cyto_J3987_model B #25.2 
    20290 --- 
    20291 Chain | Description 
    20292 B | No description available 
    20293  
    20294 Chain information for COPI_cyto_J3987_model C #25.3 
    20295 --- 
    20296 Chain | Description 
    20297 C | No description available 
    20298  
    20299 Chain information for COPI_cyto_J3987_model D #25.4 
    20300 --- 
    20301 Chain | Description 
    20302 D | No description available 
    20303  
    20304 Chain information for COPI_cyto_J3987_model E #25.5 
    20305 --- 
    20306 Chain | Description 
    20307 E | No description available 
    20308  
    20309 Chain information for COPI_cyto_J3987_model F #25.6 
    20310 --- 
    20311 Chain | Description 
    20312 F | No description available 
    20313  
    20314 Chain information for COPI_cyto_J3987_model G #25.7 
    20315 --- 
    20316 Chain | Description 
    20317 G | No description available 
    20318  
    20319 Chain information for COPI_cyto_J3987_model H #25.8 
    20320 --- 
    20321 Chain | Description 
    20322 H | No description available 
    20323  
    20324 Chain information for COPI_cyto_J3987_model I #25.9 
    20325 --- 
    20326 Chain | Description 
    20327 I | No description available 
    20328  
    20329 Chain information for COPI_cyto_J3987_model J #25.10 
    20330 --- 
    20331 Chain | Description 
    20332 J | No description available 
    20333  
    20334 Chain information for COPI_cyto_J3987_model K #25.11 
    20335 --- 
    20336 Chain | Description 
    20337 K | No description available 
    20338  
    20339 Chain information for COPI_cyto_J3987_model L #25.12 
    20340 --- 
    20341 Chain | Description 
    20342 L | No description available 
    20343  
    20344 Chain information for COPI_cyto_J3987_model M #25.13 
    20345 --- 
    20346 Chain | Description 
    20347 M | No description available 
    20348  
    20349 
    20350 > hide #!1 models
    20351 
    20352 > show #!4 models
    20353 
    20354 > fitmap #25.1 inMap #4
    20355 
    20356 Fit molecule COPI_cyto_J3987_model A (#25.1) to map
    20357 W20_J3987_consensus_resampled.mrc (#4) using 2590 atoms 
    20358 average map value = 0.3221, steps = 80 
    20359 shifted from previous position = 0.776 
    20360 rotated from previous position = 1.16 degrees 
    20361 atoms outside contour = 793, contour level = 0.27665 
    20362  
    20363 Position of COPI_cyto_J3987_model A (#25.1) relative to
    20364 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20365 Matrix rotation and translation 
    20366 -0.38698629 -0.90565681 -0.17328409 278.18136001 
    20367 -0.79448095 0.23210684 0.56118308 163.47572576 
    20368 -0.46801885 0.35484106 -0.80934924 239.73459315 
    20369 Axis -0.54794991 0.78268057 0.29523216 
    20370 Axis point 210.03344096 0.00000000 70.61465245 
    20371 Rotation angle (degrees) 169.14725684 
    20372 Shift along axis 46.29718384 
    20373  
    20374 
    20375 > fitmap #25.2 inMap #4
    20376 
    20377 Fit molecule COPI_cyto_J3987_model B (#25.2) to map
    20378 W20_J3987_consensus_resampled.mrc (#4) using 2426 atoms 
    20379 average map value = 0.3153, steps = 72 
    20380 shifted from previous position = 0.76 
    20381 rotated from previous position = 2.24 degrees 
    20382 atoms outside contour = 837, contour level = 0.27665 
    20383  
    20384 Position of COPI_cyto_J3987_model B (#25.2) relative to
    20385 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20386 Matrix rotation and translation 
    20387 -0.39446310 -0.89902146 -0.19015597 280.33015308 
    20388 -0.79147162 0.22726378 0.56738336 162.70699196 
    20389 -0.46687424 0.37431485 -0.80119714 238.32585966 
    20390 Axis -0.54517505 0.78138014 0.30369267 
    20391 Axis point 209.72584131 0.00000000 70.08251673 
    20392 Rotation angle (degrees) 169.80084660 
    20393 Shift along axis 46.68482501 
    20394  
    20395 
    20396 > fitmap #25.3 inMap #4
    20397 
    20398 Fit molecule COPI_cyto_J3987_model C (#25.3) to map
    20399 W20_J3987_consensus_resampled.mrc (#4) using 1612 atoms 
    20400 average map value = 0.3176, steps = 88 
    20401 shifted from previous position = 0.713 
    20402 rotated from previous position = 1.99 degrees 
    20403 atoms outside contour = 638, contour level = 0.27665 
    20404  
    20405 Position of COPI_cyto_J3987_model C (#25.3) relative to
    20406 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20407 Matrix rotation and translation 
    20408 -0.39593352 -0.89983916 -0.18310146 278.71276949 
    20409 -0.79448375 0.23569092 0.55968328 163.24766694 
    20410 -0.46046958 0.36706850 -0.80822553 238.88829135 
    20411 Axis -0.54450663 0.78409758 0.29783135 
    20412 Axis point 208.81546281 0.00000000 71.13107453 
    20413 Rotation angle (degrees) 169.81244748 
    20414 Shift along axis 47.38957070 
    20415  
    20416 
    20417 > fitmap #25.4 inMap #4
    20418 
    20419 Fit molecule COPI_cyto_J3987_model D (#25.4) to map
    20420 W20_J3987_consensus_resampled.mrc (#4) using 4745 atoms 
    20421 average map value = 0.3393, steps = 64 
    20422 shifted from previous position = 0.187 
    20423 rotated from previous position = 0.91 degrees 
    20424 atoms outside contour = 1720, contour level = 0.27665 
    20425  
    20426 Position of COPI_cyto_J3987_model D (#25.4) relative to
    20427 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20428 Matrix rotation and translation 
    20429 -0.36779496 -0.91688768 -0.15506087 274.91861534 
    20430 -0.80287248 0.22897373 0.55042423 165.38152260 
    20431 -0.46917233 0.32693736 -0.82035926 243.65468775 
    20432 Axis -0.55592398 0.78135279 0.28361301 
    20433 Axis point 211.28631778 0.00000000 72.30612718 
    20434 Rotation angle (degrees) 168.40427173 
    20435 Shift along axis 45.49110059 
    20436  
    20437 
    20438 > hide #!95 models
    20439 
    20440 > show #25.1 models
    20441 
    20442 > show #25.2 models
    20443 
    20444 > show #25.3 models
    20445 
    20446 > show #!25.4 models
    20447 
    20448 > show #25.5 models
    20449 
    20450 > show #25.6 models
    20451 
    20452 > show #25.7 models
    20453 
    20454 > show #25.8 models
    20455 
    20456 > show #25.9 models
    20457 
    20458 > show #25.10 models
    20459 
    20460 > show #25.11 models
    20461 
    20462 > show #25.12 models
    20463 
    20464 > show #25.13 models
    20465 
    20466 > fitmap #25.5 inMap #4
    20467 
    20468 Fit molecule COPI_cyto_J3987_model E (#25.5) to map
    20469 W20_J3987_consensus_resampled.mrc (#4) using 1876 atoms 
    20470 average map value = 0.3141, steps = 60 
    20471 shifted from previous position = 0.493 
    20472 rotated from previous position = 0.732 degrees 
    20473 atoms outside contour = 674, contour level = 0.27665 
    20474  
    20475 Position of COPI_cyto_J3987_model E (#25.5) relative to
    20476 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20477 Matrix rotation and translation 
    20478 -0.38331200 -0.90908551 -0.16320372 277.20038029 
    20479 -0.79186725 0.23250965 0.56469952 162.86818551 
    20480 -0.47541371 0.34569178 -0.80899877 242.05560365 
    20481 Axis -0.54892849 0.78253380 0.29379988 
    20482 Axis point 210.42960898 0.00000000 70.96821393 
    20483 Rotation angle (degrees) 168.49306276 
    20484 Shift along axis 46.40258047 
    20485  
    20486 
    20487 > fitmap #25.6 inMap #4
    20488 
    20489 Fit molecule COPI_cyto_J3987_model F (#25.6) to map
    20490 W20_J3987_consensus_resampled.mrc (#4) using 2400 atoms 
    20491 average map value = 0.2626, steps = 52 
    20492 shifted from previous position = 2.64 
    20493 rotated from previous position = 2.91 degrees 
    20494 atoms outside contour = 1308, contour level = 0.27665 
    20495  
    20496 Position of COPI_cyto_J3987_model F (#25.6) relative to
    20497 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20498 Matrix rotation and translation 
    20499 -0.40208359 -0.90303670 -0.15117378 274.51102549 
    20500 -0.76578539 0.24117028 0.59616243 157.61497455 
    20501 -0.50189793 0.35547381 -0.78850292 240.80443864 
    20502 Axis -0.53849728 0.78468186 0.30707499 
    20503 Axis point 207.60053656 0.00000000 67.83219255 
    20504 Rotation angle (degrees) 167.08638464 
    20505 Shift along axis 49.79919045 
    20506  
    20507 
    20508 > fitmap #25.7 inMap #4
    20509 
    20510 Fit molecule COPI_cyto_J3987_model G (#25.7) to map
    20511 W20_J3987_consensus_resampled.mrc (#4) using 2302 atoms 
    20512 average map value = 0.2759, steps = 68 
    20513 shifted from previous position = 1.66 
    20514 rotated from previous position = 2.11 degrees 
    20515 atoms outside contour = 1125, contour level = 0.27665 
    20516  
    20517 Position of COPI_cyto_J3987_model G (#25.7) relative to
    20518 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20519 Matrix rotation and translation 
    20520 -0.37470678 -0.90717007 -0.19140875 277.62743359 
    20521 -0.79108106 0.20516374 0.57627998 166.08595678 
    20522 -0.48351381 0.36735586 -0.79452130 238.82922597 
    20523 Axis -0.55354811 0.77393742 0.30757985 
    20524 Axis point 211.98563964 0.00000000 67.68895792 
    20525 Rotation angle (degrees) 169.12227850 
    20526 Shift along axis 48.31905400 
    20527  
    20528 
    20529 > fitmap #25.8 inMap #4
    20530 
    20531 Fit molecule COPI_cyto_J3987_model H (#25.8) to map
    20532 W20_J3987_consensus_resampled.mrc (#4) using 420 atoms 
    20533 average map value = 0.3391, steps = 52 
    20534 shifted from previous position = 1.47 
    20535 rotated from previous position = 4.51 degrees 
    20536 atoms outside contour = 138, contour level = 0.27665 
    20537  
    20538 Position of COPI_cyto_J3987_model H (#25.8) relative to
    20539 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20540 Matrix rotation and translation 
    20541 -0.30273203 -0.93833428 -0.16697938 274.74649750 
    20542 -0.83167276 0.17451603 0.52712864 176.16874621 
    20543 -0.46548229 0.29845092 -0.83321864 248.80226785 
    20544 Axis -0.58505795 0.76370144 0.27288698 
    20545 Axis point 220.19027093 0.00000000 73.60291153 
    20546 Rotation angle (degrees) 168.73005781 
    20547 Shift along axis 41.69260200 
    20548  
    20549 
    20550 > fitmap #25.9 inMap #4
    20551 
    20552 Fit molecule COPI_cyto_J3987_model I (#25.9) to map
    20553 W20_J3987_consensus_resampled.mrc (#4) using 1573 atoms 
    20554 average map value = 0.3297, steps = 60 
    20555 shifted from previous position = 0.422 
    20556 rotated from previous position = 0.637 degrees 
    20557 atoms outside contour = 541, contour level = 0.27665 
    20558  
    20559 Position of COPI_cyto_J3987_model I (#25.9) relative to
    20560 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20561 Matrix rotation and translation 
    20562 -0.37486313 -0.91082017 -0.17287068 276.29172892 
    20563 -0.79723061 0.22153165 0.56155775 164.41773716 
    20564 -0.47318179 0.34832509 -0.80917775 241.63479140 
    20565 Axis -0.55323087 0.77915540 0.29470744 
    20566 Axis point 210.74543880 0.00000000 70.87207510 
    20567 Rotation angle (degrees) 168.88868220 
    20568 Shift along axis 46.46542504 
    20569  
    20570 
    20571 > fitmap #25.10 inMap #4
    20572 
    20573 Fit molecule COPI_cyto_J3987_model J (#25.10) to map
    20574 W20_J3987_consensus_resampled.mrc (#4) using 1112 atoms 
    20575 average map value = 0.3174, steps = 68 
    20576 shifted from previous position = 0.699 
    20577 rotated from previous position = 4.11 degrees 
    20578 atoms outside contour = 446, contour level = 0.27665 
    20579  
    20580 Position of COPI_cyto_J3987_model J (#25.10) relative to
    20581 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20582 Matrix rotation and translation 
    20583 -0.37167949 -0.92301396 -0.09949677 269.60077643 
    20584 -0.80025326 0.26421818 0.53831543 164.62224104 
    20585 -0.47058379 0.27970342 -0.83684940 249.14141931 
    20586 Axis -0.55179431 0.79177956 0.26193160 
    20587 Axis point 209.93718651 0.00000000 75.17215989 
    20588 Rotation angle (degrees) 166.44743618 
    20589 Shift along axis 46.83836222 
    20590  
    20591 
    20592 > fitmap #25.11 inMap #4
    20593 
    20594 Fit molecule COPI_cyto_J3987_model K (#25.11) to map
    20595 W20_J3987_consensus_resampled.mrc (#4) using 319 atoms 
    20596 average map value = 0.3247, steps = 352 
    20597 shifted from previous position = 17.9 
    20598 rotated from previous position = 29.5 degrees 
    20599 atoms outside contour = 122, contour level = 0.27665 
    20600  
    20601 Position of COPI_cyto_J3987_model K (#25.11) relative to
    20602 W20_J3987_consensus_resampled.mrc (#4) coordinates: 
    20603 Matrix rotation and translation 
    20604 -0.11943694 -0.99009806 0.07376081 250.46546690 
    20605 -0.55633477 0.12827455 0.82099774 113.52890835 
    20606 -0.82232990 0.05702176 -0.56614669 259.81159734 
    20607 Axis -0.60879152 0.71407012 0.34565408 
    20608 Axis point 236.23455332 0.00000000 37.79456885 
    20609 Rotation angle (degrees) 141.13755065 
    20610 Shift along axis 18.39128867 
    20611  
    20612 
    20613 > select add #25.11
    20614 
    20615 319 atoms, 320 bonds, 37 residues, 1 model selected 
    20616 
    20617 > view matrix models
    20618 > #25.11,-0.13737,-0.98867,0.060447,253.17,-0.58792,0.1305,0.79832,118.22,-0.79717,0.074131,-0.59919,261.16
    20619 
    20620 > ui tool show Matchmaker
    20621 
    20622 > matchmaker #25.11 to #26
    20623 
    20624 Parameters 
    20625 --- 
    20626 Chain pairing | bb 
    20627 Alignment algorithm | Needleman-Wunsch 
    20628 Similarity matrix | BLOSUM-62 
    20629 SS fraction | 0.3 
    20630 Gap open (HH/SS/other) | 18/18/6 
    20631 Gap extend | 1 
    20632 SS matrix |  |  | H | S | O 
    20633 ---|---|---|--- 
    20634 H | 6 | -9 | -6 
    20635 S |  | 6 | -6 
    20636 O |  |  | 4 
    20637 Iteration cutoff | 2 
    20638  
    20639 Matchmaker COPI_cyto_J4021_model, chain K (#26) with COPI_cyto_J3987_model K,
    20640 chain K (#25.11), sequence alignment score = 192.1 
    20641 RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
    20642 0.000) 
    20643  
    20644 
    20645 > select subtract #25.11
    20646 
    20647 Nothing selected 
    20648 
    20649 > hide #!25 models
    20650 
    20651 > show #!26 models
    20652 
    20653 > split #26 chains
    20654 
    20655 Split COPI_cyto_J4021_model (#26) into 13 models 
    20656 Chain information for COPI_cyto_J4021_model A #26.1 
    20657 --- 
    20658 Chain | Description 
    20659 A | No description available 
    20660  
    20661 Chain information for COPI_cyto_J4021_model B #26.2 
    20662 --- 
    20663 Chain | Description 
    20664 B | No description available 
    20665  
    20666 Chain information for COPI_cyto_J4021_model C #26.3 
    20667 --- 
    20668 Chain | Description 
    20669 C | No description available 
    20670  
    20671 Chain information for COPI_cyto_J4021_model D #26.4 
    20672 --- 
    20673 Chain | Description 
    20674 D | No description available 
    20675  
    20676 Chain information for COPI_cyto_J4021_model E #26.5 
    20677 --- 
    20678 Chain | Description 
    20679 E | No description available 
    20680  
    20681 Chain information for COPI_cyto_J4021_model F #26.6 
    20682 --- 
    20683 Chain | Description 
    20684 F | No description available 
    20685  
    20686 Chain information for COPI_cyto_J4021_model G #26.7 
    20687 --- 
    20688 Chain | Description 
    20689 G | No description available 
    20690  
    20691 Chain information for COPI_cyto_J4021_model H #26.8 
    20692 --- 
    20693 Chain | Description 
    20694 H | No description available 
    20695  
    20696 Chain information for COPI_cyto_J4021_model I #26.9 
    20697 --- 
    20698 Chain | Description 
    20699 I | No description available 
    20700  
    20701 Chain information for COPI_cyto_J4021_model J #26.10 
    20702 --- 
    20703 Chain | Description 
    20704 J | No description available 
    20705  
    20706 Chain information for COPI_cyto_J4021_model K #26.11 
    20707 --- 
    20708 Chain | Description 
    20709 K | No description available 
    20710  
    20711 Chain information for COPI_cyto_J4021_model L #26.12 
    20712 --- 
    20713 Chain | Description 
    20714 L | No description available 
    20715  
    20716 Chain information for COPI_cyto_J4021_model M #26.13 
    20717 --- 
    20718 Chain | Description 
    20719 M | No description available 
    20720  
    20721 
    20722 > hide #!4 models
    20723 
    20724 > show #!6 models
    20725 
    20726 > fitmap #26.1 inMap #6
    20727 
    20728 Fit molecule COPI_cyto_J4021_model A (#26.1) to map
    20729 W20_J4021_consensus_resampled.mrc (#6) using 2590 atoms 
    20730 average map value = 0.2703, steps = 84 
    20731 shifted from previous position = 0.378 
    20732 rotated from previous position = 1.1 degrees 
    20733 atoms outside contour = 937, contour level = 0.25941 
    20734  
    20735 Position of COPI_cyto_J4021_model A (#26.1) relative to
    20736 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20737 Matrix rotation and translation 
    20738 -0.37414892 -0.91220652 -0.16700861 276.47462167 
    20739 -0.79157778 0.22032122 0.56996772 162.80224157 
    20740 -0.48313272 0.34545310 -0.80451534 242.25699208 
    20741 Axis -0.55289681 0.77849727 0.29706416 
    20742 Axis point 211.11351512 0.00000000 70.18074399 
    20743 Rotation angle (degrees) 168.28551633 
    20744 Shift along axis 45.84503360 
    20745  
    20746 
    20747 > fitmap #26.2 inMap #6
    20748 
    20749 Fit molecule COPI_cyto_J4021_model B (#26.2) to map
    20750 W20_J4021_consensus_resampled.mrc (#6) using 2426 atoms 
    20751 average map value = 0.2468, steps = 64 
    20752 shifted from previous position = 0.762 
    20753 rotated from previous position = 1.85 degrees 
    20754 atoms outside contour = 1379, contour level = 0.25941 
    20755  
    20756 Position of COPI_cyto_J4021_model B (#26.2) relative to
    20757 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20758 Matrix rotation and translation 
    20759 -0.37049992 -0.90946831 -0.18867225 277.51418546 
    20760 -0.80121018 0.21016989 0.56025966 165.92440083 
    20761 -0.46988517 0.35874228 -0.80654319 240.14558920 
    20762 Axis -0.55590253 0.77574936 0.29863910 
    20763 Axis point 211.54042372 0.00000000 70.27796042 
    20764 Rotation angle (degrees) 169.55728062 
    20765 Shift along axis 46.16177391 
    20766  
    20767 
    20768 > fitmap #26.3 inMap #6
    20769 
    20770 Fit molecule COPI_cyto_J4021_model C (#26.3) to map
    20771 W20_J4021_consensus_resampled.mrc (#6) using 1612 atoms 
    20772 average map value = 0.268, steps = 88 
    20773 shifted from previous position = 1.42 
    20774 rotated from previous position = 8.83 degrees 
    20775 atoms outside contour = 658, contour level = 0.25941 
    20776  
    20777 Position of COPI_cyto_J4021_model C (#26.3) relative to
    20778 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20779 Matrix rotation and translation 
    20780 -0.45746641 -0.88778349 -0.05064549 275.77079696 
    20781 -0.69608083 0.32207858 0.64166727 143.83899735 
    20782 -0.55334978 0.32879458 -0.76530919 246.76254892 
    20783 Axis -0.50270755 0.80771908 0.30801786 
    20784 Axis point 205.38970331 0.00000000 66.05855727 
    20785 Rotation angle (degrees) 161.86918570 
    20786 Shift along axis 53.55671210 
    20787  
    20788 
    20789 > fitmap #26.4 inMap #6
    20790 
    20791 Fit molecule COPI_cyto_J4021_model D (#26.4) to map
    20792 W20_J4021_consensus_resampled.mrc (#6) using 4745 atoms 
    20793 average map value = 0.3102, steps = 84 
    20794 shifted from previous position = 1.18 
    20795 rotated from previous position = 1.93 degrees 
    20796 atoms outside contour = 1692, contour level = 0.25941 
    20797  
    20798 Position of COPI_cyto_J4021_model D (#26.4) relative to
    20799 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20800 Matrix rotation and translation 
    20801 -0.36883139 -0.91668768 -0.15377619 275.04474343 
    20802 -0.80433110 0.23185065 0.54708023 165.03207524 
    20803 -0.46584859 0.32546733 -0.82283420 243.51890015 
    20804 Axis -0.55555262 0.78232196 0.28166228 
    20805 Axis point 210.98432459 0.00000000 72.73645940 
    20806 Rotation angle (degrees) 168.49504583 
    20807 Shift along axis 44.89647919 
    20808  
    20809 
    20810 > fitmap #26.5 inMap #6
    20811 
    20812 Fit molecule COPI_cyto_J4021_model E (#26.5) to map
    20813 W20_J4021_consensus_resampled.mrc (#6) using 1876 atoms 
    20814 average map value = 0.2655, steps = 44 
    20815 shifted from previous position = 0.37 
    20816 rotated from previous position = 1.44 degrees 
    20817 atoms outside contour = 812, contour level = 0.25941 
    20818  
    20819 Position of COPI_cyto_J4021_model E (#26.5) relative to
    20820 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20821 Matrix rotation and translation 
    20822 -0.37950572 -0.91098051 -0.16152380 276.55156047 
    20823 -0.78154710 0.22222838 0.58292255 160.94019650 
    20824 -0.49513590 0.34746090 -0.79631111 243.08456807 
    20825 Axis -0.54968179 0.77881257 0.30216041 
    20826 Axis point 210.99674193 0.00000000 69.29658337 
    20827 Rotation angle (degrees) 167.63257816 
    20828 Shift along axis 46.77742440 
    20829  
    20830 
    20831 > fitmap #26.6 inMap #6
    20832 
    20833 Fit molecule COPI_cyto_J4021_model F (#26.6) to map
    20834 W20_J4021_consensus_resampled.mrc (#6) using 2400 atoms 
    20835 average map value = 0.3003, steps = 72 
    20836 shifted from previous position = 3.77 
    20837 rotated from previous position = 7.24 degrees 
    20838 atoms outside contour = 749, contour level = 0.25941 
    20839  
    20840 Position of COPI_cyto_J4021_model F (#26.6) relative to
    20841 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20842 Matrix rotation and translation 
    20843 -0.50121599 -0.84817893 -0.17139150 277.75765218 
    20844 -0.73837669 0.31593590 0.59580566 148.29415474 
    20845 -0.45120108 0.42517881 -0.78462767 230.60293751 
    20846 Axis -0.49366217 0.80955254 0.31768278 
    20847 Axis point 195.53368048 0.00000000 69.77740358 
    20848 Rotation angle (degrees) 170.04832921 
    20849 Shift along axis 56.19204834 
    20850  
    20851 
    20852 > fitmap #26.7 inMap #6
    20853 
    20854 Fit molecule COPI_cyto_J4021_model G (#26.7) to map
    20855 W20_J4021_consensus_resampled.mrc (#6) using 2302 atoms 
    20856 average map value = 0.3136, steps = 76 
    20857 shifted from previous position = 3.03 
    20858 rotated from previous position = 3.18 degrees 
    20859 atoms outside contour = 723, contour level = 0.25941 
    20860  
    20861 Position of COPI_cyto_J4021_model G (#26.7) relative to
    20862 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20863 Matrix rotation and translation 
    20864 -0.43399059 -0.88593113 -0.16364048 278.30290158 
    20865 -0.75953045 0.26210802 0.59532587 156.65606797 
    20866 -0.48452624 0.38265575 -0.78664408 237.63722363 
    20867 Axis -0.52487405 0.79195238 0.31195938 
    20868 Axis point 205.37019802 0.00000000 68.21146617 
    20869 Rotation angle (degrees) 168.31145195 
    20870 Shift along axis 52.12333508 
    20871  
    20872 
    20873 > fitmap #26.8 inMap #6
    20874 
    20875 Fit molecule COPI_cyto_J4021_model H (#26.8) to map
    20876 W20_J4021_consensus_resampled.mrc (#6) using 420 atoms 
    20877 average map value = 0.4011, steps = 52 
    20878 shifted from previous position = 2.32 
    20879 rotated from previous position = 1.55 degrees 
    20880 atoms outside contour = 112, contour level = 0.25941 
    20881  
    20882 Position of COPI_cyto_J4021_model H (#26.8) relative to
    20883 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20884 Matrix rotation and translation 
    20885 -0.41519620 -0.89510830 -0.16246005 278.00922432 
    20886 -0.77921085 0.25774528 0.57131239 160.68655904 
    20887 -0.46951315 0.36379736 -0.80449295 240.32587092 
    20888 Axis -0.53442036 0.79076406 0.29847457 
    20889 Axis point 207.26688590 0.00000000 70.94580099 
    20890 Rotation angle (degrees) 168.80494855 
    20891 Shift along axis 50.22252640 
    20892  
    20893 
    20894 > fitmap #26.9 inMap #6
    20895 
    20896 Fit molecule COPI_cyto_J4021_model I (#26.9) to map
    20897 W20_J4021_consensus_resampled.mrc (#6) using 1573 atoms 
    20898 average map value = 0.2888, steps = 112 
    20899 shifted from previous position = 1.44 
    20900 rotated from previous position = 3.06 degrees 
    20901 atoms outside contour = 702, contour level = 0.25941 
    20902  
    20903 Position of COPI_cyto_J4021_model I (#26.9) relative to
    20904 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20905 Matrix rotation and translation 
    20906 -0.37846625 -0.91010040 -0.16876189 276.33040233 
    20907 -0.76836367 0.20723976 0.60553197 162.64450565 
    20908 -0.51612071 0.35884392 -0.77772133 243.67694950 
    20909 Axis -0.54941463 0.77362488 0.31567087 
    20910 Axis point 212.64433272 0.00000000 66.29298345 
    20911 Rotation angle (degrees) 167.02647454 
    20912 Shift along axis 50.92758584 
    20913  
    20914 
    20915 > fitmap #26.10 inMap #6
    20916 
    20917 Fit molecule COPI_cyto_J4021_model J (#26.10) to map
    20918 W20_J4021_consensus_resampled.mrc (#6) using 1112 atoms 
    20919 average map value = 0.3374, steps = 68 
    20920 shifted from previous position = 0.981 
    20921 rotated from previous position = 4.81 degrees 
    20922 atoms outside contour = 408, contour level = 0.25941 
    20923  
    20924 Position of COPI_cyto_J4021_model J (#26.10) relative to
    20925 W20_J4021_consensus_resampled.mrc (#6) coordinates: 
    20926 Matrix rotation and translation 
    20927 -0.36533925 -0.92641223 -0.09103639 268.10331410 
    20928 -0.79596275 0.26018434 0.54657793 163.12428402 
    20929 -0.48267023 0.27214795 -0.83244517 250.25943922 
    20930 Axis -0.55363524 0.79008238 0.26316888 
    20931 Axis point 210.17105433 0.00000000 74.56081239 
    20932 Rotation angle (degrees) 165.65005163 
    20933 Shift along axis 46.31067629 
    20934  
    20935 
    20936 > hide #!26 models
    20937 
    20938 > split #27 chains
    20939 
    20940 Split COPI_cyto_J4022_model (#27) into 13 models 
    20941 Chain information for COPI_cyto_J4022_model A #27.1 
    20942 --- 
    20943 Chain | Description 
    20944 A | No description available 
    20945  
    20946 Chain information for COPI_cyto_J4022_model B #27.2 
    20947 --- 
    20948 Chain | Description 
    20949 B | No description available 
    20950  
    20951 Chain information for COPI_cyto_J4022_model C #27.3 
    20952 --- 
    20953 Chain | Description 
    20954 C | No description available 
    20955  
    20956 Chain information for COPI_cyto_J4022_model D #27.4 
    20957 --- 
    20958 Chain | Description 
    20959 D | No description available 
    20960  
    20961 Chain information for COPI_cyto_J4022_model E #27.5 
    20962 --- 
    20963 Chain | Description 
    20964 E | No description available 
    20965  
    20966 Chain information for COPI_cyto_J4022_model F #27.6 
    20967 --- 
    20968 Chain | Description 
    20969 F | No description available 
    20970  
    20971 Chain information for COPI_cyto_J4022_model G #27.7 
    20972 --- 
    20973 Chain | Description 
    20974 G | No description available 
    20975  
    20976 Chain information for COPI_cyto_J4022_model H #27.8 
    20977 --- 
    20978 Chain | Description 
    20979 H | No description available 
    20980  
    20981 Chain information for COPI_cyto_J4022_model I #27.9 
    20982 --- 
    20983 Chain | Description 
    20984 I | No description available 
    20985  
    20986 Chain information for COPI_cyto_J4022_model J #27.10 
    20987 --- 
    20988 Chain | Description 
    20989 J | No description available 
    20990  
    20991 Chain information for COPI_cyto_J4022_model K #27.11 
    20992 --- 
    20993 Chain | Description 
    20994 K | No description available 
    20995  
    20996 Chain information for COPI_cyto_J4022_model L #27.12 
    20997 --- 
    20998 Chain | Description 
    20999 L | No description available 
    21000  
    21001 Chain information for COPI_cyto_J4022_model M #27.13 
    21002 --- 
    21003 Chain | Description 
    21004 M | No description available 
    21005  
    21006 
    21007 > hide #!6 models
    21008 
    21009 > show #!8 models
    21010 
    21011 > color #8 darkgrey models
    21012 
    21013 > color #8 #a9a9a9c0 models
    21014 
    21015 > color #8 #a9a9a9bf models
    21016 
    21017 > hide #!27 models
    21018 
    21019 > show #!27 models
    21020 
    21021 > show #27.1 models
    21022 
    21023 > show #27.2 models
    21024 
    21025 > show #27.3 models
    21026 
    21027 > show #!27.4 models
    21028 
    21029 > show #27.5 models
    21030 
    21031 > show #27.6 models
    21032 
    21033 > show #27.7 models
    21034 
    21035 > show #27.8 models
    21036 
    21037 > show #27.9 models
    21038 
    21039 > show #27.10 models
    21040 
    21041 > show #27.11 models
    21042 
    21043 > show #27.12 models
    21044 
    21045 > show #27.13 models
    21046 
    21047 > fitmap #27.1 inMap #8
    21048 
    21049 Fit molecule COPI_cyto_J4022_model A (#27.1) to map
    21050 W20_J4022_consensus_resampled.mrc (#8) using 2590 atoms 
    21051 average map value = 0.2646, steps = 56 
    21052 shifted from previous position = 1.25 
    21053 rotated from previous position = 2.42 degrees 
    21054 atoms outside contour = 957, contour level = 0.25565 
    21055  
    21056 Position of COPI_cyto_J4022_model A (#27.1) relative to
    21057 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21058 Matrix rotation and translation 
    21059 -0.39256776 -0.89898632 -0.19420133 280.18889645 
    21060 -0.78978108 0.22129853 0.57207763 162.30513777 
    21061 -0.47131349 0.37795577 -0.79687705 238.21825154 
    21062 Axis -0.54600989 0.77943814 0.30716346 
    21063 Axis point 209.81036508 0.00000000 69.55927246 
    21064 Rotation angle (degrees) 169.76045090 
    21065 Shift along axis 46.69284574 
    21066  
    21067 
    21068 > fitmap #27.2 inMap #8
    21069 
    21070 Fit molecule COPI_cyto_J4022_model B (#27.2) to map
    21071 W20_J4022_consensus_resampled.mrc (#8) using 2426 atoms 
    21072 average map value = 0.2446, steps = 52 
    21073 shifted from previous position = 1.11 
    21074 rotated from previous position = 2.79 degrees 
    21075 atoms outside contour = 1336, contour level = 0.25565 
    21076  
    21077 Position of COPI_cyto_J4022_model B (#27.2) relative to
    21078 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21079 Matrix rotation and translation 
    21080 -0.38976486 -0.89769297 -0.20550111 280.56757169 
    21081 -0.80102851 0.22038063 0.55658397 165.91242827 
    21082 -0.45435305 0.38154912 -0.80497428 236.80345949 
    21083 Axis -0.54830136 0.77953535 0.30280399 
    21084 Axis point 210.09627043 0.00000000 70.38992448 
    21085 Rotation angle (degrees) 170.81541733 
    21086 Shift along axis 47.20405452 
