Changes between Initial Version and Version 1 of Ticket #14604


Ignore:
Timestamp:
Feb 19, 2024, 9:54:09 AM (23 months ago)
Author:
Eric Pettersen
Comment:

Reported by Tim McKeithan

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #14604

    • Property Cc Tom Goddard Tristan Croll added
    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crash processing window geometry change event

  • Ticket #14604 – Description

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    2464     "queue" : "com.apple.main-thread"
    2465   }
    2466 },
    2467   "logWritingSignature" : "abc78da7148ba39a8af47839dd2684076451d939",
    2468   "trialInfo" : {
    2469   "rollouts" : [
    2470     {
    2471       "rolloutId" : "5ffde50ce2aacd000d47a95f",
    2472       "factorPackIds" : {
    2473 
    2474       },
    2475       "deploymentId" : 240000361
    2476     },
    2477     {
    2478       "rolloutId" : "63508950b3714d3622fc77f7",
    2479       "factorPackIds" : {
    2480         "SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
    2481       },
    2482       "deploymentId" : 240000014
    2483     }
    2484   ],
    2485   "experiments" : [
    2486     {
    2487       "treatmentId" : "5d51a80d-93ec-47e1-9027-675002e78e4a",
    2488       "experimentId" : "6384d56b96e8d228551ec182",
    2489       "deploymentId" : 400000027
    2490     }
    2491   ]
    2492 },
    2493   "reportNotes" : [
    2494   "PC register does not match crashing frame (0x0 vs 0x7FF8A5D9EA78)"
    2495 ]
    2496 }
    2497 ===== Log before crash start =====
    2498 Startup Messages 
    2499 --- 
    2500 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
    2501 bundle with that from NMRSTAR bundle 
    2502  
    2503 UCSF ChimeraX version: 1.7 (2023-12-19) 
    2504 © 2016-2023 Regents of the University of California. All rights reserved. 
    2505 How to cite UCSF ChimeraX 
    2506 
    2507 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    2508 > evolution/Chimera models/Alphafold models/SOS1-AF-Q07889.pdb"
    2509 
    2510 SOS1-AF-Q07889.pdb title: 
    2511 Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889)
    2512 [more info...] 
    2513  
    2514 Chain information for SOS1-AF-Q07889.pdb #1 
    2515 --- 
    2516 Chain | Description | UniProt 
    2517 A | son of sevenless homolog 1 | SOS1_HUMAN 1-1333 
    2518  
    2519 
    2520 > set bgColor white
    2521 
    2522 > graphics silhouettes true
    2523 
    2524 > ui tool show "Show Sequence Viewer"
    2525 
    2526 > sequence chain /A
    2527 
    2528 Alignment identifier is 1/A 
    2529 
    2530 > close session
    2531 
    2532 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    2533 > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"
    2534 
    2535 Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
    2536 also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb 
    2537 --- 
    2538 warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
    2539 records as basis for sequence. 
    2540  
    2541 Chain information for VAVtoSOS 2e.pdb #1 
    2542 --- 
    2543 Chain | Description 
    2544 A | No description available 
    2545 C | No description available 
    2546  
    2547 
    2548 > open /Users/tmckeithan/Downloads/Chimera/PDB/3BJI.pdb
    2549 
    2550 3BJI.pdb title: 
    2551 Structural basis of promiscuous guanine nucleotide exchange by the T- cell
    2552 essential VAV1 [more info...] 
    2553  
    2554 Chain information for 3BJI.pdb #2 
    2555 --- 
    2556 Chain | Description | UniProt 
    2557 A B | proto-oncogene vav | VAV_HUMAN 189-565 
    2558 C D | ras-related C3 botulinum toxin substrate 1 precursor | RAC1_HUMAN 1-177 
    2559  
    2560 Non-standard residues in 3BJI.pdb #2 
    2561 --- 
    2562 ZN — zinc ion 
    2563  
    2564 
    2565 > select #2/A
    2566 
    2567 2974 atoms, 2991 bonds, 8 pseudobonds, 409 residues, 2 models selected 
    2568 
    2569 > delete atoms (#!2 & sel)
    2570 
    2571 > delete bonds (#!2 & sel)
    2572 
    2573 > select #2/D
    2574 
    2575 1211 atoms, 1229 bonds, 172 residues, 1 model selected 
    2576 
    2577 > delete atoms sel
    2578 
    2579 > delete bonds sel
    2580 
    2581 > ui tool show Matchmaker
    2582 
    2583 > matchmaker #2/B to #1/A pairing ss
    2584 
    2585 Parameters 
    2586 --- 
    2587 Chain pairing | ss 
    2588 Alignment algorithm | Needleman-Wunsch 
    2589 Similarity matrix | BLOSUM-62 
    2590 SS fraction | 0.3 
    2591 Gap open (HH/SS/other) | 18/18/6 
    2592 Gap extend | 1 
    2593 SS matrix |  |  | H | S | O 
    2594 ---|---|---|--- 
    2595 H | 6 | -9 | -6 
    2596 S |  | 6 | -6 
    2597 O |  |  | 4 
    2598 Iteration cutoff | 2 
    2599  
    2600 Matchmaker VAVtoSOS 2e.pdb, chain A (#1) with 3BJI.pdb, chain B (#2), sequence
    2601 alignment score = 396.2 
    2602 RMSD between 134 pruned atom pairs is 1.045 angstroms; (across all 314 pairs:
    2603 25.295) 
    2604  
    2605 
    2606 > ui tool show Matchmaker
    2607 
    2608 > matchmaker #2/C to #1/C pairing ss
    2609 
    2610 Parameters 
    2611 --- 
    2612 Chain pairing | ss 
    2613 Alignment algorithm | Needleman-Wunsch 
    2614 Similarity matrix | BLOSUM-62 
    2615 SS fraction | 0.3 
    2616 Gap open (HH/SS/other) | 18/18/6 
    2617 Gap extend | 1 
    2618 SS matrix |  |  | H | S | O 
    2619 ---|---|---|--- 
    2620 H | 6 | -9 | -6 
    2621 S |  | 6 | -6 
    2622 O |  |  | 4 
    2623 Iteration cutoff | 2 
    2624  
    2625 Matchmaker VAVtoSOS 2e.pdb, chain C (#1) with 3BJI.pdb, chain C (#2), sequence
    2626 alignment score = 898.4 
    2627 RMSD between 158 pruned atom pairs is 0.850 angstroms; (across all 177 pairs:
    2628 1.547) 
    2629  
    2630 
    2631 > select #1/C
    2632 
    2633 2583 atoms, 2613 bonds, 177 residues, 1 model selected 
    2634 
    2635 > select add #2/C
    2636 
    2637 3902 atoms, 3947 bonds, 368 residues, 2 models selected 
    2638 
    2639 > addh
    2640 
    2641 Summary of feedback from adding hydrogens to multiple structures 
    2642 --- 
    2643 warnings | Not adding hydrogens to VAVtoSOS 2e.pdb #1/C MET 1 CA because it is
    2644 missing heavy-atom bond partners 
    2645 Not adding hydrogens to VAVtoSOS 2e.pdb #1/C GLN 2 CB because it is missing
    2646 heavy-atom bond partners 
    2647 Not adding hydrogens to VAVtoSOS 2e.pdb #1/C GLU 31 CB because it is missing
    2648 heavy-atom bond partners 
    2649 Not adding hydrogens to VAVtoSOS 2e.pdb #1/C ILE 33 CB because it is missing
    2650 heavy-atom bond partners 
    2651 Not adding hydrogens to VAVtoSOS 2e.pdb #1/C LYS 49 CB because it is missing
    2652 heavy-atom bond partners 
    2653 14 messages similar to the above omitted 
    2654 Skipped 18 atom(s) with bad connectivities; see log for details 
    2655 Not adding hydrogens to 3BJI.pdb #2/B LYS 208 CD because it is missing heavy-
    2656 atom bond partners 
    2657 Not adding hydrogens to 3BJI.pdb #2/B LYS 222 CG because it is missing heavy-
    2658 atom bond partners 
    2659 Not adding hydrogens to 3BJI.pdb #2/B ARG 226 CB because it is missing heavy-
    2660 atom bond partners 
    2661 Not adding hydrogens to 3BJI.pdb #2/B ARG 245 CB because it is missing heavy-
    2662 atom bond partners 
    2663 Not adding hydrogens to 3BJI.pdb #2/B LYS 252 CG because it is missing heavy-
    2664 atom bond partners 
    2665 54 messages similar to the above omitted 
    2666 The following atoms were skipped as donors/acceptors due to missing heavy-atom
    2667 bond partners: 3BJI.pdb #2/B GLU 415 OE2; 3BJI.pdb #2/B ARG 489 NE 
    2668 notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing
    2669 termini instead 
    2670 Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records 
    2671 Chain-initial residues that are actual N termini: VAVtoSOS 2e.pdb #1/A GLN
    2672 189, VAVtoSOS 2e.pdb #1/C MET 1, VAVtoSOS 2e.pdb #1/A GLN 189 
    2673 Chain-initial residues that are not actual N termini: 
    2674 Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #1/A ASN 583,
    2675 VAVtoSOS 2e.pdb #1/C LEU 177, VAVtoSOS 2e.pdb #1/A ASN 583 
    2676 Chain-final residues that are not actual C termini: 
    2677 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT 
    2678 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
    2679 223 OXT 
    2680  
    2681 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O 
    2682 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
