Changes between Initial Version and Version 1 of Ticket #9622


Ignore:
Timestamp:
Aug 23, 2023, 10:42:47 AM (2 years ago)
Author:
Eric Pettersen
Comment:

Reported by Thu Nguyen

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #9622

    • Property Component Unassigned → Input/Output
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash opening mmCIF file

  • Ticket #9622 – Description

    initial v1  
    24362436 
    24372437
    2438 > save /scratch/cs-
    2439 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_a_fitted.cif #1
    2440 
    2441 > close #1
    2442 
    2443 > close #2
    2444 
    2445 > open 6gsm
    2446 
    2447 6gsm title: 
    2448 Structure of a partial yeast 48S preinitiation complex in open conformation.
    2449 [more info...] 
    2450  
    2451 Chain information for 6gsm #1 
    2452 --- 
    2453 Chain | Description | UniProt 
    2454 1 | Met-tRNAi | 
    2455 2 | 18S ribosomal RNA | 
    2456 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    2457 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    2458 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    2459 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    2460 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    2461 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    2462 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    2463 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    2464 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    2465 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    2466 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    2467 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    2468 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    2469 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    2470 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    2471 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    2472 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    2473 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    2474 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    2475 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    2476 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    2477 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    2478 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    2479 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    2480 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    2481 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    2482 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    2483 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    2484 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    2485 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    2486 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    2487 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    2488 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    2489 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    2490 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    2491 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    2492 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    2493 3-265 
    2494 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    2495 90-519 
    2496 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    2497 127-270 
    2498 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    2499 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    2500 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    2501 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    2502 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    2503 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    2504 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    2505  
    2506 Non-standard residues in 6gsm #1 
    2507 --- 
    2508 7NO —
    2509 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    2510 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    2511 GCP — phosphomethylphosphonic acid guanylate ester 
    2512 MG — magnesium ion 
    2513 ZN — zinc ion 
    2514  
    2515 
    2516 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    2517 
    2518 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    2519 level 0.0673, step 2, values float32 
    2520 
    2521 > volume #2 region 115,125,134,226,196,205
    2522 
    2523 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    2524 
    2525 FYI: command is replacing existing command: "selectbox" 
    2526 executed select_box.py 
    2527 
    2528 > selectbox #1 inMap #2
    2529 
    2530 Selected 13328 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    2531 
    2532 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.cif
    2533 > #1 selectedOnly true
    2534 
    2535 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.mrc
    2536 > #2
    2537 
    2538 > close #1
    2539 
    2540 > close #2
    2541 
    2542 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.cif
    2543 
    2544 Summary of feedback from opening /scratch/cs-
    2545 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.cif 
    2546 --- 
    2547 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    2548 near line 44477 
    2549 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    2550 44478 
    2551 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    2552 44479 
    2553 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    2554 44480 
    2555 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    2556 44481 
    2557 174 messages similar to the above omitted 
    2558 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    2559 44730 
    2560 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    2561 44731 
    2562 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    2563 44732 
    2564 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    2565 44733 
    2566 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    2567 44734 
    2568 181 messages similar to the above omitted 
    2569 Atom O2' has no neighbors to form bonds with according to residue template for
    2570 C /1:39 
    2571 Atom O2 has no neighbors to form bonds with according to residue template for
    2572 C /1:39 
    2573 Atom O2' has no neighbors to form bonds with according to residue template for
    2574 C /1:40 
    2575 Atom O2 has no neighbors to form bonds with according to residue template for
    2576 C /1:40 
    2577 Atom O2' has no neighbors to form bonds with according to residue template for
    2578 C /1:41 
    2579 Atom C8 has no neighbors to form bonds with according to residue template for
    2580 A /2:1159 
    2581 Atom OP2 has no neighbors to form bonds with according to residue template for
    2582 C /2:1179 
    2583 Atom OP1 has no neighbors to form bonds with according to residue template for
    2584 A /2:1182 
    2585 Atom O5' has no neighbors to form bonds with according to residue template for
    2586 A /2:1182 
    2587 Atom OP2 has no neighbors to form bonds with according to residue template for
    2588 G /2:1262 
    2589 Atom O3' has no neighbors to form bonds with according to residue template for
    2590 U /2:1313 
    2591 Atom OP2 has no neighbors to form bonds with according to residue template for
    2592 A /2:1386 
    2593 Atom OP2 has no neighbors to form bonds with according to residue template for
    2594 A /2:1477 
    2595 Atom N3 has no neighbors to form bonds with according to residue template for
    2596 A /2:1581 
    2597 Atom N3 has no neighbors to form bonds with according to residue template for
    2598 A /3:28 
    2599 Atom OP2 has no neighbors to form bonds with according to residue template for
    2600 U /3:30 
    2601 Atom O5' has no neighbors to form bonds with according to residue template for
    2602 U /3:30 
    2603 Atom OE1 has no neighbors to form bonds with according to residue template for
    2604 GLN /D:101 
    2605 Atom O has no neighbors to form bonds with according to residue template for
    2606 ALA /D:147 
    2607 Atom CB has no neighbors to form bonds with according to residue template for
    2608 ALA /F:76 
    2609 Atom SD has no neighbors to form bonds with according to residue template for
    2610 MET /F:101 
    2611 Atom O has no neighbors to form bonds with according to residue template for
    2612 TYR /K:12 
    2613 Atom CD1 has no neighbors to form bonds with according to residue template for
    2614 PHE /K:16 
    2615 Atom N has no neighbors to form bonds with according to residue template for
    2616 VAL /K:74 
    2617 Atom N has no neighbors to form bonds with according to residue template for
    2618 LYS /P:24 
    2619 Atom O has no neighbors to form bonds with according to residue template for
    2620 SER /P:92 
    2621 Atom O has no neighbors to form bonds with according to residue template for
    2622 ASN /P:103 
    2623 Atom N has no neighbors to form bonds with according to residue template for
    2624 LYS /Q:26 
    2625 Atom C has no neighbors to form bonds with according to residue template for
    2626 LYS /Q:26 
    2627 Atom N has no neighbors to form bonds with according to residue template for
    2628 TYR /Q:92 
    2629 Atom O has no neighbors to form bonds with according to residue template for
    2630 LYS /R:32 
    2631 Atom CD has no neighbors to form bonds with according to residue template for
    2632 LYS /R:32 
    2633 Atom O has no neighbors to form bonds with according to residue template for
    2634 ARG /R:33 
    2635 Atom O has no neighbors to form bonds with according to residue template for
    2636 TRP /S:84 
    2637 Atom N has no neighbors to form bonds with according to residue template for
    2638 ASN /S:93 
    2639 Atom N has no neighbors to form bonds with according to residue template for
    2640 LEU /S:113 
    2641 Atom CD2 has no neighbors to form bonds with according to residue template for
    2642 LEU /S:131 
    2643 Atom O has no neighbors to form bonds with according to residue template for
    2644 LEU /T:45 
    2645 Atom N has no neighbors to form bonds with according to residue template for
    2646 ARG /f:92 
    2647 Atom N has no neighbors to form bonds with according to residue template for
    2648 TRP /g:93 
    2649 Atom CG2 has no neighbors to form bonds with according to residue template for
    2650 ILE /g:124 
    2651 Atom O has no neighbors to form bonds with according to residue template for
    2652 ASP /g:150 
    2653 Atom O has no neighbors to form bonds with according to residue template for
    2654 ILE /g:195 
    2655  
    2656 Chain information for 0057_6gsm_U.cif #1 
    2657 --- 
    2658 Chain | Description 
    2659 1 | Met-tRNAi 
    2660 2 | 18S ribosomal RNA 
    2661 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    2662 C | KLLA0F09812p 
    2663 D | KLLA0D08305p 
    2664 F | KLLA0D10659p 
    2665 K | KLLA0B08173p 
    2666 P | KLLA0F07843p 
    2667 Q | 40S ribosomal protein S16 
    2668 R | KLLA0B01474p 
    2669 S | KLLA0B01562p 
    2670 T | KLLA0A07194p 
    2671 U | KLLA0F25542p 
    2672 Z | KLLA0B06182p 
    2673 d | 40S ribosomal protein S29 
    2674 f | Ubiquitin-40S ribosomal protein S27a 
    2675 g | KLLA0E12277p 
    2676 i | Eukaryotic translation initiation factor 1A 
    2677  
    2678 
    2679 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U.mrc
    2680 
    2681 Opened 0057_6gsm_U.mrc as #2, grid size 112,72,72, pixel 1, shown at level
    2682 0.134, step 1, values float32 
    2683 
    2684 > fitmap #1 inMap #2
    2685 
    2686 Fit molecule 0057_6gsm_U.cif (#1) to map 0057_6gsm_U.mrc (#2) using 13328
    2687 atoms 
    2688 average map value = 0.07934, steps = 48 
    2689 shifted from previous position = 0.338 
    2690 rotated from previous position = 0.177 degrees 
    2691 atoms outside contour = 12826, contour level = 0.13392 
    2692  
    2693 Position of 0057_6gsm_U.cif (#1) relative to 0057_6gsm_U.mrc (#2) coordinates: 
    2694 Matrix rotation and translation 
    2695 0.99999647 0.00033916 0.00263397 -0.67215769 
    2696 -0.00034329 0.99999871 0.00156937 -0.49700188 
    2697 -0.00263344 -0.00157026 0.99999530 0.68166280 
    2698 Axis -0.50885627 0.85371602 -0.11060857 
    2699 Axis point 251.71663719 0.00000000 285.98413263 
    2700 Rotation angle (degrees) 0.17675705 
    2701 Shift along axis -0.15766456 
    2702  
    2703 
    2704 > save /scratch/cs-
    2705 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_U_fitted.cif #1
    2706 
    2707 > close #1
    2708 
    2709 > close #2
    2710 
    2711 > open 6gsm
    2712 
    2713 6gsm title: 
    2714 Structure of a partial yeast 48S preinitiation complex in open conformation.
    2715 [more info...] 
    2716  
    2717 Chain information for 6gsm #1 
    2718 --- 
    2719 Chain | Description | UniProt 
    2720 1 | Met-tRNAi | 
    2721 2 | 18S ribosomal RNA | 
    2722 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    2723 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    2724 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    2725 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    2726 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    2727 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    2728 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    2729 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    2730 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    2731 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    2732 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    2733 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    2734 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    2735 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    2736 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    2737 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    2738 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    2739 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    2740 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    2741 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    2742 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    2743 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    2744 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    2745 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    2746 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    2747 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    2748 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    2749 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    2750 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    2751 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    2752 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    2753 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    2754 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    2755 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    2756 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    2757 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    2758 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    2759 3-265 
    2760 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    2761 90-519 
    2762 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    2763 127-270 
    2764 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    2765 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    2766 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    2767 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    2768 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    2769 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    2770 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    2771  
    2772 Non-standard residues in 6gsm #1 
    2773 --- 
    2774 7NO —
    2775 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    2776 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    2777 GCP — phosphomethylphosphonic acid guanylate ester 
    2778 MG — magnesium ion 
    2779 ZN — zinc ion 
    2780  
    2781 
    2782 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    2783 
    2784 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    2785 level 0.0673, step 2, values float32 
    2786 
    2787 > volume #2 region 162,185,127,257,272,198
    2788 
    2789 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    2790 
    2791 FYI: command is replacing existing command: "selectbox" 
    2792 executed select_box.py 
    2793 
    2794 > selectbox #1 inMap #2
    2795 
    2796 Selected 11728 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    2797 
    2798 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_e.cif
    2799 > #1 selectedOnly true
    2800 
    2801 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_e.mrc
    2802 > #2
    2803 
    2804 > close #1
    2805 
    2806 > close #2
    2807 
    2808 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_e.cif
    2809 
    2810 Summary of feedback from opening /scratch/cs-
    2811 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_e.cif 
    2812 --- 
    2813 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    2814 near line 42816 
    2815 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    2816 42817 
    2817 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    2818 42818 
    2819 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    2820 42819 
    2821 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    2822 42820 
    2823 163 messages similar to the above omitted 
    2824 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    2825 43069 
    2826 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    2827 43070 
    2828 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    2829 43071 
    2830 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    2831 43072 
    2832 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    2833 43073 
    2834 166 messages similar to the above omitted 
    2835 Atom OP1 has no neighbors to form bonds with according to residue template for
    2836 C /2:18 
    2837 Atom OP1 has no neighbors to form bonds with according to residue template for
    2838 C /2:97 
    2839 Atom O3' has no neighbors to form bonds with according to residue template for
    2840 A /2:359 
    2841 Atom OP2 has no neighbors to form bonds with according to residue template for
    2842 G /2:389 
    2843 Atom O3' has no neighbors to form bonds with according to residue template for
    2844 A /2:411 
    2845 Atom O2' has no neighbors to form bonds with according to residue template for
    2846 A /2:411 
    2847 Atom O2' has no neighbors to form bonds with according to residue template for
    2848 G /2:421 
    2849 Atom O3' has no neighbors to form bonds with according to residue template for
    2850 G /2:425 
    2851 Atom OP2 has no neighbors to form bonds with according to residue template for
    2852 U /2:532 
    2853 Atom C3' has no neighbors to form bonds with according to residue template for
    2854 A /2:533 
    2855 Atom O3' has no neighbors to form bonds with according to residue template for
    2856 A /2:757 
    2857 Atom O4' has no neighbors to form bonds with according to residue template for
    2858 G /2:765 
    2859 Atom OP1 has no neighbors to form bonds with according to residue template for
    2860 U /2:767 
    2861 Atom O2' has no neighbors to form bonds with according to residue template for
    2862 A /2:1132 
    2863 Atom O3' has no neighbors to form bonds with according to residue template for
    2864 U /2:1256 
    2865 Atom C6 has no neighbors to form bonds with according to residue template for
    2866 U /2:1257 
    2867 Atom OP2 has no neighbors to form bonds with according to residue template for
    2868 U /2:1259 
    2869 Atom N7 has no neighbors to form bonds with according to residue template for
    2870 G /2:1266 
    2871 Atom O2 has no neighbors to form bonds with according to residue template for
    2872 U /2:1289 
    2873 Atom O2' has no neighbors to form bonds with according to residue template for
    2874 G /2:1291 
    2875 Atom O3' has no neighbors to form bonds with according to residue template for
    2876 A /2:1299 
    2877 Atom O2' has no neighbors to form bonds with according to residue template for
    2878 A /2:1299 
    2879 Atom OP1 has no neighbors to form bonds with according to residue template for
    2880 A /2:1325 
    2881 Atom N7 has no neighbors to form bonds with according to residue template for
    2882 G /2:1426 
    2883 Atom OP1 has no neighbors to form bonds with according to residue template for
    2884 A /2:1631 
    2885 Atom O2' has no neighbors to form bonds with according to residue template for
    2886 U /2:1659 
    2887 Atom C8 has no neighbors to form bonds with according to residue template for
    2888 G /2:1743 
    2889 Atom OP2 has no neighbors to form bonds with according to residue template for
    2890 G /2:1745 
    2891 Atom C5' has no neighbors to form bonds with according to residue template for
    2892 G /2:1745 
    2893 Atom O3' has no neighbors to form bonds with according to residue template for
    2894 U /2:1750 
    2895 Atom N has no neighbors to form bonds with according to residue template for
    2896 HIS /C:115 
    2897 Atom CB has no neighbors to form bonds with according to residue template for
    2898 HIS /C:115 
    2899 Atom N has no neighbors to form bonds with according to residue template for
    2900 GLY /C:117 
    2901 Atom CA has no neighbors to form bonds with according to residue template for
    2902 ILE /C:120 
    2903 Atom CG2 has no neighbors to form bonds with according to residue template for
    2904 ILE /C:120 
    2905 Atom CD1 has no neighbors to form bonds with according to residue template for
    2906 ILE /C:120 
    2907 Atom CB has no neighbors to form bonds with according to residue template for
    2908 PRO /C:178 
    2909 Atom N has no neighbors to form bonds with according to residue template for
    2910 VAL /C:201 
    2911 Atom O has no neighbors to form bonds with according to residue template for
    2912 VAL /C:201 
    2913 Atom OG1 has no neighbors to form bonds with according to residue template for
    2914 THR /C:209 