    21087  
    21088 
    21089 > fitmap #27.3 inMap #8
    21090 
    21091 Fit molecule COPI_cyto_J4022_model C (#27.3) to map
    21092 W20_J4022_consensus_resampled.mrc (#8) using 1612 atoms 
    21093 average map value = 0.2655, steps = 76 
    21094 shifted from previous position = 1.78 
    21095 rotated from previous position = 8.48 degrees 
    21096 atoms outside contour = 633, contour level = 0.25565 
    21097  
    21098 Position of COPI_cyto_J4022_model C (#27.3) relative to
    21099 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21100 Matrix rotation and translation 
    21101 -0.44384488 -0.89370270 -0.06555325 276.26301732 
    21102 -0.70850239 0.30519488 0.63630219 146.54842255 
    21103 -0.54865846 0.32886410 -0.76864967 245.76532786 
    21104 Axis -0.51083267 0.80271747 0.30772494 
    21105 Axis point 206.80155193 0.00000000 65.73198008 
    21106 Rotation angle (degrees) 162.48721631 
    21107 Shift along axis 52.14092594 
    21108  
    21109 
    21110 > fitmap #27.4 inMap #8
    21111 
    21112 Fit molecule COPI_cyto_J4022_model D (#27.4) to map
    21113 W20_J4022_consensus_resampled.mrc (#8) using 4745 atoms 
    21114 average map value = 0.3044, steps = 100 
    21115 shifted from previous position = 0.615 
    21116 rotated from previous position = 1.41 degrees 
    21117 atoms outside contour = 1677, contour level = 0.25565 
    21118  
    21119 Position of COPI_cyto_J4022_model D (#27.4) relative to
    21120 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21121 Matrix rotation and translation 
    21122 -0.37672030 -0.91435784 -0.14843034 275.26026826 
    21123 -0.79965882 0.24012360 0.55035120 163.64023290 
    21124 -0.46757631 0.32602210 -0.82163374 244.18290661 
    21125 Axis -0.55170270 0.78489010 0.28208449 
    21126 Axis point 210.28195260 0.00000000 73.03172771 
    21127 Rotation angle (degrees) 168.26963934 
    21128 Shift along axis 45.45797518 
    21129  
    21130 
    21131 > fitmap #27.5 inMap #8
    21132 
    21133 Fit molecule COPI_cyto_J4022_model E (#27.5) to map
    21134 W20_J4022_consensus_resampled.mrc (#8) using 1876 atoms 
    21135 average map value = 0.2625, steps = 52 
    21136 shifted from previous position = 0.552 
    21137 rotated from previous position = 1.61 degrees 
    21138 atoms outside contour = 794, contour level = 0.25565 
    21139  
    21140 Position of COPI_cyto_J4022_model E (#27.5) relative to
    21141 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21142 Matrix rotation and translation 
    21143 -0.39012142 -0.90485684 -0.17040949 278.02588034 
    21144 -0.78445694 0.22972243 0.57606852 161.46943730 
    21145 -0.48211265 0.35841557 -0.79944086 241.20120653 
    21146 Axis -0.54579308 0.78163622 0.30191841 
    21147 Axis point 210.00611855 0.00000000 69.84237754 
    21148 Rotation angle (degrees) 168.49862507 
    21149 Shift along axis 47.28884646 
    21150  
    21151 
    21152 > fitmap #27.6 inMap #8
    21153 
    21154 Fit molecule COPI_cyto_J4022_model F (#27.6) to map
    21155 W20_J4022_consensus_resampled.mrc (#8) using 2400 atoms 
    21156 average map value = 0.2992, steps = 68 
    21157 shifted from previous position = 0.833 
    21158 rotated from previous position = 1.23 degrees 
    21159 atoms outside contour = 836, contour level = 0.25565 
    21160  
    21161 Position of COPI_cyto_J4022_model F (#27.6) relative to
    21162 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21163 Matrix rotation and translation 
    21164 -0.37627915 -0.91501112 -0.14549456 274.06344417 
    21165 -0.78910526 0.23420927 0.56785467 161.94404988 
    21166 -0.48551716 0.32848239 -0.81016814 243.51929054 
    21167 Axis -0.55094864 0.78260937 0.28978988 
    21168 Axis point 210.19577001 0.00000000 70.73622595 
    21169 Rotation angle (degrees) 167.45323080 
    21170 Shift along axis 46.31347447 
    21171  
    21172 
    21173 > fitmap #27.7 inMap #8
    21174 
    21175 Fit molecule COPI_cyto_J4022_model G (#27.7) to map
    21176 W20_J4022_consensus_resampled.mrc (#8) using 2302 atoms 
    21177 average map value = 0.2826, steps = 96 
    21178 shifted from previous position = 2.92 
    21179 rotated from previous position = 2.79 degrees 
    21180 atoms outside contour = 976, contour level = 0.25565 
    21181  
    21182 Position of COPI_cyto_J4022_model G (#27.7) relative to
    21183 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21184 Matrix rotation and translation 
    21185 -0.33451130 -0.92639130 -0.17292012 274.85479282 
    21186 -0.79442923 0.17849847 0.58053467 167.37506321 
    21187 -0.50693629 0.33156820 -0.79566208 241.26568780 
    21188 Axis -0.56972315 0.76434688 0.30197578 
    21189 Axis point 216.29332055 0.00000000 65.86543953 
    21190 Rotation angle (degrees) 167.37918527 
    21191 Shift along axis 44.19786245 
    21192  
    21193 
    21194 > fitmap #27.8 inMap #8
    21195 
    21196 Fit molecule COPI_cyto_J4022_model H (#27.8) to map
    21197 W20_J4022_consensus_resampled.mrc (#8) using 420 atoms 
    21198 average map value = 0.3956, steps = 60 
    21199 shifted from previous position = 3.43 
    21200 rotated from previous position = 4.58 degrees 
    21201 atoms outside contour = 107, contour level = 0.25565 
    21202  
    21203 Position of COPI_cyto_J4022_model H (#27.8) relative to
    21204 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21205 Matrix rotation and translation 
    21206 -0.29409810 -0.94159516 -0.16402708 273.35842395 
    21207 -0.82182141 0.16150890 0.54637392 173.87777684 
    21208 -0.48797119 0.29548850 -0.82132252 245.93686122 
    21209 Axis -0.58771482 0.75885938 0.28057750 
    21210 Axis point 220.70161074 0.00000000 69.69363620 
    21211 Rotation angle (degrees) 167.67589275 
    21212 Shift along axis 40.29633569 
    21213  
    21214 
    21215 > fitmap #27.9 inMap #8
    21216 
    21217 Fit molecule COPI_cyto_J4022_model I (#27.9) to map
    21218 W20_J4022_consensus_resampled.mrc (#8) using 1573 atoms 
    21219 average map value = 0.2808, steps = 104 
    21220 shifted from previous position = 1.41 
    21221 rotated from previous position = 3.01 degrees 
    21222 atoms outside contour = 658, contour level = 0.25565 
    21223  
    21224 Position of COPI_cyto_J4022_model I (#27.9) relative to
    21225 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21226 Matrix rotation and translation 
    21227 -0.32433234 -0.92767253 -0.18501954 273.90297834 
    21228 -0.82148476 0.17924210 0.54132715 171.93921965 
    21229 -0.46901103 0.32756063 -0.82020284 242.13807924 
    21230 Axis -0.57622748 0.76552540 0.28623898 
    21231 Axis point 215.70475315 0.00000000 70.66930942 
    21232 Rotation angle (degrees) 169.31041717 
    21233 Shift along axis 43.10277500 
    21234  
    21235 
    21236 > fitmap #27.10 inMap #8
    21237 
    21238 Fit molecule COPI_cyto_J4022_model J (#27.10) to map
    21239 W20_J4022_consensus_resampled.mrc (#8) using 1112 atoms 
    21240 average map value = 0.33, steps = 88 
    21241 shifted from previous position = 0.662 
    21242 rotated from previous position = 3.39 degrees 
    21243 atoms outside contour = 391, contour level = 0.25565 
    21244  
    21245 Position of COPI_cyto_J4022_model J (#27.10) relative to
    21246 W20_J4022_consensus_resampled.mrc (#8) coordinates: 
    21247 Matrix rotation and translation 
    21248 -0.38171857 -0.91794952 -0.10797977 270.82825471 
    21249 -0.78627841 0.26109129 0.55999787 160.73450027 
    21250 -0.48585720 0.29866375 -0.82142727 248.07112012 
    21251 Axis -0.54679573 0.79064209 0.27549866 
    21252 Axis point 209.01509765 0.00000000 73.28198391 
    21253 Rotation angle (degrees) 166.17432003 
    21254 Shift along axis 47.33898908 
    21255  
    21256 
    21257 > hide #!27 models
    21258 
    21259 > show #!28 models
    21260 
    21261 > split #28 chains
    21262 
    21263 Split COPI_cyto_J4023_model (#28) into 13 models 
    21264 Chain information for COPI_cyto_J4023_model A #28.1 
    21265 --- 
    21266 Chain | Description 
    21267 A | No description available 
    21268  
    21269 Chain information for COPI_cyto_J4023_model B #28.2 
    21270 --- 
    21271 Chain | Description 
    21272 B | No description available 
    21273  
    21274 Chain information for COPI_cyto_J4023_model C #28.3 
    21275 --- 
    21276 Chain | Description 
    21277 C | No description available 
    21278  
    21279 Chain information for COPI_cyto_J4023_model D #28.4 
    21280 --- 
    21281 Chain | Description 
    21282 D | No description available 
    21283  
    21284 Chain information for COPI_cyto_J4023_model E #28.5 
    21285 --- 
    21286 Chain | Description 
    21287 E | No description available 
    21288  
    21289 Chain information for COPI_cyto_J4023_model F #28.6 
    21290 --- 
    21291 Chain | Description 
    21292 F | No description available 
    21293  
    21294 Chain information for COPI_cyto_J4023_model G #28.7 
    21295 --- 
    21296 Chain | Description 
    21297 G | No description available 
    21298  
    21299 Chain information for COPI_cyto_J4023_model H #28.8 
    21300 --- 
    21301 Chain | Description 
    21302 H | No description available 
    21303  
    21304 Chain information for COPI_cyto_J4023_model I #28.9 
    21305 --- 
    21306 Chain | Description 
    21307 I | No description available 
    21308  
    21309 Chain information for COPI_cyto_J4023_model J #28.10 
    21310 --- 
    21311 Chain | Description 
    21312 J | No description available 
    21313  
    21314 Chain information for COPI_cyto_J4023_model K #28.11 
    21315 --- 
    21316 Chain | Description 
    21317 K | No description available 
    21318  
    21319 Chain information for COPI_cyto_J4023_model L #28.12 
    21320 --- 
    21321 Chain | Description 
    21322 L | No description available 
    21323  
    21324 Chain information for COPI_cyto_J4023_model M #28.13 
    21325 --- 
    21326 Chain | Description 
    21327 M | No description available 
    21328  
    21329 
    21330 > hide #!8 models
    21331 
    21332 > show #!10 models
    21333 
    21334 > color #10 darkgrey models
    21335 
    21336 > color #10 #a9a9a9c3 models
    21337 
    21338 > color #10 #a9a9a9c1 models
    21339 
    21340 > color #10 #a9a9a9c0 models
    21341 
    21342 > color #10 #a9a9a9bf models
    21343 
    21344 > fitmap #28.1 inMap #10
    21345 
    21346 Fit molecule COPI_cyto_J4023_model A (#28.1) to map
    21347 W20_J4023_consensus_resampled.mrc (#10) using 2590 atoms 
    21348 average map value = 0.2661, steps = 80 
    21349 shifted from previous position = 0.302 
    21350 rotated from previous position = 1.64 degrees 
    21351 atoms outside contour = 989, contour level = 0.259 
    21352  
    21353 Position of COPI_cyto_J4023_model A (#28.1) relative to
    21354 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21355 Matrix rotation and translation 
    21356 -0.38904601 -0.90521909 -0.17094331 278.16947599 
    21357 -0.78384179 0.22779200 0.57767021 160.52070200 
    21358 -0.48397858 0.35873280 -0.79817011 240.89357120 
    21359 Axis -0.54622301 0.78098606 0.30282204 
    21360 Axis point 209.92132129 0.00000000 69.65657344 
    21361 Rotation angle (degrees) 168.43904812 
    21362 Shift along axis 46.36974623 
    21363  
    21364 
    21365 > fitmap #28.2 inMap #10
    21366 
    21367 Fit molecule COPI_cyto_J4023_model B (#28.2) to map
    21368 W20_J4023_consensus_resampled.mrc (#10) using 2426 atoms 
    21369 average map value = 0.2462, steps = 52 
    21370 shifted from previous position = 0.807 
    21371 rotated from previous position = 1.71 degrees 
    21372 atoms outside contour = 1372, contour level = 0.259 
    21373  
    21374 Position of COPI_cyto_J4023_model B (#28.2) relative to
    21375 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21376 Matrix rotation and translation 
    21377 -0.37936173 -0.90522783 -0.19143475 278.45387337 
    21378 -0.80078335 0.21757935 0.55803698 165.73257662 
    21379 -0.46349835 0.36499563 -0.80743265 238.99424212 
    21380 Axis -0.55224090 0.77830294 0.29878840 
    21381 Axis point 210.75764690 0.00000000 70.47418382 
    21382 Rotation angle (degrees) 169.93414364 
    21383 Shift along axis 46.62524128 
    21384  
    21385 
    21386 > fitmap #28.3 inMap #10
    21387 
    21388 Fit molecule COPI_cyto_J4023_model C (#28.3) to map
    21389 W20_J4023_consensus_resampled.mrc (#10) using 1612 atoms 
    21390 average map value = 0.2674, steps = 100 
    21391 shifted from previous position = 1.78 
    21392 rotated from previous position = 13.1 degrees 
    21393 atoms outside contour = 645, contour level = 0.259 
    21394  
    21395 Position of COPI_cyto_J4023_model C (#28.3) relative to
    21396 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21397 Matrix rotation and translation 
    21398 -0.48320445 -0.87548576 -0.00617812 274.93344286 
    21399 -0.65530471 0.35698291 0.66568683 136.56063023 
    21400 -0.58059385 0.32571139 -0.74620566 247.99422947 
    21401 Axis -0.48370086 0.81725132 0.31326310 
    21402 Axis point 203.45931463 0.00000000 64.26982521 
    21403 Rotation angle (degrees) 159.42510249 
    21404 Shift along axis 56.30625377 
    21405  
    21406 
    21407 > fitmap #28.4 inMap #10
    21408 
    21409 Fit molecule COPI_cyto_J4023_model D (#28.4) to map
    21410 W20_J4023_consensus_resampled.mrc (#10) using 4745 atoms 
    21411 average map value = 0.2995, steps = 72 
    21412 shifted from previous position = 0.314 
    21413 rotated from previous position = 1.26 degrees 
    21414 atoms outside contour = 1741, contour level = 0.259 
    21415  
    21416 Position of COPI_cyto_J4023_model D (#28.4) relative to
    21417 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21418 Matrix rotation and translation 
    21419 -0.37631952 -0.91385434 -0.15249221 275.60221900 
    21420 -0.80067150 0.23796533 0.54981604 164.18546643 
    21421 -0.46616391 0.32900267 -0.82124812 243.17403703 
    21422 Axis -0.55210445 0.78428015 0.28299352 
    21423 Axis point 210.42278812 0.00000000 72.60304045 
    21424 Rotation angle (degrees) 168.46454551 
    21425 Shift along axis 45.42286901 
    21426  
    21427 
    21428 > fitmap #28.5 inMap #10
    21429 
    21430 Fit molecule COPI_cyto_J4023_model E (#28.5) to map
    21431 W20_J4023_consensus_resampled.mrc (#10) using 1876 atoms 
    21432 average map value = 0.2617, steps = 64 
    21433 shifted from previous position = 0.422 
    21434 rotated from previous position = 1.48 degrees 
    21435 atoms outside contour = 839, contour level = 0.259 
    21436  
    21437 Position of COPI_cyto_J4023_model E (#28.5) relative to
    21438 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21439 Matrix rotation and translation 
    21440 -0.38829706 -0.90758205 -0.15975054 277.05830941 
    21441 -0.78302109 0.23353287 0.57648971 160.99119705 
    21442 -0.48590471 0.34893730 -0.80133600 242.27299446 
    21443 Axis -0.54602993 0.78263260 0.29889383 
    21444 Axis point 210.04637843 0.00000000 70.01691196 
    21445 Rotation angle (degrees) 167.97315842 
    21446 Shift along axis 47.12873327 
    21447  
    21448 
    21449 > fitmap #28.6 inMap #10
    21450 
    21451 Fit molecule COPI_cyto_J4023_model F (#28.6) to map
    21452 W20_J4023_consensus_resampled.mrc (#10) using 2400 atoms 
    21453 average map value = 0.3111, steps = 56 
    21454 shifted from previous position = 2.06 
    21455 rotated from previous position = 4.34 degrees 
    21456 atoms outside contour = 741, contour level = 0.259 
    21457  
    21458 Position of COPI_cyto_J4023_model F (#28.6) relative to
    21459 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21460 Matrix rotation and translation 
    21461 -0.35666068 -0.90337062 -0.23814849 281.82055176 
    21462 -0.82036020 0.18087540 0.54248801 172.36641935 
    21463 -0.44699252 0.38885168 -0.80560044 235.22166541 
    21464 Axis -0.56435649 0.76715244 0.30492440 
    21465 Axis point 214.18344574 0.00000000 69.66627251 
    21466 Rotation angle (degrees) 172.17681998 
    21467 Shift along axis 44.90888683 
    21468  
    21469 
    21470 > fitmap #28.7 inMap #10
    21471 
    21472 Fit molecule COPI_cyto_J4023_model G (#28.7) to map
    21473 W20_J4023_consensus_resampled.mrc (#10) using 2302 atoms 
    21474 average map value = 0.2755, steps = 64 
    21475 shifted from previous position = 1.24 
    21476 rotated from previous position = 2.83 degrees 
    21477 atoms outside contour = 963, contour level = 0.259 
    21478  
    21479 Position of COPI_cyto_J4023_model G (#28.7) relative to
    21480 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21481 Matrix rotation and translation 
    21482 -0.37482050 -0.90249978 -0.21214088 278.18486892 
    21483 -0.80142293 0.20037819 0.56353340 166.38017125 
    21484 -0.46608036 0.38123844 -0.79838986 235.86468916 
    21485 Axis -0.55487743 0.77295215 0.30766217 
    21486 Axis point 210.65854364 0.00000000 68.54942126 
    21487 Rotation angle (degrees) 170.54540398 
    21488 Shift along axis 46.81204878 
    21489  
    21490 
    21491 > fitmap #28.8 inMap #10
    21492 
    21493 Fit molecule COPI_cyto_J4023_model H (#28.8) to map
    21494 W20_J4023_consensus_resampled.mrc (#10) using 420 atoms 
    21495 average map value = 0.3956, steps = 56 
    21496 shifted from previous position = 0.904 
    21497 rotated from previous position = 5.89 degrees 
    21498 atoms outside contour = 91, contour level = 0.259 
    21499  
    21500 Position of COPI_cyto_J4023_model H (#28.8) relative to
    21501 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21502 Matrix rotation and translation 
    21503 -0.28058215 -0.93606717 -0.21225441 275.82091929 
    21504 -0.83301532 0.12762624 0.53832800 180.46362086 
    21505 -0.47682192 0.32785640 -0.81556793 244.72635677 
    21506 Axis -0.59550860 0.74856765 0.29157501 
    21507 Axis point 223.51865643 0.00000000 69.31481173 
    21508 Rotation angle (degrees) 169.82147556 
    21509 Shift along axis 42.19158968 
    21510  
    21511 
    21512 > fitmap #28.9 inMap #10
    21513 
    21514 Fit molecule COPI_cyto_J4023_model I (#28.9) to map
    21515 W20_J4023_consensus_resampled.mrc (#10) using 1573 atoms 
    21516 average map value = 0.285, steps = 68 
    21517 shifted from previous position = 1.1 
    21518 rotated from previous position = 2.83 degrees 
    21519 atoms outside contour = 662, contour level = 0.259 
    21520  
    21521 Position of COPI_cyto_J4023_model I (#28.9) relative to
    21522 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21523 Matrix rotation and translation 
    21524 -0.34800803 -0.91546944 -0.20200525 275.41256013 
    21525 -0.79922182 0.17708111 0.57435771 168.85645411 
    21526 -0.49003561 0.36132810 -0.79328880 241.32530949 
    21527 Axis -0.56560752 0.76473942 0.30864502 
    21528 Axis point 214.22374441 0.00000000 67.79866361 
    21529 Rotation angle (degrees) 169.14528401 
    21530 Shift along axis 47.83962632 
    21531  
    21532 
    21533 > fitmap #28.10 inMap #10
    21534 
    21535 Fit molecule COPI_cyto_J4023_model J (#28.10) to map
    21536 W20_J4023_consensus_resampled.mrc (#10) using 1112 atoms 
    21537 average map value = 0.3207, steps = 84 
    21538 shifted from previous position = 0.351 
    21539 rotated from previous position = 3.94 degrees 
    21540 atoms outside contour = 429, contour level = 0.259 
    21541  
    21542 Position of COPI_cyto_J4023_model J (#28.10) relative to
    21543 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    21544 Matrix rotation and translation 
    21545 -0.37572939 -0.92009445 -0.11069619 271.04311764 
    21546 -0.80434258 0.26444766 0.53207186 165.17448016 
    21547 -0.46028301 0.28895269 -0.83943190 247.79248250 
    21548 Axis -0.55095733 0.79223463 0.26231720 
    21549 Axis point 209.56379921 0.00000000 75.63736830 
    21550 Rotation angle (degrees) 167.25376251 
    21551 Shift along axis 46.52397993 
    21552  
    21553 
    21554 > hide #!10 models
    21555 
    21556 > show #!12 models
    21557 
    21558 > color #12 darkgrey models
    21559 
    21560 > color #12 #a9a9a9c0 models
    21561 
    21562 > color #12 #a9a9a9bf models
    21563 
    21564 > hide #!28 models
    21565 
    21566 > show #!29 models
    21567 
    21568 > split #29 chains
    21569 
    21570 Split COPI_cyto_J4024_model (#29) into 13 models 
    21571 Chain information for COPI_cyto_J4024_model A #29.1 
    21572 --- 
    21573 Chain | Description 
    21574 A | No description available 
    21575  
    21576 Chain information for COPI_cyto_J4024_model B #29.2 
    21577 --- 
    21578 Chain | Description 
    21579 B | No description available 
    21580  
    21581 Chain information for COPI_cyto_J4024_model C #29.3 
    21582 --- 
    21583 Chain | Description 
    21584 C | No description available 
    21585  
    21586 Chain information for COPI_cyto_J4024_model D #29.4 
    21587 --- 
    21588 Chain | Description 
    21589 D | No description available 
    21590  
    21591 Chain information for COPI_cyto_J4024_model E #29.5 
    21592 --- 
    21593 Chain | Description 
    21594 E | No description available 
    21595  
    21596 Chain information for COPI_cyto_J4024_model F #29.6 
    21597 --- 
    21598 Chain | Description 
    21599 F | No description available 
    21600  
    21601 Chain information for COPI_cyto_J4024_model G #29.7 
    21602 --- 
    21603 Chain | Description 
    21604 G | No description available 
    21605  
    21606 Chain information for COPI_cyto_J4024_model H #29.8 
    21607 --- 
    21608 Chain | Description 
    21609 H | No description available 
    21610  
    21611 Chain information for COPI_cyto_J4024_model I #29.9 
    21612 --- 
    21613 Chain | Description 
    21614 I | No description available 
    21615  
    21616 Chain information for COPI_cyto_J4024_model J #29.10 
    21617 --- 
    21618 Chain | Description 
    21619 J | No description available 
    21620  
    21621 Chain information for COPI_cyto_J4024_model K #29.11 
    21622 --- 
    21623 Chain | Description 
    21624 K | No description available 
    21625  
    21626 Chain information for COPI_cyto_J4024_model L #29.12 
    21627 --- 
    21628 Chain | Description 
    21629 L | No description available 
    21630  
    21631 Chain information for COPI_cyto_J4024_model M #29.13 
    21632 --- 
    21633 Chain | Description 
    21634 M | No description available 
    21635  
    21636 
    21637 > fitmap #29.1 inMap #12
    21638 
    21639 Fit molecule COPI_cyto_J4024_model A (#29.1) to map
    21640 W20_J4024_consensus_resampled.mrc (#12) using 2590 atoms 
    21641 average map value = 0.2692, steps = 100 
    21642 shifted from previous position = 0.874 
    21643 rotated from previous position = 1.25 degrees 
    21644 atoms outside contour = 892, contour level = 0.25569 
    21645  
    21646 Position of COPI_cyto_J4024_model A (#29.1) relative to
    21647 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21648 Matrix rotation and translation 
    21649 -0.38195228 -0.90644822 -0.18017798 277.95847443 
    21650 -0.79414648 0.22219499 0.56565075 163.75119780 
    21651 -0.47269847 0.35913930 -0.80472054 240.33850306 
    21652 Axis -0.55030232 0.77949527 0.29925655 
    21653 Axis point 210.52708604 0.00000000 70.30220517 
    21654 Rotation angle (degrees) 169.18522876 
    21655 Shift along axis 46.60496312 
    21656  
    21657 
    21658 > fitmap #29.2 inMap #12
    21659 
    21660 Fit molecule COPI_cyto_J4024_model B (#29.2) to map
    21661 W20_J4024_consensus_resampled.mrc (#12) using 2426 atoms 
    21662 average map value = 0.2485, steps = 64 
    21663 shifted from previous position = 0.888 
    21664 rotated from previous position = 2.24 degrees 
    21665 atoms outside contour = 1271, contour level = 0.25569 
    21666  
    21667 Position of COPI_cyto_J4024_model B (#29.2) relative to
    21668 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21669 Matrix rotation and translation 
    21670 -0.37729450 -0.90386908 -0.20166693 279.03898781 
    21671 -0.80059309 0.20887819 0.56162321 165.93012621 
    21672 -0.46551002 0.37335050 -0.80243993 238.54192108 
    21673 Axis -0.55344239 0.77558746 0.30358789 
    21674 Axis point 211.11340356 0.00000000 69.95800816 
    21675 Rotation angle (degrees) 170.20680766 
    21676 Shift along axis 46.67975878 
    21677  
    21678 
    21679 > fitmap #29.3 inMap #12
    21680 
    21681 Fit molecule COPI_cyto_J4024_model C (#29.3) to map
    21682 W20_J4024_consensus_resampled.mrc (#12) using 1612 atoms 
    21683 average map value = 0.2695, steps = 160 
    21684 shifted from previous position = 2.41 
    21685 rotated from previous position = 18.3 degrees 
    21686 atoms outside contour = 621, contour level = 0.25569 
    21687  
    21688 Position of COPI_cyto_J4024_model C (#29.3) relative to
    21689 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21690 Matrix rotation and translation 
    21691 -0.48164802 -0.86999176 0.10549661 268.61459966 
    21692 -0.62073770 0.42365137 0.65970011 129.62131912 
    21693 -0.61862744 0.25225752 -0.74408753 255.46187775 
    21694 Axis -0.46969429 0.83476038 0.28733670 
    21695 Axis point 203.50844953 0.00000000 65.15506927 
    21696 Rotation angle (degrees) 154.29538375 
    21697 Shift along axis 55.43957254 
    21698  
    21699 
    21700 > fitmap #29.4 inMap #12
    21701 
    21702 Fit molecule COPI_cyto_J4024_model D (#29.4) to map
    21703 W20_J4024_consensus_resampled.mrc (#12) using 4745 atoms 
    21704 average map value = 0.311, steps = 96 
    21705 shifted from previous position = 0.393 
    21706 rotated from previous position = 1.84 degrees 
    21707 atoms outside contour = 1582, contour level = 0.25569 
    21708  
    21709 Position of COPI_cyto_J4024_model D (#29.4) relative to
    21710 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21711 Matrix rotation and translation 
    21712 -0.36490275 -0.91923092 -0.14785303 274.26364105 
    21713 -0.80817834 0.23388135 0.54050653 165.94975145 
    21714 -0.46227025 0.31672393 -0.82824645 244.92475483 
    21715 Axis -0.55725013 0.78294306 0.27653654 
    21716 Axis point 211.24999279 0.00000000 73.77234724 
    21717 Rotation angle (degrees) 168.41673025 
    21718 Shift along axis 44.82640132 
    21719  
    21720 
    21721 > fitmap #29.5 inMap #12
    21722 
    21723 Fit molecule COPI_cyto_J4024_model E (#29.5) to map
    21724 W20_J4024_consensus_resampled.mrc (#12) using 1876 atoms 
    21725 average map value = 0.2646, steps = 56 
    21726 shifted from previous position = 0.686 
    21727 rotated from previous position = 1.54 degrees 
    21728 atoms outside contour = 791, contour level = 0.25569 
    21729  
    21730 Position of COPI_cyto_J4024_model E (#29.5) relative to
    21731 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21732 Matrix rotation and translation 
    21733 -0.38725918 -0.90565201 -0.17269853 278.00845664 
    21734 -0.78536225 0.22592118 0.57633824 161.81751759 
    21735 -0.48294563 0.35882318 -0.79875495 241.37260249 
    21736 Axis -0.54715674 0.78042314 0.30258755 
    21737 Axis point 210.33473059 0.00000000 69.77477808 
    21738 Rotation angle (degrees) 168.53504549 
    21739 Shift along axis 47.20827915 
    21740  
    21741 
    21742 > fitmap #29.6 inMap #12
    21743 
    21744 Fit molecule COPI_cyto_J4024_model F (#29.6) to map
    21745 W20_J4024_consensus_resampled.mrc (#12) using 2400 atoms 
    21746 average map value = 0.242, steps = 84 
    21747 shifted from previous position = 5.87 
    21748 rotated from previous position = 13.7 degrees 
    21749 atoms outside contour = 1297, contour level = 0.25569 
    21750  
    21751 Position of COPI_cyto_J4024_model F (#29.6) relative to
    21752 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21753 Matrix rotation and translation 
    21754 -0.53159589 -0.84531226 -0.05341354 266.88246547 
    21755 -0.64371973 0.36222400 0.67410585 127.52327824 
    21756 -0.55048227 0.39273525 -0.73670097 230.79457007 
    21757 Axis -0.46452916 0.82063626 0.33281944 
    21758 Axis point 189.53211141 0.00000000 61.79948623 
    21759 Rotation angle (degrees) 162.37079623 
    21760 Shift along axis 57.48845832 
    21761  
    21762 
    21763 > fitmap #29.7 inMap #12
    21764 
    21765 Fit molecule COPI_cyto_J4024_model G (#29.7) to map
    21766 W20_J4024_consensus_resampled.mrc (#12) using 2302 atoms 
    21767 average map value = 0.2775, steps = 60 
    21768 shifted from previous position = 3.1 
    21769 rotated from previous position = 4.14 degrees 
    21770 atoms outside contour = 948, contour level = 0.25569 
    21771  
    21772 Position of COPI_cyto_J4024_model G (#29.7) relative to
    21773 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21774 Matrix rotation and translation 
    21775 -0.36698963 -0.92232957 -0.12094124 274.70465819 
    21776 -0.76065109 0.22270273 0.60976506 158.64044193 
    21777 -0.53547040 0.31577154 -0.78330058 243.71016364 
    21778 Axis -0.55127458 0.77729395 0.30316736 
    21779 Axis point 213.68280008 0.00000000 64.72109245 
    21780 Rotation angle (degrees) 164.53504616 
    21781 Shift along axis 45.75752709 
    21782  
    21783 
    21784 > fitmap #29.8 inMap #12
    21785 
    21786 Fit molecule COPI_cyto_J4024_model H (#29.8) to map
    21787 W20_J4024_consensus_resampled.mrc (#12) using 420 atoms 
    21788 average map value = 0.3642, steps = 52 
    21789 shifted from previous position = 3.12 
    21790 rotated from previous position = 7.89 degrees 
    21791 atoms outside contour = 112, contour level = 0.25569 
    21792  
    21793 Position of COPI_cyto_J4024_model H (#29.8) relative to
    21794 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21795 Matrix rotation and translation 
    21796 -0.31100107 -0.94914560 -0.04899985 269.58279474 
    21797 -0.77806832 0.22466013 0.58663236 161.32624746 
    21798 -0.54579120 0.22056852 -0.80836966 258.53074932 
    21799 Axis -0.57164561 0.77578980 0.26715442 
    21800 Axis point 220.48916877 0.00000000 70.49015049 
    21801 Rotation angle (degrees) 161.32593230 
    21802 Shift along axis 40.11707004 
    21803  
    21804 
    21805 > fitmap #29.9 inMap #12
    21806 
    21807 Fit molecule COPI_cyto_J4024_model I (#29.9) to map
    21808 W20_J4024_consensus_resampled.mrc (#12) using 1573 atoms 
    21809 average map value = 0.308, steps = 88 
    21810 shifted from previous position = 1.06 
    21811 rotated from previous position = 3.68 degrees 
    21812 atoms outside contour = 615, contour level = 0.25569 
    21813  
    21814 Position of COPI_cyto_J4024_model I (#29.9) relative to
    21815 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21816 Matrix rotation and translation 
    21817 -0.32207758 -0.93636157 -0.13961755 272.41905490 
    21818 -0.79316925 0.18637492 0.57978181 166.78930021 
    21819 -0.51686418 0.29747507 -0.80272038 248.24026118 
    21820 Axis -0.57325903 0.76604633 0.29076985 
    21821 Axis point 217.83744421 0.00000000 68.18432836 
    21822 Rotation angle (degrees) 165.74548655 
    21823 Shift along axis 43.78243158 
    21824  
    21825 
    21826 > fitmap #29.10 inMap #12
    21827 
    21828 Fit molecule COPI_cyto_J4024_model J (#29.10) to map