    2683 223 O 
    2684  
    2685 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 O 
    2686 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY
    2687 279 O 
    2688  
    2689 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT 
    2690 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
    2691 223 OXT 
    2692  
    2693 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 OXT 
    2694 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY
    2695 279 OXT 
    2696  
    2697 13 messages similar to the above omitted 
    2698 550 hydrogen bonds 
    2699 Termini for 3BJI.pdb (#2) chain B determined from SEQRES records 
    2700 Termini for 3BJI.pdb (#2) chain C determined from SEQRES records 
    2701 Chain-initial residues that are actual N termini: 3BJI.pdb #2/B MET 189,
    2702 3BJI.pdb #2/C MET 1 
    2703 Chain-initial residues that are not actual N termini: 3BJI.pdb #2/B ASN 464,
    2704 3BJI.pdb #2/B GLN 480 
    2705 Chain-final residues that are actual C termini: 3BJI.pdb #2/B GLY 566,
    2706 3BJI.pdb #2/C LEU 177 
    2707 Chain-final residues that are not actual C termini: 3BJI.pdb #2/B ASP 457,
    2708 3BJI.pdb #2/B GLU 475 
    2709 Missing OXT added to C-terminal residue 3BJI.pdb #2/B GLY 566 
    2710 Missing OXT added to C-terminal residue 3BJI.pdb #2/C LEU 177 
    2711 513 hydrogen bonds 
    2712 Adding 'H' to 3BJI.pdb #2/B ASN 464 
    2713 Adding 'H' to 3BJI.pdb #2/B GLN 480 
    2714 3BJI.pdb #2/B ASP 457 is not terminus, removing H atom from 'C' 
    2715 3BJI.pdb #2/B GLU 475 is not terminus, removing H atom from 'C' 
    2716 4072 hydrogens added 
    2717  
    2718 
    2719 > ui tool show Matchmaker
    2720 
    2721 > select add sel : ui tool show "Show Sequence Viewer"
    2722 
    2723 > sequence chain #1/A
    2724 
    2725 Alignment identifier is 1/A 
    2726 
    2727 > sequence chain #1/C
    2728 
    2729 Alignment identifier is 1/C 
    2730 
    2731 > sequence chain #2/B
    2732 
    2733 Alignment identifier is 2/B 
    2734 
    2735 > interfaces #1
    2736 
    2737 1 buried areas: A C 1482 
    2738 
    2739 > interfaces #2
    2740 
    2741 1 buried areas: B C 1354 
    2742 
    2743 > close session
    2744 
    2745 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    2746 > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb" format pdb
    2747 
    2748 Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
    2749 also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb 
    2750 --- 
    2751 warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
    2752 records as basis for sequence. 
    2753  
    2754 Chain information for VAVtoSOS 2e.pdb #1 
    2755 --- 
    2756 Chain | Description 
    2757 A | No description available 
    2758 C | No description available 
    2759  
    2760 
    2761 > show surfaces
    2762 
    2763 > coulombic
    2764 
    2765 The following residues are missing heavy (non-hydrogen) atoms, which may
    2766 result in inaccurate electrostatics: 
    2767 /A LYS 214 
    2768 /C MET 1 
    2769 /C GLN 2 
    2770 /C GLU 31 
    2771 /C ILE 33 
    2772 /C LYS 49 
    2773 /C LYS 123 
    2774 /C ASP 124 
    2775 /C GLU 127 
    2776 /C LYS 128 
    2777 /C GLU 131 
    2778 /C LYS 132 
    2779 /C LYS 133 
    2780 /C LYS 153 
    2781 /C LEU 160 
    2782 /C THR 161 
    2783 /C LYS 166 
    2784 /C ASP 170 
    2785 /C ARG 174 
    2786 /C LEU 177 
    2787 
    2788 Using Amber 20 recommended default charges and atom types for standard
    2789 residues 
    2790 /A LYS 214 CLYS 
    2791 Nonstandard name for heavy atom /A LYS 214 OH 
    2792 
    2793 > hide surfaces
    2794 
    2795 > addh
    2796 
    2797 Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1 
    2798 --- 
    2799 warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy-
    2800 atom bond partners 
    2801 Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond
    2802 partners 
    2803 Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond
    2804 partners 
    2805 Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond
    2806 partners 
    2807 Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond
    2808 partners 
    2809 14 messages similar to the above omitted 
    2810 Skipped 18 atom(s) with bad connectivities; see log for details 
    2811 notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing
    2812 termini instead 
    2813 Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records 
    2814 Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN
    2815 189 
    2816 Chain-initial residues that are not actual N termini: 
    2817 Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN
    2818 583 
    2819 Chain-final residues that are not actual C termini: 
    2820 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2821 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2822  
    2823 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2824 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2825  
    2826 Skipping possible acceptor with bad geometry: /A GLY 279 O 
    2827 Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O 
    2828  
    2829 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2830 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2831  
    2832 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2833 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2834  
    2835 13 messages similar to the above omitted 
    2836 550 hydrogen bonds 
    2837 0 hydrogens added 
    2838  
    2839 
    2840 > swapaa /A:223 asn
    2841 
    2842 Using Dunbrack library 
    2843 /A ASN 223: phi -140.8, psi 26.7 trans 
    2844 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2845 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2846  
    2847 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2848 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2849  
    2850 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2851 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2852  
    2853 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2854 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2855  
    2856 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2857 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2858  
    2859 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2860 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2861  
    2862 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2863 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2864  
    2865 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2866 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2867  
    2868 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2869 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2870  
    2871 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2872 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2873  
    2874 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2875 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2876  
    2877 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2878 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2879  
    2880 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2881 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2882  
    2883 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2884 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2885  
    2886 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2887 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2888  
    2889 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2890 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2891  
    2892 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2893 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2894  
    2895 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2896 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2897  
    2898 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2899 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2900  
    2901 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2902 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2903  
    2904 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2905 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2906  
    2907 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2908 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2909  
