![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Changes between Initial Version and Version 1 of Ticket #19808
- Timestamp:
- Feb 5, 2026, 2:03:50 PM (3 weeks ago)
Legend:
- Unmodified
- Added
- Removed
- Modified
-
Ticket #19808
- Property Component Unassigned → Window Toolkit
- Property Owner set to
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep
-
Ticket #19808 – Description
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TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1440K 36 \nColorSync 704K 38 \nCoreAnimation 2144K 118 \nCoreGraphics 80K 5 \nCoreServices 624K 2 \nCoreUI image data 6432K 57 \nFoundation 144K 3 \nKernel Alloc Once 32K 1 \nMALLOC 6.7G 173 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 1008K 63 \nStack 213.6M 64 \nStack Guard 56.0M 1 \nVM_ALLOCATE 328.9M 220 \nVM_ALLOCATE (reserved) 768.0M 3 reserved VM address space (unallocated)\n__AUTH 5517K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 40.4M 1182 \n__DATA_CONST 38.7M 1189 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 660.4M 240 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.4G 1208 \n__TEXT (graphics) 48K 2 \n__TPRO_CONST 128K 2 \ndyld private memory 12.5M 100 \nmapped file 759.5M 107 \npage table in kernel 4487K 1 \nshared memory 3248K 30 \n=========== ======= ======= \nTOTAL 11.0G 6862 \nTOTAL, minus reserved VM space 10.3G 6862 \n", 2399 "legacyInfo" : { 2400 "threadTriggered" : { 2401 "name" : "CrBrowserMain", 2402 "queue" : "com.apple.main-thread" 2403 } 2404 }, 2405 "logWritingSignature" : "82c56b840f6684891fa68812616e7f0450124f05", 2406 "trialInfo" : { 2407 "rollouts" : [ 2408 { 2409 "rolloutId" : "63508950b3714d3622fc77f7", 2410 "factorPackIds" : { 2411 "SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8" 2412 }, 2413 "deploymentId" : 240000015 2414 }, 2415 { 2416 "rolloutId" : "661464ecda55e5192b100804", 2417 "factorPackIds" : { 2418 2419 }, 2420 "deploymentId" : 240000005 2421 } 2422 ], 2423 "experiments" : [ 2424 2425 ] 2426 } 2427 } 2428 ===== Log before crash start ===== 2429 UCSF ChimeraX version: 1.10.1 (2025-07-24) 2430 © 2016-2025 Regents of the University of California. All rights reserved. 2431 2432 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2433 > with Terns/20260111 IVC 2434 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs" 2435 2436 Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512, 2437 pixel 1.07, shown at level 0.142, step 1, values float32 2438 Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel 2439 1.07, shown at level 0.0524, step 2, values float32 2440 Log from Tue Feb 3 15:37:02 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) 2441 © 2016-2025 Regents of the University of California. All rights reserved. 2442 2443 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2444 > with Terns/20260111 IVC 2445 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs" 2446 2447 Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512, 2448 pixel 1.07, shown at level 0.142, step 1, values float32 2449 Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel 2450 1.07, shown at level 0.0524, step 2, values float32 2451 Log from Tue Feb 3 13:26:30 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) 2452 © 2016-2025 Regents of the University of California. All rights reserved. 2453 2454 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2455 > with Terns/20260111 IVC 2456 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_2_movie1.cxs" 2457 2458 Log from Mon Feb 2 10:29:38 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) 2459 © 2016-2025 Regents of the University of California. All rights reserved. 2460 2461 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2462 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM2.cxs" 2463 2464 Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 2465 1.07, shown at level 0.227, step 1, values float32 2466 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384, 2467 pixel 1.07, shown at level 0.248, step 1, values float32 2468 Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel 2469 1.07, shown at level 0.153, step 1, values float32 2470 Log from Sun Feb 1 21:27:29 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) 2471 © 2016-2025 Regents of the University of California. All rights reserved. 2472 2473 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2474 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs" 2475 2476 Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 2477 1.07, shown at level 0.145, step 1, values float32 2478 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384, 2479 pixel 1.07, shown at level 0.143, step 1, values float32 2480 Log from Thu Jan 15 09:33:23 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) 2481 © 2016-2025 Regents of the University of California. All rights reserved. 2482 2483 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2484 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs" 2485 2486 Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 2487 1.07, shown at level 0.145, step 1, values float32 2488 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384, 2489 pixel 1.07, shown at level 0.138, step 1, values float32 2490 Log from Tue Jan 13 14:05:11 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) 2491 © 2016-2025 Regents of the University of California. All rights reserved. 2492 2493 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2494 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs" 2495 2496 Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 2497 1.07, shown at level 0.145, step 1, values float32 2498 Log from Tue Jan 13 12:34:22 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) 2499 © 2016-2025 Regents of the University of California. All rights reserved. 2500 How to cite UCSF ChimeraX 2501 2502 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2503 > with Terns/20260111 IVC 2504 > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc" 2505 2506 Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 2507 1.07, shown at level 0.0524, step 2, values float32 2508 2509 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2510 > with Terns/20260111 IVC 2511 > manuscript/IVC_DNA_bound/merged_real_space_refined_007.pdb" 2512 2513 Chain information for merged_real_space_refined_007.pdb #2 2514 --- 2515 Chain | Description 2516 A | No description available 2517 C H I J K L | No description available 2518 D | No description available 2519 E | No description available 2520 F | No description available 2521 G | No description available 2522 M | No description available 2523 N O P Q R | No description available 2524 S | No description available 2525 2526 2527 > hide atoms 2528 2529 > show cartoons 2530 2531 > set bgColor white 2532 2533 > surface dust #1 size 10.7 2534 2535 > volume #1 step 1 2536 2537 > volume #1 level 0.1467 2538 2539 > hide #!1 models 2540 2541 > select #2/D 2542 2543 2438 atoms, 2496 bonds, 297 residues, 1 model selected 2544 2545 > ui tool show "Color Actions" 2546 2547 > color sel hot pink 2548 2549 > ui tool show "Color Actions" 2550 2551 > color sel pink 2552 2553 > select #2/A 2554 2555 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected 2556 2557 > ui tool show "Color Actions" 2558 2559 > color sel light sky blue 2560 2561 > select #2/S,R,Q,P,O,N 2562 2563 5281 atoms, 5363 bonds, 1 pseudobond, 664 residues, 2 models selected 2564 2565 > ui tool show "Color Actions" 2566 2567 > color sel gold 2568 2569 > color sel orange 2570 2571 > color sel gold 2572 2573 > color sel orange 2574 2575 > select #2/M,L,K,J,I,H,C, 2576 2577 Expected an objects specifier or a keyword 2578 2579 > select #2/M,L,K,J,I,H,C 2580 2581 16170 atoms, 16420 bonds, 1 pseudobond, 2079 residues, 2 models selected 2582 2583 > ui tool show "Color Actions" 2584 2585 > color sel medium sea green 2586 2587 > color sel light green 2588 2589 > color sel pale green 2590 2591 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 2592 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_color1.cxs" 2593 2594 > select add #2 2595 2596 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 2597 2598 > select subtract #2 2599 2600 Nothing selected 2601 2602 > lighting soft 2603 2604 > lighting simple 2605 2606 > lighting soft 2607 2608 > lighting flat 2609 2610 > open /Volumes/CHENGTAO/cryosparc_P6_J96_005_volume_map.mrc 2611 2612 Opened cryosparc_P6_J96_005_volume_map.mrc as #3, grid size 256,256,256, pixel 2613 1.61, shown at level 0.107, step 1, values float32 2614 2615 > surface dust #3 size 16.1 2616 2617 > lighting full 2618 2619 > lighting soft 2620 2621 > hide #!2 models 2622 2623 > open /Volumes/CHENGTAO/cryosparc_P6_J97_004_volume_map.mrc 2624 2625 Opened cryosparc_P6_J97_004_volume_map.mrc as #4, grid size 256,256,256, pixel 2626 1.61, shown at level 0.11, step 1, values float32 2627 2628 > open /Volumes/CHENGTAO/cryosparc_P6_J98_004_volume_map.mrc 2629 2630 Opened cryosparc_P6_J98_004_volume_map.mrc as #5, grid size 256,256,256, pixel 2631 1.61, shown at level 0.103, step 1, values float32 2632 2633 > open /Volumes/CHENGTAO/cryosparc_P6_J99_004_volume_map.mrc 2634 2635 Opened cryosparc_P6_J99_004_volume_map.mrc as #6, grid size 256,256,256, pixel 2636 1.61, shown at level 0.107, step 1, values float32 2637 2638 > surface dust #3 size 16.1 2639 2640 > surface dust #4 size 16.1 2641 2642 > surface dust #5 size 16.1 2643 2644 > surface dust #6 size 16.1 2645 2646 > volume #3 level 0.2172 2647 2648 > volume #4 level 0.1954 2649 2650 > volume #4 level 0.2116 2651 2652 > volume #4 level 0.2035 2653 2654 > volume #5 level 0.2178 2655 2656 > volume #6 level 0.225 2657 2658 > volume #6 level 0.2054 2659 2660 > hide #!3 models 2661 2662 > show #!2 models 2663 2664 > show #!3 models 2665 2666 > select add #2 2667 2668 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 2669 2670 > ui mousemode right "translate selected models" 2671 2672 > view matrix models 2673 > #2,-0.86578,-0.49991,0.022818,486.88,0.49898,-0.86584,-0.036613,283.9,0.03806,-0.020313,0.99907,-3.613 2674 2675 > undo 2676 2677 > select subtract #2 2678 2679 Nothing selected 2680 2681 > hide #!2 models 2682 2683 > show #!4 models 2684 2685 > show #!5 models 2686 2687 > show #!6 models 2688 2689 > hide #!3 models 2690 2691 > hide #!4 models 2692 2693 > open "/Users/xuchengtao/Documents/Building models undergoing/20251222 IVC 2694 > intermediate/20260112 IVC 2695 > intermediate/merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb" 2696 2697 Chain information for 2698 merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb #7 2699 --- 2700 Chain | Description 2701 A | No description available 2702 B E G | No description available 2703 C | No description available 2704 D | No description available 2705 F H | No description available 2706 I | No description available 2707 J | No description available 2708 K L M O | No description available 2709 N | No description available 2710 P | No description available 2711 Q | No description available 2712 2713 2714 > show #!7 cartoons 2715 2716 > hide #!7 atoms 2717 2718 > show #!4 models 2719 2720 > show #!3 models 2721 2722 > hide #!7 models 2723 2724 > volume #3 level 0.2008 2725 2726 > open "/Users/xuchengtao/Documents/Building models undergoing/20251222 IVC 2727 > intermediate/flipped_cryosparc_P6_J90_004_volume_map.mrc" 2728 2729 Opened flipped_cryosparc_P6_J90_004_volume_map.mrc as #8, grid size 2730 384,384,384, pixel 1.07, shown at level 0.0589, step 2, values float32 2731 2732 > surface dust #4 size 16.1 2733 2734 > surface dust #5 size 16.1 2735 2736 > surface dust #6 size 16.1 2737 2738 > surface dust #8 size 10.7 2739 2740 > ui tool show "Fit in Map" 2741 2742 > ui mousemode right "translate selected models" 2743 2744 > select add #8 2745 2746 2 models selected 2747 2748 > view matrix models 2749 > #8,-0.71372,-0.49135,0.49917,334.98,-0.54393,0.83781,0.046962,132.29,-0.44129,-0.238,-0.86523,550.67 2750 2751 > view matrix models 2752 > #8,0.97257,0.03667,-0.2297,35.228,0.058924,-0.99413,0.090782,387.87,-0.22503,-0.10183,-0.96902,451.87 2753 2754 > volume #8 step 1 2755 2756 > volume #8 level 0.09502 2757 2758 > fitmap #8 inMap #3 2759 2760 Fit map flipped_cryosparc_P6_J90_004_volume_map.mrc in map 2761 cryosparc_P6_J96_005_volume_map.mrc using 324674 points 2762 correlation = 0.9805, correlation about mean = 0.9142, overlap = 2.547e+04 2763 steps = 216, shift = 16.2, angle = 21 degrees 2764 2765 Position of flipped_cryosparc_P6_J90_004_volume_map.mrc (#8) relative to 2766 cryosparc_P6_J96_005_volume_map.mrc (#3) coordinates: 2767 Matrix rotation and translation 2768 0.97292447 0.21705585 0.07940239 -51.11804392 2769 0.21669675 -0.97614950 0.01321611 360.31959015 2770 0.08037724 0.00434796 -0.99675503 373.34043768 2771 Axis -0.99320802 -0.10918025 -0.04021824 2772 Axis point 0.00000000 183.38879293 187.30072229 2773 Rotation angle (degrees) 179.74420803 2774 Shift along axis -3.58402524 2775 2776 2777 > select subtract #8 2778 2779 Nothing selected 2780 2781 > show #!7 models 2782 2783 > hide #!7 models 2784 2785 > volume #8 level 0.1269 2786 2787 > hide #!6 models 2788 2789 > show #!6 models 2790 2791 > hide #!8 models 2792 2793 > show #!8 models 2794 2795 > hide #!6 models 2796 2797 > volume #8 level 0.1181 2798 2799 > hide #!8 models 2800 2801 > show #!6 models 2802 2803 > volume #6 level 0.2054 2804 2805 > show #!7 models 2806 2807 > volume #3 level 0.2069 2808 2809 > volume #4 level 0.2577 2810 2811 > volume #5 level 0.2147 2812 2813 > volume #6 level 0.2229 2814 2815 > hide #!6 models 2816 2817 > show #!8 models 2818 2819 > hide #!7 models 2820 2821 > volume #8 level 0.134 2822 2823 > volume #6 level 0.2142 2824 2825 > volume #6 level 0.2287 2826 2827 [Repeated 1 time(s)] 2828 2829 > volume #5 level 0.2392 2830 2831 > volume #5 level 0.2178 2832 2833 > volume #6 level 0.2083 2834 2835 > volume #6 level 0.2025 2836 2837 > volume #4 level 0.1914 2838 2839 > volume #5 level 0.2055 2840 2841 > volume #5 level 0.1872 2842 2843 > volume #4 level 0.2095 2844 2845 > show #!7 models 2846 2847 > volume #3 level 0.1826 2848 2849 > volume #4 showOutlineBox true 2850 2851 > volume #4 level 0.1945 2852 2853 > volume #4 showOutlineBox false 2854 2855 > volume #4 level 0.1824 2856 2857 > volume #3 level 0.1673 2858 2859 > volume #5 level 0.1903 2860 2861 > hide #!7 models 2862 2863 > volume #5 level 0.1658 2864 2865 > volume #4 level 0.1794 2866 2867 > volume #5 level 0.1933 2868 2869 > volume #5 level 0.2269 2870 2871 > volume #4 level 0.2246 2872 2873 > show #!7 models 2874 2875 > volume #3 level 0.216 2876 2877 > volume #3 level 0.1978 2878 2879 > volume #5 level 0.2086 2880 2881 > hide #!7 models 2882 2883 > show #!5 models 2884 2885 > hide #!5 models 2886 2887 > hide #!6 models 2888 2889 > show #!6 models 2890 2891 > show #!5 models 2892 2893 > hide #!6 models 2894 2895 > hide #!5 models 2896 2897 > show #!4 models 2898 2899 > volume #4 level 0.1794 2900 2901 > volume #5 level 0.1719 2902 2903 > volume #6 level 0.1734 2904 2905 > volume #5 level 0.1475 2906 2907 > volume #4 level 0.2095 2908 2909 > volume #6 level 0.22 2910 2911 > volume #3 level 0.213 2912 2913 > volume #4 level 0.2155 2914 2915 > show #!7 models 2916 2917 > color #4 #b2ffffb0 models 2918 2919 > color #4 #f4fcfeb1 models 2920 2921 > color #4 #9a9fa0b1 models 2922 2923 > color #4 #8e9293b1 models 2924 2925 > color #4 #6c7070b1 models 2926 2927 > color #4 #9ca1a2b1 models 2928 2929 > color #4 #9ca1a2b0 models 2930 2931 > color #3 #909071ff models 2932 2933 > color #3 #867f90ff models 2934 2935 > color #3 #867f90b3 models 2936 2937 > hide #!4 models 2938 2939 > show #!5 models 2940 2941 > color #5 #b2b2ffba models 2942 2943 > color #5 #f3ecfaba models 2944 2945 > color #5 #95919aba models 2946 2947 > color #6 #faf3fbff models 2948 2949 > color #6 #817d82ff models 2950 2951 > color #6 #817d82a5 models 2952 2953 > color #6 #817d82a6 models 2954 2955 > volume #5 level 0.2422 2956 2957 > volume #5 level 0.1994 2958 2959 > hide #!5 models 2960 2961 > show #!6 models 2962 2963 > volume #6 level 0.2038 2964 2965 > volume #6 level 0.2394 2966 2967 > volume #6 level 0.2167 2968 2969 > volume #6 level 0.2135 2970 2971 > volume #4 level 0.2357 2972 2973 > volume #3 level 0.2333 2974 2975 > volume #6 level 0.233 2976 2977 > copy #2 2978 2979 Unknown command: copy #2 2980 2981 > duplicate #2 2982 2983 Unknown command: duplicate #2 2984 2985 > mcopy #2 2986 2987 Missing required "to_atoms" argument 2988 2989 > combine #2 2990 2991 > hide #!7 models 2992 2993 > show #!2 models 2994 2995 > hide #!2 models 2996 2997 > show #!7 models 2998 2999 > select add #9 3000 3001 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3002 3003 > view matrix models 3004 > #9,-0.78485,0.6147,-0.07848,262.35,-0.61967,-0.77759,0.10659,471.23,0.0044959,0.13229,0.9912,-26.215 3005 3006 > mmaker #9 to #7 3007 3008 Parameters 3009 --- 3010 Chain pairing | bb 3011 Alignment algorithm | Needleman-Wunsch 3012 Similarity matrix | BLOSUM-62 3013 SS fraction | 0.3 3014 Gap open (HH/SS/other) | 18/18/6 3015 Gap extend | 1 3016 SS matrix | | | H | S | O 3017 ---|---|---|--- 3018 H | 6 | -9 | -6 3019 S | | 6 | -6 3020 O | | | 4 3021 Iteration cutoff | 2 3022 3023 Matchmaker 3024 merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb, 3025 chain A (#7) with copy of merged_real_space_refined_007.pdb, chain A (#9), 3026 sequence alignment score = 2382.1 3027 RMSD between 256 pruned atom pairs is 1.157 angstroms; (across all 517 pairs: 3028 3.343) 3029 3030 3031 > select subtract #9 3032 3033 Nothing selected 3034 3035 > hide #!9 models 3036 3037 > show #!9 models 3038 3039 > hide #!7 models 3040 3041 > show #!7 models 3042 3043 > hide #!9 models 3044 3045 > show #!9 models 3046 3047 > hide #!9 models 3048 3049 > show #!9 models 3050 3051 > hide #!9 models 3052 3053 > hide #!7 models 3054 3055 > show #!2 models 3056 3057 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 3058 > with Terns/20260111 IVC manuscript/IVC_DNA_2_states_compare.cxs" 3059 3060 > color zone #1 3061 3062 Missing required "near" argument 3063 3064 > color zone #1 near #2 3065 3066 > color zone #1 near #2 range 3 3067 3068 Expected a keyword 3069 3070 > open "/Users/xuchengtao/Documents/Building models undergoing/20251030 3071 > 8mut_ssDNA/DNA-RNA/IscB_8mut_ssDNA_DNA_model_coloring.cxc" 3072 3073 > hide #!4-13 models 3074 3075 > select #1/A:1-54 3076 3077 Nothing selected 3078 3079 > color sel hotpink 3080 3081 > select #1/A:55-85,161-196,297-374 3082 3083 Nothing selected 3084 3085 > color sel royalblue 3086 3087 > select #1/A:86-122 3088 3089 Nothing selected 3090 3091 > color sel mediumslateblue 3092 3093 > select #1/A:123-160 3094 3095 Nothing selected 3096 3097 > color sel yellow 3098 3099 > select #1/A:197-296 3100 3101 Nothing selected 3102 3103 > color sel orange 3104 3105 > select #1/A:375-429 3106 3107 Nothing selected 3108 3109 > color sel lightsalmon 3110 3111 > select #1/A:430-496 3112 3113 Nothing selected 3114 3115 > color sel blueviolet 3116 3117 > select #1/D 3118 3119 Nothing selected 3120 3121 > color sel dodgerblue 3122 3123 > select #1/B:1-16 3124 3125 Nothing selected 3126 3127 > color sel firebrick 3128 3129 > select #1/B:17-256 3130 3131 Nothing selected 3132 3133 > color sel silver 3134 3135 executed IscB_8mut_ssDNA_DNA_model_coloring.cxc 3136 3137 > color zone #1 near #2 range 3 3138 3139 Expected a keyword 3140 3141 > color zone #1 near #2 distance 3 3142 3143 > color zone #1 near #2 distance 3.5 3144 3145 > hide #!2 models 3146 3147 > show #!2 models 3148 3149 > hide #!1 models 3150 3151 > select @2/G 3152 3153 4324 atoms, 4594 bonds, 395 residues, 3 models selected 3154 3155 > select #2/G 3156 3157 983 atoms, 1100 bonds, 46 residues, 1 model selected 3158 3159 > ui tool show "Color Actions" 3160 3161 > color sel wheat 3162 3163 > color sel khaki 3164 3165 > select #2/F 3166 3167 972 atoms, 1090 bonds, 47 residues, 1 model selected 3168 3169 > ui tool show "Color Actions" 3170 3171 > color sel deep sky blue 3172 3173 > color sel dodger blue 3174 3175 > color sel cornflower blue 3176 3177 > color sel dodger blue 3178 3179 > select #2/E 3180 3181 200 atoms, 222 bonds, 10 residues, 1 model selected 3182 3183 > ui tool show "Color Actions" 3184 3185 > color sel tomato 3186 3187 > color sel dark salmon 3188 3189 > color sel hot pink 3190 3191 > color sel pale violet red 3192 3193 > color sel deep pink 3194 3195 > color sel hot pink 3196 3197 > select add #2 3198 3199 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3200 3201 > select subtract #2 3202 3203 Nothing selected 3204 3205 > color zone #1 near #2 distance 3.5 3206 3207 > show #!1 models 3208 3209 > volume #1 level 0.1611 3210 3211 > hide #!2 models 3212 3213 > volume #1 level 0.17 3214 3215 > volume #1 level 0.16 3216 3217 > color zone #1 near #2 distance 4 3218 3219 > volume #1 level 0.12 3220 3221 > volume #1 level 0.13 3222 3223 > volume #1 level 0.14 3224 3225 > volume #1 level 0.145 3226 3227 > save /Users/xuchengtao/Desktop/image166.png supersample 3 3228 3229 > color zone #1 near #2 distance 4.5 3230 3231 > save /Users/xuchengtao/Desktop/image167.png supersample 3 3232 3233 > hide #!1 models 3234 3235 > show #!7 models 3236 3237 > show #!9 models 3238 3239 > hide #!7 models 3240 3241 > hide #!9 models 3242 3243 > show #!2 models 3244 3245 > save /Users/xuchengtao/Desktop/image168.png supersample 3 3246 3247 > save /Users/xuchengtao/Desktop/image169.png supersample 3 3248 3249 > select add #2 3250 3251 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3252 3253 > cartoon style (#!2 & sel) modeHelix tube sides 20 3254 3255 > select subtract #2 3256 3257 Nothing selected 3258 3259 > save /Users/xuchengtao/Desktop/image170.png supersample 3 3260 3261 > save /Users/xuchengtao/Desktop/image171.png supersample 3 3262 3263 > show #!1 models 3264 3265 > hide #!2 models 3266 3267 > save /Users/xuchengtao/Desktop/image172.png supersample 3 3268 3269 > hide #!1 models 3270 3271 > show #!3 models 3272 3273 > show #!4 models 3274 3275 > show #!5 models 3276 3277 > close #3-6,8 3278 3279 > show #!1 models 3280 3281 > show #!2 models 3282 3283 > hide #!2 models 3284 3285 > show #!2 models 3286 3287 > hide #!2 models 3288 3289 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 3290 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_color1.cxs" 3291 3292 ——— End of log from Tue Jan 13 12:34:22 2026 ——— 3293 3294 > view name session-start 3295 3296 opened ChimeraX session 3297 3298 > show #!7 models 3299 3300 > show #!9 models 3301 3302 > hide #!7 models 3303 3304 > hide #!9 models 3305 3306 > close #7,9 3307 3308 > show #!2 models 3309 3310 > combine #2 3311 3312 > hide #!1 models 3313 3314 > hide #!2 models 3315 3316 > combine #1 3317 3318 No structures specified 3319 3320 > copy #1 3321 3322 Unknown command: copy #1 3323 3324 > duplicate #1 3325 3326 Unknown command: duplicate #1 3327 3328 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 3329 > with Terns/20260111 IVC 3330 > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc" 3331 3332 Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 3333 1.07, shown at level 0.0524, step 2, values float32 3334 3335 > close #4 3336 3337 > select #3/S,R,q,p,o,n 3338 3339 5281 atoms, 5363 bonds, 1 pseudobond, 664 residues, 2 models selected 3340 3341 > ui tool show "Color Actions" 3342 3343 > color sel light gray 3344 3345 > color sel gray 3346 3347 > color sel light gray 3348 3349 > color sel dark gray 3350 3351 > color sel light gray 3352 3353 > select #3/m,l,k,j,i,H,C 3354 3355 16170 atoms, 16420 bonds, 1 pseudobond, 2079 residues, 2 models selected 3356 3357 > ui tool show "Color Actions" 3358 3359 > color sel light gray 3360 3361 > volume copy #1 3362 3363 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384, 3364 pixel 1.07, shown at step 1, values float32 3365 3366 > color #4 #b2b2b299 models 3367 3368 > color zone #4 near #3 distance 4 3369 3370 > color #4 #b2b2b280 models 3371 3372 > color #4 #b2b2b299 models 3373 3374 > transparency 3375 3376 Missing or invalid "percent" argument: Expected a number 3377 3378 > transparency #3 60 3379 3380 > hide #!3 models 3381 3382 > show #!3 models 3383 3384 > transparency #4 60 3385 3386 > color zone #4 near #3 distance 4 3387 3388 > transparency #4 60 3389 3390 > surface dust #4 size 10.7 3391 3392 > hide #!3 models 3393 3394 > transparency #4 80 3395 3396 > color zone #4 near #3 distance 4 3397 3398 > transparency #4 90 3399 3400 > color zone #4 near #3 distance 4 3401 3402 > transparency #4 10 3403 3404 > lighting soft 3405 3406 > lighting simple 3407 3408 > lighting flat 3409 3410 > lighting soft 3411 3412 > lighting flat 3413 3414 > lighting simple 3415 3416 > lighting soft 3417 3418 > lighting full 3419 3420 > lighting soft 3421 3422 > lighting flat 3423 3424 > lighting full 3425 3426 > lighting simple 3427 3428 [Repeated 1 time(s)] 3429 3430 > lighting full 3431 3432 > save /Users/xuchengtao/Desktop/image186.png supersample 3 3433 3434 > save /Users/xuchengtao/Desktop/image187.png supersample 3 3435 3436 > select add #3 3437 3438 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3439 3440 > select subtract #3 3441 3442 Nothing selected 3443 3444 > show #!3 models 3445 3446 > hide #!4 models 3447 3448 > hide #3 cartoons 3449 3450 > show #3/A cartoons 3451 3452 > ui mousemode right select 3453 3454 > style #!3 stick 3455 3456 Changed 30522 atom styles 3457 3458 > show #!3 atoms 3459 3460 > color #!3 byhetero 3461 3462 > show #!4 models 3463 3464 > hide #!4 models 3465 3466 > transparency #4 20 3467 3468 > show #!4 models 3469 3470 > hide #!3 models 3471 3472 > show #!3 models 3473 3474 > transparency #4.1 0 3475 3476 > transparency #4 20 3477 3478 > transparency #4 50 3479 3480 > volume #4 level 0.1208 3481 3482 > color zone #4 near #3 distance 4 3483 3484 > hide #!3 atoms 3485 3486 > color zone #4 near #3 distance 4 3487 3488 > select #3/A 3489 3490 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected 3491 3492 > ui tool show "Color Actions" 3493 3494 > color sel light sky blue 3495 3496 > color zone #4 near #3 distance 4 3497 3498 > select add #3 3499 3500 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3501 3502 > select subtract #3 3503 3504 Nothing selected 3505 3506 > hide #!4 models 3507 3508 > style #!3 stick 3509 3510 Changed 30522 atom styles 3511 3512 > show #!3 atoms 3513 3514 > style #!3 stick 3515 3516 Changed 30522 atom styles 3517 3518 > color #!3 byhetero 3519 3520 > hide #3/A 3521 3522 > hide #!3 models 3523 3524 > show #!3 models 3525 3526 > hide #!3 models 3527 3528 > select #3/A:115,147,146,159,94,93,70,97,54 3529 3530 87 atoms, 85 bonds, 9 residues, 1 model selected 3531 3532 > show sel atoms 3533 3534 > show #!3 models 3535 3536 > hide #3/A cartoons 3537 3538 > select add #3 3539 3540 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3541 3542 > select subtract #3 3543 3544 Nothing selected 3545 3546 > hide #3 cartoons 3547 3548 > hide #3 atoms 3549 3550 > show sel atoms 3551 3552 > select #3/A:115,147,146,159,94,93,70,97,54 3553 3554 87 atoms, 85 bonds, 9 residues, 1 model selected 3555 3556 > show sel atoms 3557 3558 > show #!4 models 3559 3560 > combine #3 3561 3562 > hide #!3 models 3563 3564 > hide #!4 models 3565 3566 > select add #3 3567 3568 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3569 3570 > show #!1 models 3571 3572 > select subtract #3 3573 3574 Nothing selected 3575 3576 > color zone #4 near #1 distance 5 3577 3578 color zone: No atoms specified. 3579 3580 > show #!4 models 3581 3582 > hide #!1 models 3583 3584 > color #4 #b8bfbb66 models 3585 3586 > color zone #4 near #1 distance 5 3587 3588 color zone: No atoms specified. 3589 3590 > color zone #4 near #2 distance 5 3591 3592 > volume #4 level 0.13 3593 3594 > volume #4 level 0.135 3595 3596 > lighting soft 3597 3598 > hide #!4 models 3599 3600 > show #!4 models 3601 3602 > hide #!5 models 3603 3604 > show #!5 models 3605 3606 > hide #!4 models 3607 3608 > show #!4 models 3609 3610 > volume #4 level 0.14 3611 3612 > transparency #4 20 3613 3614 > ui tool show "Side View" 3615 3616 > transparency #4 50 3617 3618 > volume #4 level 0.138 3619 3620 > color zone #4 near #2 distance 5 3621 3622 > transparency #4 50 3623 3624 [Repeated 1 time(s)] 3625 3626 > transparency #4 70 3627 3628 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 3629 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs" 3630 3631 ——— End of log from Tue Jan 13 14:05:11 2026 ——— 3632 3633 > view name session-start 3634 3635 opened ChimeraX session 3636 3637 > hide #!4 models 3638 3639 > hide #!5 models 3640 3641 > show #!3 models 3642 3643 > show #!4 models 3644 3645 > hide #!3 models 3646 3647 > show #!1 models 3648 3649 > hide #!4 models 3650 3651 > hide #!1 models 3652 3653 > show #!4 models 3654 3655 > show #!5 models 3656 3657 > hide #!4 models 3658 3659 > show #!4 models 3660 3661 > hide #!5 models 3662 3663 > show #!3 models 3664 3665 > hide #!4 models 3666 3667 > show #!5 models 3668 3669 > hide #!3 models 3670 3671 > show #!3 models 3672 3673 > hide #!5 models 3674 3675 > show #!5 models 3676 3677 > show #5 cartoons 3678 3679 > show #5 atoms 3680 3681 > hide #5 atoms 3682 3683 > show #!4 models 3684 3685 > hide #!3 models 3686 3687 > show #!3 models 3688 3689 > hide #!3 models 3690 3691 > hide #!4 models 3692 3693 > show #!4 models 3694 3695 > color zone #4 near #5 distance 5 3696 3697 > hide #!5 atoms 3698 3699 > color zone #4 near #5 distance 5 3700 3701 > volume #4 level 0.09687 3702 3703 > volume #4 style mesh 3704 3705 > volume #4 style surface 3706 3707 > volume #4 level 0.1428 3708 3709 > color #!5 bychain 3710 3711 > undo 3712 3713 > hide #!4 models 3714 3715 > show #!1 models 3716 3717 > hide #!1 models 3718 3719 > show #!5 atoms 3720 3721 > select #5/E,F,A,D 3722 3723 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected 3724 3725 > hide #5 cartoons 3726 3727 > hide #5 atoms 3728 3729 > select #5/E,F,A,D 3730 3731 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected 3732 3733 > show sel cartoons 3734 3735 > select #5/A 3736 3737 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected 3738 3739 > ui tool show "Color Actions" 3740 3741 > color sel light sky blue 3742 3743 > select #5/F 3744 3745 972 atoms, 1090 bonds, 47 residues, 1 model selected 3746 3747 > ui tool show "Color Actions" 3748 3749 > color sel deep sky blue 3750 3751 > undo 3752 3753 > color sel dodger blue 3754 3755 [Repeated 3 time(s)] 3756 3757 > select #5/D 3758 3759 2438 atoms, 2496 bonds, 297 residues, 1 model selected 3760 3761 > ui tool show "Color Actions" 3762 3763 > color sel light pink 3764 3765 > select #5/E 3766 3767 200 atoms, 222 bonds, 10 residues, 1 model selected 3768 3769 > ui tool show "Color Actions" 3770 3771 > color sel hot pink 3772 3773 [Repeated 3 time(s)] 3774 3775 > select add #5 3776 3777 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3778 3779 > select subtract #5 3780 3781 Nothing selected 3782 3783 > show #!5 atoms 3784 3785 > hide #!5 atoms 3786 3787 > select #5/A,D,E,F 3788 3789 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected 3790 3791 > show #!4 models 3792 3793 > hide #!4 models 3794 3795 > show #!4 models 3796 3797 > volume zone #4 nearAtoms 5 dist 4.5 3798 3799 Invalid "nearAtoms" argument: invalid atoms specifier 3800 3801 > volume zone #4 nearAtoms #5 dist 4.5 3802 3803 Expected a keyword 3804 3805 > volume zone #4 nearAtoms #5 3806 3807 > volume zone #4 nearAtoms sel 3808 3809 > show #!4 models 3810 3811 > volume zone #4 nearAtoms sel dist 5 3812 3813 Expected a keyword 3814 3815 > volume zone #4 nearAtoms sel dis4 3816 3817 Expected a keyword 3818 3819 > volume zone #4 nearAtoms sel dis 4 3820 3821 Expected a keyword 3822 3823 > volume zone #4 nearAtoms sel range 4 3824 3825 > volume zone #4 nearAtoms sel range 3 3826 3827 > volume zone #4 nearAtoms sel range 2 3828 3829 > volume zone #4 nearAtoms sel range 2.5 3830 3831 > color zone #4 near sel distance 4 3832 3833 > select add #5 3834 3835 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3836 3837 > select subtract #5 3838 3839 Nothing selected 3840 3841 > hide #!5 models 3842 3843 > volume zone #4 nearAtoms sel range 3 3844 3845 no atoms specified for zone 3846 3847 > select #5/A,D,E,F 3848 3849 8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected 3850 3851 > volume zone #4 nearAtoms sel range 3 3852 3853 > transparency #4 50 3854 3855 > show #!5 models 3856 3857 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 3858 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs" 3859 3860 Drag select of 4 cryosparc_P6_J91_004_volume_map.mrc copy , 10 residues 3861 3862 > select clear 3863 3864 > open "/Users/xuchengtao/Documents/Building models 3865 > undergoing/20251003IVC/20251222 Xiaomeng AI 3866 > IVC/merged_real_space_refined_009.pdb" 3867 3868 Chain information for merged_real_space_refined_009.pdb #6 3869 --- 3870 Chain | Description 3871 A | No description available 3872 C H I J K L | No description available 3873 D | No description available 3874 E | No description available 3875 F | No description available 3876 G | No description available 3877 M | No description available 3878 N O P Q R | No description available 3879 S | No description available 3880 3881 3882 > hide #!4 models 3883 3884 > hide #!5 models 3885 3886 > select add #6 3887 3888 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 3889 3890 > hide sel atoms 3891 3892 > show sel cartoons 3893 3894 > select subtract #6 3895 3896 Nothing selected 3897 3898 > hide #!6 models 3899 3900 > show #!5 models 3901 3902 > show #!4 models 3903 3904 > hide #!5 models 3905 3906 > hide #!4 models 3907 3908 > show #!5 models 3909 3910 > select #5/E:8 3911 3912 19 atoms, 20 bonds, 1 residue, 1 model selected 3913 3914 > hide #5/F:1-36 3915 3916 > hide #5/F:1-36 cartoons 3917 3918 > show #5/F:34-37 cartoons 3919 3920 Drag select of 9 residues 3921 3922 > select #5/E:6 3923 3924 22 atoms, 24 bonds, 1 residue, 1 model selected 3925 Drag select of 9 residues 3926 3927 > select add #5/E:6 3928 3929 209 atoms, 24 bonds, 10 residues, 1 model selected 3930 3931 > select add #5/E:7 3932 3933 228 atoms, 44 bonds, 11 residues, 1 model selected 3934 3935 > select subtract #5/E:7 3936 3937 209 atoms, 24 bonds, 10 residues, 1 model selected 3938 3939 > select add #5/E:7 3940 3941 228 atoms, 44 bonds, 11 residues, 1 model selected 3942 3943 > select add #5/E:8 3944 3945 247 atoms, 64 bonds, 12 residues, 1 model selected 3946 3947 > select subtract #5/E:8 3948 3949 228 atoms, 44 bonds, 11 residues, 1 model selected 3950 3951 > select add #5/E:8 3952 3953 247 atoms, 64 bonds, 12 residues, 1 model selected 3954 3955 > select subtract #5/E:8 3956 3957 228 atoms, 44 bonds, 11 residues, 1 model selected 3958 3959 > select add #5/E:9 3960 3961 247 atoms, 64 bonds, 12 residues, 1 model selected 3962 3963 > select add #5/E:8 3964 3965 266 atoms, 84 bonds, 13 residues, 1 model selected 3966 3967 > select add #5/E:10 3968 3969 285 atoms, 104 bonds, 14 residues, 1 model selected 3970 3971 > select add #5/F:43 3972 3973 304 atoms, 124 bonds, 15 residues, 1 model selected 3974 3975 > select add #5/F:42 3976 3977 325 atoms, 147 bonds, 16 residues, 1 model selected 3978 3979 > select add #5/F:41 3980 3981 344 atoms, 167 bonds, 17 residues, 1 model selected 3982 3983 > select add #5/F:40 3984 3985 366 atoms, 191 bonds, 18 residues, 1 model selected 3986 3987 > select add #5/F:39 3988 3989 388 atoms, 215 bonds, 19 residues, 1 model selected 3990 3991 > select add #5/F:38 3992 3993 410 atoms, 239 bonds, 20 residues, 1 model selected 3994 3995 > select add #5/F:37 3996 3997 432 atoms, 263 bonds, 21 residues, 1 model selected 3998 3999 > select add #5/F:36 4000 4001 453 atoms, 286 bonds, 22 residues, 1 model selected 4002 4003 > select add #5/F:35 4004 4005 472 atoms, 306 bonds, 23 residues, 1 model selected 4006 4007 > select add #5/F:34 4008 4009 492 atoms, 327 bonds, 24 residues, 1 model selected 4010 4011 > show sel atoms 4012 4013 > color sel byhetero 4014 4015 > color sel bychain 4016 4017 > select add #5 4018 4019 30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected 4020 4021 > select subtract #5 4022 4023 Nothing selected 4024 4025 > select #5/A:400,405,434,532,355 4026 4027 48 atoms, 43 bonds, 5 residues, 1 model selected 4028 4029 > show sel atoms 4030 4031 > color sel byhetero 4032 4033 > hbonds sel reveal true 4034 4035 44 hydrogen bonds found 4036 4037 > undo 4038 4039 > color sel byhetero 4040 4041 > hide #5/A:403 4042 4043 > select add #5 4044 4045 30522 atoms, 31271 bonds, 13 pseudobonds, 3693 residues, 3 models selected 4046 4047 > select subtract #5 4048 4049 Nothing selected 4050 4051 > lighting simple 4052 4053 > lighting soft 4054 4055 Drag select of 1 residues 4056 4057 > select #5/D:159 4058 4059 6 atoms, 5 bonds, 1 residue, 1 model selected 4060 4061 > color sel byhetero 4062 4063 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4064 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs" 4065 4066 [Repeated 1 time(s)] 4067 4068 ——— End of log from Thu Jan 15 09:33:23 2026 ——— 4069 4070 > view name session-start 4071 4072 opened ChimeraX session 4073 4074 > close session 4075 4076 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4077 > with Terns/20260111 IVC 4078 > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc" 4079 4080 Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 4081 1.07, shown at level 0.0524, step 2, values float32 4082 4083 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4084 > with Terns/20260111 IVC 4085 > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb" 4086 4087 Chain information for merged_real_space_refined_011.pdb #2 4088 --- 4089 Chain | Description 4090 A | No description available 4091 C H I J K L | No description available 4092 D | No description available 4093 E | No description available 4094 F | No description available 4095 G | No description available 4096 M | No description available 4097 N O P Q R | No description available 4098 S | No description available 4099 4100 4101 > style stick 4102 4103 Changed 30524 atom styles 4104 4105 > show cartoons 4106 4107 > volume #1 step 1 4108 4109 > surface dust #1 size 10.7 4110 4111 > hide #!1 models 4112 4113 > hide #2 4114 4115 > hide #2 cartoons 4116 4117 > show #2/E:1-10 4118 4119 > show #2/F:37-47 4120 4121 > show #2/A 4122 4123 > select #2/A 4124 4125 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 4126 4127 > ui tool show "Color Actions" 4128 4129 > color sel light sky blue 4130 4131 > select #2/F 4132 4133 972 atoms, 1090 bonds, 47 residues, 1 model selected 4134 4135 > ui tool show "Color Actions" 4136 4137 > color sel cornflower blue 4138 4139 > ui tool show "Color Actions" 4140 4141 > color sel deep sky blue 4142 4143 > color sel royal blue 4144 4145 > select #2/E 4146 4147 200 atoms, 222 bonds, 10 residues, 1 model selected 4148 4149 > color sel hot pink 4150 4151 > select #2/D 4152 4153 2438 atoms, 2496 bonds, 297 residues, 1 model selected 4154 4155 > show 4156 4157 > Hide 4158 4159 Unknown command: Hide 4160 4161 > hide 4162 4163 > undo 4164 4165 > show #2/D 4166 4167 > color sel red 4168 4169 > select add #2 4170 4171 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 4172 4173 > select subtract #2 4174 4175 Nothing selected 4176 4177 > color byhetero 4178 4179 > undo 4180 4181 > show #2/D 4182 4183 [Repeated 1 time(s)] 4184 4185 > select #2/D 4186 4187 2438 atoms, 2496 bonds, 297 residues, 1 model selected 4188 4189 > ui tool show "Color Actions" 4190 4191 > color sel violet 4192 4193 > color sel light pink 4194 4195 > volume copy #1 4196 4197 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #3, grid size 384,384,384, 4198 pixel 1.07, shown at step 1, values float32 4199 4200 > volume #3 level 0.1685 4201 4202 > volume #1 level 0.1879 4203 4204 > color #1 #b2b2b2ad models 4205 4206 > color #3 #b2b2b2a9 models 4207 4208 > color #3 #b2b2b2a8 models 4209 4210 > volume #1 near #2/D range 3 4211 4212 Expected a keyword 4213 4214 > volume zone #1 nearAtoms #2/D range 3 4215 4216 > select add #2 4217 4218 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 4219 4220 > hide #!1 models 4221 4222 > hide #!3 models 4223 4224 > select subtract #2 4225 4226 Nothing selected 4227 4228 > select add #2 4229 4230 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 4231 4232 > select subtract #2 4233 4234 Nothing selected 4235 4236 > show #!1 models 4237 4238 > volume #1 level 0.2145 4239 4240 > volume zone #3 nearAtoms #2/A range 3 4241 4242 > hide #!1 models 4243 4244 > show #!3 models 4245 4246 > hide #!3 models 4247 4248 > select add #1 4249 4250 2 models selected 4251 4252 > show #!1 models 4253 4254 > ui tool show "Color Actions" 4255 4256 > color sel light pink 4257 4258 > color #1 #b2b2b29e models 4259 4260 [Repeated 1 time(s)] 4261 4262 > color #1 #b2b2b284 models 4263 4264 > color #1 #b2b2b280 models 4265 4266 > color #1 hotpink 4267 4268 > color #1 lightpink 4269 4270 > select ~sel & ##selected 4271 4272 Nothing selected 4273 4274 > color #1 hotpink transparency 20 4275 4276 > color #1 lightpink transparency 4277 4278 Missing "transparency" keyword's argument 4279 4280 > color #1 lightpink transparency 20 4281 4282 > color #1 lightpink transparency 60 4283 4284 > color #3 cornflowerblue transparency 60 4285 4286 > show #!3 models 4287 4288 > ui tool show "Color Actions" 4289 4290 > color #3 lightskyblue transparency 60 4291 4292 > volume #3 level 0.1491 4293 4294 > hide #2/F:42-47 4295 4296 > hide #2/F:37 4297 4298 > hide #!3 models 4299 4300 > hide #!1 models 4301 4302 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4303 > with Terns/20260111 IVC 4304 > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc" 4305 4306 Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 4307 1.07, shown at level 0.0524, step 2, values float32 4308 4309 > volume #4 step 1 4310 4311 > close #1,3 4312 4313 > volume copy #4 4314 4315 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384, 4316 pixel 1.07, shown at step 1, values float32 4317 4318 > volume #4 level 0.1491 4319 4320 > volume #1 level 0.154 4321 4322 > color #1 lightpink transparency 60 4323 4324 > color #4 lightskyblue transparency 60 4325 4326 > volume #4 level 0.2217 4327 4328 > volume #1 level 0.2217 4329 4330 > hide #2/E:1-5 4331 4332 > hide #2/E:10 4333 4334 > volume zone #1 nearAtoms #2/D range 4 4335 4336 > volume zone #4 nearAtoms #2/A range 4 4337 4338 > volume #4 level 0.1879 4339 4340 > volume #4 level 0.1927 4341 4342 > volume #4 level 0.212 4343 4344 > volume zone #4 nearAtoms #2/A range 2.5 4345 4346 > volume zone #1 nearAtoms #2/D range 2.5 4347 4348 > hide #2/A 4349 4350 > hide #2/D 4351 4352 > volume #4 level 0.1854 4353 4354 > volume #1 level 0.1951 4355 4356 > nucleotides fill 4357 4358 > style nucleic stick 4359 4360 Changed 2155 atom styles 4361 4362 > color byhetero 4363 4364 > nucleotides atoms 4365 4366 > style nucleic stick 4367 4368 Changed 2155 atom styles 4369 4370 > volume #1 level 0.1612 4371 4372 > select #2/A:434 4373 4374 11 atoms, 10 bonds, 1 residue, 1 model selected 4375 4376 > show (sel-residues & sidechain) target ab 4377 4378 > volume #4 level 0.2 4379 4380 > volume #4 level 0.1927 4381 4382 > volume #4 level 0.1975 4383 4384 > select #2/A:405 4385 4386 9 atoms, 8 bonds, 1 residue, 1 model selected 4387 4388 > show (sel-residues & sidechain) target ab 4389 4390 > select #2/D:159 4391 4392 6 atoms, 5 bonds, 1 residue, 1 model selected 4393 4394 > show (sel-residues & sidechain) target ab 4395 4396 > volume zone #4 nearAtoms #2/A range 23 4397 4398 > volume zone #4 nearAtoms #2/A range 2.3 4399 4400 > volume zone #4 nearAtoms #2/A range 2 4401 4402 > volume zone #4 nearAtoms #2/A range 2.3 4403 4404 > volume zone #4 nearAtoms #2/A range 2 4405 4406 > select add #2 4407 4408 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 4409 4410 > select subtract #2 4411 4412 Nothing selected 4413 4414 > lighting full 4415 4416 > ui tool show "Side View" 4417 4418 > hbonds reveal true 4419 4420 3027 hydrogen bonds found 4421 4422 > ~hbonds 4423 4424 > undo 4425 4426 [Repeated 3 time(s)] 4427 4428 > hide #2 4429 4430 > show #2/E:5-9 4431 4432 > show #2/F:38-41 4433 4434 > hide #2/E:5 4435 4436 > hide #2/E:6 4437 4438 > select #2/D:159 4439 4440 6 atoms, 5 bonds, 1 residue, 1 model selected 4441 4442 > show (sel-residues & sidechain) target ab 4443 4444 > select #2/A:434 4445 4446 11 atoms, 10 bonds, 1 residue, 1 model selected 4447 4448 > show (sel-residues & sidechain) target ab 4449 4450 > select #2/A:405 4451 4452 9 atoms, 8 bonds, 1 residue, 1 model selected 4453 4454 > show (sel-residues & sidechain) target ab 4455 4456 > select add #2 4457 4458 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 4459 4460 > select subtract #2 4461 4462 Nothing selected 4463 4464 > cartoon hide 4465 4466 > select add #2 4467 4468 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 4469 4470 > select subtract #2 4471 4472 Nothing selected 4473 4474 > volume #4 level 0.2175 4475 4476 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4477 > with Terns/20260111 IVC 4478 > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc" 4479 4480 Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel 4481 1.07, shown at level 0.0524, step 2, values float32 4482 4483 > color #3 #f7f9fbff models 4484 4485 > color #3 #caccce8c models 4486 4487 > volume #3 step 1 4488 4489 > volume #3 level 0.1426 4490 4491 > color #3 lighskyblue transparency 60 4492 4493 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 4494 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 4495 'fromcartoons', 'fromribbons', or 'random' or a keyword 4496 4497 > select add #3 4498 4499 4 models selected 4500 4501 > ui tool show "Color Actions" 4502 4503 > color sel light sky blue 4504 4505 > ui tool show "Color Actions" 4506 4507 > volume #3 color #87cefa66 4508 4509 > volume #3 level 0.1376 4510 4511 > volume #4 level 0.1377 4512 4513 > volume zone #4 nearAtoms #2/A range 3 4514 4515 > volume #3 level 0.1526 4516 4517 > volume #4 level 0.1477 4518 4519 > volume #4 level 0.2 4520 4521 > volume #1 level 0.1762 4522 4523 > volume #1 level 0.2484 4524 4525 > lighting full 4526 4527 > lighting flat 4528 4529 > volume #4 level 0.21 4530 4531 > volume #4 level 0.2274 4532 4533 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4534 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM1.cxs" 4535 4536 ——— End of log from Sun Feb 1 21:27:29 2026 ——— 4537 4538 > view name session-start 4539 4540 opened ChimeraX session 4541 4542 > select #2/A:1-404,406-433,435-600 4543 4544 4458 atoms, 4560 bonds, 1 pseudobond, 548 residues, 2 models selected 4545 4546 > surface (#!2 & sel) 4547 4548 > hide #!4 models 4549 4550 > surface sel transparency 90 4551 4552 > hide #!1 models 4553 4554 > select #2/D:1-158, 160-500 4555 4556 2432 atoms, 2489 bonds, 296 residues, 1 model selected 4557 4558 > surface sel 4559 4560 > surface sel transparency 90 4561 4562 > undo 4563 4564 > surface #2/A transparecy 90 4565 4566 Expected a keyword 4567 4568 > surface #2/A transparency 90 4569 4570 > surface #2/D transparency 90 4571 4572 > ui tool show "Side View" 4573 4574 > hide #2/E:6 4575 4576 > hide #2/F:41 4577 4578 > select add #2 4579 4580 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 7 models selected 4581 4582 > select subtract #2 4583 4584 2 models selected 4585 4586 > show #2/A:532 & ~@N,CA,C,O 4587 4588 > show #2/A:532 & ~@N,C,O 4589 4590 > save /Users/xuchengtao/Desktop/image216.png supersample 3 4591 4592 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4593 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM3.cxs" 4594 4595 > save /Users/xuchengtao/Desktop/image217.png supersample 3 4596 4597 > lighting soft 4598 4599 > lighting full 4600 4601 > lighting simple 4602 4603 > lighting soft 4604 4605 > lighting simple 4606 4607 > lighting soft 4608 4609 > ui tool show "Color Actions" 4610 4611 > color #2/F dodgerblue 4612 4613 > color byhetero 4614 4615 > undo 4616 4617 > color #2/F byhetero 4618 4619 > save /Users/xuchengtao/Desktop/image218.png supersample 3 4620 4621 > save /Users/xuchengtao/Desktop/image219.png supersample 3 4622 4623 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4624 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM2.cxs" 4625 4626 > close session 4627 4628 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4629 > with Terns/20260111 IVC 4630 > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb" 4631 4632 Chain information for merged_real_space_refined_011.pdb #1 4633 --- 4634 Chain | Description 4635 A | No description available 4636 C H I J K L | No description available 4637 D | No description available 4638 E | No description available 4639 F | No description available 4640 G | No description available 4641 M | No description available 4642 N O P Q R | No description available 4643 S | No description available 4644 4645 4646 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4647 > with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb" 4648 4649 Summary of feedback from opening 4650 /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with 4651 Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb 4652 --- 4653 warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 4654 4655 Chain information for merged_ivc_apo_refine_007.pdb #2 4656 --- 4657 Chain | Description 4658 A | No description available 4659 B | No description available 4660 C | No description available 4661 D | No description available 4662 E F G H | No description available 4663 I | No description available 4664 J | No description available 4665 K L M | No description available 4666 N | No description available 4667 O | No description available 4668 P | No description available 4669 Q | No description available 4670 R | No description available 4671 S | No description available 4672 4673 4674 > combine #1 4675 4676 > combine #2 4677 4678 > hide 4679 4680 > show #3/A 4681 4682 > show #4/A 4683 4684 > style stick 4685 4686 Changed 124372 atom styles 4687 4688 > color byhetero 4689 4690 > show #3/E:1-10 4691 4692 > show #3/F:37-47 4693 4694 > mmaker #4/A to #3/A 4695 4696 Parameters 4697 --- 4698 Chain pairing | bb 4699 Alignment algorithm | Needleman-Wunsch 4700 Similarity matrix | BLOSUM-62 4701 SS fraction | 0.3 4702 Gap open (HH/SS/other) | 18/18/6 4703 Gap extend | 1 4704 SS matrix | | | H | S | O 4705 ---|---|---|--- 4706 H | 6 | -9 | -6 4707 S | | 6 | -6 4708 O | | | 4 4709 Iteration cutoff | 2 4710 4711 Matchmaker copy of merged_real_space_refined_011.pdb, chain A (#3) with copy 4712 of merged_ivc_apo_refine_007.pdb, chain A (#4), sequence alignment score = 4713 2305.8 4714 RMSD between 212 pruned atom pairs is 1.103 angstroms; (across all 504 pairs: 4715 3.208) 4716 4717 4718 > show cartoons 4719 4720 > undo 4721 4722 > hide #!4 models 4723 4724 > show #!4 models 4725 4726 > hide #!4 models 4727 4728 > hide #!2 models 4729 4730 > hide #!1 models 4731 4732 > select #3/A 4733 4734 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 4735 4736 > show sel cartoons 4737 4738 > ui tool show "Color Actions" 4739 4740 > color sel light sky blue 4741 4742 > color sel byhetero 4743 4744 > cartoon style (#!3 & sel) xsection oval modeHelix default 4745 4746 > cartoon style (#!3 & sel) modeHelix tube sides 20 4747 4748 > hide (#!3 & sel) target a 4749 4750 > color #3/A transparency 10 4751 4752 > select #3/E,F 4753 4754 1172 atoms, 1312 bonds, 57 residues, 1 model selected 4755 4756 > show sel cartoons 4757 4758 > undo 4759 4760 > select #3/E:1-10 4761 4762 200 atoms, 222 bonds, 10 residues, 1 model selected 4763 4764 > show sel cartoons 4765 4766 > select #3/F:37-47 4767 4768 232 atoms, 261 bonds, 11 residues, 1 model selected 4769 4770 > show sel cartoons 4771 4772 > ui tool show "Color Actions" 4773 4774 > color sel dodger blue 4775 4776 > color sel byhetero 4777 4778 > select #3/E:1-10 4779 4780 200 atoms, 222 bonds, 10 residues, 1 model selected 4781 4782 > ui tool show "Color Actions" 4783 4784 > color sel hot pink 4785 4786 > color sel byhetero 4787 4788 > nucleotides sel fill 4789 4790 > style nucleic & sel stick 4791 4792 Changed 200 atom styles 4793 4794 > select #3/F:37-47 4795 4796 232 atoms, 261 bonds, 11 residues, 1 model selected 4797 4798 > nucleotides sel fill 4799 4800 > style nucleic & sel stick 4801 4802 Changed 232 atom styles 4803 4804 > select #4/A 4805 4806 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected 4807 4808 > show #!3 cartoons 4809 4810 > undo 4811 4812 > show sel cartoons 4813 4814 > show #!4 models 4815 4816 > hide sel atoms 4817 4818 > color sel white transcparency 70 4819 4820 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 4821 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 4822 4823 > color sel white transparency 70 4824 4825 > lighting soft 4826 4827 > select add #4 4828 4829 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 4830 4831 > select subtract #4 4832 4833 Nothing selected 4834 4835 > mmaker #4/A: 70, 93, 94, 115,146,147,159 4836 4837 > matchmaker #4/A: 70, 93, 94, 115,146,147,159 4838 4839 Missing required "to" argument 4840 4841 > mmaker #4/A: 70, 93, 94, 115,146,147,159 to #3/A 4842 4843 Parameters 4844 --- 4845 Chain pairing | bb 4846 Alignment algorithm | Needleman-Wunsch 4847 Similarity matrix | BLOSUM-62 4848 SS fraction | 0.3 4849 Gap open (HH/SS/other) | 18/18/6 4850 Gap extend | 1 4851 SS matrix | | | H | S | O 4852 ---|---|---|--- 4853 H | 6 | -9 | -6 4854 S | | 6 | -6 4855 O | | | 4 4856 Iteration cutoff | 2 4857 4858 Matchmaker copy of merged_real_space_refined_011.pdb, chain A (#3) with copy 4859 of merged_ivc_apo_refine_007.pdb, chain A (#4), sequence alignment score = 4860 45.3 4861 RMSD between 7 pruned atom pairs is 0.873 angstroms; (across all 7 pairs: 4862 0.873) 4863 4864 4865 > select #4/A 4866 4867 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected 4868 4869 > cartoon style (#!4 & sel) modeHelix tube sides 20 4870 4871 > select add #4 4872 4873 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 4874 4875 > select subtract #4 4876 4877 Nothing selected 4878 4879 > select #3/A 4880 4881 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 4882 4883 > color sel transparency 30 4884 4885 > select add #3 4886 4887 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 4888 4889 > select subtract #3 4890 4891 Nothing selected 4892 4893 > save /Users/xuchengtao/Desktop/image220.png supersample 3 4894 4895 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 4896 > with Terns/20260111 IVC 4897 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_1.cxs" 4898 4899 > measure motion #3/A toModel #4/A showVectors true color cyan 4900 4901 Missing or invalid "surface" argument: Require 1 surface, got 0 4902 4903 > measure rotation #3/A toModel #4/A showVectors true color cyan 4904 4905 Expected a keyword 4906 4907 > measure rotation #3/A toModel #4/A showAxis true color cyan 4908 4909 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 4910 merged_ivc_apo_refine_007.pdb #4 coordinates: 4911 Matrix rotation and translation 4912 -0.99736182 -0.00562907 0.07237203 460.06370117 4913 0.01683128 0.95188599 0.30598983 -17.09119514 4914 -0.07061236 0.30640068 -0.94928000 404.90437477 4915 Axis 0.00283863 0.98788229 0.15517902 4916 Axis point 237.34717297 0.00000000 195.36024542 4917 Rotation angle (degrees) 175.84992537 4918 Shift along axis 47.25452561 4919 4920 4921 > measure rotation #3/A toModel #4/A coordinateSystem#4/A showAxis true color 4922 > cyan 4923 4924 Expected a keyword 4925 4926 > measure rotation #3/A toModel #4/A coordinateSystem #4/A showAxis true color 4927 > cyan 4928 4929 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 4930 merged_ivc_apo_refine_007.pdb #4 in copy of merged_ivc_apo_refine_007.pdb #4 4931 coordinate system: 4932 Matrix rotation and translation 4933 -0.99736182 -0.00562907 0.07237203 460.06370117 4934 0.01683128 0.95188599 0.30598983 -17.09119514 4935 -0.07061236 0.30640068 -0.94928000 404.90437477 4936 Axis 0.00283863 0.98788229 0.15517902 4937 Axis point 237.34717297 0.00000000 195.36024542 4938 Rotation angle (degrees) 175.84992537 4939 Shift along axis 47.25452561 4940 4941 4942 > measure rotation #3/A toModel #4/A coordinateSystem #4/A showSlabs true 4943 > color cyan 4944 4945 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 4946 merged_ivc_apo_refine_007.pdb #4 in copy of merged_ivc_apo_refine_007.pdb #4 4947 coordinate system: 4948 Matrix rotation and translation 4949 -0.99736182 -0.00562907 0.07237203 460.06370117 4950 0.01683128 0.95188599 0.30598983 -17.09119514 4951 -0.07061236 0.30640068 -0.94928000 404.90437477 4952 Axis 0.00283863 0.98788229 0.15517902 4953 Axis point 237.34717297 0.00000000 195.36024542 4954 Rotation angle (degrees) 175.84992537 4955 Shift along axis 47.25452561 4956 4957 4958 > measure rotation #3/A toModel #4/A showSlabs true color cyan 4959 4960 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 4961 merged_ivc_apo_refine_007.pdb #4 coordinates: 4962 Matrix rotation and translation 4963 -0.99736182 -0.00562907 0.07237203 460.06370117 4964 0.01683128 0.95188599 0.30598983 -17.09119514 4965 -0.07061236 0.30640068 -0.94928000 404.90437477 4966 Axis 0.00283863 0.98788229 0.15517902 4967 Axis point 237.34717297 0.00000000 195.36024542 4968 Rotation angle (degrees) 175.84992537 4969 Shift along axis 47.25452561 4970 4971 4972 > measure rotation #3 toModel #4/A showSlabs true color cyan 4973 4974 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 4975 merged_ivc_apo_refine_007.pdb #4 coordinates: 4976 Matrix rotation and translation 4977 -0.99736182 -0.00562907 0.07237203 460.06370117 4978 0.01683128 0.95188599 0.30598983 -17.09119514 4979 -0.07061236 0.30640068 -0.94928000 404.90437477 4980 Axis 0.00283863 0.98788229 0.15517902 4981 Axis point 237.34717297 0.00000000 195.36024542 4982 Rotation angle (degrees) 175.84992537 4983 Shift along axis 47.25452561 4984 4985 4986 > measure rotation #3 toModel #4 showSlabs true color cyan 4987 4988 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 4989 merged_ivc_apo_refine_007.pdb #4 coordinates: 4990 Matrix rotation and translation 4991 -0.99736182 -0.00562907 0.07237203 460.06370117 4992 0.01683128 0.95188599 0.30598983 -17.09119514 4993 -0.07061236 0.30640068 -0.94928000 404.90437477 4994 Axis 0.00283863 0.98788229 0.15517902 4995 Axis point 237.34717297 0.00000000 195.36024542 4996 Rotation angle (degrees) 175.84992537 4997 Shift along axis 47.25452561 4998 4999 5000 > measure rotation #3 toModel #4 showSlabs true color cyan 5001 5002 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 5003 merged_ivc_apo_refine_007.pdb #4 coordinates: 5004 Matrix rotation and translation 5005 -0.99736182 -0.00562907 0.07237203 460.06370117 5006 0.01683128 0.95188599 0.30598983 -17.09119514 5007 -0.07061236 0.30640068 -0.94928000 404.90437477 5008 Axis 0.00283863 0.98788229 0.15517902 5009 Axis point 237.34717297 0.00000000 195.36024542 5010 Rotation angle (degrees) 175.84992537 5011 Shift along axis 47.25452561 5012 5013 5014 > measure rotation #3 toModel #4 showSlabs true color cyan 5015 5016 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 5017 merged_ivc_apo_refine_007.pdb #4 coordinates: 5018 Matrix rotation and translation 5019 -0.99736182 -0.00562907 0.07237203 460.06370117 5020 0.01683128 0.95188599 0.30598983 -17.09119514 5021 -0.07061236 0.30640068 -0.94928000 404.90437477 5022 Axis 0.00283863 0.98788229 0.15517902 5023 Axis point 237.34717297 0.00000000 195.36024542 5024 Rotation angle (degrees) 175.84992537 5025 Shift along axis 47.25452561 5026 5027 5028 > measure rotation #3 toModel #4 showSlabs true color cyan 5029 5030 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 5031 merged_ivc_apo_refine_007.pdb #4 coordinates: 5032 Matrix rotation and translation 5033 -0.99736182 -0.00562907 0.07237203 460.06370117 5034 0.01683128 0.95188599 0.30598983 -17.09119514 5035 -0.07061236 0.30640068 -0.94928000 404.90437477 5036 Axis 0.00283863 0.98788229 0.15517902 5037 Axis point 237.34717297 0.00000000 195.36024542 5038 Rotation angle (degrees) 175.84992537 5039 Shift along axis 47.25452561 5040 5041 5042 > measure rotation #3 toModel #4 showSlabs true color cyan 5043 5044 Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of 5045 merged_ivc_apo_refine_007.pdb #4 coordinates: 5046 Matrix rotation and translation 5047 -0.99736182 -0.00562907 0.07237203 460.06370117 5048 0.01683128 0.95188599 0.30598983 -17.09119514 5049 -0.07061236 0.30640068 -0.94928000 404.90437477 5050 Axis 0.00283863 0.98788229 0.15517902 5051 Axis point 237.34717297 0.00000000 195.36024542 5052 Rotation angle (degrees) 175.84992537 5053 Shift along axis 47.25452561 5054 5055 5056 > close #5-22 5057 5058 > morph #4/A,#3/A frames 2 showVectors true 5059 5060 Missing or invalid "structures" argument: only initial part "#4/A" of atom 5061 specifier valid 5062 5063 > morph #4/A #3/A frames 2 showVectors true 5064 5065 Expected a keyword 5066 5067 > morph #4/A #3/A frames 60 5068 5069 models have different number of chains, 19 (Morph - copy of 5070 merged_ivc_apo_refine_007.pdb #/A,Morph - copy of 5071 merged_ivc_apo_refine_007.pdb #/B,Morph - copy of 5072 merged_ivc_apo_refine_007.pdb #/C,Morph - copy of 5073 merged_ivc_apo_refine_007.pdb #/D,Morph - copy of 5074 merged_ivc_apo_refine_007.pdb #/E,Morph - copy of 5075 merged_ivc_apo_refine_007.pdb #/F,Morph - copy of 5076 merged_ivc_apo_refine_007.pdb #/G,Morph - copy of 5077 merged_ivc_apo_refine_007.pdb #/H,Morph - copy of 5078 merged_ivc_apo_refine_007.pdb #/I,Morph - copy of 5079 merged_ivc_apo_refine_007.pdb #/J,Morph - copy of 5080 merged_ivc_apo_refine_007.pdb #/K,Morph - copy of 5081 merged_ivc_apo_refine_007.pdb #/L,Morph - copy of 5082 merged_ivc_apo_refine_007.pdb #/M,Morph - copy of 5083 merged_ivc_apo_refine_007.pdb #/N,Morph - copy of 5084 merged_ivc_apo_refine_007.pdb #/O,Morph - copy of 5085 merged_ivc_apo_refine_007.pdb #/P,Morph - copy of 5086 merged_ivc_apo_refine_007.pdb #/Q,Morph - copy of 5087 merged_ivc_apo_refine_007.pdb #/R,Morph - copy of 5088 merged_ivc_apo_refine_007.pdb #/S) and 18 (copy of 5089 merged_real_space_refined_011.pdb #3/A,copy of 5090 merged_real_space_refined_011.pdb #3/C,copy of 5091 merged_real_space_refined_011.pdb #3/D,copy of 5092 merged_real_space_refined_011.pdb #3/E,copy of 5093 merged_real_space_refined_011.pdb #3/F,copy of 5094 merged_real_space_refined_011.pdb #3/G,copy of 5095 merged_real_space_refined_011.pdb #3/H,copy of 5096 merged_real_space_refined_011.pdb #3/I,copy of 5097 merged_real_space_refined_011.pdb #3/J,copy of 5098 merged_real_space_refined_011.pdb #3/K,copy of 5099 merged_real_space_refined_011.pdb #3/L,copy of 5100 merged_real_space_refined_011.pdb #3/M,copy of 5101 merged_real_space_refined_011.pdb #3/N,copy of 5102 merged_real_space_refined_011.pdb #3/O,copy of 5103 merged_real_space_refined_011.pdb #3/P,copy of 5104 merged_real_space_refined_011.pdb #3/Q,copy of 5105 merged_real_space_refined_011.pdb #3/R,copy of 5106 merged_real_space_refined_011.pdb #3/S) 5107 5108 > morph #4/A,#3/A frames 60 5109 5110 Missing or invalid "structures" argument: only initial part "#4/A" of atom 5111 specifier valid 5112 5113 > select #3/A 5114 5115 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5116 5117 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5118 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb" models #3 5119 > selectedOnly true relModel #3 5120 5121 > select #4/A 5122 5123 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected 5124 5125 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5126 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb" models #4 5127 > selectedOnly true relModel #3 5128 5129 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5130 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb" 5131 5132 Summary of feedback from opening 5133 /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with 5134 Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb 5135 --- 5136 warnings | Start residue of secondary structure not found: HELIX 19 19 LEU B 30 ASN B 46 1 17 5137 Start residue of secondary structure not found: HELIX 20 20 ARG B 51 THR B 60 5138 1 10 5139 Start residue of secondary structure not found: HELIX 21 21 LYS B 135 LEU B 5140 143 1 9 5141 Start residue of secondary structure not found: HELIX 22 22 GLN B 187 LYS B 5142 199 1 13 5143 Start residue of secondary structure not found: HELIX 23 23 PRO B 249 THR B 5144 257 1 9 5145 209 messages similar to the above omitted 5146 5147 Chain information for Cas10_apo.pdb #5 5148 --- 5149 Chain | Description 5150 A | No description available 5151 5152 5153 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5154 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb" 5155 5156 Summary of feedback from opening 5157 /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with 5158 Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb 5159 --- 5160 warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27 5161 Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88 5162 1 8 5163 Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C 5164 111 1 7 5165 Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C 5166 122 1 6 5167 Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C 5168 184 1 5 5169 203 messages similar to the above omitted 5170 5171 Chain information for Cas10_bound.pdb #6 5172 --- 5173 Chain | Description 5174 A | No description available 5175 5176 5177 > hide #!3 models 5178 5179 > hide #!4 