    2915 Atom O has no neighbors to form bonds with according to residue template for
    2916 GLY /D:36 
    2917 Atom CD1 has no neighbors to form bonds with according to residue template for
    2918 ILE /D:50 
    2919 Atom ND2 has no neighbors to form bonds with according to residue template for
    2920 ASN /D:62 
    2921 Atom CG has no neighbors to form bonds with according to residue template for
    2922 GLN /J:139 
    2923 Atom NE2 has no neighbors to form bonds with according to residue template for
    2924 GLN /J:139 
    2925 Atom OE1 has no neighbors to form bonds with according to residue template for
    2926 GLU /J:151 
    2927 Atom O has no neighbors to form bonds with according to residue template for
    2928 GLU /J:183 
    2929 Atom CE2 has no neighbors to form bonds with according to residue template for
    2930 TYR /K:12 
    2931 Atom OH has no neighbors to form bonds with according to residue template for
    2932 TYR /K:12 
    2933 Atom NE2 has no neighbors to form bonds with according to residue template for
    2934 GLN /K:47 
    2935 Atom N has no neighbors to form bonds with according to residue template for
    2936 GLN /K:58 
    2937 Atom CB has no neighbors to form bonds with according to residue template for
    2938 LYS /l:216 
    2939 Atom N has no neighbors to form bonds with according to residue template for
    2940 SER /l:219 
    2941 Atom OG has no neighbors to form bonds with according to residue template for
    2942 SER /l:219 
    2943 Atom N has no neighbors to form bonds with according to residue template for
    2944 GLN /m:31 
    2945 Atom C has no neighbors to form bonds with according to residue template for
    2946 GLN /m:31 
    2947 Atom N has no neighbors to form bonds with according to residue template for
    2948 CYS /m:89 
    2949 Atom SG has no neighbors to form bonds with according to residue template for
    2950 CYS /m:89 
    2951 Atom CD1 has no neighbors to form bonds with according to residue template for
    2952 LEU /p:390 
    2953 Atom CD2 has no neighbors to form bonds with according to residue template for
    2954 LEU /p:390 
    2955 Atom N has no neighbors to form bonds with according to residue template for
    2956 GLU /p:398 
    2957 Atom O has no neighbors to form bonds with according to residue template for
    2958 ASN /p:412 
    2959 Atom N has no neighbors to form bonds with according to residue template for
    2960 VAL /p:480 
    2961 Atom O has no neighbors to form bonds with according to residue template for
    2962 VAL /p:480 
    2963 Atom OE1 has no neighbors to form bonds with according to residue template for
    2964 GLU /p:530 
    2965 Atom OE2 has no neighbors to form bonds with according to residue template for
    2966 GLU /p:530 
    2967  
    2968 Chain information for 0057_6gsm_e.cif #1 
    2969 --- 
    2970 Chain | Description 
    2971 2 | 18S ribosomal RNA 
    2972 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    2973 C | KLLA0F09812p 
    2974 D | KLLA0D08305p 
    2975 J | KLLA0E23673p 
    2976 K | KLLA0B08173p 
    2977 M | 40S ribosomal protein S12 
    2978 X | KLLA0B11231p 
    2979 e | 40S ribosomal protein S30 
    2980 i | Eukaryotic translation initiation factor 1A 
    2981 l | Eukaryotic translation initiation factor 2 subunit beta 
    2982 m | Eukaryotic translation initiation factor eIF-1 
    2983 p | Eukaryotic translation initiation factor 3 subunit B 
    2984  
    2985 
    2986 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_e.mrc
    2987 
    2988 Opened 0057_6gsm_e.mrc as #2, grid size 96,88,72, pixel 1, shown at level
    2989 0.14, step 1, values float32 
    2990 
    2991 > fitmap #1 inMap #2
    2992 
    2993 Fit molecule 0057_6gsm_e.cif (#1) to map 0057_6gsm_e.mrc (#2) using 11728
    2994 atoms 
    2995 average map value = 0.07883, steps = 48 
    2996 shifted from previous position = 0.345 
    2997 rotated from previous position = 0.156 degrees 
    2998 atoms outside contour = 11229, contour level = 0.14039 
    2999  
    3000 Position of 0057_6gsm_e.cif (#1) relative to 0057_6gsm_e.mrc (#2) coordinates: 
    3001 Matrix rotation and translation 
    3002 0.99999931 -0.00096213 -0.00066854 0.07989544 
    3003 0.00096378 0.99999650 0.00246569 -0.83572949 
    3004 0.00066616 -0.00246633 0.99999674 0.52309429 
    3005 Axis -0.90324313 -0.24443575 0.35270810 
    3006 Axis point 0.00000000 166.40782257 307.79255316 
    3007 Rotation angle (degrees) 0.15642749 
    3008 Shift along axis 0.31661676 
    3009  
    3010 
    3011 > save /scratch/cs-
    3012 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_e_fitted.cif #1
    3013 
    3014 > close #1
    3015 
    3016 > close #2
    3017 
    3018 > open 6gsm
    3019 
    3020 6gsm title: 
    3021 Structure of a partial yeast 48S preinitiation complex in open conformation.
    3022 [more info...] 
    3023  
    3024 Chain information for 6gsm #1 
    3025 --- 
    3026 Chain | Description | UniProt 
    3027 1 | Met-tRNAi | 
    3028 2 | 18S ribosomal RNA | 
    3029 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    3030 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    3031 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    3032 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    3033 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    3034 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    3035 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    3036 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    3037 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    3038 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    3039 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    3040 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    3041 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    3042 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    3043 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    3044 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    3045 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    3046 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    3047 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    3048 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    3049 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    3050 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    3051 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    3052 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    3053 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    3054 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    3055 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    3056 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    3057 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    3058 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    3059 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    3060 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    3061 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    3062 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    3063 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    3064 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    3065 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    3066 3-265 
    3067 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    3068 90-519 
    3069 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    3070 127-270 
    3071 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    3072 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    3073 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    3074 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    3075 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    3076 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    3077 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    3078  
    3079 Non-standard residues in 6gsm #1 
    3080 --- 
    3081 7NO —
    3082 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    3083 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    3084 GCP — phosphomethylphosphonic acid guanylate ester 
    3085 MG — magnesium ion 
    3086 ZN — zinc ion 
    3087  
    3088 
    3089 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    3090 
    3091 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    3092 level 0.0673, step 2, values float32 
    3093 
    3094 > volume #2 region 130,174,165,225,277,244
    3095 
    3096 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    3097 
    3098 FYI: command is replacing existing command: "selectbox" 
    3099 executed select_box.py 
    3100 
    3101 > selectbox #1 inMap #2
    3102 
    3103 Selected 19056 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    3104 
    3105 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.cif
    3106 > #1 selectedOnly true
    3107 
    3108 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.mrc
    3109 > #2
    3110 
    3111 > close #1
    3112 
    3113 > close #2
    3114 
    3115 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.cif
    3116 
    3117 Summary of feedback from opening /scratch/cs-
    3118 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.cif 
    3119 --- 
    3120 warnings | Invalid residue range for struct_conf "HELX41": invalid chain "J",
    3121 near line 50359 
    3122 Invalid residue range for struct_conf "HELX42": invalid chain "J", near line
    3123 50360 
    3124 Invalid residue range for struct_conf "HELX43": invalid chain "J", near line
    3125 50361 
    3126 Invalid residue range for struct_conf "HELX51": invalid chain "L", near line
    3127 50369 
    3128 Invalid residue range for struct_conf "HELX52": invalid chain "L", near line
    3129 50370 
    3130 119 messages similar to the above omitted 
    3131 Invalid sheet range for struct_sheet_range "? 49": invalid chain "J", near
    3132 line 50620 
    3133 Invalid sheet range for struct_sheet_range "? 50": invalid chain "J", near
    3134 line 50621 
    3135 Invalid sheet range for struct_sheet_range "? 51": invalid chain "J", near
    3136 line 50622 
    3137 Invalid sheet range for struct_sheet_range "? 52": invalid chain "J", near
    3138 line 50623 
    3139 Invalid sheet range for struct_sheet_range "? 53": invalid chain "J", near
    3140 line 50624 
    3141 110 messages similar to the above omitted 
    3142 Atom O4' has no neighbors to form bonds with according to residue template for
    3143 U /1:36 
    3144 Atom OP2 has no neighbors to form bonds with according to residue template for
    3145 A /2:28 
    3146 Atom O2' has no neighbors to form bonds with according to residue template for
    3147 U /2:33 
    3148 Atom O4' has no neighbors to form bonds with according to residue template for
    3149 A /2:41 
    3150 Atom O3' has no neighbors to form bonds with according to residue template for
    3151 C /2:107 
    3152 Atom O2 has no neighbors to form bonds with according to residue template for
    3153 C /2:107 
    3154 Atom P has no neighbors to form bonds with according to residue template for U
    3155 /2:110 
    3156 Atom O3' has no neighbors to form bonds with according to residue template for
    3157 G /2:461 
    3158 Atom O5' has no neighbors to form bonds with according to residue template for
    3159 U /2:465 
    3160 Atom O3' has no neighbors to form bonds with according to residue template for
    3161 G /2:486 
    3162 Atom O2' has no neighbors to form bonds with according to residue template for
    3163 G /2:486 
    3164 Atom OP2 has no neighbors to form bonds with according to residue template for
    3165 C /2:565 
    3166 Atom O2 has no neighbors to form bonds with according to residue template for
    3167 U /2:587 
    3168 Atom N3 has no neighbors to form bonds with according to residue template for
    3169 U /2:587 
    3170 Atom O4 has no neighbors to form bonds with according to residue template for
    3171 U /2:587 
    3172 Atom OP2 has no neighbors to form bonds with according to residue template for
    3173 A /2:600 
    3174 Atom OP2 has no neighbors to form bonds with according to residue template for
    3175 C /2:644 
    3176 Atom N4 has no neighbors to form bonds with according to residue template for
    3177 C /2:644 
    3178 Atom C5 has no neighbors to form bonds with according to residue template for
    3179 C /2:644 
    3180 Atom OP2 has no neighbors to form bonds with according to residue template for
    3181 U /2:664 
    3182 Atom O4 has no neighbors to form bonds with according to residue template for
    3183 U /2:664 
    3184 Atom N4 has no neighbors to form bonds with according to residue template for
    3185 C /2:675 
    3186 Atom C5 has no neighbors to form bonds with according to residue template for
    3187 C /2:675 
    3188 Atom N7 has no neighbors to form bonds with according to residue template for
    3189 G /2:689 
    3190 Atom O6 has no neighbors to form bonds with according to residue template for
    3191 G /2:689 
    3192 Atom C3' has no neighbors to form bonds with according to residue template for
    3193 A /2:755 
    3194 Atom C5' has no neighbors to form bonds with according to residue template for
    3195 A /2:756 
    3196 Atom OP1 has no neighbors to form bonds with according to residue template for
    3197 A /2:864 
    3198 Atom O2' has no neighbors to form bonds with according to residue template for
    3199 A /2:864 
    3200 Atom N4 has no neighbors to form bonds with according to residue template for
    3201 C /2:942 
    3202 Atom C5 has no neighbors to form bonds with according to residue template for
    3203 C /2:942 
    3204 Atom O3' has no neighbors to form bonds with according to residue template for
    3205 A /2:1024 
    3206 Atom O2' has no neighbors to form bonds with according to residue template for
    3207 U /2:1186 
    3208 Atom N3 has no neighbors to form bonds with according to residue template for
    3209 A /2:1188 
    3210 Atom OP2 has no neighbors to form bonds with according to residue template for
    3211 C /2:1191 
    3212 Atom O5' has no neighbors to form bonds with according to residue template for
    3213 C /2:1191 
    3214 Atom OP1 has no neighbors to form bonds with according to residue template for
    3215 A /2:1192 
    3216 Atom O5' has no neighbors to form bonds with according to residue template for
    3217 A /2:1311 
    3218 Atom OP2 has no neighbors to form bonds with according to residue template for
    3219 U /2:1394 
    3220 Atom O3' has no neighbors to form bonds with according to residue template for
    3221 U /2:1394 
    3222 Atom O3' has no neighbors to form bonds with according to residue template for
    3223 G /2:1417 
    3224 Atom OP1 has no neighbors to form bonds with according to residue template for
    3225 U /2:1430 
    3226 Atom O3' has no neighbors to form bonds with according to residue template for
    3227 C /2:1618 
    3228 Atom O2' has no neighbors to form bonds with according to residue template for
    3229 C /2:1638 
    3230 Atom O2' has no neighbors to form bonds with according to residue template for
    3231 U /2:1767 
    3232 Atom OP1 has no neighbors to form bonds with according to residue template for
    3233 G /2:1787 
    3234 Atom OD1 has no neighbors to form bonds with according to residue template for
    3235 ASP /A:8 
    3236 Atom OP2 has no neighbors to form bonds with according to residue template for
    3237 A /3:29 
    3238 Atom CE2 has no neighbors to form bonds with according to residue template for
    3239 TYR /D:34 
    3240 Atom OH has no neighbors to form bonds with according to residue template for
    3241 TYR /D:34 
    3242 Atom N has no neighbors to form bonds with according to residue template for
    3243 VAL /D:39 
    3244 Atom O has no neighbors to form bonds with according to residue template for
    3245 VAL /D:39 
    3246 Atom CB has no neighbors to form bonds with according to residue template for
    3247 ARG /D:90 
    3248 Atom CG2 has no neighbors to form bonds with according to residue template for
    3249 ILE /E:248 
    3250 Atom CD1 has no neighbors to form bonds with according to residue template for
    3251 ILE /E:248 
    3252 Atom CE has no neighbors to form bonds with according to residue template for
    3253 LYS /H:105 
    3254 Atom CG2 has no neighbors to form bonds with according to residue template for
    3255 VAL /J:113 
    3256 Atom N has no neighbors to form bonds with according to residue template for
    3257 TYR /J:114 
    3258 Atom C has no neighbors to form bonds with according to residue template for
    3259 TYR /J:114 
    3260 Atom N has no neighbors to form bonds with according to residue template for
    3261 LYS /J:138 
    3262 Atom CE has no neighbors to form bonds with according to residue template for
    3263 LYS /J:138 
    3264 Atom O has no neighbors to form bonds with according to residue template for
    3265 GLN /J:139 
    3266 Atom N has no neighbors to form bonds with according to residue template for
    3267 ASN /J:142 
    3268 Atom O has no neighbors to form bonds with according to residue template for
    3269 LYS /L:105 
    3270 Atom N has no neighbors to form bonds with according to residue template for
    3271 SER /L:144 
    3272 Atom NZ has no neighbors to form bonds with according to residue template for
    3273 LYS /O:92 
    3274 Atom CB has no neighbors to form bonds with according to residue template for
    3275 LEU /O:137 
    3276 Atom CD1 has no neighbors to form bonds with according to residue template for
    3277 LEU /O:137 
    3278 Atom N has no neighbors to form bonds with according to residue template for
    3279 GLY /R:2 
    3280 Atom N has no neighbors to form bonds with according to residue template for
    3281 LYS /R:44 
    3282 Atom O has no neighbors to form bonds with according to residue template for
    3283 LYS /R:44 
    3284 Atom N has no neighbors to form bonds with according to residue template for
    3285 SER /X:66 
    3286 Atom OG has no neighbors to form bonds with according to residue template for
    3287 SER /X:66 
    3288 Atom NH1 has no neighbors to form bonds with according to residue template for
    3289 ARG /X:69 
    3290 Atom NH2 has no neighbors to form bonds with according to residue template for
    3291 ARG /X:69 
    3292 Atom N has no neighbors to form bonds with according to residue template for
    3293 SER /a:27 
    3294 Atom N has no neighbors to form bonds with according to residue template for
    3295 LEU /b:8 
    3296 Atom O has no neighbors to form bonds with according to residue template for
    3297 ARG /c:67 
    3298 Atom N has no neighbors to form bonds with according to residue template for
    3299 PHE /d:43 
    3300 Atom O has no neighbors to form bonds with according to residue template for
    3301 ARG /e:37 
    3302 Atom N has no neighbors to form bonds with according to residue template for
    3303 THR /g:131 
    3304 Atom CG2 has no neighbors to form bonds with according to residue template for
    3305 THR /g:131 
    3306 Atom CG2 has no neighbors to form bonds with according to residue template for
    3307 VAL /g:152 
    3308 Atom OG has no neighbors to form bonds with according to residue template for
    3309 SER /g:176 
    3310 Atom N has no neighbors to form bonds with according to residue template for
    3311 ASN /g:207 
    3312 Atom N has no neighbors to form bonds with according to residue template for
    3313 TRP /g:230 
    3314 Atom CE has no neighbors to form bonds with according to residue template for
    3315 MET /g:239 
    3316 Atom N has no neighbors to form bonds with according to residue template for
    3317 VAL /g:247 
    3318 Atom CD has no neighbors to form bonds with according to residue template for
    3319 LYS /i:23 
    3320 Atom NZ has no neighbors to form bonds with according to residue template for
    3321 LYS /i:23 
    3322 Atom O has no neighbors to form bonds with according to residue template for
    3323 LYS /i:67 
    3324  
    3325 Chain information for 0057_6gsm_C.cif #1 
    3326 --- 
    3327 Chain | Description 
    3328 1 | Met-tRNAi 
    3329 2 | 18S ribosomal RNA 
    3330 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    3331 A | 40S ribosomal protein S0 
    3332 B | 40S ribosomal protein S1 
    3333 C | KLLA0F09812p 
    3334 D | KLLA0D08305p 
    3335 E | 40S ribosomal protein S4 
    3336 H | 40S ribosomal protein S7 
    3337 J | KLLA0E23673p 
    3338 L | KLLA0A10483p 
    3339 N | KLLA0F18040p 
    3340 O | 40S ribosomal protein S14 
    3341 R | KLLA0B01474p 
    3342 U | KLLA0F25542p 
    3343 V | 40S ribosomal protein S21 
    3344 W | 40S ribosomal protein S22 
    3345 X | KLLA0B11231p 
    3346 a | 40S ribosomal protein S26 
    3347 b | 40S ribosomal protein S27 
    3348 c | 40S ribosomal protein S28 
    3349 d | 40S ribosomal protein S29 
    3350 e | 40S ribosomal protein S30 
    3351 g | KLLA0E12277p 
    3352 i | Eukaryotic translation initiation factor 1A 
    3353  
    3354 
    3355 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C.mrc
    3356 
    3357 Opened 0057_6gsm_C.mrc as #2, grid size 96,104,80, pixel 1, shown at level
    3358 0.146, step 1, values float32 
    3359 
    3360 > fitmap #1 inMap #2
    3361 
    3362 Fit molecule 0057_6gsm_C.cif (#1) to map 0057_6gsm_C.mrc (#2) using 19056
    3363 atoms 
    3364 average map value = 0.0813, steps = 60 
    3365 shifted from previous position = 0.29 
    3366 rotated from previous position = 0.049 degrees 
    3367 atoms outside contour = 18418, contour level = 0.14602 
    3368  
    3369 Position of 0057_6gsm_C.cif (#1) relative to 0057_6gsm_C.mrc (#2) coordinates: 
    3370 Matrix rotation and translation 
    3371 0.99999999 -0.00002143 0.00013169 -0.07370813 
    3372 0.00002132 0.99999964 0.00084431 -0.39245208 
    3373 -0.00013171 -0.00084430 0.99999963 0.02626946 
    3374 Axis -0.98774211 0.15407786 0.02501082 
    3375 Axis point 0.00000000 30.52682018 467.20587978 
    3376 Rotation angle (degrees) 0.04897546 
    3377 Shift along axis 0.01299346 
    3378  
    3379 
    3380 > save /scratch/cs-
    3381 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_C_fitted.cif #1
    3382 
    3383 > close #1
    3384 
    3385 > close #2
    3386 
    3387 > open 6gsm
    3388 
    3389 6gsm title: 