    2910 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2911 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2912  
    2913 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2914 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2915  
    2916 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2917 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2918  
    2919 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2920 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2921  
    2922 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2923 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2924  
    2925 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2926 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2927  
    2928 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2929 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2930  
    2931 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2932 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2933  
    2934 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2935 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2936  
    2937 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2938 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2939  
    2940 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2941 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2942  
    2943 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2944 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2945  
    2946 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2947 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2948  
    2949 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2950 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2951  
    2952 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2953 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2954  
    2955 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2956 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2957  
    2958 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2959 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2960  
    2961 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2962 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2963  
    2964 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2965 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2966  
    2967 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2968 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2969  
    2970 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2971 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2972  
    2973 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2974 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2975  
    2976 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2977 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2978  
    2979 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2980 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2981  
    2982 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2983 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2984  
    2985 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2986 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2987  
    2988 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2989 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2990  
    2991 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2992 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2993  
    2994 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    2995 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    2996  
    2997 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    2998 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    2999  
    3000 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    3001 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    3002  
    3003 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    3004 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    3005  
    3006 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    3007 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    3008  
    3009 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    3010 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    3011  
    3012 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    3013 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    3014  
    3015 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    3016 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    3017  
    3018 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    3019 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    3020  
    3021 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    3022 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    3023  
    3024 
    3025 Skipped 70 atom(s) with bad connectivities; see log for details 
    3026 
    3027 Applying ASN rotamer (chi angles: -163.3 -54.4) to /A ASN 223 
    3028 
    3029 > addh
    3030 
    3031 Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1 
    3032 --- 
    3033 warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy-
    3034 atom bond partners 
    3035 Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond
    3036 partners 
    3037 Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond
    3038 partners 
    3039 Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond
    3040 partners 
    3041 Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond
    3042 partners 
    3043 14 messages similar to the above omitted 
    3044 Skipped 17 atom(s) with bad connectivities; see log for details 
    3045 notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing
    3046 termini instead 
    3047 Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records 
    3048 Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN
    3049 189 
    3050 Chain-initial residues that are not actual N termini: 
    3051 Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN
    3052 583 
    3053 Chain-final residues that are not actual C termini: 
    3054 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    3055 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    3056  
    3057 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    3058 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    3059  
    3060 Skipping possible acceptor with bad geometry: /A GLY 279 O 
    3061 Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O 
    3062  
    3063 Skipping possible acceptor with bad geometry: /A GLY 279 OXT 
    3064 Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 OXT 
    3065  
    3066 Skipping possible acceptor with bad geometry: /A GLY 279 O 
    3067 Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O 
    3068  
    3069 12 messages similar to the above omitted 
    3070 551 hydrogen bonds 
    3071 4 hydrogens added 
    3072  
    3073 
    3074 > swapaa /A:279 gly
    3075 
    3076 Using Dunbrack library 
    3077 Swapping /A GLY 279 to GLY 
    3078 
    3079 > addh
    3080 
    3081 Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1 
    3082 --- 
    3083 warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy-
    3084 atom bond partners 
    3085 Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond
    3086 partners 
    3087 Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond
    3088 partners 
    3089 Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond
    3090 partners 
    3091 Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond
    3092 partners 
    3093 14 messages similar to the above omitted 
    3094 Skipped 17 atom(s) with bad connectivities; see log for details 
    3095 notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing
    3096 termini instead 
    3097 Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records 
    3098 Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN
    3099 189 
    3100 Chain-initial residues that are not actual N termini: 
    3101 Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN
    3102 583 
    3103 Chain-final residues that are not actual C termini: 
    3104 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    3105 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    3106  
    3107 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    3108 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    3109  
    3110 Skipping possible acceptor with bad geometry: /A GLY 279 O 
