Changes between Initial Version and Version 1 of Ticket #18310


Ignore:
Timestamp:
Jul 29, 2025, 11:55:10 AM (4 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #18310

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

  • Ticket #18310 – Description

    initial v1  
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    2390     "path" : "\/usr\/lib\/libc++.1.dylib",
    2391     "name" : "libc++.1.dylib"
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    2407   "trialInfo" : {
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    2419 
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    2424   "experiments" : [
    2425 
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    2428 }
    2429 ===== Log before crash start =====
    2430 Startup Messages 
    2431 --- 
    2432 warning | Registration file '/Users/ctn700/Library/Application Support/ChimeraX/registration' has expired 
    2433 note | available bundle cache has not been initialized yet 
    2434  
    2435 UCSF ChimeraX version: 1.8 (2024-06-10) 
    2436 © 2016-2024 Regents of the University of California. All rights reserved. 
    2437 How to cite UCSF ChimeraX 
    2438 
    2439 > open 5J4I
    2440 
    2441 Summary of feedback from opening 5J4I fetched from pdb 
    2442 --- 
    2443 note | Fetching compressed mmCIF 5j4i from http://files.rcsb.org/download/5j4i.cif 
    2444  
    2445 5j4i title: 
    2446 Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2
    2447 Angstroem resolution [more info...] 
    2448  
    2449 Chain information for 5j4i #1 
    2450 --- 
    2451 Chain | Description | UniProt 
    2452 A B | Arginine/agmatine antiporter | ADIC_ECO57 1-445 
    2453  
    2454 
    2455 > open 8kdp
    2456 
    2457 Summary of feedback from opening 8kdp fetched from pdb 
    2458 --- 
    2459 note | Fetching compressed mmCIF 8kdp from http://files.rcsb.org/download/8kdp.cif 
    2460  
    2461 8kdp title: 
    2462 Structure of apo outward-open LAT1-CD98h in nanodisc, focused on TMD [more
    2463 info...] 
    2464  
    2465 Chain information for 8kdp #2 
    2466 --- 
    2467 Chain | Description | UniProt 
    2468 A | 4F2 cell-surface antigen heavy chain | 4F2_HUMAN 2-630 
    2469 B | Large neutral amino acids transporter small subunit 1 | LAT1_HUMAN 1-507 
    2470  
    2471 
    2472 > hide #1 models
    2473 
    2474 > show #!2 atoms
    2475 
    2476 > dssp
    2477 
    2478 > hide #!2 atoms
    2479 
    2480 > open 7O82
    2481 
    2482 Summary of feedback from opening 7O82 fetched from pdb 
    2483 --- 
    2484 note | Fetching compressed mmCIF 7o82 from http://files.rcsb.org/download/7o82.cif 
    2485  
    2486 7o82 title: 
    2487 The L-arginine/agmatine antiporter from E. coli at 1.7 A resolution [more
    2488 info...] 
    2489  
    2490 Chain information for 7o82 #3 
    2491 --- 
    2492 Chain | Description | UniProt 
    2493 A B | Arginine/agmatine antiporter | ADIC_ECO57 1-445 
    2494  
    2495 Non-standard residues in 7o82 #3 
    2496 --- 
    2497 BNG — nonyl beta-D-glucopyranoside (Beta-NONYLGLUCOSIDE; nonyl beta-D-
    2498 glucoside; nonyl D-glucoside; nonyl glucoside) 
    2499 D10 — decane 
    2500 HEX — hexane 
    2501 OCT — N-octane 
    2502 TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) 
    2503  
    2504 78 atoms have alternate locations. Control/examine alternate locations with
    2505 Altloc Explorer [start tool...] or the altlocs command. 
    2506 
    2507 > hide #!2 models
    2508 
    2509 > view
    2510 
    2511 > dssp
    2512 
    2513 > show #3:HOH
    2514 
    2515 > select #3/A:209
    2516 
    2517 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2518 
    2519 > select add #3/A:22
    2520 
    2521 14 atoms, 12 bonds, 2 residues, 1 model selected 
    2522 
    2523 > view sel
    2524 
    2525 > select clear
    2526 
    2527 > show #3 atoms
    2528 
    2529 > rainbow #3
    2530 
    2531 > color #3 byhetero
    2532 
    2533 > show #!2 models
    2534 
    2535 > matchmaker #3 to #2
    2536 
    2537 Parameters 
    2538 --- 
    2539 Chain pairing | bb 
    2540 Alignment algorithm | Needleman-Wunsch 
    2541 Similarity matrix | BLOSUM-62 
    2542 SS fraction | 0.3 
    2543 Gap open (HH/SS/other) | 18/18/6 
    2544 Gap extend | 1 
    2545 SS matrix |  |  | H | S | O 
    2546 ---|---|---|--- 
    2547 H | 6 | -9 | -6 
    2548 S |  | 6 | -6 
    2549 O |  |  | 4 
    2550 Iteration cutoff | 2 
    2551  
    2552 Matchmaker 8kdp, chain B (#2) with 7o82, chain B (#3), sequence alignment
    2553 score = 634 
    2554 RMSD between 190 pruned atom pairs is 1.228 angstroms; (across all 407 pairs:
    2555 5.717) 
    2556  
    2557 
    2558 > view
    2559 
    2560 > dssp
    2561 
    2562 > hide #3#!2 cartoons
    2563 
    2564 > show #3#!2 cartoons
    2565 
    2566 > hide #3#!2 atoms
    2567 
    2568 > open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
    2569 > Newstead Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
    2570 > step7_3_whole_nojump_center_rotxyz-transxyz.pdb"
    2571 
    2572 Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
    2573 Nexus365/Dimitris - Newstead
    2574 Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
    2575 step7_3_whole_nojump_center_rotxyz-transxyz.pdb 
    2576 --- 
    2577 warnings | Ignored bad PDB record found on line 1 
    2578 REMARK GENERATED BY TRJCONV 
    2579  
    2580 Ignored bad PDB record found on line 3 
    2581 REMARK THIS IS A SIMULATION BOX 
    2582  
    2583 nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb title: 
    2584 AtCAT4-Leu in POPC-Cholesterol in water t= 1000000.00000 step= 500000000 [more
    2585 info...] 
    2586  
    2587 Chain information for nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb
    2588 #4 
    2589 --- 
    2590 Chain | Description 
    2591 A | No description available 
    2592  
    2593 Non-standard residues in nowaters-step7_3_whole_nojump_center_rotxyz-
    2594 transxyz.pdb #4 
    2595 --- 
    2596 ACE — (ACE) 
    2597 CHL1 — (CHL1) 
    2598 NME — (NME) 
    2599 POPC — (popc) 
    2600  
    2601 
    2602 > hide #3 models
    2603 
    2604 > hide #!2 models
    2605 
    2606 > view
    2607 
    2608 > hide :POPC,CHL1
    2609 
    2610 > dssp
    2611 
    2612 > open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
    2613 > Newstead Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
    2614 > step7_2_whole_nojump_center_rotxyz-transxyz.pdb"
    2615 
    2616 Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
    2617 Nexus365/Dimitris - Newstead
    2618 Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
    2619 step7_2_whole_nojump_center_rotxyz-transxyz.pdb 
    2620 --- 
    2621 warnings | Ignored bad PDB record found on line 1 
    2622 REMARK GENERATED BY TRJCONV 
    2623  
    2624 Ignored bad PDB record found on line 3 
    2625 REMARK THIS IS A SIMULATION BOX 
    2626  
    2627 nowaters-step7_2_whole_nojump_center_rotxyz-transxyz.pdb title: 
    2628 AtCAT4-Leu in POPC-Cholesterol in water t= 1000000.00000 step= 500000000 [more
    2629 info...] 
    2630  
    2631 Chain information for nowaters-step7_2_whole_nojump_center_rotxyz-transxyz.pdb
    2632 #5 
    2633 --- 
    2634 Chain | Description 
    2635 A | No description available 
    2636  
    2637 Non-standard residues in nowaters-step7_2_whole_nojump_center_rotxyz-
    2638 transxyz.pdb #5 
    2639 --- 
    2640 ACE — (ACE) 
    2641 CHL1 — (CHL1) 
    2642 NME — (NME) 
    2643 POPC — (popc) 
    2644  
    2645 
    2646 > hide #4 models
    2647 
    2648 > hide :POPC,CHL1
    2649 
    2650 > dssp
    2651 
    2652 > open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
    2653 > Newstead Lab/Postdoc/MD/AtCAT4_new_model_to_test_TM1/pr1000ns/nowaters-
    2654 > step7_3_whole_nojump_center_rotxyz-transxyz.pdb"
    2655 
    2656 Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
    2657 Nexus365/Dimitris - Newstead
    2658 Lab/Postdoc/MD/AtCAT4_new_model_to_test_TM1/pr1000ns/nowaters-
    2659 step7_3_whole_nojump_center_rotxyz-transxyz.pdb 
    2660 --- 
    2661 warnings | Ignored bad PDB record found on line 1 
    2662 REMARK GENERATED BY TRJCONV 
    2663  
    2664 Ignored bad PDB record found on line 3 
    2665 REMARK THIS IS A SIMULATION BOX 
    2666  
    2667 nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb title: 
    2668 AtCAT4 cryoEM structure in POPC-Cholesterol in water t= 1000000.00000 step=
    2669 500000000 [more info...] 
    2670  
    2671 Chain information for nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb
    2672 #6 
    2673 --- 
    2674 Chain | Description 
    2675 A | No description available 
    2676  
    2677 Non-standard residues in nowaters-step7_3_whole_nojump_center_rotxyz-
    2678 transxyz.pdb #6 
    2679 --- 
    2680 ACE — (ACE) 
    2681 CHL1 — (CHL1) 
    2682 NME — (NME) 
    2683 POPC — (popc) 
    2684  
    2685 
    2686 > hide #5 models
    2687 
    2688 > hide :POPC,CHL1
    2689 
    2690 > close #1,3-6#2
    2691 
    2692 > open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
    2693 > Newstead
    2694 > Lab/Postdoc/MD/SLC7A4_homology_model_leucine/SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb"
    2695 
    2696 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    2697 title: 
    2698 Alphafold monomer V2.0 prediction for cationic amino acid transporter 4
    2699 (O43246) [more info...] 
    2700  
    2701 Chain information for
    2702 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    2703 #1 
    2704 --- 
    2705 Chain | Description 
    2706 A | No description available 
    2707  
    2708 Non-standard residues in
    2709 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    2710 #1 
    2711 --- 
    2712 CLR — (CLR) 
    2713  
    2714 
    2715 > dssp
    2716 
    2717 > open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
    2718 > Newstead
    2719 > Lab/Postdoc/MD/AtCAT4_ornithine_EM_model/production_from_IFD/pr1000ns_run1_whole_nojump_center_rotxyz-
    2720 > transxyz.pdb"
    2721 
    2722 Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
    2723 Nexus365/Dimitris - Newstead
    2724 Lab/Postdoc/MD/AtCAT4_ornithine_EM_model/production_from_IFD/pr1000ns_run1_whole_nojump_center_rotxyz-
    2725 transxyz.pdb 
    2726 --- 
    2727 warnings | Ignored bad PDB record found on line 1 
    2728 REMARK GENERATED BY TRJCONV 
    2729  
    2730 Ignored bad PDB record found on line 3 
    2731 REMARK THIS IS A SIMULATION BOX 
    2732  
    2733 pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb title: 
    2734 AtCAT4-Orn cryoEM structure in POPC-Cholesterol in water t= 137500.00000 step=
    2735 68750000 [more info...] 
    2736  
    2737 Chain information for pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb #2 
    2738 --- 
    2739 Chain | Description 
    2740 A | No description available 
    2741  
    2742 Non-standard residues in pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb
    2743 #2 
    2744 --- 
    2745 ACE — (ACE) 
    2746 CHL1 — (CHL1) 
    2747 CL — (CL) 
    2748 NA — (NA) 
    2749 NME — (NME) 
    2750 ORN — (ORN) 
    2751 POPC — (popc) 
    2752 SOL — (SOL) 
    2753  
    2754 
    2755 > matchmaker #2 to #1
    2756 
    2757 Parameters 
    2758 --- 
    2759 Chain pairing | bb 
    2760 Alignment algorithm | Needleman-Wunsch 
    2761 Similarity matrix | BLOSUM-62 
    2762 SS fraction | 0.3 
    2763 Gap open (HH/SS/other) | 18/18/6 
    2764 Gap extend | 1 
    2765 SS matrix |  |  | H | S | O 
    2766 ---|---|---|--- 
    2767 H | 6 | -9 | -6 
    2768 S |  | 6 | -6 
    2769 O |  |  | 4 
    2770 Iteration cutoff | 2 
    2771  
    2772 Matchmaker
    2773 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    2774 chain A (#1) with pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb, chain
    2775 A (#2), sequence alignment score = 1246.3 
    2776 RMSD between 357 pruned atom pairs is 1.098 angstroms; (across all 547 pairs:
    2777 7.014) 
    2778  
    2779 
    2780 > hide atoms
    2781 
    2782 > view
    2783 
    2784 > dssp
    2785 
    2786 > hide #!1 models
    2787 
    2788 > hide #2 models
    2789 
    2790 > open /Users/ctn700/Library/CloudStorage/OneDrive-
    2791 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Apo_Sybody/RealSpaceRefine_34/AtCAT4_final-
    2792 > coot-17_H_real_space_refined_034_ARG-fixed_H.pdb
    2793 
    2794 Chain information for AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
    2795 fixed_H.pdb #3 
    2796 --- 
    2797 Chain | Description 
    2798 A | No description available 
    2799 B | No description available 
    2800  
    2801 
    2802 > view
    2803 
    2804 > dssp
    2805 
    2806 > undo
    2807 
    2808 > dssp
    2809 
    2810 > undo
    2811 
    2812 > dssp
    2813 
    2814 > ui tool show "Modeller Comparative"
    2815 
    2816 Populating font family aliases took 61 ms. Replace uses of missing font family
    2817 "Times" with one that exists to avoid this cost. 
    2818 
    2819 > ui tool show "Modeller Comparative"
    2820 
    2821 > ui tool show "Show Sequence Viewer"
    2822 
    2823 > open /Users/ctn700/Downloads/AF-O43246-F1-model_v4.pdb
    2824 
    2825 AF-O43246-F1-model_v4.pdb title: 
    2826 Alphafold monomer V2.0 prediction for cationic amino acid transporter 4
    2827 (O43246) [more info...] 