    21829 W20_J4024_consensus_resampled.mrc (#12) using 1112 atoms 
    21830 average map value = 0.3363, steps = 72 
    21831 shifted from previous position = 0.618 
    21832 rotated from previous position = 4.66 degrees 
    21833 atoms outside contour = 406, contour level = 0.25569 
    21834  
    21835 Position of COPI_cyto_J4024_model J (#29.10) relative to
    21836 W20_J4024_consensus_resampled.mrc (#12) coordinates: 
    21837 Matrix rotation and translation 
    21838 -0.36498462 -0.92690394 -0.08738035 267.73871712 
    21839 -0.79378094 0.26076630 0.54946590 162.75689323 
    21840 -0.48651625 0.26990746 -0.83093436 251.13764208 
    21841 Axis -0.55340845 0.79012166 0.26352770 
    21842 Axis point 210.27082462 0.00000000 74.58174748 
    21843 Rotation angle (degrees) 165.36983736 
    21844 Shift along axis 46.61060410 
    21845  
    21846 
    21847 > hide #!12 models
    21848 
    21849 > hide #!29 models
    21850 
    21851 > show #!30 models
    21852 
    21853 > split #30 chains
    21854 
    21855 Split COPI_cyto_J4025_model (#30) into 13 models 
    21856 Chain information for COPI_cyto_J4025_model A #30.1 
    21857 --- 
    21858 Chain | Description 
    21859 A | No description available 
    21860  
    21861 Chain information for COPI_cyto_J4025_model B #30.2 
    21862 --- 
    21863 Chain | Description 
    21864 B | No description available 
    21865  
    21866 Chain information for COPI_cyto_J4025_model C #30.3 
    21867 --- 
    21868 Chain | Description 
    21869 C | No description available 
    21870  
    21871 Chain information for COPI_cyto_J4025_model D #30.4 
    21872 --- 
    21873 Chain | Description 
    21874 D | No description available 
    21875  
    21876 Chain information for COPI_cyto_J4025_model E #30.5 
    21877 --- 
    21878 Chain | Description 
    21879 E | No description available 
    21880  
    21881 Chain information for COPI_cyto_J4025_model F #30.6 
    21882 --- 
    21883 Chain | Description 
    21884 F | No description available 
    21885  
    21886 Chain information for COPI_cyto_J4025_model G #30.7 
    21887 --- 
    21888 Chain | Description 
    21889 G | No description available 
    21890  
    21891 Chain information for COPI_cyto_J4025_model H #30.8 
    21892 --- 
    21893 Chain | Description 
    21894 H | No description available 
    21895  
    21896 Chain information for COPI_cyto_J4025_model I #30.9 
    21897 --- 
    21898 Chain | Description 
    21899 I | No description available 
    21900  
    21901 Chain information for COPI_cyto_J4025_model J #30.10 
    21902 --- 
    21903 Chain | Description 
    21904 J | No description available 
    21905  
    21906 Chain information for COPI_cyto_J4025_model K #30.11 
    21907 --- 
    21908 Chain | Description 
    21909 K | No description available 
    21910  
    21911 Chain information for COPI_cyto_J4025_model L #30.12 
    21912 --- 
    21913 Chain | Description 
    21914 L | No description available 
    21915  
    21916 Chain information for COPI_cyto_J4025_model M #30.13 
    21917 --- 
    21918 Chain | Description 
    21919 M | No description available 
    21920  
    21921 
    21922 > show #!14 models
    21923 
    21924 > color #14 darkgrey models
    21925 
    21926 > color #14 #a9a9a9be models
    21927 
    21928 > color #14 #a9a9a9bf models
    21929 
    21930 > fitmap #30.1 inMap #14
    21931 
    21932 Fit molecule COPI_cyto_J4025_model A (#30.1) to map
    21933 W20_J4025_consensus_resampled.mrc (#14) using 2590 atoms 
    21934 average map value = 0.2675, steps = 76 
    21935 shifted from previous position = 0.303 
    21936 rotated from previous position = 0.916 degrees 
    21937 atoms outside contour = 971, contour level = 0.25978 
    21938  
    21939 Position of COPI_cyto_J4025_model A (#30.1) relative to
    21940 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    21941 Matrix rotation and translation 
    21942 -0.38101620 -0.91006695 -0.16310984 276.49091025 
    21943 -0.78874603 0.22789915 0.57091304 162.02364661 
    21944 -0.48239649 0.34617935 -0.80464495 242.12831797 
    21945 Axis -0.54965686 0.78091585 0.29672844 
    21946 Axis point 210.37135033 0.00000000 70.30651243 
    21947 Rotation angle (degrees) 168.20381385 
    21948 Shift along axis 46.39806523 
    21949  
    21950 
    21951 > fitmap #30.2 inMap #14
    21952 
    21953 Fit molecule COPI_cyto_J4025_model B (#30.2) to map
    21954 W20_J4025_consensus_resampled.mrc (#14) using 2426 atoms 
    21955 average map value = 0.2464, steps = 56 
    21956 shifted from previous position = 0.713 
    21957 rotated from previous position = 1.44 degrees 
    21958 atoms outside contour = 1409, contour level = 0.25978 
    21959  
    21960 Position of COPI_cyto_J4025_model B (#30.2) relative to
    21961 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    21962 Matrix rotation and translation 
    21963 -0.37124088 -0.90903393 -0.18930807 277.53484582 
    21964 -0.80004519 0.20967074 0.56210843 165.71657123 
    21965 -0.47128327 0.36013264 -0.80510656 240.05521807 
    21966 Axis -0.55553559 0.77557441 0.29977415 
    21967 Axis point 211.48229973 0.00000000 70.08195116 
    21968 Rotation angle (degrees) 169.52626651 
    21969 Shift along axis 46.30739501 
    21970  
    21971 
    21972 > fitmap #30.3 inMap #14
    21973 
    21974 Fit molecule COPI_cyto_J4025_model C (#30.3) to map
    21975 W20_J4025_consensus_resampled.mrc (#14) using 1612 atoms 
    21976 average map value = 0.2632, steps = 96 
    21977 shifted from previous position = 1.92 
    21978 rotated from previous position = 10.7 degrees 
    21979 atoms outside contour = 694, contour level = 0.25978 
    21980  
    21981 Position of COPI_cyto_J4025_model C (#30.3) relative to
    21982 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    21983 Matrix rotation and translation 
    21984 -0.44316515 -0.89625169 -0.01837289 273.18677871 
    21985 -0.69089200 0.32841899 0.64405685 142.84601321 
    21986 -0.57120303 0.29811723 -0.76475697 249.76514069 
    21987 Axis -0.50596953 0.80856656 0.30035804 
    21988 Axis point 206.79517933 0.00000000 65.69504944 
    21989 Rotation angle (degrees) 160.00987675 
    21990 Shift along axis 52.29529270 
    21991  
    21992 
    21993 > fitmap #30.4 inMap #14
    21994 
    21995 Fit molecule COPI_cyto_J4025_model D (#30.4) to map
    21996 W20_J4025_consensus_resampled.mrc (#14) using 4745 atoms 
    21997 average map value = 0.2994, steps = 96 
    21998 shifted from previous position = 0.519 
    21999 rotated from previous position = 1.3 degrees 
    22000 atoms outside contour = 1727, contour level = 0.25978 
    22001  
    22002 Position of COPI_cyto_J4025_model D (#30.4) relative to
    22003 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    22004 Matrix rotation and translation 
    22005 -0.37140408 -0.91616900 -0.15064322 274.98034054 
    22006 -0.80234855 0.23505413 0.54862225 164.28861064 
    22007 -0.46722138 0.32462891 -0.82238693 243.65233050 
    22008 Axis -0.55421176 0.78328822 0.28161834 
    22009 Axis point 210.66577055 0.00000000 72.75003830 
    22010 Rotation angle (degrees) 168.34121758 
    22011 Shift along axis 44.90495816 
    22012  
    22013 
    22014 > fitmap #30.5 inMap #14
    22015 
    22016 Fit molecule COPI_cyto_J4025_model E (#30.5) to map
    22017 W20_J4025_consensus_resampled.mrc (#14) using 1876 atoms 
    22018 average map value = 0.2637, steps = 64 
    22019 shifted from previous position = 0.305 
    22020 rotated from previous position = 1.58 degrees 
    22021 atoms outside contour = 846, contour level = 0.25978 
    22022  
    22023 Position of COPI_cyto_J4025_model E (#30.5) relative to
    22024 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    22025 Matrix rotation and translation 
    22026 -0.38354345 -0.90936875 -0.16106801 276.77746085 
    22027 -0.78111798 0.22638522 0.58189729 160.60505785 
    22028 -0.49269579 0.34899601 -0.79715284 242.75004629 
    22029 Axis -0.54793741 0.78020725 0.30173041 
    22030 Axis point 210.53234092 0.00000000 69.48347841 
    22031 Rotation angle (degrees) 167.72960946 
    22032 Shift along axis 46.89357823 
    22033  
    22034 
    22035 > fitmap #30.6 inMap #14
    22036 
    22037 Fit molecule COPI_cyto_J4025_model F (#30.6) to map
    22038 W20_J4025_consensus_resampled.mrc (#14) using 2400 atoms 
    22039 average map value = 0.3154, steps = 76 
    22040 shifted from previous position = 4.38 
    22041 rotated from previous position = 6.32 degrees 
    22042 atoms outside contour = 716, contour level = 0.25978 
    22043  
    22044 Position of COPI_cyto_J4025_model F (#30.6) relative to
    22045 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    22046 Matrix rotation and translation 
    22047 -0.46916307 -0.86826583 -0.16124662 276.76831771 
    22048 -0.75844576 0.30262715 0.57721474 152.99334716 
    22049 -0.45237823 0.39310465 -0.80051401 236.07204224 
    22050 Axis -0.50923185 0.80524369 0.30375239 
    22051 Axis point 199.19186600 0.00000000 71.96275109 
    22052 Rotation angle (degrees) 169.58524914 
    22053 Shift along axis 53.96513192 
    22054  
    22055 
    22056 > fitmap #30.7 inMap #14
    22057 
    22058 Fit molecule COPI_cyto_J4025_model G (#30.7) to map
    22059 W20_J4025_consensus_resampled.mrc (#14) using 2302 atoms 
    22060 average map value = 0.2919, steps = 76 
    22061 shifted from previous position = 4.85 
    22062 rotated from previous position = 4.34 degrees 
    22063 atoms outside contour = 830, contour level = 0.25978 
    22064  
    22065 Position of COPI_cyto_J4025_model G (#30.7) relative to
    22066 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    22067 Matrix rotation and translation 
    22068 -0.43043084 -0.88252203 -0.18943119 279.00638393 
    22069 -0.77202835 0.25122185 0.58383201 159.76771478 
    22070 -0.46765535 0.39754556 -0.78946565 235.51132473 
    22071 Axis -0.52833633 0.78908543 0.31337663 
    22072 Axis point 205.32244175 0.00000000 68.76349381 
    22073 Rotation angle (degrees) 169.84595276 
    22074 Shift along axis 52.46491169 
    22075  
    22076 
    22077 > fitmap #30.8 inMap #14
    22078 
    22079 Fit molecule COPI_cyto_J4025_model H (#30.8) to map
    22080 W20_J4025_consensus_resampled.mrc (#14) using 420 atoms 
    22081 average map value = 0.3536, steps = 80 
    22082 shifted from previous position = 3.69 
    22083 rotated from previous position = 5.02 degrees 
    22084 atoms outside contour = 122, contour level = 0.25978 
    22085  
    22086 Position of COPI_cyto_J4025_model H (#30.8) relative to
    22087 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    22088 Matrix rotation and translation 
    22089 -0.35116806 -0.91592354 -0.19433237 278.04382885 
    22090 -0.84420748 0.21996160 0.48880532 174.65406664 
    22091 -0.40496263 0.33570965 -0.85047299 242.78401221 
    22092 Axis -0.56683990 0.77986296 0.26553022 
    22093 Axis point 212.55649174 0.00000000 78.50487362 
    22094 Rotation angle (degrees) 172.23888649 
    22095 Shift along axis 43.06639339 
    22096  
    22097 
    22098 > fitmap #30.9 inMap #14
    22099 
    22100 Fit molecule COPI_cyto_J4025_model I (#30.9) to map
    22101 W20_J4025_consensus_resampled.mrc (#14) using 1573 atoms 
    22102 average map value = 0.2801, steps = 68 
    22103 shifted from previous position = 1.75 
    22104 rotated from previous position = 3.58 degrees 
    22105 atoms outside contour = 701, contour level = 0.25978 
    22106  
    22107 Position of COPI_cyto_J4025_model I (#30.9) relative to
    22108 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    22109 Matrix rotation and translation 
    22110 -0.38742239 -0.89858889 -0.20601436 277.54357463 
    22111 -0.78023576 0.20056569 0.59245724 165.02578227 
    22112 -0.49105608 0.39027097 -0.77881481 238.87427461 
    22113 Axis -0.54798153 0.77254303 0.32077019 
    22114 Axis point 210.67928153 0.00000000 66.74726373 
    22115 Rotation angle (degrees) 169.36902321 
    22116 Shift along axis 52.02451216 
    22117  
    22118 
    22119 > fitmap #30.10 inMap #14
    22120 
    22121 Fit molecule COPI_cyto_J4025_model J (#30.10) to map
    22122 W20_J4025_consensus_resampled.mrc (#14) using 1112 atoms 
    22123 average map value = 0.3297, steps = 72 
    22124 shifted from previous position = 0.309 
    22125 rotated from previous position = 4.19 degrees 
    22126 atoms outside contour = 404, contour level = 0.25978 
    22127  
    22128 Position of COPI_cyto_J4025_model J (#30.10) relative to
    22129 W20_J4025_consensus_resampled.mrc (#14) coordinates: 
    22130 Matrix rotation and translation 
    22131 -0.35980949 -0.92767682 -0.09976404 268.82850280 
    22132 -0.80210592 0.25292807 0.54097459 164.87500239 
    22133 -0.47661645 0.27466912 -0.83510098 249.92805127 
    22134 Axis -0.55685591 0.78801420 0.26257402 
    22135 Axis point 210.98119167 0.00000000 74.83620925 
    22136 Rotation angle (degrees) 166.16567308 
    22137 Shift along axis 45.84971671 
    22138  
    22139 
    22140 > hide #!30 models
    22141 
    22142 > split #31 chains
    22143 
    22144 Split COPI_cyto_J4026_model (#31) into 13 models 
    22145 Chain information for COPI_cyto_J4026_model A #31.1 
    22146 --- 
    22147 Chain | Description 
    22148 A | No description available 
    22149  
    22150 Chain information for COPI_cyto_J4026_model B #31.2 
    22151 --- 
    22152 Chain | Description 
    22153 B | No description available 
    22154  
    22155 Chain information for COPI_cyto_J4026_model C #31.3 
    22156 --- 
    22157 Chain | Description 
    22158 C | No description available 
    22159  
    22160 Chain information for COPI_cyto_J4026_model D #31.4 
    22161 --- 
    22162 Chain | Description 
    22163 D | No description available 
    22164  
    22165 Chain information for COPI_cyto_J4026_model E #31.5 
    22166 --- 
    22167 Chain | Description 
    22168 E | No description available 
    22169  
    22170 Chain information for COPI_cyto_J4026_model F #31.6 
    22171 --- 
    22172 Chain | Description 
    22173 F | No description available 
    22174  
    22175 Chain information for COPI_cyto_J4026_model G #31.7 
    22176 --- 
    22177 Chain | Description 
    22178 G | No description available 
    22179  
    22180 Chain information for COPI_cyto_J4026_model H #31.8 
    22181 --- 
    22182 Chain | Description 
    22183 H | No description available 
    22184  
    22185 Chain information for COPI_cyto_J4026_model I #31.9 
    22186 --- 
    22187 Chain | Description 
    22188 I | No description available 
    22189  
    22190 Chain information for COPI_cyto_J4026_model J #31.10 
    22191 --- 
    22192 Chain | Description 
    22193 J | No description available 
    22194  
    22195 Chain information for COPI_cyto_J4026_model K #31.11 
    22196 --- 
    22197 Chain | Description 
    22198 K | No description available 
    22199  
    22200 Chain information for COPI_cyto_J4026_model L #31.12 
    22201 --- 
    22202 Chain | Description 
    22203 L | No description available 
    22204  
    22205 Chain information for COPI_cyto_J4026_model M #31.13 
    22206 --- 
    22207 Chain | Description 
    22208 M | No description available 
    22209  
    22210 
    22211 > show #31.1 models
    22212 
    22213 > show #31.2 models
    22214 
    22215 > show #31.3 models
    22216 
    22217 > show #!31.4 models
    22218 
    22219 > show #31.5 models
    22220 
    22221 > show #31.6 models
    22222 
    22223 > show #31.7 models
    22224 
    22225 > show #31.8 models
    22226 
    22227 > show #31.9 models
    22228 
    22229 > show #31.10 models
    22230 
    22231 > show #31.11 models
    22232 
    22233 > show #31.12 models
    22234 
    22235 > show #31.13 models
    22236 
    22237 > hide #!14 models
    22238 
    22239 > color #16 darkgrey models
    22240 
    22241 > color #16 #a9a9a9bf models
    22242 
    22243 > show #!16 models
    22244 
    22245 > fitmap #31.1 inMap #16
    22246 
    22247 Fit molecule COPI_cyto_J4026_model A (#31.1) to map
    22248 W20_J4026_consensus_resampled.mrc (#16) using 2590 atoms 
    22249 average map value = 0.3888, steps = 44 
    22250 shifted from previous position = 1.29 
    22251 rotated from previous position = 3.47 degrees 
    22252 atoms outside contour = 601, contour level = 0.25963 
    22253  
    22254 Position of COPI_cyto_J4026_model A (#31.1) relative to
    22255 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22256 Matrix rotation and translation 
    22257 -0.42179573 -0.88868235 -0.17981118 281.30883739 
    22258 -0.78142467 0.25572018 0.56919478 159.93267883 
    22259 -0.45985201 0.38059282 -0.80229998 237.51658930 
    22260 Axis -0.53238793 0.79050266 0.30276829 
    22261 Axis point 207.09091155 0.00000000 70.78659039 
    22262 Rotation angle (degrees) 169.79746249 
    22263 Shift along axis 48.57427120 
    22264  
    22265 
    22266 > fitmap #31.2 inMap #16
    22267 
    22268 Fit molecule COPI_cyto_J4026_model B (#31.2) to map
    22269 W20_J4026_consensus_resampled.mrc (#16) using 2426 atoms 
    22270 average map value = 0.3729, steps = 96 
    22271 shifted from previous position = 1.87 
    22272 rotated from previous position = 3.62 degrees 
    22273 atoms outside contour = 599, contour level = 0.25963 
    22274  
    22275 Position of COPI_cyto_J4026_model B (#31.2) relative to
    22276 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22277 Matrix rotation and translation 
    22278 -0.41831806 -0.88734205 -0.19399514 282.19270881 
    22279 -0.78598077 0.24658443 0.56694830 161.68081011 
    22280 -0.45524088 0.38964115 -0.80058449 236.37167847 
    22281 Axis -0.53469530 0.78782425 0.30566958 
    22282 Axis point 207.69640372 0.00000000 70.48893010 
    22283 Rotation angle (degrees) 170.45617020 
    22284 Shift along axis 48.74057955 
    22285  
    22286 
    22287 > fitmap #31.3 inMap #16
    22288 
    22289 Fit molecule COPI_cyto_J4026_model C (#31.3) to map
    22290 W20_J4026_consensus_resampled.mrc (#16) using 1612 atoms 
    22291 average map value = 0.3193, steps = 132 
    22292 shifted from previous position = 1.47 
    22293 rotated from previous position = 4.65 degrees 
    22294 atoms outside contour = 561, contour level = 0.25963 
    22295  
    22296 Position of COPI_cyto_J4026_model C (#31.3) relative to
    22297 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22298 Matrix rotation and translation 
    22299 -0.38059936 -0.91824851 -0.10937920 274.00313195 
    22300 -0.75305941 0.23911656 0.61296396 156.01911017 
    22301 -0.53669887 0.31566272 -0.78250328 246.73459431 
    22302 Axis -0.54436027 0.78242476 0.30246220 
    22303 Axis point 211.94174234 0.00000000 66.53857749 
    22304 Rotation angle (degrees) 164.15273201 
    22305 Shift along axis 47.54468445 
    22306  
    22307 
    22308 > fitmap #31.4 inMap #16
    22309 
    22310 Fit molecule COPI_cyto_J4026_model D (#31.4) to map
    22311 W20_J4026_consensus_resampled.mrc (#16) using 4745 atoms 
    22312 average map value = 0.2725, steps = 48 
    22313 shifted from previous position = 0.247 
    22314 rotated from previous position = 2.27 degrees 
    22315 atoms outside contour = 1838, contour level = 0.25963 
    22316  
    22317 Position of COPI_cyto_J4026_model D (#31.4) relative to
    22318 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22319 Matrix rotation and translation 
    22320 -0.36032627 -0.92283158 -0.13618688 272.90164046 
    22321 -0.80657650 0.23487967 0.54246282 165.85713835 
    22322 -0.46861429 0.30530874 -0.82896757 246.32646884 
    22323 Axis -0.55856608 0.78296216 0.27381417 
    22324 Axis point 211.65908561 0.00000000 73.73169378 
    22325 Rotation angle (degrees) 167.74351385 
    22326 Shift along axis 44.87394129 
    22327  
    22328 
    22329 > fitmap #31.5 inMap #16
    22330 
    22331 Fit molecule COPI_cyto_J4026_model E (#31.5) to map
    22332 W20_J4026_consensus_resampled.mrc (#16) using 1876 atoms 
    22333 average map value = 0.3337, steps = 68 
    22334 shifted from previous position = 0.775 
    22335 rotated from previous position = 3.95 degrees 
    22336 atoms outside contour = 584, contour level = 0.25963 
    22337  
    22338 Position of COPI_cyto_J4026_model E (#31.5) relative to
    22339 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22340 Matrix rotation and translation 
    22341 -0.41217203 -0.89272092 -0.18210871 281.24771125 
    22342 -0.76396069 0.22971791 0.60298736 156.90992899 
    22343 -0.49646580 0.38765842 -0.77668699 239.04221312 
    22344 Axis -0.53537564 0.78159084 0.32013853 
    22345 Axis point 208.88799304 0.00000000 67.41763702 
    22346 Rotation angle (degrees) 168.39866163 
    22347 Shift along axis 48.59281177 
    22348  
    22349 
    22350 > fitmap #31.10 inMap #16
    22351 
    22352 Fit molecule COPI_cyto_J4026_model J (#31.10) to map
    22353 W20_J4026_consensus_resampled.mrc (#16) using 1112 atoms 
    22354 average map value = 0.275, steps = 132 
    22355 shifted from previous position = 1.13 
    22356 rotated from previous position = 6.46 degrees 
    22357 atoms outside contour = 480, contour level = 0.25963 
    22358  
    22359 Position of COPI_cyto_J4026_model J (#31.10) relative to
    22360 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22361 Matrix rotation and translation 
    22362 -0.39165506 -0.91840010 -0.05610338 267.15064982 
    22363 -0.77630145 0.29709402 0.55595973 158.01112550 
    22364 -0.49392549 0.26129757 -0.82931369 252.31232484 
    22365 Axis -0.53914103 0.80107967 0.25999678 
    22366 Axis point 207.59429240 0.00000000 75.03244785 
    22367 Rotation angle (degrees) 164.14105481 
    22368 Shift along axis 48.14801546 
    22369  
    22370 
    22371 > fitmap #31.10 inMap #16
    22372 
    22373 Fit molecule COPI_cyto_J4026_model J (#31.10) to map
    22374 W20_J4026_consensus_resampled.mrc (#16) using 1112 atoms 
    22375 average map value = 0.275, steps = 48 
    22376 shifted from previous position = 0.0181 
    22377 rotated from previous position = 0.0479 degrees 
    22378 atoms outside contour = 481, contour level = 0.25963 
    22379  
    22380 Position of COPI_cyto_J4026_model J (#31.10) relative to
    22381 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22382 Matrix rotation and translation 
    22383 -0.39111474 -0.91864714 -0.05582756 267.08423778 
    22384 -0.77617700 0.29664639 0.55637235 158.00648729 
    22385 -0.49454882 0.26093749 -0.82905555 252.36987731 
    22386 Axis -0.53933760 0.80091724 0.26008948 
    22387 Axis point 207.64765628 0.00000000 74.98798493 
    22388 Rotation angle (degrees) 164.10431634 
    22389 Shift along axis 48.14029770 
    22390  
    22391 
    22392 > fitmap #31.12 inMap #16
    22393 
    22394 Fit molecule COPI_cyto_J4026_model L (#31.12) to map
    22395 W20_J4026_consensus_resampled.mrc (#16) using 1420 atoms 
    22396 average map value = 0.246, steps = 148 
    22397 shifted from previous position = 18 
    22398 rotated from previous position = 21.2 degrees 
    22399 atoms outside contour = 781, contour level = 0.25963 
    22400  
    22401 Position of COPI_cyto_J4026_model L (#31.12) relative to
    22402 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22403 Matrix rotation and translation 
    22404 -0.20471014 -0.86077408 -0.46600619 296.00976398 
    22405 -0.82456258 -0.10488916 0.55596297 187.90289621 
    22406 -0.52743751 0.49806252 -0.68829022 207.63206185 
    22407 Axis -0.63033876 0.66877783 0.39421981 
    22408 Axis point 239.98122179 0.00000000 43.12371251 
    22409 Rotation angle (degrees) 177.36759071 
    22410 Shift along axis 20.93153367 
    22411  
    22412 
    22413 > fitmap #31.13 inMap #16
    22414 
    22415 Fit molecule COPI_cyto_J4026_model M (#31.13) to map
    22416 W20_J4026_consensus_resampled.mrc (#16) using 4552 atoms 
    22417 average map value = 0.2784, steps = 240 
    22418 shifted from previous position = 13.3 
    22419 rotated from previous position = 28.4 degrees 
    22420 atoms outside contour = 2174, contour level = 0.25963 
    22421  
    22422 Position of COPI_cyto_J4026_model M (#31.13) relative to
    22423 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    22424 Matrix rotation and translation 
    22425 -0.19059508 -0.97763486 0.08890226 232.38163718 
    22426 -0.95481798 0.20565637 0.21454160 224.73228555 
    22427 -0.22802666 -0.04399490 -0.97266043 250.13777446 
    22428 Axis -0.63112960 0.77367498 0.05569971 
    22429 Axis point 224.43338633 0.00000000 99.69760848 
    22430 Rotation angle (degrees) 168.18101146 
    22431 Shift along axis 41.13941809 
    22432  
    22433 
    22434 > hide #!31 models
    22435 
    22436 > show #!32 models
    22437 
    22438 > split #32 chains
    22439 
    22440 Split COPI_cyto_J4027_model (#32) into 13 models 
    22441 Chain information for COPI_cyto_J4027_model A #32.1 
    22442 --- 
    22443 Chain | Description 
    22444 A | No description available 
    22445  
    22446 Chain information for COPI_cyto_J4027_model B #32.2 
    22447 --- 
    22448 Chain | Description 
    22449 B | No description available 
    22450  
    22451 Chain information for COPI_cyto_J4027_model C #32.3 
    22452 --- 
    22453 Chain | Description 
    22454 C | No description available 
    22455  
    22456 Chain information for COPI_cyto_J4027_model D #32.4 
    22457 --- 
    22458 Chain | Description 
    22459 D | No description available 
    22460  
    22461 Chain information for COPI_cyto_J4027_model E #32.5 
    22462 --- 
    22463 Chain | Description 
    22464 E | No description available 
    22465  
    22466 Chain information for COPI_cyto_J4027_model F #32.6 
    22467 --- 
    22468 Chain | Description 
    22469 F | No description available 
    22470  
    22471 Chain information for COPI_cyto_J4027_model G #32.7 
    22472 --- 
    22473 Chain | Description 
    22474 G | No description available 
    22475  
    22476 Chain information for COPI_cyto_J4027_model H #32.8 
    22477 --- 
    22478 Chain | Description 
    22479 H | No description available 
    22480  
    22481 Chain information for COPI_cyto_J4027_model I #32.9 
    22482 --- 
    22483 Chain | Description 
    22484 I | No description available 
    22485  
    22486 Chain information for COPI_cyto_J4027_model J #32.10 
    22487 --- 
    22488 Chain | Description 
    22489 J | No description available 
    22490  
    22491 Chain information for COPI_cyto_J4027_model K #32.11 
    22492 --- 
    22493 Chain | Description 
    22494 K | No description available 
    22495  
    22496 Chain information for COPI_cyto_J4027_model L #32.12 
    22497 --- 
    22498 Chain | Description 
    22499 L | No description available 
    22500  
    22501 Chain information for COPI_cyto_J4027_model M #32.13 
    22502 --- 
    22503 Chain | Description 
    22504 M | No description available 
    22505  
    22506 
    22507 > hide #!16 models
    22508 
    22509 > show #!18 models
    22510 
    22511 > color #18 darkgrey models
    22512 
    22513 > color #18 #a9a9a9be models
    22514 
    22515 > color #18 #a9a9a9bf models
    22516 
    22517 > fitmap #32.1 inMap #18
    22518 
    22519 Fit molecule COPI_cyto_J4027_model A (#32.1) to map
    22520 W20_J4027_consensus_resampled.mrc (#18) using 2590 atoms 
    22521 average map value = 0.3669, steps = 68 
    22522 shifted from previous position = 0.35 
    22523 rotated from previous position = 0.41 degrees 
    22524 atoms outside contour = 652, contour level = 0.25259 
    22525  
    22526 Position of COPI_cyto_J4027_model A (#32.1) relative to
    22527 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    22528 Matrix rotation and translation 
    22529 -0.36484420 -0.91715830 -0.16034147 275.00307794 
    22530 -0.79726014 0.21879492 0.56258783 164.15850506 
    22531 -0.48090019 0.33309077 -0.81103980 243.29869461 
    22532 Axis -0.55693597 0.77792142 0.29096492 
    22533 Axis point 211.66585714 0.00000000 70.85307433 
    22534 Rotation angle (degrees) 168.10988229 
    22535 Shift along axis 45.33469685 
    22536  
    22537 
    22538 > fitmap #32.2 inMap #18
    22539 
    22540 Fit molecule COPI_cyto_J4027_model B (#32.2) to map
    22541 W20_J4027_consensus_resampled.mrc (#18) using 2426 atoms 
    22542 average map value = 0.354, steps = 64 
    22543 shifted from previous position = 0.279 
    22544 rotated from previous position = 0.915 degrees 
    22545 atoms outside contour = 634, contour level = 0.25259 
    22546  
    22547 Position of COPI_cyto_J4027_model B (#32.2) relative to
    22548 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    22549 Matrix rotation and translation 
    22550 -0.37575375 -0.90933745 -0.17864639 277.57875572 
    22551 -0.79848110 0.21984249 0.56044378 165.00984098 
    22552 -0.47035845 0.35323462 -0.80869540 240.85491140 
    22553 Axis -0.55315660 0.77874186 0.29593731 
    22554 Axis point 211.17574622 0.00000000 70.68321054 
    22555 Rotation angle (degrees) 169.20491693 
    22556 Shift along axis 46.23350389 
    22557  
    22558 
    22559 > fitmap #32.3 inMap #18
    22560 
    22561 Fit molecule COPI_cyto_J4027_model C (#32.3) to map
    22562 W20_J4027_consensus_resampled.mrc (#18) using 1612 atoms 
    22563 average map value = 0.307, steps = 124 
    22564 shifted from previous position = 0.916 
    22565 rotated from previous position = 4.06 degrees 
    22566 atoms outside contour = 549, contour level = 0.25259 
    22567  
    22568 Position of COPI_cyto_J4027_model C (#32.3) relative to
    22569 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    22570 Matrix rotation and translation 
    22571 -0.38280043 -0.91660120 -0.11535204 274.19904393 
    22572 -0.75859054 0.24060781 0.60551491 157.21505378 
    22573 -0.52726108 0.31929633 -0.78742976 246.39824143 
    22574 Axis -0.54425835 0.78326479 0.30046485 
    22575 Axis point 211.53956724 0.00000000 67.39140608 
    22576 Rotation angle (degrees) 164.75519865 
    22577 Shift along axis 47.93990763 
    22578  
    22579 
    22580 > fitmap #32.4 inMap #18
    22581 
    22582 Fit molecule COPI_cyto_J4027_model D (#32.4) to map
    22583 W20_J4027_consensus_resampled.mrc (#18) using 4745 atoms 
    22584 average map value = 0.2737, steps = 64 
    22585 shifted from previous position = 0.424 
    22586 rotated from previous position = 0.652 degrees 
    22587 atoms outside contour = 1745, contour level = 0.25259 
    22588  
    22589 Position of COPI_cyto_J4027_model D (#32.4) relative to
    22590 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    22591 Matrix rotation and translation 
    22592 -0.37438641 -0.91150980 -0.17024900 276.33175026 
    22593 -0.80075946 0.22523142 0.55502712 164.71539509 
    22594 -0.46756723 0.34412311 -0.81422367 240.98992687 
    22595 Axis -0.55358575 0.78040778 0.29070004 
    22596 Axis point 210.61143312 0.00000000 71.24312694 
    22597 Rotation angle (degrees) 169.01867576 
    22598 Shift along axis 45.62763928 
    22599  
    22600 
    22601 > fitmap #32.5 inMap #18
    22602 
    22603 Fit molecule COPI_cyto_J4027_model E (#32.5) to map
    22604 W20_J4027_consensus_resampled.mrc (#18) using 1876 atoms 