    3111 Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O 
    3112  
    3113 Skipping possible acceptor with bad geometry: /A ASN 223 O 
    3114 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O 
    3115  
    3116 Skipping possible acceptor with bad geometry: /A ASN 223 OXT 
    3117 Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT 
    3118  
    3119 12 messages similar to the above omitted 
    3120 551 hydrogen bonds 
    3121 3 hydrogens added 
    3122  
    3123 
    3124 > show surfaces
    3125 
    3126 > coulombic
    3127 
    3128 The following residues are missing heavy (non-hydrogen) atoms, which may
    3129 result in inaccurate electrostatics: 
    3130 /A LYS 214 
    3131 /C MET 1 
    3132 /C GLN 2 
    3133 /C GLU 31 
    3134 /C ILE 33 
    3135 /C LYS 49 
    3136 /C LYS 123 
    3137 /C ASP 124 
    3138 /C GLU 127 
    3139 /C LYS 128 
    3140 /C GLU 131 
    3141 /C LYS 132 
    3142 /C LYS 133 
    3143 /C LYS 153 
    3144 /C LEU 160 
    3145 /C THR 161 
    3146 /C LYS 166 
    3147 /C ASP 170 
    3148 /C ARG 174 
    3149 /C LEU 177 
    3150 
    3151 Using Amber 20 recommended default charges and atom types for standard
    3152 residues 
    3153 /A LYS 214 CLYS 
    3154 Nonstandard name for heavy atom /A LYS 214 OH 
    3155 
    3156 > swapaa /A:214 lys
    3157 
    3158 Using Dunbrack library 
    3159 /A LYS 214: phi -51.4, psi -27.4 trans 
    3160 Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 214 
    3161 
    3162 > swapaa /C:1 met
    3163 
    3164 Using Dunbrack library 
    3165 /C MET 1: phi none, psi -163.4 trans 
    3166 Applying MET rotamer (chi angles: 72.6 -72.0 -71.4) to /C MET 1 
    3167 
    3168 > swapaa /C:2 gln
    3169 
    3170 Using Dunbrack library 
    3171 /C GLN 2: phi 54.0, psi 43.2 trans 
    3172 Applying GLN rotamer (chi angles: -63.1 -69.2 -63.4) to /C GLN 2 
    3173 
    3174 > swapaa /C:31 glu
    3175 
    3176 Using Dunbrack library 
    3177 /C GLU 31: phi -67.8, psi -17.2 trans 
    3178 Applying GLU rotamer (chi angles: 66.6 -85.0 17.8) to /C GLU 31 
    3179 
    3180 > swapaa /C:33 ile
    3181 
    3182 Using Dunbrack library 
    3183 /C ILE 33: phi -128.5, psi 129.8 trans 
    3184 Applying ILE rotamer (chi angles: 66.2 -71.1) to /C ILE 33 
    3185 
    3186 > swapaa /C:49 lys
    3187 
    3188 Using Dunbrack library 
    3189 /C LYS 49: phi -105.8, psi 132.8 trans 
    3190 Applying LYS rotamer (chi angles: -177.7 178.5 -176.1 -64.2) to /C LYS 49 
    3191 
    3192 > swapaa /C:123 lys
    3193 
    3194 Using Dunbrack library 
    3195 /C LYS 123: phi -59.5, psi -24.4 trans 
    3196 Applying LYS rotamer (chi angles: -66.0 -66.1 -174.7 -67.0) to /C LYS 123 
    3197 
    3198 > swapaa /C:124 asp
    3199 
    3200 Using Dunbrack library 
    3201 /C ASP 124: phi -65.8, psi -32.0 trans 
    3202 Applying ASP rotamer (chi angles: -71.2 -15.9) to /C ASP 124 
    3203 
    3204 > swapaa /C:127 glu
    3205 
    3206 Using Dunbrack library 
    3207 /C GLU 127: phi -60.7, psi -29.0 trans 
    3208 Applying GLU rotamer (chi angles: -69.3 177.9 -8.3) to /C GLU 127 
    3209 
    3210 > swapaa /C:128 lys
    3211 
    3212 Using Dunbrack library 
    3213 /C LYS 128: phi -79.9, psi -47.4 trans 
    3214 Applying LYS rotamer (chi angles: -66.0 -173.5 -71.5 -66.9) to /C LYS 128 
    3215 
    3216 > swapaa /C:131 glu
    3217 
    3218 Using Dunbrack library 
    3219 /C GLU 131: phi -67.4, psi -28.1 trans 
    3220 Applying GLU rotamer (chi angles: -68.4 178.8 -8.3) to /C GLU 131 
    3221 
    3222 > swapaa /C:132 lys
    3223 
    3224 Using Dunbrack library 
    3225 /C LYS 132: phi -92.6, psi 6.9 trans 
    3226 Applying LYS rotamer (chi angles: -64.3 -174.6 -70.2 -66.8) to /C LYS 132 
    3227 
    3228 > swapaa /C:133 lys
    3229 
    3230 Using Dunbrack library 
    3231 /C LYS 133: phi 60.7, psi 17.9 trans 
    3232 Applying LYS rotamer (chi angles: -83.6 68.4 178.6 177.6) to /C LYS 133 
    3233 
    3234 > swapaa /C:153 lys
    3235 
    3236 Using Dunbrack library 
    3237 /C LYS 153: phi -147.1, psi 155.7 trans 
    3238 Applying LYS rotamer (chi angles: -61.9 -73.1 -174.8 -67.0) to /C LYS 153 
    3239 
    3240 > swapaa /C:160 leu
    3241 
    3242 Using Dunbrack library 
    3243 /C LEU 160: phi -72.4, psi -31.1 trans 
    3244 Applying LEU rotamer (chi angles: -67.8 174.1) to /C LEU 160 
    3245 
    3246 > swapaa /C:161 thr
    3247 
    3248 Using Dunbrack library 
    3249 /C THR 161: phi -153.7, psi 150.8 trans 
    3250 Applying THR rotamer (chi angles: -174.5) to /C THR 161 
    3251 
    3252 > swapaa /C:166 lys
    3253 
    3254 Using Dunbrack library 
    3255 /C LYS 166: phi -57.5, psi -38.2 trans 
    3256 Applying LYS rotamer (chi angles: -171.7 -89.7 -173.2 -177.4) to /C LYS 166 
    3257 
    3258 > swapaa /C:170 asp
    3259 
    3260 Using Dunbrack library 
    3261 /C ASP 170: phi -62.4, psi -45.3 trans 
    3262 Applying ASP rotamer (chi angles: -71.6 -15.7) to /C ASP 170 
    3263 
    3264 > swapaa /C:174 arg
    3265 
    3266 Using Dunbrack library 
    3267 /C ARG 174: phi -63.3, psi -17.3 trans 
    3268 Applying ARG rotamer (chi angles: -172.3 178.2 -63.1 -83.0) to /C ARG 174 
    3269 
    3270 > swapaa /C:177 leu
    3271 
    3272 Using Dunbrack library 
    3273 /C LEU 177: phi -148.8, psi none trans 
    3274 Applying LEU rotamer (chi angles: -64.7 174.5) to /C LEU 177 
    3275 
    3276 > hide surfaces
    3277 
    3278 > show surfaces
    3279 
    3280 > coulombic
    3281 
    3282 The following heavy (non-hydrogen) atoms are missing, which may result in
    3283 inaccurate electrostatics: 
    3284 /A LYS 214 O 
    3285 
    3286 Using Amber 20 recommended default charges and atom types for standard
    3287 residues 
    3288 Coulombic values for VAVtoSOS 2e.pdb_A SES surface #1.1: minimum, -22.41, mean
    3289 -1.75, maximum 15.42 
    3290 Coulombic values for VAVtoSOS 2e.pdb_C SES surface #1.2: minimum, -14.81, mean
    3291 -0.22, maximum 9.43 
    3292 To also show corresponding color key, enter the above coulombic command and
    3293 add key true 
    3294 
    3295 > hide surfaces
    3296 
    3297 > select /C
    3298 
    3299 2639 atoms, 2669 bonds, 177 residues, 1 model selected 
    3300 
    3301 > select /A
    3302 
    3303 6240 atoms, 6299 bonds, 386 residues, 1 model selected 
    3304 
    3305 > show sel surfaces
    3306 
    3307 > hide sel surfaces
    3308 
    3309 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3310 > evolution/Chimera models/Alphafold models/SOS1-AF-Q07889.pdb"
    3311 
    3312 SOS1-AF-Q07889.pdb title: 
    3313 Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889)
    3314 [more info...] 
    3315  
    3316 Chain information for SOS1-AF-Q07889.pdb #2 
    3317 --- 
    3318 Chain | Description | UniProt 
    3319 A | son of sevenless homolog 1 | SOS1_HUMAN 1-1333 
    3320  
    3321 
    3322 > ui tool show "Show Sequence Viewer"
    3323 
    3324 > sequence chain #1/A
    3325 
    3326 Alignment identifier is 1/A 
    3327 
    3328 > sequence chain #1/C
    3329 
    3330 Alignment identifier is 1/C 
    3331 
    3332 > sequence chain #2/A
    3333 
    3334 Alignment identifier is 2/A 
    3335 
    3336 > select #2/A:1040-1041
    3337 
    3338 18 atoms, 17 bonds, 2 residues, 1 model selected 
    3339 
    3340 > select #2/A:1040-1333
    3341 
    3342 2241 atoms, 2331 bonds, 294 residues, 1 model selected 
    3343 
    3344 > cartoon hide sel
    3345 
    3346 > select clear
    3347 
    3348 > select #2/A:565
    3349 
    3350 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3351 
    3352 > select #2/A:554-565
    3353 
    3354 100 atoms, 99 bonds, 12 residues, 1 model selected 
    3355 
    3356 > ui tool show Matchmaker
    3357 
    3358 > matchmaker #2/A & sel to #1/A pairing ss
    3359 
    3360 Parameters 
    3361 --- 
    3362 Chain pairing | ss 
    3363 Alignment algorithm | Needleman-Wunsch 
    3364 Similarity matrix | BLOSUM-62 
    3365 SS fraction | 0.3 
    3366 Gap open (HH/SS/other) | 18/18/6 
    3367 Gap extend | 1 
    3368 SS matrix |  |  | H | S | O 
    3369 ---|---|---|--- 
    3370 H | 6 | -9 | -6 
    3371 S |  | 6 | -6 
    3372 O |  |  | 4 
    3373 Iteration cutoff | 2 
    3374  
    3375 Matchmaker VAVtoSOS 2e.pdb, chain A (#1) with SOS1-AF-Q07889.pdb, chain A
    3376 (#2), sequence alignment score = 61.6 
    3377 RMSD between 12 pruned atom pairs is 0.349 angstroms; (across all 12 pairs:
    3378 0.349) 