    2828  
    2829 Chain information for AF-O43246-F1-model_v4.pdb #4 
    2830 --- 
    2831 Chain | Description | UniProt 
    2832 A | cationic amino acid transporter 4 | CTR4_HUMAN 1-635 
    2833  
    2834 
    2835 > matchmaker #4 to #3
    2836 
    2837 Parameters 
    2838 --- 
    2839 Chain pairing | bb 
    2840 Alignment algorithm | Needleman-Wunsch 
    2841 Similarity matrix | BLOSUM-62 
    2842 SS fraction | 0.3 
    2843 Gap open (HH/SS/other) | 18/18/6 
    2844 Gap extend | 1 
    2845 SS matrix |  |  | H | S | O 
    2846 ---|---|---|--- 
    2847 H | 6 | -9 | -6 
    2848 S |  | 6 | -6 
    2849 O |  |  | 4 
    2850 Iteration cutoff | 2 
    2851  
    2852 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    2853 chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
    2854 score = 1197.6 
    2855 RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
    2856 5.348) 
    2857  
    2858 
    2859 > view
    2860 
    2861 > ui tool show "Show Sequence Viewer"
    2862 
    2863 > sequence chain #3/A
    2864 
    2865 Alignment identifier is 3/A 
    2866 
    2867 > sequence chain #4/A
    2868 
    2869 Alignment identifier is 4/A 
    2870 
    2871 > select add #3
    2872 
    2873 9769 atoms, 9888 bonds, 1 pseudobond, 634 residues, 2 models selected 
    2874 
    2875 > select add #4
    2876 
    2877 14590 atoms, 14841 bonds, 1 pseudobond, 1269 residues, 3 models selected 
    2878 
    2879 > select clear
    2880 
    2881 > select #3/A,#4
    2882 
    2883 Expected an objects specifier or a keyword 
    2884 
    2885 > select #3/A#4
    2886 
    2887 12861 atoms, 13090 bonds, 1 pseudobond, 1154 residues, 3 models selected 
    2888 
    2889 > ui tool show "Modeller Comparative"
    2890 
    2891 Alignment identifier is 3/A 
    2892 Alignment identifier is 4/A 
    2893 
    2894 > ui tool show Matchmaker
    2895 
    2896 > matchmaker #4 to #3
    2897 
    2898 Parameters 
    2899 --- 
    2900 Chain pairing | bb 
    2901 Alignment algorithm | Needleman-Wunsch 
    2902 Similarity matrix | BLOSUM-62 
    2903 SS fraction | 0.3 
    2904 Gap open (HH/SS/other) | 18/18/6 
    2905 Gap extend | 1 
    2906 SS matrix |  |  | H | S | O 
    2907 ---|---|---|--- 
    2908 H | 6 | -9 | -6 
    2909 S |  | 6 | -6 
    2910 O |  |  | 4 
    2911 Iteration cutoff | 2 
    2912  
    2913 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    2914 chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
    2915 score = 1197.6 
    2916 RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
    2917 5.348) 
    2918  
    2919 
    2920 > ui tool show Matchmaker
    2921 
    2922 > matchmaker #4 to #1
    2923 
    2924 Parameters 
    2925 --- 
    2926 Chain pairing | bb 
    2927 Alignment algorithm | Needleman-Wunsch 
    2928 Similarity matrix | BLOSUM-62 
    2929 SS fraction | 0.3 
    2930 Gap open (HH/SS/other) | 18/18/6 
    2931 Gap extend | 1 
    2932 SS matrix |  |  | H | S | O 
    2933 ---|---|---|--- 
    2934 H | 6 | -9 | -6 
    2935 S |  | 6 | -6 
    2936 O |  |  | 4 
    2937 Iteration cutoff | 2 
    2938  
    2939 Matchmaker
    2940 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    2941 chain A (#1) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
    2942 score = 2556.8 
    2943 RMSD between 251 pruned atom pairs is 1.141 angstroms; (across all 556 pairs:
    2944 9.086) 
    2945  
    2946 
    2947 > ui tool show Matchmaker
    2948 
    2949 > matchmaker #4 to #3
    2950 
    2951 Parameters 
    2952 --- 
    2953 Chain pairing | bb 
    2954 Alignment algorithm | Needleman-Wunsch 
    2955 Similarity matrix | BLOSUM-62 
    2956 SS fraction | 0.3 
    2957 Gap open (HH/SS/other) | 18/18/6 
    2958 Gap extend | 1 
    2959 SS matrix |  |  | H | S | O 
    2960 ---|---|---|--- 
    2961 H | 6 | -9 | -6 
    2962 S |  | 6 | -6 
    2963 O |  |  | 4 
    2964 Iteration cutoff | 2 
    2965  
    2966 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    2967 chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
    2968 score = 1197.6 
    2969 RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
    2970 5.348) 
    2971  
    2972 
    2973 > ui tool show "Modeller Comparative"
    2974 
    2975 > ui tool show "Blast Protein"
    2976 
    2977 > ui tool show Matchmaker
    2978 
    2979 > matchmaker #4 to #3/A pairing bs
    2980 
    2981 Parameters 
    2982 --- 
    2983 Chain pairing | bs 
    2984 Alignment algorithm | Needleman-Wunsch 
    2985 Similarity matrix | BLOSUM-62 
    2986 SS fraction | 0.3 
    2987 Gap open (HH/SS/other) | 18/18/6 
    2988 Gap extend | 1 
    2989 SS matrix |  |  | H | S | O 
    2990 ---|---|---|--- 
    2991 H | 6 | -9 | -6 
    2992 S |  | 6 | -6 
    2993 O |  |  | 4 
    2994 Iteration cutoff | 2 
    2995  
    2996 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    2997 chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
    2998 score = 1197.6 
    2999 RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
    3000 5.348) 
    3001  
    3002 
    3003 > matchmaker #4 to #3/A pairing bs showAlignment true
    3004 
    3005 Parameters 
    3006 --- 
    3007 Chain pairing | bs 
    3008 Alignment algorithm | Needleman-Wunsch 
    3009 Similarity matrix | BLOSUM-62 
    3010 SS fraction | 0.3 
    3011 Gap open (HH/SS/other) | 18/18/6 
    3012 Gap extend | 1 
    3013 SS matrix |  |  | H | S | O 
    3014 ---|---|---|--- 
    3015 H | 6 | -9 | -6 
    3016 S |  | 6 | -6 
    3017 O |  |  | 4 
    3018 Iteration cutoff | 2 
    3019  
    3020 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3021 chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
    3022 score = 1197.6 
    3023 Alignment identifier is 1 
    3024 Showing conservation header ("seq_conservation" residue attribute) for
    3025 alignment 1 
    3026 Hiding conservation header for alignment 1 
    3027 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    3028 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3029 AF-O43246-F1-model_v4.pdb #4/A 
    3030 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    3031 RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
    3032 5.348) 
    3033  
    3034 
    3035 > matchmaker #4 to #3/A pairing bs showAlignment true
    3036 
    3037 Parameters 
    3038 --- 
    3039 Chain pairing | bs 
    3040 Alignment algorithm | Needleman-Wunsch 
    3041 Similarity matrix | BLOSUM-62 
    3042 SS fraction | 0.3 
    3043 Gap open (HH/SS/other) | 18/18/6 
    3044 Gap extend | 1 
    3045 SS matrix |  |  | H | S | O 
    3046 ---|---|---|--- 
    3047 H | 6 | -9 | -6 
    3048 S |  | 6 | -6 
    3049 O |  |  | 4 
    3050 Iteration cutoff | 2 
    3051  
    3052 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3053 chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
    3054 score = 1197.6 
    3055 Alignment identifier is 2 
    3056 Showing conservation header ("seq_conservation" residue attribute) for
    3057 alignment 2 
    3058 Hiding conservation header for alignment 2 
    3059 Chains used in RMSD evaluation for alignment 2: AtCAT4_final-
    3060 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3061 AF-O43246-F1-model_v4.pdb #4/A 
    3062 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    3063 RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
    3064 5.348) 
    3065  
    3066 
    3067 > ui tool show "Modeller Comparative"
    3068 
    3069 > modeller comparative 1:2 numModels 5 fast false multichain false hetPreserve
    3070 > true hydrogens true waterPreserve true
    3071 
    3072 Webservices job id: 63RUMTGUXZHWP15D 
    3073 Modeller job (ID 63RUMTGUXZHWP15D) finished 
    3074 Parameters 
    3075 --- 
    3076 Chain pairing | ss 
    3077 Alignment algorithm | Needleman-Wunsch 
    3078 Similarity matrix | BLOSUM-62 
    3079 SS fraction | 0.3 
    3080 Gap open (HH/SS/other) | 18/18/6 
    3081 Gap extend | 1 
    3082 SS matrix |  |  | H | S | O 
    3083 ---|---|---|--- 
    3084 H | 6 | -9 | -6 
    3085 S |  | 6 | -6 
    3086 O |  |  | 4 
    3087 Iteration cutoff | 2 
    3088  
    3089 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3090 chain A (#3) with chain_A, chain A (#), sequence alignment score = 531.6 
    3091 RMSD between 8 pruned atom pairs is 1.367 angstroms; (across all 501 pairs:
    3092 22.621) 
    3093  
    3094 Parameters 
    3095 --- 
    3096 Chain pairing | ss 
    3097 Alignment algorithm | Needleman-Wunsch 
    3098 Similarity matrix | BLOSUM-62 
    3099 SS fraction | 0.3 
    3100 Gap open (HH/SS/other) | 18/18/6 
    3101 Gap extend | 1 
    3102 SS matrix |  |  | H | S | O 
    3103 ---|---|---|--- 
    3104 H | 6 | -9 | -6 
    3105 S |  | 6 | -6 
    3106 O |  |  | 4 
    3107 Iteration cutoff | 2 
    3108  
    3109 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3110 chain A (#3) with chain_A, chain A (#), sequence alignment score = 404.2 
    3111 RMSD between 8 pruned atom pairs is 1.235 angstroms; (across all 501 pairs:
    3112 32.296) 
    3113  
    3114 Parameters 
    3115 --- 
    3116 Chain pairing | ss 
    3117 Alignment algorithm | Needleman-Wunsch 
    3118 Similarity matrix | BLOSUM-62 
    3119 SS fraction | 0.3 
    3120 Gap open (HH/SS/other) | 18/18/6 
    3121 Gap extend | 1 
    3122 SS matrix |  |  | H | S | O 
    3123 ---|---|---|--- 
    3124 H | 6 | -9 | -6 
    3125 S |  | 6 | -6 
    3126 O |  |  | 4 
    3127 Iteration cutoff | 2 
    3128  
    3129 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3130 chain A (#3) with chain_A, chain A (#), sequence alignment score = 452.9 
    3131 RMSD between 5 pruned atom pairs is 0.956 angstroms; (across all 494 pairs:
    3132 21.034) 
    3133  
    3134 Parameters 
    3135 --- 
    3136 Chain pairing | ss 
    3137 Alignment algorithm | Needleman-Wunsch 
    3138 Similarity matrix | BLOSUM-62 
    3139 SS fraction | 0.3 
    3140 Gap open (HH/SS/other) | 18/18/6 
    3141 Gap extend | 1 
    3142 SS matrix |  |  | H | S | O 
    3143 ---|---|---|--- 
    3144 H | 6 | -9 | -6 
    3145 S |  | 6 | -6 
    3146 O |  |  | 4 
    3147 Iteration cutoff | 2 
    3148  
    3149 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3150 chain A (#3) with chain_A, chain A (#), sequence alignment score = 472.8 
    3151 RMSD between 10 pruned atom pairs is 1.324 angstroms; (across all 492 pairs:
    3152 23.779) 
    3153  
    3154 Parameters 
    3155 --- 
    3156 Chain pairing | ss 
    3157 Alignment algorithm | Needleman-Wunsch 
    3158 Similarity matrix | BLOSUM-62 
    3159 SS fraction | 0.3 
    3160 Gap open (HH/SS/other) | 18/18/6 
    3161 Gap extend | 1 
    3162 SS matrix |  |  | H | S | O 
    3163 ---|---|---|--- 
    3164 H | 6 | -9 | -6 
    3165 S |  | 6 | -6 
    3166 O |  |  | 4 
    3167 Iteration cutoff | 2 
    3168  
    3169 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3170 chain A (#3) with chain_A, chain A (#), sequence alignment score = 449.9 
    3171 RMSD between 7 pruned atom pairs is 0.902 angstroms; (across all 494 pairs:
    3172 24.766) 
    3173  
    3174 Associated chain_A chain A to AF-O43246-F1-model_v4.pdb, chain A with 0
    3175 mismatches 
    3176 Chain information for chain_A 
    3177 --- 
    3178 Chain | Description 
    3179 5.1/A 5.2/A 5.3/A 5.4/A 5.5/A | No description available 
    3180  
    3181 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    3182 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3183 AF-O43246-F1-model_v4.pdb #4/A, chain_A #5.1/A, chain_A #5.2/A, chain_A
    3184 #5.3/A, chain_A #5.4/A, chain_A #5.5/A 
    3185 
    3186 > hide #4 models
    3187 
    3188 > matchmaker #5 to #3
    3189 
    3190 Parameters 
    3191 --- 
    3192 Chain pairing | bb 
    3193 Alignment algorithm | Needleman-Wunsch 
    3194 Similarity matrix | BLOSUM-62 
    3195 SS fraction | 0.3 
    3196 Gap open (HH/SS/other) | 18/18/6 
    3197 Gap extend | 1 
    3198 SS matrix |  |  | H | S | O 
    3199 ---|---|---|--- 
    3200 H | 6 | -9 | -6 
    3201 S |  | 6 | -6 
    3202 O |  |  | 4 
    3203 Iteration cutoff | 2 
    3204  
    3205 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3206 chain A (#3) with chain_A, chain A (#5.1), sequence alignment score = 531.6 
    3207 RMSD between 8 pruned atom pairs is 1.367 angstroms; (across all 501 pairs:
    3208 22.621) 
    3209  
    3210 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3211 chain A (#3) with chain_A, chain A (#5.2), sequence alignment score = 404.2 
    3212 RMSD between 8 pruned atom pairs is 1.235 angstroms; (across all 501 pairs:
    3213 32.296) 
    3214  
    3215 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3216 chain A (#3) with chain_A, chain A (#5.3), sequence alignment score = 452.9 
    3217 RMSD between 5 pruned atom pairs is 0.956 angstroms; (across all 494 pairs:
    3218 21.034) 
    3219  
    3220 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3221 chain A (#3) with chain_A, chain A (#5.4), sequence alignment score = 472.8 
    3222 RMSD between 10 pruned atom pairs is 1.324 angstroms; (across all 492 pairs:
    3223 23.779) 
    3224  
    3225 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3226 chain A (#3) with chain_A, chain A (#5.5), sequence alignment score = 449.9 
    3227 RMSD between 7 pruned atom pairs is 0.902 angstroms; (across all 494 pairs:
    3228 24.766) 
    3229  
    3230 
    3231 > hide #!3 models
    3232 
    3233 > hide #5.2 models
    3234 
    3235 > hide #5.3 models
    3236 
    3237 > hide #5.4 models
    3238 
    3239 > hide #5.5 models
    3240 
    3241 > hide #5.1 models
    3242 
    3243 > show #5.2 models
    3244 
    3245 > hide #5.2 models
    3246 
    3247 > show #5.3 models
    3248 
    3249 > hide #5.3 models
    3250 
    3251 > show #5.4 models
    3252 
    3253 > hide #5.4 models
    3254 
    3255 > show #5.5 models
    3256 
    3257 > hide #5.5 models
    3258 
    3259 > close #5
    3260 
    3261 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    3262 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3263 AF-O43246-F1-model_v4.pdb #4/A 
    3264 
    3265 > ui tool show "Modeller Comparative"
    3266 
    3267 > modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
    3268 > false hydrogens true waterPreserve true directory
    3269 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    3270 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    3271 > model_modeller"
    3272 
    3273 Webservices job id: 4HXLBUSRUEWDV4Z9 
    3274 Modeller job (ID 4HXLBUSRUEWDV4Z9) finished 
    3275 Parameters 
    3276 --- 
    3277 Chain pairing | ss 
    3278 Alignment algorithm | Needleman-Wunsch 
    3279 Similarity matrix | BLOSUM-62 
    3280 SS fraction | 0.3 
    3281 Gap open (HH/SS/other) | 18/18/6 
    3282 Gap extend | 1 
    3283 SS matrix |  |  | H | S | O 
    3284 ---|---|---|--- 
    3285 H | 6 | -9 | -6 
    3286 S |  | 6 | -6 
    3287 O |  |  | 4 
    3288 Iteration cutoff | 2 
    3289  
    3290 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3291 chain A (#3) with chain_A, chain A (#), sequence alignment score = 377.6 
    3292 RMSD between 11 pruned atom pairs is 1.363 angstroms; (across all 494 pairs:
    3293 19.118) 
    3294  
    3295 Associated chain_A chain A to AF-O43246-F1-model_v4.pdb, chain A with 0
    3296 mismatches 
    3297 Chain information for chain_A 
    3298 --- 
    3299 Chain | Description 
    3300 5.1/A | No description available 
    3301  
    3302 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    3303 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3304 AF-O43246-F1-model_v4.pdb #4/A, chain_A #5.1/A 
    3305 
    3306 > close #5
    3307 
    3308 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    3309 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3310 AF-O43246-F1-model_v4.pdb #4/A 
    3311 
    3312 > ui tool show "Modeller Comparative"
    3313 
    3314 > modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
    3315 > false hydrogens false waterPreserve false directory
    3316 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    3317 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    3318 > model_modeller"
    3319 
    3320 Webservices job id: SQ53K70VGRRVFOCB 
    3321 Modeller job (ID SQ53K70VGRRVFOCB) finished 
    3322 Parameters 
    3323 --- 
    3324 Chain pairing | ss 
    3325 Alignment algorithm | Needleman-Wunsch 
    3326 Similarity matrix | BLOSUM-62 
    3327 SS fraction | 0.3 
    3328 Gap open (HH/SS/other) | 18/18/6 
    3329 Gap extend | 1 
    3330 SS matrix |  |  | H | S | O 
    3331 ---|---|---|--- 
    3332 H | 6 | -9 | -6 
    3333 S |  | 6 | -6 
    3334 O |  |  | 4 
    3335 Iteration cutoff | 2 
    3336  
    3337 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3338 chain A (#3) with chain_A, chain A (#), sequence alignment score = 533.4 
    3339 RMSD between 9 pruned atom pairs is 1.333 angstroms; (across all 494 pairs:
    3340 16.579) 
    3341  
    3342 Associated chain_A chain A to AF-O43246-F1-model_v4.pdb, chain A with 0
    3343 mismatches 
    3344 Chain information for chain_A 
    3345 --- 
    3346 Chain | Description 
    3347 5.1/A | No description available 
    3348  
    3349 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    3350 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3351 AF-O43246-F1-model_v4.pdb #4/A, chain_A #5.1/A 
    3352 
    3353 > show #!3 models
    3354 
    3355 > hide #!3 models
    3356 
    3357 > close #5
    3358 
    3359 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    3360 coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    3361 AF-O43246-F1-model_v4.pdb #4/A 
    3362 
    3363 > open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
    3364 > Newstead
    3365 > Lab/Postdoc/MD/AtCAT4_new_model_to_test_TM1/setup_new/system_solvated_ions.gro"
    3366 
    3367 Chain information for AtCAT4 cryoEM structure in POPC-Cholesterol in water #5 
    3368 --- 
    3369 Chain | Description 
    3370 ? | No description available 
    3371  
    3372 
    3373 > hide #5:POPC,CHL1,SOL
    3374 
    3375 > view
    3376 
    3377 > matchmaker #5 to #3
    3378 
    3379 Parameters 
    3380 --- 
    3381 Chain pairing | bb 
    3382 Alignment algorithm | Needleman-Wunsch 
    3383 Similarity matrix | BLOSUM-62 
    3384 SS fraction | 0.3 
    3385 Gap open (HH/SS/other) | 18/18/6 
    3386 Gap extend | 1 
    3387 SS matrix |  |  | H | S | O 
    3388 ---|---|---|--- 
    3389 H | 6 | -9 | -6 
    3390 S |  | 6 | -6 
    3391 O |  |  | 4 
    3392 Iteration cutoff | 2 
    3393  
    3394 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    3395 chain A (#3) with AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain
    3396 (blank) (#5), sequence alignment score = 2528.4 
    3397 RMSD between 504 pruned atom pairs is 0.372 angstroms; (across all 517 pairs:
    3398 0.601) 
    3399  
    3400 
    3401 > show #!3 models
    3402 
    3403 > view
    3404 
    3405 > hide #!3 models
    3406 
    3407 > select add #3
    3408 
    3409 14590 atoms, 14841 bonds, 1 pseudobond, 1269 residues, 3 models selected 
    3410 
    3411 > select subtract #3
    3412 
    3413 4821 atoms, 4953 bonds, 635 residues, 1 model selected 
    3414 
    3415 > select #5,4
    3416 
    3417 162643 atoms, 128423 bonds, 35494 residues, 2 models selected 
    3418 
    3419 > ui tool show Matchmaker
    3420 
    3421 > matchmaker #4 to #5/? pairing bs showAlignment true
    3422 
    3423 Parameters 
    3424 --- 
    3425 Chain pairing | bs 
    3426 Alignment algorithm | Needleman-Wunsch 
    3427 Similarity matrix | BLOSUM-62 
    3428 SS fraction | 0.3 
    3429 Gap open (HH/SS/other) | 18/18/6 
    3430 Gap extend | 1 
    3431 SS matrix |  |  | H | S | O 
    3432 ---|---|---|--- 
    3433 H | 6 | -9 | -6 
    3434 S |  | 6 | -6 
    3435 O |  |  | 4 
    3436 Iteration cutoff | 2 
    3437  
    3438 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    3439 (#5) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment score =
    3440 1209.8 
    3441 Alignment identifier is 2 
    3442 Showing conservation header ("seq_conservation" residue attribute) for
    3443 alignment 2 
    3444 Hiding conservation header for alignment 2 
    3445 Chains used in RMSD evaluation for alignment 2: AF-O43246-F1-model_v4.pdb
    3446 #4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? 