models 5180 5181 > select add #4 5182 5183 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 5184 5185 > select subtract #4 5186 5187 Nothing selected 5188 5189 > select add #6 5190 5191 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5192 5193 > ui tool show "Color Actions" 5194 5195 > color sel light sky blue 5196 5197 > select add #5 5198 5199 8577 atoms, 8775 bonds, 4 pseudobonds, 1054 residues, 4 models selected 5200 5201 > select subtract #6 5202 5203 4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected 5204 5205 > ui tool show "Color Actions" 5206 5207 > color sel white 5208 5209 > color #5 #ffffffb3 5210 5211 > color #5 #ffffff4d 5212 5213 > select add #6 5214 5215 8577 atoms, 8775 bonds, 4 pseudobonds, 1054 residues, 4 models selected 5216 5217 > cartoon style (#!5-6 & sel) modeHelix tube sides 20 5218 5219 > select subtract #5 5220 5221 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5222 5223 > select subtract #6 5224 5225 Nothing selected 5226 5227 > morph #5,#6 frames 60 5228 5229 Missing or invalid "structures" argument: only initial part "#5" of atom 5230 specifier valid 5231 5232 > morph #5 #6 frames 60 5233 5234 Computed 61 frame morph #7 5235 5236 > coordset #7 1,61 5237 5238 > morph #5 #6 frames 30 5239 5240 Computed 31 frame morph #8 5241 5242 > coordset #8 1,31 5243 5244 > close #7 5245 5246 > select add #8 5247 5248 4095 atoms, 4189 bonds, 3 pseudobonds, 504 residues, 2 models selected 5249 5250 > ui tool show "Color Actions" 5251 5252 > color sel light sky blue 5253 5254 > select subtract #8 5255 5256 Nothing selected 5257 5258 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5259 > with Terns/20260111 IVC 5260 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_2_movie1.cxs" 5261 5262 ——— End of log from Mon Feb 2 10:29:38 2026 ——— 5263 5264 > view name session-start 5265 5266 opened ChimeraX session 5267 5268 > show #!3 models 5269 5270 > hide #!3 models 5271 5272 > show #!3 models 5273 5274 > hide #!3 models 5275 5276 > show #!3 models 5277 5278 > hide #!3 models 5279 5280 > show #!1 models 5281 5282 > show #1 5283 5284 > hide #!1 models 5285 5286 > show #!2 models 5287 5288 > show #2 5289 5290 > mmaker #2 to #1 5291 5292 Parameters 5293 --- 5294 Chain pairing | bb 5295 Alignment algorithm | Needleman-Wunsch 5296 Similarity matrix | BLOSUM-62 5297 SS fraction | 0.3 5298 Gap open (HH/SS/other) | 18/18/6 5299 Gap extend | 1 5300 SS matrix | | | H | S | O 5301 ---|---|---|--- 5302 H | 6 | -9 | -6 5303 S | | 6 | -6 5304 O | | | 4 5305 Iteration cutoff | 2 5306 5307 Matchmaker merged_real_space_refined_011.pdb, chain A (#1) with 5308 merged_ivc_apo_refine_007.pdb, chain A (#2), sequence alignment score = 2305.8 5309 RMSD between 212 pruned atom pairs is 1.103 angstroms; (across all 504 pairs: 5310 3.208) 5311 5312 5313 > show #!1 models 5314 5315 > hide #!1 models 5316 5317 > hide #!2 models 5318 5319 > show #!1 models 5320 5321 > show #!2 models 5322 5323 > hide #!1 models 5324 5325 > hide #!2 models 5326 5327 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5328 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb" 5329 5330 Summary of feedback from opening 5331 /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with 5332 Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb 5333 --- 5334 warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27 5335 Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88 5336 1 8 5337 Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C 5338 111 1 7 5339 Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C 5340 122 1 6 5341 Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C 5342 184 1 5 5343 203 messages similar to the above omitted 5344 5345 Chain information for Cas10_bound.pdb #7 5346 --- 5347 Chain | Description 5348 A | No description available 5349 5350 5351 > close session 5352 5353 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5354 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb" format pdb 5355 5356 Summary of feedback from opening 5357 /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with 5358 Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb 5359 --- 5360 warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27 5361 Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88 5362 1 8 5363 Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C 5364 111 1 7 5365 Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C 5366 122 1 6 5367 Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C 5368 184 1 5 5369 203 messages similar to the above omitted 5370 5371 Chain information for Cas10_bound.pdb #1 5372 --- 5373 Chain | Description 5374 A | No description available 5375 5376 5377 > select #1/A:1-335 5378 5379 2374 atoms, 2430 bonds, 1 pseudobond, 290 residues, 2 models selected 5380 5381 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5382 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_1_335.pdb" 5383 > selectedOnly true relModel #1 5384 5385 > select #1/A:335-437 5386 5387 801 atoms, 815 bonds, 103 residues, 1 model selected 5388 5389 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5390 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb" 5391 > selectedOnly true relModel #1 5392 5393 > select #1/A:437-900 5394 5395 1314 atoms, 1347 bonds, 159 residues, 1 model selected 5396 5397 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5398 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_437_Cterm.pdb" 5399 > relModel #1 5400 5401 > view matrix models #1,1,0,0,0.00059032,0,1,0,-0.020052,0,0,1,0.0076704 5402 5403 > select #1/A:50-180 5404 5405 1058 atoms, 1086 bonds, 131 residues, 1 model selected 5406 5407 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5408 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_50_180.pdb" 5409 > selectedOnly true relModel #1 5410 5411 > open 7tr8 5412 5413 7tr8 title: 5414 Cascade complex from type I-A CRISPR-Cas system [more info...] 5415 5416 Chain information for 7tr8 #2 5417 --- 5418 Chain | Description | UniProt 5419 A | CRISPR-associated helicase Cas3 | A0A5C0XNV5_PYRFU 10-516 5420 C | Cas8 | Q8U338_PYRFU 2-342 5421 D E F G H | Cas11a | Q8U332_PYRFU 2-109 5422 I J K L M N O | Cas7a | Q8U333_PYRFU 1-336 5423 P | Cas5a | A0A5C0XNV9_PYRFU 1-256 5424 Q | CRISPR-associated endonuclease Cas3-HD | CS3HD_PYRFU 2-216 5425 R | crRNA (45-MER) | 5426 5427 Non-standard residues in 7tr8 #2 5428 --- 5429 NI — nickel (II) ion 5430 5431 5432 > select add #1 5433 5434 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5435 5436 > hide #!1 models 5437 5438 > select subtract #1 5439 5440 Nothing selected 5441 5442 > style #!2 stick 5443 5444 Changed 33581 atom styles 5445 5446 > show #!2 atoms 5447 5448 > show #!2 cartoons 5449 5450 > color #!2 byhetero 5451 5452 > hide #!2 atoms 5453 5454 > cartoon style #2 modeHelix tube sides 20 5455 5456 > show #!2 cartoons 5457 5458 > show #!2 atoms 5459 5460 > hide #!2 cartoons 5461 5462 > show #!2 atoms 5463 5464 > show #!2 cartoons 5465 5466 > hide #!2 atoms 5467 5468 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5469 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb" 5470 5471 Summary of feedback from opening 5472 /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with 5473 Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb 5474 --- 5475 warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 40 SER A 44 1 5 5476 Start residue of secondary structure not found: HELIX 2 2 LEU A 67 PHE A 81 1 5477 15 5478 Start residue of secondary structure not found: HELIX 3 3 GLY A 84 ILE A 92 1 5479 9 5480 Start residue of secondary structure not found: HELIX 4 4 GLN A 120 PHE A 130 5481 1 11 5482 Start residue of secondary structure not found: HELIX 5 5 LYS A 138 LYS A 144 5483 1 7 5484 18 messages similar to the above omitted 5485 Cannot find LINK/SSBOND residue CYS (152 ) 5486 5487 Chain information for Cas10_bound_335_437.pdb #3 5488 --- 5489 Chain | Description 5490 A | No description available 5491 5492 5493 > mmaker #3 to #2 5494 5495 Parameters 5496 --- 5497 Chain pairing | bb 5498 Alignment algorithm | Needleman-Wunsch 5499 Similarity matrix | BLOSUM-62 5500 SS fraction | 0.3 5501 Gap open (HH/SS/other) | 18/18/6 5502 Gap extend | 1 5503 SS matrix | | | H | S | O 5504 ---|---|---|--- 5505 H | 6 | -9 | -6 5506 S | | 6 | -6 5507 O | | | 4 5508 Iteration cutoff | 2 5509 5510 Matchmaker 7tr8, chain A (#2) with Cas10_bound_335_437.pdb, chain A (#3), 5511 sequence alignment score = 65.9 5512 RMSD between 7 pruned atom pairs is 1.051 angstroms; (across all 100 pairs: 5513 14.603) 5514 5515 5516 > close #2 5517 5518 > open /Users/xuchengtao/Downloads/AF-A0A7V6NIE4-F1-model_v6.pdb 5519 5520 Summary of feedback from opening 5521 /Users/xuchengtao/Downloads/AF-A0A7V6NIE4-F1-model_v6.pdb 5522 --- 5523 warning | Ignored bad PDB record found on line 38 5524 DBREF XXXX A 1 478 UNP A0A7V6NIE4 A0A7V6NIE4_9CLOT 1 478 5525 5526 AF-A0A7V6NIE4-F1-model_v6.pdb title: 5527 Alphafold monomer V2.0 prediction for type I-B crispr-associated protein 5528 CAS8B1/CST1 (A0A7V6NIE4) [more info...] 5529 5530 Chain information for AF-A0A7V6NIE4-F1-model_v6.pdb #2 5531 --- 5532 Chain | Description 5533 A | type I-B crispr-associated protein CAS8B1/CST1 5534 5535 Computing secondary structure 5536 5537 > mmaker #3 to #2 5538 5539 Parameters 5540 --- 5541 Chain pairing | bb 5542 Alignment algorithm | Needleman-Wunsch 5543 Similarity matrix | BLOSUM-62 5544 SS fraction | 0.3 5545 Gap open (HH/SS/other) | 18/18/6 5546 Gap extend | 1 5547 SS matrix | | | H | S | O 5548 ---|---|---|--- 5549 H | 6 | -9 | -6 5550 S | | 6 | -6 5551 O | | | 4 5552 Iteration cutoff | 2 5553 5554 Matchmaker AF-A0A7V6NIE4-F1-model_v6.pdb, chain A (#2) with 5555 Cas10_bound_335_437.pdb, chain A (#3), sequence alignment score = 104.6 5556 RMSD between 26 pruned atom pairs is 0.744 angstroms; (across all 98 pairs: 5557 9.407) 5558 5559 5560 > ui tool show "Selection Inspector" 5561 5562 > center #2 5563 5564 Unknown command: center #2 5565 5566 > center 5567 5568 Unknown command: center 5569 5570 > cofr 5571 5572 Center of rotation: -9.0432 -2.4508 11.129 front center 5573 5574 > cofr #2 5575 5576 > show #!1 models 5577 5578 > hide #!1 models 5579 5580 > show #!1 models 5581 5582 > select #1/A:55-150 5583 5584 785 atoms, 809 bonds, 96 residues, 1 model selected 5585 5586 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5587 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_55_150.pdb" 5588 > models #1 selectedOnly true relModel #1 5589 5590 > select #1/A:437-500 5591 5592 539 atoms, 550 bonds, 64 residues, 1 model selected 5593 5594 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 5595 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_437_Cterm.pdb" 5596 > models #1 selectedOnly true relModel #1 5597 5598 > open 6TH 5599 5600 '6TH' has no suffix 5601 5602 > open 6THH 5603 5604 Summary of feedback from opening 6THH fetched from pdb 5605 --- 5606 note | Fetching compressed mmCIF 6thh from http://files.rcsb.org/download/6thh.cif 5607 5608 6thh title: 5609 Crystal structure of type I-D CRISPR-Cas nuclease Cas10d in complex with the 5610 SIRV3 AcrID1 (gp02) anti-CRISPR protein [more info...] 5611 5612 Chain information for 6thh #4 5613 --- 5614 Chain | Description | UniProt 5615 A B | SIRV3 AcrID1 (gp02) anti-CRISPR protein | A0A1B3SN05_9VIRU 1-96 5616 C | CRISPR-associated protein, CscA | M9U4Y8_SULIS 1-847 5617 5618 Non-standard residues in 6thh #4 5619 --- 5620 PO4 — phosphate ion 5621 ZN — zinc ion 5622 5623 6thh mmCIF Assemblies 5624 --- 5625 1| author_defined_assembly 5626 5627 5628 > select add #1 5629 5630 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5631 5632 > select add #4 5633 5634 12721 atoms, 12994 bonds, 8 pseudobonds, 1560 residues, 6 models selected 5635 5636 > mmaker #1 to #4 5637 5638 Parameters 5639 --- 5640 Chain pairing | bb 5641 Alignment algorithm | Needleman-Wunsch 5642 Similarity matrix | BLOSUM-62 5643 SS fraction | 0.3 5644 Gap open (HH/SS/other) | 18/18/6 5645 Gap extend | 1 5646 SS matrix | | | H | S | O 5647 ---|---|---|--- 5648 H | 6 | -9 | -6 5649 S | | 6 | -6 5650 O | | | 4 5651 Iteration cutoff | 2 5652 5653 Matchmaker 6thh, chain C (#4) with Cas10_bound.pdb, chain A (#1), sequence 5654 alignment score = 154.1 5655 RMSD between 22 pruned atom pairs is 1.050 angstroms; (across all 409 pairs: 5656 40.667) 5657 5658 5659 > select subtract #4 5660 5661 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5662 5663 > select subtract #1 5664 5665 Nothing selected 5666 5667 > cofr #4/C 5668 5669 > open 6Yes 5670 5671 Summary of feedback from opening 6Yes fetched from pdb 5672 --- 5673 note | Fetching compressed mmCIF 6yes from http://files.rcsb.org/download/6yes.cif 5674 5675 6yes title: 5676 Crystal structure of type I-D CRISPR-Cas nuclease Cas10d [more info...] 5677 5678 Chain information for 6yes #5 5679 --- 5680 Chain | Description | UniProt 5681 A B | CRISPR-associated protein, CscA | M9U4Y8_SULIS 1-847 5682 5683 Non-standard residues in 6yes #5 5684 --- 5685 ZN — zinc ion 5686 5687 6yes mmCIF Assemblies 5688 --- 5689 1| author_defined_assembly 5690 2| author_defined_assembly 5691 5692 5693 > select #5/A:14-847 5694 5695 6325 atoms, 6448 bonds, 3 pseudobonds, 791 residues, 2 models selected 5696 5697 > hide #2 models 5698 5699 > hide #3 models 5700 5701 > mmaker #1 to #5 5702 5703 Parameters 5704 --- 5705 Chain pairing | bb 5706 Alignment algorithm | Needleman-Wunsch 5707 Similarity matrix | BLOSUM-62 5708 SS fraction | 0.3 5709 Gap open (HH/SS/other) | 18/18/6 5710 Gap extend | 1 5711 SS matrix | | | H | S | O 5712 ---|---|---|--- 5713 H | 6 | -9 | -6 5714 S | | 6 | -6 5715 O | | | 4 5716 Iteration cutoff | 2 5717 5718 Matchmaker 6yes, chain A (#5) with Cas10_bound.pdb, chain A (#1), sequence 5719 alignment score = 135.7 5720 RMSD between 11 pruned atom pairs is 1.193 angstroms; (across all 431 pairs: 5721 32.783) 5722 5723 5724 > hide #!1 models 5725 5726 > select add #5 5727 5728 12534 atoms, 12775 bonds, 10 pseudobonds, 1569 residues, 4 models selected 5729 5730 > show #!1 models 5731 5732 > select subtract #5 5733 5734 Nothing selected 5735 5736 > select #5/B:14-844 5737 5738 6207 atoms, 6327 bonds, 2 pseudobonds, 776 residues, 2 models selected 5739 5740 > hide #5/B cartoons 5741 5742 > hide #5/B 5743 5744 > select add #1 5745 5746 10685 atoms, 10909 bonds, 3 pseudobonds, 1326 residues, 4 models selected 5747 5748 > select add #5 5749 5750 17012 atoms, 17357 bonds, 11 pseudobonds, 2119 residues, 6 models selected 5751 5752 > select subtract #5 5753 5754 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5755 5756 > view matrix models 5757 > #1,0.66911,0.7076,-0.22714,-278.82,-0.74159,0.61589,-0.26594,125.06,-0.048282,0.34639,0.93685,-320.82 5758 5759 > view matrix models 5760 > #1,0.10857,0.58169,-0.80613,28.689,-0.99406,0.069538,-0.083697,235.53,0.0073718,0.81043,0.58578,-325.5 5761 5762 > view matrix models 5763 > #1,-0.049471,0.44584,-0.89374,113.79,-0.99529,0.052664,0.081364,193.82,0.083344,0.89356,0.44114,-318.66 5764 5765 > view matrix models 5766 > #1,0.21172,0.80335,-0.5566,-104.87,-0.96736,0.091101,-0.23648,267.3,-0.13927,0.5885,0.79641,-308.2 5767 5768 > view matrix models 5769 > #1,0.30895,0.91561,-0.25732,-216.38,-0.8958,0.18925,-0.40214,261.48,-0.31951,0.35475,0.87867,-230.9 5770 5771 > select subtract #1 5772 5773 Nothing selected 5774 5775 > select add #1 5776 5777 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5778 5779 > select subtract #1 5780 5781 Nothing selected 5782 5783 > cofr #1 5784 5785 > select add #1 5786 5787 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5788 5789 > view matrix models 5790 > #1,0.30895,0.91561,-0.25732,-257.59,-0.8958,0.18925,-0.40214,262.52,-0.31951,0.35475,0.87867,-278.37 5791 5792 > ui tool show "Show Sequence Viewer" 5793 5794 > sequence chain #4/C #5/A #5/B 5795 5796 Alignment identifier is 1 5797 5798 > close #4 5799 5800 > ui tool show "Show Sequence Viewer" 5801 5802 > sequence chain #5/A #5/B 5803 5804 Alignment identifier is 1 5805 5806 > select #5/A-B:93 5807 5808 20 atoms, 20 bonds, 2 residues, 1 model selected 5809 5810 > select #5/A-B:93-94 5811 5812 36 atoms, 36 bonds, 4 residues, 1 model selected 5813 5814 > show sel atoms 5815 5816 > select add #5 5817 5818 12534 atoms, 12775 bonds, 10 pseudobonds, 1569 residues, 4 models selected 5819 5820 > show sel atoms 5821 5822 > close #5 5823 5824 > open 7SBA 5825 