    3379  
    3380 
    3381 > select #2/A:565
    3382 
    3383 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3384 
    3385 > select #2/A:271-565
    3386 
    3387 2380 atoms, 2424 bonds, 295 residues, 1 model selected 
    3388 
    3389 > cartoon hide sel
    3390 
    3391 > select #2/A:1
    3392 
    3393 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3394 
    3395 > select #2/A:1-315
    3396 
    3397 2556 atoms, 2610 bonds, 315 residues, 1 model selected 
    3398 
    3399 > cartoon hide sel
    3400 
    3401 > select #2/A:563@CA
    3402 
    3403 1 atom, 1 residue, 1 model selected 
    3404 
    3405 > cofr sel
    3406 
    3407 No displayed objects specified. 
    3408 
    3409 > select #1/A:563@CA
    3410 
    3411 1 atom, 1 residue, 1 model selected 
    3412 
    3413 > cofr sel
    3414 
    3415 > ui mousemode right zoom
    3416 
    3417 > select add #1
    3418 
    3419 8879 atoms, 8968 bonds, 563 residues, 2 models selected 
    3420 
    3421 > ui mousemode right "rotate selected models"
    3422 
    3423 > view matrix models
    3424 > #1,0.70271,-0.27973,0.65418,-92.749,0.51877,0.8307,-0.20204,54.743,-0.48691,0.48134,0.72886,1.1474
    3425 
    3426 > ui mousemode right "translate selected models"
    3427 
    3428 > view matrix models
    3429 > #1,0.70271,-0.27973,0.65418,-120.91,0.51877,0.8307,-0.20204,77.907,-0.48691,0.48134,0.72886,-7.8518
    3430 
    3431 > roll x 2 180
    3432 
    3433 > cofr sel
    3434 
    3435 > roll x 1 60
    3436 
    3437 > roll x 1 300
    3438 
    3439 > roll x 1 90
    3440 
    3441 > show sel surfaces
    3442 
    3443 > hide #!1 models
    3444 
    3445 > addh
    3446 
    3447 Summary of feedback from adding hydrogens to multiple structures 
    3448 --- 
    3449 warning | Skipped 17 atom(s) with bad connectivities; see log for details 
    3450 notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing
    3451 termini instead 
    3452 Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records 
    3453 Chain-initial residues that are actual N termini: VAVtoSOS 2e.pdb #1/A GLN
    3454 189, VAVtoSOS 2e.pdb #1/C MET 1, VAVtoSOS 2e.pdb #1/A GLN 189 
    3455 Chain-initial residues that are not actual N termini: 
    3456 Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #1/A ASN 583,
    3457 VAVtoSOS 2e.pdb #1/C LEU 177, VAVtoSOS 2e.pdb #1/A ASN 583 
    3458 Chain-final residues that are not actual C termini: 
    3459 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT 
    3460 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
    3461 223 OXT 
    3462  
    3463 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O 
    3464 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
    3465 223 O 
    3466  
    3467 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 O 
    3468 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY
    3469 279 O 
    3470  
    3471 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O 
    3472 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
    3473 223 O 
    3474  
    3475 Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT 
    3476 Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
    3477 223 OXT 
    3478  
    3479 12 messages similar to the above omitted 
    3480 565 hydrogen bonds 
    3481 Termini for SOS1-AF-Q07889.pdb (#2) chain A determined from SEQRES records 
    3482 Chain-initial residues that are actual N termini: SOS1-AF-Q07889.pdb #2/A MET
    3483 1 
    3484 Chain-initial residues that are not actual N termini: 
    3485 Chain-final residues that are actual C termini: SOS1-AF-Q07889.pdb #2/A SER
    3486 1333 
    3487 Chain-final residues that are not actual C termini: 
    3488 1018 hydrogen bonds 
    3489 10869 hydrogens added 
    3490  
    3491 Drag select of 474 residues 
    3492 
    3493 > show sel surfaces
    3494 
    3495 > coulombic sel
    3496 
    3497 Using Amber 20 recommended default charges and atom types for standard
    3498 residues 
    3499 Coulombic values for SOS1-AF-Q07889.pdb_A SES surface #2.1: minimum, -18.25,
    3500 mean -0.78, maximum 27.88 
    3501 To also show corresponding color key, enter the above coulombic command and
    3502 add key true 
    3503 
    3504 > show #!1 models
    3505 
    3506 > hide #!2 models
    3507 
    3508 > show #!2 models
    3509 
    3510 > hide #!1 models
    3511 
    3512 > select add #1
    3513 
    3514 16908 atoms, 9129 bonds, 1037 residues, 3 models selected 
    3515 
    3516 > select subtract #1
    3517 
    3518 7868 atoms, 474 residues, 4 models selected 
    3519 
    3520 > show #!1 models
    3521 
    3522 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3523 > evolution/Chimera models/Working models/SPTBN2 working 4n.pdb"
    3524 
    3525 Chain information for SPTBN2 working 4n.pdb #3 
    3526 --- 
    3527 Chain | Description 
    3528 A B C D F G | No description available 
    3529 H | No description available 
    3530 J | No description available 
    3531 K | No description available 
    3532 Q | No description available 
    3533 b | No description available 
    3534  
    3535 
    3536 > select #2/A:1085
    3537 
    3538 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3539 
    3540 > select #2/A:1085
    3541 
    3542 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3543 
    3544 > select #2/A:819
    3545 
    3546 14 atoms, 14 bonds, 1 residue, 1 model selected 
    3547 
    3548 > select #2/A:819-864
    3549 
    3550 786 atoms, 791 bonds, 46 residues, 1 model selected 
    3551 
    3552 > ui tool show Matchmaker
    3553 
    3554 > matchmaker #3/H to #2/A & sel pairing ss