    3390 Structure of a partial yeast 48S preinitiation complex in open conformation.
    3391 [more info...] 
    3392  
    3393 Chain information for 6gsm #1 
    3394 --- 
    3395 Chain | Description | UniProt 
    3396 1 | Met-tRNAi | 
    3397 2 | 18S ribosomal RNA | 
    3398 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    3399 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    3400 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    3401 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    3402 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    3403 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    3404 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    3405 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    3406 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    3407 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    3408 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    3409 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    3410 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    3411 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    3412 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    3413 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    3414 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    3415 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    3416 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    3417 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    3418 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    3419 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    3420 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    3421 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    3422 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    3423 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    3424 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    3425 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    3426 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    3427 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    3428 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    3429 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    3430 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    3431 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    3432 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    3433 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    3434 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    3435 3-265 
    3436 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    3437 90-519 
    3438 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    3439 127-270 
    3440 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    3441 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    3442 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    3443 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    3444 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    3445 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    3446 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    3447  
    3448 Non-standard residues in 6gsm #1 
    3449 --- 
    3450 7NO —
    3451 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    3452 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    3453 GCP — phosphomethylphosphonic acid guanylate ester 
    3454 MG — magnesium ion 
    3455 ZN — zinc ion 
    3456  
    3457 
    3458 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    3459 
    3460 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    3461 level 0.0673, step 2, values float32 
    3462 
    3463 > volume #2 region 179,79,129,258,182,224
    3464 
    3465 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    3466 
    3467 FYI: command is replacing existing command: "selectbox" 
    3468 executed select_box.py 
    3469 
    3470 > selectbox #1 inMap #2
    3471 
    3472 Selected 13752 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    3473 
    3474 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.cif
    3475 > #1 selectedOnly true
    3476 
    3477 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.mrc
    3478 > #2
    3479 
    3480 > close #1
    3481 
    3482 > close #2
    3483 
    3484 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.cif
    3485 
    3486 Summary of feedback from opening /scratch/cs-
    3487 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.cif 
    3488 --- 
    3489 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    3490 near line 44865 
    3491 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    3492 44866 
    3493 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    3494 44867 
    3495 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    3496 44868 
    3497 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    3498 44869 
    3499 168 messages similar to the above omitted 
    3500 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    3501 45118 
    3502 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    3503 45119 
    3504 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    3505 45120 
    3506 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    3507 45121 
    3508 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    3509 45122 
    3510 203 messages similar to the above omitted 
    3511 Atom OP1 has no neighbors to form bonds with according to residue template for
    3512 C /1:6 
    3513 Atom O2' has no neighbors to form bonds with according to residue template for
    3514 C /1:6 
    3515 Atom O3' has no neighbors to form bonds with according to residue template for
    3516 U /1:50 
    3517 Atom C5' has no neighbors to form bonds with according to residue template for
    3518 G /2:1232 
    3519 Atom OP1 has no neighbors to form bonds with according to residue template for
    3520 U /2:1258 
    3521 Atom OP1 has no neighbors to form bonds with according to residue template for
    3522 G /2:1266 
    3523 Atom N2 has no neighbors to form bonds with according to residue template for
    3524 G /2:1266 
    3525 Atom N3 has no neighbors to form bonds with according to residue template for
    3526 G /2:1266 
    3527 Atom O4' has no neighbors to form bonds with according to residue template for
    3528 A /2:1286 
    3529 Atom O4' has no neighbors to form bonds with according to residue template for
    3530 G /2:1329 
    3531 Atom C5 has no neighbors to form bonds with according to residue template for
    3532 A /2:1398 
    3533 Atom N6 has no neighbors to form bonds with according to residue template for
    3534 A /2:1398 
    3535 Atom O3' has no neighbors to form bonds with according to residue template for
    3536 G /2:1426 
    3537 Atom OP1 has no neighbors to form bonds with according to residue template for
    3538 G /2:1484 
    3539 Atom O2' has no neighbors to form bonds with according to residue template for
    3540 U /2:1487 
    3541 Atom O2' has no neighbors to form bonds with according to residue template for
    3542 C /2:1489 
    3543 Atom OP2 has no neighbors to form bonds with according to residue template for
    3544 G /2:1496 
    3545 Atom OP2 has no neighbors to form bonds with according to residue template for
    3546 G /2:1497 
    3547 Atom OP2 has no neighbors to form bonds with according to residue template for
    3548 U /2:1508 
    3549 Atom O3' has no neighbors to form bonds with according to residue template for
    3550 U /2:1517 
    3551 Atom O2 has no neighbors to form bonds with according to residue template for
    3552 U /2:1517 
    3553 Atom CG2 has no neighbors to form bonds with according to residue template for
    3554 ILE /F:66 
    3555 Atom N has no neighbors to form bonds with according to residue template for
    3556 SER /F:67 
    3557 Atom C has no neighbors to form bonds with according to residue template for
    3558 SER /F:67 
    3559 Atom OD1 has no neighbors to form bonds with according to residue template for
    3560 ASP /F:128 
    3561 Atom CD1 has no neighbors to form bonds with according to residue template for
    3562 TYR /K:12 
    3563 Atom N has no neighbors to form bonds with according to residue template for
    3564 LEU /K:46 
    3565 Atom N has no neighbors to form bonds with according to residue template for
    3566 TYR /K:66 
    3567 Atom CD2 has no neighbors to form bonds with according to residue template for
    3568 LEU /Q:38 
    3569 Atom N has no neighbors to form bonds with according to residue template for
    3570 LYS /Q:47 
    3571 Atom N has no neighbors to form bonds with according to residue template for
    3572 ARG /T:63 
    3573 Atom CB has no neighbors to form bonds with according to residue template for
    3574 ARG /T:63 
    3575 Atom CD has no neighbors to form bonds with according to residue template for
    3576 ARG /T:63 
    3577 Atom N has no neighbors to form bonds with according to residue template for
    3578 THR /c:26 
    3579 Atom CG2 has no neighbors to form bonds with according to residue template for
    3580 THR /c:26 
    3581 Atom N has no neighbors to form bonds with according to residue template for
    3582 VAL /c:48 
    3583 Atom O has no neighbors to form bonds with according to residue template for
    3584 VAL /c:48 
    3585 Atom N has no neighbors to form bonds with according to residue template for
    3586 ASN /d:48 
    3587 Atom ND2 has no neighbors to form bonds with according to residue template for
    3588 ASN /d:48 
    3589 Atom O has no neighbors to form bonds with according to residue template for
    3590 ASN /j:41 
    3591 Atom ND2 has no neighbors to form bonds with according to residue template for
    3592 ASN /j:41 
    3593 Atom N has no neighbors to form bonds with according to residue template for
    3594 ALA /j:71 
    3595 Atom CB has no neighbors to form bonds with according to residue template for
    3596 ALA /j:71 
    3597 Atom O has no neighbors to form bonds with according to residue template for
    3598 ARG /j:88 
    3599 Atom CA has no neighbors to form bonds with according to residue template for
    3600 GLU /j:93 
    3601 Atom CG has no neighbors to form bonds with according to residue template for
    3602 GLU /j:93 
    3603 Atom N has no neighbors to form bonds with according to residue template for
    3604 ASP /j:94 
    3605 Atom N has no neighbors to form bonds with according to residue template for
    3606 ALA /j:116 
    3607 Atom C has no neighbors to form bonds with according to residue template for
    3608 ALA /j:116 
    3609 Atom O has no neighbors to form bonds with according to residue template for
    3610 GLN /j:120 
    3611 Atom N has no neighbors to form bonds with according to residue template for
    3612 ILE /j:173 
    3613 Atom CG1 has no neighbors to form bonds with according to residue template for
    3614 ILE /j:173 
    3615 Atom O has no neighbors to form bonds with according to residue template for
    3616 VAL /l:225 
    3617 Atom CG1 has no neighbors to form bonds with according to residue template for
    3618 VAL /l:225 
    3619 Atom CA has no neighbors to form bonds with according to residue template for
    3620 LEU /l:226 
    3621 Atom O has no neighbors to form bonds with according to residue template for
    3622 LEU /l:226 
    3623 Atom O has no neighbors to form bonds with according to residue template for
    3624 MET /m:74 
    3625  
    3626 Chain information for 0057_6gsm_S.cif #1 
    3627 --- 
    3628 Chain | Description 
    3629 1 | Met-tRNAi 
    3630 2 | 18S ribosomal RNA 
    3631 D | KLLA0D08305p 
    3632 F | KLLA0D10659p 
    3633 K | KLLA0B08173p 
    3634 P | KLLA0F07843p 
    3635 Q | 40S ribosomal protein S16 
    3636 R | KLLA0B01474p 
    3637 S | KLLA0B01562p 
    3638 T | KLLA0A07194p 
    3639 U | KLLA0F25542p 
    3640 Z | KLLA0B06182p 
    3641 c | 40S ribosomal protein S28 
    3642 d | 40S ribosomal protein S29 
    3643 f | Ubiquitin-40S ribosomal protein S27a 
    3644 j | Eukaryotic translation initiation factor 2 subunit alpha 
    3645 l | Eukaryotic translation initiation factor 2 subunit beta 
    3646 m | Eukaryotic translation initiation factor eIF-1 
    3647  
    3648 
    3649 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S.mrc
    3650 
    3651 Opened 0057_6gsm_S.mrc as #2, grid size 80,104,96, pixel 1, shown at level
    3652 0.127, step 1, values float32 
    3653 
    3654 > fitmap #1 inMap #2
    3655 
    3656 Fit molecule 0057_6gsm_S.cif (#1) to map 0057_6gsm_S.mrc (#2) using 13752
    3657 atoms 
    3658 average map value = 0.07525, steps = 48 
    3659 shifted from previous position = 0.41 
    3660 rotated from previous position = 0.0854 degrees 
    3661 atoms outside contour = 13058, contour level = 0.12703 
    3662  
    3663 Position of 0057_6gsm_S.cif (#1) relative to 0057_6gsm_S.mrc (#2) coordinates: 
    3664 Matrix rotation and translation 
    3665 0.99999906 0.00133714 0.00031755 -0.63883129 
    3666 -0.00133696 0.99999894 -0.00057716 0.36463028 
    3667 -0.00031832 0.00057673 0.99999978 -0.16205439 
    3668 Axis 0.38707716 0.21330452 -0.89703537 
    3669 Axis point 276.20794680 470.96878257 0.00000000 
    3670 Rotation angle (degrees) 0.08540052 
    3671 Shift along axis -0.02413119 
    3672  
    3673 
    3674 > save /scratch/cs-
    3675 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_S_fitted.cif #1
    3676 
    3677 > close #1
    3678 
    3679 > close #2
    3680 
    3681 > open 6gsm
    3682 
    3683 6gsm title: 
    3684 Structure of a partial yeast 48S preinitiation complex in open conformation.
    3685 [more info...] 