    3447 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    3448 RMSD between 285 pruned atom pairs is 1.152 angstroms; (across all 545 pairs:
    3449 8.655) 
    3450  
    3451 
    3452 > show #4 models
    3453 
    3454 > ui tool show "Modeller Comparative"
    3455 
    3456 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    3457 > false hydrogens true waterPreserve false directory
    3458 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    3459 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    3460 > model_modeller"
    3461 
    3462 Webservices job id: I9KJIO2YLDJMCQO1 
    3463 Modeller job (ID I9KJIO2YLDJMCQO1) finished 
    3464  
    3465 Modeller error output 
    3466 Traceback (most recent call last): 
    3467 File "ModellerModelling.py", line 76, in   
    3468 a.make() 
    3469 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    3470 line 141, in make 
    3471 self.homcsr(exit_stage) 
    3472 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    3473 line 624, in homcsr 
    3474 self.check_alignment(aln) 
    3475 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    3476 line 577, in check_alignment 
    3477 aln.check() 
    3478 File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 215, in
    3479 check 
    3480 self.check_structure_structure(io=io) 
    3481 File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 224, in
    3482 check_structure_structure 
    3483 return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) 
    3484 _modeller.SequenceMismatchError: read_te_291E> Sequence difference between
    3485 alignment and pdb : 
    3486  
    3487  
    3488 Modeller run output 
    3489  
    3490 MODELLER 10.6, 2024/10/17, r12888 
    3491  
    3492 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 
    3493  
    3494  
    3495 Copyright(c) 1989-2024 Andrej Sali 
    3496 All Rights Reserved 
    3497  
    3498 Written by A. Sali 
    3499 with help from 
    3500 B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 
    3501 M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, 
    3502 A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, 
    3503 F. Melo, J.P. Overington, E. Feyfant 
    3504 University of California, San Francisco, USA 
    3505 Rockefeller University, New York, USA 
    3506 Harvard University, Cambridge, USA 
    3507 Imperial Cancer Research Fund, London, UK 
    3508 Birkbeck College, University of London, London, UK 
    3509  
    3510  
    3511 Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
    3512 4.18.0-553.62.1.el8_10.x86_64 x86_64 
    3513 Date and time of compilation : 2024/10/17 20:43:03 
    3514 MODELLER executable type : x86_64-intel8 
    3515 Job starting time (YY/MM/DD HH:MM:SS): 2025/07/27 11:39:01 
    3516  
    3517 environ____W> The class 'environ' is deprecated; use 'Environ' instead 
    3518 openf___224_> Open $(LIB)/restyp.lib 
    3519 openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib 
    3520 rdresgr_266_> Number of residue groups: 2 
    3521 openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib 
    3522  
    3523 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
    3524 0.183 
    3525  
    3526 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
    3527 0.183 
    3528 openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib 
    3529  
    3530 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
    3531 0.230 
    3532 rdrdih__263_> Number of dihedral angle types : 9 
    3533 Maximal number of dihedral angle optima: 3 
    3534 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 
    3535 openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib 
    3536  
    3537 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
    3538 0.242 
    3539 openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib 
    3540 rdwilmo_274_> Mainchain residue conformation classes: APBLE 
    3541 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib 
    3542 rdclass_257_> Number of classes: 5 
    3543 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib 
    3544 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib 
    3545 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib 
    3546 openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat 
    3547 rdrrwgh_268_> Number of residue types: 21 
    3548 allhmodel__W> The class 'allhmodel' is deprecated; use 'AllHModel' instead 
    3549 openf___224_> Open alignment.ali 
    3550  
    3551 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 283002 276.369
    3552 0.270 
    3553  
    3554 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 298535 291.538
    3555 0.285 
    3556  
    3557 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 314385 307.017
    3558 0.300 
    3559  
    3560 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 346085 337.974
    3561 0.330 
    3562  
    3563 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 409485 399.888
    3564 0.391 
    3565  
    3566 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 536285 523.716
    3567 0.511 
    3568  
    3569 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 538537 525.915 0.514 
    3570  
    3571 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 541073 528.392 0.516 
    3572  
    3573 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543609 530.868 0.518 
    3574 read_al_374_> Non-standard residue type,position,sequence: . 1 1 
    3575 read_al_374_> Non-standard residue type,position,sequence: . 564 1 
    3576  
    3577 Read the alignment from file : alignment.ali 
    3578  
    3579 Total number of alignment positions: 652 
    3580  
    3581 # Code #_Res #_Segm PDB_code Name 
    3582 \------------------------------------------------------------------------------- 
    3583 1 AtCAT4_cr 564 1 AtCAT4_cryo 
    3584 2 AF-O43246 635 1 AF-O43246-F 
    3585 3 chain_A 635 1 chain_A 
    3586 check_a_343_> >> BEGINNING OF COMMAND 
    3587 openf___224_> Open ./AtCAT4_cryoEM_structure_in_POPC-
    3588 Cholesterol_in_water_5.pdb 
    3589  
    3590 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 714534 697.787
    3591 0.681 
    3592 read_pd_459W> Residue type ACE not recognized. 'AutoModel' model building 
    3593 will treat this residue as a rigid body. 
    3594 To use real parameters, add the residue type to ${LIB}/restyp.lib, 
    3595 its topology to ${LIB}/top_*.lib, and suitable forcefield 
    3596 parameters to ${LIB}/par.lib. 
    3597  
    3598 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 714534 697.787 0.681 
    3599  
    3600 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 714705 697.954
    3601 0.682 
    3602 read_pd_459W> Residue type HID not recognized. 'AutoModel' model building 
    3603 will treat this residue as a rigid body. 
    3604 To use real parameters, add the residue type to ${LIB}/restyp.lib, 
    3605 its topology to ${LIB}/top_*.lib, and suitable forcefield 
    3606 parameters to ${LIB}/par.lib. 
    3607  
    3608 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 715555 698.784
    3609 0.682 
    3610  
    3611 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 716813 700.013
    3612 0.684 
    3613  
    3614 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 718717 701.872
    3615 0.685 
    3616  
    3617 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 721573 704.661
    3618 0.688 
    3619  
    3620 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 725857 708.845
    3621 0.692 
    3622  
    3623 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 725857 708.845 0.692 
    3624  
    3625 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 725947 708.933
    3626 0.692 
    3627  
    3628 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 732373 715.208
    3629 0.698 
    3630  
    3631 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 732373 715.208 0.698 
    3632  
    3633 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 732508 715.340
    3634 0.699 
    3635  
    3636 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 742130 724.736
    3637 0.708 
    3638  
    3639 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 742130 724.736 0.708 
    3640  
    3641 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 742328 724.930
    3642 0.708 
    3643  
    3644 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 756778 739.041
    3645 0.722 
    3646  
    3647 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 756778 739.041 0.722 
    3648  
    3649 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 757075 739.331
    3650 0.722 
    3651  
    3652 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 778733 760.481
    3653 0.743 
    3654  
    3655 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778733 760.481 0.743 
    3656  
    3657 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779183 760.921
    3658 0.743 
    3659  
    3660 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 811687 792.663
    3661 0.774 
    3662  
    3663 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 811687 792.663 0.774 
    3664  
    3665 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 812362 793.322
    3666 0.775 
    3667  
    3668 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 861118 840.936
    3669 0.821 
    3670  
    3671 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 861118 840.936 0.821 
    3672  
    3673 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 862126 841.920
    3674 0.822 
    3675  
    3676 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 935260 913.340
    3677 0.892 
    3678  
    3679 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 935260 913.340 0.892 
    3680  
    3681 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 936772 914.816
    3682 0.893 
    3683  
    3684 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1046456 1021.930
    3685 0.998 
    3686  
    3687 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1046456 1021.930
    3688 0.998 
    3689  
    3690 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1048724 1024.145
    3691 1.000 
    3692 rdpdb___459W> Residue type NME not recognized. 'AutoModel' model building 
    3693 will treat this residue as a rigid body. 
    3694 To use real parameters, add the residue type to ${LIB}/restyp.lib, 
    3695 its topology to ${LIB}/top_*.lib, and suitable forcefield 
    3696 parameters to ${LIB}/par.lib. 
    3697  
    3698 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1046987 1022.448
    3699 0.998 
    3700 read_te_291E> Sequence difference between alignment and pdb : 
    3701 x (mismatch at alignment position 3) 
    3702 Alignment .PHQLAKKLSAVDLVAIGVGTTIGAGVYILVGTVAREHTGPALAVSFFIAGVAAALS 
    3703 PDB .P.QLAKKLSAVDLVAIGVGTTIGAGVYILVGTVARE.TGPALAVSFFIAGVAAALS 
    3704 Match ** ********************************** ******************* 
    3705 Alignment residue type 7 (H, HIS) does not match pdb 
    3706 residue type 68 (., HID), 
    3707 for align code AtCAT4_cryoEM_structure_in_POPC-Choleste (atom file
    3708 AtCAT4_cryoEM_structure_in_POPC-Cholesterol_in_water_5), pdb residue number "
    3709 22", chain "" 
    3710  
    3711 Please check your alignment file header to be sure you correctly specified 
    3712 the starting and ending residue numbers and chains. The alignment sequence 
    3713 must match that from the atom file exactly. 
    3714  
    3715 Another possibility is that some residues in the atom file are missing, 
    3716 perhaps because they could not be resolved experimentally. (Note that Modeller 
    3717 reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) 
    3718 In this case, simply replace the section of your alignment corresponding 
    3719 to these missing residues with gaps. 
    3720 read_te_288W> Protein not accepted: 1 AtCAT4_cryoEM_structure_in_POPC-Choleste 
    3721  
    3722 No output models from Modeller; see log for Modeller text output. 
    3723 
    3724 > hide #4 models
    3725 
    3726 > select subtract #4
    3727 
    3728 157822 atoms, 123470 bonds, 34859 residues, 1 model selected 
    3729 
    3730 > select #5:HID
    3731 
    3732 102 atoms, 102 bonds, 6 residues, 1 model selected 
    3733 
    3734 > show sel atoms
    3735 
    3736 > style sel sphere
    3737 
    3738 Changed 102 atom styles 
    3739 
    3740 > style sel ball
    3741 
    3742 Changed 102 atom styles 
    3743 
    3744 > hide #5 atoms
    3745 
    3746 > select #5:HID
    3747 
    3748 102 atoms, 102 bonds, 6 residues, 1 model selected 
    3749 
    3750 > show sel atoms
    3751 
    3752 > style sel ball
    3753 
    3754 Changed 102 atom styles 
    3755 
    3756 > ui mousemode right swapaa
    3757 
    3758 > swappa
    3759 
    3760 Unknown command: swappa 
    3761 
    3762 > swapaa
    3763 
    3764 Missing or invalid "residues" argument: empty atom specifier 
    3765 
    3766 > help swapaa
    3767 
    3768 > swapaa #5:HID
    3769 
    3770 Missing or invalid "resTypes" argument: Expected a text string 
    3771 
    3772 > swapaa #5:HID HIS
    3773 
    3774 Using Dunbrack library 
    3775 AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 22: phi -77.6,
    3776 psi 67.8 trans 
    3777 AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 57: phi -136.9,
    3778 psi 159.9 trans 
    3779 AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 95: phi -58.0,
    3780 psi -46.7 trans 
    3781 AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 520: phi -53.6,
    3782 psi 134.2 trans 
    3783 AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 524: phi -157.4,
    3784 psi -172.6 trans 
    3785 AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 577: phi -103.8,
    3786 psi 7.8 trans 
    3787 Applying HIS rotamer (chi angles: -64.5 -70.6) to AtCAT4 cryoEM structure in
    3788 POPC-Cholesterol in water #5/? HIS 22 
    3789 Applying HIS rotamer (chi angles: -62.6 -79.6) to AtCAT4 cryoEM structure in
    3790 POPC-Cholesterol in water #5/? HIS 57 
    3791 Applying HIS rotamer (chi angles: -179.8 72.7) to AtCAT4 cryoEM structure in
    3792 POPC-Cholesterol in water #5/? HIS 95 
    3793 Applying HIS rotamer (chi angles: -173.8 -75.5) to AtCAT4 cryoEM structure in
    3794 POPC-Cholesterol in water #5/? HIS 520 
    3795 Applying HIS rotamer (chi angles: 61.8 81.6) to AtCAT4 cryoEM structure in
    3796 POPC-Cholesterol in water #5/? HIS 524 
    3797 Applying HIS rotamer (chi angles: -173.8 -172.5) to AtCAT4 cryoEM structure in
    3798 POPC-Cholesterol in water #5/? HIS 577 
    3799 
    3800 > delete #5:POPC,CHL1,SOL
    3801 
    3802 > select add #5
    3803 
    3804 8746 atoms, 8530 bonds, 869 residues, 1 model selected 
    3805 
    3806 > show sel atoms
    3807 
    3808 > undo
    3809 
    3810 > delete #5:POPC,CHL1,SOL,CL,NA
    3811 
    3812 > show sel atoms
    3813 
    3814 > undo
    3815 
    3816 > addh #5:HIS
    3817 
    3818 Summary of feedback from adding hydrogens to AtCAT4 cryoEM structure in POPC-
    3819 Cholesterol in water #5 
    3820 --- 
    3821 warnings | Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? PRO 152 CG because it is missing heavy-atom bond partners 
    3822 Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
    3823 #5/? PRO 152 CB because it is missing heavy-atom bond partners 
    3824 Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
    3825 #5/? LEU 476 CG because it is missing heavy-atom bond partners 
    3826 Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
    3827 #5/? LEU 476 HG because it is missing heavy-atom bond partners 
    3828 Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
    3829 #5/? LEU 476 CD1 because it is missing heavy-atom bond partners 
    3830 1 messages similar to the above omitted 
    3831 notes | No usable SEQRES records for AtCAT4 cryoEM structure in POPC-Cholesterol in water (#5) chain (blank); guessing termini instead 
    3832 Chain-initial residues that are actual N termini: AtCAT4 cryoEM structure in
    3833 POPC-Cholesterol in water #5/? ACE 20 
    3834 Chain-initial residues that are not actual N termini: 
    3835 Chain-final residues that are actual C termini: AtCAT4 cryoEM structure in
    3836 POPC-Cholesterol in water #5/? NME 583 
    3837 Chain-final residues that are not actual C termini: 
    3838 462 hydrogen bonds 
    3839 33 hydrogens added 
    3840  
    3841 
    3842 > select clear
    3843 
    3844 > show #4 models
    3845 
    3846 > hide #4 models
    3847 
    3848 > select add #4
    3849 
    3850 4821 atoms, 4953 bonds, 635 residues, 1 model selected 
    3851 
    3852 > select add #5
    3853 
    3854 13295 atoms, 13516 bonds, 1199 residues, 2 models selected 
    3855 
    3856 > ui tool show Matchmaker
    3857 
    3858 > matchmaker #4 to #5/? pairing bs showAlignment true
    3859 
    3860 Parameters 
    3861 --- 
    3862 Chain pairing | bs 
    3863 Alignment algorithm | Needleman-Wunsch 
    3864 Similarity matrix | BLOSUM-62 
    3865 SS fraction | 0.3 
    3866 Gap open (HH/SS/other) | 18/18/6 
    3867 Gap extend | 1 
    3868 SS matrix |  |  | H | S | O 
    3869 ---|---|---|--- 
    3870 H | 6 | -9 | -6 
    3871 S |  | 6 | -6 
    3872 O |  |  | 4 
    3873 Iteration cutoff | 2 
    3874  
    3875 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    3876 (#5) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment score =
    3877 1209.8 
    3878 Alignment identifier is 1 
    3879 Showing conservation header ("seq_conservation" residue attribute) for
    3880 alignment 1 
    3881 Hiding conservation header for alignment 1 
    3882 Chains used in RMSD evaluation for alignment 1: AF-O43246-F1-model_v4.pdb
    3883 #4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? 
    3884 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    3885 RMSD between 285 pruned atom pairs is 1.152 angstroms; (across all 545 pairs:
    3886 8.655) 
    3887  
    3888 
    3889 > ui tool show "Modeller Comparative"
    3890 
    3891 > modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
    3892 > false hydrogens true waterPreserve false directory
    3893 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    3894 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    3895 > model_modeller"
    3896 
    3897 Webservices job id: 03PC2J0R944H8KUG 
    3898 Modeller job (ID 03PC2J0R944H8KUG) finished 
    3899 Parameters 
    3900 --- 
    3901 Chain pairing | ss 
    3902 Alignment algorithm | Needleman-Wunsch 
    3903 Similarity matrix | BLOSUM-62 
    3904 SS fraction | 0.3 
    3905 Gap open (HH/SS/other) | 18/18/6 
    3906 Gap extend | 1 
    3907 SS matrix |  |  | H | S | O 
    3908 ---|---|---|--- 
    3909 H | 6 | -9 | -6 
    3910 S |  | 6 | -6 
    3911 O |  |  | 4 
    3912 Iteration cutoff | 2 
    3913  
    3914 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    3915 (#5) with chain_A, chain (blank) (#), sequence alignment score = 284.4 
    3916 RMSD between 12 pruned atom pairs is 1.489 angstroms; (across all 530 pairs:
    3917 29.745) 
    3918  
    3919 Associated chain_A chain to AF-O43246-F1-model_v4.pdb, chain A with 0
    3920 mismatches 
    3921 Chain information for chain_A 
    3922 --- 
    3923 Chain | Description 
    3924 6.1/? | No description available 
    3925  
    3926 Chains used in RMSD evaluation for alignment 1: AF-O43246-F1-model_v4.pdb
    3927 #4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?, chain_A
    3928 #6.1/? 
    3929 
    3930 > hide #5 models
    3931 
    3932 > close #6
    3933 
    3934 Chains used in RMSD evaluation for alignment 1: AF-O43246-F1-model_v4.pdb
    3935 #4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? 
    3936 
    3937 > show #4 models
    3938 
    3939 > show #5 models
    3940 
    3941 > select clear
    3942 
    3943 > delete #4:1-30
    3944 
    3945 > delete #4:594-600
    3946 
    3947 > delete #4:594-636
    3948 
    3949 > ui tool show Matchmaker
    3950 
    3951 > matchmaker #!4 to #5/? pairing bs showAlignment true
    3952 
    3953 Parameters 
    3954 --- 
    3955 Chain pairing | bs 
    3956 Alignment algorithm | Needleman-Wunsch 
    3957 Similarity matrix | BLOSUM-62 
    3958 SS fraction | 0.3 
    3959 Gap open (HH/SS/other) | 18/18/6 
    3960 Gap extend | 1 
    3961 SS matrix |  |  | H | S | O 
    3962 ---|---|---|--- 
    3963 H | 6 | -9 | -6 
    3964 S |  | 6 | -6 
    3965 O |  |  | 4 
    3966 Iteration cutoff | 2 
    3967  
    3968 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    3969 (#5) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment score =
    3970 1214.1 
    3971 Alignment identifier is 2 
    3972 Showing conservation header ("seq_conservation" residue attribute) for
    3973 alignment 2 
    3974 Hiding conservation header for alignment 2 
    3975 Chains used in RMSD evaluation for alignment 2: AF-O43246-F1-model_v4.pdb
    3976 #4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? 
    3977 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    3978 RMSD between 286 pruned atom pairs is 1.148 angstroms; (across all 543 pairs:
    3979 8.534) 
    3980  
    3981 
    3982 > ui tool show "Modeller Comparative"
    3983 
    3984 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    3985 > false hydrogens true waterPreserve false directory
    3986 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    3987 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    3988 > model_modeller"
    3989 
    3990 Webservices job id: 12UKJZ1RC6WQUGV9 
    3991 Modeller job (ID 12UKJZ1RC6WQUGV9) finished 
    3992 Parameters 
    3993 --- 
    3994 Chain pairing | ss 
    3995 Alignment algorithm | Needleman-Wunsch 
    3996 Similarity matrix | BLOSUM-62 
    3997 SS fraction | 0.3 
    3998 Gap open (HH/SS/other) | 18/18/6 
    3999 Gap extend | 1 
    4000 SS matrix |  |  | H | S | O 
    4001 ---|---|---|--- 
    4002 H | 6 | -9 | -6 
    4003 S |  | 6 | -6 
    4004 O |  |  | 4 
    4005 Iteration cutoff | 2 
    4006  
    4007 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    4008 (#5) with chain_A, chain (blank) (#), sequence alignment score = 268 
    4009 RMSD between 6 pruned atom pairs is 1.324 angstroms; (across all 537 pairs:
    4010 25.813) 
    4011  
    4012 Associated chain_A chain to AF-O43246-F1-model_v4.pdb, chain A with 0
    4013 mismatches 
    4014 Chain information for chain_A 
    4015 --- 
    4016 Chain | Description 
    4017 6.1/? | No description available 
    4018  
    4019 Chains used in RMSD evaluation for alignment 2: AF-O43246-F1-model_v4.pdb
    4020 #4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?, chain_A
    4021 #6.1/? 