    3555 
    3556 Parameters 
    3557 --- 
    3558 Chain pairing | ss 
    3559 Alignment algorithm | Needleman-Wunsch 
    3560 Similarity matrix | BLOSUM-62 
    3561 SS fraction | 0.3 
    3562 Gap open (HH/SS/other) | 18/18/6 
    3563 Gap extend | 1 
    3564 SS matrix |  |  | H | S | O 
    3565 ---|---|---|--- 
    3566 H | 6 | -9 | -6 
    3567 S |  | 6 | -6 
    3568 O |  |  | 4 
    3569 Iteration cutoff | 2 
    3570  
    3571 Matchmaker SOS1-AF-Q07889.pdb, chain A (#2) with SPTBN2 working 4n.pdb, chain
    3572 H (#3), sequence alignment score = 242.8 
    3573 RMSD between 46 pruned atom pairs is 0.746 angstroms; (across all 46 pairs:
    3574 0.746) 
    3575  
    3576 
    3577 > hide sel atoms
    3578 
    3579 > select
    3580 
    3581 98252 atoms, 99312 bonds, 10 pseudobonds, 6212 residues, 4 models selected 
    3582 
    3583 > hide sel atoms
    3584 
    3585 > show sel cartoons
    3586 
    3587 > select #2/A:1289-1333
    3588 
    3589 705 atoms, 720 bonds, 45 residues, 1 model selected 
    3590 
    3591 > select #2/A:1040-1333
    3592 
    3593 4434 atoms, 4524 bonds, 294 residues, 1 model selected 
    3594 
    3595 > cartoon hide (#!2 & sel)
    3596 
    3597 > select #2/A:564-565
    3598 
    3599 30 atoms, 29 bonds, 2 residues, 1 model selected 
    3600 
    3601 > select #2/A:271-565
    3602 
    3603 4737 atoms, 4781 bonds, 295 residues, 1 model selected 
    3604 
    3605 > cartoon hide (#!2 & sel)
    3606 
    3607 > select #2/A:313-314
    3608 
    3609 28 atoms, 27 bonds, 2 residues, 1 model selected 
    3610 
    3611 > select #2/A:138-314
    3612 
    3613 2837 atoms, 2865 bonds, 177 residues, 1 model selected 
    3614 
    3615 > select #2/A:93
    3616 
    3617 10 atoms, 9 bonds, 1 residue, 1 model selected 
    3618 
    3619 > select #2/A:1-93
    3620 
    3621 1476 atoms, 1493 bonds, 93 residues, 1 model selected 
    3622 
    3623 > select #2/A:1
    3624 
    3625 19 atoms, 18 bonds, 1 residue, 1 model selected 
    3626 
    3627 > select #2/A:1-246
    3628 
    3629 4024 atoms, 4064 bonds, 246 residues, 1 model selected 
    3630 
    3631 > cartoon hide (#!2 & sel)
    3632 
    3633 > select #2/A:566
    3634 
    3635 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3636 
    3637 > select #2/A:271-566
    3638 
    3639 4754 atoms, 4798 bonds, 296 residues, 1 model selected 
    3640 
    3641 > select clear
    3642 
    3643 > select #2/A:566
    3644 
    3645 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3646 
    3647 > select #2/A:271-566
    3648 
    3649 4754 atoms, 4798 bonds, 296 residues, 1 model selected 
    3650 
    3651 > cartoon hide (#!2 & sel)
    3652 
    3653 > ui tool show "Show Sequence Viewer"
    3654 
    3655 > sequence chain #3/H
    3656 
    3657 Alignment identifier is 3/H 
    3658 
    3659 > select #3/H:520-565
    3660 
    3661 738 atoms, 741 bonds, 46 residues, 1 model selected 
    3662 
    3663 > select #3/H:201-565
    3664 
    3665 5911 atoms, 5966 bonds, 365 residues, 1 model selected 
    3666 
    3667 > cartoon hide sel
    3668 
    3669 > select clear
    3670 
    3671 > select #2/A
    3672 
    3673 21448 atoms, 21723 bonds, 1333 residues, 1 model selected 
    3674 
    3675 > hide sel surfaces
    3676 
    3677 > hide sel cartoons
    3678 
    3679 > view matrix models
    3680 > #2,-0.16721,0.025947,0.98558,-73.706,0.98583,0.018113,0.16677,74.81,-0.013525,0.9995,-0.028608,160.35
    3681 
    3682 > select #1/A
    3683 
    3684 6251 atoms, 6310 bonds, 386 residues, 1 model selected 
    3685 
    3686 > hide sel surfaces
    3687 
    3688 > select #3/Q
    3689 
    3690 2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected 
    3691 
    3692 > delete atoms (#!3 & sel)
    3693 
    3694 > delete bonds (#!3 & sel)
    3695 
    3696 > close #2
    3697 
    3698 > select #3/H:519-565
    3699 
    3700 760 atoms, 763 bonds, 47 residues, 1 model selected 
    3701 
    3702 > select #3/H:201-565
    3703 
    3704 5911 atoms, 5966 bonds, 365 residues, 1 model selected 
    3705 
    3706 > delete atoms sel
    3707 
    3708 > delete bonds sel
    3709 
    3710 > combine #1,3 name SOS-RacGEF
    3711 
    3712 Remapping chain ID 'A' in SPTBN2 working 4n.pdb #3 to 'E' 
    3713 Remapping chain ID 'C' in SPTBN2 working 4n.pdb #3 to 'I' 
    3714 
    3715 > close #1-2
    3716 
    3717 > close session
    3718 
    3719 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3720 > evolution/Chimera models/Working models/SPTBN2 working 7g.pdb"
    3721 
    3722 Chain information for SPTBN2 working 7g.pdb #1 
    3723 --- 
    3724 Chain | Description 
    3725 B C D E F | No description available 
    3726 J | No description available 
    3727 K | No description available 
    3728 Q | No description available 
    3729 S | No description available 
    3730  
    3731 
    3732 > select ::name="ADP"
    3733 
    3734 195 atoms, 205 bonds, 5 residues, 1 model selected 
    3735 
    3736 > color sel byelement
    3737 
    3738 > select clear
    3739 
    3740 > select ::name="ADP"
    3741 
    3742 195 atoms, 205 bonds, 5 residues, 1 model selected 
    3743 
    3744 > show sel atoms
    3745 
    3746 > select clear
    3747 
    3748 > open "/Users/tmckeithan/Desktop/Cell biology and also early
    3749 > evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"
    3750 
    3751 Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
    3752 also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb 
    3753 --- 
    3754 warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
    3755 records as basis for sequence. 