    3686  
    3687 Chain information for 6gsm #1 
    3688 --- 
    3689 Chain | Description | UniProt 
    3690 1 | Met-tRNAi | 
    3691 2 | 18S ribosomal RNA | 
    3692 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    3693 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    3694 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    3695 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    3696 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    3697 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    3698 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    3699 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    3700 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    3701 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    3702 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    3703 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    3704 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    3705 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    3706 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    3707 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    3708 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    3709 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    3710 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    3711 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    3712 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    3713 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    3714 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    3715 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    3716 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    3717 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    3718 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    3719 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    3720 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    3721 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    3722 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    3723 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    3724 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    3725 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    3726 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    3727 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    3728 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    3729 3-265 
    3730 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    3731 90-519 
    3732 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    3733 127-270 
    3734 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    3735 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    3736 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    3737 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    3738 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    3739 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    3740 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    3741  
    3742 Non-standard residues in 6gsm #1 
    3743 --- 
    3744 7NO —
    3745 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    3746 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    3747 GCP — phosphomethylphosphonic acid guanylate ester 
    3748 MG — magnesium ion 
    3749 ZN — zinc ion 
    3750  
    3751 
    3752 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    3753 
    3754 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    3755 level 0.0673, step 2, values float32 
    3756 
    3757 > volume #2 region 206,188,189,285,251,244
    3758 
    3759 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    3760 
    3761 FYI: command is replacing existing command: "selectbox" 
    3762 executed select_box.py 
    3763 
    3764 > selectbox #1 inMap #2
    3765 
    3766 Selected 8610 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    3767 
    3768 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.cif
    3769 > #1 selectedOnly true
    3770 
    3771 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.mrc
    3772 > #2
    3773 
    3774 > close #1
    3775 
    3776 > close #2
    3777 
    3778 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.cif
    3779 
    3780 Summary of feedback from opening /scratch/cs-
    3781 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.cif 
    3782 --- 
    3783 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    3784 near line 39713 
    3785 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    3786 39714 
    3787 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    3788 39715 
    3789 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    3790 39716 
    3791 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    3792 39717 
    3793 114 messages similar to the above omitted 
    3794 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    3795 39966 
    3796 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    3797 39967 
    3798 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    3799 39968 
    3800 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    3801 39969 
    3802 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    3803 39970 
    3804 157 messages similar to the above omitted 
    3805 Atom N6 has no neighbors to form bonds with according to residue template for
    3806 A /2:11 
    3807 Atom OP2 has no neighbors to form bonds with according to residue template for
    3808 G /2:20 
    3809 Atom OP1 has no neighbors to form bonds with according to residue template for
    3810 C /2:309 
    3811 Atom OP1 has no neighbors to form bonds with according to residue template for
    3812 U /2:373 
    3813 Atom OP1 has no neighbors to form bonds with according to residue template for
    3814 A /2:605 
    3815 Atom OP2 has no neighbors to form bonds with according to residue template for
    3816 U /2:611 
    3817 Atom O2' has no neighbors to form bonds with according to residue template for
    3818 G /2:612 
    3819 Atom OP2 has no neighbors to form bonds with according to residue template for
    3820 C /2:613 
    3821 Atom O5' has no neighbors to form bonds with according to residue template for
    3822 C /2:613 
    3823 Atom P has no neighbors to form bonds with according to residue template for G
    3824 /2:633 
    3825 Atom N4 has no neighbors to form bonds with according to residue template for
    3826 C /2:942 
    3827 Atom C5 has no neighbors to form bonds with according to residue template for
    3828 C /2:942 
    3829 Atom N6 has no neighbors to form bonds with according to residue template for
    3830 A /2:997 
    3831 Atom N1 has no neighbors to form bonds with according to residue template for
    3832 A /2:997 
    3833 Atom O2' has no neighbors to form bonds with according to residue template for
    3834 A /2:1000 
    3835 Atom OP2 has no neighbors to form bonds with according to residue template for
    3836 U /2:1008 
    3837 Atom OP2 has no neighbors to form bonds with according to residue template for
    3838 C /2:1009 
    3839 Atom N6 has no neighbors to form bonds with according to residue template for
    3840 A /2:1018 
    3841 Atom N1 has no neighbors to form bonds with according to residue template for
    3842 A /2:1018 
    3843 Atom O2' has no neighbors to form bonds with according to residue template for
    3844 C /2:1074 
    3845 Atom OP2 has no neighbors to form bonds with according to residue template for
    3846 A /2:1142 
    3847 Atom O2' has no neighbors to form bonds with according to residue template for
    3848 G /2:1734 
    3849 Atom O3' has no neighbors to form bonds with according to residue template for
    3850 C /2:1794 
    3851 Atom C8 has no neighbors to form bonds with according to residue template for
    3852 A /3:29 
    3853 Atom CA has no neighbors to form bonds with according to residue template for
    3854 LYS /N:9 
    3855 Atom CB has no neighbors to form bonds with according to residue template for
    3856 LYS /O:92 
    3857 Atom NZ has no neighbors to form bonds with according to residue template for
    3858 LYS /O:92 
    3859 Atom O has no neighbors to form bonds with according to residue template for
    3860 ASN /X:79 
    3861 Atom O has no neighbors to form bonds with according to residue template for
    3862 ALA /X:113 
    3863 Atom C has no neighbors to form bonds with according to residue template for
    3864 LEU /i:42 
    3865 Atom CD2 has no neighbors to form bonds with according to residue template for
    3866 LEU /i:42 
    3867 Atom N has no neighbors to form bonds with according to residue template for
    3868 ASN /i:44 
    3869 Atom N has no neighbors to form bonds with according to residue template for
    3870 GLY /m:107 
    3871 Atom O has no neighbors to form bonds with according to residue template for
    3872 GLY /m:107 
    3873 Atom N has no neighbors to form bonds with according to residue template for
    3874 GLY /p:132 
    3875 Atom O has no neighbors to form bonds with according to residue template for
    3876 GLY /p:132 
    3877 Atom O has no neighbors to form bonds with according to residue template for
    3878 PRO /p:181 
    3879 Atom CB has no neighbors to form bonds with according to residue template for
    3880 LEU /p:189 
    3881 Atom CD2 has no neighbors to form bonds with according to residue template for
    3882 LEU /p:189 
    3883 Atom O has no neighbors to form bonds with according to residue template for
    3884 LYS /p:241 
    3885 Atom N has no neighbors to form bonds with according to residue template for
    3886 ARG /p:266 
    3887 Atom N has no neighbors to form bonds with according to residue template for
    3888 LEU /p:284 
    3889 Atom N has no neighbors to form bonds with according to residue template for
    3890 GLU /p:295 
    3891 Atom CB has no neighbors to form bonds with according to residue template for
    3892 GLU /p:295 
    3893 Atom OE2 has no neighbors to form bonds with according to residue template for
    3894 GLU /p:295 
    3895 Atom O has no neighbors to form bonds with according to residue template for
    3896 GLU /p:308 
    3897 Atom CA has no neighbors to form bonds with according to residue template for
    3898 ASP /p:397 
    3899 Atom O has no neighbors to form bonds with according to residue template for
    3900 THR /q:141 
    3901 Atom CB has no neighbors to form bonds with according to residue template for
    3902 THR /q:141 
    3903 Atom O has no neighbors to form bonds with according to residue template for
    3904 GLN /q:159 
    3905  
    3906 Chain information for 0057_6gsm_h.cif #1 
    3907 --- 
    3908 Chain | Description 
    3909 2 | 18S ribosomal RNA 
    3910 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    3911 C | KLLA0F09812p 
    3912 L | KLLA0A10483p 
    3913 N | KLLA0F18040p 
    3914 O | 40S ribosomal protein S14 
    3915 X | KLLA0B11231p 
    3916 a | 40S ribosomal protein S26 
    3917 h | 60S ribosomal protein L41-A 
    3918 i | Eukaryotic translation initiation factor 1A 
    3919 k | Eukaryotic translation initiation factor 2 subunit gamma 
    3920 m | Eukaryotic translation initiation factor eIF-1 
    3921 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    3922 translation initiation factor 3 subunit A,eIF3a 
    3923 p | Eukaryotic translation initiation factor 3 subunit B 
    3924 q | Eukaryotic translation initiation factor 3 subunit C 
    3925  
    3926 
    3927 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h.mrc
    3928 
    3929 Opened 0057_6gsm_h.mrc as #2, grid size 80,64,56, pixel 1, shown at level
    3930 0.155, step 1, values float32 
    3931 
    3932 > fitmap #1 inMap #2
    3933 
    3934 Fit molecule 0057_6gsm_h.cif (#1) to map 0057_6gsm_h.mrc (#2) using 8610 atoms 
    3935 average map value = 0.08394, steps = 76 
    3936 shifted from previous position = 0.502 
    3937 rotated from previous position = 0.277 degrees 
    3938 atoms outside contour = 8377, contour level = 0.1553 
    3939  
    3940 Position of 0057_6gsm_h.cif (#1) relative to 0057_6gsm_h.mrc (#2) coordinates: 
    3941 Matrix rotation and translation 
    3942 0.99999390 0.00244455 0.00249314 -1.49360317 
    3943 -0.00245288 0.99999140 0.00334522 -0.36462362 
    3944 -0.00248494 -0.00335131 0.99999130 1.17721721 
    3945 Axis -0.69213279 0.51451966 -0.50618349 
    3946 Axis point 0.00000000 388.68717064 148.49285133 
    3947 Rotation angle (degrees) 0.27717525 
    3948 Shift along axis 0.25027779 
    3949  
    3950 
    3951 > save /scratch/cs-
    3952 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_h_fitted.cif #1
    3953 
    3954 > close #1
    3955 
    3956 > close #2
    3957 
    3958 > open 6gsm
    3959 
    3960 6gsm title: 
    3961 Structure of a partial yeast 48S preinitiation complex in open conformation.
    3962 [more info...] 
    3963  
    3964 Chain information for 6gsm #1 
    3965 --- 
    3966 Chain | Description | UniProt 
    3967 1 | Met-tRNAi | 
    3968 2 | 18S ribosomal RNA | 
    3969 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    3970 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    3971 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    3972 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    3973 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    3974 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    3975 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    3976 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    3977 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    3978 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    3979 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    3980 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    3981 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    3982 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    3983 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    3984 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    3985 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    3986 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    3987 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    3988 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    3989 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    3990 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    3991 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    3992 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    3993 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    3994 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    3995 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    3996 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    3997 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    3998 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    3999 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    4000 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    4001 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    4002 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    4003 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    4004 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    4005 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    4006 3-265 
    4007 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    4008 90-519 
    4009 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    4010 127-270 
    4011 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    4012 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4013 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    4014 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    4015 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    4016 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    4017 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    4018  
    4019 Non-standard residues in 6gsm #1 
    4020 --- 
    4021 7NO —
    4022 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    4023 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    4024 GCP — phosphomethylphosphonic acid guanylate ester 
    4025 MG — magnesium ion 
    4026 ZN — zinc ion 
    4027  
    4028 
    4029 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    4030 
    4031 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    4032 level 0.0673, step 2, values float32 
    4033 
    4034 > volume #2 region 216,241,180,287,360,275
    4035 
    4036 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    4037 
    4038 FYI: command is replacing existing command: "selectbox" 
    4039 executed select_box.py 
    4040 
    4041 > selectbox #1 inMap #2
    4042 
    4043 Selected 14447 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    4044 
    4045 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.cif
    4046 > #1 selectedOnly true
    4047 
    4048 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.mrc
    4049 > #2
    4050 
    4051 > close #1
    4052 
    4053 > close #2
    4054 
    4055 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.cif
    4056 
    4057 Summary of feedback from opening /scratch/cs-
    4058 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.cif 
    4059 --- 
    4060 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    4061 near line 45675 
    4062 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    4063 45676 
    4064 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    4065 45677 
    4066 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    4067 45678 
    4068 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    4069 45679 
    4070 127 messages similar to the above omitted 
    4071 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    4072 45928 
    4073 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    4074 45929 
    4075 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    4076 45930 
    4077 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    4078 45931 
    4079 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    4080 45932 
    4081 179 messages similar to the above omitted 
    4082 Atom O2' has no neighbors to form bonds with according to residue template for
    4083 U /2:24 
    4084 Atom O2' has no neighbors to form bonds with according to residue template for
    4085 C /2:25 
    4086 Atom OP1 has no neighbors to form bonds with according to residue template for
    4087 A /2:40 
    4088 Atom O3' has no neighbors to form bonds with according to residue template for
    4089 A /2:41 
    4090 Atom O2' has no neighbors to form bonds with according to residue template for
    4091 U /2:64 
    4092 Atom OP2 has no neighbors to form bonds with according to residue template for
    4093 U /2:110 
    4094 Atom O5' has no neighbors to form bonds with according to residue template for
    4095 U /2:110 
    4096 Atom OP2 has no neighbors to form bonds with according to residue template for
    4097 U /2:111 
    4098 Atom O2' has no neighbors to form bonds with according to residue template for
    4099 A /2:146 
    4100 Atom O3' has no neighbors to form bonds with according to residue template for
    4101 G /2:162 
    4102 Atom N2 has no neighbors to form bonds with according to residue template for
    4103 G /2:162 
    4104 Atom OP2 has no neighbors to form bonds with according to residue template for
    4105 A /2:221 
    4106 Atom O5' has no neighbors to form bonds with according to residue template for
    4107 G /2:272 
    4108 Atom O2' has no neighbors to form bonds with according to residue template for
    4109 G /2:364 
    4110 Atom O2' has no neighbors to form bonds with according to residue template for
    4111 A /2:365 
    4112 Atom O2' has no neighbors to form bonds with according to residue template for
    4113 U /2:373 
    4114 Atom OP2 has no neighbors to form bonds with according to residue template for
    4115 G /2:417 
    4116 Atom C6 has no neighbors to form bonds with according to residue template for
    4117 C /2:423 
    4118 Atom N2 has no neighbors to form bonds with according to residue template for
    4119 G /2:433 
    4120 Atom N3 has no neighbors to form bonds with according to residue template for
    4121 G /2:433 
    4122 Atom O5' has no neighbors to form bonds with according to residue template for
    4123 A /2:459 
    4124 Atom O2' has no neighbors to form bonds with according to residue template for
    4125 C /2:468 
    4126 Atom O2 has no neighbors to form bonds with according to residue template for
    4127 C /2:468 
    4128 Atom OP1 has no neighbors to form bonds with according to residue template for
    4129 G /2:627 
    4130 Atom N2 has no neighbors to form bonds with according to residue template for
    4131 G /2:627 
    4132 Atom N3 has no neighbors to form bonds with according to residue template for
    4133 G /2:627 
    4134 Atom O4 has no neighbors to form bonds with according to residue template for
    4135 U /2:631 
    4136 Atom C5 has no neighbors to form bonds with according to residue template for
    4137 U /2:631 
    4138 Atom O2' has no neighbors to form bonds with according to residue template for
    4139 A /2:795 
    4140 Atom N3 has no neighbors to form bonds with according to residue template for
    4141 A /2:795 
    4142 Atom O4 has no neighbors to form bonds with according to residue template for
    4143 U /2:830 
    4144 Atom C5 has no neighbors to form bonds with according to residue template for
    4145 U /2:830 
    4146 Atom O2 has no neighbors to form bonds with according to residue template for
    4147 C /2:848 
    4148 Atom O3' has no neighbors to form bonds with according to residue template for
    4149 U /2:1103 
    4150 Atom O2' has no neighbors to form bonds with according to residue template for
    4151 G /2:1118 
    4152 Atom NH2 has no neighbors to form bonds with according to residue template for
    4153 ARG /E:11 
    4154 Atom CD1 has no neighbors to form bonds with according to residue template for
    4155 LEU /E:12 
    4156 Atom O has no neighbors to form bonds with according to residue template for
    4157 VAL /E:61 
    4158 Atom N has no neighbors to form bonds with according to residue template for
    4159 THR /E:141 
    4160 Atom O has no neighbors to form bonds with according to residue template for
    4161 THR /E:141 
    4162 Atom O has no neighbors to form bonds with according to residue template for
    4163 GLY /G:55 
    4164 Atom O has no neighbors to form bonds with according to residue template for
    4165 ILE /G:112 
    4166 Atom N has no neighbors to form bonds with according to residue template for
    4167 ILE /G:141 
    4168 Atom C has no neighbors to form bonds with according to residue template for
    4169 ILE /G:141 
    4170 Atom OD1 has no neighbors to form bonds with according to residue template for
    4171 ASP /G:152 
    4172 Atom N has no neighbors to form bonds with according to residue template for
    4173 GLU /N:86 
    4174 Atom O has no neighbors to form bonds with according to residue template for
    4175 GLU /N:86 
    4176 Atom N has no neighbors to form bonds with according to residue template for
    4177 VAL /N:132 
    4178 Atom N has no neighbors to form bonds with according to residue template for
    4179 ASN /X:22 
    4180 Atom OD1 has no neighbors to form bonds with according to residue template for
    4181 ASN /X:22 
    4182 Atom N has no neighbors to form bonds with according to residue template for
    4183 TRP /X:24 
    4184 Atom N has no neighbors to form bonds with according to residue template for
    4185 LYS /X:50 
    4186 Atom N has no neighbors to form bonds with according to residue template for
    4187 UNK /o:703 
    4188 Atom N has no neighbors to form bonds with according to residue template for
    4189 LEU /p:189 
    4190 Atom OG1 has no neighbors to form bonds with according to residue template for
    4191 THR /p:243 
    4192 Atom CG2 has no neighbors to form bonds with according to residue template for
    4193 THR /p:243 
    4194 Atom ND2 has no neighbors to form bonds with according to residue template for
    4195 ASN /p:445 
    4196  
    4197 Chain information for 0057_6gsm_I.cif #1 
    4198 --- 
    4199 Chain | Description 
    4200 2 | 18S ribosomal RNA 
    4201 E | 40S ribosomal protein S4 
    4202 G | 40S ribosomal protein S6 
    4203 I | 40S ribosomal protein S8 
    4204 J | KLLA0E23673p 
    4205 L | KLLA0A10483p 
    4206 N | KLLA0F18040p 
    4207 X | KLLA0B11231p 
    4208 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4209 translation initiation factor 3 subunit A,eIF3a 
    4210 p | Eukaryotic translation initiation factor 3 subunit B 
    4211 q | Eukaryotic translation initiation factor 3 subunit C 
    4212  
    4213 
    4214 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I.mrc
    4215 
    4216 Opened 0057_6gsm_I.mrc as #2, grid size 72,120,96, pixel 1, shown at level
    4217 0.144, step 1, values float32 
    4218 
    4219 > fitmap #1 inMap #2
    4220 
    4221 Fit molecule 0057_6gsm_I.cif (#1) to map 0057_6gsm_I.mrc (#2) using 14447
    4222 atoms 
    4223 average map value = 0.08325, steps = 64 
    4224 shifted from previous position = 0.639 
    4225 rotated from previous position = 0.171 degrees 
    4226 atoms outside contour = 13697, contour level = 0.14363 
    4227  
    4228 Position of 0057_6gsm_I.cif (#1) relative to 0057_6gsm_I.mrc (#2) coordinates: 
    4229 Matrix rotation and translation 
    4230 0.99999700 0.00094952 -0.00225603 -0.15605800 
    4231 -0.00094564 0.99999807 0.00172043 -0.49124166 
    4232 0.00225766 -0.00171829 0.99999598 -0.43873210 
    4233 Axis -0.57480111 -0.75448682 -0.31678593 
    4234 Axis point 110.38476831 0.00000000 83.37759510 
    4235 Rotation angle (degrees) 0.17138502 
    4236 Shift along axis 0.59932182 
    4237  
    4238 
    4239 > save /scratch/cs-
    4240 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_I_fitted.cif #1
    4241 
    4242 > close #1
    4243 
    4244 > close #2
    4245 
    4246 > open 6gsm
    4247 
    4248 6gsm title: 