    4022 
    4023 > hide #5 models
    4024 
    4025 > hide #!4 models
    4026 
    4027 > show #5 models
    4028 
    4029 > show #!4 models
    4030 
    4031 > show #!1 models
    4032 
    4033 > hide #!4 models
    4034 
    4035 > hide #!6 models
    4036 
    4037 > hide #6.1 models
    4038 
    4039 > hide #5 models
    4040 
    4041 > show #!4 models
    4042 
    4043 > show #2 models
    4044 
    4045 > hide #2 models
    4046 
    4047 > hide #!4 models
    4048 
    4049 > view
    4050 
    4051 > select add #1
    4052 
    4053 8573 atoms, 8694 bonds, 1 pseudobond, 558 residues, 2 models selected 
    4054 
    4055 > show sel atoms
    4056 
    4057 > select subtract #1
    4058 
    4059 Nothing selected 
    4060 
    4061 > open uniprot:O43246
    4062 
    4063 Summary of feedback from opening O43246 fetched from uniprot 
    4064 --- 
    4065 notes | Fetching compressed O43246 UniProt info from https://www.uniprot.org/uniprot/O43246.xml 
    4066 Alignment identifier is O43246 
    4067 Associated
    4068 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    4069 chain A to O43246 with 0 mismatches 
    4070 Associated AF-O43246-F1-model_v4.pdb chain A to O43246 with 0 mismatches 
    4071 Associated chain_A (6.1) chain to O43246 with 0 mismatches 
    4072  
    4073 Opened UniProt O43246 
    4074 
    4075 > select #1/A:38-592 #4/A #6.1/*
    4076 
    4077 22461 atoms, 22833 bonds, 1753 residues, 3 models selected 
    4078 
    4079 > hide #!1 models
    4080 
    4081 > view
    4082 
    4083 > select #1/A:151,195,221,500 #4/A:151,195,221,500 #6.1/*:151,195,221,500,601
    4084 
    4085 158 atoms, 145 bonds, 13 residues, 3 models selected 
    4086 
    4087 > select #1/A:422,427 #4/A:422,427 #6.1/*:422,427
    4088 
    4089 56 atoms, 50 bonds, 6 residues, 3 models selected 
    4090 
    4091 > select #1/A:155-192 #4/A:155-192 #6.1/*:155-192
    4092 
    4093 1388 atoms, 1412 bonds, 114 residues, 3 models selected 
    4094 
    4095 > select #6.1/*:28,349,608 #1/A:349 #4/A:349
    4096 
    4097 59 atoms, 55 bonds, 5 residues, 3 models selected 
    4098 
    4099 > select
    4100 > #1/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4101 > #4/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4102 > #6.1/*:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4103 
    4104 10371 atoms, 10473 bonds, 819 residues, 3 models selected 
    4105 
    4106 > select #1/A:422,427 #4/A:422,427 #6.1/*:422,427
    4107 
    4108 56 atoms, 50 bonds, 6 residues, 3 models selected 
    4109 
    4110 > select #1/A:38-592 #4/A #6.1/*
    4111 
    4112 22461 atoms, 22833 bonds, 1753 residues, 3 models selected 
    4113 
    4114 > select #1/A:38-592 #4/A #6.1/*
    4115 
    4116 22461 atoms, 22833 bonds, 1753 residues, 3 models selected 
    4117 
    4118 > ~select
    4119 
    4120 Nothing selected 
    4121 
    4122 > select #1/A:151,195,221,500 #4/A:151,195,221,500 #6.1/*:151,195,221,500,601
    4123 
    4124 158 atoms, 145 bonds, 13 residues, 3 models selected 
    4125 
    4126 > select #1/A:422,427 #4/A:422,427 #6.1/*:422,427
    4127 
    4128 56 atoms, 50 bonds, 6 residues, 3 models selected 
    4129 
    4130 > select #1/A:155-192 #4/A:155-192 #6.1/*:155-192
    4131 
    4132 1388 atoms, 1412 bonds, 114 residues, 3 models selected 
    4133 
    4134 > select #1/A:155-192 #4/A:155-192 #6.1/*:155-192
    4135 
    4136 1388 atoms, 1412 bonds, 114 residues, 3 models selected 
    4137 
    4138 > ~select
    4139 
    4140 Nothing selected 
    4141 
    4142 > select #6.1/*:28,349,608 #1/A:349 #4/A:349
    4143 
    4144 59 atoms, 55 bonds, 5 residues, 3 models selected 
    4145 
    4146 > select #1/A:349 #4/A:349 #6.1/*:349
    4147 
    4148 25 atoms, 22 bonds, 3 residues, 3 models selected 
    4149 
    4150 > select
    4151 > #1/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4152 > #4/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4153 > #6.1/*:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4154 
    4155 10371 atoms, 10473 bonds, 819 residues, 3 models selected 
    4156 
    4157 > select
    4158 > #1/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4159 > #4/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4160 > #6.1/*:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
    4161 
    4162 10371 atoms, 10473 bonds, 819 residues, 3 models selected 
    4163 
    4164 > open /Users/ctn700/Library/CloudStorage/OneDrive-
    4165 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Apo_Sybody/RealSpaceRefine_34/AtCAT4_final-
    4166 > coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
    4167 
    4168 Chain information for AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
    4169 fixed_noH.pdb #7 
    4170 --- 
    4171 Chain | Description 
    4172 A | No description available 
    4173 B | No description available 
    4174  
    4175 
    4176 > view
    4177 
    4178 > select add #6.1
    4179 
    4180 15910 atoms, 16110 bonds, 1181 residues, 3 models selected 
    4181 
    4182 > select add #6
    4183 
    4184 15910 atoms, 16110 bonds, 1181 residues, 4 models selected 
    4185 
    4186 > select subtract #6
    4187 
    4188 6188 atoms, 6256 bonds, 546 residues, 2 models selected 
    4189 
    4190 > select add #4
    4191 
    4192 8448 atoms, 8602 bonds, 836 residues, 2 models selected 
    4193 
    4194 > select subtract #4
    4195 
    4196 4183 atoms, 4217 bonds, 273 residues, 1 model selected 
    4197 
    4198 > select add #1
    4199 
    4200 8573 atoms, 8694 bonds, 1 pseudobond, 558 residues, 2 models selected 
    4201 
    4202 > select subtract #1
    4203 
    4204 Nothing selected 
    4205 
    4206 > select add #6.1
    4207 
    4208 9722 atoms, 9854 bonds, 635 residues, 1 model selected 
    4209 
    4210 > select add #7
    4211 
    4212 14540 atoms, 14789 bonds, 1 pseudobond, 1269 residues, 3 models selected 
    4213 
    4214 > ui tool show "Show Sequence Viewer"
    4215 
    4216 > sequence chain #5/?
    4217 
    4218 Alignment identifier is 5/ 
    4219 
    4220 > ui tool show "Modeller Comparative"
    4221 
    4222 > select #5/*:20
    4223 
    4224 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4225 
    4226 > select #5/*
    4227 
    4228 8474 atoms, 8563 bonds, 564 residues, 1 model selected 
    4229 
    4230 > modeller comparative "5/ :1" numModels 5 fast true multichain false
    4231 > hetPreserve false hydrogens true waterPreserve false directory
    4232 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    4233 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    4234 > model_modeller"
    4235 
    4236 Webservices job id: TBAIP49CM3LNEJ9G 
    4237 Modeller job (ID TBAIP49CM3LNEJ9G) finished 
    4238 Parameters 
    4239 --- 
    4240 Chain pairing | ss 
    4241 Alignment algorithm | Needleman-Wunsch 
    4242 Similarity matrix | BLOSUM-62 
    4243 SS fraction | 0.3 
    4244 Gap open (HH/SS/other) | 18/18/6 
    4245 Gap extend | 1 
    4246 SS matrix |  |  | H | S | O 
    4247 ---|---|---|--- 
    4248 H | 6 | -9 | -6 
    4249 S |  | 6 | -6 
    4250 O |  |  | 4 
    4251 Iteration cutoff | 2 
    4252  
    4253 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    4254 (#5) with chain_(blank), chain (blank) (#), sequence alignment score = 2835.8 
    4255 RMSD between 562 pruned atom pairs is 0.171 angstroms; (across all 562 pairs:
    4256 0.171) 
    4257  
    4258 Associated chain_(blank) chain to chain (blank) with 0 mismatches 
    4259 Chain information for chain_(blank) 
    4260 --- 
    4261 Chain | Description 
    4262 8.1/? | No description available 
    4263  
    4264 
    4265 > hide #!7 models
    4266 
    4267 > select #8.1/?:25
    4268 
    4269 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4270 
    4271 > select up
    4272 
    4273 294 atoms, 294 bonds, 21 residues, 1 model selected 
    4274 
    4275 > show sel atoms
    4276 
    4277 > close #8
    4278 
    4279 > ui tool show "Modeller Comparative"
    4280 
    4281 > ui tool show Matchmaker
    4282 
    4283 > matchmaker #!7 to #6.1/? pairing bs showAlignment true
    4284 
    4285 Parameters 
    4286 --- 
    4287 Chain pairing | bs 
    4288 Alignment algorithm | Needleman-Wunsch 
    4289 Similarity matrix | BLOSUM-62 
    4290 SS fraction | 0.3 
    4291 Gap open (HH/SS/other) | 18/18/6 
    4292 Gap extend | 1 
    4293 SS matrix |  |  | H | S | O 
    4294 ---|---|---|--- 
    4295 H | 6 | -9 | -6 
    4296 S |  | 6 | -6 
    4297 O |  |  | 4 
    4298 Iteration cutoff | 2 
    4299  
    4300 Matchmaker chain_A, chain (blank) (#6.1) with AtCAT4_final-
    4301 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain A (#7), sequence
    4302 alignment score = 192.8 
    4303 Alignment identifier is 1 
    4304 Showing conservation header ("seq_conservation" residue attribute) for
    4305 alignment 1 
    4306 Hiding conservation header for alignment 1 
    4307 Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
    4308 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    4309 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    4310 RMSD between 9 pruned atom pairs is 1.656 angstroms; (across all 492 pairs:
    4311 25.311) 
    4312  
    4313 
    4314 > ui tool show "Modeller Comparative"
    4315 
    4316 > modeller comparative 1:1 numModels 5 fast true multichain false hetPreserve
    4317 > false hydrogens false waterPreserve true directory
    4318 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    4319 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    4320 > model_modeller"
    4321 
    4322 Webservices job id: W5UOTIFQA72M2SV2 
    4323 Modeller job (ID W5UOTIFQA72M2SV2) finished 
    4324 Parameters 
    4325 --- 
    4326 Chain pairing | ss 
    4327 Alignment algorithm | Needleman-Wunsch 
    4328 Similarity matrix | BLOSUM-62 
    4329 SS fraction | 0.3 
    4330 Gap open (HH/SS/other) | 18/18/6 
    4331 Gap extend | 1 
    4332 SS matrix |  |  | H | S | O 
    4333 ---|---|---|--- 
    4334 H | 6 | -9 | -6 
    4335 S |  | 6 | -6 
    4336 O |  |  | 4 
    4337 Iteration cutoff | 2 
    4338  
    4339 Matchmaker chain_A, chain (blank) (#6.1) with chain_(blank), chain (blank)
    4340 (#), sequence alignment score = 2716.2 
    4341 RMSD between 29 pruned atom pairs is 1.279 angstroms; (across all 635 pairs:
    4342 30.341) 
    4343  
    4344 Associated chain_(blank) chain to chain_A, chain (blank) with 0 mismatches 
    4345 Chain information for chain_(blank) 
    4346 --- 
    4347 Chain | Description 
    4348 8.1/? | No description available 
    4349  
    4350 Associated chain_(blank) (8.1) chain to O43246 with 0 mismatches 
    4351 Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
    4352 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A, chain_(blank) #8.1/? 
    4353 
    4354 > close #8
    4355 
    4356 Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
    4357 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    4358 Alignment identifier is 1/A 
    4359 Alignment identifier is 2/A 
    4360 Alignment identifier is 2 
    4361 Alignment identifier is 3 
    4362 Missing or invalid "chains" argument: only initial part "#4/A#6.1" of atom
    4363 specifier valid 
    4364 
    4365 > show #5 models
    4366 
    4367 > matchmaker #5 to #6.1/? pairing bs showAlignment true
    4368 
    4369 Parameters 
    4370 --- 
    4371 Chain pairing | bs 
    4372 Alignment algorithm | Needleman-Wunsch 
    4373 Similarity matrix | BLOSUM-62 
    4374 SS fraction | 0.3 
    4375 Gap open (HH/SS/other) | 18/18/6 
    4376 Gap extend | 1 
    4377 SS matrix |  |  | H | S | O 
    4378 ---|---|---|--- 
    4379 H | 6 | -9 | -6 
    4380 S |  | 6 | -6 
    4381 O |  |  | 4 
    4382 Iteration cutoff | 2 
    4383  
    4384 Matchmaker chain_A, chain (blank) (#6.1) with AtCAT4 cryoEM structure in POPC-
    4385 Cholesterol in water, chain (blank) (#5), sequence alignment score = 268 
    4386 Alignment identifier is 2 
    4387 Showing conservation header ("seq_conservation" residue attribute) for
    4388 alignment 2 
    4389 Hiding conservation header for alignment 2 
    4390 Chains used in RMSD evaluation for alignment 2: AtCAT4 cryoEM structure in
    4391 POPC-Cholesterol in water #5/?, chain_A #6.1/? 
    4392 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    4393 RMSD between 6 pruned atom pairs is 1.324 angstroms; (across all 537 pairs:
    4394 25.813) 
    4395  
    4396 
    4397 > ui tool show "Modeller Comparative"
    4398 
    4399 > modeller comparative 2:1 numModels 5 fast true multichain false hetPreserve
    4400 > false hydrogens false waterPreserve true directory
    4401 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    4402 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    4403 > model_modeller"
    4404 
    4405 Webservices job id: SEB9H6EJPN7GVBAZ 
    4406 Modeller job (ID SEB9H6EJPN7GVBAZ) finished 
    4407 Parameters 
    4408 --- 
    4409 Chain pairing | ss 
    4410 Alignment algorithm | Needleman-Wunsch 
    4411 Similarity matrix | BLOSUM-62 
    4412 SS fraction | 0.3 
    4413 Gap open (HH/SS/other) | 18/18/6 
    4414 Gap extend | 1 
    4415 SS matrix |  |  | H | S | O 
    4416 ---|---|---|--- 
    4417 H | 6 | -9 | -6 
    4418 S |  | 6 | -6 
    4419 O |  |  | 4 
    4420 Iteration cutoff | 2 
    4421  
    4422 Matchmaker chain_A, chain (blank) (#6.1) with chain_(blank), chain (blank)
    4423 (#), sequence alignment score = 2749.8 
    4424 RMSD between 90 pruned atom pairs is 1.442 angstroms; (across all 635 pairs:
    4425 28.278) 
    4426  
    4427 Associated chain_(blank) chain to chain_A, chain (blank) with 0 mismatches 
    4428 Chain information for chain_(blank) 
    4429 --- 
    4430 Chain | Description 
    4431 8.1/? | No description available 
    4432  
    4433 Associated chain_(blank) (8.1) chain to O43246 with 0 mismatches 
    4434 Associated chain_(blank) (8.1) chain to chain_A, chain (blank) with 0
    4435 mismatches 
    4436 Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
    4437 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A, chain_(blank) #8.1/? 
    4438 Chains used in RMSD evaluation for alignment 2: AtCAT4 cryoEM structure in
    4439 POPC-Cholesterol in water #5/?, chain_A #6.1/?, chain_(blank) #8.1/? 
    4440 
    4441 > close #8
    4442 
    4443 Chains used in RMSD evaluation for alignment 2: AtCAT4 cryoEM structure in
    4444 POPC-Cholesterol in water #5/?, chain_A #6.1/? 
    4445 Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
    4446 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    4447 
    4448 > open /Users/ctn700/Downloads/9fqw.cif
    4449 
    4450 9fqw.cif title: 
    4451 Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the ornithine-bound
    4452 inward-occluded state [more info...] 
    4453  
    4454 Chain information for 9fqw.cif #8 
    4455 --- 
    4456 Chain | Description | UniProt 
    4457 A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871 
    4458 B | Surface protein | ENV_MLVF5 35-270 
    4459  
    4460 Non-standard residues in 9fqw.cif #8 
    4461 --- 
    4462 BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 
    4463 FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
    4464 L-fucose; fucose) 
    4465 MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 
    4466 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    4467 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    4468 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    4469 ORN — L-ornithine 
    4470 Y01 — cholesterol hemisuccinate 
    4471  
    4472 
    4473 > hide #5 models
    4474 
    4475 > dssp #8
    4476 
    4477 > set bgColor white
    4478 
    4479 > lighting soft
    4480 
    4481 > view
    4482 
    4483 > undo
    4484 
    4485 > select #8/A:1003@OXT
    4486 
    4487 1 atom, 1 residue, 1 model selected 
    4488 
    4489 > select up
    4490 
    4491 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4492 
    4493 > view sel
    4494 
    4495 > open /Users/ctn700/Downloads/emd_50671.map
    4496 
    4497 Opened emd_50671.map as #9, grid size 256,256,256, pixel 0.825, shown at level
    4498 0.0937, step 1, values float32 
    4499 
    4500 > transparency 50
    4501 
    4502 > volume #9 level 0.1513
    4503 
    4504 > view
    4505 
    4506 > surface dust #9 size 8.25
    4507 
    4508 > open 9fqu
    4509 
    4510 Summary of feedback from opening 9fqu fetched from pdb 
    4511 --- 
    4512 note | Fetching compressed mmCIF 9fqu from http://files.rcsb.org/download/9fqu.cif 
    4513  
    4514 9fqu title: 
    4515 Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the arginine-bound inward-
    4516 occluded state [more info...] 