    3756  
    3757 Chain information for VAVtoSOS 2e.pdb #2 
    3758 --- 
    3759 Chain | Description 
    3760 A | No description available 
    3761 C | No description available 
    3762  
    3763 
    3764 > ui tool show "Show Sequence Viewer"
    3765 
    3766 > sequence chain #1/S
    3767 
    3768 Alignment identifier is 1/S 
    3769 
    3770 > select #1/S:570
    3771 
    3772 14 atoms, 14 bonds, 1 residue, 1 model selected 
    3773 
    3774 > select #1/S:565-570
    3775 
    3776 108 atoms, 108 bonds, 6 residues, 1 model selected 
    3777 
    3778 > ui tool show Matchmaker
    3779 
    3780 > matchmaker #2/A to #1/S pairing ss
    3781 
    3782 Parameters 
    3783 --- 
    3784 Chain pairing | ss 
    3785 Alignment algorithm | Needleman-Wunsch 
    3786 Similarity matrix | BLOSUM-62 
    3787 SS fraction | 0.3 
    3788 Gap open (HH/SS/other) | 18/18/6 
    3789 Gap extend | 1 
    3790 SS matrix |  |  | H | S | O 
    3791 ---|---|---|--- 
    3792 H | 6 | -9 | -6 
    3793 S |  | 6 | -6 
    3794 O |  |  | 4 
    3795 Iteration cutoff | 2 
    3796  
    3797 Matchmaker SPTBN2 working 7g.pdb, chain S (#1) with VAVtoSOS 2e.pdb, chain A
    3798 (#2), sequence alignment score = 117 
    3799 RMSD between 8 pruned atom pairs is 1.292 angstroms; (across all 276 pairs:
    3800 36.428) 
    3801  
    3802 
    3803 > ui tool show "Show Sequence Viewer"
    3804 
    3805 > sequence chain #2/A
    3806 
    3807 Alignment identifier is 2/A 
    3808 
    3809 > select #2/A:563
    3810 
    3811 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3812 
    3813 > select #2/A:563-569
    3814 
    3815 117 atoms, 117 bonds, 7 residues, 1 model selected 
    3816 
    3817 > select #1/S:570
    3818 
    3819 14 atoms, 14 bonds, 1 residue, 1 model selected 
    3820 
    3821 > select #1/S:565-570
    3822 
    3823 108 atoms, 108 bonds, 6 residues, 1 model selected 
    3824 
    3825 > name frozen temp sel
    3826 
    3827 > select #2/A:569
    3828 
    3829 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3830 
    3831 > select #2/A:564-569
    3832 
    3833 102 atoms, 102 bonds, 6 residues, 1 model selected 
    3834 
    3835 > select add temp
    3836 
    3837 210 atoms, 210 bonds, 12 residues, 2 models selected 
    3838 
    3839 > matchmaker #2/A & sel to #1/S & sel pairing ss
    3840 
    3841 Parameters 
    3842 --- 
    3843 Chain pairing | ss 
    3844 Alignment algorithm | Needleman-Wunsch 
    3845 Similarity matrix | BLOSUM-62 
    3846 SS fraction | 0.3 
    3847 Gap open (HH/SS/other) | 18/18/6 
    3848 Gap extend | 1 
    3849 SS matrix |  |  | H | S | O 
    3850 ---|---|---|--- 
    3851 H | 6 | -9 | -6 
    3852 S |  | 6 | -6 
    3853 O |  |  | 4 
    3854 Iteration cutoff | 2 
    3855  
    3856 Matchmaker SPTBN2 working 7g.pdb, chain S (#1) with VAVtoSOS 2e.pdb, chain A
    3857 (#2), sequence alignment score = 24.2 
    3858 RMSD between 5 pruned atom pairs is 0.794 angstroms; (across all 5 pairs:
    3859 0.794) 
    3860  
    3861 
    3862 > select #1/S
    3863 
    3864 8017 atoms, 8116 bonds, 483 residues, 1 model selected 
    3865 
    3866 > show sel cartoons
    3867 
    3868 > hide sel atoms
    3869 
    3870 > select clear
    3871 
    3872 > select add #2
    3873 
    3874 8835 atoms, 8924 bonds, 563 residues, 1 model selected 
    3875 
    3876 > ui mousemode right "rotate selected models"
    3877 
    3878 > view matrix models
    3879 > #2,-0.81869,0.30503,0.48652,-105.62,-0.32525,-0.94456,0.044877,60.514,0.47324,-0.1215,0.87251,-275.68
    3880 
    3881 > undo
    3882 
    3883 > view matrix models
    3884 > #2,-0.33213,0.84204,-0.42503,19.323,-0.92921,-0.21469,0.30078,-30.599,0.16202,0.49484,0.85374,-311.62
    3885 
    3886 > view matrix models
    3887 > #2,-0.17531,0.79237,-0.58431,50.14,-0.96584,-0.023367,0.2581,-34.351,0.19086,0.60959,0.7694,-303.58
    3888 
    3889 > ui mousemode right "translate selected models"
    3890 
    3891 > view matrix models
    3892 > #2,-0.17531,0.79237,-0.58431,95.476,-0.96584,-0.023367,0.2581,-65.593,0.19086,0.60959,0.7694,-309.48
    3893 
    3894 > open /Users/tmckeithan/Downloads/Chimera/PDB/6ZNL.pdb
    3895 
    3896 6ZNL.pdb title: 
    3897 Cryo-em structure of the dynactin complex [more info...] 
    3898  
    3899 Chain information for 6ZNL.pdb #3 
    3900 --- 
    3901 Chain | Description | UniProt 
    3902 A B C D E F G I | ARP1 actin related protein 1 homolog A | F2Z5G5_PIG 1-376 
    3903 H | β-actin | ACTB_PIG 1-375 
    3904 J | ARP11 | I3LHK5_PIG 1-417 
    3905 K | capping protein (actin filament) muscle Z-line, α 1 | A0PFK5_PIG 1-286 
    3906 L | F-actin capping protein β subunit | A9XFX6_PIG 1-272 
    3907 M N m n | dynactin subunit 2 | 
    3908 O o | dynactin subunit 3 isoform 1 | F1SEC0_PIG 1-186 
    3909 U | dynactin 6 | D0G6S1_PIG 1-190 
    3910 V | dynactin subunit 5 | 
    3911 Y | dynactin subunit 4 | 
    3912 Z z | dynactin subunit 1 | 
    3913  
    3914 Non-standard residues in 6ZNL.pdb #3 
    3915 --- 
    3916 ADP — adenosine-5'-diphosphate 
    3917 ATP — adenosine-5'-triphosphate 
    3918 ZN — zinc ion 
    3919  
    3920 
    3921 > close #3
    3922 
    3923 > open /Users/tmckeithan/Downloads/Chimera/PDB/8DNH.pdb
    3924 
    3925 8DNH.pdb title: 
    3926 Cryo-em structure of nonmuscle β-actin [more info...] 
    3927  
    3928 Chain information for 8DNH.pdb #3 
    3929 --- 
    3930 Chain | Description | UniProt 
    3931 A B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374 
    3932  
    3933 Non-standard residues in 8DNH.pdb #3 
    3934 --- 
    3935 ACE — acetyl group 
    3936 ADP — adenosine-5'-diphosphate 
    3937 MG — magnesium ion 
    3938  
    3939 
    3940 > ui tool show Matchmaker
    3941 
    3942 > matchmaker #3/A to #1/B pairing ss
    3943 
    3944 Parameters 
    3945 --- 
    3946 Chain pairing | ss 
    3947 Alignment algorithm | Needleman-Wunsch 
    3948 Similarity matrix | BLOSUM-62 
    3949 SS fraction | 0.3 
    3950 Gap open (HH/SS/other) | 18/18/6 
    3951 Gap extend | 1 
    3952 SS matrix |  |  | H | S | O 
    3953 ---|---|---|--- 
    3954 H | 6 | -9 | -6 
    3955 S |  | 6 | -6 
    3956 O |  |  | 4 
    3957 Iteration cutoff | 2 
    3958  
    3959 Matchmaker SPTBN2 working 7g.pdb, chain B (#1) with 8DNH.pdb, chain A (#3),
    3960 sequence alignment score = 1845.7 
    3961 RMSD between 263 pruned atom pairs is 1.168 angstroms; (across all 374 pairs:
    3962 2.458) 
    3963  
    3964 
    3965 > matchmaker #3/A to #1/D pairing ss