    4249 Structure of a partial yeast 48S preinitiation complex in open conformation.
    4250 [more info...] 
    4251  
    4252 Chain information for 6gsm #1 
    4253 --- 
    4254 Chain | Description | UniProt 
    4255 1 | Met-tRNAi | 
    4256 2 | 18S ribosomal RNA | 
    4257 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    4258 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    4259 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    4260 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    4261 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    4262 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    4263 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    4264 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    4265 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    4266 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    4267 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    4268 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    4269 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    4270 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    4271 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    4272 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    4273 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    4274 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    4275 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    4276 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    4277 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    4278 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    4279 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    4280 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    4281 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    4282 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    4283 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    4284 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    4285 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    4286 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    4287 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    4288 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    4289 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    4290 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    4291 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    4292 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    4293 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    4294 3-265 
    4295 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    4296 90-519 
    4297 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    4298 127-270 
    4299 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    4300 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4301 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    4302 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    4303 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    4304 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    4305 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    4306  
    4307 Non-standard residues in 6gsm #1 
    4308 --- 
    4309 7NO —
    4310 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    4311 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    4312 GCP — phosphomethylphosphonic acid guanylate ester 
    4313 MG — magnesium ion 
    4314 ZN — zinc ion 
    4315  
    4316 
    4317 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    4318 
    4319 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    4320 level 0.0673, step 2, values float32 
    4321 
    4322 > volume #2 region 192,95,185,327,198,264
    4323 
    4324 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    4325 
    4326 FYI: command is replacing existing command: "selectbox" 
    4327 executed select_box.py 
    4328 
    4329 > selectbox #1 inMap #2
    4330 
    4331 Selected 14398 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    4332 
    4333 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.cif
    4334 > #1 selectedOnly true
    4335 
    4336 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.mrc
    4337 > #2
    4338 
    4339 > close #1
    4340 
    4341 > close #2
    4342 
    4343 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.cif
    4344 
    4345 Summary of feedback from opening /scratch/cs-
    4346 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.cif 
    4347 --- 
    4348 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    4349 near line 45481 
    4350 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    4351 45482 
    4352 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    4353 45483 
    4354 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    4355 45484 
    4356 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    4357 45485 
    4358 121 messages similar to the above omitted 
    4359 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    4360 45734 
    4361 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    4362 45735 
    4363 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    4364 45736 
    4365 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    4366 45737 
    4367 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    4368 45738 
    4369 141 messages similar to the above omitted 
    4370 Atom O5' has no neighbors to form bonds with according to residue template for
    4371 U /2:920 
    4372 Atom OP2 has no neighbors to form bonds with according to residue template for
    4373 A /2:923 
    4374 Atom N3 has no neighbors to form bonds with according to residue template for
    4375 A /2:987 
    4376 Atom OP1 has no neighbors to form bonds with according to residue template for
    4377 G /2:1145 
    4378 Atom O2' has no neighbors to form bonds with according to residue template for
    4379 G /2:1145 
    4380 Atom N2 has no neighbors to form bonds with according to residue template for
    4381 G /2:1280 
    4382 Atom O3' has no neighbors to form bonds with according to residue template for
    4383 A /2:1286 
    4384 Atom O2' has no neighbors to form bonds with according to residue template for
    4385 A /2:1286 
    4386 Atom OP1 has no neighbors to form bonds with according to residue template for
    4387 G /2:1287 
    4388 Atom O2' has no neighbors to form bonds with according to residue template for
    4389 G /2:1287 
    4390 Atom O2' has no neighbors to form bonds with according to residue template for
    4391 U /2:1306 
    4392 Atom OP1 has no neighbors to form bonds with according to residue template for
    4393 C /2:1308 
    4394 Atom OP2 has no neighbors to form bonds with according to residue template for
    4395 C /2:1308 
    4396 Atom OP1 has no neighbors to form bonds with according to residue template for
    4397 G /2:1460 
    4398 Atom C8 has no neighbors to form bonds with according to residue template for
    4399 G /2:1462 
    4400 Atom C6 has no neighbors to form bonds with according to residue template for
    4401 C /2:1463 
    4402 Atom OP2 has no neighbors to form bonds with according to residue template for
    4403 U /2:1526 
    4404 Atom OP1 has no neighbors to form bonds with according to residue template for
    4405 U /2:1756 
    4406 Atom O3' has no neighbors to form bonds with according to residue template for
    4407 U /2:1756 
    4408 Atom OP1 has no neighbors to form bonds with according to residue template for
    4409 U /2:1783 
    4410 Atom C5' has no neighbors to form bonds with according to residue template for
    4411 U /2:1783 
    4412 Atom OP2 has no neighbors to form bonds with according to residue template for
    4413 U /2:1796 
    4414 Atom N has no neighbors to form bonds with according to residue template for
    4415 ARG /B:26 
    4416 Atom O has no neighbors to form bonds with according to residue template for
    4417 PHE /B:81 
    4418 Atom NZ has no neighbors to form bonds with according to residue template for
    4419 LYS /B:116 
    4420 Atom N has no neighbors to form bonds with according to residue template for
    4421 PHE /B:142 
    4422 Atom CG1 has no neighbors to form bonds with according to residue template for
    4423 VAL /F:55 
    4424 Atom CB has no neighbors to form bonds with according to residue template for
    4425 ARG /F:94 
    4426 Atom N has no neighbors to form bonds with according to residue template for
    4427 ASN /F:130 
    4428 Atom N has no neighbors to form bonds with according to residue template for
    4429 LEU /F:132 
    4430 Atom NE2 has no neighbors to form bonds with according to residue template for
    4431 GLN /F:133 
    4432 Atom OD1 has no neighbors to form bonds with according to residue template for
    4433 ASP /O:124 
    4434 Atom O has no neighbors to form bonds with according to residue template for
    4435 VAL /S:28 
    4436 Atom N has no neighbors to form bonds with according to residue template for
    4437 ALA /S:31 
    4438 Atom CB has no neighbors to form bonds with according to residue template for
    4439 ALA /S:31 
    4440 Atom CG has no neighbors to form bonds with according to residue template for
    4441 LEU /S:61 
    4442 Atom N has no neighbors to form bonds with according to residue template for
    4443 THR /S:62 
    4444 Atom CG2 has no neighbors to form bonds with according to residue template for
    4445 THR /S:62 
    4446 Atom N has no neighbors to form bonds with according to residue template for
    4447 VAL /Z:92 
    4448 Atom CG2 has no neighbors to form bonds with according to residue template for
    4449 VAL /Z:92 
    4450 Atom N has no neighbors to form bonds with according to residue template for
    4451 SER /a:88 
    4452 Atom CB has no neighbors to form bonds with according to residue template for
    4453 SER /a:88 
    4454 Atom OE2 has no neighbors to form bonds with according to residue template for
    4455 GLU /c:31 
    4456 Atom N has no neighbors to form bonds with according to residue template for
    4457 ASP /k:193 
    4458 Atom N has no neighbors to form bonds with according to residue template for
    4459 MET /k:211 
    4460 Atom SD has no neighbors to form bonds with according to residue template for
    4461 MET /k:211 
    4462 Atom CB has no neighbors to form bonds with according to residue template for
    4463 ALA /k:234 
    4464 Atom O has no neighbors to form bonds with according to residue template for
    4465 PHE /k:435 
    4466 Atom CD2 has no neighbors to form bonds with according to residue template for
    4467 PHE /k:435 
    4468 Atom NE has no neighbors to form bonds with according to residue template for
    4469 ARG /k:474 
    4470 Atom NH2 has no neighbors to form bonds with according to residue template for
    4471 ARG /k:474 
    4472 Atom C has no neighbors to form bonds with according to residue template for
    4473 ARG /l:167 
    4474 Atom CD has no neighbors to form bonds with according to residue template for
    4475 ARG /l:167 
    4476 Atom NH1 has no neighbors to form bonds with according to residue template for
    4477 ARG /l:167 
    4478 Atom N has no neighbors to form bonds with according to residue template for
    4479 ILE /p:116 
    4480 Atom OE1 has no neighbors to form bonds with according to residue template for
    4481 GLU /p:118 
    4482 Atom OE2 has no neighbors to form bonds with according to residue template for
    4483 GLU /p:118 
    4484 Atom C has no neighbors to form bonds with according to residue template for
    4485 LEU /p:127 
    4486  
    4487 Chain information for 0057_6gsm_j.cif #1 
    4488 --- 
    4489 Chain | Description 
    4490 1 | Met-tRNAi 
    4491 2 | 18S ribosomal RNA 
    4492 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    4493 B | 40S ribosomal protein S1 
    4494 C | KLLA0F09812p 
    4495 F | KLLA0D10659p 
    4496 O | 40S ribosomal protein S14 
    4497 Q | 40S ribosomal protein S16 
    4498 S | KLLA0B01562p 
    4499 T | KLLA0A07194p 
    4500 U | KLLA0F25542p 
    4501 Z | KLLA0B06182p 
    4502 a | 40S ribosomal protein S26 
    4503 c | 40S ribosomal protein S28 
    4504 i | Eukaryotic translation initiation factor 1A 
    4505 j | Eukaryotic translation initiation factor 2 subunit alpha 
    4506 k | Eukaryotic translation initiation factor 2 subunit gamma 
    4507 l | Eukaryotic translation initiation factor 2 subunit beta 
    4508 m | Eukaryotic translation initiation factor eIF-1 
    4509 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4510 translation initiation factor 3 subunit A,eIF3a 
    4511 p | Eukaryotic translation initiation factor 3 subunit B 
    4512  
    4513 
    4514 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j.mrc
    4515 
    4516 Opened 0057_6gsm_j.mrc as #2, grid size 136,104,80, pixel 1, shown at level
    4517 0.119, step 1, values float32 
    4518 
    4519 > fitmap #1 inMap #2
    4520 
    4521 Fit molecule 0057_6gsm_j.cif (#1) to map 0057_6gsm_j.mrc (#2) using 14398
    4522 atoms 
    4523 average map value = 0.06882, steps = 56 
    4524 shifted from previous position = 0.502 
    4525 rotated from previous position = 0.155 degrees 
    4526 atoms outside contour = 13409, contour level = 0.11916 
    4527  
    4528 Position of 0057_6gsm_j.cif (#1) relative to 0057_6gsm_j.mrc (#2) coordinates: 
    4529 Matrix rotation and translation 
    4530 0.99999853 0.00013427 0.00170961 -0.74251221 
    4531 -0.00013069 0.99999780 -0.00209394 0.48762654 
    4532 -0.00170989 0.00209372 0.99999635 -0.29123892 
    4533 Axis 0.77364167 0.63172986 -0.04894843 
    4534 Axis point 0.00000000 145.53493310 308.78942974 
    4535 Rotation angle (degrees) 0.15506880 
    4536 Shift along axis -0.25213445 
    4537  
    4538 
    4539 > save /scratch/cs-
    4540 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_j_fitted.cif #1
    4541 
    4542 > close #1
    4543 
    4544 > close #2
    4545 
    4546 > open 6gsm
    4547 
    4548 6gsm title: 
    4549 Structure of a partial yeast 48S preinitiation complex in open conformation.
    4550 [more info...] 