    22605 average map value = 0.3307, steps = 48 
    22606 shifted from previous position = 0.367 
    22607 rotated from previous position = 3.19 degrees 
    22608 atoms outside contour = 589, contour level = 0.25259 
    22609  
    22610 Position of COPI_cyto_J4027_model E (#32.5) relative to
    22611 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    22612 Matrix rotation and translation 
    22613 -0.38890629 -0.90726627 -0.16006193 277.40112056 
    22614 -0.76465276 0.22097260 0.60537367 157.20851597 
    22615 -0.51386581 0.35782543 -0.77968129 242.84222727 
    22616 Axis -0.54436333 0.77802149 0.31360984 
    22617 Axis point 210.57407631 0.00000000 67.28775591 
    22618 Rotation angle (degrees) 166.85747662 
    22619 Shift along axis 47.46231881 
    22620  
    22621 
    22622 > fitmap #32.6 inMap #18
    22623 
    22624 Fit molecule COPI_cyto_J4027_model F (#32.6) to map
    22625 W20_J4027_consensus_resampled.mrc (#18) using 2400 atoms 
    22626 average map value = 0.1739, steps = 100 
    22627 shifted from previous position = 2.11 
    22628 rotated from previous position = 17.6 degrees 
    22629 atoms outside contour = 2400, contour level = 0.25259 
    22630  
    22631 Position of COPI_cyto_J4027_model F (#32.6) relative to
    22632 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    22633 Matrix rotation and translation 
    22634 -0.22469468 -0.97442669 0.00222317 252.72099618 
    22635 -0.68062183 0.15857762 0.71526714 144.63194145 
    22636 -0.69732793 0.15920358 -0.69884762 265.52538785 
    22637 Axis -0.59112239 0.74365656 0.31232874 
    22638 Axis point 226.29273798 0.00000000 55.85483264 
    22639 Rotation angle (degrees) 151.94327126 
    22640 Shift along axis 41.09866330 
    22641  
    22642 
    22643 > ui tool show Matchmaker
    22644 
    22645 > matchmaker #32.6 to #33
    22646 
    22647 Parameters 
    22648 --- 
    22649 Chain pairing | bb 
    22650 Alignment algorithm | Needleman-Wunsch 
    22651 Similarity matrix | BLOSUM-62 
    22652 SS fraction | 0.3 
    22653 Gap open (HH/SS/other) | 18/18/6 
    22654 Gap extend | 1 
    22655 SS matrix |  |  | H | S | O 
    22656 ---|---|---|--- 
    22657 H | 6 | -9 | -6 
    22658 S |  | 6 | -6 
    22659 O |  |  | 4 
    22660 Iteration cutoff | 2 
    22661  
    22662 Matchmaker COPI_cyto_J4028_model, chain F (#33) with COPI_cyto_J4027_model F,
    22663 chain F (#32.6), sequence alignment score = 1592 
    22664 RMSD between 299 pruned atom pairs is 0.000 angstroms; (across all 299 pairs:
    22665 0.000) 
    22666  
    22667 
    22668 > hide #!32 models
    22669 
    22670 > show #!32 models
    22671 
    22672 > hide #!32 models
    22673 
    22674 > hide #!18 models
    22675 
    22676 > show #!20 models
    22677 
    22678 > color #20 darkgrey models
    22679 
    22680 > color #20 #a9a9a9c2 models
    22681 
    22682 > show #!33 models
    22683 
    22684 > split #33 chains
    22685 
    22686 Split COPI_cyto_J4028_model (#33) into 13 models 
    22687 Chain information for COPI_cyto_J4028_model A #33.1 
    22688 --- 
    22689 Chain | Description 
    22690 A | No description available 
    22691  
    22692 Chain information for COPI_cyto_J4028_model B #33.2 
    22693 --- 
    22694 Chain | Description 
    22695 B | No description available 
    22696  
    22697 Chain information for COPI_cyto_J4028_model C #33.3 
    22698 --- 
    22699 Chain | Description 
    22700 C | No description available 
    22701  
    22702 Chain information for COPI_cyto_J4028_model D #33.4 
    22703 --- 
    22704 Chain | Description 
    22705 D | No description available 
    22706  
    22707 Chain information for COPI_cyto_J4028_model E #33.5 
    22708 --- 
    22709 Chain | Description 
    22710 E | No description available 
    22711  
    22712 Chain information for COPI_cyto_J4028_model F #33.6 
    22713 --- 
    22714 Chain | Description 
    22715 F | No description available 
    22716  
    22717 Chain information for COPI_cyto_J4028_model G #33.7 
    22718 --- 
    22719 Chain | Description 
    22720 G | No description available 
    22721  
    22722 Chain information for COPI_cyto_J4028_model H #33.8 
    22723 --- 
    22724 Chain | Description 
    22725 H | No description available 
    22726  
    22727 Chain information for COPI_cyto_J4028_model I #33.9 
    22728 --- 
    22729 Chain | Description 
    22730 I | No description available 
    22731  
    22732 Chain information for COPI_cyto_J4028_model J #33.10 
    22733 --- 
    22734 Chain | Description 
    22735 J | No description available 
    22736  
    22737 Chain information for COPI_cyto_J4028_model K #33.11 
    22738 --- 
    22739 Chain | Description 
    22740 K | No description available 
    22741  
    22742 Chain information for COPI_cyto_J4028_model L #33.12 
    22743 --- 
    22744 Chain | Description 
    22745 L | No description available 
    22746  
    22747 Chain information for COPI_cyto_J4028_model M #33.13 
    22748 --- 
    22749 Chain | Description 
    22750 M | No description available 
    22751  
    22752 
    22753 > fitmap #33.1 inMap #20
    22754 
    22755 Fit molecule COPI_cyto_J4028_model A (#33.1) to map
    22756 W20_J4028_consensus_resampled.mrc (#20) using 2590 atoms 
    22757 average map value = 0.3839, steps = 84 
    22758 shifted from previous position = 1.3 
    22759 rotated from previous position = 3.69 degrees 
    22760 atoms outside contour = 606, contour level = 0.25474 
    22761  
    22762 Position of COPI_cyto_J4028_model A (#33.1) relative to
    22763 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22764 Matrix rotation and translation 
    22765 -0.42505705 -0.88684737 -0.18118571 281.77112295 
    22766 -0.78040543 0.25764379 0.56972543 159.62921913 
    22767 -0.45857812 0.38356412 -0.80161381 237.17247148 
    22768 Axis -0.53095306 0.79115444 0.30358443 
    22769 Axis point 206.86596376 0.00000000 70.78540234 
    22770 Rotation angle (degrees) 169.90338089 
    22771 Shift along axis 48.68599577 
    22772  
    22773 
    22774 > fitmap #33.2 inMap #20
    22775 
    22776 Fit molecule COPI_cyto_J4028_model B (#33.2) to map
    22777 W20_J4028_consensus_resampled.mrc (#20) using 2426 atoms 
    22778 average map value = 0.3703, steps = 76 
    22779 shifted from previous position = 2 
    22780 rotated from previous position = 3.77 degrees 
    22781 atoms outside contour = 594, contour level = 0.25474 
    22782  
    22783 Position of COPI_cyto_J4028_model B (#33.2) relative to
    22784 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22785 Matrix rotation and translation 
    22786 -0.42163847 -0.88604192 -0.19274527 282.36522569 
    22787 -0.78360399 0.24908325 0.56914176 161.05650807 
    22788 -0.45627383 0.39100801 -0.79932906 236.28096107 
    22789 Axis -0.53305638 0.78859614 0.30654042 
    22790 Axis point 207.42054850 0.00000000 70.38397992 
    22791 Rotation angle (degrees) 170.38149718 
    22792 Shift along axis 48.92162012 
    22793  
    22794 
    22795 > fitmap #33.3 inMap #20
    22796 
    22797 Fit molecule COPI_cyto_J4028_model C (#33.3) to map
    22798 W20_J4028_consensus_resampled.mrc (#20) using 1612 atoms 
    22799 average map value = 0.2936, steps = 120 
    22800 shifted from previous position = 1.59 
    22801 rotated from previous position = 5.86 degrees 
    22802 atoms outside contour = 556, contour level = 0.25474 
    22803  
    22804 Position of COPI_cyto_J4028_model C (#33.3) relative to
    22805 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22806 Matrix rotation and translation 
    22807 -0.38874794 -0.91700982 -0.08926390 273.70817090 
    22808 -0.74150605 0.25389180 0.62105374 153.76404568 
    22809 -0.54684900 0.30762308 -0.77866824 247.74574422 
    22810 Axis -0.53877892 0.78657655 0.30168628 
    22811 Axis point 211.55093832 0.00000000 66.06733162 
    22812 Rotation angle (degrees) 163.08987268 
    22813 Shift along axis 48.22049311 
    22814  
    22815 
    22816 > fitmap #33.4 inMap #20
    22817 
    22818 Fit molecule COPI_cyto_J4028_model D (#33.4) to map
    22819 W20_J4028_consensus_resampled.mrc (#20) using 4745 atoms 
    22820 average map value = 0.2743, steps = 52 
    22821 shifted from previous position = 0.325 
    22822 rotated from previous position = 2.63 degrees 
    22823 atoms outside contour = 1777, contour level = 0.25474 
    22824  
    22825 Position of COPI_cyto_J4028_model D (#33.4) relative to
    22826 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22827 Matrix rotation and translation 
    22828 -0.35425466 -0.92574203 -0.13230776 272.21729531 
    22829 -0.80879167 0.23228423 0.54027779 166.54524500 
    22830 -0.46942484 0.29840534 -0.83102021 247.09025195 
    22831 Axis -0.56108841 0.78203404 0.27129791 
    22832 Axis point 212.23977312 0.00000000 73.93457988 
    22833 Rotation angle (degrees) 167.55287093 
    22834 Shift along axis 44.54114989 
    22835  
    22836 
    22837 > fitmap #33.5 inMap #20
    22838 
    22839 Fit molecule COPI_cyto_J4028_model E (#33.5) to map
    22840 W20_J4028_consensus_resampled.mrc (#20) using 1876 atoms 
    22841 average map value = 0.3337, steps = 68 
    22842 shifted from previous position = 0.86 
    22843 rotated from previous position = 3.26 degrees 
    22844 atoms outside contour = 607, contour level = 0.25474 
    22845  
    22846 Position of COPI_cyto_J4028_model E (#33.5) relative to
    22847 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22848 Matrix rotation and translation 
    22849 -0.40812036 -0.89487089 -0.18067614 280.82990976 
    22850 -0.77162408 0.23236180 0.59211848 158.56716868 
    22851 -0.48788736 0.38106967 -0.78533550 239.27651010 
    22852 Axis -0.53761002 0.78256694 0.31394976 
    22853 Axis point 209.07381918 0.00000000 68.40687366 
    22854 Rotation angle (degrees) 168.68024136 
    22855 Shift along axis 48.23325430 
    22856  
    22857 
    22858 > fitmap #33.10 inMap #20
    22859 
    22860 Fit molecule COPI_cyto_J4028_model J (#33.10) to map
    22861 W20_J4028_consensus_resampled.mrc (#20) using 1112 atoms 
    22862 average map value = 0.2746, steps = 88 
    22863 shifted from previous position = 1.18 
    22864 rotated from previous position = 6.07 degrees 
    22865 atoms outside contour = 487, contour level = 0.25474 
    22866  
    22867 Position of COPI_cyto_J4028_model J (#33.10) relative to
    22868 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22869 Matrix rotation and translation 
    22870 -0.37976892 -0.92311743 -0.06024771 266.93454127 
    22871 -0.77672422 0.28281318 0.56277545 158.41114514 
    22872 -0.50246898 0.26052048 -0.82441132 252.69246283 
    22873 Axis -0.54431763 0.79637675 0.26363308 
    22874 Axis point 208.95699781 0.00000000 74.09614523 
    22875 Rotation angle (degrees) 163.88025316 
    22876 Shift along axis 47.47586703 
    22877  
    22878 
    22879 > fitmap #33.12 inMap #20
    22880 
    22881 Fit molecule COPI_cyto_J4028_model L (#33.12) to map
    22882 W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms 
    22883 average map value = 0.2305, steps = 152 
    22884 shifted from previous position = 15.6 
    22885 rotated from previous position = 25.9 degrees 
    22886 atoms outside contour = 812, contour level = 0.25474 
    22887  
    22888 Position of COPI_cyto_J4028_model L (#33.12) relative to
    22889 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22890 Matrix rotation and translation 
    22891 -0.06107414 -0.89318761 -0.44551751 275.05032468 
    22892 -0.79982244 -0.22322988 0.55718265 197.31395144 
    22893 -0.59712146 0.39036435 -0.70075791 230.69793847 
    22894 Axis -0.68372085 0.62136335 0.38266615 
    22895 Axis point 0.00000000 233.57747065 184.11991319 
    22896 Rotation angle (degrees) 172.99286255 
    22897 Shift along axis 22.82630694 
    22898  
    22899 
    22900 > select add #33.12
    22901 
    22902 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    22903 
    22904 > view matrix models
    22905 > #33.12,-0.71047,-0.45523,-0.53665,342.29,-0.62968,0.75173,0.19595,130.11,0.31422,0.47714,-0.82074,104.42
    22906 
    22907 > view matrix models
    22908 > #33.12,-0.87976,-0.194,-0.43403,328.35,-0.31813,0.91866,0.23421,62.94,0.35329,0.34413,-0.86992,118.06
    22909 
    22910 > fitmap #33.12 inMap #20
    22911 
    22912 Fit molecule COPI_cyto_J4028_model L (#33.12) to map
    22913 W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms 
    22914 average map value = 0.219, steps = 148 
    22915 shifted from previous position = 4.64 
    22916 rotated from previous position = 34.8 degrees 
    22917 atoms outside contour = 813, contour level = 0.25474 
    22918  
    22919 Position of COPI_cyto_J4028_model L (#33.12) relative to
    22920 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22921 Matrix rotation and translation 
    22922 -0.65509662 -0.64625356 -0.39141380 328.46645180 
    22923 -0.75535360 0.57185725 0.32003163 147.76949721 
    22924 0.01701124 0.50530746 -0.86277170 152.27605950 
    22925 Axis 0.40140909 -0.88487271 -0.23637052 
    22926 Axis point 188.23063104 0.00000000 79.03730027 
    22927 Rotation angle (degrees) 166.65689588 
    22928 Shift along axis -34.90134836 
    22929  
    22930 
    22931 > ui mousemode right "rotate selected models"
    22932 
    22933 > view matrix models
    22934 > #33.12,-0.03029,-0.7598,0.64945,102.21,-0.99925,0.0072683,-0.038101,287,0.024229,-0.65012,-0.75945,246.16
    22935 
    22936 > fitmap #33.12 inMap #20
    22937 
    22938 Fit molecule COPI_cyto_J4028_model L (#33.12) to map
    22939 W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms 
    22940 average map value = 0.2032, steps = 160 
    22941 shifted from previous position = 13.1 
    22942 rotated from previous position = 20.8 degrees 
    22943 atoms outside contour = 909, contour level = 0.25474 
    22944  
    22945 Position of COPI_cyto_J4028_model L (#33.12) relative to
    22946 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22947 Matrix rotation and translation 
    22948 0.16998318 -0.52866209 0.83163822 33.05834902 
    22949 -0.98535039 -0.07936651 0.15094897 271.66299549 
    22950 -0.01379677 -0.84511382 -0.53440836 228.58308709 
    22951 Axis -0.71969674 0.61086190 -0.32997627 
    22952 Axis point 0.00000000 219.83009454 42.24482979 
    22953 Rotation angle (degrees) 136.21122723 
    22954 Shift along axis 66.72959442 
    22955  
    22956 
    22957 > ui mousemode right "translate selected models"
    22958 
    22959 > view matrix models
    22960 > #33.12,0.16998,-0.52866,0.83164,40.813,-0.98535,-0.079367,0.15095,266.5,-0.013797,-0.84511,-0.53441,239.35
    22961 
    22962 > ui mousemode right "rotate selected models"
    22963 
    22964 > view matrix models
    22965 > #33.12,-0.43029,-0.87383,0.22644,246.31,-0.87355,0.46631,0.13952,199.93,-0.22751,-0.13778,-0.96398,263.72
    22966 
    22967 > ui mousemode right "translate selected models"
    22968 
    22969 > view matrix models
    22970 > #33.12,-0.43029,-0.87383,0.22644,240.63,-0.87355,0.46631,0.13952,199.48,-0.22751,-0.13778,-0.96398,257.34
    22971 
    22972 > fitmap #33.12 inMap #20
    22973 
    22974 Fit molecule COPI_cyto_J4028_model L (#33.12) to map
    22975 W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms 
    22976 average map value = 0.259, steps = 136 
    22977 shifted from previous position = 2.22 
    22978 rotated from previous position = 19 degrees 
    22979 atoms outside contour = 643, contour level = 0.25474 
    22980  
    22981 Position of COPI_cyto_J4028_model L (#33.12) relative to
    22982 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    22983 Matrix rotation and translation 
    22984 -0.11376158 -0.96773135 0.22484296 202.04835591 
    22985 -0.96542922 0.16110229 0.20492070 231.97393999 
    22986 -0.23453090 -0.19375786 -0.95260336 262.84035133 
    22987 Axis -0.65544634 0.75523227 0.00378481 
    22988 Axis point 228.77213631 0.00000000 107.04713970 
    22989 Rotation angle (degrees) 162.29431769 
    22990 Shift along axis 43.75715061 
    22991  
    22992 
    22993 > select subtract #33.12
    22994 
    22995 Nothing selected 
    22996 
    22997 > fitmap #33.13 inMap #20
    22998 
    22999 Fit molecule COPI_cyto_J4028_model M (#33.13) to map
    23000 W20_J4028_consensus_resampled.mrc (#20) using 4552 atoms 
    23001 average map value = 0.2597, steps = 164 
    23002 shifted from previous position = 11.9 
    23003 rotated from previous position = 21.2 degrees 
    23004 atoms outside contour = 2429, contour level = 0.25474 
    23005  
    23006 Position of COPI_cyto_J4028_model M (#33.13) relative to
    23007 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    23008 Matrix rotation and translation 
    23009 -0.41064746 -0.90764367 0.08690026 262.06407158 
    23010 -0.84733447 0.41507760 0.33126258 174.12202496 
    23011 -0.33673873 0.06239856 -0.93952832 256.95292530 
    23012 Axis -0.53201816 0.83828111 0.11933760 
    23013 Axis point 205.62822196 0.00000000 94.49206914 
    23014 Rotation angle (degrees) 165.36365713 
    23015 Shift along axis 37.20450278 
    23016  
    23017 
    23018 > show #!32 models
    23019 
    23020 > hide #!33 models
    23021 
    23022 > hide #!32 models
    23023 
    23024 > show #!33 models
    23025 
    23026 > hide #!33 models
    23027 
    23028 > split #34 chains
    23029 
    23030 Split COPI_cyto_J3988_model (#34) into 13 models 
    23031 Chain information for COPI_cyto_J3988_model A #34.1 
    23032 --- 
    23033 Chain | Description 
    23034 A | No description available 
    23035  
    23036 Chain information for COPI_cyto_J3988_model B #34.2 
    23037 --- 
    23038 Chain | Description 
    23039 B | No description available 
    23040  
    23041 Chain information for COPI_cyto_J3988_model C #34.3 
    23042 --- 
    23043 Chain | Description 
    23044 C | No description available 
    23045  
    23046 Chain information for COPI_cyto_J3988_model D #34.4 
    23047 --- 
    23048 Chain | Description 
    23049 D | No description available 
    23050  
    23051 Chain information for COPI_cyto_J3988_model E #34.5 
    23052 --- 
    23053 Chain | Description 
    23054 E | No description available 
    23055  
    23056 Chain information for COPI_cyto_J3988_model F #34.6 
    23057 --- 
    23058 Chain | Description 
    23059 F | No description available 
    23060  
    23061 Chain information for COPI_cyto_J3988_model G #34.7 
    23062 --- 
    23063 Chain | Description 
    23064 G | No description available 
    23065  
    23066 Chain information for COPI_cyto_J3988_model H #34.8 
    23067 --- 
    23068 Chain | Description 
    23069 H | No description available 
    23070  
    23071 Chain information for COPI_cyto_J3988_model I #34.9 
    23072 --- 
    23073 Chain | Description 
    23074 I | No description available 
    23075  
    23076 Chain information for COPI_cyto_J3988_model J #34.10 
    23077 --- 
    23078 Chain | Description 
    23079 J | No description available 
    23080  
    23081 Chain information for COPI_cyto_J3988_model K #34.11 
    23082 --- 
    23083 Chain | Description 
    23084 K | No description available 
    23085  
    23086 Chain information for COPI_cyto_J3988_model L #34.12 
    23087 --- 
    23088 Chain | Description 
    23089 L | No description available 
    23090  
    23091 Chain information for COPI_cyto_J3988_model M #34.13 
    23092 --- 
    23093 Chain | Description 
    23094 M | No description available 
    23095  
    23096 
    23097 > show #34.1 models
    23098 
    23099 > show #34.2 models
    23100 
    23101 > show #34.3 models
    23102 
    23103 > show #!34.4 models
    23104 
    23105 > show #34.5 models
    23106 
    23107 > show #34.6 models
    23108 
    23109 > show #34.7 models
    23110 
    23111 > show #34.8 models
    23112 
    23113 > show #34.9 models
    23114 
    23115 > show #34.10 models
    23116 
    23117 > show #34.11 models
    23118 
    23119 > show #34.12 models
    23120 
    23121 > show #34.13 models
    23122 
    23123 > hide #!20 models
    23124 
    23125 > show #!22 models
    23126 
    23127 > color #22 darkgrey models
    23128 
    23129 > color #22 #a9a9a9bf models
    23130 
    23131 > fitmap #34.1 inMap #22
    23132 
    23133 Fit molecule COPI_cyto_J3988_model A (#34.1) to map
    23134 W20_J3988_consensus_resampled.mrc (#22) using 2590 atoms 
    23135 average map value = 0.3688, steps = 88 
    23136 shifted from previous position = 1.25 
    23137 rotated from previous position = 3.5 degrees 
    23138 atoms outside contour = 749, contour level = 0.28583 
    23139  
    23140 Position of COPI_cyto_J3988_model A (#34.1) relative to
    23141 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23142 Matrix rotation and translation 
    23143 -0.41785370 -0.88839960 -0.19011695 282.28257009 
    23144 -0.78880679 0.25093956 0.56108217 162.05511406 
    23145 -0.45075731 0.38441580 -0.80563165 235.85823021 
    23146 Axis -0.53495212 0.78922836 0.30157060 
    23147 Axis point 207.72235198 0.00000000 70.74799729 
    23148 Rotation angle (degrees) 170.49558915 
    23149 Shift along axis 48.01874106 
    23150  
    23151 
    23152 > fitmap #34.2 inMap #22
    23153 
    23154 Fit molecule COPI_cyto_J3988_model B (#34.2) to map
    23155 W20_J3988_consensus_resampled.mrc (#22) using 2426 atoms 
    23156 average map value = 0.3348, steps = 104 
    23157 shifted from previous position = 1.68 
    23158 rotated from previous position = 3.88 degrees 
    23159 atoms outside contour = 828, contour level = 0.28583 
    23160  
    23161 Position of COPI_cyto_J3988_model B (#34.2) relative to
    23162 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23163 Matrix rotation and translation 
    23164 -0.42101840 -0.88538396 -0.19707555 283.10669504 
    23165 -0.78443773 0.24632045 0.56919566 160.85163308 
    23166 -0.45541296 0.39423534 -0.79823402 235.48770247 
    23167 Axis -0.53352603 0.78777711 0.30782658 
    23168 Axis point 207.58242660 0.00000000 70.13942680 
    23169 Rotation angle (degrees) 170.56282406 
    23170 Shift along axis 48.15981832 
    23171  
    23172 
    23173 > fitmap #34.3 inMap #22
    23174 
    23175 Fit molecule COPI_cyto_J3988_model C (#34.3) to map
    23176 W20_J3988_consensus_resampled.mrc (#22) using 1612 atoms 
    23177 average map value = 0.3235, steps = 80 
    23178 shifted from previous position = 1.01 
    23179 rotated from previous position = 1.39 degrees 
    23180 atoms outside contour = 647, contour level = 0.28583 
    23181  
    23182 Position of COPI_cyto_J3988_model C (#34.3) relative to
    23183 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23184 Matrix rotation and translation 
    23185 -0.38953007 -0.90460759 -0.17306487 278.08945587 
    23186 -0.79075902 0.23214543 0.56639976 162.53472037 
    23187 -0.47219330 0.35748234 -0.80575423 240.06559363 
    23188 Axis -0.54660128 0.78262495 0.29786781 
    23189 Axis point 209.73775516 0.00000000 70.39505904 
    23190 Rotation angle (degrees) 168.98267188 
    23191 Shift along axis 46.70748572 
    23192  
    23193 
    23194 > fitmap #34.4 inMap #22
    23195 
    23196 Fit molecule COPI_cyto_J3988_model D (#34.4) to map
    23197 W20_J3988_consensus_resampled.mrc (#22) using 4745 atoms 
    23198 average map value = 0.341, steps = 72 
    23199 shifted from previous position = 0.451 
    23200 rotated from previous position = 2.53 degrees 
    23201 atoms outside contour = 1760, contour level = 0.28583 
    23202  
    23203 Position of COPI_cyto_J3988_model D (#34.4) relative to
    23204 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23205 Matrix rotation and translation 
    23206 -0.35609850 -0.92473928 -0.13435451 272.54654270 
    23207 -0.80894027 0.23309315 0.53970662 166.76836324 
    23208 -0.46777080 0.30087349 -0.83106296 247.02887626 
    23209 Axis -0.56042334 0.78236325 0.27172306 
    23210 Axis point 212.17904341 0.00000000 74.04958983 
    23211 Rotation angle (degrees) 167.69692699 
    23212 Shift along axis 44.85543655 
    23213  
    23214 
    23215 > fitmap #34.5 inMap #22
    23216 
    23217 Fit molecule COPI_cyto_J3988_model E (#34.5) to map
    23218 W20_J3988_consensus_resampled.mrc (#22) using 1876 atoms 
    23219 average map value = 0.3399, steps = 68 
    23220 shifted from previous position = 0.902 
    23221 rotated from previous position = 1.88 degrees 
    23222 atoms outside contour = 644, contour level = 0.28583 
    23223  
    23224 Position of COPI_cyto_J3988_model E (#34.5) relative to
    23225 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23226 Matrix rotation and translation 
    23227 -0.38559316 -0.90595853 -0.17480580 278.32647192 
    23228 -0.80563868 0.23824013 0.54239099 166.10780051 
    23229 -0.44973798 0.34997256 -0.82173899 240.13441550 
    23230 Axis -0.54937100 0.78495483 0.28642174 
    23231 Axis point 210.04384962 0.00000000 72.68833745 
    23232 Rotation angle (degrees) 169.91400249 
    23233 Shift along axis 46.26234424 
    23234  
    23235 
    23236 > fitmap #34.10 inMap #22
    23237 
    23238 Fit molecule COPI_cyto_J3988_model J (#34.10) to map
    23239 W20_J3988_consensus_resampled.mrc (#22) using 1112 atoms 
    23240 average map value = 0.314, steps = 56 
    23241 shifted from previous position = 0.967 
    23242 rotated from previous position = 5.85 degrees 
    23243 atoms outside contour = 470, contour level = 0.28583 
    23244  
    23245 Position of COPI_cyto_J3988_model J (#34.10) relative to
    23246 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23247 Matrix rotation and translation 
    23248 -0.37577208 -0.92422463 -0.06785421 266.88773036 
    23249 -0.79027325 0.28134549 0.54434632 161.90561717 
    23250 -0.48400780 0.25817351 -0.83611178 252.25402649 
    23251 Axis -0.54768370 0.79644372 0.25635904 
    23252 Axis point 209.14918816 0.00000000 75.62770199 
    23253 Rotation angle (degrees) 164.85531677 
    23254 Shift along axis 47.44625196 
    23255  
    23256 
    23257 > fitmap #34.12 inMap #22
    23258 
    23259 Fit molecule COPI_cyto_J3988_model L (#34.12) to map
    23260 W20_J3988_consensus_resampled.mrc (#22) using 1420 atoms 
    23261 average map value = 0.2477, steps = 128 
    23262 shifted from previous position = 15.9 
    23263 rotated from previous position = 23.9 degrees 
    23264 atoms outside contour = 825, contour level = 0.28583 
    23265  
    23266 Position of COPI_cyto_J3988_model L (#34.12) relative to
    23267 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23268 Matrix rotation and translation 
    23269 -0.13744140 -0.87706877 -0.46028280 286.39333689 
    23270 -0.79755718 -0.17757218 0.57651599 190.01595705 
    23271 -0.58737759 0.44633901 -0.67510671 220.17263411 
    23272 Axis -0.65564558 0.64012190 0.40046576 
    23273 Axis point 0.00000000 242.83430967 190.87489306 
    23274 Rotation angle (degrees) 174.30264049 
    23275 Shift along axis 22.03245138 
    23276  
    23277 
    23278 > ui mousemode right "rotate selected models"
    23279 
    23280 > select add #34.12
    23281 
    23282 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    23283 
    23284 > view matrix models
    23285 > #34.12,0.094052,-0.95592,0.27815,157.02,-0.86993,0.056954,0.48988,190.57,-0.48413,-0.28805,-0.82622,295.38
    23286 
    23287 > fitmap #34.12 inMap #22
    23288 
    23289 Fit molecule COPI_cyto_J3988_model L (#34.12) to map
    23290 W20_J3988_consensus_resampled.mrc (#22) using 1420 atoms 
    23291 average map value = 0.265, steps = 180 
    23292 shifted from previous position = 7.48 
    23293 rotated from previous position = 16.7 degrees 
    23294 atoms outside contour = 709, contour level = 0.28583 
    23295  
    23296 Position of COPI_cyto_J3988_model L (#34.12) relative to
    23297 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23298 Matrix rotation and translation 
    23299 -0.10354097 -0.97915690 0.17473139 207.46054459 
    23300 -0.94372455 0.15219348 0.29363435 218.75648454 
    23301 -0.31410708 -0.13449511 -0.93981265 267.23328820 
    23302 Axis -0.65787226 0.75115891 0.05444605 
    23303 Axis point 229.01761440 0.00000000 99.48866389 
    23304 Rotation angle (degrees) 161.01082491 
    23305 Shift along axis 42.38814162 
    23306  
    23307 
    23308 > select subtract #34.12
    23309 
    23310 Nothing selected 
    23311 
    23312 > fitmap #34.13 inMap #22
    23313 
    23314 Fit molecule COPI_cyto_J3988_model M (#34.13) to map
    23315 W20_J3988_consensus_resampled.mrc (#22) using 4552 atoms 
    23316 average map value = 0.2757, steps = 176 
    23317 shifted from previous position = 11.7 
    23318 rotated from previous position = 23.1 degrees 
    23319 atoms outside contour = 2512, contour level = 0.28583 
    23320  
    23321 Position of COPI_cyto_J3988_model M (#34.13) relative to
    23322 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    23323 Matrix rotation and translation 
    23324 -0.23360378 -0.97224105 0.01329047 246.50433978 
    23325 -0.93813795 0.22896058 0.25975806 213.83868979 
    23326 -0.25559044 0.04821217 -0.96558227 246.39586728 
    23327 Axis -0.61528240 0.78204162 0.09918904 
    23328 Axis point 220.79513963 0.00000000 94.62595818 
    23329 Rotation angle (degrees) 170.10113474 
    23330 Shift along axis 40.00074310 
    23331  
    23332 
    23333 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    23334 > resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
    23335 
    23336 > open
    23337 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_29/denmod_map.ccp4
    23338 
    23339 Opened denmod_map.ccp4 as #35, grid size 99,98,133, pixel 1.19, shown at level
    23340 0.318, step 1, values float32 
    23341 
    23342 > open
    23343 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_30/denmod_map.ccp4
    23344 
    23345 Opened denmod_map.ccp4 as #36, grid size 97,98,137, pixel 1.19, shown at level
    23346 0.404, step 1, values float32 
    23347 
    23348 > hide #!34 models
    23349 
    23350 > hide #!22 models
    23351 
    23352 > hide #!36 models
    23353 
    23354 > volume #35 level 0.105
    23355 
    23356 > show #!34 models
    23357 
    23358 > hide #!35 models
    23359 
    23360 > show #!36 models
    23361 
    23362 > volume #36 level 0.1681
    23363 
    23364 > hide #!36 models
    23365 
    23366 > close #35-36
    23367 
    23368 > open
    23369 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_29/denmod_map.ccp4
    23370 
    23371 Opened denmod_map.ccp4 as #35, grid size 99,98,133, pixel 1.19, shown at level
    23372 0.318, step 1, values float32 
    23373 
    23374 > close #35
    23375 
    23376 > show #!47 models
    23377 
    23378 > hide #!47 models
    23379 
    23380 > close #56#47-55,57
    23381 
    23382 > show #!94 models
    23383 
    23384 > hide #!94 models
    23385 
    23386 > close #71-72,76,78-80,83,86-88#58-70,73-75,77,81-82,84-85,89-95
    23387 
    23388 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    23389 > files/COPI_soluble_job155_dhelix.pdb"
    23390 
    23391 Chain information for COPI_soluble_job155_dhelix.pdb #35 
    23392 --- 
    23393 Chain | Description 