    3966 
    3967 Parameters 
    3968 --- 
    3969 Chain pairing | ss 
    3970 Alignment algorithm | Needleman-Wunsch 
    3971 Similarity matrix | BLOSUM-62 
    3972 SS fraction | 0.3 
    3973 Gap open (HH/SS/other) | 18/18/6 
    3974 Gap extend | 1 
    3975 SS matrix |  |  | H | S | O 
    3976 ---|---|---|--- 
    3977 H | 6 | -9 | -6 
    3978 S |  | 6 | -6 
    3979 O |  |  | 4 
    3980 Iteration cutoff | 2 
    3981  
    3982 Matchmaker SPTBN2 working 7g.pdb, chain D (#1) with 8DNH.pdb, chain A (#3),
    3983 sequence alignment score = 1823.5 
    3984 RMSD between 224 pruned atom pairs is 1.340 angstroms; (across all 374 pairs:
    3985 2.714) 
    3986  
    3987 
    3988 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    3989 > evolution/Chimera models/Working models/SPTBN2 working 8.pdb"
    3990 
    3991 > ui mousemode right zoom
    3992 
    3993 > show sel atoms
    3994 
    3995 > style sel sphere
    3996 
    3997 Changed 8835 atom styles 
    3998 
    3999 > save "/Users/tmckeithan/Desktop/Cell biology and also early
    4000 > evolution/Chimera models/Working models/SPTBN2 working 8.cxs"
    4001 
    4002 > select
    4003 
    4004 74563 atoms, 75470 bonds, 13 pseudobonds, 5520 residues, 5 models selected 
    4005 
    4006 > show sel cartoons
    4007 
    4008 > hide sel atoms
    4009 
    4010 > select clear
    4011 
    4012 > select #1/S:586-588,601-604,947-950,953-956
    4013 
    4014 272 atoms, 269 bonds, 15 residues, 1 model selected 
    4015 
    4016 > select add #2
    4017 
    4018 9107 atoms, 9193 bonds, 578 residues, 2 models selected 
    4019 
    4020 > select sel : ui tool show "Show Sequence Viewer"
    4021 
    4022 > sequence chain #1/S
    4023 
    4024 Destroying pre-existing alignment with identifier 1/S 
    4025 Alignment identifier is 1/S 
    4026 
    4027 > sequence chain #1/J
    4028 
    4029 Alignment identifier is 1/J 
    4030 
    4031 > sequence chain #1/K
    4032 
    4033 Alignment identifier is 1/K 
    4034 
    4035 > sequence chain #1/Q
    4036 
    4037 Alignment identifier is 1/Q 
    4038 
    4039 > select clear
    4040 
    4041 > select #2/A
    4042 
    4043 6252 atoms, 6311 bonds, 386 residues, 1 model selected 
    4044 
    4045 > select sel : select add #1
    4046 
    4047 60614 atoms, 61233 bonds, 9 pseudobonds, 3865 residues, 3 models selected 
    4048 
    4049 > select subtract #1
    4050 
    4051 6682 atoms, 6739 bonds, 416 residues, 1 model selected 
    4052 
    4053 > select add #2
    4054 
    4055 8835 atoms, 8924 bonds, 563 residues, 1 model selected 
    4056 
    4057 > ui mousemode right "translate selected atoms"
    4058 
    4059 > select sel : undo
    4060 
    4061 > ui mousemode right zoom
    4062 
    4063 > ui mousemode right "rotate selected models"
    4064 
    4065 > view matrix models
    4066 > #1,0.99927,0.033374,0.018352,2.1816,-0.033789,0.99917,0.022784,6.2974,-0.017577,-0.023387,0.99957,1.8691,#2,-0.20392,0.8022,-0.56115,89.719,-0.95476,-0.036233,0.29516,-69.519,0.21644,0.59595,0.7733,-307.62
    4067 
    4068 > undo
    4069 
    4070 > select add #1
    4071 
    4072 62767 atoms, 63418 bonds, 9 pseudobonds, 4012 residues, 3 models selected 
    4073 
    4074 > select subtract #1
    4075 
    4076 8835 atoms, 8924 bonds, 563 residues, 1 model selected 
    4077 
    4078 > view matrix models
    4079 > #2,-0.12312,0.77457,-0.62039,102.93,-0.97518,0.021485,0.22035,-62.423,0.18401,0.63212,0.7527,-308.28
    4080 
    4081 > ui mousemode right "translate selected models"
    4082 
    4083 > view matrix models
    4084 > #2,-0.12312,0.77457,-0.62039,105.45,-0.97518,0.021485,0.22035,-62.22,0.18401,0.63212,0.7527,-308.29
    4085 
    4086 > view matrix models
    4087 > #2,-0.12312,0.77457,-0.62039,105.25,-0.97518,0.021485,0.22035,-61.883,0.18401,0.63212,0.7527,-308.73
    4088 
    4089 > select sel : view matrix models
    4090 > #1,1,0,0,2.5099,0,1,0,-5.5645,0,0,1,5.9637,#2,-0.12312,0.77457,-0.62039,107.76,-0.97518,0.021485,0.22035,-67.448,0.18401,0.63212,0.7527,-302.77
    4091 
    4092 > undo
    4093 
    4094 > ui mousemode right zoom
    4095 
    4096 > select add #1
    4097 
    4098 62767 atoms, 63418 bonds, 9 pseudobonds, 4012 residues, 3 models selected 
    4099 
    4100 > select subtract #1
    4101 
    4102 8835 atoms, 8924 bonds, 563 residues, 1 model selected 
    4103 
    4104 > ui mousemode right "translate selected models"
    4105 
    4106 > view matrix models
    4107 > #2,-0.12312,0.77457,-0.62039,104.94,-0.97518,0.021485,0.22035,-59.617,0.18401,0.63212,0.7527,-307.1
    4108 
    4109 > ui mousemode right zoom
    4110 
    4111 > select sel : select #3/A
    4112 
    4113 2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected 
    4114 
    4115 > select clear
    4116 
    4117 > select #3/A
    4118 
    4119 2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected 
    4120 
    4121 > delete atoms (#!3 & sel)
    4122 
    4123 > delete bonds (#!3 & sel)
    4124 
    4125 > ui tool show "Show Sequence Viewer"
    4126 
    4127 > sequence chain #2/A
    4128 
    4129 Destroying pre-existing alignment with identifier 2/A 
    4130 Alignment identifier is 2/A 
    4131 
    4132 > select #2/A:582-583
    4133 
    4134 30 atoms, 29 bonds, 2 residues, 1 model selected 
    4135 
    4136 > select #2/A:567-583
    4137 
    4138 254 atoms, 257 bonds, 17 residues, 1 model selected 
    4139 
    4140 > select #2/A:564-583
    4141 
    4142 312 atoms, 315 bonds, 20 residues, 1 model selected 
    4143 
    4144 > delete atoms sel
    4145 
    4146 > delete bonds sel
    4147 
    4148 Drag select of 5097 residues 
    4149 
    4150 > select add ::name="ACE"::name="ADP"::name="GTP"::name="MG"
    4151 
    4152 71302 atoms, 369 bonds, 10 pseudobonds, 5123 residues, 5 models selected 
    4153 
    4154 > cartoon hide (#2#!1,3 & sel)
    4155 
    4156 > select ~sel
    4157 
    4158 Nothing selected 
    4159 
    4160 > cartoon
    4161 
    4162 > select ~sel
    4163 
    4164 71302 atoms, 72141 bonds, 12 pseudobonds, 5123 residues, 5 models selected 
    4165 
    4166 > select ~sel
    4167 
    4168 Nothing selected 
    4169 
    4170 > combine #1,2,3 name combo
    4171 
    4172 Remapping chain ID 'C' in VAVtoSOS 2e.pdb #2 to 'G' 
    4173 Remapping chain ID 'B' in 8DNH.pdb #3 to 'H' 
    4174 Remapping chain ID 'C' in 8DNH.pdb #3 to 'I' 
    4175 Remapping chain ID 'D' in 8DNH.pdb #3 to 'L' 
     304
     305[deleted to fit within ticket limits]
    4176306
    4177307> addh