    4551  
    4552 Chain information for 6gsm #1 
    4553 --- 
    4554 Chain | Description | UniProt 
    4555 1 | Met-tRNAi | 
    4556 2 | 18S ribosomal RNA | 
    4557 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    4558 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    4559 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    4560 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    4561 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    4562 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    4563 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    4564 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    4565 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    4566 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    4567 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    4568 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    4569 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    4570 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    4571 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    4572 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    4573 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    4574 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    4575 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    4576 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    4577 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    4578 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    4579 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    4580 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    4581 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    4582 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    4583 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    4584 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    4585 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    4586 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    4587 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    4588 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    4589 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    4590 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    4591 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    4592 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    4593 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    4594 3-265 
    4595 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    4596 90-519 
    4597 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    4598 127-270 
    4599 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    4600 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4601 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    4602 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    4603 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    4604 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    4605 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    4606  
    4607 Non-standard residues in 6gsm #1 
    4608 --- 
    4609 7NO —
    4610 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    4611 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    4612 GCP — phosphomethylphosphonic acid guanylate ester 
    4613 MG — magnesium ion 
    4614 ZN — zinc ion 
    4615  
    4616 
    4617 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    4618 
    4619 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    4620 level 0.0673, step 2, values float32 
    4621 
    4622 > volume #2 region 211,155,169,314,226,240
    4623 
    4624 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    4625 
    4626 FYI: command is replacing existing command: "selectbox" 
    4627 executed select_box.py 
    4628 
    4629 > selectbox #1 inMap #2
    4630 
    4631 Selected 12721 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    4632 
    4633 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.cif
    4634 > #1 selectedOnly true
    4635 
    4636 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.mrc
    4637 > #2
    4638 
    4639 > close #1
    4640 
    4641 > close #2
    4642 
    4643 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.cif
    4644 
    4645 Summary of feedback from opening /scratch/cs-
    4646 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.cif 
    4647 --- 
    4648 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    4649 near line 43790 
    4650 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    4651 43791 
    4652 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    4653 43792 
    4654 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    4655 43793 
    4656 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    4657 43794 
    4658 100 messages similar to the above omitted 
    4659 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    4660 44043 
    4661 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    4662 44044 
    4663 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    4664 44045 
    4665 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    4666 44046 
    4667 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    4668 44047 
    4669 153 messages similar to the above omitted 
    4670 Atom O6 has no neighbors to form bonds with according to residue template for
    4671 1MG /1:9 
    4672 Atom OP2 has no neighbors to form bonds with according to residue template for
    4673 2MG /1:10 
    4674 Atom O3' has no neighbors to form bonds with according to residue template for
    4675 G /1:22 
    4676 Atom OP1 has no neighbors to form bonds with according to residue template for
    4677 G /2:10 
    4678 Atom OP2 has no neighbors to form bonds with according to residue template for
    4679 G /2:10 
    4680 Atom O2' has no neighbors to form bonds with according to residue template for
    4681 U /2:15 
    4682 Atom O2 has no neighbors to form bonds with according to residue template for
    4683 U /2:15 
    4684 Atom OP1 has no neighbors to form bonds with according to residue template for
    4685 C /2:571 
    4686 Atom OP2 has no neighbors to form bonds with according to residue template for
    4687 C /2:571 
    4688 Atom O2 has no neighbors to form bonds with according to residue template for
    4689 U /2:617 
    4690 Atom N6 has no neighbors to form bonds with according to residue template for
    4691 A /2:620 
    4692 Atom OP1 has no neighbors to form bonds with according to residue template for
    4693 A /2:621 
    4694 Atom OP2 has no neighbors to form bonds with according to residue template for
    4695 A /2:621 
    4696 Atom OP2 has no neighbors to form bonds with according to residue template for
    4697 G /2:623 
    4698 Atom N2 has no neighbors to form bonds with according to residue template for
    4699 G /2:623 
    4700 Atom OP2 has no neighbors to form bonds with according to residue template for
    4701 A /2:899 
    4702 Atom O4' has no neighbors to form bonds with according to residue template for
    4703 C /2:909 
    4704 Atom OP2 has no neighbors to form bonds with according to residue template for
    4705 U /2:910 
    4706 Atom N3 has no neighbors to form bonds with according to residue template for
    4707 A /2:939 
    4708 Atom O3' has no neighbors to form bonds with according to residue template for
    4709 G /2:1108 
    4710 Atom O2' has no neighbors to form bonds with according to residue template for
    4711 C /2:1133 
    4712 Atom O2 has no neighbors to form bonds with according to residue template for
    4713 C /2:1133 
    4714 Atom C8 has no neighbors to form bonds with according to residue template for
    4715 G /2:1140 
    4716 Atom OP1 has no neighbors to form bonds with according to residue template for
    4717 A /2:1141 
    4718 Atom OP2 has no neighbors to form bonds with according to residue template for
    4719 A /2:1141 
    4720 Atom OP2 has no neighbors to form bonds with according to residue template for
    4721 C /2:1176 
    4722 Atom C5' has no neighbors to form bonds with according to residue template for
    4723 A /2:1188 
    4724 Atom O3' has no neighbors to form bonds with according to residue template for
    4725 C /2:1454 
    4726 Atom O2' has no neighbors to form bonds with according to residue template for
    4727 C /2:1454 
    4728 Atom OP2 has no neighbors to form bonds with according to residue template for
    4729 G /2:1456 
    4730 Atom OP2 has no neighbors to form bonds with according to residue template for
    4731 C /2:1463 
    4732 Atom N4 has no neighbors to form bonds with according to residue template for
    4733 C /2:1463 
    4734 Atom O3' has no neighbors to form bonds with according to residue template for
    4735 C /2:1617 
    4736 Atom O2' has no neighbors to form bonds with according to residue template for
    4737 C /2:1617 
    4738 Atom O3' has no neighbors to form bonds with according to residue template for
    4739 U /2:1619 
    4740 Atom OP1 has no neighbors to form bonds with according to residue template for
    4741 C /2:1632 
    4742 Atom O5' has no neighbors to form bonds with according to residue template for
    4743 A /2:1744 
    4744 Atom O4' has no neighbors to form bonds with according to residue template for
    4745 U /2:1793 
    4746 Atom N has no neighbors to form bonds with according to residue template for
    4747 ARG /B:8 
    4748 Atom O has no neighbors to form bonds with according to residue template for
    4749 ARG /B:8 
    4750 Atom CG1 has no neighbors to form bonds with according to residue template for
    4751 VAL /F:222 
    4752 Atom O has no neighbors to form bonds with according to residue template for
    4753 ARG /O:90 
    4754 Atom NH1 has no neighbors to form bonds with according to residue template for
    4755 ARG /O:103 
    4756 Atom NH2 has no neighbors to form bonds with according to residue template for
    4757 ARG /O:103 
    4758 Atom N has no neighbors to form bonds with according to residue template for
    4759 THR /S:140 
    4760 Atom CG2 has no neighbors to form bonds with according to residue template for
    4761 THR /S:140 
    4762 Atom O has no neighbors to form bonds with according to residue template for
    4763 CYS /X:71 
    4764 Atom N has no neighbors to form bonds with according to residue template for
    4765 VAL /X:120 
    4766 Atom CG2 has no neighbors to form bonds with according to residue template for
    4767 VAL /X:120 
    4768 Atom O has no neighbors to form bonds with according to residue template for
    4769 ASN /a:8 
    4770 Atom N has no neighbors to form bonds with according to residue template for
    4771 VAL /a:18 
    4772 Atom O has no neighbors to form bonds with according to residue template for
    4773 VAL /a:18 
    4774 Atom CG1 has no neighbors to form bonds with according to residue template for
    4775 VAL /a:21 
    4776 Atom O has no neighbors to form bonds with according to residue template for
    4777 LEU /a:71 
    4778 Atom CD1 has no neighbors to form bonds with according to residue template for
    4779 LEU /a:71 
    4780 Atom N has no neighbors to form bonds with according to residue template for
    4781 ILE /a:83 
    4782 Atom N has no neighbors to form bonds with according to residue template for
    4783 ARG /h:21 
    4784 Atom NH1 has no neighbors to form bonds with according to residue template for
    4785 ARG /h:21 
    4786 Atom CG has no neighbors to form bonds with according to residue template for
    4787 ARG /i:24 
    4788 Atom O has no neighbors to form bonds with according to residue template for
    4789 GLU /i:34 
    4790 Atom N has no neighbors to form bonds with according to residue template for
    4791 ASP /i:53 
    4792 Atom C has no neighbors to form bonds with according to residue template for
    4793 ASP /i:53 
    4794 Atom N has no neighbors to form bonds with according to residue template for
    4795 ASP /i:83 
    4796 Atom C has no neighbors to form bonds with according to residue template for
    4797 ASP /i:83 
    4798 Atom N has no neighbors to form bonds with according to residue template for
    4799 ARG /i:101 
    4800 Atom CD1 has no neighbors to form bonds with according to residue template for
    4801 LEU /i:109 
    4802 Atom CD2 has no neighbors to form bonds with according to residue template for
    4803 LEU /i:109 
    4804 Atom CG2 has no neighbors to form bonds with according to residue template for
    4805 ILE /j:19 
    4806 Atom CD1 has no neighbors to form bonds with according to residue template for
    4807 ILE /j:19 
    4808 Atom CG2 has no neighbors to form bonds with according to residue template for
    4809 ILE /j:46 
    4810 Atom OE1 has no neighbors to form bonds with according to residue template for
    4811 GLN /j:60 
    4812 Atom N has no neighbors to form bonds with according to residue template for
    4813 ARG /j:75 
    4814 Atom N has no neighbors to form bonds with according to residue template for
    4815 GLY /k:277 
    4816 Atom O has no neighbors to form bonds with according to residue template for
    4817 GLY /k:277 
    4818 Atom O has no neighbors to form bonds with according to residue template for
    4819 ILE /k:291 
    4820 Atom O has no neighbors to form bonds with according to residue template for
    4821 ASN /k:295 
    4822 Atom N has no neighbors to form bonds with according to residue template for
    4823 LYS /k:300 
    4824 Atom N has no neighbors to form bonds with according to residue template for
    4825 ILE /k:495 
    4826 Atom CD1 has no neighbors to form bonds with according to residue template for
    4827 TYR /p:248 
    4828 Atom OG has no neighbors to form bonds with according to residue template for
    4829 SER /p:275 
    4830 Atom CD2 has no neighbors to form bonds with according to residue template for
    4831 LEU /p:284 
    4832 Atom CD1 has no neighbors to form bonds with according to residue template for
    4833 TRP /p:336 
    4834 Atom N has no neighbors to form bonds with according to residue template for
    4835 ASP /p:360 
    4836 Atom O has no neighbors to form bonds with according to residue template for
    4837 ASP /p:360 
    4838 Atom N has no neighbors to form bonds with according to residue template for
    4839 ALA /p:370 
    4840 Atom O has no neighbors to form bonds with according to residue template for
    4841 ALA /p:370 
    4842 Atom N has no neighbors to form bonds with according to residue template for
    4843 VAL /q:112 
    4844  
    4845 Chain information for 0057_6gsm_m.cif #1 
    4846 --- 
    4847 Chain | Description 
    4848 1 | Met-tRNAi 
    4849 2 | 18S ribosomal RNA 
    4850 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    4851 B | 40S ribosomal protein S1 
    4852 F | KLLA0D10659p 
    4853 O | 40S ribosomal protein S14 
    4854 P | KLLA0F07843p 
    4855 Q | 40S ribosomal protein S16 
    4856 S | KLLA0B01562p 
    4857 X | KLLA0B11231p 
    4858 a | 40S ribosomal protein S26 
    4859 c | 40S ribosomal protein S28 
    4860 e | 40S ribosomal protein S30 
    4861 h | 60S ribosomal protein L41-A 
    4862 i | Eukaryotic translation initiation factor 1A 
    4863 j | Eukaryotic translation initiation factor 2 subunit alpha 
    4864 k | Eukaryotic translation initiation factor 2 subunit gamma 
    4865 l | Eukaryotic translation initiation factor 2 subunit beta 
    4866 m | Eukaryotic translation initiation factor eIF-1 
    4867 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4868 translation initiation factor 3 subunit A,eIF3a 
    4869 p | Eukaryotic translation initiation factor 3 subunit B 
    4870 q | Eukaryotic translation initiation factor 3 subunit C 
    4871  
    4872 
    4873 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m.mrc
    4874 
    4875 Opened 0057_6gsm_m.mrc as #2, grid size 104,72,72, pixel 1, shown at level
    4876 0.134, step 1, values float32 
    4877 
    4878 > fitmap #1 inMap #2
    4879 
    4880 Fit molecule 0057_6gsm_m.cif (#1) to map 0057_6gsm_m.mrc (#2) using 12721
    4881 atoms 
    4882 average map value = 0.0659, steps = 112 
    4883 shifted from previous position = 0.523 
    4884 rotated from previous position = 0.124 degrees 
    4885 atoms outside contour = 12229, contour level = 0.13429 
    4886  
    4887 Position of 0057_6gsm_m.cif (#1) relative to 0057_6gsm_m.mrc (#2) coordinates: 
    4888 Matrix rotation and translation 
    4889 0.99999779 0.00130994 0.00164375 -1.03339978 
    4890 -0.00130910 0.99999901 -0.00050917 0.23869542 
    4891 -0.00164441 0.00050701 0.99999852 0.15046608 
    4892 Axis 0.23496469 0.76030197 -0.60558444 
    4893 Axis point 34.81184266 0.00000000 606.93991431 
    4894 Rotation angle (degrees) 0.12389672 
    4895 Shift along axis -0.15245178 
    4896  
    4897 
    4898 > save /scratch/cs-
    4899 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_m_fitted.cif #1
    4900 
    4901 > close #1
    4902 
    4903 > close #2
    4904 
    4905 > open 6gsm
    4906 
    4907 6gsm title: 
    4908 Structure of a partial yeast 48S preinitiation complex in open conformation.
    4909 [more info...] 