    4517  
    4518 Chain information for 9fqu #10 
    4519 --- 
    4520 Chain | Description | UniProt 
    4521 A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871 
    4522 B | Surface protein | ENV_MLVF5 35-270 
    4523  
    4524 Non-standard residues in 9fqu #10 
    4525 --- 
    4526 ARG — arginine 
    4527 BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 
    4528 FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
    4529 L-fucose; fucose) 
    4530 MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 
    4531 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    4532 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    4533 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    4534 Y01 — cholesterol hemisuccinate 
    4535  
    4536 
    4537 > matchmaker #10 to #8
    4538 
    4539 Parameters 
    4540 --- 
    4541 Chain pairing | bb 
    4542 Alignment algorithm | Needleman-Wunsch 
    4543 Similarity matrix | BLOSUM-62 
    4544 SS fraction | 0.3 
    4545 Gap open (HH/SS/other) | 18/18/6 
    4546 Gap extend | 1 
    4547 SS matrix |  |  | H | S | O 
    4548 ---|---|---|--- 
    4549 H | 6 | -9 | -6 
    4550 S |  | 6 | -6 
    4551 O |  |  | 4 
    4552 Iteration cutoff | 2 
    4553  
    4554 Matchmaker 9fqw.cif, chain A (#8) with 9fqu, chain A (#10), sequence alignment
    4555 score = 4093.9 
    4556 RMSD between 543 pruned atom pairs is 0.305 angstroms; (across all 544 pairs:
    4557 0.317) 
    4558  
    4559 
    4560 > hide #!9 models
    4561 
    4562 > camera mono
    4563 
    4564 > view sel
    4565 
    4566 > select #10/A:263
    4567 
    4568 12 atoms, 11 bonds, 1 residue, 1 model selected 
    4569 
    4570 > show sel atoms
    4571 
    4572 > select clear
    4573 
    4574 > hide #!8 models
    4575 
    4576 > matchmaker #10 to #7
    4577 
    4578 Parameters 
    4579 --- 
    4580 Chain pairing | bb 
    4581 Alignment algorithm | Needleman-Wunsch 
    4582 Similarity matrix | BLOSUM-62 
    4583 SS fraction | 0.3 
    4584 Gap open (HH/SS/other) | 18/18/6 
    4585 Gap extend | 1 
    4586 SS matrix |  |  | H | S | O 
    4587 ---|---|---|--- 
    4588 H | 6 | -9 | -6 
    4589 S |  | 6 | -6 
    4590 O |  |  | 4 
    4591 Iteration cutoff | 2 
    4592  
    4593 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    4594 chain A (#7) with 9fqu, chain A (#10), sequence alignment score = 1155.9 
    4595 RMSD between 156 pruned atom pairs is 1.204 angstroms; (across all 494 pairs:
    4596 6.473) 
    4597  
    4598 
    4599 > show #!7 models
    4600 
    4601 > matchmaker #10 to #3
    4602 
    4603 Parameters 
    4604 --- 
    4605 Chain pairing | bb 
    4606 Alignment algorithm | Needleman-Wunsch 
    4607 Similarity matrix | BLOSUM-62 
    4608 SS fraction | 0.3 
    4609 Gap open (HH/SS/other) | 18/18/6 
    4610 Gap extend | 1 
    4611 SS matrix |  |  | H | S | O 
    4612 ---|---|---|--- 
    4613 H | 6 | -9 | -6 
    4614 S |  | 6 | -6 
    4615 O |  |  | 4 
    4616 Iteration cutoff | 2 
    4617  
    4618 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
    4619 chain A (#3) with 9fqu, chain A (#10), sequence alignment score = 1127.7 
    4620 RMSD between 157 pruned atom pairs is 1.208 angstroms; (across all 494 pairs:
    4621 6.467) 
    4622  
    4623 
    4624 > show #!3 models
    4625 
    4626 > hide #!7 models
    4627 
    4628 > hide #!3 models
    4629 
    4630 > show #!3 models
    4631 
    4632 > hide #!3 models
    4633 
    4634 > open "/Users/ctn700/Library/CloudStorage/OneDrive-
    4635 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Ornithine/250630 -
    4636 > newmodel_TM1 induced
    4637 > fit/RealSpaceRefine_72/ORN_real_space_refined_063_mapJ510-coot-sn.pdb"
    4638 
    4639 Chain information for ORN_real_space_refined_063_mapJ510-coot-sn.pdb #11 
    4640 --- 
    4641 Chain | Description 
    4642 A | No description available 
    4643 B | No description available 
    4644  
    4645 
    4646 > matchmaker #11 to #10
    4647 
    4648 Parameters 
    4649 --- 
    4650 Chain pairing | bb 
    4651 Alignment algorithm | Needleman-Wunsch 
    4652 Similarity matrix | BLOSUM-62 
    4653 SS fraction | 0.3 
    4654 Gap open (HH/SS/other) | 18/18/6 
    4655 Gap extend | 1 
    4656 SS matrix |  |  | H | S | O 
    4657 ---|---|---|--- 
    4658 H | 6 | -9 | -6 
    4659 S |  | 6 | -6 
    4660 O |  |  | 4 
    4661 Iteration cutoff | 2 
    4662  
    4663 Matchmaker 9fqu, chain A (#10) with ORN_real_space_refined_063_mapJ510-coot-
    4664 sn.pdb, chain A (#11), sequence alignment score = 1139.9 
    4665 RMSD between 142 pruned atom pairs is 1.235 angstroms; (across all 491 pairs:
    4666 6.291) 
    4667  
    4668 
    4669 > hide #!10 models
    4670 
    4671 > show #!8 models
    4672 
    4673 > matchmaker #8 to #11
    4674 
    4675 Parameters 
    4676 --- 
    4677 Chain pairing | bb 
    4678 Alignment algorithm | Needleman-Wunsch 
    4679 Similarity matrix | BLOSUM-62 
    4680 SS fraction | 0.3 
    4681 Gap open (HH/SS/other) | 18/18/6 
    4682 Gap extend | 1 
    4683 SS matrix |  |  | H | S | O 
    4684 ---|---|---|--- 
    4685 H | 6 | -9 | -6 
    4686 S |  | 6 | -6 
    4687 O |  |  | 4 
    4688 Iteration cutoff | 2 
    4689  
    4690 Matchmaker ORN_real_space_refined_063_mapJ510-coot-sn.pdb, chain A (#11) with
    4691 9fqw.cif, chain A (#8), sequence alignment score = 1167.5 
    4692 RMSD between 140 pruned atom pairs is 1.231 angstroms; (across all 491 pairs:
    4693 6.347) 
    4694  
    4695 
    4696 > show #!9 models
    4697 
    4698 > hide #!9 models
    4699 
    4700 > view
    4701 
    4702 > hide #!11 models
    4703 
    4704 > view
    4705 
    4706 > open 9FQT
    4707 
    4708 Summary of feedback from opening 9FQT fetched from pdb 
    4709 --- 
    4710 note | Fetching compressed mmCIF 9fqt from http://files.rcsb.org/download/9fqt.cif 
    4711  
    4712 9fqt title: 
    4713 Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the apo inward-open state
    4714 [more info...] 
    4715  
    4716 Chain information for 9fqt #12 
    4717 --- 
    4718 Chain | Description | UniProt 
    4719 A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871 
    4720 B | Surface protein | ENV_MLVF5 1-236 
    4721  
    4722 Non-standard residues in 9fqt #12 
    4723 --- 
    4724 BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 
    4725 FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
    4726 L-fucose; fucose) 
    4727 MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 
    4728 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    4729 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    4730 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    4731 Y01 — cholesterol hemisuccinate 
    4732  
    4733 
    4734 > matchmaker #12 to #11
    4735 
    4736 Parameters 
    4737 --- 
    4738 Chain pairing | bb 
    4739 Alignment algorithm | Needleman-Wunsch 
    4740 Similarity matrix | BLOSUM-62 
    4741 SS fraction | 0.3 
    4742 Gap open (HH/SS/other) | 18/18/6 
    4743 Gap extend | 1 
    4744 SS matrix |  |  | H | S | O 
    4745 ---|---|---|--- 
    4746 H | 6 | -9 | -6 
    4747 S |  | 6 | -6 
    4748 O |  |  | 4 
    4749 Iteration cutoff | 2 
    4750  
    4751 Matchmaker ORN_real_space_refined_063_mapJ510-coot-sn.pdb, chain A (#11) with
    4752 9fqt, chain A (#12), sequence alignment score = 1179.2 
    4753 RMSD between 121 pruned atom pairs is 1.230 angstroms; (across all 487 pairs:
    4754 7.631) 
    4755  
    4756 
    4757 > select up
    4758 
    4759 2 atoms, 1 bond, 1 residue, 1 model selected 
    4760 
    4761 > select up
    4762 
    4763 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4764 
    4765 > view sel
    4766 
    4767 > show #!7 models
    4768 
    4769 > show #!10 models
    4770 
    4771 > hide #!7 models
    4772 
    4773 > hide #!8 models
    4774 
    4775 > close #8-12
    4776 
    4777 > show #!7 models
    4778 
    4779 > view
    4780 
    4781 > open 9FQT
    4782 
    4783 9fqt title: 
    4784 Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the apo inward-open state
    4785 [more info...] 
    4786  
    4787 Chain information for 9fqt #8 
    4788 --- 
    4789 Chain | Description | UniProt 
    4790 A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871 
    4791 B | Surface protein | ENV_MLVF5 1-236 
    4792  
    4793 Non-standard residues in 9fqt #8 
    4794 --- 
    4795 BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 
    4796 FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
    4797 L-fucose; fucose) 
    4798 MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 
    4799 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    4800 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    4801 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    4802 Y01 — cholesterol hemisuccinate 
    4803  
    4804 
    4805 > matchmaker #8 to #7
    4806 
    4807 Parameters 
    4808 --- 
    4809 Chain pairing | bb 
    4810 Alignment algorithm | Needleman-Wunsch 
    4811 Similarity matrix | BLOSUM-62 
    4812 SS fraction | 0.3 
    4813 Gap open (HH/SS/other) | 18/18/6 
    4814 Gap extend | 1 
    4815 SS matrix |  |  | H | S | O 
    4816 ---|---|---|--- 
    4817 H | 6 | -9 | -6 
    4818 S |  | 6 | -6 
    4819 O |  |  | 4 
    4820 Iteration cutoff | 2 
    4821  
    4822 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    4823 chain A (#7) with 9fqt, chain A (#8), sequence alignment score = 1188.6 
    4824 RMSD between 121 pruned atom pairs is 1.131 angstroms; (across all 490 pairs:
    4825 7.971) 
    4826  
    4827 
    4828 > matchmaker #8 to #7:87-224,282-405,465-579
    4829 
    4830 Parameters 
    4831 --- 
    4832 Chain pairing | bb 
    4833 Alignment algorithm | Needleman-Wunsch 
    4834 Similarity matrix | BLOSUM-62 
    4835 SS fraction | 0.3 
    4836 Gap open (HH/SS/other) | 18/18/6 
    4837 Gap extend | 1 
    4838 SS matrix |  |  | H | S | O 
    4839 ---|---|---|--- 
    4840 H | 6 | -9 | -6 
    4841 S |  | 6 | -6 
    4842 O |  |  | 4 
    4843 Iteration cutoff | 2 
    4844  
    4845 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    4846 chain A (#7) with 9fqt, chain A (#8), sequence alignment score = 787.4 
    4847 RMSD between 103 pruned atom pairs is 1.145 angstroms; (across all 349 pairs:
    4848 12.749) 
    4849  
    4850 
    4851 > view
    4852 
    4853 > dssp
    4854 
    4855 > lighting soft
    4856 
    4857 > ui tool show Matchmaker
    4858 
    4859 > matchmaker #!7 to #8/A pairing bs showAlignment true
    4860 
    4861 Parameters 
    4862 --- 
    4863 Chain pairing | bs 
    4864 Alignment algorithm | Needleman-Wunsch 
    4865 Similarity matrix | BLOSUM-62 
    4866 SS fraction | 0.3 
    4867 Gap open (HH/SS/other) | 18/18/6 
    4868 Gap extend | 1 
    4869 SS matrix |  |  | H | S | O 
    4870 ---|---|---|--- 
    4871 H | 6 | -9 | -6 
    4872 S |  | 6 | -6 
    4873 O |  |  | 4 
    4874 Iteration cutoff | 2 
    4875  
    4876 Matchmaker 9fqt, chain A (#8) with AtCAT4_final-
    4877 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain A (#7), sequence
    4878 alignment score = 1188.6 
    4879 Alignment identifier is 1 
    4880 Showing conservation header ("seq_conservation" residue attribute) for
    4881 alignment 1 
    4882 Hiding conservation header for alignment 1 
    4883 Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
    4884 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A, 9fqt #8/A 
    4885 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    4886 RMSD between 121 pruned atom pairs is 1.131 angstroms; (across all 490 pairs:
    4887 7.971) 
    4888  
    4889 
    4890 > select #7:87-224,282-405,465-579
    4891 
    4892 3022 atoms, 3096 bonds, 405 residues, 1 model selected 
    4893 
    4894 > select #8/A:91
    4895 
    4896 16 atoms, 15 bonds, 1 residue, 1 model selected 
    4897 
    4898 > select #8/A:91-92
    4899 
    4900 30 atoms, 30 bonds, 2 residues, 1 model selected 
    4901 
    4902 > select #7:87-224,282-405,465-579
    4903 
    4904 3022 atoms, 3096 bonds, 405 residues, 1 model selected 
    4905 
    4906 The cached device pixel ratio value was stale on window expose. Please file a
    4907 QTBUG which explains how to reproduce. 
    4908 
    4909 > matchmaker #8/A:91-244,302-425,498-602 to #7/A:87-224,282-405,465-579
    4910 
    4911 Parameters 
    4912 --- 
    4913 Chain pairing | bb 
    4914 Alignment algorithm | Needleman-Wunsch 
    4915 Similarity matrix | BLOSUM-62 
    4916 SS fraction | 0.3 
    4917 Gap open (HH/SS/other) | 18/18/6 
    4918 Gap extend | 1 
    4919 SS matrix |  |  | H | S | O 
    4920 ---|---|---|--- 
    4921 H | 6 | -9 | -6 
    4922 S |  | 6 | -6 
    4923 O |  |  | 4 
    4924 Iteration cutoff | 2 
    4925  
    4926 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    4927 chain A (#7) with 9fqt, chain A (#8), sequence alignment score = 781.8 
    4928 RMSD between 104 pruned atom pairs is 1.155 angstroms; (across all 359 pairs:
    4929 8.462) 
    4930  
    4931 
    4932 > ui tool show Matchmaker
    4933 
    4934 > matchmaker #!8 to #6.1/? pairing bs showAlignment true
    4935 
    4936 Parameters 
    4937 --- 
    4938 Chain pairing | bs 
    4939 Alignment algorithm | Needleman-Wunsch 
    4940 Similarity matrix | BLOSUM-62 
    4941 SS fraction | 0.3 
    4942 Gap open (HH/SS/other) | 18/18/6 
    4943 Gap extend | 1 
    4944 SS matrix |  |  | H | S | O 
    4945 ---|---|---|--- 
    4946 H | 6 | -9 | -6 
    4947 S |  | 6 | -6 
    4948 O |  |  | 4 
    4949 Iteration cutoff | 2 
    4950  
    4951 Matchmaker chain_A, chain (blank) (#6.1) with 9fqt, chain A (#8), sequence
    4952 alignment score = 409.2 
    4953 Alignment identifier is 2 
    4954 Showing conservation header ("seq_conservation" residue attribute) for
    4955 alignment 2 
    4956 Hiding conservation header for alignment 2 
    4957 Chains used in RMSD evaluation for alignment 2: chain_A #6.1/?, 9fqt #8/A 
    4958 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    4959 RMSD between 7 pruned atom pairs is 1.033 angstroms; (across all 513 pairs:
    4960 22.270) 
    4961  
    4962 
    4963 > show #!6 models
    4964 
    4965 > undo
    4966 
    4967 > hide #!7 models
    4968 
    4969 > show #!6 models
    4970 
    4971 > show #6.1 models
    4972 
    4973 > hide #!8 models
    4974 
    4975 > close #6.1
    4976 
    4977 > close #6
    4978 
    4979 > open uniprot:O43246
    4980 
    4981 Summary of feedback from opening O43246 fetched from uniprot 
    4982 --- 
    4983 notes | Alignment identifier is O43246 
    4984 Associated
    4985 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    4986 chain A to O43246 with 0 mismatches 
    4987 Associated AF-O43246-F1-model_v4.pdb chain A to O43246 with 0 mismatches 
    4988  
    4989 Opened UniProt O43246 
    4990 
    4991 > ui tool show Matchmaker
    4992 
    4993 > open uniprot:O43246
    4994 
    4995 Summary of feedback from opening O43246 fetched from uniprot 
    4996 --- 
    4997 notes | Alignment identifier is O43246 
    4998 Associated
    4999 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5000 chain A to O43246 with 0 mismatches 
    5001 Associated AF-O43246-F1-model_v4.pdb chain A to O43246 with 0 mismatches 
    5002  
    5003 Opened UniProt O43246 
    5004 
    5005 > select #1/A:38-592 #4/A
    5006 
    5007 12739 atoms, 12979 bonds, 1118 residues, 2 models selected 
    5008 
    5009 > select #1/A:38-592 #4/A
    5010 
    5011 12739 atoms, 12979 bonds, 1118 residues, 2 models selected 
    5012 
    5013 > ~select
    5014 
    5015 Nothing selected 
    5016 
    5017 > select #1/A:151,195,221,500 #4/A:151,195,221,500
    5018 
    5019 88 atoms, 80 bonds, 8 residues, 2 models selected 
    5020 
    5021 > select #1/A:38-592 #4/A
    5022 
    5023 12739 atoms, 12979 bonds, 1118 residues, 2 models selected 
    5024 
    5025 > ~select
    5026 
    5027 Nothing selected 
    5028 
    5029 > select clear
    5030 
    5031 > select #1/A:38-592 #4/A
    5032 
    5033 12739 atoms, 12979 bonds, 1118 residues, 2 models selected 
    5034 O43246 [ID: O43246] region O43246 [1-635] RMSD: 181.955 
    5035  
    5036 
    5037 > ui tool show Matchmaker
    5038 
    5039 Traceback (most recent call last): 
    5040 File
    5041 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5042 packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh 
    5043 self._items_change() 
    5044 File
    5045 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5046 packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change 
    5047 item_names = self._item_names() 
    5048 ^^^^^^^^^^^^^^^^^^ 
    5049 File
    5050 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5051 packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names 
    5052 values = [v for v in self.list_func() if self.filter_func(v)] 
    5053 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    5054 File
    5055 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5056 packages/chimerax/ui/widgets/item_chooser.py", line 47, in   
    5057 values = [v for v in self.list_func() if self.filter_func(v)] 
    5058 ^^^^^^^^^^^^^^^^^^^ 
    5059 File
    5060 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5061 packages/chimerax/ui/widgets/item_chooser.py", line 22, in   
    5062 filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
    5063 isinstance(x, cf) 
    5064 ^^^^^ 
    5065 File
    5066 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5067 packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models 
    5068 ref_structures = [ref_value.structure] 
    5069 ^^^^^^^^^^^^^^^^^^^ 
    5070 AttributeError: 'NoneType' object has no attribute 'structure' 
    5071  
    5072 AttributeError: 'NoneType' object has no attribute 'structure' 
    5073  
    5074 File
    5075 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5076 packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models 
    5077 ref_structures = [ref_value.structure] 
    5078 ^^^^^^^^^^^^^^^^^^^ 
    5079  
    5080 See log for complete Python traceback. 
    5081  
    5082 Traceback (most recent call last): 
    5083 File
    5084 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5085 packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh 
    5086 self._items_change() 
    5087 File
    5088 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5089 packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change 
    5090 item_names = self._item_names() 
    5091 ^^^^^^^^^^^^^^^^^^ 
    5092 File
    5093 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5094 packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names 
    5095 values = [v for v in self.list_func() if self.filter_func(v)] 
    5096 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    5097 File
    5098 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5099 packages/chimerax/ui/widgets/item_chooser.py", line 47, in   
    5100 values = [v for v in self.list_func() if self.filter_func(v)] 
    5101 ^^^^^^^^^^^^^^^^^^^ 
    5102 File
    5103 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5104 packages/chimerax/ui/widgets/item_chooser.py", line 22, in   
    5105 filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
    5106 isinstance(x, cf) 
    5107 ^^^^^ 
    5108 File
    5109 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5110 packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models 
    5111 ref_structures = [ref_value.structure] 
    5112 ^^^^^^^^^^^^^^^^^^^ 
    5113 AttributeError: 'NoneType' object has no attribute 'structure' 
    5114  
    5115 AttributeError: 'NoneType' object has no attribute 'structure' 
    5116  
    5117 File
    5118 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5119 packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models 
    5120 ref_structures = [ref_value.structure] 