    23394 D | No description available 
    23395 E | No description available 
    23396 F | No description available 
    23397 G | No description available 
    23398 H | No description available 
    23399 I | No description available 
    23400 J | No description available 
    23401 K | No description available 
    23402 L | No description available 
    23403 M | No description available 
    23404 N | No description available 
    23405 O | No description available 
    23406 P | No description available 
    23407 Q | No description available 
    23408  
    23409 
    23410 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
    23411 > files/COPI_soluble_job160_dhelix.pdb"
    23412 
    23413 Chain information for COPI_soluble_job160_dhelix.pdb #36 
    23414 --- 
    23415 Chain | Description 
    23416 D | No description available 
    23417 E | No description available 
    23418 F | No description available 
    23419 G | No description available 
    23420 H | No description available 
    23421 I | No description available 
    23422 J | No description available 
    23423 K | No description available 
    23424 L | No description available 
    23425 M | No description available 
    23426 N | No description available 
    23427 O | No description available 
    23428 P | No description available 
    23429 Q | No description available 
    23430  
    23431 
    23432 > ui tool show Matchmaker
    23433 
    23434 > matchmaker #!35-36 to #34.4
    23435 
    23436 Parameters 
    23437 --- 
    23438 Chain pairing | bb 
    23439 Alignment algorithm | Needleman-Wunsch 
    23440 Similarity matrix | BLOSUM-62 
    23441 SS fraction | 0.3 
    23442 Gap open (HH/SS/other) | 18/18/6 
    23443 Gap extend | 1 
    23444 SS matrix |  |  | H | S | O 
    23445 ---|---|---|--- 
    23446 H | 6 | -9 | -6 
    23447 S |  | 6 | -6 
    23448 O |  |  | 4 
    23449 Iteration cutoff | 2 
    23450  
    23451 Matchmaker COPI_cyto_J3988_model D, chain D (#34.4) with
    23452 COPI_soluble_job155_dhelix.pdb, chain I (#35), sequence alignment score = 1535 
    23453 RMSD between 291 pruned atom pairs is 0.541 angstroms; (across all 305 pairs:
    23454 0.988) 
    23455  
    23456 Matchmaker COPI_cyto_J3988_model D, chain D (#34.4) with
    23457 COPI_soluble_job160_dhelix.pdb, chain I (#36), sequence alignment score = 1538 
    23458 RMSD between 291 pruned atom pairs is 0.541 angstroms; (across all 305 pairs:
    23459 0.988) 
    23460  
    23461 
    23462 > hide #34.1-3,5-13#!35-36#!34.4 atoms
    23463 
    23464 > show #34.1-3,5-13#!35-36#!34.4 cartoons
    23465 
    23466 > hide #!34 models
    23467 
    23468 > hide #!36 models
    23469 
    23470 > show #!16 models
    23471 
    23472 > show #!18 models
    23473 
    23474 > hide #!16 models
    23475 
    23476 > hide #!18 models
    23477 
    23478 > show #!20 models
    23479 
    23480 > hide #!20 models
    23481 
    23482 > show #!22 models
    23483 
    23484 > hide #!35 models
    23485 
    23486 > show #!36 models
    23487 
    23488 > show #!20 models
    23489 
    23490 > hide #!20 models
    23491 
    23492 > show #!18 models
    23493 
    23494 > hide #!22 models
    23495 
    23496 > hide #!18 models
    23497 
    23498 > hide #!36 models
    23499 
    23500 > split #35 chains
    23501 
    23502 Split COPI_soluble_job155_dhelix.pdb (#35) into 14 models 
    23503 Chain information for COPI_soluble_job155_dhelix.pdb D #35.1 
    23504 --- 
    23505 Chain | Description 
    23506 D | No description available 
    23507  
    23508 Chain information for COPI_soluble_job155_dhelix.pdb E #35.2 
    23509 --- 
    23510 Chain | Description 
    23511 E | No description available 
    23512  
    23513 Chain information for COPI_soluble_job155_dhelix.pdb F #35.3 
    23514 --- 
    23515 Chain | Description 
    23516 F | No description available 
    23517  
    23518 Chain information for COPI_soluble_job155_dhelix.pdb G #35.4 
    23519 --- 
    23520 Chain | Description 
    23521 G | No description available 
    23522  
    23523 Chain information for COPI_soluble_job155_dhelix.pdb H #35.5 
    23524 --- 
    23525 Chain | Description 
    23526 H | No description available 
    23527  
    23528 Chain information for COPI_soluble_job155_dhelix.pdb I #35.6 
    23529 --- 
    23530 Chain | Description 
    23531 I | No description available 
    23532  
    23533 Chain information for COPI_soluble_job155_dhelix.pdb J #35.7 
    23534 --- 
    23535 Chain | Description 
    23536 J | No description available 
    23537  
    23538 Chain information for COPI_soluble_job155_dhelix.pdb K #35.8 
    23539 --- 
    23540 Chain | Description 
    23541 K | No description available 
    23542  
    23543 Chain information for COPI_soluble_job155_dhelix.pdb L #35.9 
    23544 --- 
    23545 Chain | Description 
    23546 L | No description available 
    23547  
    23548 Chain information for COPI_soluble_job155_dhelix.pdb M #35.10 
    23549 --- 
    23550 Chain | Description 
    23551 M | No description available 
    23552  
    23553 Chain information for COPI_soluble_job155_dhelix.pdb N #35.11 
    23554 --- 
    23555 Chain | Description 
    23556 N | No description available 
    23557  
    23558 Chain information for COPI_soluble_job155_dhelix.pdb O #35.12 
    23559 --- 
    23560 Chain | Description 
    23561 O | No description available 
    23562  
    23563 Chain information for COPI_soluble_job155_dhelix.pdb P #35.13 
    23564 --- 
    23565 Chain | Description 
    23566 P | No description available 
    23567  
    23568 Chain information for COPI_soluble_job155_dhelix.pdb Q #35.14 
    23569 --- 
    23570 Chain | Description 
    23571 Q | No description available 
    23572  
    23573 
    23574 > split #36 chains
    23575 
    23576 Split COPI_soluble_job160_dhelix.pdb (#36) into 14 models 
    23577 Chain information for COPI_soluble_job160_dhelix.pdb D #36.1 
    23578 --- 
    23579 Chain | Description 
    23580 D | No description available 
    23581  
    23582 Chain information for COPI_soluble_job160_dhelix.pdb E #36.2 
    23583 --- 
    23584 Chain | Description 
    23585 E | No description available 
    23586  
    23587 Chain information for COPI_soluble_job160_dhelix.pdb F #36.3 
    23588 --- 
    23589 Chain | Description 
    23590 F | No description available 
    23591  
    23592 Chain information for COPI_soluble_job160_dhelix.pdb G #36.4 
    23593 --- 
    23594 Chain | Description 
    23595 G | No description available 
    23596  
    23597 Chain information for COPI_soluble_job160_dhelix.pdb H #36.5 
    23598 --- 
    23599 Chain | Description 
    23600 H | No description available 
    23601  
    23602 Chain information for COPI_soluble_job160_dhelix.pdb I #36.6 
    23603 --- 
    23604 Chain | Description 
    23605 I | No description available 
    23606  
    23607 Chain information for COPI_soluble_job160_dhelix.pdb J #36.7 
    23608 --- 
    23609 Chain | Description 
    23610 J | No description available 
    23611  
    23612 Chain information for COPI_soluble_job160_dhelix.pdb K #36.8 
    23613 --- 
    23614 Chain | Description 
    23615 K | No description available 
    23616  
    23617 Chain information for COPI_soluble_job160_dhelix.pdb L #36.9 
    23618 --- 
    23619 Chain | Description 
    23620 L | No description available 
    23621  
    23622 Chain information for COPI_soluble_job160_dhelix.pdb M #36.10 
    23623 --- 
    23624 Chain | Description 
    23625 M | No description available 
    23626  
    23627 Chain information for COPI_soluble_job160_dhelix.pdb N #36.11 
    23628 --- 
    23629 Chain | Description 
    23630 N | No description available 
    23631  
    23632 Chain information for COPI_soluble_job160_dhelix.pdb O #36.12 
    23633 --- 
    23634 Chain | Description 
    23635 O | No description available 
    23636  
    23637 Chain information for COPI_soluble_job160_dhelix.pdb P #36.13 
    23638 --- 
    23639 Chain | Description 
    23640 P | No description available 
    23641  
    23642 Chain information for COPI_soluble_job160_dhelix.pdb Q #36.14 
    23643 --- 
    23644 Chain | Description 
    23645 Q | No description available 
    23646  
    23647 
    23648 > open
    23649 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_32/J4028_denmod_map.ccp4
    23650 
    23651 Opened J4028_denmod_map.ccp4 as #37, grid size 98,99,135, pixel 1.19, shown at
    23652 level 0.424, step 1, values float32 
    23653 
    23654 > volume #37 level 0.2276
    23655 
    23656 > hide #!35 models
    23657 
    23658 > hide #!36 models
    23659 
    23660 > show #!35.14 models
    23661 
    23662 > show #!35.13 models
    23663 
    23664 > show #35.12 models
    23665 
    23666 > show #!35.11 models
    23667 
    23668 > show #35.10 models
    23669 
    23670 > show #35.9 models
    23671 
    23672 > show #35.8 models
    23673 
    23674 > show #!35.7 models
    23675 
    23676 > show #!35.6 models
    23677 
    23678 > show #35.5 models
    23679 
    23680 > show #35.4 models
    23681 
    23682 > show #35.3 models
    23683 
    23684 > show #35.2 models
    23685 
    23686 > show #35.1 models
    23687 
    23688 > hide #!35 models
    23689 
    23690 > volume #37 level 0.1206
    23691 
    23692 > close #37
    23693 
    23694 > show #!16 models
    23695 
    23696 > show #!31 models
    23697 
    23698 > show #!35 models
    23699 
    23700 > hide #35.1 models
    23701 
    23702 > hide #35.2 models
    23703 
    23704 > hide #35.3 models
    23705 
    23706 > hide #35.4 models
    23707 
    23708 > hide #35.5 models
    23709 
    23710 > hide #!35.6 models
    23711 
    23712 > hide #!35.7 models
    23713 
    23714 > hide #35.8 models
    23715 
    23716 > hide #35.9 models
    23717 
    23718 > show #35.9 models
    23719 
    23720 > hide #35.10 models
    23721 
    23722 > show #35.10 models
    23723 
    23724 > hide #35.10 models
    23725 
    23726 > show #35.10 models
    23727 
    23728 > hide #!35.11 models
    23729 
    23730 > show #!35.11 models
    23731 
    23732 > hide #35.12 models
    23733 
    23734 > hide #!35.13 models
    23735 
    23736 > hide #!35.14 models
    23737 
    23738 > fitmap #35.9 inMap #16
    23739 
    23740 Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
    23741 W20_J4026_consensus_resampled.mrc (#16) using 1163 atoms 
    23742 average map value = 0.3245, steps = 56 
    23743 shifted from previous position = 1.07 
    23744 rotated from previous position = 3.98 degrees 
    23745 atoms outside contour = 440, contour level = 0.25963 
    23746  
    23747 Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
    23748 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    23749 Matrix rotation and translation 
    23750 -0.90987894 0.24236896 -0.33671591 435.50395252 
    23751 0.06606031 -0.71661672 -0.69433170 604.82381864 
    23752 -0.40958070 -0.65400135 0.63602349 262.39041137 
    23753 Axis 0.20683441 0.37368744 -0.90419977 
    23754 Axis point 263.30917938 345.30538105 0.00000000 
    23755 Rotation angle (degrees) 174.40510072 
    23756 Shift along axis 78.83891898 
    23757  
    23758 
    23759 > fitmap #35.10 inMap #16
    23760 
    23761 Fit molecule COPI_soluble_job155_dhelix.pdb M (#35.10) to map
    23762 W20_J4026_consensus_resampled.mrc (#16) using 2212 atoms 
    23763 average map value = 0.3306, steps = 92 
    23764 shifted from previous position = 2.46 
    23765 rotated from previous position = 6.1 degrees 
    23766 atoms outside contour = 710, contour level = 0.25963 
    23767  
    23768 Position of COPI_soluble_job155_dhelix.pdb M (#35.10) relative to
    23769 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    23770 Matrix rotation and translation 
    23771 -0.91287694 0.27628102 -0.30054033 410.29266882 
    23772 -0.00773154 -0.74776328 -0.66392040 629.67159952 
    23773 -0.40816163 -0.60375398 0.68475193 227.42100406 
    23774 Axis 0.19432248 0.34758987 -0.91728952 
    23775 Axis point 254.63604518 341.25031476 0.00000000 
    23776 Rotation angle (degrees) 171.09417945 
    23777 Shift along axis 89.98565405 
    23778  
    23779 
    23780 > fitmap #35.11 inMap #16
    23781 
    23782 Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
    23783 W20_J4026_consensus_resampled.mrc (#16) using 1064 atoms 
    23784 average map value = 0.3024, steps = 52 
    23785 shifted from previous position = 1.19 
    23786 rotated from previous position = 1.61 degrees 
    23787 atoms outside contour = 298, contour level = 0.25963 
    23788  
    23789 Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
    23790 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    23791 Matrix rotation and translation 
    23792 -0.93792901 0.21017775 -0.27588855 435.11677592 
    23793 0.06068204 -0.68374702 -0.72719166 606.90260953 
    23794 -0.34147748 -0.69879563 0.62855215 261.30949009 
    23795 Axis 0.17136788 0.39582419 -0.90219524 
    23796 Axis point 255.61353944 351.07885546 0.00000000 
    23797 Rotation angle (degrees) 175.24753470 
    23798 Shift along axis 79.03959464 
    23799  
    23800 
    23801 > hide #31.13 models
    23802 
    23803 > hide #31.12 models
    23804 
    23805 > show #31.12 models
    23806 
    23807 > select add #31.12
    23808 
    23809 1420 atoms, 1441 bonds, 177 residues, 1 model selected 
    23810 
    23811 > view matrix models
    23812 > #31.12,-0.23372,-0.97024,-0.063385,254.71,-0.96642,0.23897,-0.094492,266.72,0.10683,0.039172,-0.99351,199.68
    23813 
    23814 > fitmap #31.12 inMap #16
    23815 
    23816 Fit molecule COPI_cyto_J4026_model L (#31.12) to map
    23817 W20_J4026_consensus_resampled.mrc (#16) using 1420 atoms 
    23818 average map value = 0.2882, steps = 136 
    23819 shifted from previous position = 4.88 
    23820 rotated from previous position = 24.5 degrees 
    23821 atoms outside contour = 593, contour level = 0.25963 
    23822  
    23823 Position of COPI_cyto_J4026_model L (#31.12) relative to
    23824 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    23825 Matrix rotation and translation 
    23826 -0.11780824 -0.96709435 0.22549890 202.70773070 
    23827 -0.96549277 0.16465999 0.20176923 232.00719445 
    23828 -0.23226052 -0.19394747 -0.95312090 262.37235731 
    23829 Axis -0.65397629 0.75651041 0.00264684 
    23830 Axis point 228.48470686 0.00000000 107.10492224 
    23831 Rotation angle (degrees) 162.38937332 
    23832 Shift along axis 43.64426578 
    23833  
    23834 
    23835 > select subtract #31.12
    23836 
    23837 Nothing selected 
    23838 
    23839 > show #31.13 models
    23840 
    23841 > hide #31.13 models
    23842 
    23843 > hide #31.12 models
    23844 
    23845 > hide #31.11 models
    23846 
    23847 > hide #31.10 models
    23848 
    23849 > hide #31.9 models
    23850 
    23851 > hide #31.8 models
    23852 
    23853 > hide #31.7 models
    23854 
    23855 > hide #31.6 models
    23856 
    23857 > hide #31.5 models
    23858 
    23859 > hide #!31.4 models
    23860 
    23861 > hide #31.3 models
    23862 
    23863 > hide #31.2 models
    23864 
    23865 > hide #31.1 models
    23866 
    23867 > hide #!16 models
    23868 
    23869 > show #31.13 models
    23870 
    23871 > hide #35.9 models
    23872 
    23873 > hide #!35.11 models
    23874 
    23875 > hide #35.10 models
    23876 
    23877 > ui mousemode right select
    23878 
    23879 Drag select of 228 residues 
    23880 
    23881 > select up
    23882 
    23883 2019 atoms, 2046 bonds, 257 residues, 1 model selected 
    23884 
    23885 > delete sel
    23886 
    23887 > show #35.10 models
    23888 
    23889 Drag select of 6 residues, 1 pseudobonds 
    23890 
    23891 > select up
    23892 
    23893 61 atoms, 60 bonds, 1 pseudobond, 8 residues, 2 models selected 
    23894 
    23895 > delete sel
    23896 
    23897 Drag select of 3 residues 
    23898 
    23899 > select up
    23900 
    23901 130 atoms, 130 bonds, 17 residues, 1 model selected 
    23902 
    23903 > delete sel
    23904 
    23905 > fitmap #31.13 inMap #16
    23906 
    23907 Fit molecule COPI_cyto_J4026_model M (#31.13) to map
    23908 W20_J4026_consensus_resampled.mrc (#16) using 2342 atoms 
    23909 average map value = 0.3254, steps = 72 
    23910 shifted from previous position = 2.25 
    23911 rotated from previous position = 5.92 degrees 
    23912 atoms outside contour = 789, contour level = 0.25963 
    23913  
    23914 Position of COPI_cyto_J4026_model M (#31.13) relative to
    23915 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    23916 Matrix rotation and translation 
    23917 -0.14741636 -0.97480443 0.16740596 215.74618933 
    23918 -0.97007287 0.17551559 0.16778831 236.68236999 
    23919 -0.19294315 -0.13766124 -0.97150519 252.55946622 
    23920 Axis -0.64657421 0.76278534 0.01001574 
    23921 Axis point 227.98326837 0.00000000 105.57175219 
    23922 Rotation angle (degrees) 166.33727095 
    23923 Shift along axis 43.57149027 
    23924  
    23925 
    23926 > hide #!31.13 models
    23927 
    23928 > show #!31.13 models
    23929 
    23930 > show #!16 models
    23931 
    23932 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    23933 > predictions/fold_20250401_ct_alpha1_350_gamma1_350/fold_20250401_ct_alpha1_350_gamma1_350_model_0.cif"
    23934 
    23935 Chain information for fold_20250401_ct_alpha1_350_gamma1_350_model_0.cif #37 
    23936 --- 
    23937 Chain | Description 
    23938 A | . 
    23939 B | . 
    23940  
    23941 Computing secondary structure 
    23942 
    23943 > ui tool show Matchmaker
    23944 
    23945 > matchmaker #37 to #31.1
    23946 
    23947 Parameters 
    23948 --- 
    23949 Chain pairing | bb 
    23950 Alignment algorithm | Needleman-Wunsch 
    23951 Similarity matrix | BLOSUM-62 
    23952 SS fraction | 0.3 
    23953 Gap open (HH/SS/other) | 18/18/6 
    23954 Gap extend | 1 
    23955 SS matrix |  |  | H | S | O 
    23956 ---|---|---|--- 
    23957 H | 6 | -9 | -6 
    23958 S |  | 6 | -6 
    23959 O |  |  | 4 
    23960 Iteration cutoff | 2 
    23961  
    23962 Matchmaker COPI_cyto_J4026_model A, chain A (#31.1) with
    23963 fold_20250401_ct_alpha1_350_gamma1_350_model_0.cif, chain A (#37), sequence
    23964 alignment score = 1357.6 
    23965 RMSD between 278 pruned atom pairs is 0.471 angstroms; (across all 313 pairs:
    23966 6.653) 
    23967  
    23968 
    23969 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    23970 > predictions/fold_20250401_ct_alpha1_350_gamma1_50/fold_20250401_ct_alpha1_350_gamma1_50_model_0.cif"
    23971 
    23972 Chain information for fold_20250401_ct_alpha1_350_gamma1_50_model_0.cif #38 
    23973 --- 
    23974 Chain | Description 
    23975 A | . 
    23976 B | . 
    23977  
    23978 Computing secondary structure 
    23979 
    23980 > ui tool show Matchmaker
    23981 
    23982 > matchmaker #38 to #24.1
    23983 
    23984 Parameters 
    23985 --- 
    23986 Chain pairing | bb 
    23987 Alignment algorithm | Needleman-Wunsch 
    23988 Similarity matrix | BLOSUM-62 
    23989 SS fraction | 0.3 
    23990 Gap open (HH/SS/other) | 18/18/6 
    23991 Gap extend | 1 
    23992 SS matrix |  |  | H | S | O 
    23993 ---|---|---|--- 
    23994 H | 6 | -9 | -6 
    23995 S |  | 6 | -6 
    23996 O |  |  | 4 
    23997 Iteration cutoff | 2 
    23998  
    23999 Matchmaker COPI_cyto_for_J4027_v1 A, chain A (#24.1) with
    24000 fold_20250401_ct_alpha1_350_gamma1_50_model_0.cif, chain A (#38), sequence
    24001 alignment score = 1354 
    24002 RMSD between 279 pruned atom pairs is 0.445 angstroms; (across all 313 pairs:
    24003 6.676) 
    24004  
    24005 
    24006 > hide #!16 models
    24007 
    24008 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
    24009 > predictions/fold_2025_01_17_alpha1_330gamma1_330zeta/fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif"
    24010 
    24011 Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif #39 
    24012 --- 
    24013 Chain | Description 
    24014 A | . 
    24015 B | . 
    24016 C | . 
    24017  
    24018 Computing secondary structure 
    24019 
    24020 > ui tool show Matchmaker
    24021 
    24022 > matchmaker #39 to #24.1
    24023 
    24024 Parameters 
    24025 --- 
    24026 Chain pairing | bb 
    24027 Alignment algorithm | Needleman-Wunsch 
    24028 Similarity matrix | BLOSUM-62 
    24029 SS fraction | 0.3 
    24030 Gap open (HH/SS/other) | 18/18/6 
    24031 Gap extend | 1 
    24032 SS matrix |  |  | H | S | O 
    24033 ---|---|---|--- 
    24034 H | 6 | -9 | -6 
    24035 S |  | 6 | -6 
    24036 O |  |  | 4 
    24037 Iteration cutoff | 2 
    24038  
    24039 Matchmaker COPI_cyto_for_J4027_v1 A, chain A (#24.1) with
    24040 fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain B (#39), sequence
    24041 alignment score = 1688.7 
    24042 RMSD between 283 pruned atom pairs is 0.307 angstroms; (across all 318 pairs:
    24043 4.917) 
    24044  
    24045 
    24046 > hide #38 models
    24047 
    24048 > hide #37 models
    24049 
    24050 > fitmap #39 inMap #16
    24051 
    24052 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#39) to map
    24053 W20_J4026_consensus_resampled.mrc (#16) using 6676 atoms 
    24054 average map value = 0.2973, steps = 112 
    24055 shifted from previous position = 5.99 
    24056 rotated from previous position = 14.7 degrees 
    24057 atoms outside contour = 2828, contour level = 0.25963 
    24058  
    24059 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#39)
    24060 relative to W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    24061 Matrix rotation and translation 
    24062 0.75236864 0.61844958 -0.22685138 135.89900591 
    24063 0.54481378 -0.77776674 -0.31345947 141.53555984 
    24064 -0.37029633 0.11224532 -0.92210716 89.13598609 
    24065 Axis 0.93516725 0.31511280 -0.16175949 
    24066 Axis point 0.00000000 40.80728347 61.99249889 
    24067 Rotation angle (degrees) 166.84366143 
    24068 Shift along axis 157.26937502 
    24069  
    24070 
    24071 > split #39 chains
    24072 
    24073 Split fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#39) into 3 models 
    24074 Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A
    24075 #39.1 
    24076 --- 
    24077 Chain | Description 
    24078 A | No description available 
    24079  
    24080 Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif B
    24081 #39.2 
    24082 --- 
    24083 Chain | Description 
    24084 B | No description available 
    24085  
    24086 Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif C
    24087 #39.3 
    24088 --- 
    24089 Chain | Description 
    24090 C | No description available 
    24091  
    24092 
    24093 > show #!16 models
    24094 
    24095 > hide #!31.13 models
    24096 
    24097 > hide #39.2 models
    24098 
    24099 > show #39.2 models
    24100 
    24101 > hide #39.2 models
    24102 
    24103 > hide #39.1 models
    24104 
    24105 > show #39.1 models
    24106 
    24107 > hide #39.3 models
    24108 
    24109 > show #31.12 models
    24110 
    24111 > show #31.1 models
    24112 
    24113 > fitmap #39.1 inMap #16
    24114 
    24115 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24116 map W20_J4026_consensus_resampled.mrc (#16) using 2567 atoms 
    24117 average map value = 0.332, steps = 92 
    24118 shifted from previous position = 1.08 
    24119 rotated from previous position = 8.07 degrees 
    24120 atoms outside contour = 837, contour level = 0.25963 
    24121  
    24122 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24123 relative to W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    24124 Matrix rotation and translation 
    24125 0.83404122 0.50639742 -0.21894494 135.37114526 
    24126 0.43420964 -0.84733835 -0.30574452 138.37406207 
    24127 -0.34034868 0.15993553 -0.92659775 89.77783066 
    24128 Axis 0.95695074 0.24947901 -0.14834252 
    24129 Axis point 0.00000000 44.30433155 61.88415197 
    24130 Rotation angle (degrees) 165.91774988 
    24131 Shift along axis 150.74707237 
    24132  
    24133 
    24134 > hide #!16 models
    24135 
    24136 > hide #31.12 models
    24137 
    24138 > show #35.9 models
    24139 
    24140 > hide #35.9 models
    24141 
    24142 > show #35.9 models
    24143 
    24144 > show #!16 models
    24145 
    24146 > hide #!16 models
    24147 
    24148 > hide #35.9 models
    24149 
    24150 > hide #35.10 models
    24151 
    24152 > show #35.9 models
    24153 
    24154 > hide #39.1 models
    24155 
    24156 Drag select of 11 residues 
    24157 
    24158 > select up
    24159 
    24160 130 atoms, 130 bonds, 17 residues, 1 model selected 
    24161 
    24162 > delete sel
    24163 
    24164 > show #39.1 models
    24165 
    24166 > select #35.9/L:317
    24167 
    24168 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24169 
    24170 > delete sel
    24171 
    24172 > hide #39.1 models
    24173 
    24174 Drag select of 4 residues 
    24175 
    24176 > delete sel
    24177 
    24178 Drag select of 5 residues 
    24179 
    24180 > delete sel
    24181 
    24182 > select #35.9/L:327
    24183 
    24184 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24185 
    24186 > delete sel
    24187 
    24188 > show #39.1 models
    24189 
    24190 > hide #39.1 models
    24191 
    24192 > select #35.9/L:328
    24193 
    24194 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24195 
    24196 > delete sel
    24197 
    24198 > select #35.9/L:329
    24199 
    24200 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24201 
    24202 > delete sel
    24203 
    24204 > show #39.1 models
    24205 
    24206 > select #35.9/L:330
    24207 
    24208 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24209 
    24210 > delete sel
    24211 
    24212 > show #!16 models
    24213 
    24214 > fitmap #35.9 inMap #16
    24215 
    24216 Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
    24217 W20_J4026_consensus_resampled.mrc (#16) using 930 atoms 
    24218 average map value = 0.3516, steps = 52 
    24219 shifted from previous position = 0.499 
    24220 rotated from previous position = 6.25 degrees 
    24221 atoms outside contour = 295, contour level = 0.25963 
    24222  
    24223 Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
    24224 W20_J4026_consensus_resampled.mrc (#16) coordinates: 
    24225 Matrix rotation and translation 
    24226 -0.93642912 0.16612187 -0.30903727 462.34398677 
    24227 0.11986381 -0.67634146 -0.72677018 585.05727704 
    24228 -0.32974714 -0.71761114 0.61343384 270.00020679 
    24229 Axis 0.17783383 0.40210728 -0.89815637 
    24230 Axis point 261.88005557 349.74957427 0.00000000 
    24231 Rotation angle (degrees) 178.52437469 
    24232 Shift along axis 74.97378580 
    24233  
    24234 
    24235 > show #35.8 models
    24236 
    24237 > hide #35.8 models
    24238 
    24239 > show #!35.11 models
    24240 
    24241 > show #31.12 models
    24242 
    24243 > show #31.11 models
    24244 
    24245 > show #31.10 models
    24246 
    24247 > show #31.9 models
    24248 
    24249 > show #31.8 models
    24250 
    24251 > show #31.7 models
    24252 
    24253 > show #31.6 models
    24254 
    24255 > show #31.5 models
    24256 
    24257 > show #!31.4 models
    24258 
    24259 > show #31.3 models
    24260 
    24261 > show #31.2 models
    24262 
    24263 > combine #31.1 #31.2 #31.3 #31.4 #31.5 #31.6 #31.7 #31.8 #31.9 #31.10 #31.11
    24264 > #31.12 #39.1 #35.9 #35.11
    24265 
    24266 Remapping chain ID 'A' in fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif
    24267 A #39.1 to 'M' 
    24268 Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N' 
    24269 Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O' 
    24270 
    24271 > rename #40 COPI_cyto_J4026_model
    24272 
    24273 > hide #!40 models
    24274 
    24275 > show #!40 models
    24276 
    24277 > hide #!40 models
    24278 
    24279 > hide #!16 models
    24280 
    24281 > show #!18 models
    24282 
    24283 > fitmap #35.11 inMap #18
    24284 
    24285 Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
    24286 W20_J4027_consensus_resampled.mrc (#18) using 1064 atoms 
    24287 average map value = 0.345, steps = 52 
    24288 shifted from previous position = 0.96 
    24289 rotated from previous position = 4.13 degrees 
    24290 atoms outside contour = 305, contour level = 0.25259 
    24291  
    24292 Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
    24293 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    24294 Matrix rotation and translation 
    24295 -0.95797163 0.17569317 -0.22676476 434.71371371 
    24296 0.05774245 -0.65621750 -0.75235923 607.00290226 
    24297 -0.28099138 -0.73383275 0.61849280 258.09556438 
    24298 Axis 0.14127895 0.41352064 -0.89946703 
    24299 Axis point 248.09458414 355.10604389 0.00000000 
    24300 Rotation angle (degrees) 176.24059016 
    24301 Shift along axis 80.27567222 
    24302  
    24303 
    24304 > fitmap #35.9 inMap #18
    24305 
    24306 Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
    24307 W20_J4027_consensus_resampled.mrc (#18) using 930 atoms 
    24308 average map value = 0.3717, steps = 64 
    24309 shifted from previous position = 4.09 
    24310 rotated from previous position = 12 degrees 
    24311 atoms outside contour = 279, contour level = 0.25259 
    24312  
    24313 Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
    24314 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    24315 Matrix rotation and translation 
    24316 -0.98236672 0.03849512 -0.18295835 476.12367349 
    24317 0.12352589 -0.60093803 -0.78969288 580.42963487 
    24318 -0.14034595 -0.79836809 0.58558637 250.87293860 
    24319 Axis -0.09083469 -0.44617724 0.89032293 
    24320 Axis point 243.54419066 359.36795920 0.00000000 
    24321 Rotation angle (degrees) 177.26292686 
    24322 Shift along axis -78.86510835 
    24323  
    24324 
    24325 > fitmap #39.1 inMap #18
    24326 
    24327 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24328 map W20_J4027_consensus_resampled.mrc (#18) using 2567 atoms 
    24329 average map value = 0.2497, steps = 140 
    24330 shifted from previous position = 20.2 
    24331 rotated from previous position = 23.5 degrees 
    24332 atoms outside contour = 1358, contour level = 0.25259 
    24333  
    24334 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24335 relative to W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    24336 Matrix rotation and translation 
    24337 0.71011541 0.46894974 -0.52518782 133.17594101 
    24338 0.50811821 -0.85767517 -0.07879844 140.50399717 
    24339 -0.48739306 -0.21090151 -0.84733026 102.37727978 
    24340 Axis -0.92459305 -0.26452658 0.27414118 
    24341 Axis point 0.00000000 53.88234017 68.89098797 
    24342 Rotation angle (degrees) 175.90338628 
    24343 Shift along axis -132.23476323 
    24344  
    24345 
    24346 > select add #39.1
    24347 
    24348 2567 atoms, 2609 bonds, 330 residues, 1 model selected 
    24349 
    24350 > ui mousemode right "translate selected models"
    24351 