    4910  
    4911 Chain information for 6gsm #1 
    4912 --- 
    4913 Chain | Description | UniProt 
    4914 1 | Met-tRNAi | 
    4915 2 | 18S ribosomal RNA | 
    4916 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    4917 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    4918 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    4919 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    4920 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    4921 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    4922 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    4923 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    4924 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    4925 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    4926 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    4927 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    4928 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    4929 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    4930 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    4931 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    4932 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    4933 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    4934 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    4935 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    4936 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    4937 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    4938 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    4939 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    4940 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    4941 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    4942 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    4943 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    4944 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    4945 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    4946 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    4947 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    4948 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    4949 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    4950 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    4951 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    4952 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    4953 3-265 
    4954 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    4955 90-519 
    4956 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    4957 127-270 
    4958 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    4959 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4960 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    4961 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    4962 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    4963 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    4964 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    4965  
    4966 Non-standard residues in 6gsm #1 
    4967 --- 
    4968 7NO —
    4969 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    4970 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    4971 GCP — phosphomethylphosphonic acid guanylate ester 
    4972 MG — magnesium ion 
    4973 ZN — zinc ion 
    4974  
    4975 
    4976 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    4977 
    4978 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    4979 level 0.0673, step 2, values float32 
    4980 
    4981 > volume #2 region 144,82,144,231,169,223
    4982 
    4983 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    4984 
    4985 FYI: command is replacing existing command: "selectbox" 
    4986 executed select_box.py 
    4987 
    4988 > selectbox #1 inMap #2
    4989 
    4990 Selected 13497 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    4991 
    4992 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.cif
    4993 > #1 selectedOnly true
    4994 
    4995 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.mrc
    4996 > #2
    4997 
    4998 > close #1
    4999 
    5000 > close #2
    5001 
    5002 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.cif
    5003 
    5004 Summary of feedback from opening /scratch/cs-
    5005 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.cif 
    5006 --- 
    5007 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    5008 near line 44599 
    5009 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    5010 44600 
    5011 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    5012 44601 
    5013 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    5014 44602 
    5015 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    5016 44603 
    5017 174 messages similar to the above omitted 
    5018 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    5019 44852 
    5020 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    5021 44853 
    5022 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    5023 44854 
    5024 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    5025 44855 
    5026 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    5027 44856 
    5028 183 messages similar to the above omitted 
    5029 Atom O4' has no neighbors to form bonds with according to residue template for
    5030 G /1:43 
    5031 Atom O3' has no neighbors to form bonds with according to residue template for
    5032 C /2:1158 
    5033 Atom O2' has no neighbors to form bonds with according to residue template for
    5034 C /2:1158 
    5035 Atom OP2 has no neighbors to form bonds with according to residue template for
    5036 A /2:1159 
    5037 Atom O6 has no neighbors to form bonds with according to residue template for
    5038 G /2:1197 
    5039 Atom OP1 has no neighbors to form bonds with according to residue template for
    5040 U /2:1448 
    5041 Atom O2 has no neighbors to form bonds with according to residue template for
    5042 C /2:1617 
    5043 Atom N3 has no neighbors to form bonds with according to residue template for
    5044 C /2:1617 
    5045 Atom CG1 has no neighbors to form bonds with according to residue template for
    5046 VAL /D:41 
    5047 Atom CG2 has no neighbors to form bonds with according to residue template for
    5048 VAL /D:41 
    5049 Atom CD1 has no neighbors to form bonds with according to residue template for
    5050 ILE /F:42 
    5051 Atom CG2 has no neighbors to form bonds with according to residue template for
    5052 ILE /F:64 
    5053 Atom C has no neighbors to form bonds with according to residue template for
    5054 VAL /F:134 
    5055 Atom CB has no neighbors to form bonds with according to residue template for
    5056 ALA /F:138 
    5057 Atom O has no neighbors to form bonds with according to residue template for
    5058 SER /F:142 
    5059 Atom N has no neighbors to form bonds with according to residue template for
    5060 ARG /F:159 
    5061 Atom CG1 has no neighbors to form bonds with according to residue template for
    5062 VAL /F:222 
    5063 Atom CG2 has no neighbors to form bonds with according to residue template for
    5064 VAL /F:222 
    5065 Atom C has no neighbors to form bonds with according to residue template for
    5066 ASN /K:28 
    5067 Atom CB has no neighbors to form bonds with according to residue template for
    5068 ASN /K:28 
    5069 Atom OE1 has no neighbors to form bonds with according to residue template for
    5070 GLU /P:23 
    5071 Atom OE2 has no neighbors to form bonds with according to residue template for
    5072 GLU /P:23 
    5073 Atom O has no neighbors to form bonds with according to residue template for
    5074 GLY /P:48 
    5075 Atom O has no neighbors to form bonds with according to residue template for
    5076 ILE /P:85 
    5077 Atom O has no neighbors to form bonds with according to residue template for
    5078 VAL /P:94 
    5079 Atom CG2 has no neighbors to form bonds with according to residue template for
    5080 VAL /P:94 
    5081 Atom N has no neighbors to form bonds with according to residue template for
    5082 ARG /P:127 
    5083 Atom O has no neighbors to form bonds with according to residue template for
    5084 ARG /P:127 
    5085 Atom N has no neighbors to form bonds with according to residue template for
    5086 TRP /S:129 
    5087 Atom C has no neighbors to form bonds with according to residue template for
    5088 TRP /S:129 
    5089 Atom CB has no neighbors to form bonds with according to residue template for
    5090 TRP /S:129 
    5091 Atom CD1 has no neighbors to form bonds with according to residue template for
    5092 TRP /S:129 
    5093 Atom N has no neighbors to form bonds with according to residue template for
    5094 GLU /U:46 
    5095 Atom CD1 has no neighbors to form bonds with according to residue template for
    5096 ILE /U:99 
    5097 Atom CG2 has no neighbors to form bonds with according to residue template for
    5098 VAL /c:25 
    5099 Atom C has no neighbors to form bonds with according to residue template for
    5100 LYS /c:45 
    5101 Atom O has no neighbors to form bonds with according to residue template for
    5102 TYR /d:8 
    5103 Atom OH has no neighbors to form bonds with according to residue template for
    5104 TYR /d:8 
    5105 Atom O has no neighbors to form bonds with according to residue template for
    5106 ILE /d:38 
    5107 Atom CG1 has no neighbors to form bonds with according to residue template for
    5108 VAL /g:35 
    5109 Atom N has no neighbors to form bonds with according to residue template for
    5110 VAL /g:72 
    5111 Atom CD2 has no neighbors to form bonds with according to residue template for
    5112 LEU /g:112 
    5113 Atom N has no neighbors to form bonds with according to residue template for
    5114 ALA /g:249 
    5115 Atom CB has no neighbors to form bonds with according to residue template for
    5116 ALA /g:249 
    5117 Atom N has no neighbors to form bonds with according to residue template for
    5118 ARG /j:54 
    5119 Atom NZ has no neighbors to form bonds with according to residue template for
    5120 LYS /j:87 
    5121  
    5122 Chain information for 0057_6gsm_T.cif #1 
    5123 --- 
    5124 Chain | Description 
    5125 1 | Met-tRNAi 
    5126 2 | 18S ribosomal RNA 
    5127 D | KLLA0D08305p 
    5128 F | KLLA0D10659p 
    5129 K | KLLA0B08173p 
    5130 P | KLLA0F07843p 
    5131 Q | 40S ribosomal protein S16 
    5132 R | KLLA0B01474p 
    5133 S | KLLA0B01562p 
    5134 T | KLLA0A07194p 
    5135 U | KLLA0F25542p 
    5136 Z | KLLA0B06182p 
    5137 c | 40S ribosomal protein S28 
    5138 d | 40S ribosomal protein S29 
    5139 g | KLLA0E12277p 
    5140 j | Eukaryotic translation initiation factor 2 subunit alpha 
    5141  
    5142 
    5143 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T.mrc
    5144 
    5145 Opened 0057_6gsm_T.mrc as #2, grid size 88,88,80, pixel 1, shown at level
    5146 0.133, step 1, values float32 
    5147 
    5148 > fitmap #1 inMap #2
    5149 
    5150 Fit molecule 0057_6gsm_T.cif (#1) to map 0057_6gsm_T.mrc (#2) using 13497
    5151 atoms 
    5152 average map value = 0.07745, steps = 60 
    5153 shifted from previous position = 0.338 
    5154 rotated from previous position = 0.083 degrees 
    5155 atoms outside contour = 12958, contour level = 0.13258 
    5156  
    5157 Position of 0057_6gsm_T.cif (#1) relative to 0057_6gsm_T.mrc (#2) coordinates: 
    5158 Matrix rotation and translation 
    5159 0.99999979 -0.00028336 0.00058636 -0.30702594 
    5160 0.00028412 0.99999912 -0.00129319 0.23254354 
    5161 -0.00058599 0.00129335 0.99999899 -0.30519742 
    5162 Axis 0.89315267 0.40482004 0.19595673 
    5163 Axis point -0.00000000 199.82647397 254.78106719 
    5164 Rotation angle (degrees) 0.08296346 
    5165 Shift along axis -0.23988825 
    5166  
    5167 
    5168 > save /scratch/cs-
    5169 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_T_fitted.cif #1
    5170 
    5171 > close #1
    5172 
    5173 > close #2
    5174 
    5175 > open 6gsm
    5176 
    5177 6gsm title: 
    5178 Structure of a partial yeast 48S preinitiation complex in open conformation.
    5179 [more info...] 
    5180  
    5181 Chain information for 6gsm #1 
    5182 --- 
    5183 Chain | Description | UniProt 
    5184 1 | Met-tRNAi | 
    5185 2 | 18S ribosomal RNA | 
    5186 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    5187 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    5188 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    5189 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    5190 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    5191 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    5192 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    5193 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    5194 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    5195 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    5196 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    5197 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    5198 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    5199 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    5200 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    5201 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    5202 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    5203 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    5204 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    5205 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    5206 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    5207 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    5208 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    5209 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    5210 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    5211 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    5212 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    5213 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    5214 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    5215 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    5216 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    5217 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    5218 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    5219 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    5220 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    5221 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    5222 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    5223 3-265 
    5224 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    5225 90-519 
    5226 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    5227 127-270 
    5228 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    5229 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    5230 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    5231 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    5232 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    5233 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    5234 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    5235  
    5236 Non-standard residues in 6gsm #1 
    5237 --- 
    5238 7NO —
    5239 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    5240 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    5241 GCP — phosphomethylphosphonic acid guanylate ester 
    5242 MG — magnesium ion 
    5243 ZN — zinc ion 
    5244  
    5245 
    5246 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    5247 
    5248 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    5249 level 0.0673, step 2, values float32 
    5250 
    5251 > volume #2 region 169,249,127,296,328,198
    5252 
    5253 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    5254 
    5255 FYI: command is replacing existing command: "selectbox" 
    5256 executed select_box.py 
    5257 
    5258 > selectbox #1 inMap #2
    5259 
    5260 Selected 12319 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    5261 
    5262 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.cif
    5263 > #1 selectedOnly true
    5264 
    5265 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.mrc
    5266 > #2
    5267 
    5268 > close #1
    5269 
    5270 > close #2
    5271 
    5272 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.cif
    5273 
    5274 Summary of feedback from opening /scratch/cs-
    5275 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.cif 
    5276 --- 
    5277 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    5278 near line 43436 
    5279 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    5280 43437 
    5281 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    5282 43438 
    5283 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    5284 43439 
    5285 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    5286 43440 
    5287 161 messages similar to the above omitted 
    5288 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    5289 43689 
    5290 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    5291 43690 
    5292 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    5293 43691 
    5294 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    5295 43692 
    5296 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    5297 43693 
    5298 187 messages similar to the above omitted 
    5299 Atom N2 has no neighbors to form bonds with according to residue template for
    5300 G /2:23 
    5301 Atom C8 has no neighbors to form bonds with according to residue template for
    5302 A /2:28 
    5303 Atom O4 has no neighbors to form bonds with according to residue template for
    5304 U /2:29 
    5305 Atom O3' has no neighbors to form bonds with according to residue template for
    5306 U /2:77 
    5307 Atom O2' has no neighbors to form bonds with according to residue template for
    5308 U /2:173 
    5309 Atom OP2 has no neighbors to form bonds with according to residue template for
    5310 U /2:271 
    5311 Atom N7 has no neighbors to form bonds with according to residue template for
    5312 G /2:290 
    5313 Atom O6 has no neighbors to form bonds with according to residue template for
    5314 G /2:290 
    5315 Atom C4' has no neighbors to form bonds with according to residue template for
    5316 C /2:297 
    5317 Atom O2' has no neighbors to form bonds with according to residue template for
    5318 C /2:297 
    5319 Atom O3' has no neighbors to form bonds with according to residue template for
    5320 A /2:359 
    5321 Atom OP2 has no neighbors to form bonds with according to residue template for
    5322 G /2:389 
    5323 Atom N4 has no neighbors to form bonds with according to residue template for
    5324 C /2:392 
    5325 Atom N3 has no neighbors to form bonds with according to residue template for
    5326 G /2:395 
    5327 Atom OP1 has no neighbors to form bonds with according to residue template for
    5328 A /2:396 
    5329 Atom O2' has no neighbors to form bonds with according to residue template for
    5330 A /2:398 
    5331 Atom O3' has no neighbors to form bonds with according to residue template for
    5332 G /2:508 
    5333 Atom OP1 has no neighbors to form bonds with according to residue template for
    5334 C /2:542 
    5335 Atom C5' has no neighbors to form bonds with according to residue template for
    5336 U /2:592 
    5337 Atom N6 has no neighbors to form bonds with according to residue template for
    5338 A /2:593 
    5339 Atom O2' has no neighbors to form bonds with according to residue template for
    5340 U /2:1659 
    5341 Atom N4 has no neighbors to form bonds with according to residue template for
    5342 C /2:1684 
    5343 Atom C8 has no neighbors to form bonds with according to residue template for
    5344 G /2:1711 
    5345 Atom N3 has no neighbors to form bonds with according to residue template for
    5346 A /2:1720 
    5347 Atom N has no neighbors to form bonds with according to residue template for
    5348 GLN /C:155 
    5349 Atom O has no neighbors to form bonds with according to residue template for
    5350 GLN /C:155 
    5351 Atom CB has no neighbors to form bonds with according to residue template for
    5352 PRO /C:178 
    5353 Atom O has no neighbors to form bonds with according to residue template for
    5354 ALA /E:2 
    5355 Atom CB has no neighbors to form bonds with according to residue template for
    5356 ALA /E:2 
    5357 Atom N has no neighbors to form bonds with according to residue template for
    5358 TYR /E:121 
    5359 Atom O has no neighbors to form bonds with according to residue template for
    5360 TYR /E:121 
    5361 Atom N has no neighbors to form bonds with according to residue template for
    5362 PHE /G:145 
    5363 Atom CG1 has no neighbors to form bonds with according to residue template for
    5364 VAL /G:153 
    5365 Atom CG2 has no neighbors to form bonds with according to residue template for
    5366 VAL /G:153 
    5367 Atom NH1 has no neighbors to form bonds with according to residue template for
    5368 ARG /G:159 
    5369 Atom O has no neighbors to form bonds with according to residue template for
    5370 GLU /J:183 
    5371 Atom O has no neighbors to form bonds with according to residue template for
    5372 ARG /p:663 
    5373 Atom N has no neighbors to form bonds with according to residue template for
    5374 ALA /p:692 
    5375 Atom CB has no neighbors to form bonds with according to residue template for
    5376 ALA /p:692 
    5377  
    5378 Chain information for 0057_6gsm_Y.cif #1 
    5379 --- 
    5380 Chain | Description 
    5381 2 | 18S ribosomal RNA 
    5382 C | KLLA0F09812p 
    5383 E | 40S ribosomal protein S4 
    5384 G | 40S ribosomal protein S6 
    5385 J | KLLA0E23673p 
    5386 Y | 40S ribosomal protein S24 
    5387 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    5388 translation initiation factor 3 subunit A,eIF3a 
    5389 p | Eukaryotic translation initiation factor 3 subunit B 
    5390  
    5391 
    5392 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y.mrc
    5393 
    5394 Opened 0057_6gsm_Y.mrc as #2, grid size 128,80,72, pixel 1, shown at level
    5395 0.142, step 1, values float32 
    5396 
    5397 > fitmap #1 inMap #2
    5398 
    5399 Fit molecule 0057_6gsm_Y.cif (#1) to map 0057_6gsm_Y.mrc (#2) using 12319
    5400 atoms 
    5401 average map value = 0.08353, steps = 48 
    5402 shifted from previous position = 0.466 
    5403 rotated from previous position = 0.137 degrees 
    5404 atoms outside contour = 11679, contour level = 0.14216 
    5405  
    5406 Position of 0057_6gsm_Y.cif (#1) relative to 0057_6gsm_Y.mrc (#2) coordinates: 
    5407 Matrix rotation and translation 
    5408 0.99999809 -0.00071326 -0.00182141 0.23329565 
    5409 0.00071574 0.99999882 0.00136215 -0.76507248 
    5410 0.00182043 -0.00136345 0.99999741 0.02693523 
    5411 Axis -0.57164385 -0.76380649 0.29970477 
    5412 Axis point 61.17022831 0.00000000 272.10136371 
    5413 Rotation angle (degrees) 0.13659378 
    5414 Shift along axis 0.45907793 
    5415  
    5416 
    5417 > save /scratch/cs-
    5418 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Y_fitted.cif #1
    5419 
    5420 > close #1
    5421 
    5422 > close #2
    5423 
    5424 > open 6gsm
    5425 
    5426 6gsm title: 
    5427 Structure of a partial yeast 48S preinitiation complex in open conformation.
    5428 [more info...] 