    5121 ^^^^^^^^^^^^^^^^^^^ 
    5122  
    5123 See log for complete Python traceback. 
    5124  
    5125 
    5126 > select subtract #4
    5127 
    5128 8474 atoms, 8594 bonds, 555 residues, 1 model selected 
    5129 
    5130 > select add #4
    5131 
    5132 12739 atoms, 12979 bonds, 1118 residues, 2 models selected 
    5133 
    5134 > close #4
    5135 
    5136 > open uniprot:O43246
    5137 
    5138 Summary of feedback from opening O43246 fetched from uniprot 
    5139 --- 
    5140 notes | Alignment identifier is O43246 
    5141 Associated
    5142 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5143 chain A to O43246 with 0 mismatches 
    5144  
    5145 Opened UniProt O43246 
    5146 
    5147 > select #1/A:38-592
    5148 
    5149 8474 atoms, 8594 bonds, 555 residues, 1 model selected 
    5150 
    5151 > show #!1 models
    5152 
    5153 > view
    5154 
    5155 > select #1/A:38-592
    5156 
    5157 8474 atoms, 8594 bonds, 555 residues, 1 model selected 
    5158 
    5159 > ui tool show Matchmaker
    5160 
    5161 > matchmaker #!8 to #1/A pairing bs showAlignment true
    5162 
    5163 Parameters 
    5164 --- 
    5165 Chain pairing | bs 
    5166 Alignment algorithm | Needleman-Wunsch 
    5167 Similarity matrix | BLOSUM-62 
    5168 SS fraction | 0.3 
    5169 Gap open (HH/SS/other) | 18/18/6 
    5170 Gap extend | 1 
    5171 SS matrix |  |  | H | S | O 
    5172 ---|---|---|--- 
    5173 H | 6 | -9 | -6 
    5174 S |  | 6 | -6 
    5175 O |  |  | 4 
    5176 Iteration cutoff | 2 
    5177  
    5178 Matchmaker
    5179 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    5180 chain A (#1) with 9fqt, chain A (#8), sequence alignment score = 1397.2 
    5181 Alignment identifier is 2 
    5182 Showing conservation header ("seq_conservation" residue attribute) for
    5183 alignment 2 
    5184 Hiding conservation header for alignment 2 
    5185 Chains used in RMSD evaluation for alignment 2:
    5186 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5187 #1/A, 9fqt #8/A 
    5188 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    5189 RMSD between 117 pruned atom pairs is 1.190 angstroms; (across all 518 pairs:
    5190 9.154) 
    5191  
    5192 
    5193 > ui tool show "Modeller Comparative"
    5194 
    5195 > modeller comparative 2:1 numModels 5 fast true multichain false hetPreserve
    5196 > false hydrogens false waterPreserve true directory
    5197 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5198 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5199 > model_modeller"
    5200 
    5201 Invalid "directory" argument: File
    5202 '/Users/ctn700/Library/CloudStorage/OneDrive-
    5203 Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5204 model_modeller' does not exist 
    5205 
    5206 > ui tool show "Modeller Comparative"
    5207 
    5208 > modeller comparative 2:1 numModels 5 fast true multichain false hetPreserve
    5209 > false hydrogens false waterPreserve true directory
    5210 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5211 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5212 > model_modeller_for SN"
    5213 
    5214 Webservices job id: GYL3LLFYDXWXZROT 
    5215 Modeller job (ID GYL3LLFYDXWXZROT) finished 
    5216 Parameters 
    5217 --- 
    5218 Chain pairing | ss 
    5219 Alignment algorithm | Needleman-Wunsch 
    5220 Similarity matrix | BLOSUM-62 
    5221 SS fraction | 0.3 
    5222 Gap open (HH/SS/other) | 18/18/6 
    5223 Gap extend | 1 
    5224 SS matrix |  |  | H | S | O 
    5225 ---|---|---|--- 
    5226 H | 6 | -9 | -6 
    5227 S |  | 6 | -6 
    5228 O |  |  | 4 
    5229 Iteration cutoff | 2 
    5230  
    5231 Matchmaker
    5232 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    5233 chain A (#1) with chain_A, chain A (#), sequence alignment score = 1904.7 
    5234 RMSD between 16 pruned atom pairs is 1.391 angstroms; (across all 556 pairs:
    5235 20.824) 
    5236  
    5237 Associated chain_A chain A to
    5238 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    5239 chain A with 0 mismatches 
    5240 Chain information for chain_A 
    5241 --- 
    5242 Chain | Description 
    5243 4.1/A | No description available 
    5244  
    5245 Associated chain_A (4.1) chain A to O43246 with 1 mismatch 
    5246 Chains used in RMSD evaluation for alignment 2:
    5247 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5248 #1/A, chain_A #4.1/A, 9fqt #8/A 
    5249 
    5250 > hide #!1 models
    5251 
    5252 > hide #4.1 models
    5253 
    5254 > show #4.1 models
    5255 
    5256 > close #4
    5257 
    5258 Chains used in RMSD evaluation for alignment 2:
    5259 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5260 #1/A, 9fqt #8/A 
    5261 
    5262 > select #1/A:421 #8/A:428
    5263 
    5264 26 atoms, 24 bonds, 2 residues, 2 models selected 
    5265 
    5266 > ui tool show AlphaFold
    5267 
    5268 > alphafold match #1
    5269 
    5270 Fetching AlphaFold database settings from
    5271 https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json 
    5272 Fetching compressed AlphaFold O43246 from
    5273 https://alphafold.ebi.ac.uk/files/AF-O43246-F1-model_v4.cif 
    5274 1 AlphaFold model found using sequence similarity searches: O43246 (chain A) 
    5275 AlphaFold prediction matching
    5276 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb 
    5277 --- 
    5278 Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id 
    5279 A | O43246 | CTR4_HUMAN | 9.09 | 556 | 556 | 100   
    5280  
    5281 Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to O43246 with 0
    5282 mismatches 
    5283 Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
    5284 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    5285 chain A with 1 mismatch 
    5286 Chains used in RMSD evaluation for alignment 2:
    5287 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5288 #1/A, AlphaFold CTR4_HUMAN chain A #4.1/A, 9fqt #8/A 
    5289 Opened 1 AlphaFold model 
    5290 
    5291 > dssp #4.1
    5292 
    5293 > ui tool show Matchmaker
    5294 
    5295 > matchmaker #4.1 to #7 showAlignment true
    5296 
    5297 Parameters 
    5298 --- 
    5299 Chain pairing | bb 
    5300 Alignment algorithm | Needleman-Wunsch 
    5301 Similarity matrix | BLOSUM-62 
    5302 SS fraction | 0.3 
    5303 Gap open (HH/SS/other) | 18/18/6 
    5304 Gap extend | 1 
    5305 SS matrix |  |  | H | S | O 
    5306 ---|---|---|--- 
    5307 H | 6 | -9 | -6 
    5308 S |  | 6 | -6 
    5309 O |  |  | 4 
    5310 Iteration cutoff | 2 
    5311  
    5312 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    5313 chain A (#7) with AlphaFold CTR4_HUMAN chain A, chain A (#4.1), sequence
    5314 alignment score = 1224.4 
    5315 Alignment identifier is 2 
    5316 Showing conservation header ("seq_conservation" residue attribute) for
    5317 alignment 2 
    5318 Hiding conservation header for alignment 2 
    5319 Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
    5320 #4.1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5321 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    5322 RMSD between 286 pruned atom pairs is 1.182 angstroms; (across all 496 pairs:
    5323 5.090) 
    5324  
    5325 
    5326 > show #!7 models
    5327 
    5328 > view
    5329 
    5330 > ui tool show "Modeller Comparative"
    5331 
    5332 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    5333 > false hydrogens false waterPreserve true directory
    5334 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5335 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5336 > model_modeller_for SN"
    5337 
    5338 Webservices job id: R93DCQWMX3LHTMN8 
    5339 Modeller job (ID R93DCQWMX3LHTMN8) finished 
    5340 Parameters 
    5341 --- 
    5342 Chain pairing | ss 
    5343 Alignment algorithm | Needleman-Wunsch 
    5344 Similarity matrix | BLOSUM-62 
    5345 SS fraction | 0.3 
    5346 Gap open (HH/SS/other) | 18/18/6 
    5347 Gap extend | 1 
    5348 SS matrix |  |  | H | S | O 
    5349 ---|---|---|--- 
    5350 H | 6 | -9 | -6 
    5351 S |  | 6 | -6 
    5352 O |  |  | 4 
    5353 Iteration cutoff | 2 
    5354  
    5355 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    5356 chain A (#7) with chain_A, chain A (#), sequence alignment score = 474 
    5357 RMSD between 12 pruned atom pairs is 1.156 angstroms; (across all 489 pairs:
    5358 17.569) 
    5359  
    5360 Associated chain_A chain A to AlphaFold CTR4_HUMAN chain A, chain A with 0
    5361 mismatches 
    5362 Chain information for chain_A 
    5363 --- 
    5364 Chain | Description 
    5365 6.1/A | No description available 
    5366  
    5367 Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
    5368 #4.1/A, chain_A #6.1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
    5369 fixed_noH.pdb #7/A 
    5370 
    5371 > hide #!7 models
    5372 
    5373 > hide #!4 models
    5374 
    5375 > view
    5376 
    5377 > select add #1
    5378 
    5379 8588 atoms, 8708 bonds, 1 pseudobond, 559 residues, 3 models selected 
    5380 
    5381 > select subtract #1
    5382 
    5383 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5384 
    5385 > hide #4.1 models
    5386 
    5387 > view
    5388 
    5389 > select add #8
    5390 
    5391 11733 atoms, 11908 bonds, 1 pseudobond, 771 residues, 2 models selected 
    5392 
    5393 > select subtract #8
    5394 
    5395 Nothing selected 
    5396 
    5397 > view
    5398 
    5399 > select clear
    5400 
    5401 > close #6
    5402 
    5403 Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
    5404 #4.1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5405 
    5406 > open
    5407 > /Users/ctn700/Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5408 
    5409 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5410 title: 
    5411 Model of AF-O43246-F1_A based on AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1
    5412 [more info...] 
    5413  
    5414 Chain information for
    5415 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5416 #6 
    5417 --- 
    5418 Chain | Description 
    5419 A | No description available 
    5420  
    5421 Non-standard residues in
    5422 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5423 #6 
    5424 --- 
    5425 CHL — (CHL) 
    5426  
    5427 Associated
    5428 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5429 chain A to AlphaFold CTR4_HUMAN chain A, chain A with 0 mismatches 
    5430 Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
    5431 #4.1/A,
    5432 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5433 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5434 
    5435 > view
    5436 
    5437 > dssp #6
    5438 
    5439 > show #!7 models
    5440 
    5441 > ui tool show Matchmaker
    5442 
    5443 > matchmaker #!7 to #6 showAlignment true
    5444 
    5445 Parameters 
    5446 --- 
    5447 Chain pairing | bb 
    5448 Alignment algorithm | Needleman-Wunsch 
    5449 Similarity matrix | BLOSUM-62 
    5450 SS fraction | 0.3 
    5451 Gap open (HH/SS/other) | 18/18/6 
    5452 Gap extend | 1 
    5453 SS matrix |  |  | H | S | O 
    5454 ---|---|---|--- 
    5455 H | 6 | -9 | -6 
    5456 S |  | 6 | -6 
    5457 O |  |  | 4 
    5458 Iteration cutoff | 2 
    5459  
    5460 Matchmaker
    5461 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5462 chain A (#6) with AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
    5463 fixed_noH.pdb, chain A (#7), sequence alignment score = 1294.7 
    5464 Alignment identifier is 1 
    5465 Showing conservation header ("seq_conservation" residue attribute) for
    5466 alignment 1 
    5467 Hiding conservation header for alignment 1 
    5468 Chains used in RMSD evaluation for alignment 1:
    5469 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5470 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5471 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    5472 RMSD between 484 pruned atom pairs is 0.363 angstroms; (across all 515 pairs:
    5473 1.488) 
    5474  
    5475 
    5476 > ui tool show "Modeller Comparative"
    5477 
    5478 > modeller comparative 1:1 numModels 5 fast true multichain false hetPreserve
    5479 > false hydrogens false waterPreserve true directory
    5480 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5481 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5482 > model_modeller_for SN"
    5483 
    5484 Webservices job id: HCW2TZFM5IIN2SBS 
    5485 Modeller job (ID HCW2TZFM5IIN2SBS) finished 
    5486 Parameters 
    5487 --- 
    5488 Chain pairing | ss 
    5489 Alignment algorithm | Needleman-Wunsch 
    5490 Similarity matrix | BLOSUM-62 
    5491 SS fraction | 0.3 
    5492 Gap open (HH/SS/other) | 18/18/6 
    5493 Gap extend | 1 
    5494 SS matrix |  |  | H | S | O 
    5495 ---|---|---|--- 
    5496 H | 6 | -9 | -6 
    5497 S |  | 6 | -6 
    5498 O |  |  | 4 
    5499 Iteration cutoff | 2 
    5500  
    5501 Matchmaker
    5502 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5503 chain A (#6) with chain_A, chain A (#), sequence alignment score = 2390.7 
    5504 RMSD between 188 pruned atom pairs is 0.881 angstroms; (across all 565 pairs:
    5505 9.658) 
    5506  
    5507 Associated chain_A chain A to
    5508 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5509 chain A with 0 mismatches 
    5510 Chain information for chain_A 
    5511 --- 
    5512 Chain | Description 
    5513 9.1/A | No description available 
    5514  
    5515 Chains used in RMSD evaluation for alignment 1:
    5516 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5517 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
    5518 chain_A #9.1/A 
    5519 
    5520 > hide #6 models
    5521 
    5522 > hide #!7 models
    5523 
    5524 > close #9
    5525 
    5526 Chains used in RMSD evaluation for alignment 1:
    5527 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5528 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5529 
    5530 > select #6/A:416
    5531 
    5532 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5533 
    5534 > select #6/A:416-418
    5535 
    5536 44 atoms, 43 bonds, 3 residues, 1 model selected 
    5537 
    5538 > select #6/A:415
    5539 
    5540 17 atoms, 16 bonds, 1 residue, 1 model selected 
    5541 
    5542 > select #6/A:415-464
    5543 
    5544 722 atoms, 734 bonds, 50 residues, 1 model selected 
    5545 
    5546 > delete sel
    5547 
    5548 > show #!6 models
    5549 
    5550 > show #!7 models
    5551 
    5552 > ui tool show Matchmaker
    5553 
    5554 > matchmaker #!6 to #7 showAlignment true
    5555 
    5556 Parameters 
    5557 --- 
    5558 Chain pairing | bb 
    5559 Alignment algorithm | Needleman-Wunsch 
    5560 Similarity matrix | BLOSUM-62 
    5561 SS fraction | 0.3 
    5562 Gap open (HH/SS/other) | 18/18/6 
    5563 Gap extend | 1 
    5564 SS matrix |  |  | H | S | O 
    5565 ---|---|---|--- 
    5566 H | 6 | -9 | -6 
    5567 S |  | 6 | -6 
    5568 O |  |  | 4 
    5569 Iteration cutoff | 2 
    5570  
    5571 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    5572 chain A (#7) with
    5573 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5574 chain A (#6), sequence alignment score = 1287.2 
    5575 Alignment identifier is 1 
    5576 Showing conservation header ("seq_conservation" residue attribute) for
    5577 alignment 1 
    5578 Hiding conservation header for alignment 1 
    5579 Chains used in RMSD evaluation for alignment 1:
    5580 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5581 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5582 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    5583 RMSD between 484 pruned atom pairs is 0.363 angstroms; (across all 510 pairs:
    5584 1.172) 
    5585  
    5586 
    5587 > select clear
    5588 
    5589 > ui tool show "Modeller Comparative"
    5590 
    5591 > modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
    5592 > false hydrogens false waterPreserve true directory
    5593 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5594 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5595 > model_modeller_for SN"
    5596 
    5597 Webservices job id: F41JDLRP50L7I36W 
    5598 Modeller job (ID F41JDLRP50L7I36W) finished 
    5599 Parameters 
    5600 --- 
    5601 Chain pairing | ss 
    5602 Alignment algorithm | Needleman-Wunsch 
    5603 Similarity matrix | BLOSUM-62 
    5604 SS fraction | 0.3 
    5605 Gap open (HH/SS/other) | 18/18/6 
    5606 Gap extend | 1 
    5607 SS matrix |  |  | H | S | O 
    5608 ---|---|---|--- 
    5609 H | 6 | -9 | -6 
    5610 S |  | 6 | -6 
    5611 O |  |  | 4 
    5612 Iteration cutoff | 2 
    5613  
    5614 Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    5615 chain A (#7) with chain_A, chain A (#), sequence alignment score = 1030 
    5616 RMSD between 187 pruned atom pairs is 0.807 angstroms; (across all 488 pairs:
    5617 6.590) 
    5618  
    5619 Associated chain_A chain A to
    5620 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5621 chain A with 0 mismatches 
    5622 Chain information for chain_A 
    5623 --- 
    5624 Chain | Description 
    5625 9.1/A | No description available 
    5626  
    5627 Chains used in RMSD evaluation for alignment 1:
    5628 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5629 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
    5630 chain_A #9.1/A 
    5631 
    5632 > hide #!6 models
    5633 
    5634 > hide #!7 models
    5635 
    5636 > show #!6 models
    5637 
    5638 > hide #!6 models
    5639 
    5640 > show #!6 models
    5641 
    5642 > show #!7 models
    5643 
    5644 > hide #!7 models
    5645 
    5646 > show #!7 models
    5647 
    5648 > hide #!6 models
    5649 
    5650 > hide #!7 models
    5651 
    5652 > close #9
    5653 
    5654 Chains used in RMSD evaluation for alignment 1:
    5655 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5656 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5657 
    5658 > select clear
    5659 
    5660 > select #7/A:21
    5661 
    5662 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5663 
    5664 > select #7/A:21-582 #6/A
    5665 
    5666 11760 atoms, 11956 bonds, 2 pseudobonds, 1032 residues, 4 models selected 
    5667 MatchMaker Alignment [ID: 1] region AtCAT4_final-
    5668 coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain
    5669 A..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5670 chain A [1-567] RMSD: 1.172 
    5671  
    5672 
    5673 > sequence align 1 program clustalOmega
    5674 
    5675 Alignment identifier is 2 
    5676 Associated
    5677 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5678 chain A to
    5679 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5680 chain A with 0 mismatches 
    5681 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
    5682 A to AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain A
    5683 with 0 mismatches 
    5684 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
    5685 chain A to AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
    5686 chain A with 0 mismatches 
    5687 Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
    5688 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5689 chain A with 0 mismatches 
    5690 Associated
    5691 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5692 chain A to
    5693 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5694 chain A with 0 mismatches 
    5695 Showing conservation header ("seq_conservation" residue attribute) for
    5696 alignment 2 
    5697 Webservices job id: H4DAM594BYRTK18Y 
    5698 
    5699 > select #1/A:473 #4.1/A:473 #6/A:473
    5700 
    5701 28 atoms, 25 bonds, 3 residues, 3 models selected 
    5702 
    5703 > select #1/A:473 #4.1/A:473 #6/A:473
    5704 
    5705 28 atoms, 25 bonds, 3 residues, 3 models selected 
    5706 
    5707 > ui tool show "Modeller Comparative"
    5708 
    5709 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    5710 > false hydrogens false waterPreserve true directory
    5711 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5712 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5713 > model_modeller_for SN"
    5714 
    5715 Webservices job id: WYDGTY7T5OQLN5PB 
    5716 Modeller job (ID WYDGTY7T5OQLN5PB) finished 
    5717 Parameters 
    5718 --- 
    5719 Chain pairing | ss 
    5720 Alignment algorithm | Needleman-Wunsch 
    5721 Similarity matrix | BLOSUM-62 
    5722 SS fraction | 0.3 
    5723 Gap open (HH/SS/other) | 18/18/6 
    5724 Gap extend | 1 
    5725 SS matrix |  |  | H | S | O 
    5726 ---|---|---|--- 
    5727 H | 6 | -9 | -6 
    5728 S |  | 6 | -6 
    5729 O |  |  | 4 
    5730 Iteration cutoff | 2 
    5731  
    5732 Matchmaker
    5733 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    5734 chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
    5735 2353.4 
    5736 RMSD between 150 pruned atom pairs is 0.879 angstroms; (across all 556 pairs:
    5737 11.307) 
    5738  
    5739 Associated Model_of_AF-O432 chain A to
    5740 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5741 chain A with 0 mismatches 
    5742 Chain information for Model_of_AF-O432 
    5743 --- 
    5744 Chain | Description 
    5745 9.1/A | No description available 
    5746  
    5747 Associated Model_of_AF-O432 (9.1) chain A to
    5748 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5749 chain A with 0 mismatches 
    5750 Chains used in RMSD evaluation for alignment 1:
    5751 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5752 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
    5753 Model_of_AF-O432 #9.1/A 
    5754 
    5755 > close #9
    5756 
    5757 Chains used in RMSD evaluation for alignment 1:
    5758 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5759 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5760 