    24352 > view matrix models
    24353 > #39.1,0.71012,0.46895,-0.52519,127.98,0.50812,-0.85768,-0.078798,150.01,-0.48739,-0.2109,-0.84733,99.315
    24354 
    24355 > fitmap #39.1 inMap #18
    24356 
    24357 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24358 map W20_J4027_consensus_resampled.mrc (#18) using 2567 atoms 
    24359 average map value = 0.2908, steps = 104 
    24360 shifted from previous position = 3.89 
    24361 rotated from previous position = 15.2 degrees 
    24362 atoms outside contour = 938, contour level = 0.25259 
    24363  
    24364 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24365 relative to W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    24366 Matrix rotation and translation 
    24367 0.65350179 0.33145691 -0.68049373 127.41590893 
    24368 0.52879246 -0.84317616 0.09712103 144.98236935 
    24369 -0.54158466 -0.42330872 -0.72628905 97.39971457 
    24370 Axis -0.90721165 -0.24214590 0.34399476 
    24371 Axis point 0.00000000 66.60547701 63.44217524 
    24372 Rotation angle (degrees) 163.33177472 
    24373 Shift along axis -117.19509172 
    24374  
    24375 
    24376 > hide #31.12 models
    24377 
    24378 > hide #!31 models
    24379 
    24380 > show #!32 models
    24381 
    24382 > hide #32.13 models
    24383 
    24384 > fitmap #32.12 inMap #18
    24385 
    24386 Fit molecule COPI_cyto_J4027_model L (#32.12) to map
    24387 W20_J4027_consensus_resampled.mrc (#18) using 1420 atoms 
    24388 average map value = 0.249, steps = 84 
    24389 shifted from previous position = 0.209 
    24390 rotated from previous position = 0.257 degrees 
    24391 atoms outside contour = 664, contour level = 0.25259 
    24392  
    24393 Position of COPI_cyto_J4027_model L (#32.12) relative to
    24394 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    24395 Matrix rotation and translation 
    24396 -0.36763985 -0.91576410 -0.16191685 275.33631018 
    24397 -0.79632880 0.22007538 0.56340686 164.04444754 
    24398 -0.48031386 0.33606986 -0.81015780 242.91724000 
    24399 Axis -0.55576549 0.77837779 0.29198072 
    24400 Axis point 211.47624167 0.00000000 70.72859152 
    24401 Rotation angle (degrees) 168.19824647 
    24402 Shift along axis 45.59328469 
    24403  
    24404 
    24405 > view matrix models
    24406 > #39.1,0.6535,0.33146,-0.68049,127.38,0.52879,-0.84318,0.097121,144.98,-0.54158,-0.42331,-0.72629,97.387
    24407 
    24408 > select subtract #39.1
    24409 
    24410 Nothing selected 
    24411 
    24412 > fitmap #32.5 inMap #18
    24413 
    24414 Fit molecule COPI_cyto_J4027_model E (#32.5) to map
    24415 W20_J4027_consensus_resampled.mrc (#18) using 1876 atoms 
    24416 average map value = 0.3307, steps = 28 
    24417 shifted from previous position = 0.0226 
    24418 rotated from previous position = 0.025 degrees 
    24419 atoms outside contour = 588, contour level = 0.25259 
    24420  
    24421 Position of COPI_cyto_J4027_model E (#32.5) relative to
    24422 W20_J4027_consensus_resampled.mrc (#18) coordinates: 
    24423 Matrix rotation and translation 
    24424 -0.38917297 -0.90711538 -0.16026883 277.45394634 
    24425 -0.76472866 0.22115752 0.60521025 157.23067335 
    24426 -0.51355087 0.35809364 -0.77976565 242.80657971 
    24427 Axis -0.54426642 0.77809236 0.31360219 
    24428 Axis point 210.56184964 0.00000000 67.30315702 
    24429 Rotation angle (degrees) 166.87842423 
    24430 Shift along axis 47.47579529 
    24431  
    24432 
    24433 > combine #32.1 #32.2 #32.3 #32.4 #32.5 #32.6 #32.7 #32.8 #32.9 #32.10 #32.11
    24434 > #32.12 #39.1 #35.9 #35.11
    24435 
    24436 Remapping chain ID 'A' in fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif
    24437 A #39.1 to 'M' 
    24438 Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N' 
    24439 Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O' 
    24440 
    24441 > rename #41 COPI_cyto_J4017_model
    24442 
    24443 > hide #39.1 models
    24444 
    24445 > show #39.1 models
    24446 
    24447 > hide #!41 models
    24448 
    24449 > hide #!32 models
    24450 
    24451 > hide #!18 models
    24452 
    24453 > show #!20 models
    24454 
    24455 > fitmap #35.9 inMap #10
    24456 
    24457 Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
    24458 W20_J4023_consensus_resampled.mrc (#10) using 930 atoms 
    24459 average map value = 0.2393, steps = 52 
    24460 shifted from previous position = 2.69 
    24461 rotated from previous position = 6.1 degrees 
    24462 atoms outside contour = 585, contour level = 0.259 
    24463  
    24464 Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
    24465 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24466 Matrix rotation and translation 
    24467 -0.98125869 0.10123862 -0.16395770 446.50000833 
    24468 0.05661840 -0.66183176 -0.74751126 606.96394850 
    24469 -0.18418942 -0.74278494 0.64369619 224.44341669 
    24470 Axis 0.09602403 0.41104534 -0.90654350 
    24471 Axis point 239.00882222 351.39277051 0.00000000 
    24472 Rotation angle (degrees) 178.58980379 
    24473 Shift along axis 88.89671334 
    24474  
    24475 
    24476 > fitmap #35.11 inMap #10
    24477 
    24478 Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
    24479 W20_J4023_consensus_resampled.mrc (#10) using 1064 atoms 
    24480 average map value = 0.2705, steps = 48 
    24481 shifted from previous position = 1.17 
    24482 rotated from previous position = 3.69 degrees 
    24483 atoms outside contour = 361, contour level = 0.259 
    24484  
    24485 Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
    24486 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24487 Matrix rotation and translation 
    24488 -0.95447536 0.16472623 -0.24868064 445.72556094 
    24489 0.09748552 -0.61564640 -0.78196936 592.79673482 
    24490 -0.28191020 -0.77061325 0.57156090 289.62220826 
    24491 Axis 0.14970170 0.43804800 -0.88639909 
    24492 Axis point 253.33667423 363.30405703 0.00000000 
    24493 Rotation angle (degrees) 177.82629912 
    24494 Shift along axis 69.67843860 
    24495  
    24496 
    24497 > fitmap #39.1 inMap #10
    24498 
    24499 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24500 map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms 
    24501 average map value = 0.197, steps = 180 
    24502 shifted from previous position = 18.8 
    24503 rotated from previous position = 39.4 degrees 
    24504 atoms outside contour = 2326, contour level = 0.259 
    24505  
    24506 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24507 relative to W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24508 Matrix rotation and translation 
    24509 0.77937618 0.53787625 -0.32134390 138.00151844 
    24510 0.38455520 -0.81555599 -0.43241846 137.27793171 
    24511 -0.49466156 0.21344218 -0.84246803 102.09006947 
    24512 Axis 0.94140147 0.25262649 -0.22347958 
    24513 Axis point 0.00000000 37.55487421 76.95697173 
    24514 Rotation angle (degrees) 159.93832539 
    24515 Shift along axis 141.77982886 
    24516  
    24517 
    24518 > select add #39.1
    24519 
    24520 2567 atoms, 2609 bonds, 330 residues, 1 model selected 
    24521 
    24522 > view matrix models
    24523 > #39.1,0.77938,0.53788,-0.32134,133.03,0.38456,-0.81556,-0.43242,136.21,-0.49466,0.21344,-0.84247,87.787
    24524 
    24525 > fitmap #39.1 inMap #10
    24526 
    24527 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24528 map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms 
    24529 average map value = 0.197, steps = 148 
    24530 shifted from previous position = 15.2 
    24531 rotated from previous position = 0.0116 degrees 
    24532 atoms outside contour = 2326, contour level = 0.259 
    24533  
    24534 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24535 relative to W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24536 Matrix rotation and translation 
    24537 0.77933517 0.53786894 -0.32145559 138.00257192 
    24538 0.38460571 -0.81561140 -0.43226900 137.27863469 
    24539 -0.49468691 0.21324878 -0.84250212 102.09071968 
    24540 Axis 0.94139228 0.25263228 -0.22351177 
    24541 Axis point 0.00000000 37.56089500 76.95480112 
    24542 Rotation angle (degrees) 159.94922815 
    24543 Shift along axis 141.77709241 
    24544  
    24545 
    24546 > view matrix models
    24547 > #39.1,0.77934,0.53787,-0.32146,130.24,0.38461,-0.81561,-0.43227,141.73,-0.49469,0.21325,-0.8425,88.079
    24548 
    24549 > view matrix models
    24550 > #39.1,0.77934,0.53787,-0.32146,135.31,0.38461,-0.81561,-0.43227,140.11,-0.49469,0.21325,-0.8425,84.463
    24551 
    24552 > fitmap #39.1 inMap #10
    24553 
    24554 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24555 map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms 
    24556 average map value = 0.197, steps = 172 
    24557 shifted from previous position = 18.1 
    24558 rotated from previous position = 0.0154 degrees 
    24559 atoms outside contour = 2326, contour level = 0.259 
    24560  
    24561 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24562 relative to W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24563 Matrix rotation and translation 
    24564 0.77924517 0.53791820 -0.32159133 138.00026966 
    24565 0.38472109 -0.81564702 -0.43209909 137.28065889 
    24566 -0.49473897 0.21298817 -0.84253747 102.08755822 
    24567 Axis 0.94137014 0.25267283 -0.22355918 
    24568 Axis point 0.00000000 37.56685145 76.95023483 
    24569 Rotation angle (degrees) 159.96268257 
    24570 Shift along axis 141.77381369 
    24571  
    24572 
    24573 > view matrix models
    24574 > #39.1,0.77925,0.53792,-0.32159,128.09,0.38472,-0.81565,-0.4321,135.26,-0.49474,0.21299,-0.84254,82.235
    24575 
    24576 > view matrix models
    24577 > #39.1,0.77925,0.53792,-0.32159,135.47,0.38472,-0.81565,-0.4321,136.17,-0.49474,0.21299,-0.84254,76.831
    24578 
    24579 > view matrix models
    24580 > #39.1,0.77925,0.53792,-0.32159,139.06,0.38472,-0.81565,-0.4321,133.92,-0.49474,0.21299,-0.84254,83.878
    24581 
    24582 > view matrix models
    24583 > #39.1,0.77925,0.53792,-0.32159,133.59,0.38472,-0.81565,-0.4321,136.36,-0.49474,0.21299,-0.84254,86.161
    24584 
    24585 > view matrix models
    24586 > #39.1,0.77925,0.53792,-0.32159,137.64,0.38472,-0.81565,-0.4321,140.68,-0.49474,0.21299,-0.84254,88.092
    24587 
    24588 > ui mousemode right "rotate selected models"
    24589 
    24590 > view matrix models
    24591 > #39.1,0.88557,0.46445,-0.0069167,134.98,0.45496,-0.87029,-0.18867,138.57,-0.093649,0.16394,-0.98202,91.009
    24592 
    24593 > fitmap #39.1 inMap #10
    24594 
    24595 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24596 map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms 
    24597 average map value = 0.197, steps = 144 
    24598 shifted from previous position = 19.4 
    24599 rotated from previous position = 24.7 degrees 
    24600 atoms outside contour = 2327, contour level = 0.259 
    24601  
    24602 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24603 relative to W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24604 Matrix rotation and translation 
    24605 0.77925174 0.53807988 -0.32130481 137.99460111 
    24606 0.38488292 -0.81549555 -0.43224086 137.29386764 
    24607 -0.49460275 0.21315971 -0.84257407 102.10795439 
    24608 Axis 0.94137004 0.25276936 -0.22345043 
    24609 Axis point 0.00000000 37.55980635 76.95624722 
    24610 Rotation angle (degrees) 159.95253140 
    24611 Shift along axis 141.79160050 
    24612  
    24613 
    24614 > view matrix models
    24615 > #39.1,0.68606,0.65344,-0.3199,137.9,0.57062,-0.75605,-0.32059,137.24,-0.45135,0.037399,-0.89156,102.26
    24616 
    24617 > ui mousemode right "translate selected models"
    24618 
    24619 > view matrix models
    24620 > #39.1,0.68606,0.65344,-0.3199,131.56,0.57062,-0.75605,-0.32059,145.97,-0.45135,0.037399,-0.89156,83.123
    24621 
    24622 > view matrix models
    24623 > #39.1,0.68606,0.65344,-0.3199,134.43,0.57062,-0.75605,-0.32059,139.6,-0.45135,0.037399,-0.89156,83.125
    24624 
    24625 > view matrix models
    24626 > #39.1,0.68606,0.65344,-0.3199,130.69,0.57062,-0.75605,-0.32059,139.63,-0.45135,0.037399,-0.89156,81.892
    24627 
    24628 > view matrix models
    24629 > #39.1,0.68606,0.65344,-0.3199,132.35,0.57062,-0.75605,-0.32059,136.91,-0.45135,0.037399,-0.89156,85.265
    24630 
    24631 > view matrix models
    24632 > #39.1,0.68606,0.65344,-0.3199,127.51,0.57062,-0.75605,-0.32059,139.3,-0.45135,0.037399,-0.89156,87.993
    24633 
    24634 > view matrix models
    24635 > #39.1,0.68606,0.65344,-0.3199,131.61,0.57062,-0.75605,-0.32059,143.53,-0.45135,0.037399,-0.89156,89.59
    24636 
    24637 > fitmap #39.1 inMap #10
    24638 
    24639 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    24640 map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms 
    24641 average map value = 0.197, steps = 144 
    24642 shifted from previous position = 14.5 
    24643 rotated from previous position = 13.3 degrees 
    24644 atoms outside contour = 2327, contour level = 0.259 
    24645  
    24646 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    24647 relative to W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24648 Matrix rotation and translation 
    24649 0.77919349 0.53804611 -0.32150254 137.99342007 
    24650 0.38489409 -0.81557949 -0.43207249 137.29343954 
    24651 -0.49468580 0.21292364 -0.84258500 102.10246297 
    24652 Axis 0.94135648 0.25275684 -0.22352173 
    24653 Axis point 0.00000000 37.56820104 76.95313719 
    24654 Rotation angle (degrees) 159.96533135 
    24655 Shift along axis 141.78073688 
    24656  
    24657 
    24658 > select subtract #39.1
    24659 
    24660 Nothing selected 
    24661 
    24662 > hide #39.1 models
    24663 
    24664 > show #!33 models
    24665 
    24666 > hide #33.1 models
    24667 
    24668 > hide #33.2 models
    24669 
    24670 > hide #33.3 models
    24671 
    24672 > hide #!33.4 models
    24673 
    24674 > hide #33.5 models
    24675 
    24676 > hide #33.6 models
    24677 
    24678 > hide #33.7 models
    24679 
    24680 > hide #33.8 models
    24681 
    24682 > hide #33.9 models
    24683 
    24684 > hide #33.10 models
    24685 
    24686 > hide #33.11 models
    24687 
    24688 > hide #33.12 models
    24689 
    24690 > fitmap #33.13 inMap #10
    24691 
    24692 Fit molecule COPI_cyto_J4028_model M (#33.13) to map
    24693 W20_J4023_consensus_resampled.mrc (#10) using 4552 atoms 
    24694 average map value = 0.2144, steps = 128 
    24695 shifted from previous position = 5.65 
    24696 rotated from previous position = 7.59 degrees 
    24697 atoms outside contour = 3456, contour level = 0.259 
    24698  
    24699 Position of COPI_cyto_J4028_model M (#33.13) relative to
    24700 W20_J4023_consensus_resampled.mrc (#10) coordinates: 
    24701 Matrix rotation and translation 
    24702 -0.35039846 -0.93657228 -0.00730075 262.48644706 
    24703 -0.86127456 0.31914510 0.39541441 178.27483489 
    24704 -0.36800418 0.14484055 -0.91847382 254.98975169 
    24705 Axis -0.56232261 0.80946867 0.16897857 
    24706 Axis point 210.46623440 0.00000000 89.03589265 
    24707 Rotation angle (degrees) 167.12630425 
    24708 Shift along axis 39.79363149 
    24709  
    24710 
    24711 > hide #!20 models
    24712 
    24713 > hide #!35.11 models
    24714 
    24715 > show #!35.11 models
    24716 
    24717 > hide #!35.11 models
    24718 
    24719 > hide #35.9 models
    24720 
    24721 > show #35.9 models
    24722 
    24723 > hide #33.13 models
    24724 
    24725 > hide #35.9 models
    24726 
    24727 > show #33.13 models
    24728 
    24729 > ui mousemode right select
    24730 
    24731 Drag select of 242 residues 
    24732 
    24733 > select up
    24734 
    24735 2060 atoms, 2089 bonds, 262 residues, 1 model selected 
    24736 
    24737 > select clear
    24738 
    24739 Drag select of 128 residues 
    24740 
    24741 > select up
    24742 
    24743 1192 atoms, 1211 bonds, 151 residues, 1 model selected 
    24744 
    24745 > delete sel
    24746 
    24747 > select clear
    24748 
    24749 Drag select of 5 residues 
    24750 Drag select of 16 residues 
    24751 Drag select of 64 residues, 1 pseudobonds 
    24752 
    24753 > select up
    24754 
    24755 587 atoms, 592 bonds, 1 pseudobond, 73 residues, 2 models selected 
    24756 
    24757 > delete sel
    24758 
    24759 Drag select of 4 residues, 1 pseudobonds 
    24760 
    24761 > delete sel
    24762 
    24763 Drag select of 1 pseudobonds 
    24764 
    24765 > delete sel
    24766 
    24767 > select add #33.13
    24768 
    24769 2744 atoms, 2786 bonds, 1 pseudobond, 354 residues, 2 models selected 
    24770 
    24771 > select subtract #33.13
    24772 
    24773 Nothing selected 
    24774 
    24775 > combine #30.13
    24776 
    24777 > hide #!33.13 models
    24778 
    24779 Drag select of 172 residues 
    24780 
    24781 > select up
    24782 
    24783 1391 atoms, 1413 bonds, 176 residues, 1 model selected 
    24784 
    24785 > delete sel
    24786 
    24787 Drag select of 24 residues 
    24788 
    24789 > select up
    24790 
    24791 388 atoms, 392 bonds, 48 residues, 1 model selected 
    24792 
    24793 > delete sel
    24794 
    24795 Drag select of 15 residues, 1 pseudobonds 
    24796 
    24797 > select up
    24798 
    24799 269 atoms, 268 bonds, 1 pseudobond, 37 residues, 2 models selected 
    24800 
    24801 > select clear
    24802 
    24803 Drag select of 9 residues, 1 pseudobonds 
    24804 
    24805 > select up
    24806 
    24807 155 atoms, 154 bonds, 1 pseudobond, 21 residues, 2 models selected 
    24808 
    24809 > delete sel
    24810 
    24811 Drag select of 7 residues 
    24812 
    24813 > select up
    24814 
    24815 136 atoms, 136 bonds, 19 residues, 1 model selected 
    24816 
    24817 > select clear
    24818 
    24819 > fitmap #42 inMap #20
    24820 
    24821 Fit molecule copy of COPI_cyto_J4025_model M (#42) to map
    24822 W20_J4028_consensus_resampled.mrc (#20) using 2618 atoms 
    24823 average map value = 0.306, steps = 180 
    24824 shifted from previous position = 23.6 
    24825 rotated from previous position = 33.1 degrees 
    24826 atoms outside contour = 931, contour level = 0.25474 
    24827  
    24828 Position of copy of COPI_cyto_J4025_model M (#42) relative to
    24829 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    24830 Matrix rotation and translation 
    24831 -0.14963361 -0.97522083 0.16295437 216.33302484 
    24832 -0.96633931 0.17912766 0.18466631 233.37303521 
    24833 -0.20928006 -0.12983692 -0.96919773 254.43371461 
    24834 Axis -0.64527959 0.76372913 0.01822260 
    24835 Axis point 227.29901935 0.00000000 104.64971477 
    24836 Rotation angle (degrees) 165.89525591 
    24837 Shift along axis 43.27494515 
    24838  
    24839 
    24840 > show #!20 models
    24841 
    24842 > show #35.9 models
    24843 
    24844 > hide #35.9 models
    24845 
    24846 > show #35.9 models
    24847 
    24848 > fitmap #35.9 inMap #20
    24849 
    24850 Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
    24851 W20_J4028_consensus_resampled.mrc (#20) using 930 atoms 
    24852 average map value = 0.3762, steps = 56 
    24853 shifted from previous position = 2.58 
    24854 rotated from previous position = 5.97 degrees 
    24855 atoms outside contour = 300, contour level = 0.25474 
    24856  
    24857 Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
    24858 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    24859 Matrix rotation and translation 
    24860 -0.95707237 0.18100601 -0.22638311 433.92940718 
    24861 0.05310912 -0.65830260 -0.75087756 607.96749602 
    24862 -0.28494194 -0.73066717 0.62043016 258.74353581 
    24863 Axis 0.14221667 0.41206734 -0.89998607 
    24864 Axis point 248.77691524 354.86529873 0.00000000 
    24865 Rotation angle (degrees) 175.92541914 
    24866 Shift along axis 79.36996533 
    24867  
    24868 
    24869 > show #35.8 models
    24870 
    24871 > hide #35.8 models
    24872 
    24873 > show #!35.11 models
    24874 
    24875 > fitmap #35.11 inMap #20
    24876 
    24877 Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
    24878 W20_J4028_consensus_resampled.mrc (#20) using 1064 atoms 
    24879 average map value = 0.3378, steps = 88 
    24880 shifted from previous position = 0.716 
    24881 rotated from previous position = 7.18 degrees 
    24882 atoms outside contour = 284, contour level = 0.25474 
    24883  
    24884 Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
    24885 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    24886 Matrix rotation and translation 
    24887 -0.94111577 0.21871586 -0.25780707 426.29452223 
    24888 0.03665885 -0.69203983 -0.72092788 614.47706636 
    24889 -0.33609112 -0.68792750 0.64327172 250.03704434 
    24890 Axis 0.16425992 0.38966017 -0.90619183 
    24891 Axis point 251.98330593 349.53072602 0.00000000 
    24892 Rotation angle (degrees) 174.23481815 
    24893 Shift along axis 82.87881842 
    24894  
    24895 
    24896 > hide #!20 models
    24897 
    24898 > show #!20 models
    24899 
    24900 > hide #!20 models
    24901 
    24902 > select #35.9/L:331
    24903 
    24904 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24905 
    24906 > show #!20 models
    24907 
    24908 > hide #!20 models
    24909 
    24910 > delete sel
    24911 
    24912 > select #35.9/L:332
    24913 
    24914 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24915 
    24916 > delete sel
    24917 
    24918 > select #35.9/L:333
    24919 
    24920 7 atoms, 6 bonds, 1 residue, 1 model selected 
    24921 
    24922 > delete sel
    24923 
    24924 > select #35.9/L:334
    24925 
    24926 7 atoms, 6 bonds, 1 residue, 1 model selected 
    24927 
    24928 > delete sel
    24929 
    24930 > select #35.9/L:335
    24931 
    24932 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24933 
    24934 > delete sel
    24935 
    24936 > select #35.9/L:336
    24937 
    24938 6 atoms, 5 bonds, 1 residue, 1 model selected 
    24939 
    24940 > delete sel
    24941 
    24942 > select #35.9/L:337
    24943 
    24944 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24945 
    24946 > delete sel
    24947 
    24948 > fitmap #35.9 inMap #20
    24949 
    24950 Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
    24951 W20_J4028_consensus_resampled.mrc (#20) using 878 atoms 
    24952 average map value = 0.3829, steps = 44 
    24953 shifted from previous position = 0.138 
    24954 rotated from previous position = 1.65 degrees 
    24955 atoms outside contour = 274, contour level = 0.25474 
    24956  
    24957 Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
    24958 W20_J4028_consensus_resampled.mrc (#20) coordinates: 
    24959 Matrix rotation and translation 
    24960 -0.96329901 0.17783180 -0.20107426 427.85994614 
    24961 0.03340558 -0.66383109 -0.74713610 614.70583444 
    24962 -0.26634390 -0.72643247 0.63352726 246.72265827 
    24963 Axis 0.12953006 0.40835260 -0.90358736 
    24964 Axis point 244.47252749 353.86664751 0.00000000 
    24965 Rotation angle (degrees) 175.41613396 
    24966 Shift along axis 83.50197716 
    24967  
    24968 
    24969 > show #!20 models
    24970 
    24971 > show #33.1 models
    24972 
    24973 > show #33.2 models
    24974 
    24975 > show #33.3 models
    24976 
    24977 > show #!33.4 models
    24978 
    24979 > show #33.5 models
    24980 
    24981 > show #33.6 models
    24982 
    24983 > show #33.7 models
    24984 
    24985 > show #33.8 models
    24986 
    24987 > show #33.9 models
    24988 
    24989 > show #33.10 models
    24990 
    24991 > show #33.11 models
    24992 
    24993 > show #33.12 models
    24994 
    24995 > combine #33.1 #33.2 #33.3 #33.4 #33.5 #33.6 #33.7 #33.8 #33.9 #33.10 #33.11
    24996 > #33.12 #41 #35.9 #35.11
    24997 
    24998 Remapping chain ID 'A' in COPI_cyto_J4017_model #41 to 'P' 
    24999 Remapping chain ID 'B' in COPI_cyto_J4017_model #41 to 'Q' 
    25000 Remapping chain ID 'C' in COPI_cyto_J4017_model #41 to 'R' 
    25001 Remapping chain ID 'D' in COPI_cyto_J4017_model #41 to 'S' 
    25002 Remapping chain ID 'E' in COPI_cyto_J4017_model #41 to 'T' 
    25003 Remapping chain ID 'F' in COPI_cyto_J4017_model #41 to 'U' 
    25004 Remapping chain ID 'G' in COPI_cyto_J4017_model #41 to 'V' 
    25005 Remapping chain ID 'H' in COPI_cyto_J4017_model #41 to 'W' 
    25006 Remapping chain ID 'I' in COPI_cyto_J4017_model #41 to 'X' 
    25007 Remapping chain ID 'J' in COPI_cyto_J4017_model #41 to 'Y' 
    25008 Remapping chain ID 'K' in COPI_cyto_J4017_model #41 to 'Z' 
    25009 Remapping chain ID 'L' in COPI_cyto_J4017_model #41 to 'a' 
    25010 Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'b' 
    25011 Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'c' 
    25012 
    25013 > rename #41 COPI_cyto_J4027_model
    25014 
    25015 > rename #43 COPI_cyto_J4028_model
    25016 
    25017 > hide #!20 models
    25018 
    25019 > show #!22 models
    25020 
    25021 > hide #!43 models
    25022 
    25023 > show #!43 models
    25024 
    25025 > hide #!22 models
    25026 
    25027 > show #!20 models
    25028 
    25029 > hide #!20 models
    25030 
    25031 > hide #!43 models
    25032 
    25033 > hide #!42 models
    25034 
    25035 > hide #!33 models
    25036 
    25037 > show #!16 models
    25038 
    25039 > hide #35.9 models
    25040 
    25041 > show #35.9 models
    25042 
    25043 > hide #!35 models
    25044 
    25045 > show #!40 models
    25046 
    25047 > hide #!40 models
    25048 
    25049 > hide #!16 models
    25050 
    25051 > show #!18 models
    25052 
    25053 > show #!41 models
    25054 
    25055 > hide #!41 models
    25056 
    25057 > show #!43 models
    25058 
    25059 > hide #!18 models
    25060 
    25061 > show #!20 models
    25062 
    25063 > close #43
    25064 
    25065 > show #!42 models
    25066 
    25067 > show #!35 models
    25068 
    25069 > show #!33 models
    25070 
    25071 > combine #33.1 #33.2 #33.3 #33.4 #33.5 #33.6 #33.7 #33.8 #33.9 #33.10 #33.11
    25072 > #33.12 #42 #35.9 #35.11
    25073 
    25074 Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N' 
    25075 Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O' 
    25076 
    25077 > rename #43 COPI_cyto_J4028_model
    25078 
    25079 > hide #!43 models
    25080 
    25081 > show #!43 models
    25082 
    25083 > hide #!42 models
    25084 
    25085 > hide #!35 models
    25086 
    25087 > hide #!33 models
    25088 
    25089 > hide #!43 models
    25090 
    25091 > show #!43 models
    25092 
    25093 > hide #!43 models
    25094 
    25095 > hide #!20 models
    25096 
    25097 > show #!22 models
    25098 
    25099 > show #!34 models
    25100 
    25101 > hide #34.13 models
    25102 
    25103 > show #!35 models
    25104 
    25105 > show #39.1 models
    25106 
    25107 > fitmap #35.9 inMap #22
    25108 
    25109 Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
    25110 W20_J3988_consensus_resampled.mrc (#22) using 878 atoms 
    25111 average map value = 0.3662, steps = 64 
    25112 shifted from previous position = 1.16 
    25113 rotated from previous position = 1.8 degrees 
    25114 atoms outside contour = 302, contour level = 0.28583 
    25115  
    25116 Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
    25117 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    25118 Matrix rotation and translation 
    25119 -0.95887497 0.16676765 -0.22966788 440.72789628 
    25120 0.05962226 -0.67277255 -0.73744307 605.37107525 
    25121 -0.27749589 -0.72080903 0.63516169 247.24016866 
    25122 Axis 0.14036124 0.40358181 -0.90411307 
    25123 Axis point 248.93620927 350.83028914 0.00000000 
    25124 Rotation angle (degrees) 176.60298227 
    25125 Shift along axis 82.64480207 
    25126  
    25127 
    25128 > fitmap #35.11 inMap #22
    25129 
    25130 Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
    25131 W20_J3988_consensus_resampled.mrc (#22) using 1064 atoms 
    25132 average map value = 0.384, steps = 72 
    25133 shifted from previous position = 0.949 
    25134 rotated from previous position = 1.29 degrees 
    25135 atoms outside contour = 322, contour level = 0.28583 
    25136  
    25137 Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
    25138 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    25139 Matrix rotation and translation 
    25140 -0.93994555 0.23565898 -0.24691539 415.54469230 
    25141 0.01481361 -0.69455698 -0.71928517 620.65417336 
    25142 -0.34100282 -0.67974661 0.64935478 246.72523257 
    25143 Axis 0.16251841 0.38673478 -0.90775767 
    25144 Axis point 249.64126104 349.36740731 0.00000000 
    25145 Rotation angle (degrees) 173.01304550 
    25146 Shift along axis 83.59549488 
    25147  
    25148 
    25149 > fitmap #39.1 inMap #22
    25150 
    25151 Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
    25152 map W20_J3988_consensus_resampled.mrc (#22) using 2567 atoms 
    25153 average map value = 0.2763, steps = 92 
    25154 shifted from previous position = 10.5 
    25155 rotated from previous position = 9.1 degrees 
    25156 atoms outside contour = 1395, contour level = 0.28583 
    25157  
    25158 Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
    25159 relative to W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    25160 Matrix rotation and translation 
    25161 0.78195191 0.59824553 -0.17508140 136.85372786 
    25162 0.46784009 -0.74887041 -0.46938125 138.09735041 
    25163 -0.41191852 0.28512347 -0.86546389 93.90913619 
    25164 Axis 0.94138597 0.29549867 -0.16270522 
    25165 Axis point 0.00000000 34.34868013 69.05412162 
    25166 Rotation angle (degrees) 156.37546309 
    25167 Shift along axis 154.36025614 
    25168  
    25169 
    25170 > fitmap #42 inMap #22
    25171 
    25172 Fit molecule copy of COPI_cyto_J4025_model M (#42) to map
    25173 W20_J3988_consensus_resampled.mrc (#22) using 2618 atoms 
    25174 average map value = 0.3079, steps = 52 
    25175 shifted from previous position = 1.27 
    25176 rotated from previous position = 2.32 degrees 
    25177 atoms outside contour = 1148, contour level = 0.28583 
    25178  
    25179 Position of copy of COPI_cyto_J4025_model M (#42) relative to
    25180 W20_J3988_consensus_resampled.mrc (#22) coordinates: 
    25181 Matrix rotation and translation 
    25182 -0.16260849 -0.97678601 0.13945458 220.44563836 
    25183 -0.95843463 0.18994779 0.21289181 227.66250748 
    25184 -0.23443883 -0.09904008 -0.96707265 255.16502900 
    25185 Axis -0.64015894 0.76731881 0.03766144 
    25186 Axis point 225.62353549 0.00000000 102.00127381 
    25187 Rotation angle (degrees) 165.89874346 
    25188 Shift along axis 43.17936097 
    25189  
    25190 
    25191 > hide #39.1 models
    25192 
    25193 > show #!42 models
    25194 
    25195 > combine #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 #34.9 #34.10 #34.11
    25196 > #34.12 #42 #35.9 #35.11
    25197 
    25198 Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N' 