5826 Summary of feedback from opening 7SBA fetched from pdb 5827 --- 5828 note | Fetching compressed mmCIF 7sba from http://files.rcsb.org/download/7sba.cif 5829 5830 7sba title: 5831 Structure of type I-D Cascade bound to a dsDNA target [more info...] 5832 5833 Chain information for 7sba #4 5834 --- 5835 Chain | Description | UniProt 5836 A B C D E F G | Cas7d | Q6ZEI6_SYNY3 1-329 5837 H | Cas5d | Q6ZEI5_SYNY3 1-254 5838 I | Cas10d | Q6ZEI7_SYNY3 1-975 5839 J K | Cas11d | Q6ZEI7_SYNY3 1-146 5840 X | DNA target strand | 5841 Y | DNA non-target strand | 5842 Z | crRNA | 5843 5844 5845 > sequence chain #4/I 5846 5847 Alignment identifier is 4/I 5848 5849 > mmaker #1 to #4/I 5850 5851 Parameters 5852 --- 5853 Chain pairing | bb 5854 Alignment algorithm | Needleman-Wunsch 5855 Similarity matrix | BLOSUM-62 5856 SS fraction | 0.3 5857 Gap open (HH/SS/other) | 18/18/6 5858 Gap extend | 1 5859 SS matrix | | | H | S | O 5860 ---|---|---|--- 5861 H | 6 | -9 | -6 5862 S | | 6 | -6 5863 O | | | 4 5864 Iteration cutoff | 2 5865 5866 Matchmaker 7sba, chain I (#4) with Cas10_bound.pdb, chain A (#1), sequence 5867 alignment score = 131.1 5868 RMSD between 14 pruned atom pairs is 1.230 angstroms; (across all 409 pairs: 5869 37.869) 5870 5871 5872 > cofr #4/I 5873 5874 > show #!1,4 atoms 5875 5876 > hide #!1,4 atoms 5877 5878 > show #!1,4 cartoons 5879 5880 > select #4/I:975 5881 5882 9 atoms, 8 bonds, 1 residue, 1 model selected 5883 5884 > select #4/I:767-975 5885 5886 1719 atoms, 1747 bonds, 209 residues, 1 model selected 5887 5888 > select add #4 5889 5890 30651 atoms, 31399 bonds, 35 pseudobonds, 3741 residues, 3 models selected 5891 5892 > select subtract #4 5893 5894 Nothing selected 5895 5896 > select clear 5897 5898 > select #4/I:2-226 5899 5900 1300 atoms, 1329 bonds, 3 pseudobonds, 159 residues, 2 models selected 5901 5902 > select #4/I:115-116 5903 5904 18 atoms, 18 bonds, 2 residues, 1 model selected 5905 5906 > select #4/I:115-116 5907 5908 18 atoms, 18 bonds, 2 residues, 1 model selected 5909 5910 > show sel atoms 5911 5912 > style sel stick 5913 5914 Changed 18 atom styles 5915 5916 > color sel byhetero 5917 5918 > select #4/I:210 5919 5920 8 atoms, 7 bonds, 1 residue, 1 model selected 5921 5922 > select #4/I:210-211 5923 5924 15 atoms, 14 bonds, 2 residues, 1 model selected 5925 5926 > show sel atoms 5927 5928 > style sel stick 5929 5930 Changed 15 atom styles 5931 5932 > color sel byhetero 5933 5934 > select #4/I:81 5935 5936 10 atoms, 10 bonds, 1 residue, 1 model selected 5937 5938 > select #4/I:81-83 5939 5940 26 atoms, 26 bonds, 3 residues, 1 model selected 5941 5942 > show sel atoms 5943 5944 > style sel stick 5945 5946 Changed 26 atom styles 5947 5948 > color sel byhetero 5949 5950 > select add #1 5951 5952 4504 atoms, 4608 bonds, 1 pseudobond, 553 residues, 3 models selected 5953 5954 > select subtract #1 5955 5956 26 atoms, 26 bonds, 3 residues, 1 model selected 5957 5958 > select add #4 5959 5960 30651 atoms, 31399 bonds, 35 pseudobonds, 3741 residues, 3 models selected 5961 5962 > select subtract #4 5963 5964 Nothing selected 5965 5966 > select add #1 5967 5968 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 5969 5970 > ui mousemode right "translate selected models" 5971 5972 > view matrix models 5973 > #1,-0.92899,-0.15763,0.33486,365.26,0.26402,-0.9163,0.30113,305.54,0.25937,0.36815,0.89286,-130.81 5974 5975 > view matrix models 5976 > #1,-0.92168,0.011683,0.38778,316.88,0.0013436,-0.99944,0.033304,453.28,0.38795,0.031217,0.92115,-103.03 5977 5978 > view matrix models 5979 > #1,-0.97299,-0.20139,0.11281,444.21,0.17741,-0.96509,-0.19269,469.37,0.14768,-0.16747,0.97475,-26.294 5980 5981 > view matrix models 5982 > #1,-0.95377,-0.085947,0.28798,372.04,0.068101,-0.99512,-0.071442,471.83,0.29272,-0.048527,0.95497,-83.653 5983 5984 > view matrix models 5985 > #1,-0.95377,-0.085947,0.28798,372.22,0.068101,-0.99512,-0.071442,471.54,0.29272,-0.048527,0.95497,-83.902 5986 5987 > view matrix models 5988 > #1,-0.95377,-0.085947,0.28798,372.37,0.068101,-0.99512,-0.071442,467.5,0.29272,-0.048527,0.95497,-81.992 5989 5990 > view matrix models 5991 > #1,-0.92916,-0.3413,0.14206,455.49,0.36415,-0.77877,0.51079,200.84,-0.063704,0.52634,0.84789,-82.728 5992 5993 > view matrix models 5994 > #1,-0.92916,-0.3413,0.14206,455.32,0.36415,-0.77877,0.51079,188.2,-0.063704,0.52634,0.84789,-75.666 5995 5996 > view matrix models 5997 > #1,-0.92916,-0.3413,0.14206,451.36,0.36415,-0.77877,0.51079,174.97,-0.063704,0.52634,0.84789,-54.964 5998 5999 > view matrix models 6000 > #1,-0.92916,-0.3413,0.14206,455.29,0.36415,-0.77877,0.51079,178.31,-0.063704,0.52634,0.84789,-63.121 6001 6002 > view matrix models 6003 > #1,-0.86919,-0.39526,0.29711,409.74,0.49112,-0.75998,0.42572,169.72,0.057532,0.51595,0.85469,-90.031 6004 6005 > select #1/A:94,93,159,115 6006 6007 37 atoms, 36 bonds, 4 residues, 1 model selected 6008 6009 > show sel atoms 6010 6011 > style sel stick 6012 6013 Changed 37 atom styles 6014 6015 > color sel byhetero 6016 6017 > view matrix models 6018 > #1,-0.86919,-0.39526,0.29711,405.12,0.49112,-0.75998,0.42572,166.84,0.057532,0.51595,0.85469,-75.68 6019 6020 > view matrix models 6021 > #1,-0.86919,-0.39526,0.29711,405.72,0.49112,-0.75998,0.42572,169.37,0.057532,0.51595,0.85469,-78.05 6022 6023 > view matrix models 6024 > #1,-0.87411,-0.48334,0.048136,491.77,0.45718,-0.78522,0.41763,183.96,-0.16406,0.38706,0.90734,-18.514 6025 6026 > view matrix models 6027 > #1,-0.87491,-0.482,0.047025,492.94,0.45544,-0.78588,0.41829,184.36,-0.16466,0.38738,0.90709,-21.008 6028 6029 > view matrix models 6030 > #1,-0.87491,-0.482,0.047025,492.77,0.45544,-0.78588,0.41829,184.58,-0.16466,0.38738,0.90709,-20.838 6031 6032 > view matrix models 6033 > #1,-0.88733,-0.45747,-0.058039,519.63,0.3877,-0.80823,0.44324,197.11,-0.24968,0.37079,0.89452,4.7181 6034 6035 > view matrix models 6036 > #1,-0.88334,-0.46707,-0.039382,515.36,0.40537,-0.80343,0.4361,193.64,-0.23533,0.36926,0.89904,0.93621 6037 6038 > view matrix models 6039 > #1,-0.89367,-0.4487,0.0058692,501.77,0.40237,-0.79548,0.45312,188.13,-0.19864,0.4073,0.89143,-12.406 6040 6041 > view matrix models 6042 > #1,-0.86852,-0.49445,-0.034478,515.93,0.43488,-0.79355,0.42562,188.05,-0.23781,0.35467,0.90424,2.8431 6043 6044 > view matrix models 6045 > #1,-0.86852,-0.49445,-0.034478,517.42,0.43488,-0.79355,0.42562,188.02,-0.23781,0.35467,0.90424,1.6296 6046 6047 > view matrix models 6048 > #1,-0.78923,-0.58513,-0.18638,558.61,0.48029,-0.77727,0.40641,180.06,-0.38267,0.23123,0.89448,60.114 6049 6050 > view matrix models 6051 > #1,-0.78129,-0.59771,-0.17979,558.76,0.50063,-0.77212,0.39142,178.15,-0.37278,0.2158,0.90248,57.532 6052 6053 > view matrix models 6054 > #1,-0.78129,-0.59771,-0.17979,558.66,0.50063,-0.77212,0.39142,178.63,-0.37278,0.2158,0.90248,57.646 6055 6056 > select #1/A:94,93,159,115,70 6057 6058 47 atoms, 46 bonds, 5 residues, 1 model selected 6059 6060 > show sel atoms 6061 6062 > view matrix models 6063 > #1,-0.80502,-0.59205,0.037748,503.3,0.57171,-0.75722,0.31587,180.64,-0.15843,0.27586,0.94805,-14.063 6064 6065 > view matrix models 6066 > #1,-0.80502,-0.59205,0.037748,503.39,0.57171,-0.75722,0.31587,182.05,-0.15843,0.27586,0.94805,-14.885 6067 6068 > view matrix models 6069 > #1,-0.81791,-0.57123,-0.068667,531.44,0.51406,-0.77917,0.35866,187.37,-0.25838,0.25805,0.93094,15.477 6070 6071 > view matrix models 6072 > #1,-0.81791,-0.57123,-0.068667,531,0.51406,-0.77917,0.35866,185.96,-0.25838,0.25805,0.93094,14.32 6073 6074 > view matrix models 6075 > #1,-0.81791,-0.57123,-0.068667,530.06,0.51406,-0.77917,0.35866,188.55,-0.25838,0.25805,0.93094,13.985 6076 6077 > view matrix models 6078 > #1,-0.77362,-0.6252,-0.1032,539.92,0.57011,-0.75783,0.31728,183.31,-0.27657,0.18662,0.9427,28.429 6079 6080 > view matrix models 6081 > #1,-0.76784,-0.63464,-0.087455,536.13,0.57323,-0.74157,0.34853,170.97,-0.28605,0.21749,0.93321,27.261 6082 6083 > view matrix models 6084 > #1,-0.76784,-0.63464,-0.087455,535.05,0.57323,-0.74157,0.34853,169.78,-0.28605,0.21749,0.93321,28.598 6085 6086 > view matrix models 6087 > #1,-0.76784,-0.63464,-0.087455,535.06,0.57323,-0.74157,0.34853,170.38,-0.28605,0.21749,0.93321,28.285 6088 6089 > view matrix models 6090 > #1,-0.76784,-0.63464,-0.087455,534.8,0.57323,-0.74157,0.34853,170.74,-0.28605,0.21749,0.93321,28.066 6091 6092 > view matrix models 6093 > #1,-0.75284,-0.64687,-0.12158,543.13,0.56806,-0.73187,0.37639,162.41,-0.33246,0.2143,0.91845,43.062 6094 6095 > view matrix models 6096 > #1,-0.75284,-0.64687,-0.12158,542.71,0.56806,-0.73187,0.37639,162.76,-0.33246,0.2143,0.91845,42.834 6097 6098 > view matrix models 6099 > #1,-0.75284,-0.64687,-0.12158,542.66,0.56806,-0.73187,0.37639,162.54,-0.33246,0.2143,0.91845,43.02 6100 6101 > view matrix models 6102 > #1,-0.75838,-0.63698,-0.13826,546.58,0.5545,-0.74197,0.37685,167.36,-0.34263,0.20913,0.9159,46.971 6103 6104 > view matrix models 6105 > #1,-0.7596,-0.63718,-0.13043,544.75,0.54112,-0.7304,0.41678,157.21,-0.36083,0.24601,0.8996,48.465 6106 6107 > view matrix models 6108 > #1,-0.7596,-0.63718,-0.13043,544.49,0.54112,-0.7304,0.41678,155.79,-0.36083,0.24601,0.8996,48.75 6109 6110 > select add #1 6111 6112 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 6113 6114 > select subtract #1 6115 6116 Nothing selected 6117 6118 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 6119 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_ID.cxs" 6120 6121 > hide #!1 models 6122 6123 > show #!1 models 6124 6125 > hide #!4 models 6126 6127 > combine #1 6128 6129 > hide #!1 models 6130 6131 > open 8BMW 6132 6133 Summary of feedback from opening 8BMW fetched from pdb 6134 --- 6135 note | Fetching compressed mmCIF 8bmw from http://files.rcsb.org/download/8bmw.cif 6136 6137 8bmw title: 6138 SsoCsm [more info...] 6139 6140 Chain information for 8bmw #6 6141 --- 6142 Chain | Description | UniProt 6143 A B C D E | CRISPR-associated small subunit protein (Type III-D) | A0A157T170_SACSO 1-139 6144 F G | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T0X8_SACSO 1-248 6145 H I | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T120_SACSO 1-278 6146 J | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T1A2_SACSO 3-274 6147 K | CRISPR-associated protein Cas10 (Type III-D) | A0A157T112_SACSO 1-829 6148 L | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T2I3_SACSO 1-202 6149 M | CRISPR-associated protein Cas5 (Type III-D) | A0A157T1I2_SACSO 1-300 6150 N | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T1J6_SACSO 1-252 6151 R | RNA (48-MER) | 6152 6153 6154 > select add #6 6155 6156 28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected 6157 6158 > show sel cartoons 6159 6160 > hide sel atoms 6161 6162 > select #6/K:1-829 6163 6164 6678 atoms, 6805 bonds, 829 residues, 1 model selected 6165 6166 > mmaker #5 to #6/K 6167 6168 Parameters 6169 --- 6170 Chain pairing | bb 6171 Alignment algorithm | Needleman-Wunsch 6172 Similarity matrix | BLOSUM-62 6173 SS fraction | 0.3 6174 Gap open (HH/SS/other) | 18/18/6 6175 Gap extend | 1 6176 SS matrix | | | H | S | O 6177 ---|---|---|--- 6178 H | 6 | -9 | -6 6179 S | | 6 | -6 6180 O | | | 4 6181 Iteration cutoff | 2 6182 6183 Matchmaker 8bmw, chain K (#6) with copy of Cas10_bound.pdb, chain A (#5), 6184 sequence alignment score = 185.2 6185 RMSD between 25 pruned atom pairs is 1.021 angstroms; (across all 419 pairs: 6186 31.068) 6187 6188 6189 > hide #!5 models 6190 6191 > select add #6 6192 6193 28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected 6194 6195 > select subtract #6 6196 6197 Nothing selected 6198 6199 > cofr #6 6200 6201 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 6202 > with Terns/20260111 IVC 6203 > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb" 6204 6205 Chain information for merged_real_space_refined_011.pdb #7 6206 --- 6207 Chain | Description 6208 A | No description available 6209 C H I J K L | No description available 6210 D | No description available 6211 E | No description available 6212 F | No description available 6213 G | No description available 6214 M | No description available 6215 N O P Q R | No description available 6216 S | No description available 6217 6218 6219 > select add #7 6220 6221 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 6222 6223 > show sel atoms 6224 6225 > style sel stick 6226 6227 Changed 30524 atom styles 6228 6229 > hide sel cartoons 6230 6231 > show sel cartoons 6232 6233 > hide sel atoms 6234 6235 [Repeated 1 time(s)] 6236 6237 > view matrix models #7,1,0,0,13.762,0,1,0,40.121,0,0,1,-62.573 6238 6239 > view matrix models 6240 > #7,-0.64946,0.021277,-0.7601,502.79,0.039004,0.99922,-0.0053566,33.191,0.7594,-0.033126,-0.64979,109.51 6241 6242 > view matrix models 6243 > #7,-0.64946,0.021277,-0.7601,532.01,0.039004,0.99922,-0.0053566,-59.316,0.7594,-0.033126,-0.64979,98.523 6244 6245 > view matrix models 6246 > #7,0.40297,0.91334,0.058558,-49.62,0.80765,-0.32479,-0.49215,160.87,-0.43048,0.24562,-0.86854,307.91 6247 6248 > view matrix models 6249 > #7,0.051556,0.95685,0.28596,-29.803,0.88581,0.088412,-0.45554,53.02,-0.46117,0.27679,-0.84304,302.94 6250 6251 > view matrix models 6252 > #7,-0.0029515,0.95165,0.30718,-42.665,0.90473,0.1334,-0.40456,25.462,-0.42598,0.27672,-0.86137,309.92 6253 6254 > view matrix models 6255 > #7,-0.53098,0.81849,0.2194,111.93,0.79275,0.57127,-0.21258,-78.241,-0.29934,0.061054,-0.95219,345.35 6256 6257 > view matrix models 6258 > #7,-0.53098,0.81849,0.2194,77.406,0.79275,0.57127,-0.21258,-90.854,-0.29934,0.061054,-0.95219,352.18 6259 6260 > view matrix models 6261 > #7,-0.8291,0.55788,0.037085,228.61,0.5408,0.81702,-0.20006,-90.982,-0.14191,-0.14581,-0.97908,367.19 6262 6263 > view matrix models 6264 > #7,-0.8291,0.55788,0.037085,228.55,0.5408,0.81702,-0.20006,-87.866,-0.14191,-0.14581,-0.97908,380.33 6265 6266 > view matrix models 6267 > #7,-0.85422,0.50761,-0.11238,273.39,0.51975,0.82842,-0.20876,-84.094,-0.01287,-0.23674,-0.97149,370.47 6268 6269 > view matrix models 6270 > #7,-0.96768,0.25114,-0.023036,331.89,0.25206,0.9601,-0.12111,-72.32,-0.0082982,-0.123,-0.99237,350.4 6271 6272 > view matrix models 6273 > #7,-0.70511,0.64449,0.29573,126.28,0.63304,0.76003,-0.14699,-101.62,-0.3195,0.083564,-0.9439,358.76 6274 6275 > view matrix models 6276 > #7,-0.65421,0.65946,0.37029,97.966,0.59449,0.75105,-0.28724,-64.214,-0.46753,0.032215,-0.88339,388.26 6277 6278 > view matrix models 6279 > #7,-0.65961,0.62754,0.41365,97.099,0.4846,0.77577,-0.40415,-23.387,-0.57452,-0.066127,-0.81582,417.4 6280 6281 > view matrix models 6282 > #7,-0.65961,0.62754,0.41365,89.815,0.4846,0.77577,-0.40415,-26.954,-0.57452,-0.066127,-0.81582,416.99 6283 6284 > view matrix models 6285 > #7,-0.65961,0.62754,0.41365,89.768,0.4846,0.77577,-0.40415,-27.843,-0.57452,-0.066127,-0.81582,415.91 6286 6287 > view matrix models 6288 > #7,-0.21793,0.93874,0.26696,-37.188,0.86475,0.31254,-0.3931,-14.808,-0.45246,0.14518,-0.87989,359.85 6289 6290 > view matrix models 6291 > #7,-0.21793,0.93874,0.26696,-36.18,0.86475,0.31254,-0.3931,-15.08,-0.45246,0.14518,-0.87989,359.07 6292 6293 > select subtract #7 6294 6295 Nothing selected 6296 6297 > color #6 #e49e9eff 6298 6299 > color #6 #e4e4e0ff 6300 6301 > color #7 #6e7cf9ff 6302 6303 > color #6 #8c8d8bff 6304 6305 > color #6 #fefffdff 6306 6307 > color #6 #f0ff73ff 6308 6309 > select add #7 6310 6311 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 6312 6313 > view matrix models 6314 > #7,-0.21793,0.93874,0.26696,-34.672,0.86475,0.31254,-0.3931,-15.515,-0.45246,0.14518,-0.87989,358.27 6315 6316 > view matrix models 6317 > #7,-0.29187,0.88991,0.35052,-25.674,0.67377,0.45141,-0.58503,33.657,-0.67886,0.065411,-0.73135,392.65 6318 6319 > view matrix models 6320 > #7,-0.29187,0.88991,0.35052,67.353,0.67377,0.45141,-0.58503,97.803,-0.67886,0.065411,-0.73135,380.41 6321 6322 > view matrix models 6323 > #7,0.12179,0.95469,0.27155,-16.692,0.79285,0.071016,-0.60526,154.58,-0.59712,0.28901,-0.74828,321.03 6324 6325 > view matrix models 6326 > #7,0.12179,0.95469,0.27155,-77.534,0.79285,0.071016,-0.60526,142.09,-0.59712,0.28901,-0.74828,314.91 6327 6328 > view matrix models 6329 > #7,-0.234,0.83803,0.4929,-22.917,0.69423,0.49895,-0.51874,58.323,-0.68066,0.2208,-0.69854,336.51 6330 6331 > view matrix models 6332 > #7,-0.234,0.83803,0.4929,-34.186,0.69423,0.49895,-0.51874,25.983,-0.68066,0.2208,-0.69854,350.78 6333 6334 > view matrix models 6335 > #7,-0.62708,0.76066,0.16784,127.43,0.6775,0.63893,-0.36437,-29.398,-0.3844,-0.11478,-0.916,400.14 6336 6337 > view matrix models 6338 > #7,-0.70238,0.68776,0.18344,149.83,0.60673,0.71324,-0.35096,-50.542,-0.37221,-0.13521,-0.91825,400.1 6339 6340 > view matrix models 6341 > #7,-0.69971,0.63699,0.32348,132.15,0.59564,0.77016,-0.22816,-83.951,-0.39447,0.033031,-0.91831,370.41 6342 6343 > view matrix models 6344 > #7,-0.69971,0.63699,0.32348,125.08,0.59564,0.77016,-0.22816,-76.844,-0.39447,0.033031,-0.91831,378.06 6345 6346 > view matrix models 6347 > #7,-0.69971,0.63699,0.32348,117.6,0.59564,0.77016,-0.22816,-76.942,-0.39447,0.033031,-0.91831,379.71 6348 6349 > view matrix models 6350 > #7,-0.83123,0.42438,0.35909,181.46,0.45119,0.89237,-0.010192,-114.53,-0.32477,0.15355,-0.93325,343.49 6351 6352 > view matrix models 6353 > #7,-0.88372,0.30166,0.35783,217.72,0.35464,0.93053,0.091374,-122.1,-0.3054,0.20765,-0.92931,327.63 6354 6355 > view matrix models 6356 > #7,-0.88372,0.30166,0.35783,211.66,0.35464,0.93053,0.091374,-122.07,-0.3054,0.20765,-0.92931,324.25 6357 6358 > view matrix models 6359 > #7,-0.56247,0.70283,0.43549,47.486,0.70514,0.6828,-0.19122,-89.18,-0.43175,0.19953,-0.87965,342.53 6360 6361 > mmaker #7 to #6 6362 6363 Parameters 6364 --- 6365 Chain pairing | bb 6366 Alignment algorithm | Needleman-Wunsch 6367 Similarity matrix | BLOSUM-62 6368 SS fraction | 0.3 6369 Gap open (HH/SS/other) | 18/18/6 6370 Gap extend | 1 6371 SS matrix | | | H | S | O 6372 ---|---|---|--- 6373 H | 6 | -9 | -6 6374 S | | 6 | -6 6375 O | | | 4 6376 Iteration cutoff | 2 6377 6378 Matchmaker 8bmw, chain K (#6) with merged_real_space_refined_011.pdb, chain A 6379 (#7), sequence alignment score = 185.2 6380 RMSD between 25 pruned atom pairs is 1.021 angstroms; (across all 419 pairs: 6381 31.068) 6382 6383 6384 > view matrix models 6385 > #7,0.30911,0.95069,0.025143,-88.754,0.88584,-0.27821,-0.37134,98.811,-0.34604,0.13706,-0.92816,340.69 6386 6387 > view matrix models 6388 > #7,0.30911,0.95069,0.025143,-90.701,0.88584,-0.27821,-0.37134,94.742,-0.34604,0.13706,-0.92816,346.99 6389 6390 > view matrix models 6391 > #7,-0.59825,0.78378,0.16671,104.93,0.78192,0.61649,-0.092444,-120.96,-0.17523,0.075052,-0.98166,334.5 6392 6393 > view matrix models 6394 > #7,-0.59825,0.78378,0.16671,98.447,0.78192,0.61649,-0.092444,-120.88,-0.17523,0.075052,-0.98166,337.15 6395 6396 > view matrix models 6397 > #7,-0.56838,0.80004,0.19201,83.93,0.77689,0.59871,-0.19489,-96.101,-0.27088,0.038403,-0.96185,360.7 6398 6399 > select subtract #7 6400 6401 Nothing selected 6402 6403 > select add #7 6404 6405 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 6406 6407 > view matrix models 6408 > #7,-0.56838,0.80004,0.19201,123.42,0.77689,0.59871,-0.19489,-29.729,-0.27088,0.038403,-0.96185,321.74 6409 6410 > view matrix models 6411 > #7,-0.81366,0.51412,0.27137,216.79,0.4764,0.8572,-0.19558,-20.449,-0.33317,-0.029854,-0.94239,344.64 6412 6413 > view matrix models 6414 > #7,-0.81292,0.51564,0.27069,170.28,0.47811,0.8563,-0.19535,-67.438,-0.33253,-0.029381,-0.94264,371.27 6415 6416 > view matrix models 6417 > #7,-0.81292,0.51564,0.27069,164.44,0.47811,0.8563,-0.19535,-70.198,-0.33253,-0.029381,-0.94264,377.77 6418 6419 > view matrix models 6420 > #7,-0.6748,0.63257,0.38012,92.37,0.6264,0.76328,-0.15819,-91.803,-0.39021,0.13137,-0.91131,350.78 6421 6422 > view matrix models 6423 > #7,-0.6748,0.63257,0.38012,105.27,0.6264,0.76328,-0.15819,-106.57,-0.39021,0.13137,-0.91131,348.68 6424 6425 > view matrix models 6426 > #7,-0.6748,0.63257,0.38012,102.03,0.6264,0.76328,-0.15819,-106.9,-0.39021,0.13137,-0.91131,344.75 6427 6428 > view matrix models 6429 > #7,-0.73464,0.5535,0.39235,128.26,0.6362,0.76291,0.11497,-162.48,-0.2357,0.33407,-0.9126,271.38 6430 6431 > view matrix models 6432 > #7,-0.73464,0.5535,0.39235,123.54,0.6362,0.76291,0.11497,-161.88,-0.2357,0.33407,-0.9126,275.9 6433 6434 > view matrix models 6435 > #7,-0.92912,0.23184,0.28807,250.25,0.23464,0.97175,-0.025291,-93.191,-0.2858,0.044095,-0.95727,354.33 6436 6437 > view matrix models 6438 > #7,-0.92912,0.23184,0.28807,250.78,0.23464,0.97175,-0.025291,-92.605,-0.2858,0.044095,-0.95727,360 6439 6440 > view matrix models 6441 > #7,-0.92912,0.23184,0.28807,250.51,0.23464,0.97175,-0.025291,-94.297,-0.2858,0.044095,-0.95727,360.58 6442 6443 > view matrix models 6444 > #7,-0.86677,0.46943,0.16836,212.49,0.47815,0.87818,0.013035,-133.53,-0.14173,0.091799,-0.98564,326.35 6445 6446 > view matrix models 6447 > #7,-0.75369,0.55111,0.3581,134.98,0.59561,0.80308,0.017645,-143.61,-0.27786,0.22659,-0.93352,317.01 6448 6449 > view matrix models 6450 > #7,-0.75369,0.55111,0.3581,134.9,0.59561,0.80308,0.017645,-139.03,-0.27786,0.22659,-0.93352,317.56 6451 6452 > view matrix models 6453 > #7,-0.75562,0.53048,0.38422,134.39,0.61149,0.78155,0.12352,-158.73,-0.23476,0.32828,-0.91494,284.16 6454 6455 > view matrix models 6456 > #7,-0.87839,0.1055,0.46616,230.69,0.23165,0.94709,0.22217,-132.62,-0.41806,0.30314,-0.85635,316.04 6457 6458 > view matrix models 6459 > #7,-0.87839,0.1055,0.46616,233.2,0.23165,0.94709,0.22217,-133.27,-0.41806,0.30314,-0.85635,318.67 6460 6461 > view matrix models 6462 > #7,-0.87839,0.1055,0.46616,227.55,0.23165,0.94709,0.22217,-131.84,-0.41806,0.30314,-0.85635,320.35 6463 6464 > view matrix models 6465 > #7,-0.93225,-0.14612,0.33099,316.69,-0.11028,0.98605,0.12469,-49.31,-0.34459,0.079745,-0.93536,366.13 6466 6467 > view matrix models 6468 > #7,-0.92482,0.31305,0.21613,243.94,0.26945,0.94012,-0.20873,-53.736,-0.26853,-0.1348,-0.95379,397.68 6469 6470 > view matrix models 6471 > #7,-0.92482,0.31305,0.21613,245.77,0.26945,0.94012,-0.20873,-54.196,-0.26853,-0.1348,-0.95379,393.98 6472 6473 > view matrix models 6474 > #7,-0.91926,0.28285,0.27379,239.46,0.2527,0.95729,-0.14052,-67.592,-0.30184,-0.059985,-0.95147,385.2 6475 6476 > view matrix models 6477 > #7,-0.87025,0.40939,0.27398,203.36,0.38118,0.91193,-0.15192,-82.905,-0.31205,-0.027772,-0.94966,380.4 6478 6479 > select subtract #7 6480 6481 Nothing selected 6482 6483 > color #!6-7 bychain 6484 6485 > hide #!6 models 6486 6487 > show #!6 models 6488 6489 > hide #!7 models 6490 6491 > show #!7 models 6492 6493 > hide #!6 models 6494 6495 > hide #!7 models 6496 6497 > show #!6 models 6498 6499 > hide #!6 models 6500 6501 > show #!7 models 6502 6503 > show #!6 models 6504 6505 > hide #!7 models 6506 6507 > show #!7 models 6508 6509 > hide #!7 models 6510 6511 > show #!7 models 6512 6513 > hide #!6 models 6514 6515 > show #!6 models 6516 6517 > hide #!7 models 6518 6519 > hide #!6 models 6520 6521 > show #!7 models 6522 6523 > show #!6 models 6524 6525 > select add #7 6526 6527 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 6528 6529 > view matrix models 6530 > #7,-0.82295,0.51309,0.24391,178.13,0.50778,0.85685,-0.089235,-110.38,-0.25478,0.050415,-0.96568,355.72 6531 6532 > view matrix models 6533 > #7,-0.78408,0.52693,0.32797,150.7,0.521,0.84596,-0.11358,-106.14,-0.3373,0.081817,-0.93783,361.06 6534 6535 > view matrix models 6536 > #7,-0.89777,0.38001,0.22271,225.07,0.38215,0.92343,-0.035182,-108.37,-0.21903,0.053522,-0.97425,349.31 6537 6538 > view matrix models 6539 > #7,-0.89849,0.35157,0.2629,223.14,0.33404,0.9361,-0.11019,-86.193,-0.28484,-0.011191,-0.95851,373.16 6540 6541 > view matrix models 6542 > #7,-0.89999,0.33607,0.27763,223.72,0.34879,0.93719,-0.0037997,-110.38,-0.26147,0.093416,-0.96068,347.35 6543 6544 > view matrix models 6545 > #7,-0.86687,0.36718,0.33723,198.77,0.38136,0.92407,-0.025835,-110.17,-0.32111,0.10621,-0.94107,353.34 6546 6547 > view matrix models 6548 > #7,-0.85053,0.42931,0.3038,189.23,0.44771,0.89412,-0.010102,-120.99,-0.27597,0.12742,-0.95268,341.87 6549 6550 > view matrix models 6551 > #7,-0.85053,0.42931,0.3038,188.25,0.44771,0.89412,-0.010102,-122.75,-0.27597,0.12742,-0.95268,342.46 6552 6553 > select subtract #7 6554 6555 Nothing selected 6556 6557 > hide #!6 models 6558 6559 > show #!6 models 6560 6561 > hide #!7 models 6562 6563 > show #!7 models 6564 6565 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 6566 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_IIIA.cxs" 6567 6568 > open 7uzz 6569 6570 Summary of feedback from opening 7uzz fetched from pdb 6571 --- 6572 note | Fetching compressed mmCIF 7uzz from http://files.rcsb.org/download/7uzz.cif 6573 6574 7uzz title: 6575 Staphylococcus epidermidis RP62a CRISPR tall effector complex [more info...] 6576 6577 Chain information for 7uzz #8 6578 --- 6579 Chain | Description | UniProt 6580 A B C D | CRISPR system Cms endoribonuclease Csm3 | Q5HK91_STAEQ 1-214 6581 E | CRISPR system Cms protein Csm5 | Q5HK93_STAEQ 1-340 6582 F | CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) | Q5HK89_STAEQ 1-757 6583 G | RNA (37-MER) | 6584 H | CRISPR system Cms protein Csm4 | Q5HK92_STAEQ 1-304 6585 I J K | CRISPR system Cms protein Csm2 | Q5HK90_STAEQ 14-141 6586 6587 6588 > select add #8 6589 6590 19967 atoms, 20391 bonds, 20 pseudobonds, 2410 residues, 2 models selected 6591 6592 > show sel cartoons 6593 6594 > hide sel atoms 6595 6596 > mmaker #8 to #6 6597 6598 Parameters 6599 --- 6600 Chain pairing | bb 6601 Alignment algorithm | Needleman-Wunsch 6602 Similarity matrix | BLOSUM-62 6603 SS fraction | 0.3 6604 Gap open (HH/SS/other) | 18/18/6 6605 Gap extend | 1 6606 SS matrix | | | H | S | O 6607 ---|---|---|--- 6608 H | 6 | -9 | -6 6609 S | | 6 | -6 6610 O | | | 4 6611 Iteration cutoff | 2 6612 6613 Matchmaker 8bmw, chain K (#6) with 7uzz, chain F (#8), sequence alignment 6614 score = 511.8 6615 RMSD between 93 pruned atom pairs is 1.318 angstroms; (across all 573 pairs: 6616 19.490) 6617 6618 6619 > hide #!6 models 6620 6621 > hide #!7 models 6622 6623 > select subtract #8 6624 6625 Nothing selected 6626 6627 > show #!7 models 6628 6629 > select add #8 6630 6631 19967 atoms, 20391 bonds, 20 pseudobonds, 2410 residues, 2 models selected 6632 6633 > view matrix models 6634 > #8,0.0845,-0.98012,-0.1795,412.25,0.90669,0.00092228,0.4218,-142.16,-0.41325,-0.19839,0.88875,35.585 6635 6636 > undo 6637 6638 > select subtract #8 6639 6640 Nothing selected 6641 6642 > select add #7 6643 6644 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 6645 6646 > view matrix models 6647 > #7,-0.81633,0.44067,0.37339,165.14,0.45487,0.88888,-0.054584,-114.45,-0.35596,0.12529,-0.92607,354.36 6648 6649 > view matrix models 6650 > #7,-0.81662,0.49226,0.30135,168.81,0.46376,0.87044,-0.16511,-90.847,-0.34358,0.0049201,-0.93911,378.91 6651 6652 > view matrix models 6653 > #7,-0.81662,0.49226,0.30135,172.72,0.46376,0.87044,-0.16511,-86.119,-0.34358,0.0049201,-0.93911,377.93 6654 6655 > view matrix models 6656 > #7,-0.81662,0.49226,0.30135,172.89,0.46376,0.87044,-0.16511,-82.532,-0.34358,0.0049201,-0.93911,372.99 6657 6658 > view matrix models 6659 > #7,-0.82887,0.49346,0.26357,182.62,0.47056,0.86977,-0.14859,-87.056,-0.30257,0.00086647,-0.95313,368.01 6660 6661 > view matrix models 6662 > #7,-0.82416,0.50826,0.24988,181.3,0.47514,0.86059,-0.18336,-79.315,-0.30824,-0.032389,-0.95076,375.52 6663 6664 > view matrix models 6665 > #7,-0.83782,0.38323,0.38884,182.4,0.3359,0.92331,-0.18621,-62.502,-0.43038,-0.0254,-0.90229,390.07 6666 6667 > view matrix models 6668 > #7,-0.86925,0.25505,0.4235,207.88,0.18583,0.96239,-0.19816,-33.763,-0.45811,-0.093551,-0.88396,406.02 6669 6670 > view matrix models 6671 > #7,-0.88198,0.25193,0.3983,216.12,0.1757,0.95997,-0.21814,-27.234,-0.43731,-0.12241,-0.89094,408.95 6672 6673 > view matrix models 6674 > #7,-0.90652,0.17807,0.38277,239.36,0.088975,0.96691,-0.23911,-6.4377,-0.41268,-0.1827,-0.89237,416.39 6675 6676 > view matrix models 6677 > #7,-0.90652,0.17807,0.38277,245.13,0.088975,0.96691,-0.23911,-7.8887,-0.41268,-0.1827,-0.89237,419.89 6678 6679 > view matrix models 6680 > #7,-0.90652,0.17807,0.38277,245.84,0.088975,0.96691,-0.23911,-4.2885,-0.41268,-0.1827,-0.89237,420.93 6681 6682 > view matrix models 6683 > #7,-0.90652,0.17807,0.38277,246.4,0.088975,0.96691,-0.23911,-5.0303,-0.41268,-0.1827,-0.89237,419.99 6684 6685 > view matrix models 6686 > #7,-0.89684,0.24239,0.37004,233.75,0.15668,0.95634,-0.24671,-15.509,-0.41368,-0.16328,-0.89566,416.88 6687 6688 > select subtract #7 6689 6690 Nothing selected 6691 6692 > select add #6 6693 6694 28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected 6695 6696 > show #!6 models 6697 6698 > hide #!8 models 6699 6700 > select subtract #6 6701 6702 Nothing selected 6703 6704 > hide #!6 models 6705 6706 > show #!6 models 6707 6708 > hide #!6 models 6709 6710 > show #!6 models 6711 6712 > hide #!6 models 6713 6714 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 6715 > with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_IIIA_2.cxs" 6716 6717 [Repeated 1 time(s)] 6718 6719 > close session 6720 6721 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 6722 > with Terns/20260111 IVC 6723 > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc" 6724 6725 Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel 6726 1.07, shown at level 0.0524, step 2, values float32 6727 6728 > close 6729 6730 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 6731 > with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb" 6732 6733 Summary of feedback from opening 6734 /Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with 6735 Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb 6736 --- 6737 warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 6738 6739 Chain information for merged_ivc_apo_refine_007.pdb #1 6740 --- 6741 Chain | Description 6742 A | No description available 6743 B | No description available 6744 C | No description available 6745 D | No description available 6746 E F G H | No description available 6747 I | No description available 6748 J | No description available 6749 K L M | No description available 6750 N | No description available 6751 O | No description available 6752 P | No description available 6753 Q | No description available 6754 R | No description available 6755 S | No description available 6756 6757 6758 > open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC 6759 > apo/cryosparc_P38_J47_006_volume_map.mrc" 6760 6761 Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512, 6762 pixel 1.07, shown at level 0.0338, step 2, values float32 6763 6764 > volume #2 step 1 6765 6766 > surface dust #2 size 10.7 6767 6768 > volume #2 level 0.1238 6769 6770 > hide cartoons 6771 6772 > hide atoms 6773 6774 > volume #2 level 0.1508 6775 6776 > volume #2 color #8d8d8d81 6777 6778 > volume #2 color #7d8d8d81 6779 6780 > volume #2 color #7d8d8d82 6781 6782 > select add #2 6783 6784 2 models selected 6785 6786 > ui tool show "Color Actions" 6787 6788 > color sel light sky blue 6789 6790 > volume #2 color #87cefa60 6791 6792 > select subtract #2 6793 6794 Nothing selected 6795 6796 > volume #2 color #87cefa61 6797 6798 > combine #1 6799 6800 > select add #2 6801 6802 2 models selected 6803 6804 > select add #1 6805 6806 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 4 models selected 6807 6808 > select add #3 6809 6810 63324 atoms, 64720 bonds, 34 pseudobonds, 7776 residues, 6 models selected 6811 6812 > ui tool show "Color Actions" 6813 6814 > color sel white 6815 6816 > color #2 #ffffff6c models 6817 6818 > color #2 #ffffff6b models 6819 6820 > lighting soft 6821 6822 > color #2 #e6e8e86b models 6823 6824 > color #2 #e6e8e8d0 models 6825 6826 > color #2 #969797d0 models 6827 6828 > color #2 #aeb0b0d0 models 6829 6830 > lighting full 6831 6832 > select subtract #1 6833 6834 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 4 models selected 6835 6836 > select subtract #3 6837 6838 2 models selected 6839 6840 > select subtract #2 6841 6842 Nothing selected 6843 6844 > select #1/A:54,70,93,97,115,146,159 6845 6846 69 atoms, 66 bonds, 7 residues, 1 model selected 6847 6848 > show (sel-residues & sidechain) target ab 6849 6850 > style sel stick 6851 6852 Changed 69 atom styles 6853 6854 > color sel byhetero 6855 6856 > cofr #1/A 6857 6858 > volume #2 level 0.2093 6859 6860 > volume #2 level 0.18 6861 6862 > volume #2 level 0.15 6863 6864 > volume #2 color #aeb0b03b 6865 6866 > select add #1 6867 6868 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 6869 6870 > select subtract #1 6871 6872 Nothing selected 6873 6874 > volume #2 level 0.14 6875 6876 > select /S:2-31 6877 6878 1232 atoms, 1380 bonds, 60 residues, 2 models selected 6879 6880 > select /R:1-46 6881 6882 1960 atoms, 