    5761 > sequence header 2 rmsd show
    5762 
    5763 Chains used in RMSD evaluation for alignment 2:
    5764 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5765 #1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    5766 AlphaFold CTR4_HUMAN chain A #4.1/A,
    5767 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5768 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5769 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2 
    5770 
    5771 > show #!6 models
    5772 
    5773 > show #!7 models
    5774 
    5775 > hide #!7 models
    5776 
    5777 > save "/Users/ctn700/Library/CloudStorage/OneDrive-
    5778 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5779 > model_modeller_for SN/AtCAT4 apo template/SLC7A4_HM_based_apo_AtCAT4_EM.pdb"
    5780 > models #6
    5781 
    5782 > ui tool show "Modeller Comparative"
    5783 
    5784 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    5785 > false hydrogens false waterPreserve true directory
    5786 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5787 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5788 > model_modeller_for SN"
    5789 
    5790 Webservices job id: I908NAOT9O4F2GS3 
    5791 Modeller job (ID I908NAOT9O4F2GS3) finished 
    5792 Parameters 
    5793 --- 
    5794 Chain pairing | ss 
    5795 Alignment algorithm | Needleman-Wunsch 
    5796 Similarity matrix | BLOSUM-62 
    5797 SS fraction | 0.3 
    5798 Gap open (HH/SS/other) | 18/18/6 
    5799 Gap extend | 1 
    5800 SS matrix |  |  | H | S | O 
    5801 ---|---|---|--- 
    5802 H | 6 | -9 | -6 
    5803 S |  | 6 | -6 
    5804 O |  |  | 4 
    5805 Iteration cutoff | 2 
    5806  
    5807 Matchmaker
    5808 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    5809 chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
    5810 2353.4 
    5811 RMSD between 150 pruned atom pairs is 0.879 angstroms; (across all 556 pairs:
    5812 11.307) 
    5813  
    5814 Associated Model_of_AF-O432 chain A to
    5815 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5816 chain A with 0 mismatches 
    5817 Chain information for Model_of_AF-O432 
    5818 --- 
    5819 Chain | Description 
    5820 9.1/A | No description available 
    5821  
    5822 Associated Model_of_AF-O432 (9.1) chain A to
    5823 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5824 chain A with 0 mismatches 
    5825 Chains used in RMSD evaluation for alignment 1:
    5826 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5827 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
    5828 Model_of_AF-O432 #9.1/A 
    5829 Chains used in RMSD evaluation for alignment 2:
    5830 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5831 #1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    5832 AlphaFold CTR4_HUMAN chain A #4.1/A,
    5833 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5834 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
    5835 Model_of_AF-O432 #9.1/A 
    5836 
    5837 > save "/Users/ctn700/Library/CloudStorage/OneDrive-
    5838 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5839 > model_modeller_for SN/AtCAT4 apo template/test.pdb" models #9
    5840 
    5841 > hide #!6 models
    5842 
    5843 > show #5 models
    5844 
    5845 > view
    5846 
    5847 > close #9
    5848 
    5849 Chains used in RMSD evaluation for alignment 2:
    5850 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    5851 #1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
    5852 AlphaFold CTR4_HUMAN chain A #4.1/A,
    5853 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5854 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5855 Chains used in RMSD evaluation for alignment 1:
    5856 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5857 #6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A 
    5858 
    5859 > show #!6 models
    5860 
    5861 > select add #6
    5862 
    5863 8012 atoms, 8119 bonds, 1 pseudobond, 518 residues, 4 models selected 
    5864 
    5865 > select subtract #6
    5866 
    5867 17 atoms, 15 bonds, 2 residues, 2 models selected 
    5868 
    5869 > select add #4.1
    5870 
    5871 4219 atoms, 4338 bonds, 557 residues, 2 models selected 
    5872 
    5873 > select subtract #4.1
    5874 
    5875 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5876 
    5877 > select add #1
    5878 
    5879 8573 atoms, 8694 bonds, 1 pseudobond, 558 residues, 2 models selected 
    5880 
    5881 > select subtract #1
    5882 
    5883 Nothing selected 
    5884 
    5885 > close #6
    5886 
    5887 > open "/Users/ctn700/Library/CloudStorage/OneDrive-
    5888 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5889 > model_modeller_for SN/AtCAT4 apo template/SLC7A4_HM_based_apo_AtCAT4_EM.pdb"
    5890 
    5891 SLC7A4_HM_based_apo_AtCAT4_EM.pdb title: 
    5892 Model of AF-O43246-F1_A based on AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1
    5893 [more info...] 
    5894  
    5895 Chain information for SLC7A4_HM_based_apo_AtCAT4_EM.pdb #6 
    5896 --- 
    5897 Chain | Description 
    5898 A | No description available 
    5899  
    5900 Non-standard residues in SLC7A4_HM_based_apo_AtCAT4_EM.pdb #6 
    5901 --- 
    5902 CHL — (CHL) 
    5903  
    5904 
    5905 > close #6
    5906 
    5907 > open
    5908 > /Users/ctn700/Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5909 
    5910 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5911 title: 
    5912 Model of AF-O43246-F1_A based on AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1
    5913 [more info...] 
    5914  
    5915 Chain information for
    5916 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5917 #6 
    5918 --- 
    5919 Chain | Description 
    5920 A | No description available 
    5921  
    5922 Non-standard residues in
    5923 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5924 #6 
    5925 --- 
    5926 CHL — (CHL) 
    5927  
    5928 
    5929 > ui tool show Matchmaker
    5930 
    5931 > matchmaker #6 to #5 showAlignment true
    5932 
    5933 Parameters 
    5934 --- 
    5935 Chain pairing | bb 
    5936 Alignment algorithm | Needleman-Wunsch 
    5937 Similarity matrix | BLOSUM-62 
    5938 SS fraction | 0.3 
    5939 Gap open (HH/SS/other) | 18/18/6 
    5940 Gap extend | 1 
    5941 SS matrix |  |  | H | S | O 
    5942 ---|---|---|--- 
    5943 H | 6 | -9 | -6 
    5944 S |  | 6 | -6 
    5945 O |  |  | 4 
    5946 Iteration cutoff | 2 
    5947  
    5948 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    5949 (#5) with
    5950 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    5951 chain A (#6), sequence alignment score = 1440.8 
    5952 Alignment identifier is 1 
    5953 Showing conservation header ("seq_conservation" residue attribute) for
    5954 alignment 1 
    5955 Hiding conservation header for alignment 1 
    5956 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    5957 POPC-Cholesterol in water #5/?,
    5958 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    5959 #6/A 
    5960 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    5961 RMSD between 538 pruned atom pairs is 0.076 angstroms; (across all 556 pairs:
    5962 1.444) 
    5963  
    5964 
    5965 > view
    5966 
    5967 > select #6/A:497
    5968 
    5969 16 atoms, 15 bonds, 1 residue, 1 model selected 
    5970 
    5971 > select clear
    5972 
    5973 > ui tool show "Modeller Comparative"
    5974 
    5975 > modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
    5976 > false hydrogens false waterPreserve true directory
    5977 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    5978 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    5979 > model_modeller_for SN"
    5980 
    5981 Webservices job id: WVXA273V473CHSCK 
    5982 Modeller job (ID WVXA273V473CHSCK) finished 
    5983 Parameters 
    5984 --- 
    5985 Chain pairing | ss 
    5986 Alignment algorithm | Needleman-Wunsch 
    5987 Similarity matrix | BLOSUM-62 
    5988 SS fraction | 0.3 
    5989 Gap open (HH/SS/other) | 18/18/6 
    5990 Gap extend | 1 
    5991 SS matrix |  |  | H | S | O 
    5992 ---|---|---|--- 
    5993 H | 6 | -9 | -6 
    5994 S |  | 6 | -6 
    5995 O |  |  | 4 
    5996 Iteration cutoff | 2 
    5997  
    5998 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    5999 (#5) with chain_A, chain (blank) (#), sequence alignment score = 1079.1 
    6000 RMSD between 135 pruned atom pairs is 0.924 angstroms; (across all 549 pairs:
    6001 6.141) 
    6002  
    6003 Associated chain_A chain to
    6004 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6005 chain A with 0 mismatches 
    6006 Chain information for chain_A 
    6007 --- 
    6008 Chain | Description 
    6009 9.1/? | No description available 
    6010  
    6011 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6012 POPC-Cholesterol in water #5/?,
    6013 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6014 #6/A, chain_A #9.1/? 
    6015 
    6016 > hide #5 models
    6017 
    6018 > hide #6 models
    6019 
    6020 > close #9
    6021 
    6022 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6023 POPC-Cholesterol in water #5/?,
    6024 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6025 #6/A 
    6026 
    6027 > select #5/*:20
    6028 
    6029 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6030 
    6031 > select #5/* #6/A
    6032 
    6033 17117 atoms, 17326 bonds, 1129 residues, 2 models selected 
    6034 MatchMaker Alignment [ID: 1] region AtCAT4 cryoEM structure in POPC-
    6035 Cholesterol in water, chain
    6036 (blank)..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6037 chain A [1-573] RMSD: 1.444 
    6038  
    6039 
    6040 > sequence align 1 program muscle
    6041 
    6042 Alignment identifier is 2 
    6043 Associated
    6044 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    6045 chain A to
    6046 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6047 chain A with 0 mismatches 
    6048 Associated pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb chain A to
    6049 AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 1
    6050 mismatch 
    6051 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
    6052 A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with
    6053 0 mismatches 
    6054 Associated AtCAT4 cryoEM structure in POPC-Cholesterol in water chain (blank)
    6055 to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 0
    6056 mismatches 
    6057 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
    6058 chain A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    6059 with 0 mismatches 
    6060 Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
    6061 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6062 chain A with 0 mismatches 
    6063 Associated
    6064 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6065 chain A to
    6066 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6067 chain A with 0 mismatches 
    6068 Showing conservation header ("seq_conservation" residue attribute) for
    6069 alignment 2 
    6070 Webservices job id: 2I19WRMM0U2SUAYT 
    6071 
    6072 > ui tool show "Modeller Comparative"
    6073 
    6074 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    6075 > false hydrogens false waterPreserve true directory
    6076 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    6077 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    6078 > model_modeller_for SN"
    6079 
    6080 Webservices job id: Q0L10UTRKYWYBZ1C 
    6081 Modeller job (ID Q0L10UTRKYWYBZ1C) finished 
    6082  
    6083 Modeller error output 
    6084 Traceback (most recent call last): 
    6085 File "ModellerModelling.py", line 80, in   
    6086 a.make() 
    6087 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    6088 line 141, in make 
    6089 self.homcsr(exit_stage) 
    6090 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    6091 line 624, in homcsr 
    6092 self.check_alignment(aln) 
    6093 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    6094 line 577, in check_alignment 
    6095 aln.check() 
    6096 File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 215, in
    6097 check 
    6098 self.check_structure_structure(io=io) 
    6099 File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 224, in
    6100 check_structure_structure 
    6101 return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) 
    6102 _modeller.SequenceMismatchError: read_te_291E> Sequence difference between
    6103 alignment and pdb : 
    6104  
    6105  
    6106 Modeller run output 
    6107  
    6108 MODELLER 10.6, 2024/10/17, r12888 
    6109  
    6110 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 
    6111  
    6112  
    6113 Copyright(c) 1989-2024 Andrej Sali 
    6114 All Rights Reserved 
    6115  
    6116 Written by A. Sali 
    6117 with help from 
    6118 B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 
    6119 M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, 
    6120 A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, 
    6121 F. Melo, J.P. Overington, E. Feyfant 
    6122 University of California, San Francisco, USA 
    6123 Rockefeller University, New York, USA 
    6124 Harvard University, Cambridge, USA 
    6125 Imperial Cancer Research Fund, London, UK 
    6126 Birkbeck College, University of London, London, UK 
    6127  
    6128  
    6129 Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
    6130 4.18.0-553.62.1.el8_10.x86_64 x86_64 
    6131 Date and time of compilation : 2024/10/17 20:43:03 
    6132 MODELLER executable type : x86_64-intel8 
    6133 Job starting time (YY/MM/DD HH:MM:SS): 2025/07/28 03:41:28 
    6134  
    6135 environ____W> The class 'environ' is deprecated; use 'Environ' instead 
    6136 openf___224_> Open $(LIB)/restyp.lib 
    6137 openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib 
    6138 rdresgr_266_> Number of residue groups: 2 
    6139 openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib 
    6140  
    6141 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
    6142 0.183 
    6143  
    6144 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
    6145 0.183 
    6146 openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib 
    6147  
    6148 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
    6149 0.230 
    6150 rdrdih__263_> Number of dihedral angle types : 9 
    6151 Maximal number of dihedral angle optima: 3 
    6152 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 
    6153 openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib 
    6154  
    6155 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
    6156 0.242 
    6157 openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib 
    6158 rdwilmo_274_> Mainchain residue conformation classes: APBLE 
    6159 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib 
    6160 rdclass_257_> Number of classes: 5 
    6161 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib 
    6162 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib 
    6163 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib 
    6164 openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat 
    6165 rdrrwgh_268_> Number of residue types: 21 
    6166 automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead 
    6167 openf___224_> Open alignment.ali 
    6168  
    6169 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285887 279.187
    6170 0.273 
    6171  
    6172 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 303625 296.509
    6173 0.290 
    6174  
    6175 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 321725 314.185
    6176 0.307 
    6177  
    6178 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 357925 349.536
    6179 0.341 
    6180  
    6181 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 430325 420.239
    6182 0.410 
    6183  
    6184 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 575125 561.646
    6185 0.548 
    6186  
    6187 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 577349 563.817 0.551 
    6188  
    6189 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 579605 566.021 0.553 
    6190  
    6191 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 581669 568.036 0.555 
    6192  
    6193 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 583921 570.235 0.557 
    6194  
    6195 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 585985 572.251 0.559 
    6196  
    6197 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 588205 574.419 0.561 
    6198  
    6199 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 590461 576.622 0.563 
    6200  
    6201 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 592721 578.829 0.565 
    6202 read_al_374_> Non-standard residue type,position,sequence: w 580 1 
    6203 read_al_374_> Non-standard residue type,position,sequence: . 1 2 
    6204 read_al_374_> Non-standard residue type,position,sequence: X 566 2 
    6205 read_al_374_> Non-standard residue type,position,sequence: . 1 4 
    6206 read_al_374_> Non-standard residue type,position,sequence: . 565 4 
    6207 read_al_374_> Non-standard residue type,position,sequence: w 580 8 
    6208  
    6209 Read the alignment from file : alignment.ali 
    6210  
    6211 Total number of alignment positions: 580 
    6212  
    6213 # Code #_Res #_Segm PDB_code Name 
    6214 \------------------------------------------------------------------------------- 
    6215 1 SLC7A4_ho 557 1 SLC7A4_homo 
    6216 2 pr1000ns_ 565 1 pr1000ns_ru 
    6217 3 AtCAT4_fi 517 1 AtCAT4_fina 
    6218 4 AtCAT4_cr 564 1 AtCAT4_cryo 
    6219 5 AtCAT4_fi 517 1 AtCAT4_fina 
    6220 6 AlphaFold 556 1 AlphaFold_C 
    6221 7 Model_of_ 565 1 Model_of_AF 
    6222 8 Model_of_ 566 1 Model_of_AF 
    6223 check_a_343_> >> BEGINNING OF COMMAND 
    6224 openf___224_> Open
    6225 ./SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb_1.pdb 
    6226  
    6227 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761546 743.697
    6228 0.726 
    6229  
    6230 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 761546 743.697 0.726 
    6231  
    6232 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761717 743.864
    6233 0.726 
    6234  
    6235 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 762567 744.694
    6236 0.727 
    6237  
    6238 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 763825 745.923
    6239 0.728 
    6240  
    6241 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 765729 747.782
    6242 0.730 
    6243  
    6244 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 765729 747.782 0.730 
    6245  
    6246 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 765819 747.870
    6247 0.730 
    6248  
    6249 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 768675 750.659
    6250 0.733 
    6251  
    6252 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 768675 750.659 0.733 
    6253  
    6254 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 768810 750.791
    6255 0.733 
    6256  
    6257 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 773094 754.975
    6258 0.737 
    6259  
    6260 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 773094 754.975 0.737 
    6261  
    6262 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 773292 755.168
    6263 0.737 
    6264  
    6265 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779718 761.443
    6266 0.744 
    6267  
    6268 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 779718 761.443 0.744 
    6269  
    6270 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 780015 761.733
    6271 0.744 
    6272  
    6273 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 789637 771.130
    6274 0.753 
    6275  
    6276 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 789637 771.130 0.753 
    6277  
    6278 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 790087 771.569
    6279 0.753 
    6280  
    6281 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 804537 785.681
    6282 0.767 
    6283  
    6284 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 804537 785.681 0.767 
    6285  
    6286 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 805212 786.340
    6287 0.768 
    6288  
    6289 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 826870 807.490
    6290 0.789 
    6291  
    6292 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 826870 807.490 0.789 
    6293  
    6294 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 827878 808.475
    6295 0.790 
    6296  
    6297 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 860382 840.217
    6298 0.821 
    6299  
    6300 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 860382 840.217 0.821 
    6301  
    6302 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 861894 841.693
    6303 0.822 
    6304  
    6305 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 910650 889.307
    6306 0.868 
    6307  
    6308 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 910650 889.307 0.868 
    6309  
    6310 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 912918 891.521
    6311 0.871 
    6312  
    6313 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 911118 889.764
    6314 0.869 
    6315 openf___224_> Open ./pr1000ns_run1_whole_nojump_center_rotxyz-
    6316 transxyz.pdb_2.pdb 
    6317 readlinef__W> File: ./pr1000ns_run1_whole_nojump_center_rotxyz-
    6318 transxyz.pdb_2.pdb, Line: 1 
    6319 Modeller will only read the first 80 characters of this line. 
    6320  
    6321  
    6322 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1082343 1056.976
    6323 1.032 
    6324 read_pd_459W> Residue type ACE not recognized. 'AutoModel' model building 
    6325 will treat this residue as a rigid body. 