    25199 Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O' 
    25200 
    25201 > rename #44 COPI_cyto_J3988_model
    25202 
    25203 > hide #!42 models
    25204 
    25205 > hide #!22 models
    25206 
    25207 > show #!24 models
    25208 
    25209 > hide #!44 models
    25210 
    25211 > hide #!35 models
    25212 
    25213 > hide #!24 models
    25214 
    25215 > hide #!34 models
    25216 
    25217 > show #!24 models
    25218 
    25219 > show #!1 models
    25220 
    25221 > hide #!1 models
    25222 
    25223 > show #!3 models
    25224 
    25225 > hide #!3 models
    25226 
    25227 > show #!4 models
    25228 
    25229 > hide #!24 models
    25230 
    25231 > show #!25 models
    25232 
    25233 > hide #!4 models
    25234 
    25235 > show #!5 models
    25236 
    25237 > hide #!5 models
    25238 
    25239 > show #!6 models
    25240 
    25241 > hide #!25 models
    25242 
    25243 > show #!26 models
    25244 
    25245 > hide #!26 models
    25246 
    25247 > show #!27 models
    25248 
    25249 > hide #!6 models
    25250 
    25251 > show #!8 models
    25252 
    25253 > hide #!27 models
    25254 
    25255 > close #35
    25256 
    25257 > close #36
    25258 
    25259 > close #37-39
    25260 
    25261 > close #42
    25262 
    25263 > combine #24.1 #24.2 #24.3 #24.4 #24.5 #24.6 #24.7 #24.8 #24.9 #24.10 #24.11
    25264 > #24.12 #24.13
    25265 
    25266 > hide #!8 models
    25267 
    25268 > show #!1 models
    25269 
    25270 > rename #35 COPI_cyto_J3623_model
    25271 
    25272 > hide #!35 models
    25273 
    25274 > show #!35 models
    25275 
    25276 > combine #25.1 #25.2 #25.3 #25.4 #25.5 #25.6 #25.7 #25.8 #25.9 #25.10 #25.11
    25277 > #25.12 #25.13
    25278 
    25279 > rename #36 COPI_cyto_J3987_model
    25280 
    25281 > combine #26.1 #26.2 #26.3 #26.4 #26.5 #26.6 #26.7 #26.8 #26.9 #26.10 #26.11
    25282 > #26.12 #26.13
    25283 
    25284 > rename #37 COPI_cyto_J4021_model
    25285 
    25286 > combine #27.1 #27.2 #27.3 #27.4 #27.5 #27.6 #27.7 #27.8 #27.9 #27.10 #27.11
    25287 > #27.12 #27.13
    25288 
    25289 > rename #38 COPI_cyto_J4022_model
    25290 
    25291 > combine #28.1 #28.2 #28.3 #28.4 #28.5 #28.6 #28.7 #28.8 #28.9 #28.10 #28.11
    25292 > #28.12 #28.13
    25293 
    25294 > rename #39 COPI_cyto_J4023_model
    25295 
    25296 > combine #29.1 #29.2 #29.3 #29.4 #29.5 #29.6 #29.7 #29.8 #29.9 #29.10 #29.11
    25297 > #29.12 #29.13
    25298 
    25299 > rename #42 COPI_cyto_J4024_model
    25300 
    25301 > combine #30.1 #30.2 #30.3 #30.4 #30.5 #30.6 #30.7 #30.8 #30.9 #30.10 #30.11
    25302 > #30.12 #30.13
    25303 
    25304 > hide #!42 models
    25305 
    25306 > hide #!39 models
    25307 
    25308 > hide #!38 models
    25309 
    25310 > hide #!37 models
    25311 
    25312 > hide #!36 models
    25313 
    25314 > hide #!35 models
    25315 
    25316 > rename #45 COPI_cyto_J4025_model
    25317 
    25318 > save COPI_cyto_J3623_model.pdb #35
    25319 
    25320 > save COPI_cyto_J3987_model.pdb #36
    25321 
    25322 > save COPI_cyto_J4021_model.pdb #37
    25323 
    25324 > save COPI_cyto_J4022_model.pdb #38
    25325 
    25326 > save COPI_cyto_J4023_model.pdb #39
    25327 
    25328 > save COPI_cyto_J4026_model.pdb #40
    25329 
    25330 > save COPI_cyto_J4027_model.pdb #41
    25331 
    25332 > save COPI_cyto_J4024_model.pdb #42
    25333 
    25334 > save COPI_cyto_J4028_model.pdb #43
    25335 
    25336 > save COPI_cyto_J3988_model.pdb #44
    25337 
    25338 > save COPI_cyto_J4025_model.pdb #45
    25339 
    25340 > hide #!45 models
    25341 
    25342 > show #!5 models
    25343 
    25344 > hide #!1 models
    25345 
    25346 > hide #!5 models
    25347 
    25348 > show #!4 models
    25349 
    25350 > hide #!4 models
    25351 
    25352 > show #!6 models
    25353 
    25354 > hide #!6 models
    25355 
    25356 > show #!8 models
    25357 
    25358 > hide #!8 models
    25359 
    25360 > show #!10 models
    25361 
    25362 > hide #!10 models
    25363 
    25364 > show #!10 models
    25365 
    25366 > hide #!10 models
    25367 
    25368 > show #!6 models
    25369 
    25370 > show #!31 models
    25371 
    25372 > open
    25373 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_33/composite_map.ccp4
    25374 
    25375 Opened composite_map.ccp4 as #46, grid size 240,240,240, pixel 1.19, shown at
    25376 level 5.84, step 1, values float32 
    25377 
    25378 > rename #46 composite_map_J4021_J4026.ccp4
    25379 
    25380 > hide #!46 models
    25381 
    25382 > show #!46 models
    25383 
    25384 > hide #!6 models
    25385 
    25386 > volume #46 level 4.356
    25387 
    25388 > color #46 darkgrey models
    25389 
    25390 > color #46 #a9a9a9c3 models
    25391 
    25392 > color #46 #a9a9a9c0 models
    25393 
    25394 > color #46 #a9a9a9bf models
    25395 
    25396 > hide #!31 models
    25397 
    25398 > show #!40 models
    25399 
    25400 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    25401 > resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
    25402 
    25403 > hide #!46 models
    25404 
    25405 > show #!46 models
    25406 
    25407 > hide #!46 models
    25408 
    25409 > open
    25410 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J3987_ResolveCryoEM_34/J3987_denmod_map.ccp4
    25411 
    25412 Opened J3987_denmod_map.ccp4 as #47, grid size 100,124,124, pixel 1.19, shown
    25413 at level 0.316, step 1, values float32 
    25414 
    25415 > volume #47 level 0.168
    25416 
    25417 > volume #47 level 0.08306
    25418 
    25419 > close #47
    25420 
    25421 > open
    25422 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4021_ResolveCryoEM_35/J4021_denmod_map.ccp4
    25423 
    25424 Opened J4021_denmod_map.ccp4 as #47, grid size 92,128,121, pixel 1.19, shown
    25425 at level 0.263, step 1, values float32 
    25426 
    25427 > volume #47 level 0.1546
    25428 
    25429 > volume #47 level 0.0986
    25430 
    25431 > close #47
    25432 
    25433 > open
    25434 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4022_ResolveCryoEM_36/J4022_denmod_map.ccp4
    25435 
    25436 Opened J4022_denmod_map.ccp4 as #47, grid size 92,126,116, pixel 1.19, shown
    25437 at level 0.256, step 1, values float32 
    25438 
    25439 > volume #47 level 0.1136
    25440 
    25441 > close #47
    25442 
    25443 > open
    25444 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4023_ResolveCryoEM_37/J4023_denmod_map.ccp4
    25445 
    25446 Opened J4023_denmod_map.ccp4 as #47, grid size 92,125,117, pixel 1.19, shown
    25447 at level 0.26, step 1, values float32 
    25448 
    25449 > volume #47 level 0.06747
    25450 
    25451 > open
    25452 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4024_ResolveCryoEM_38/J4024_denmod_map.ccp4
    25453 
    25454 Opened J4024_denmod_map.ccp4 as #48, grid size 92,126,119, pixel 1.19, shown
    25455 at level 0.262, step 1, values float32 
    25456 
    25457 > close #47
    25458 
    25459 > volume #48 level 0.1111
    25460 
    25461 > close #48
    25462 
    25463 > open
    25464 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4025_ResolveCryoEM_40/J4025_denmod_map.ccp4
    25465 
    25466 Opened J4025_denmod_map.ccp4 as #47, grid size 91,128,120, pixel 1.19, shown
    25467 at level 0.235, step 1, values float32 
    25468 
    25469 > volume #47 level 0.1354
    25470 
    25471 > volume #47 level 0.09666
    25472 
    25473 > close #47
    25474 
    25475 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    25476 > resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
    25477 
    25478 ——— End of log from Mon Jul 7 09:47:13 2025 ———
    25479 
    25480 > view name session-start
    25481 
    25482 opened ChimeraX session 
    25483 
    25484 > show #!46 models
    25485 
    25486 > open
    25487 > /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4021_J4027_CombineFocusedMaps_41/J4021_J4027_composite_map.ccp4
    25488 
    25489 Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
    25490 1.19, shown at level 5.81, step 1, values float32 
    25491 
    25492 > color #47 darkgrey models
    25493 
    25494 > color #47 #a9a9a9c1 models
    25495 
    25496 > hide #!47 models
    25497 
    25498 > hide #!46 models
    25499 
    25500 > hide #!40 models
    25501 
    25502 > show #!40 models
    25503 
    25504 > hide #!40 models
    25505 
    25506 > combine #40
    25507 
    25508 > split #48 chains
    25509 
    25510 Split copy of COPI_cyto_J4026_model (#48) into 15 models 
    25511 Chain information for copy of COPI_cyto_J4026_model A #48.1 
    25512 --- 
    25513 Chain | Description 
    25514 A | No description available 
    25515  
    25516 Chain information for copy of COPI_cyto_J4026_model B #48.2 
    25517 --- 
    25518 Chain | Description 
    25519 B | No description available 
    25520  
    25521 Chain information for copy of COPI_cyto_J4026_model C #48.3 
    25522 --- 
    25523 Chain | Description 
    25524 C | No description available 
    25525  
    25526 Chain information for copy of COPI_cyto_J4026_model D #48.4 
    25527 --- 
    25528 Chain | Description 
    25529 D | No description available 
    25530  
    25531 Chain information for copy of COPI_cyto_J4026_model E #48.5 
    25532 --- 
    25533 Chain | Description 
    25534 E | No description available 
    25535  
    25536 Chain information for copy of COPI_cyto_J4026_model F #48.6 
    25537 --- 
    25538 Chain | Description 
    25539 F | No description available 
    25540  
    25541 Chain information for copy of COPI_cyto_J4026_model G #48.7 
    25542 --- 
    25543 Chain | Description 
    25544 G | No description available 
    25545  
    25546 Chain information for copy of COPI_cyto_J4026_model H #48.8 
    25547 --- 
    25548 Chain | Description 
    25549 H | No description available 
    25550  
    25551 Chain information for copy of COPI_cyto_J4026_model I #48.9 
    25552 --- 
    25553 Chain | Description 
    25554 I | No description available 
    25555  
    25556 Chain information for copy of COPI_cyto_J4026_model J #48.10 
    25557 --- 
    25558 Chain | Description 
    25559 J | No description available 
    25560  
    25561 Chain information for copy of COPI_cyto_J4026_model K #48.11 
    25562 --- 
    25563 Chain | Description 
    25564 K | No description available 
    25565  
    25566 Chain information for copy of COPI_cyto_J4026_model L #48.12 
    25567 --- 
    25568 Chain | Description 
    25569 L | No description available 
    25570  
    25571 Chain information for copy of COPI_cyto_J4026_model M #48.13 
    25572 --- 
    25573 Chain | Description 
    25574 M | No description available 
    25575  
    25576 Chain information for copy of COPI_cyto_J4026_model N #48.14 
    25577 --- 
    25578 Chain | Description 
    25579 N | No description available 
    25580  
    25581 Chain information for copy of COPI_cyto_J4026_model O #48.15 
    25582 --- 
    25583 Chain | Description 
    25584 O | No description available 
    25585  
    25586 
    25587 > show #!46 models
    25588 
    25589 > fitmap #48.1 inMap #46
    25590 
    25591 Fit molecule copy of COPI_cyto_J4026_model A (#48.1) to map
    25592 composite_map_J4021_J4026.ccp4 (#46) using 2590 atoms 
    25593 average map value = 8.012, steps = 44 
    25594 shifted from previous position = 0.024 
    25595 rotated from previous position = 0.0413 degrees 
    25596 atoms outside contour = 449, contour level = 4.3561 
    25597  
    25598 Position of copy of COPI_cyto_J4026_model A (#48.1) relative to
    25599 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25600 Matrix rotation and translation 
    25601 -0.42161671 -0.88866766 -0.18030295 281.35767523 
    25602 -0.78137178 0.25516130 0.56951811 159.89900138 
    25603 -0.46010598 0.38100198 -0.80196009 237.46670115 
    25604 Axis -0.53247943 0.79032688 0.30306613 
    25605 Axis point 207.11724288 0.00000000 70.73686916 
    25606 Rotation angle (degrees) 169.80392724 
    25607 Shift along axis 48.52341756 
    25608  
    25609 
    25610 > fitmap #48.2 inMap #46
    25611 
    25612 Fit molecule copy of COPI_cyto_J4026_model B (#48.2) to map
    25613 composite_map_J4021_J4026.ccp4 (#46) using 2426 atoms 
    25614 average map value = 7.643, steps = 48 
    25615 shifted from previous position = 0.0352 
    25616 rotated from previous position = 0.149 degrees 
    25617 atoms outside contour = 405, contour level = 4.3561 
    25618  
    25619 Position of copy of COPI_cyto_J4026_model B (#48.2) relative to
    25620 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25621 Matrix rotation and translation 
    25622 -0.42061793 -0.88953902 -0.17832811 281.05427064 
    25623 -0.78226434 0.25604617 0.56789336 160.17141808 
    25624 -0.45950307 0.37836585 -0.80355226 237.63647217 
    25625 Axis -0.53290254 0.79059154 0.30162873 
    25626 Axis point 207.14962646 0.00000000 70.86650714 
    25627 Rotation angle (degrees) 169.75686245 
    25628 Shift along axis 48.53362146 
    25629  
    25630 
    25631 > fitmap #48.3 inMap #46
    25632 
    25633 Fit molecule copy of COPI_cyto_J4026_model C (#48.3) to map
    25634 composite_map_J4021_J4026.ccp4 (#46) using 1612 atoms 
    25635 average map value = 6.339, steps = 64 
    25636 shifted from previous position = 0.137 
    25637 rotated from previous position = 1.31 degrees 
    25638 atoms outside contour = 282, contour level = 4.3561 
    25639  
    25640 Position of copy of COPI_cyto_J4026_model C (#48.3) relative to
    25641 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25642 Matrix rotation and translation 
    25643 -0.43767621 -0.88321497 -0.16843654 281.87335410 
    25644 -0.76783552 0.26967498 0.58112309 157.06406865 
    25645 -0.46783349 0.38367530 -0.79619414 237.77730124 
    25646 Axis -0.52408907 0.79469449 0.30625367 
    25647 Axis point 206.03117664 0.00000000 70.20592740 
    25648 Rotation angle (degrees) 169.14218802 
    25649 Shift along axis 49.91138003 
    25650  
    25651 
    25652 > fitmap #48.4 inMap #46
    25653 
    25654 Fit molecule copy of COPI_cyto_J4026_model D (#48.4) to map
    25655 composite_map_J4021_J4026.ccp4 (#46) using 4745 atoms 
    25656 average map value = 6.217, steps = 64 
    25657 shifted from previous position = 0.346 
    25658 rotated from previous position = 0.851 degrees 
    25659 atoms outside contour = 894, contour level = 4.3561 
    25660  
    25661 Position of copy of COPI_cyto_J4026_model D (#48.4) relative to
    25662 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25663 Matrix rotation and translation 
    25664 -0.42924156 -0.88289723 -0.19037904 282.64245635 
    25665 -0.77884347 0.25509758 0.57299920 159.11506089 
    25666 -0.45733417 0.39423054 -0.79713722 235.42666761 
    25667 Axis -0.52934994 0.79047793 0.30811245 
    25668 Axis point 206.45398809 0.00000000 70.11358015 
    25669 Rotation angle (degrees) 170.27864285 
    25670 Shift along axis 48.69806493 
    25671  
    25672 
    25673 > fitmap #48.5 inMap #46
    25674 
    25675 Fit molecule copy of COPI_cyto_J4026_model E (#48.5) to map
    25676 composite_map_J4021_J4026.ccp4 (#46) using 1876 atoms 
    25677 average map value = 6.728, steps = 28 
    25678 shifted from previous position = 0.0537 
    25679 rotated from previous position = 0.205 degrees 
    25680 atoms outside contour = 414, contour level = 4.3561 
    25681  
    25682 Position of copy of COPI_cyto_J4026_model E (#48.5) relative to
    25683 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25684 Matrix rotation and translation 
    25685 -0.41906414 -0.89016033 -0.17888502 280.98895035 
    25686 -0.78296435 0.25453348 0.56760863 160.29649800 
    25687 -0.45973045 0.37792501 -0.80362965 237.75201321 
    25688 Axis -0.53364295 0.79011139 0.30157785 
    25689 Axis point 207.27636606 0.00000000 70.89197237 
    25690 Rotation angle (degrees) 169.76271203 
    25691 Shift along axis 48.40505872 
    25692  
    25693 
    25694 > fitmap #48.6 inMap #46
    25695 
    25696 Fit molecule copy of COPI_cyto_J4026_model F (#48.6) to map
    25697 composite_map_J4021_J4026.ccp4 (#46) using 2400 atoms 
    25698 average map value = 4.933, steps = 60 
    25699 shifted from previous position = 4.71 
    25700 rotated from previous position = 7.6 degrees 
    25701 atoms outside contour = 678, contour level = 4.3561 
    25702  
    25703 Position of copy of COPI_cyto_J4026_model F (#48.6) relative to
    25704 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25705 Matrix rotation and translation 
    25706 -0.53669929 -0.82504557 -0.17678715 281.80609510 
    25707 -0.72189432 0.34051286 0.60242808 144.12665157 
    25708 -0.43683232 0.45094436 -0.77834872 227.64701078 
    25709 Axis -0.47615916 0.81740061 0.32423556 
    25710 Axis point 193.11631392 -0.00000000 70.10143524 
    25711 Rotation angle (degrees) 170.84717448 
    25712 Shift along axis 57.43591697 
    25713  
    25714 
    25715 > fitmap #48.7 inMap #46
    25716 
    25717 Fit molecule copy of COPI_cyto_J4026_model G (#48.7) to map
    25718 composite_map_J4021_J4026.ccp4 (#46) using 2302 atoms 
    25719 average map value = 5.406, steps = 80 
    25720 shifted from previous position = 4.73 
    25721 rotated from previous position = 4.21 degrees 
    25722 atoms outside contour = 580, contour level = 4.3561 
    25723  
    25724 Position of copy of COPI_cyto_J4026_model G (#48.7) relative to
    25725 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25726 Matrix rotation and translation 
    25727 -0.48330635 -0.85702087 -0.17869027 283.39251275 
    25728 -0.74444396 0.29492363 0.59901858 152.16224396 
    25729 -0.46067144 0.42253437 -0.78054247 232.42661347 
    25730 Axis -0.50253361 0.80293313 0.32055945 
    25731 Axis point 201.16168457 -0.00000000 68.72114991 
    25732 Rotation angle (degrees) 169.88674773 
    25733 Shift along axis 54.26839065 
    25734  
    25735 
    25736 > fitmap #48.8 inMap #46
    25737 
    25738 Fit molecule copy of COPI_cyto_J4026_model H (#48.8) to map
    25739 composite_map_J4021_J4026.ccp4 (#46) using 420 atoms 
    25740 average map value = 7.082, steps = 56 
    25741 shifted from previous position = 3.46 
    25742 rotated from previous position = 2.58 degrees 
    25743 atoms outside contour = 93, contour level = 4.3561 
    25744  
    25745 Position of copy of COPI_cyto_J4026_model H (#48.8) relative to
    25746 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25747 Matrix rotation and translation 
    25748 -0.46181347 -0.87023765 -0.17150736 282.95432862 
    25749 -0.76161078 0.28994955 0.57955009 156.07549407 
    25750 -0.45461782 0.39826589 -0.79668497 236.09755101 
    25751 Axis -0.51312841 0.80134959 0.30747044 
    25752 Axis point 203.66513828 0.00000000 70.89396293 
    25753 Rotation angle (degrees) 169.82553836 
    25754 Shift along axis 52.47214622 
    25755  
    25756 
    25757 > fitmap #48.9 inMap #46
    25758 
    25759 Fit molecule copy of COPI_cyto_J4026_model I (#48.9) to map
    25760 composite_map_J4021_J4026.ccp4 (#46) using 1573 atoms 
    25761 average map value = 5.892, steps = 72 
    25762 shifted from previous position = 1.08 
    25763 rotated from previous position = 2.82 degrees 
    25764 atoms outside contour = 307, contour level = 4.3561 
    25765  
    25766 Position of copy of COPI_cyto_J4026_model I (#48.9) relative to
    25767 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25768 Matrix rotation and translation 
    25769 -0.44042374 -0.87092293 -0.21799127 283.13278743 
    25770 -0.77489855 0.24614258 0.58219077 160.68330197 
    25771 -0.45338635 0.42533175 -0.78328394 232.61931758 
    25772 Axis -0.52509607 0.78800081 0.32144805 
    25773 Axis point 205.38082265 0.00000000 68.72443099 
    25774 Rotation angle (degrees) 171.41003245 
    25775 Shift along axis 52.72168395 
    25776  
    25777 
    25778 > fitmap #48.10 inMap #46
    25779 
    25780 Fit molecule copy of COPI_cyto_J4026_model J (#48.10) to map
    25781 composite_map_J4021_J4026.ccp4 (#46) using 1112 atoms 
    25782 average map value = 6.367, steps = 68 
    25783 shifted from previous position = 0.853 
    25784 rotated from previous position = 2.18 degrees 
    25785 atoms outside contour = 324, contour level = 4.3561 
    25786  
    25787 Position of copy of COPI_cyto_J4026_model J (#48.10) relative to
    25788 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25789 Matrix rotation and translation 
    25790 -0.39606742 -0.89516479 -0.20447643 281.46766551 
    25791 -0.80125621 0.22817550 0.55310438 165.26116045 
    25792 -0.44846305 0.38290463 -0.80762922 236.59702773 
    25793 Axis -0.54558979 0.78211990 0.30103197 
    25794 Axis point 209.53544999 0.00000000 71.09106362 
    25795 Rotation angle (degrees) 171.02649245 
    25796 Shift along axis 46.91142523 
    25797  
    25798 
    25799 > fitmap #48.12 inMap #46
    25800 
    25801 Fit molecule copy of COPI_cyto_J4026_model L (#48.12) to map
    25802 composite_map_J4021_J4026.ccp4 (#46) using 1420 atoms 
    25803 average map value = 6, steps = 48 
    25804 shifted from previous position = 0.00534 
    25805 rotated from previous position = 0.0308 degrees 
    25806 atoms outside contour = 490, contour level = 4.3561 
    25807  
    25808 Position of copy of COPI_cyto_J4026_model L (#48.12) relative to
    25809 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25810 Matrix rotation and translation 
    25811 -0.42201385 -0.88851995 -0.18010170 281.36850791 
    25812 -0.78123838 0.25562354 0.56949383 159.86937778 
    25813 -0.45996839 0.38103664 -0.80202255 237.46846236 
    25814 Axis -0.53229101 0.79047409 0.30301320 
    25815 Axis point 207.08142201 0.00000000 70.75583573 
    25816 Rotation angle (degrees) 169.80350204 
    25817 Shift along axis 48.55875296 
    25818  
    25819 
    25820 > fitmap #48.13 inMap #46
    25821 
    25822 Fit molecule copy of COPI_cyto_J4026_model M (#48.13) to map
    25823 composite_map_J4021_J4026.ccp4 (#46) using 2567 atoms 
    25824 average map value = 6.934, steps = 48 
    25825 shifted from previous position = 0.0327 
    25826 rotated from previous position = 0.0247 degrees 
    25827 atoms outside contour = 577, contour level = 4.3561 
    25828  
    25829 Position of copy of COPI_cyto_J4026_model M (#48.13) relative to
    25830 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25831 Matrix rotation and translation 
    25832 -0.42198871 -0.88852999 -0.18011109 281.34034070 
    25833 -0.78150296 0.25580865 0.56904751 159.96958762 
    25834 -0.45954180 0.38088898 -0.80233717 237.44017007 
    25835 Axis -0.53232061 0.79053934 0.30279089 
    25836 Axis point 207.07606122 0.00000000 70.77828437 
    25837 Rotation angle (degrees) 169.82040522 
    25838 Shift along axis 48.59371022 
    25839  
    25840 
    25841 > fitmap #48.14 inMap #46
    25842 
    25843 Fit molecule copy of COPI_cyto_J4026_model N (#48.14) to map
    25844 composite_map_J4021_J4026.ccp4 (#46) using 930 atoms 
    25845 average map value = 7.254, steps = 40 
    25846 shifted from previous position = 0.0472 
    25847 rotated from previous position = 0.247 degrees 
    25848 atoms outside contour = 214, contour level = 4.3561 
    25849  
    25850 Position of copy of COPI_cyto_J4026_model N (#48.14) relative to
    25851 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25852 Matrix rotation and translation 
    25853 -0.42294225 -0.88896586 -0.17566891 281.09587079 
    25854 -0.78004341 0.25851684 0.56982571 159.40297655 
    25855 -0.46114222 0.37803274 -0.80276965 237.94268675 
    25856 Axis -0.53164432 0.79132341 0.30192975 
    25857 Axis point 206.92420625 0.00000000 70.92756128 
    25858 Rotation angle (degrees) 169.60827201 
    25859 Shift along axis 48.53825925 
    25860  
    25861 
    25862 > fitmap #48.15 inMap #46
    25863 
    25864 Fit molecule copy of COPI_cyto_J4026_model O (#48.15) to map
    25865 composite_map_J4021_J4026.ccp4 (#46) using 1064 atoms 
    25866 average map value = 6.216, steps = 60 
    25867 shifted from previous position = 0.0698 
    25868 rotated from previous position = 0.468 degrees 
    25869 atoms outside contour = 130, contour level = 4.3561 
    25870  
    25871 Position of copy of COPI_cyto_J4026_model O (#48.15) relative to
    25872 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    25873 Matrix rotation and translation 
    25874 -0.41919869 -0.88836490 -0.18729731 281.44552791 
    25875 -0.78315395 0.24946223 0.56959504 160.73613068 
    25876 -0.45928463 0.38545612 -0.80030071 236.81019199 
    25877 Axis -0.53389619 0.78860565 0.30505080 
    25878 Axis point 207.35794189 0.00000000 70.38133823 
    25879 Rotation angle (degrees) 170.06980434 
    25880 Shift along axis 48.73386479 
    25881  
    25882 
    25883 > color #48.13 gammav3
    25884 
    25885 > color #48.14 gammav3
    25886 
    25887 > color #48.15 gammav3
    25888 
    25889 > combine #48.1 #48.2 #48.3 #48.4 #48.5 #48.6 #48.7 #48.8 #48.9 #48.10 #48.11
    25890 > #48.12 #48.13 #48.14 #48.15
    25891 
    25892 > rename #49 Model_for_composite_J4021_J4026
    25893 
    25894 > hide #!49 models
    25895 
    25896 > hide #!46 models
    25897 
    25898 > show #!47 models
    25899 
    25900 > close #48
    25901 
    25902 > combine #41
    25903 
    25904 > split #48 chains
    25905 
    25906 Split copy of COPI_cyto_J4027_model (#48) into 15 models 
    25907 Chain information for copy of COPI_cyto_J4027_model A #48.1 
    25908 --- 
    25909 Chain | Description 
    25910 A | No description available 
    25911  
    25912 Chain information for copy of COPI_cyto_J4027_model B #48.2 
    25913 --- 
    25914 Chain | Description 
    25915 B | No description available 
    25916  
    25917 Chain information for copy of COPI_cyto_J4027_model C #48.3 
    25918 --- 
    25919 Chain | Description 
    25920 C | No description available 
    25921  
    25922 Chain information for copy of COPI_cyto_J4027_model D #48.4 
    25923 --- 
    25924 Chain | Description 
    25925 D | No description available 
    25926  
    25927 Chain information for copy of COPI_cyto_J4027_model E #48.5 
    25928 --- 
    25929 Chain | Description 
    25930 E | No description available 
    25931  
    25932 Chain information for copy of COPI_cyto_J4027_model F #48.6 
    25933 --- 
    25934 Chain | Description 
    25935 F | No description available 
    25936  
    25937 Chain information for copy of COPI_cyto_J4027_model G #48.7 
    25938 --- 
    25939 Chain | Description 
    25940 G | No description available 
    25941  
    25942 Chain information for copy of COPI_cyto_J4027_model H #48.8 
    25943 --- 
    25944 Chain | Description 
    25945 H | No description available 
    25946  
    25947 Chain information for copy of COPI_cyto_J4027_model I #48.9 
    25948 --- 
    25949 Chain | Description 
    25950 I | No description available 
    25951  
    25952 Chain information for copy of COPI_cyto_J4027_model J #48.10 
    25953 --- 
    25954 Chain | Description 
    25955 J | No description available 
    25956  
    25957 Chain information for copy of COPI_cyto_J4027_model K #48.11 
    25958 --- 
    25959 Chain | Description 
    25960 K | No description available 
    25961  
    25962 Chain information for copy of COPI_cyto_J4027_model L #48.12 
    25963 --- 
    25964 Chain | Description 
    25965 L | No description available 
    25966  
    25967 Chain information for copy of COPI_cyto_J4027_model M #48.13 
    25968 --- 
    25969 Chain | Description 
    25970 M | No description available 
    25971  
    25972 Chain information for copy of COPI_cyto_J4027_model N #48.14 
    25973 --- 
    25974 Chain | Description 
    25975 N | No description available 
    25976  
    25977 Chain information for copy of COPI_cyto_J4027_model O #48.15 
    25978 --- 
    25979 Chain | Description 
    25980 O | No description available 
    25981  
    25982 
    25983 > color #48.13 gammav3
    25984 
    25985 > color #48.14 gammav3
    25986 
    25987 > color #48.15 gammav3
    25988 
    25989 > fitmap #48.15 inMap #46
    25990 
    25991 Fit molecule copy of COPI_cyto_J4027_model O (#48.15) to map
    25992 composite_map_J4021_J4026.ccp4 (#46) using 1064 atoms 
    25993 average map value = 6.216, steps = 68 
    25994 shifted from previous position = 0.926 
    25995 rotated from previous position = 3.78 degrees 
    25996 atoms outside contour = 131, contour level = 4.3561 
    25997  
    25998 Position of copy of COPI_cyto_J4027_model O (#48.15) relative to
    25999 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    26000 Matrix rotation and translation 
    26001 -0.34404909 -0.93260747 -0.10896575 269.91254838 
    26002 -0.80984309 0.23600764 0.53707968 166.69850821 
    26003 -0.47516777 0.27302693 -0.83646393 251.15790315 
    26004 Axis -0.56437651 0.78270657 0.26239203 
    26005 Axis point 213.21055464 0.00000000 75.30227951 
    26006 Rotation angle (degrees) 166.47125621 
    26007 Shift along axis 44.04554723 
    26008  
    26009 
    26010 > fitmap #48.14 inMap #46
    26011 
    26012 Fit molecule copy of COPI_cyto_J4027_model N (#48.14) to map
    26013 composite_map_J4021_J4026.ccp4 (#46) using 930 atoms 
    26014 average map value = 7.254, steps = 68 
    26015 shifted from previous position = 4.09 
    26016 rotated from previous position = 12.1 degrees 
    26017 atoms outside contour = 214, contour level = 4.3561 
    26018  
    26019 Position of copy of COPI_cyto_J4027_model N (#48.14) relative to
    26020 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    26021 Matrix rotation and translation 
    26022 -0.29521822 -0.95538003 0.00975828 254.00941556 
    26023 -0.83564878 0.26314499 0.48212638 171.86630354 
    26024 -0.46318175 0.13417799 -0.87604735 264.92556241 
    26025 Axis -0.58065970 0.78924699 0.19980868 
    26026 Axis point 215.16338827 0.00000000 83.71664964 
    26027 Rotation angle (degrees) 162.56553634 
    26028 Shift along axis 41.08635962 
    26029  
    26030 
    26031 > fitmap #48.13 inMap #46
    26032 
    26033 Fit molecule copy of COPI_cyto_J4027_model M (#48.13) to map
    26034 composite_map_J4021_J4026.ccp4 (#46) using 2567 atoms 
    26035 average map value = 6.934, steps = 184 
    26036 shifted from previous position = 24.3 
    26037 rotated from previous position = 38.5 degrees 
    26038 atoms outside contour = 574, contour level = 4.3561 
    26039  
    26040 Position of copy of COPI_cyto_J4027_model M (#48.13) relative to
    26041 composite_map_J4021_J4026.ccp4 (#46) coordinates: 
    26042 Matrix rotation and translation 
    26043 -0.06511231 -0.96101824 0.26870867 188.55069019 
    26044 -0.97216064 0.12183140 0.20015198 237.48407748 
    26045 -0.22508686 -0.24819563 -0.94219682 265.26082374 
    26046 Axis -0.67212131 0.74025262 -0.01670366 
    26047 Axis point 232.93504959 0.00000000 109.96611159 
    26048 Rotation angle (degrees) 160.51672010 
    26049 Shift along axis 44.63844706 
    26050  
    26051 
    26052 > fitmap #48.13 inMap #47
    26053 
    26054 Fit molecule copy of COPI_cyto_J4027_model M (#48.13) to map
    26055 J4021_J4027_composite_map.ccp4 (#47) using 2567 atoms 