2194 bonds, 92 residues, 2 models selected 6883 6884 > select /Q:43-121 6885 6886 452 atoms, 460 bonds, 2 pseudobonds, 56 residues, 4 models selected 6887 6888 > select /P:17-124 6889 6890 1552 atoms, 1570 bonds, 4 pseudobonds, 196 residues, 4 models selected 6891 6892 > select /O:15-124 6893 6894 1674 atoms, 1698 bonds, 4 pseudobonds, 210 residues, 4 models selected 6895 6896 > select /N:15-124 6897 6898 1728 atoms, 1754 bonds, 2 pseudobonds, 218 residues, 4 models selected 6899 6900 > select /B:1-297 6901 6902 4712 atoms, 4822 bonds, 2 pseudobonds, 570 residues, 4 models selected 6903 6904 > select /C:1-303 6905 6906 4576 atoms, 4646 bonds, 2 pseudobonds, 588 residues, 4 models selected 6907 6908 > select /D:1-303 6909 6910 4608 atoms, 4678 bonds, 2 pseudobonds, 592 residues, 4 models selected 6911 6912 > select /I:1-303 6913 6914 4578 atoms, 4648 bonds, 2 pseudobonds, 586 residues, 4 models selected 6915 6916 > select /J:1-303 6917 6918 4056 atoms, 4124 bonds, 2 pseudobonds, 524 residues, 4 models selected 6919 6920 > select /K:16-124 6921 6922 1710 atoms, 1736 bonds, 2 pseudobonds, 216 residues, 4 models selected 6923 6924 > select /L:16-124 6925 6926 1710 atoms, 1736 bonds, 2 pseudobonds, 216 residues, 4 models selected 6927 6928 > select /H:1-303 6929 6930 4716 atoms, 4788 bonds, 606 residues, 2 models selected 6931 6932 > select /G:1-303 6933 6934 4716 atoms, 4788 bonds, 606 residues, 2 models selected 6935 6936 > select /F:1-303 6937 6938 4716 atoms, 4788 bonds, 606 residues, 2 models selected 6939 6940 > select /E:1-303 6941 6942 4716 atoms, 4788 bonds, 606 residues, 2 models selected 6943 6944 > select /C:1-303 6945 6946 4576 atoms, 4646 bonds, 2 pseudobonds, 588 residues, 4 models selected 6947 6948 > select /B:1-297 6949 6950 4712 atoms, 4822 bonds, 2 pseudobonds, 570 residues, 4 models selected 6951 6952 > select /A:40-593 6953 6954 8198 atoms, 8386 bonds, 6 pseudobonds, 1008 residues, 4 models selected 6955 6956 > select /S:2-31 6957 6958 1232 atoms, 1380 bonds, 60 residues, 2 models selected 6959 6960 > select /R:1-46 6961 6962 1960 atoms, 2194 bonds, 92 residues, 2 models selected 6963 6964 > select /Q:43-121 6965 6966 452 atoms, 460 bonds, 2 pseudobonds, 56 residues, 4 models selected 6967 6968 > select /P:17-124 6969 6970 1552 atoms, 1570 bonds, 4 pseudobonds, 196 residues, 4 models selected 6971 6972 > show #1/T 6973 6974 > select #1/T 6975 6976 2 atoms, 2 residues, 1 model selected 6977 6978 > ui tool show "Color Actions" 6979 6980 > color sel slate gray 6981 6982 > select add #1 6983 6984 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 6985 6986 > select subtract #1 6987 6988 Nothing selected 6989 6990 > ui tool show "Side View" 6991 6992 > select #3/A:94,147 6993 6994 18 atoms, 17 bonds, 2 residues, 1 model selected 6995 6996 > show (sel-residues & sidechain) target ab 6997 6998 > style sel stick 6999 7000 Changed 18 atom styles 7001 7002 > color sel byhetero 7003 7004 > select add #3 7005 7006 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 7007 7008 > select subtract #3 7009 7010 Nothing selected 7011 7012 > volume #2 level 0.135 7013 7014 > volume #2 level 0.138 7015 7016 > volume #2 level 0.139 7017 7018 > volume #2 color #8585872e 7019 7020 > volume #2 color #7272732e 7021 7022 > volume #2 color #7368732e 7023 7024 > volume #2 color #d5c1d62e 7025 7026 > volume #2 color #e5cfe62e 7027 7028 > volume #2 color #d6c2d72e 7029 7030 > lighting soft 7031 7032 > lighting simple 7033 7034 > lighting full 7035 7036 > volume #2 color #e1769a2e 7037 7038 > volume #2 color #e87a9f1b 7039 7040 > volume #2 level 0.142 7041 7042 > select add #1 7043 7044 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 7045 7046 > select add #3 7047 7048 63324 atoms, 64720 bonds, 34 pseudobonds, 7776 residues, 4 models selected 7049 7050 > ui tool show "Color Actions" 7051 7052 > color sel pale violet red 7053 7054 > color sel plum 7055 7056 > color sel pink 7057 7058 > color sel light pink 7059 7060 > color sel byhetero 7061 7062 > select #1/T 7063 7064 2 atoms, 2 residues, 1 model selected 7065 7066 > ui tool show "Color Actions" 7067 7068 > color sel slate gray 7069 7070 > select add #1 7071 7072 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 7073 7074 > select subtract #1 7075 7076 Nothing selected 7077 7078 > save /Users/xuchengtao/Desktop/image221.png supersample 3 7079 7080 > save /Users/xuchengtao/Desktop/image222.png supersample 3 7081 7082 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 7083 > with Terns/20260111 IVC manuscript/IVC_Apo/IVC_apo_HD_1.cxs" 7084 7085 > lighting full 7086 7087 > lighting soft 7088 7089 > volume zone #2 nearAtoms #1range 3 7090 7091 Invalid "nearAtoms" argument: only initial part "#1" of atom specifier valid 7092 7093 > volume zone #2 nearAtoms #1/A range 3 7094 7095 > volume zone #2 nearAtoms #1/A range 4 7096 7097 > save /Users/xuchengtao/Desktop/image223.png supersample 3 7098 7099 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 7100 > with Terns/20260111 IVC manuscript/IVC_Apo/IVC_apo_HD_1.cxs" 7101 7102 > hide #!1 models 7103 7104 > hide #!3 models 7105 7106 > show #!3 models 7107 7108 > show #!1 models 7109 7110 > hide #!2 models 7111 7112 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 7113 > with Terns/20260111 IVC 7114 > manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb" 7115 7116 Chain information for merged_real_space_refined_011.pdb #4 7117 --- 7118 Chain | Description 7119 A | No description available 7120 C H I J K L | No description available 7121 D | No description available 7122 E | No description available 7123 F | No description available 7124 G | No description available 7125 M | No description available 7126 N O P Q R | No description available 7127 S | No description available 7128 7129 7130 > mmaker #4/A: 54, 70,93,94,115,146,147,97 7131 7132 > matchmaker #4/A: 54, 70,93,94,115,146,147,97 7133 7134 Missing required "to" argument 7135 7136 > mmaker #4/A: 54, 70,93,94,115,146,147,97 to #1 7137 7138 Parameters 7139 --- 7140 Chain pairing | bb 7141 Alignment algorithm | Needleman-Wunsch 7142 Similarity matrix | BLOSUM-62 7143 SS fraction | 0.3 7144 Gap open (HH/SS/other) | 18/18/6 7145 Gap extend | 1 7146 SS matrix | | | H | S | O 7147 ---|---|---|--- 7148 H | 6 | -9 | -6 7149 S | | 6 | -6 7150 O | | | 4 7151 Iteration cutoff | 2 7152 7153 Matchmaker merged_ivc_apo_refine_007.pdb, chain A (#1) with 7154 merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score = 7155 49.4 7156 RMSD between 8 pruned atom pairs is 0.822 angstroms; (across all 8 pairs: 7157 0.822) 7158 7159 7160 > style stick 7161 7162 Changed 93848 atom styles 7163 7164 > hide atoms 7165 7166 [Repeated 1 time(s)] 7167 7168 > show atoms 7169 7170 > undo 7171 7172 [Repeated 3 time(s)] 7173 7174 > style stick 7175 7176 Changed 93848 atom styles 7177 7178 > color byhetero 7179 7180 > hide #4 7181 7182 > show #4/A:54,70,93,94,115,146,147,159 7183 7184 > select #4/A:54,70,93,97,115,146,159 7185 7186 69 atoms, 66 bonds, 7 residues, 1 model selected 7187 7188 > show (sel-residues & sidechain) target ab 7189 7190 > select #4/A 7191 7192 4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected 7193 7194 > ui tool show "Color Actions" 7195 7196 > color sel light sky blue 7197 7198 > color sel byhetero 7199 7200 > combine #4/A 7201 7202 > select add #4 7203 7204 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 7205 7206 > hide #!5 models 7207 7208 > show #!5 models 7209 7210 > hide #5 7211 7212 > show #5/A:94,147 7213 7214 > select #5/A:94,147 7215 7216 18 atoms, 17 bonds, 2 residues, 1 model selected 7217 7218 > show (sel-residues & sidechain) target ab 7219 7220 > color #1 #ffb6c17c 7221 7222 [Repeated 1 time(s)] 7223 7224 > color sel byhetero 7225 7226 > color #1 #ffb6c17d 7227 7228 > select add #1 7229 7230 31680 atoms, 32377 bonds, 17 pseudobonds, 3890 residues, 3 models selected 7231 7232 > color sel byhetero 7233 7234 > select subtract #1 7235 7236 18 atoms, 17 bonds, 2 residues, 1 model selected 7237 7238 > color #3 #f1c3caff 7239 7240 > color #3 #f1c3ca81 7241 7242 > color #3 #f1c3ca82 7243 7244 > select add #3 7245 7246 31680 atoms, 32377 bonds, 17 pseudobonds, 3890 residues, 3 models selected 7247 7248 > color sel byhetero 7249 7250 > select subtract #3 7251 7252 18 atoms, 17 bonds, 2 residues, 1 model selected 7253 7254 > hide #1/T 7255 7256 > select #1/T 7257 7258 2 atoms, 2 residues, 1 model selected 7259 7260 > show (sel-residues & sidechain) target ab 7261 7262 > show #1/T 7263 7264 > ui tool show "Color Actions" 7265 7266 > color sel slate gray 7267 7268 > select add #1 7269 7270 31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected 7271 7272 > select subtract #1 7273 7274 Nothing selected 7275 7276 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 7277 > with Terns/20260111 IVC 7278 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs" 7279 7280 > show #4/A:67-81, 86-96,112-118,136-160 cartoons 7281 7282 > select #4/A:67-81, 86-96,112-118,136-160 cartoon 7283 7284 Expected a keyword 7285 7286 > select #4/A:67-81, 86-96,112-118,136-160 7287 7288 470 atoms, 480 bonds, 58 residues, 1 model selected 7289 7290 > cartoon style sel modeHelix tube sides 20 7291 7292 > select #4/A:67-81, 86-98,112-118,136-160 7293 7294 486 atoms, 497 bonds, 60 residues, 1 model selected 7295 7296 > show sel cartoons 7297 7298 > select add #4 7299 7300 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 7301 7302 > select subtract #4 7303 7304 Nothing selected 7305 7306 > hide #1/T 7307 7308 > show #4/B 7309 7310 > select #4/B 7311 7312 2 atoms, 2 residues, 1 model selected 7313 7314 > ui tool show "Color Actions" 7315 7316 > color sel slate gray 7317 7318 > select add #4 7319 7320 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 7321 7322 > select subtract #4 7323 7324 Nothing selected 7325 7326 > select #4/B 7327 7328 2 atoms, 2 residues, 1 model selected 7329 7330 > color sel byhetero 7331 7332 > undo 7333 7334 > color sel bychain 7335 7336 > undo 7337 7338 > style sel sphere 7339 7340 Changed 2 atom styles 7341 7342 > select add #4 7343 7344 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 7345 7346 > select subtract #4 7347 7348 Nothing selected 7349 7350 > save /Users/xuchengtao/Desktop/image224.png supersample 3 7351 7352 > open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 7353 > with Terns/20260111 IVC 7354 > manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc" 7355 7356 Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel 7357 1.07, shown at level 0.0524, step 2, values float32 7358 7359 > save /Users/xuchengtao/Desktop/image225.png supersample 3 7360 7361 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 7362 > with Terns/20260111 IVC 7363 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs" 7364 7365 ——— End of log from Tue Feb 3 13:26:30 2026 ——— 7366 7367 > view name session-start 7368 7369 opened ChimeraX session 7370 7371 > hide #!3 models 7372 7373 > show #!3 models 7374 7375 > show #1/A:136-160 cartoons 7376 7377 > show #1/A:136-180 cartoons 7378 7379 [Repeated 1 time(s)] 7380 7381 > show #4/A:136-180 cartoons 7382 7383 > select #4/A:136-180 7384 7385 352 atoms, 357 bonds, 45 residues, 1 model selected 7386 7387 > cartoon style sel xsection oval modeHelix default 7388 7389 > select add #4 7390 7391 30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected 7392 7393 > select subtract #4 7394 7395 Nothing selected 7396 7397 > 7398 7399 Unknown command: measure #1/A:159@CA #4/A:159@CA 7400 7401 > ui tool show Distances 7402 7403 > select #1/A:159@CA #4/A:159@CA 7404 7405 2 atoms, 2 residues, 2 models selected 7406 7407 > distance #1/A:159@CA #4/A:159@CA 7408 7409 Distance between merged_ivc_apo_refine_007.pdb #1/A GLU 159 CA and 7410 merged_real_space_refined_011.pdb #4/A GLU 159 CA: 1.998Å 7411 7412 > hide #1/A:59 7413 7414 > hide #1/A:59 atoms 7415 7416 > hide #1/A:54 atoms 7417 7418 > hide #4/A:54 atoms 7419 7420 > mmaker #4/A:115,94,146,147 to #1/A 7421 7422 Parameters 7423 --- 7424 Chain pairing | bb 7425 Alignment algorithm | Needleman-Wunsch 7426 Similarity matrix | BLOSUM-62 7427 SS fraction | 0.3 7428 Gap open (HH/SS/other) | 18/18/6 7429 Gap extend | 1 7430 SS matrix | | | H | S | O 7431 ---|---|---|--- 7432 H | 6 | -9 | -6 7433 S | | 6 | -6 7434 O | | | 4 7435 Iteration cutoff | 2 7436 7437 Matchmaker merged_ivc_apo_refine_007.pdb, chain A (#1) with 7438 merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score = 7439 25.8 7440 RMSD between 4 pruned atom pairs is 0.509 angstroms; (across all 4 pairs: 7441 0.509) 7442 7443 7444 > mmaker #4/A:115,94,146,147,70 to #1/A 7445 7446 Parameters 7447 --- 7448 Chain pairing | bb 7449 Alignment algorithm | Needleman-Wunsch 7450 Similarity matrix | BLOSUM-62 7451 SS fraction | 0.3 7452 Gap open (HH/SS/other) | 18/18/6 7453 Gap extend | 1 7454 SS matrix | | | H | S | O 7455 ---|---|---|--- 7456 H | 6 | -9 | -6 7457 S | | 6 | -6 7458 O | | | 4 7459 Iteration cutoff | 2 7460 7461 Matchmaker merged_ivc_apo_refine_007.pdb, chain A (#1) with 7462 merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score = 7463 33.2 7464 RMSD between 5 pruned atom pairs is 0.579 angstroms; (across all 5 pairs: 7465 0.579) 7466 7467 7468 > save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV 7469 > with Terns/20260111 IVC 7470 > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs" 7471 7472 ——— End of log from Tue Feb 3 15:37:02 2026 ——— 7473 7474 > view name session-start 7475 7476 opened ChimeraX session 7477 7478 > show #!2 models 7479 7480 > hide #!2 models 7481 7482 > hide #!1 models 7483 7484 > hide #!3 models 7485 7486 > hide #!4 models 7487 7488 > hide #!5 models 7489 7490 > close #7#1-6 7491 7492 > open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC 7493 > apo/merged_ivc_apo_refine_007.pdb" 7494 7495 Summary of feedback from opening /Users/xuchengtao/Documents/Building models 7496 undergoing/20260114 IVC apo/merged_ivc_apo_refine_007.pdb 7497 --- 7498 warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 7499 7500 Chain information for merged_ivc_apo_refine_007.pdb #1 7501 --- 7502 Chain | Description 7503 A | No description available 7504 B | No description available 7505 C | No description available 7506 D | No description available 7507 E F G H | No description available 7508 I | No description available 7509 J | No description available 7510 K L M | No description available 7511 N | No description available 7512 O | No description available 7513 P | No description available 7514 Q | No description available 7515 R | No description available 7516 S | No description available 7517 7518 7519 > style stick 7520 7521 Changed 31663 atom styles 7522 7523 > hide atoms 7524 7525 > show atoms 7526 7527 > style stick 7528 7529 Changed 31663 atom styles 7530 7531 > show cartoons 7532 7533 > hide cartoons 7534 7535 > hide #1 7536 7537 > open "/Users/xuchengtao/Documents/Building models 7538 > undergoing/20251003IVC/20251222 Xiaomeng AI 7539 > IVC/merged_real_space_refined_014.pdb" 7540 7541 Chain information for merged_real_space_refined_014.pdb #2 7542 --- 7543 Chain | Description 7544 A | No description available 7545 C H I J K L | No description available 7546 D | No description available 7547 E | No description available 7548 F | No description available 7549 G | No description available 7550 M | No description available 7551 N O P Q R | No description available 7552 S | No description available 7553 7554 7555 > hide atoms 7556 7557 > mmaker #1/A:70,93,94,146,147 to #2/A 7558 7559 Parameters 7560 --- 7561 Chain pairing | bb 7562 Alignment algorithm | Needleman-Wunsch 7563 Similarity matrix | BLOSUM-62 7564 SS fraction | 0.3 7565 Gap open (HH/SS/other) | 18/18/6 7566 Gap extend | 1 7567 SS matrix | | | H | S | O 7568 ---|---|---|--- 7569 H | 6 | -9 | -6 7570 S | | 6 | -6 7571 O | | | 4 7572 Iteration cutoff | 2 7573 7574 Matchmaker merged_real_space_refined_014.pdb, chain A (#2) with 7575 merged_ivc_apo_refine_007.pdb, chain A (#1), sequence alignment score = 33.2 7576 RMSD between 5 pruned atom pairs is 0.530 angstroms; (across all 5 pairs: 7577 0.530) 7578 7579 7580 > show #1/A:70,93,94,146,147 7581 7582 > select #1/A:70,93,94,146,147 7583 7584 48 atoms, 49 bonds, 5 residues, 1 model selected 7585 7586 > style sel stick 7587 7588 Changed 48 atom styles 81 [deleted to fit within ticket limits] 82 7589 83 7590 84 > color sel byhetero