    6326 To use real parameters, add the residue type to ${LIB}/restyp.lib, 
    6327 its topology to ${LIB}/top_*.lib, and suitable forcefield 
    6328 parameters to ${LIB}/par.lib. 
    6329  
    6330 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1082343 1056.976
    6331 1.032 
    6332  
    6333 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1082514 1057.143
    6334 1.032 
    6335  
    6336 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1083364 1057.973
    6337 1.033 
    6338  
    6339 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1084622 1059.201
    6340 1.034 
    6341  
    6342 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1086526 1061.061
    6343 1.036 
    6344  
    6345 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1086526 1061.061
    6346 1.036 
    6347  
    6348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1086616 1061.148
    6349 1.036 
    6350  
    6351 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1089472 1063.938
    6352 1.039 
    6353  
    6354 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1089472 1063.938
    6355 1.039 
    6356  
    6357 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1089607 1064.069
    6358 1.039 
    6359  
    6360 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1093891 1068.253
    6361 1.043 
    6362  
    6363 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1093891 1068.253
    6364 1.043 
    6365  
    6366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1094089 1068.446
    6367 1.043 
    6368  
    6369 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1100515 1074.722
    6370 1.050 
    6371  
    6372 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1100515 1074.722
    6373 1.050 
    6374  
    6375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1100812 1075.012
    6376 1.050 
    6377  
    6378 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1110434 1084.408
    6379 1.059 
    6380  
    6381 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1110434 1084.408
    6382 1.059 
    6383  
    6384 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1110884 1084.848
    6385 1.059 
    6386  
    6387 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1125334 1098.959
    6388 1.073 
    6389  
    6390 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1125334 1098.959
    6391 1.073 
    6392  
    6393 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1126009 1099.618
    6394 1.074 
    6395  
    6396 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1147667 1120.769
    6397 1.095 
    6398  
    6399 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1147667 1120.769
    6400 1.095 
    6401  
    6402 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1148675 1121.753
    6403 1.095 
    6404  
    6405 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1181179 1153.495
    6406 1.126 
    6407  
    6408 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1181179 1153.495
    6409 1.126 
    6410  
    6411 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1182691 1154.972
    6412 1.128 
    6413  
    6414 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1231447 1202.585
    6415 1.174 
    6416  
    6417 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1231447 1202.585
    6418 1.174 
    6419  
    6420 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1233715 1204.800
    6421 1.177 
    6422 rdpdb___459W> Residue type NME not recognized. 'AutoModel' model building 
    6423 will treat this residue as a rigid body. 
    6424 To use real parameters, add the residue type to ${LIB}/restyp.lib, 
    6425 its topology to ${LIB}/top_*.lib, and suitable forcefield 
    6426 parameters to ${LIB}/par.lib. 
    6427  
    6428 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1231987 1203.112
    6429 1.175 
    6430 read_te_291E> Sequence difference between alignment and pdb : 
    6431 x (mismatch at alignment position 565) 
    6432 Alignment LLNNAX/ 
    6433 PDB LLNNA./ 
    6434 Match ***** * 
    6435 Alignment residue type 24 (X, UNK) does not match pdb 
    6436 residue type 68 (., NME), 
    6437 for align code pr1000ns_run1_whole_nojump_center_rotxyz (atom file
    6438 pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb_2), pdb residue number "
    6439 584", chain "A" 
    6440  
    6441 Please check your alignment file header to be sure you correctly specified 
    6442 the starting and ending residue numbers and chains. The alignment sequence 
    6443 must match that from the atom file exactly. 
    6444  
    6445 Another possibility is that some residues in the atom file are missing, 
    6446 perhaps because they could not be resolved experimentally. (Note that Modeller 
    6447 reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) 
    6448 In this case, simply replace the section of your alignment corresponding 
    6449 to these missing residues with gaps. 
    6450 read_te_288W> Protein not accepted: 2 pr1000ns_run1_whole_nojump_center_rotxyz 
    6451  
    6452 No output models from Modeller; see log for Modeller text output. 
    6453 
    6454 > delete :ACE,NME
    6455 
    6456 > show #5 models
    6457 
    6458 > show #6 models
    6459 
    6460 > ui tool show Matchmaker
    6461 
    6462 > matchmaker #6 to #5 showAlignment true
    6463 
    6464 Parameters 
    6465 --- 
    6466 Chain pairing | bb 
    6467 Alignment algorithm | Needleman-Wunsch 
    6468 Similarity matrix | BLOSUM-62 
    6469 SS fraction | 0.3 
    6470 Gap open (HH/SS/other) | 18/18/6 
    6471 Gap extend | 1 
    6472 SS matrix |  |  | H | S | O 
    6473 ---|---|---|--- 
    6474 H | 6 | -9 | -6 
    6475 S |  | 6 | -6 
    6476 O |  |  | 4 
    6477 Iteration cutoff | 2 
    6478  
    6479 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    6480 (#5) with
    6481 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6482 chain A (#6), sequence alignment score = 1440.8 
    6483 Alignment identifier is 1 
    6484 Showing conservation header ("seq_conservation" residue attribute) for
    6485 alignment 1 
    6486 Hiding conservation header for alignment 1 
    6487 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6488 POPC-Cholesterol in water #5/?,
    6489 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6490 #6/A 
    6491 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1 
    6492 RMSD between 538 pruned atom pairs is 0.076 angstroms; (across all 556 pairs:
    6493 1.444) 
    6494  
    6495 
    6496 > select #5/*:21
    6497 
    6498 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6499 
    6500 > select #5/* #6/A
    6501 
    6502 17105 atoms, 17314 bonds, 1127 residues, 2 models selected 
    6503 MatchMaker Alignment [ID: 1] region AtCAT4 cryoEM structure in POPC-
    6504 Cholesterol in water, chain
    6505 (blank)..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6506 chain A [2-572] RMSD: 1.444 
    6507  
    6508 
    6509 > sequence align 1 program muscle
    6510 
    6511 Alignment identifier is 2 
    6512 Associated
    6513 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    6514 chain A to
    6515 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6516 chain A with 0 mismatches 
    6517 Associated pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb chain A to
    6518 AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 1
    6519 mismatch 
    6520 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
    6521 A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with
    6522 0 mismatches 
    6523 Associated AtCAT4 cryoEM structure in POPC-Cholesterol in water chain (blank)
    6524 to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 0
    6525 mismatches 
    6526 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
    6527 chain A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    6528 with 0 mismatches 
    6529 Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
    6530 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6531 chain A with 0 mismatches 
    6532 Associated
    6533 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6534 chain A to
    6535 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6536 chain A with 0 mismatches 
    6537 Showing conservation header ("seq_conservation" residue attribute) for
    6538 alignment 2 
    6539 Webservices job id: XA5T2F4O3417BWXW 
    6540 
    6541 > ui tool show "Modeller Comparative"
    6542 
    6543 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    6544 > false hydrogens false waterPreserve true directory
    6545 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    6546 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    6547 > model_modeller_for SN"
    6548 
    6549 Webservices job id: TD16QG7CO0YGYIPG 
    6550 Modeller job (ID TD16QG7CO0YGYIPG) finished 
    6551 Parameters 
    6552 --- 
    6553 Chain pairing | ss 
    6554 Alignment algorithm | Needleman-Wunsch 
    6555 Similarity matrix | BLOSUM-62 
    6556 SS fraction | 0.3 
    6557 Gap open (HH/SS/other) | 18/18/6 
    6558 Gap extend | 1 
    6559 SS matrix |  |  | H | S | O 
    6560 ---|---|---|--- 
    6561 H | 6 | -9 | -6 
    6562 S |  | 6 | -6 
    6563 O |  |  | 4 
    6564 Iteration cutoff | 2 
    6565  
    6566 Matchmaker
    6567 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    6568 chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
    6569 2450 
    6570 RMSD between 90 pruned atom pairs is 0.789 angstroms; (across all 556 pairs:
    6571 9.819) 
    6572  
    6573 Associated Model_of_AF-O432 chain A to
    6574 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6575 chain A with 0 mismatches 
    6576 Chain information for Model_of_AF-O432 
    6577 --- 
    6578 Chain | Description 
    6579 9.1/A | No description available 
    6580  
    6581 Associated Model_of_AF-O432 (9.1) chain A to
    6582 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6583 chain A with 0 mismatches 
    6584 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6585 POPC-Cholesterol in water #5/?,
    6586 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6587 #6/A, Model_of_AF-O432 #9.1/A 
    6588 
    6589 > hide #6 models
    6590 
    6591 > hide #5 models
    6592 
    6593 > hide #9.1 models
    6594 
    6595 > show #9.1 models
    6596 
    6597 > view
    6598 
    6599 > matchmaker #9 to #5
    6600 
    6601 Parameters 
    6602 --- 
    6603 Chain pairing | bb 
    6604 Alignment algorithm | Needleman-Wunsch 
    6605 Similarity matrix | BLOSUM-62 
    6606 SS fraction | 0.3 
    6607 Gap open (HH/SS/other) | 18/18/6 
    6608 Gap extend | 1 
    6609 SS matrix |  |  | H | S | O 
    6610 ---|---|---|--- 
    6611 H | 6 | -9 | -6 
    6612 S |  | 6 | -6 
    6613 O |  |  | 4 
    6614 Iteration cutoff | 2 
    6615  
    6616 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    6617 (#5) with Model_of_AF-O432, chain A (#9.1), sequence alignment score = 1083.3 
    6618 RMSD between 133 pruned atom pairs is 0.829 angstroms; (across all 543 pairs:
    6619 9.086) 
    6620  
    6621 
    6622 > view
    6623 
    6624 > show #5 models
    6625 
    6626 > select clear
    6627 
    6628 > select #1/A:99 #2/A:90 #3/A:90 #4.1/A:99 #5/?:90 #6/A:99 #7/A:90 #9.1/A:70
    6629 
    6630 77 atoms, 69 bonds, 8 residues, 8 models selected 
    6631 
    6632 > select #6/A:30-37,593-594 #9.1/A:1-8,564-565 #4.1/A:593
    6633 
    6634 263 atoms, 258 bonds, 21 residues, 3 models selected 
    6635 
    6636 > close #9
    6637 
    6638 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6639 POPC-Cholesterol in water #5/?,
    6640 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6641 #6/A 
    6642 
    6643 > select clear
    6644 
    6645 > select #2/A #3/A:21-582 #5/* #7/A:21-582 #1/A:38-592 #4.1/A #6/A
    6646 
    6647 49904 atoms, 50628 bonds, 2 pseudobonds, 3835 residues, 9 models selected 
    6648 MUSCLE Realignment of MatchMaker Alignment [ID: 2] region AtCAT4 cryoEM
    6649 structure in POPC-Cholesterol in water, chain
    6650 (blank)..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6651 chain A [1-578] RMSD: 137.214 
    6652  
    6653 
    6654 > sequence align 2 program clustalOmega replace true
    6655 
    6656 Webservices job id: PAFA5I3BRFITLR34 
    6657 
    6658 > ui tool show "Modeller Comparative"
    6659 
    6660 > modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
    6661 > false hydrogens false waterPreserve true directory
    6662 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    6663 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    6664 > model_modeller_for SN"
    6665 
    6666 Webservices job id: V898UGAC0RRASVGL 
    6667 Modeller job (ID V898UGAC0RRASVGL) finished 
    6668 Parameters 
    6669 --- 
    6670 Chain pairing | ss 
    6671 Alignment algorithm | Needleman-Wunsch 
    6672 Similarity matrix | BLOSUM-62 
    6673 SS fraction | 0.3 
    6674 Gap open (HH/SS/other) | 18/18/6 
    6675 Gap extend | 1 
    6676 SS matrix |  |  | H | S | O 
    6677 ---|---|---|--- 
    6678 H | 6 | -9 | -6 
    6679 S |  | 6 | -6 
    6680 O |  |  | 4 
    6681 Iteration cutoff | 2 
    6682  
    6683 Matchmaker
    6684 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    6685 chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
    6686 2436.2 
    6687 RMSD between 90 pruned atom pairs is 0.812 angstroms; (across all 556 pairs:
    6688 11.736) 
    6689  
    6690 Associated Model_of_AF-O432 chain A to
    6691 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6692 chain A with 0 mismatches 
    6693 Chain information for Model_of_AF-O432 
    6694 --- 
    6695 Chain | Description 
    6696 9.1/A | No description available 
    6697  
    6698 Associated Model_of_AF-O432 (9.1) chain A to
    6699 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6700 chain A with 0 mismatches 
    6701 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6702 POPC-Cholesterol in water #5/?,
    6703 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6704 #6/A, Model_of_AF-O432 #9.1/A 
    6705 
    6706 > matchmaker #9 to #5
    6707 
    6708 Parameters 
    6709 --- 
    6710 Chain pairing | bb 
    6711 Alignment algorithm | Needleman-Wunsch 
    6712 Similarity matrix | BLOSUM-62 
    6713 SS fraction | 0.3 
    6714 Gap open (HH/SS/other) | 18/18/6 
    6715 Gap extend | 1 
    6716 SS matrix |  |  | H | S | O 
    6717 ---|---|---|--- 
    6718 H | 6 | -9 | -6 
    6719 S |  | 6 | -6 
    6720 O |  |  | 4 
    6721 Iteration cutoff | 2 
    6722  
    6723 Matchmaker AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
    6724 (#5) with Model_of_AF-O432, chain A (#9.1), sequence alignment score = 1097.6 
    6725 RMSD between 126 pruned atom pairs is 0.780 angstroms; (across all 541 pairs:
    6726 10.794) 
    6727  
    6728 
    6729 > hide #5 models
    6730 
    6731 > open "/Users/ctn700/Library/CloudStorage/OneDrive-
    6732 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/sequence alignments whole
    6733 > family/alignment.praln"
    6734 
    6735 Unrecognized file suffix '.praln' 
    6736 
    6737 > open "/Users/ctn700/Library/CloudStorage/OneDrive-
    6738 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/sequence alignments whole
    6739 > family/alignment.fasta"
    6740 
    6741 Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
    6742 Nexus365/SLC7_shared_DK/SLC7A4_paper_all/sequence alignments whole
    6743 family/alignment.fasta 
    6744 --- 
    6745 notes | Alignment identifier is alignment.fasta 
    6746 Associated
    6747 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
    6748 chain A to NAME:SLC7A4_CAT4|CHAIN: with 0 mismatches 
    6749 Associated pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb chain A to
    6750 NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches 
    6751 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
    6752 A to NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches 
    6753 Associated AtCAT4 cryoEM structure in POPC-Cholesterol in water chain (blank)
    6754 to NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches 
    6755 Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
    6756 chain A to NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches 
    6757 3 messages similar to the above omitted 
    6758 Showing conservation header ("seq_conservation" residue attribute) for
    6759 alignment alignment.fasta 
    6760  
    6761 Opened 14 sequences from alignment.fasta 
    6762 
    6763 > close #9
    6764 
    6765 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6766 POPC-Cholesterol in water #5/?,
    6767 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6768 #6/A 
    6769 
    6770 > ui tool show "Modeller Comparative"
    6771 
    6772 > modeller comparative alignment.fasta:1 numModels 5 fast true multichain
    6773 > false hetPreserve false hydrogens false waterPreserve true directory
    6774 > "/Users/ctn700/Library/CloudStorage/OneDrive-
    6775 > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
    6776 > model_modeller_for SN"
    6777 
    6778 Webservices job id: Z233MIUGDOLV28ED 
    6779 Modeller job (ID Z233MIUGDOLV28ED) finished 
    6780 Parameters 
    6781 --- 
    6782 Chain pairing | ss 
    6783 Alignment algorithm | Needleman-Wunsch 
    6784 Similarity matrix | BLOSUM-62 
    6785 SS fraction | 0.3 
    6786 Gap open (HH/SS/other) | 18/18/6 
    6787 Gap extend | 1 
    6788 SS matrix |  |  | H | S | O 
    6789 ---|---|---|--- 
    6790 H | 6 | -9 | -6 
    6791 S |  | 6 | -6 
    6792 O |  |  | 4 
    6793 Iteration cutoff | 2 
    6794  
    6795 Matchmaker
    6796 SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
    6797 chain A (#1) with NAME_SLC7A4_CAT4, chain A (#), sequence alignment score =
    6798 1905.2 
    6799 RMSD between 5 pruned atom pairs is 1.226 angstroms; (across all 556 pairs:
    6800 109.289) 
    6801  
    6802 Associated NAME_SLC7A4_CAT4 chain A to NAME:SLC7A4_CAT4|CHAIN: with 0
    6803 mismatches 
    6804 Chain information for NAME_SLC7A4_CAT4 
    6805 --- 
    6806 Chain | Description 
    6807 9.1/A | No description available 
    6808  
    6809 Associated NAME_SLC7A4_CAT4 (9.1) chain A to
    6810 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6811 chain A with 0 mismatches 
    6812 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6813 POPC-Cholesterol in water #5/?,
    6814 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6815 #6/A, NAME_SLC7A4_CAT4 #9.1/A 
    6816 
    6817 > close #9
    6818 
    6819 Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
    6820 POPC-Cholesterol in water #5/?,
    6821 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
    6822 #6/A 
    6823 
    6824 > show #!4 models
    6825 
    6826 > hide #!4 models
    6827 
    6828 > show #!4 models
    6829 
    6830 > view
    6831 
    6832 > select clear
    6833 
    6834 > view
    6835 
    6836 > show #4.1 models
    6837 
    6838 > view
    6839 
    6840 > hide #!4 models
    6841 
    6842 > hide #4.1 models
    6843 
    6844 > show #6 models
    6845 
    6846 > show #4.1 models
    6847 
    6848 > hide #6 models
    6849 
    6850 > show #6 models
    6851 
    6852 > hide #6 models
    6853 
    6854 > matchmaker #6 to #4
    6855 
    6856 Parameters 
    6857 --- 
    6858 Chain pairing | bb 
    6859 Alignment algorithm | Needleman-Wunsch 
    6860 Similarity matrix | BLOSUM-62 
    6861 SS fraction | 0.3 
    6862 Gap open (HH/SS/other) | 18/18/6 
    6863 Gap extend | 1 
    6864 SS matrix |  |  | H | S | O 
    6865 ---|---|---|--- 
    6866 H | 6 | -9 | -6 
    6867 S |  | 6 | -6 
    6868 O |  |  | 4 
    6869 Iteration cutoff | 2 
    6870  
    6871 Matchmaker AlphaFold CTR4_HUMAN chain A, chain A (#4.1) with
    6872 Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
    6873 chain A (#6), sequence alignment score = 2554.5 
    6874 RMSD between 260 pruned atom pairs is 1.171 angstroms; (across all 556 pairs:
    6875 8.899) 
    6876  
     443  "threads" : 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