    26056 average map value = 5.305, steps = 140 
    26057 shifted from previous position = 20.1 
    26058 rotated from previous position = 23.5 degrees 
    26059 atoms outside contour = 1497, contour level = 5.8074 
    26060  
    26061 Position of copy of COPI_cyto_J4027_model M (#48.13) relative to
    26062 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26063 Matrix rotation and translation 
    26064 -0.20584357 -0.97794249 -0.03545317 247.21508377 
    26065 -0.89336671 0.17300799 0.41468563 196.10217944 
    26066 -0.39940501 0.11703305 -0.90927384 267.43384909 
    26067 Axis -0.62307640 0.76186070 0.17704255 
    26068 Axis point 224.46487691 0.00000000 89.15375612 
    26069 Rotation angle (degrees) 166.18089851 
    26070 Shift along axis 42.71583076 
    26071  
    26072 
    26073 > close #48
    26074 
    26075 > combine #41
    26076 
    26077 > split #48 chains
    26078 
    26079 Split copy of COPI_cyto_J4027_model (#48) into 15 models 
    26080 Chain information for copy of COPI_cyto_J4027_model A #48.1 
    26081 --- 
    26082 Chain | Description 
    26083 A | No description available 
    26084  
    26085 Chain information for copy of COPI_cyto_J4027_model B #48.2 
    26086 --- 
    26087 Chain | Description 
    26088 B | No description available 
    26089  
    26090 Chain information for copy of COPI_cyto_J4027_model C #48.3 
    26091 --- 
    26092 Chain | Description 
    26093 C | No description available 
    26094  
    26095 Chain information for copy of COPI_cyto_J4027_model D #48.4 
    26096 --- 
    26097 Chain | Description 
    26098 D | No description available 
    26099  
    26100 Chain information for copy of COPI_cyto_J4027_model E #48.5 
    26101 --- 
    26102 Chain | Description 
    26103 E | No description available 
    26104  
    26105 Chain information for copy of COPI_cyto_J4027_model F #48.6 
    26106 --- 
    26107 Chain | Description 
    26108 F | No description available 
    26109  
    26110 Chain information for copy of COPI_cyto_J4027_model G #48.7 
    26111 --- 
    26112 Chain | Description 
    26113 G | No description available 
    26114  
    26115 Chain information for copy of COPI_cyto_J4027_model H #48.8 
    26116 --- 
    26117 Chain | Description 
    26118 H | No description available 
    26119  
    26120 Chain information for copy of COPI_cyto_J4027_model I #48.9 
    26121 --- 
    26122 Chain | Description 
    26123 I | No description available 
    26124  
    26125 Chain information for copy of COPI_cyto_J4027_model J #48.10 
    26126 --- 
    26127 Chain | Description 
    26128 J | No description available 
    26129  
    26130 Chain information for copy of COPI_cyto_J4027_model K #48.11 
    26131 --- 
    26132 Chain | Description 
    26133 K | No description available 
    26134  
    26135 Chain information for copy of COPI_cyto_J4027_model L #48.12 
    26136 --- 
    26137 Chain | Description 
    26138 L | No description available 
    26139  
    26140 Chain information for copy of COPI_cyto_J4027_model M #48.13 
    26141 --- 
    26142 Chain | Description 
    26143 M | No description available 
    26144  
    26145 Chain information for copy of COPI_cyto_J4027_model N #48.14 
    26146 --- 
    26147 Chain | Description 
    26148 N | No description available 
    26149  
    26150 Chain information for copy of COPI_cyto_J4027_model O #48.15 
    26151 --- 
    26152 Chain | Description 
    26153 O | No description available 
    26154  
    26155 
    26156 > color #48.13 gammav3
    26157 
    26158 > color #48.14 gammav3
    26159 
    26160 > color #48.15 gammav3
    26161 
    26162 > fitmap #48.15 inMap #47
    26163 
    26164 Fit molecule copy of COPI_cyto_J4027_model O (#48.15) to map
    26165 J4021_J4027_composite_map.ccp4 (#47) using 1064 atoms 
    26166 average map value = 7.175, steps = 80 
    26167 shifted from previous position = 0.0377 
    26168 rotated from previous position = 0.0512 degrees 
    26169 atoms outside contour = 362, contour level = 5.8074 
    26170  
    26171 Position of copy of COPI_cyto_J4027_model O (#48.15) relative to
    26172 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26173 Matrix rotation and translation 
    26174 -0.36445970 -0.91742956 -0.15966261 274.93147533 
    26175 -0.79741803 0.21892271 0.56231428 164.22520611 
    26176 -0.48092997 0.33225874 -0.81136337 243.41623113 
    26177 Axis -0.55708089 0.77795083 0.29060864 
    26178 Axis point 211.70950704 0.00000000 70.89847596 
    26179 Rotation angle (degrees) 168.08366956 
    26180 Shift along axis 45.33892553 
    26181  
    26182 
    26183 > fitmap #48.14 inMap #47
    26184 
    26185 Fit molecule copy of COPI_cyto_J4027_model N (#48.14) to map
    26186 J4021_J4027_composite_map.ccp4 (#47) using 930 atoms 
    26187 average map value = 7.843, steps = 48 
    26188 shifted from previous position = 0.0452 
    26189 rotated from previous position = 0.236 degrees 
    26190 atoms outside contour = 308, contour level = 5.8074 
    26191  
    26192 Position of copy of COPI_cyto_J4027_model N (#48.14) relative to
    26193 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26194 Matrix rotation and translation 
    26195 -0.36749036 -0.91663154 -0.15728153 275.08372435 
    26196 -0.79611294 0.22261900 0.56271217 163.59058237 
    26197 -0.48078586 0.33200516 -0.81155255 243.40917516 
    26198 Axis -0.55562941 0.77912031 0.29025419 
    26199 Axis point 211.38295724 0.00000000 71.01177343 
    26200 Rotation angle (degrees) 168.01774651 
    26201 Shift along axis 45.26267005 
    26202  
    26203 
    26204 > fitmap #48.13 inMap #47
    26205 
    26206 Fit molecule copy of COPI_cyto_J4027_model M (#48.13) to map
    26207 J4021_J4027_composite_map.ccp4 (#47) using 2567 atoms 
    26208 average map value = 6.181, steps = 48 
    26209 shifted from previous position = 0.0646 
    26210 rotated from previous position = 0.137 degrees 
    26211 atoms outside contour = 1105, contour level = 5.8074 
    26212  
    26213 Position of copy of COPI_cyto_J4027_model M (#48.13) relative to
    26214 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26215 Matrix rotation and translation 
    26216 -0.36546244 -0.91673285 -0.16136328 275.21816301 
    26217 -0.79822949 0.21948305 0.56094285 164.44314904 
    26218 -0.47881823 0.33380847 -0.81197600 242.98792253 
    26219 Axis -0.55679103 0.77820041 0.29049589 
    26220 Axis point 211.65663706 0.00000000 70.90505517 
    26221 Rotation angle (degrees) 168.23094482 
    26222 Shift along axis 45.31771373 
    26223  
    26224 
    26225 > fitmap #48.12 inMap #47
    26226 
    26227 Fit molecule copy of COPI_cyto_J4027_model L (#48.12) to map
    26228 J4021_J4027_composite_map.ccp4 (#47) using 1420 atoms 
    26229 average map value = 5.269, steps = 64 
    26230 shifted from previous position = 0.0436 
    26231 rotated from previous position = 0.124 degrees 
    26232 atoms outside contour = 716, contour level = 5.8074 
    26233  
    26234 Position of copy of COPI_cyto_J4027_model L (#48.12) relative to
    26235 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26236 Matrix rotation and translation 
    26237 -0.36575950 -0.91679867 -0.16031284 275.10067764 
    26238 -0.79603501 0.21891045 0.56427520 163.73853261 
    26239 -0.48223259 0.33400364 -0.80987241 243.20437721 
    26240 Axis -0.55646287 0.77793538 0.29183150 
    26241 Axis point 211.57205619 0.00000000 70.70465662 
    26242 Rotation angle (degrees) 168.05887425 
    26243 Shift along axis 45.26938091 
    26244  
    26245 
    26246 > fitmap #48.11 inMap #47
    26247 
    26248 Fit molecule copy of COPI_cyto_J4027_model K (#48.11) to map
    26249 J4021_J4027_composite_map.ccp4 (#47) using 319 atoms 
    26250 average map value = 6.544, steps = 680 
    26251 shifted from previous position = 34.4 
    26252 rotated from previous position = 55.2 degrees 
    26253 atoms outside contour = 122, contour level = 5.8074 
    26254  
    26255 Position of copy of COPI_cyto_J4027_model K (#48.11) relative to
    26256 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26257 Matrix rotation and translation 
    26258 0.24248330 -0.95058432 0.19388478 218.57357673 
    26259 -0.33056267 0.10693534 0.93770633 73.53913137 
    26260 -0.91210207 -0.29146919 -0.28829766 267.39969287 
    26261 Axis -0.69605025 0.62629170 0.35110220 
    26262 Axis point 0.00000000 252.37218567 153.78684989 
    26263 Rotation angle (degrees) 117.99791989 
    26264 Shift along axis -12.19662658 
    26265  
    26266 
    26267 > ui tool show Matchmaker
    26268 
    26269 > matchmaker #48.11 to #49
    26270 
    26271 Parameters 
    26272 --- 
    26273 Chain pairing | bb 
    26274 Alignment algorithm | Needleman-Wunsch 
    26275 Similarity matrix | BLOSUM-62 
    26276 SS fraction | 0.3 
    26277 Gap open (HH/SS/other) | 18/18/6 
    26278 Gap extend | 1 
    26279 SS matrix |  |  | H | S | O 
    26280 ---|---|---|--- 
    26281 H | 6 | -9 | -6 
    26282 S |  | 6 | -6 
    26283 O |  |  | 4 
    26284 Iteration cutoff | 2 
    26285  
    26286 Matchmaker Model_for_composite_J4021_J4026, chain K (#49) with copy of
    26287 COPI_cyto_J4027_model K, chain K (#48.11), sequence alignment score = 192.1 
    26288 RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
    26289 0.000) 
    26290  
    26291 
    26292 > fitmap #48.10 inMap #47
    26293 
    26294 Fit molecule copy of COPI_cyto_J4027_model J (#48.10) to map
    26295 J4021_J4027_composite_map.ccp4 (#47) using 1112 atoms 
    26296 average map value = 6.595, steps = 68 
    26297 shifted from previous position = 0.392 
    26298 rotated from previous position = 3.79 degrees 
    26299 atoms outside contour = 449, contour level = 5.8074 
    26300  
    26301 Position of copy of COPI_cyto_J4027_model J (#48.10) relative to
    26302 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26303 Matrix rotation and translation 
    26304 -0.36954265 -0.92395010 -0.09876469 269.14351053 
    26305 -0.79489549 0.25928902 0.54855298 162.57033903 
    26306 -0.48122698 0.28122133 -0.83026211 249.17503135 
    26307 Axis -0.55216997 0.78997075 0.26656057 
    26308 Axis point 209.80677258 0.00000000 74.24424921 
    26309 Rotation angle (degrees) 165.99103601 
    26310 Shift along axis 46.23308621 
    26311  
    26312 
    26313 > fitmap #48.9 inMap #47
    26314 
    26315 Fit molecule copy of COPI_cyto_J4027_model I (#48.9) to map
    26316 J4021_J4027_composite_map.ccp4 (#47) using 1573 atoms 
    26317 average map value = 5.861, steps = 68 
    26318 shifted from previous position = 1.24 
    26319 rotated from previous position = 3.45 degrees 
    26320 atoms outside contour = 773, contour level = 5.8074 
    26321  
    26322 Position of copy of COPI_cyto_J4027_model I (#48.9) relative to
    26323 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26324 Matrix rotation and translation 
    26325 -0.37973756 -0.89954761 -0.21590159 277.24792433 
    26326 -0.80457095 0.20595800 0.55699812 167.23271540 
    26327 -0.45657967 0.38522125 -0.80195986 236.87971276 
    26328 Axis -0.55310174 0.77495569 0.30581391 
    26329 Axis point 209.49101626 0.00000000 70.11224809 
    26330 Rotation angle (degrees) 171.06667095 
    26331 Shift along axis 48.69274569 
    26332  
    26333 
    26334 > fitmap #48.8 inMap #47
    26335 
    26336 Fit molecule copy of COPI_cyto_J4027_model H (#48.8) to map
    26337 J4021_J4027_composite_map.ccp4 (#47) using 420 atoms 
    26338 average map value = 6.824, steps = 56 
    26339 shifted from previous position = 3.38 
    26340 rotated from previous position = 2.53 degrees 
    26341 atoms outside contour = 149, contour level = 5.8074 
    26342  
    26343 Position of copy of COPI_cyto_J4027_model H (#48.8) relative to
    26344 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26345 Matrix rotation and translation 
    26346 -0.40542761 -0.90093167 -0.15475978 276.94991852 
    26347 -0.78307394 0.25494593 0.56727223 160.97102962 
    26348 -0.47161814 0.35117617 -0.80885823 241.79873195 
    26349 Axis -0.53858123 0.78971345 0.29373956 
    26350 Axis point 207.95662584 0.00000000 71.49993787 
    26351 Rotation angle (degrees) 168.42701468 
    26352 Shift along axis 48.98681208 
    26353  
    26354 
    26355 > fitmap #48.7 inMap #47
    26356 
    26357 Fit molecule copy of COPI_cyto_J4027_model G (#48.7) to map
    26358 J4021_J4027_composite_map.ccp4 (#47) using 2302 atoms 
    26359 average map value = 5.298, steps = 64 
    26360 shifted from previous position = 4.62 
    26361 rotated from previous position = 4.04 degrees 
    26362 atoms outside contour = 1402, contour level = 5.8074 
    26363  
    26364 Position of copy of COPI_cyto_J4027_model G (#48.7) relative to
    26365 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26366 Matrix rotation and translation 
    26367 -0.42560093 -0.89008522 -0.16313234 277.69917989 
    26368 -0.76548490 0.25798571 0.58947118 157.21311144 
    26369 -0.48259377 0.37575482 -0.79114574 238.50649670 
    26370 Axis -0.52893684 0.79065037 0.30837932 
    26371 Axis point 205.81643686 0.00000000 68.93017279 
    26372 Rotation angle (degrees) 168.34463133 
    26373 Shift along axis 50.96574868 
    26374  
    26375 
    26376 > fitmap #48.6 inMap #47
    26377 
    26378 Fit molecule copy of COPI_cyto_J4027_model F (#48.6) to map
    26379 J4021_J4027_composite_map.ccp4 (#47) using 2400 atoms 
    26380 average map value = 4.862, steps = 56 
    26381 shifted from previous position = 4.53 
    26382 rotated from previous position = 7.12 degrees 
    26383 atoms outside contour = 1891, contour level = 5.8074 
    26384  
    26385 Position of copy of COPI_cyto_J4027_model F (#48.6) relative to
    26386 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26387 Matrix rotation and translation 
    26388 -0.47631791 -0.86443647 -0.16084418 276.54476513 
    26389 -0.74836077 0.30252539 0.59028346 150.15879842 
    26390 -0.46160309 0.40153206 -0.79100860 234.60647851 
    26391 Axis -0.50526012 0.80508798 0.31071780 
    26392 Axis point 198.13646970 0.00000000 70.54602612 
    26393 Rotation angle (degrees) 169.23470102 
    26394 Shift along axis 54.06041328 
    26395  
    26396 
    26397 > fitmap #48.5 inMap #47
    26398 
    26399 Fit molecule copy of COPI_cyto_J4027_model E (#48.5) to map
    26400 J4021_J4027_composite_map.ccp4 (#47) using 1876 atoms 
    26401 average map value = 6.882, steps = 40 
    26402 shifted from previous position = 0.0401 
    26403 rotated from previous position = 0.0808 degrees 
    26404 atoms outside contour = 679, contour level = 5.8074 
    26405  
    26406 Position of copy of COPI_cyto_J4027_model E (#48.5) relative to
    26407 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26408 Matrix rotation and translation 
    26409 -0.36460635 -0.91721639 -0.16055006 274.96464339 
    26410 -0.79803633 0.21895894 0.56142232 164.31313284 
    26411 -0.47979187 0.33282292 -0.81180581 243.25738221 
    26412 Axis -0.55710084 0.77799805 0.29044395 
    26413 Axis point 211.64530256 0.00000000 70.95305334 
    26414 Rotation angle (degrees) 168.16062068 
    26415 Shift along axis 45.30489541 
    26416  
    26417 
    26418 > fitmap #48.4 inMap #47
    26419 
    26420 Fit molecule copy of COPI_cyto_J4027_model D (#48.4) to map
    26421 J4021_J4027_composite_map.ccp4 (#47) using 4745 atoms 
    26422 average map value = 6.326, steps = 80 
    26423 shifted from previous position = 0.232 
    26424 rotated from previous position = 0.637 degrees 
    26425 atoms outside contour = 1901, contour level = 5.8074 
    26426  
    26427 Position of copy of COPI_cyto_J4027_model D (#48.4) relative to
    26428 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26429 Matrix rotation and translation 
    26430 -0.36403643 -0.91927407 -0.14970864 274.32296003 
    26431 -0.79661223 0.22402751 0.56144514 163.63243958 
    26432 -0.48258310 0.32364622 -0.81385913 244.76587458 
    26433 Axis -0.55679826 0.77941446 0.28720862 
    26434 Axis point 211.67256763 0.00000000 71.48567291 
    26435 Rotation angle (degrees) 167.67003358 
    26436 Shift along axis 45.09381034 
    26437  
    26438 
    26439 > fitmap #48.3 inMap #47
    26440 
    26441 Fit molecule copy of COPI_cyto_J4027_model C (#48.3) to map
    26442 J4021_J4027_composite_map.ccp4 (#47) using 1612 atoms 
    26443 average map value = 6.318, steps = 80 
    26444 shifted from previous position = 0.228 
    26445 rotated from previous position = 1.41 degrees 
    26446 atoms outside contour = 653, contour level = 5.8074 
    26447  
    26448 Position of copy of COPI_cyto_J4027_model C (#48.3) relative to
    26449 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26450 Matrix rotation and translation 
    26451 -0.38173446 -0.91224090 -0.14864510 275.71683603 
    26452 -0.78322797 0.23388065 0.57606754 161.04568217 
    26453 -0.49074715 0.33632783 -0.80377288 243.57494299 
    26454 Axis -0.54833896 0.78246479 0.29508175 
    26455 Axis point 210.53404344 0.00000000 70.11714477 
    26456 Rotation angle (degrees) 167.37286555 
    26457 Shift along axis 46.70081412 
    26458  
    26459 
    26460 > fitmap #48.2 inMap #47
    26461 
    26462 Fit molecule copy of COPI_cyto_J4027_model B (#48.2) to map
    26463 J4021_J4027_composite_map.ccp4 (#47) using 2426 atoms 
    26464 average map value = 7.483, steps = 48 
    26465 shifted from previous position = 0.0329 
    26466 rotated from previous position = 0.105 degrees 
    26467 atoms outside contour = 734, contour level = 5.8074 
    26468  
    26469 Position of copy of COPI_cyto_J4027_model B (#48.2) relative to
    26470 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26471 Matrix rotation and translation 
    26472 -0.36430973 -0.91755945 -0.15925792 274.83521303 
    26473 -0.79785551 0.21931761 0.56153930 164.30315268 
    26474 -0.48031762 0.33163904 -0.81197940 243.32909311 
    26475 Axis -0.55716005 0.77808367 0.29010081 
    26476 Axis point 211.66844489 0.00000000 70.92695219 
    26477 Rotation angle (degrees) 168.09354740 
    26478 Shift along axis 45.30436790 
    26479  
    26480 
    26481 > fitmap #48.1 inMap #47
    26482 
    26483 Fit molecule copy of COPI_cyto_J4027_model A (#48.1) to map
    26484 J4021_J4027_composite_map.ccp4 (#47) using 2590 atoms 
    26485 average map value = 7.767, steps = 64 
    26486 shifted from previous position = 0.0157 
    26487 rotated from previous position = 0.0377 degrees 
    26488 atoms outside contour = 732, contour level = 5.8074 
    26489  
    26490 Position of copy of COPI_cyto_J4027_model A (#48.1) relative to
    26491 J4021_J4027_composite_map.ccp4 (#47) coordinates: 
    26492 Matrix rotation and translation 
    26493 -0.36433385 -0.91729312 -0.16073020 274.99544480 
    26494 -0.79752965 0.21821532 0.56243093 164.22320875 
    26495 -0.48084022 0.33309973 -0.81107168 243.29313210 
    26496 Axis -0.55718331 0.77773961 0.29097743 
    26497 Axis point 211.71070241 0.00000000 70.85027180 
    26498 Rotation angle (degrees) 168.12395214 
    26499 Shift along axis 45.29283319 
    26500  
    26501 
    26502 > combine #48.1 #48.2 #48.3 #48.4 #48.5 #48.6 #48.7 #48.8 #48.9 #48.10 #48.11
    26503 > #48.12 #48.13 #48.14 #48.15
    26504 
    26505 > rename #50 Model_for_composite_J4021_J4027
    26506 
    26507 > close #48
    26508 
    26509 > show #!49 models
    26510 
    26511 > hide #!49 models
    26512 
    26513 > hide #!50 models
    26514 
    26515 > save composite_model_J4021_J4026.pdb #49
    26516 
    26517 > save composite_model_J4021_J4027.pdb #50
    26518 
    26519 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    26520 > resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
    26521 
    26522 > hide #!47 models
    26523 
    26524 > show #!1 models
    26525 
    26526 > color #1 #a9a9a9bf models
    26527 
    26528 > ui tool show "Surface Color"
    26529 
    26530 > ui tool show "Color Zone"
    26531 
    26532 > color zone #1 near #35 distance 6
    26533 
    26534 > hide #!1 models
    26535 
    26536 > show #!1 models
    26537 
    26538 > select #35/K
    26539 
    26540 319 atoms, 320 bonds, 37 residues, 1 model selected 
    26541 
    26542 > hide #!1 models
    26543 
    26544 > show #!35 models
    26545 
    26546 > select #35/M
    26547 
    26548 4552 atoms, 4624 bonds, 582 residues, 1 model selected 
    26549 
    26550 > color sel gammav3
    26551 
    26552 > select add #35
    26553 
    26554 27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected 
    26555 
    26556 > hide #!35 models
    26557 
    26558 > select subtract #35
    26559 
    26560 Nothing selected 
    26561 
    26562 > show #!36 models
    26563 
    26564 > hide #!36 models
    26565 
    26566 > show #!37 models
    26567 
    26568 > select #36/M
    26569 
    26570 4552 atoms, 4624 bonds, 582 residues, 1 model selected 
    26571 
    26572 > color sel gammav3
    26573 
    26574 > select #37/M
    26575 
    26576 4552 atoms, 4624 bonds, 582 residues, 1 model selected 
    26577 
    26578 > color sel gammav3
    26579 
    26580 > select add #37
    26581 
    26582 27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected 
    26583 
    26584 > select subtract #37
    26585 
    26586 Nothing selected 
    26587 
    26588 > hide #!37 models
    26589 
    26590 > show #!38 models
    26591 
    26592 > select #38/M
    26593 
    26594 4552 atoms, 4624 bonds, 582 residues, 1 model selected 
    26595 
    26596 > color sel gammav3
    26597 
    26598 > select #39/m
    26599 
    26600 4552 atoms, 4624 bonds, 582 residues, 1 model selected 
    26601 
    26602 > color sel gammav3
    26603 
    26604 > select add #39
    26605 
    26606 27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected 
    26607 
    26608 > select subtract #39
    26609 
    26610 Nothing selected 
    26611 
    26612 > hide #!38 models
    26613 
    26614 > show #!39 models
    26615 
    26616 > hide #!39 models
    26617 
    26618 > show #!40 models
    26619 
    26620 > select #40/m
    26621 
    26622 2567 atoms, 2609 bonds, 330 residues, 1 model selected 
    26623 
    26624 > color sel gammav3
    26625 
    26626 > select #40/n
    26627 
    26628 930 atoms, 941 bonds, 118 residues, 1 model selected 
    26629 
    26630 > color sel gammav3
    26631 
    26632 > select #40/o
    26633 
    26634 1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected 
    26635 
    26636 > color sel gammav3
    26637 
    26638 > select #41/m
    26639 
    26640 2567 atoms, 2609 bonds, 330 residues, 1 model selected 
    26641 
    26642 > hide #!40 models
    26643 
    26644 > show #!41 models
    26645 
    26646 > color sel gammav3
    26647 
    26648 > select #41/n
    26649 
    26650 930 atoms, 941 bonds, 118 residues, 1 model selected 
    26651 
    26652 > color sel gammav3
    26653 
    26654 > select #41/o
    26655 
    26656 1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected 
    26657 
    26658 > color sel gammav3
    26659 
    26660 > select add #41
    26661 
    26662 27356 atoms, 27866 bonds, 2 pseudobonds, 3436 residues, 2 models selected 
    26663 
    26664 > select subtract #41
    26665 
    26666 Nothing selected 
    26667 
    26668 > hide #!41 models
    26669 
    26670 > show #!42 models
    26671 
    26672 > select #42/m
    26673 
    26674 4552 atoms, 4624 bonds, 582 residues, 1 model selected 
    26675 
    26676 > color sel gammav3
    26677 
    26678 > select add #42
    26679 
    26680 27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected 
    26681 
    26682 > select subtract #42
    26683 
    26684 Nothing selected 
    26685 
    26686 > hide #!42 models
    26687 
    26688 > show #!43 models
    26689 
    26690 > select #43/m
    26691 
    26692 2618 atoms, 2660 bonds, 337 residues, 1 model selected 
    26693 
    26694 > color sel gammav3
    26695 
    26696 > select #43/n
    26697 
    26698 878 atoms, 889 bonds, 111 residues, 1 model selected 
    26699 
    26700 > color sel gammav3
    26701 
    26702 > select #43/o
    26703 
    26704 1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected 
    26705 
    26706 > color sel gammav3
    26707 
    26708 > select add #43
    26709 
    26710 27355 atoms, 27865 bonds, 2 pseudobonds, 3436 residues, 2 models selected 
    26711 
    26712 > hide #!43 models
    26713 
    26714 > select subtract #43
    26715 
    26716 Nothing selected 
    26717 
    26718 > show #!44 models
    26719 
    26720 > select #44/o
    26721 
    26722 1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected 
    26723 
    26724 > color sel gammav3
    26725 
    26726 > select #44/n
    26727 
    26728 878 atoms, 889 bonds, 111 residues, 1 model selected 
    26729 
    26730 > color sel gammav3
    26731 
    26732 > select #44/m
    26733 
    26734 2618 atoms, 2660 bonds, 337 residues, 1 model selected 
    26735 
    26736 > color sel gammav3
    26737 
    26738 > select add #44
    26739 
    26740 27355 atoms, 27865 bonds, 2 pseudobonds, 3436 residues, 2 models selected 
    26741 
    26742 > hide #!44 models
    26743 
    26744 > select subtract #44
    26745 
    26746 Nothing selected 
    26747 
    26748 > show #!45 models
    26749 
    26750 > select #45/m
    26751 
    26752 4552 atoms, 4624 bonds, 582 residues, 1 model selected 
    26753 
    26754 > color sel gammav3
    26755 
    26756 > select add #45
    26757 
    26758 27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected 
    26759 
    26760 > select subtract #45
    26761 
    26762 Nothing selected 
    26763 
    26764 > hide #!45 models
    26765 
    26766 > show #!1 models
    26767 
    26768 > color zone #1 near #35 distance 6
    26769 
    26770 > volume #1 level 0.1319
    26771 
    26772 > color zone #1 near #35 distance 6.1
    26773 
    26774 > color zone #1 near #35 distance 6.2
    26775 
    26776 > color zone #1 near #35 distance 6.3
    26777 
    26778 > color zone #1 near #35 distance 6.4
    26779 
    26780 > color zone #1 near #35 distance 6.5
    26781 
    26782 > color zone #1 near #35 distance 6.6
    26783 
    26784 > color zone #1 near #35 distance 6.7
    26785 
    26786 > color zone #1 near #35 distance 9
    26787 
    26788 [Repeated 1 time(s)]
    26789 
    26790 > volume #1 level 0.1857
    26791 
    26792 > view view1
    26793 
    26794 Expected an objects specifier or a view name or a keyword 
    26795 
    26796 > view name view1
    26797 
    26798 > rotate 90
    26799 
    26800 Unknown command: rotate 90 
    26801 
    26802 > turn 90
    26803 
    26804 Expected an axis vector or a keyword 
    26805 
    26806 > turn x 90
    26807 
    26808 [Repeated 3 time(s)]
    26809 
    26810 > turn y 90
    26811 
    26812 [Repeated 3 time(s)]
    26813 
    26814 > turn y -90
    26815 
    26816 > view name view2
    26817 
    26818 > turn y 90
    26819 
    26820 > view view2
    26821 
    26822 > turn y 180
    26823 
    26824 > view name view3
    26825 
    26826 > view view3
    26827 
    26828 > turn y 180
    26829 
    26830 > view name view4
    26831 
    26832 [Repeated 1 time(s)]
    26833 
    26834 > view view3
    26835 
    26836 > view name view3
    26837 
    26838 > view name view5
    26839 
    26840 > lighting soft
    26841 
    26842 > set silhouetteWidth 1.5
    26843 
    26844 > ui tool show "Side View"
    26845 
    26846 > save
    26847 > /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view5.png
    26848 > width 823 height 607 supersample 3 transparentBackground true
    26849 
    26850 > view view3
    26851 
    26852 > save
    26853 > /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view3.png
    26854 > width 823 height 607 supersample 3 transparentBackground true
    26855 
    26856 > view view4
    26857 
    26858 > save
    26859 > /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view4.png
    26860 > width 823 height 607 supersample 3 transparentBackground true
    26861 
    26862 > save "/Users/becca/Desktop/Postdoc/COPI notebooks and
    26863 > resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
    26864 
    26865 > open "/Users/becca/Desktop/Postdoc/COPI notebooks and
    26866 > resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4479_map_locres_J3623.mrc"
    26867 
    26868 Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
    26869 240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32 
    26870 
    26871 > ui tool show "Surface Color"
    26872 
    26873 > color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
    26874 > #808080
    26875 
    26876 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26877 
    26878 > color sample #1.1 map #48 palette 2,#ff0000:4,#ffffff:10,#0000ff
    26879 > outsideColor #808080
    26880 
    26881 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26882 
    26883 > color sample #1.1 map #48 palette 3,#ff0000:4,#ffffff:10,#0000ff
    26884 > outsideColor #808080
    26885 
    26886 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26887 
    26888 > color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
    26889 > #808080
    26890 
    26891 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26892 
    26893 > color sample #1.1 map #48 palette 4,#ff0000:6,#ffffff:8,#0000ff outsideColor
    26894 > #808080
    26895 
    26896 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26897 
    26898 > color single #1.1
    26899 
    26900 > key red-white-blue :4 :6 :8 showTool true
    26901 
    26902 > ui mousemode right "color key"
    26903 
    26904 > color sample #1.1 map #48 palette 2.5,#ff0000:6,#ffffff:8,#0000ff
    26905 > outsideColor #808080
    26906 
    26907 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26908 
    26909 > key red-white-blue :2.5 :6.0 :8.0 showTool true
    26910 
    26911 > color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:8,#0000ff
    26912 > outsideColor #808080
    26913 
    26914 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26915 
    26916 > key red-white-blue :2.5 :4.0 :8.0 showTool true
    26917 
    26918 > color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:6.5,#0000ff
    26919 > outsideColor #808080
    26920 
    26921 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26922 
    26923 > key red-white-blue :2.5 :4.0 :6.5 showTool true
    26924 
    26925 > color single #1.1
    26926 
    26927 > color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:6.5,#0000ff
    26928 > outsideColor #808080
    26929 
    26930 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26931 
    26932 > color sample #1.1 map #48 palette 3,#ff0000:4,#ffffff:6.5,#0000ff
    26933 > outsideColor #808080
    26934 
    26935 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
    26936 
    26937 > key red-white-blue :3.0 :4.0 :6.5 showTool true
    26938 
    26939 > color sample #1.1 map #48 palette 3,#ff0000:4.5,#ffffff:6.5,#0000ff
    26940 > outsideColor #808080
    26941 
    26942 Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766 
     2424[deleted to fit within ticket limits]
    269432425
    269442426> key red-white-blue :3.0 :4.5 :6.5 showTool true