    5429  
    5430 Chain information for 6gsm #1 
    5431 --- 
    5432 Chain | Description | UniProt 
    5433 1 | Met-tRNAi | 
    5434 2 | 18S ribosomal RNA | 
    5435 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    5436 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    5437 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    5438 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    5439 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    5440 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    5441 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    5442 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    5443 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    5444 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    5445 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    5446 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    5447 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    5448 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    5449 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    5450 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    5451 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    5452 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    5453 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    5454 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    5455 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    5456 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    5457 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    5458 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    5459 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    5460 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    5461 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    5462 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    5463 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    5464 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    5465 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    5466 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    5467 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    5468 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    5469 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    5470 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    5471 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    5472 3-265 
    5473 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    5474 90-519 
    5475 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    5476 127-270 
    5477 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    5478 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    5479 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    5480 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    5481 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    5482 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    5483 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    5484  
    5485 Non-standard residues in 6gsm #1 
    5486 --- 
    5487 7NO —
    5488 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    5489 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    5490 GCP — phosphomethylphosphonic acid guanylate ester 
    5491 MG — magnesium ion 
    5492 ZN — zinc ion 
    5493  
    5494 
    5495 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    5496 
    5497 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    5498 level 0.0673, step 2, values float32 
    5499 
    5500 > volume #2 region 144,95,177,239,198,256
    5501 
    5502 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    5503 
    5504 FYI: command is replacing existing command: "selectbox" 
    5505 executed select_box.py 
    5506 
    5507 > selectbox #1 inMap #2
    5508 
    5509 Selected 16573 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    5510 
    5511 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.cif
    5512 > #1 selectedOnly true
    5513 
    5514 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.mrc
    5515 > #2
    5516 
    5517 > close #1
    5518 
    5519 > close #2
    5520 
    5521 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.cif
    5522 
    5523 Summary of feedback from opening /scratch/cs-
    5524 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.cif 
    5525 --- 
    5526 warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
    5527 near line 47739 
    5528 Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
    5529 47740 
    5530 Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
    5531 47741 
    5532 Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
    5533 47742 
    5534 Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
    5535 47743 
    5536 112 messages similar to the above omitted 
    5537 Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
    5538 line 47997 
    5539 Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
    5540 line 47998 
    5541 Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
    5542 line 47999 
    5543 Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
    5544 line 48000 
    5545 Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
    5546 line 48001 
    5547 139 messages similar to the above omitted 
    5548 Atom OP1 has no neighbors to form bonds with according to residue template for
    5549 G /1:22 
    5550 Atom OP2 has no neighbors to form bonds with according to residue template for
    5551 G /1:22 
    5552 Atom C5' has no neighbors to form bonds with according to residue template for
    5553 G /1:22 
    5554 Atom O3' has no neighbors to form bonds with according to residue template for
    5555 G /1:22 
    5556 Atom O3' has no neighbors to form bonds with according to residue template for
    5557 C /1:23 
    5558 Atom O3' has no neighbors to form bonds with according to residue template for
    5559 G /1:24 
    5560 Atom O4 has no neighbors to form bonds with according to residue template for
    5561 U /1:45 
    5562 Atom C5 has no neighbors to form bonds with according to residue template for
    5563 U /1:45 
    5564 Atom C8 has no neighbors to form bonds with according to residue template for
    5565 A /2:899 
    5566 Atom O2' has no neighbors to form bonds with according to residue template for
    5567 A /2:987 
    5568 Atom N3 has no neighbors to form bonds with according to residue template for
    5569 A /2:987 
    5570 Atom O2 has no neighbors to form bonds with according to residue template for
    5571 C /2:999 
    5572 Atom OP1 has no neighbors to form bonds with according to residue template for
    5573 G /2:1145 
    5574 Atom O2' has no neighbors to form bonds with according to residue template for
    5575 G /2:1145 
    5576 Atom OP2 has no neighbors to form bonds with according to residue template for
    5577 C /2:1273 
    5578 Atom OP2 has no neighbors to form bonds with according to residue template for
    5579 C /2:1278 
    5580 Atom OP2 has no neighbors to form bonds with according to residue template for
    5581 A /2:1347 
    5582 Atom O4' has no neighbors to form bonds with according to residue template for
    5583 C /2:1354 
    5584 Atom OP2 has no neighbors to form bonds with according to residue template for
    5585 U /2:1355 
    5586 Atom C2' has no neighbors to form bonds with according to residue template for
    5587 A /2:1371 
    5588 Atom C6 has no neighbors to form bonds with according to residue template for
    5589 U /2:1520 
    5590 Atom O3' has no neighbors to form bonds with according to residue template for
    5591 A /2:1598 
    5592 Atom O2' has no neighbors to form bonds with according to residue template for
    5593 A /2:1598 
    5594 Atom OP1 has no neighbors to form bonds with according to residue template for
    5595 U /2:1783 
    5596 Atom C5' has no neighbors to form bonds with according to residue template for
    5597 U /2:1783 
    5598 Atom OP2 has no neighbors to form bonds with according to residue template for
    5599 U /2:1796 
    5600 Atom N has no neighbors to form bonds with according to residue template for
    5601 TYR /A:81 
    5602 Atom CB has no neighbors to form bonds with according to residue template for
    5603 GLN /A:83 
    5604 Atom N has no neighbors to form bonds with according to residue template for
    5605 VAL /B:3 
    5606 Atom OG1 has no neighbors to form bonds with according to residue template for
    5607 THR /B:107 
    5608 Atom NZ has no neighbors to form bonds with according to residue template for
    5609 LYS /B:116 
    5610 Atom CG1 has no neighbors to form bonds with according to residue template for
    5611 VAL /D:126 
    5612 Atom CG2 has no neighbors to form bonds with according to residue template for
    5613 VAL /D:126 
    5614 Atom N has no neighbors to form bonds with according to residue template for
    5615 ILE /D:138 
    5616 Atom N has no neighbors to form bonds with according to residue template for
    5617 MET /D:150 
    5618 Atom N has no neighbors to form bonds with according to residue template for
    5619 ASP /D:154 
    5620 Atom CG1 has no neighbors to form bonds with according to residue template for
    5621 VAL /D:186 
    5622 Atom N has no neighbors to form bonds with according to residue template for
    5623 GLU /D:214 
    5624 Atom N has no neighbors to form bonds with according to residue template for
    5625 LYS /O:72 
    5626 Atom OD1 has no neighbors to form bonds with according to residue template for
    5627 ASP /O:124 
    5628 Atom N has no neighbors to form bonds with according to residue template for
    5629 LEU /S:18 
    5630 Atom O has no neighbors to form bonds with according to residue template for
    5631 LEU /S:18 
    5632 Atom O has no neighbors to form bonds with according to residue template for
    5633 LYS /T:38 
    5634 Atom CG has no neighbors to form bonds with according to residue template for
    5635 LYS /T:38 
    5636 Atom N has no neighbors to form bonds with according to residue template for
    5637 ASN /U:36 
    5638 Atom OD1 has no neighbors to form bonds with according to residue template for
    5639 ASN /U:36 
    5640 Atom ND2 has no neighbors to form bonds with according to residue template for
    5641 ASN /U:36 
    5642 Atom N has no neighbors to form bonds with according to residue template for
    5643 LYS /U:61 
    5644 Atom OG1 has no neighbors to form bonds with according to residue template for
    5645 THR /U:67 
    5646 Atom N has no neighbors to form bonds with according to residue template for
    5647 SER /a:57 
    5648 Atom OG has no neighbors to form bonds with according to residue template for
    5649 SER /a:57 
    5650 Atom N has no neighbors to form bonds with according to residue template for
    5651 SER /a:88 
    5652 Atom CB has no neighbors to form bonds with according to residue template for
    5653 SER /a:88 
    5654 Atom OD1 has no neighbors to form bonds with according to residue template for
    5655 ASN /d:48 
    5656 Atom ND2 has no neighbors to form bonds with according to residue template for
    5657 ASN /d:48 
    5658 Atom CG1 has no neighbors to form bonds with according to residue template for
    5659 VAL /g:35 
    5660 Atom CD2 has no neighbors to form bonds with according to residue template for
    5661 LEU /g:48 
    5662 Atom N has no neighbors to form bonds with according to residue template for
    5663 VAL /g:72 
    5664 Atom N has no neighbors to form bonds with according to residue template for
    5665 ALA /g:249 
    5666 Atom CB has no neighbors to form bonds with according to residue template for
    5667 ALA /g:249 
    5668 Atom N has no neighbors to form bonds with according to residue template for
    5669 LYS /g:268 
    5670 Atom N has no neighbors to form bonds with according to residue template for
    5671 LEU /g:299 
    5672 Atom CD2 has no neighbors to form bonds with according to residue template for
    5673 LEU /g:299 
    5674 Atom CB has no neighbors to form bonds with according to residue template for
    5675 TYR /j:9 
    5676 Atom OG has no neighbors to form bonds with according to residue template for
    5677 SER /j:91 
    5678 Atom N has no neighbors to form bonds with according to residue template for
    5679 LEU /j:123 
    5680 Atom C has no neighbors to form bonds with according to residue template for
    5681 LEU /j:123 
    5682 Atom NE1 has no neighbors to form bonds with according to residue template for
    5683 TRP /j:132 
    5684 Atom O has no neighbors to form bonds with according to residue template for
    5685 ILE /l:173 
    5686 Atom NH1 has no neighbors to form bonds with according to residue template for
    5687 ARG /m:36 
    5688  
    5689 Chain information for 0057_6gsm_F.cif #1 
    5690 --- 
    5691 Chain | Description 
    5692 1 | Met-tRNAi 
    5693 2 | 18S ribosomal RNA 
    5694 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    5695 A | 40S ribosomal protein S0 
    5696 B | 40S ribosomal protein S1 
    5697 C | KLLA0F09812p 
    5698 D | KLLA0D08305p 
    5699 F | KLLA0D10659p 
    5700 O | 40S ribosomal protein S14 
    5701 Q | 40S ribosomal protein S16 
    5702 R | KLLA0B01474p 
    5703 S | KLLA0B01562p 
    5704 T | KLLA0A07194p 
    5705 U | KLLA0F25542p 
    5706 Z | KLLA0B06182p 
    5707 a | 40S ribosomal protein S26 
    5708 c | 40S ribosomal protein S28 
    5709 d | 40S ribosomal protein S29 
    5710 g | KLLA0E12277p 
    5711 i | Eukaryotic translation initiation factor 1A 
    5712 j | Eukaryotic translation initiation factor 2 subunit alpha 
    5713 l | Eukaryotic translation initiation factor 2 subunit beta 
    5714 m | Eukaryotic translation initiation factor eIF-1 
    5715  
    5716 
    5717 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F.mrc
    5718 
    5719 Opened 0057_6gsm_F.mrc as #2, grid size 96,104,80, pixel 1, shown at level
    5720 0.132, step 1, values float32 
    5721 
    5722 > fitmap #1 inMap #2
    5723 
    5724 Fit molecule 0057_6gsm_F.cif (#1) to map 0057_6gsm_F.mrc (#2) using 16573
    5725 atoms 
    5726 average map value = 0.07465, steps = 48 
    5727 shifted from previous position = 0.482 
    5728 rotated from previous position = 0.311 degrees 
    5729 atoms outside contour = 15915, contour level = 0.13241 
    5730  
    5731 Position of 0057_6gsm_F.cif (#1) relative to 0057_6gsm_F.mrc (#2) coordinates: 
    5732 Matrix rotation and translation 
    5733 0.99999869 -0.00155151 -0.00047107 0.19682187 
    5734 0.00154904 0.99998536 -0.00518424 0.71416720 
    5735 0.00047911 0.00518351 0.99998645 -1.35461568 
    5736 Axis 0.95440247 -0.08746900 0.28542090 
    5737 Axis point -0.00000000 247.29302550 132.65108473 
    5738 Rotation angle (degrees) 0.31120585 
    5739 Shift along axis -0.26125584 
    5740  
    5741 
    5742 > save /scratch/cs-
    5743 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_F_fitted.cif #1
    5744 
    5745 > close #1
    5746 
    5747 > close #2
    5748 
    5749 > open 6gsm
    5750 
    5751 6gsm title: 
    5752 Structure of a partial yeast 48S preinitiation complex in open conformation.
    5753 [more info...] 
    5754  
    5755 Chain information for 6gsm #1 
    5756 --- 
    5757 Chain | Description | UniProt 
    5758 1 | Met-tRNAi | 
    5759 2 | 18S ribosomal RNA | 
    5760 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    5761 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    5762 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    5763 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    5764 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    5765 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    5766 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    5767 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    5768 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    5769 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    5770 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    5771 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    5772 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    5773 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    5774 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    5775 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    5776 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    5777 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    5778 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    5779 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    5780 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    5781 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    5782 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    5783 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    5784 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    5785 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    5786 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    5787 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    5788 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    5789 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    5790 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    5791 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    5792 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    5793 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    5794 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    5795 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    5796 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    5797 3-265 
    5798 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    5799 90-519 
    5800 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    5801 127-270 
    5802 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    5803 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    5804 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    5805 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    5806 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    5807 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    5808 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    5809  
    5810 Non-standard residues in 6gsm #1 
    5811 --- 
    5812 7NO —
    5813 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    5814 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    5815 GCP — phosphomethylphosphonic acid guanylate ester 
    5816 MG — magnesium ion 
    5817 ZN — zinc ion 
    5818  
    5819 
    5820 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    5821 
    5822 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    5823 level 0.0673, step 2, values float32 
    5824 
    5825 > volume #2 region 187,227,189,274,338,292
    5826 
    5827 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    5828 
    5829 FYI: command is replacing existing command: "selectbox" 
    5830 executed select_box.py 
    5831 
    5832 > selectbox #1 inMap #2
    5833 
    5834 Selected 20625 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    5835 
    5836 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.cif
    5837 > #1 selectedOnly true
    5838 
    5839 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.mrc
    5840 > #2
    5841 
    5842 > close #1
    5843 
    5844 > close #2
    5845 
    5846 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.cif
    5847 
    5848 Summary of feedback from opening /scratch/cs-
    5849 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.cif 
    5850 --- 
    5851 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    5852 near line 51957 
    5853 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    5854 51958 
    5855 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    5856 51959 
    5857 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    5858 51960 
    5859 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    5860 51961 
    5861 107 messages similar to the above omitted 
    5862 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    5863 52210 
    5864 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    5865 52211 
    5866 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    5867 52212 
    5868 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    5869 52213 
    5870 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    5871 52214 
    5872 152 messages similar to the above omitted 
    5873 Atom OP2 has no neighbors to form bonds with according to residue template for
    5874 G /2:20 
    5875 Atom O2' has no neighbors to form bonds with according to residue template for
    5876 U /2:24 
    5877 Atom O2 has no neighbors to form bonds with according to residue template for
    5878 U /2:24 
    5879 Atom OP1 has no neighbors to form bonds with according to residue template for
    5880 A /2:26 
    5881 Atom O2' has no neighbors to form bonds with according to residue template for
    5882 A /2:43 
    5883 Atom OP1 has no neighbors to form bonds with according to residue template for
    5884 A /2:47 
    5885 Atom C6 has no neighbors to form bonds with according to residue template for
    5886 C /2:90 
    5887 Atom OP1 has no neighbors to form bonds with according to residue template for
    5888 A /2:135 
    5889 Atom O3' has no neighbors to form bonds with according to residue template for
    5890 A /2:135 
    5891 Atom OP2 has no neighbors to form bonds with according to residue template for
    5892 A /2:196 
    5893 Atom N7 has no neighbors to form bonds with according to residue template for
    5894 A /2:196 
    5895 Atom N6 has no neighbors to form bonds with according to residue template for
    5896 A /2:196 
    5897 Atom O4' has no neighbors to form bonds with according to residue template for
    5898 C /2:229 
    5899 Atom O2 has no neighbors to form bonds with according to residue template for
    5900 C /2:229 
    5901 Atom O2' has no neighbors to form bonds with according to residue template for
    5902 G /2:273 
    5903 Atom N2 has no neighbors to form bonds with according to residue template for
    5904 G /2:273 
    5905 Atom OP1 has no neighbors to form bonds with according to residue template for
    5906 C /2:281 
    5907 Atom OP2 has no neighbors to form bonds with according to residue template for
    5908 G /2:286 
    5909 Atom C5' has no neighbors to form bonds with according to residue template for
    5910 G /2:286 
    5911 Atom N7 has no neighbors to form bonds with according to residue template for
    5912 G /2:286 
    5913 Atom O6 has no neighbors to form bonds with according to residue template for
    5914 G /2:286 
    5915 Atom OP1 has no neighbors to form bonds with according to residue template for
    5916 A /2:287 
    5917 Atom OP2 has no neighbors to form bonds with according to residue template for
    5918 A /2:287 
    5919 Atom OP2 has no neighbors to form bonds with according to residue template for
    5920 U /2:288 
    5921 Atom OP1 has no neighbors to form bonds with according to residue template for
    5922 G /2:387 
    5923 Atom C5' has no neighbors to form bonds with according to residue template for
    5924 C /2:571 
    5925 Atom O4' has no neighbors to form bonds with according to residue template for
    5926 C /2:571 
    5927 Atom O2' has no neighbors to form bonds with according to residue template for
    5928 A /2:619 
    5929 Atom OP1 has no neighbors to form bonds with according to residue template for
    5930 U /2:695 
    5931 Atom OP2 has no neighbors to form bonds with according to residue template for
    5932 U /2:695 
    5933 Atom O3' has no neighbors to form bonds with according to residue template for
    5934 U /2:695 
    5935 Atom OP1 has no neighbors to form bonds with according to residue template for
    5936 G /2:729 
    5937 Atom O3' has no neighbors to form bonds with according to residue template for
    5938 G /2:729 
    5939 Atom O3' has no neighbors to form bonds with according to residue template for
    5940 C /2:731 
    5941 Atom O3' has no neighbors to form bonds with according to residue template for
    5942 G /2:786 
    5943 Atom O2' has no neighbors to form bonds with according to residue template for
    5944 C /2:949 
    5945 Atom OP1 has no neighbors to form bonds with according to residue template for
    5946 A /2:1019 
    5947 Atom O3' has no neighbors to form bonds with according to residue template for
    5948 A /2:1019 
    5949 Atom O3' has no neighbors to form bonds with according to residue template for
    5950 U /2:1048 
    5951 Atom O2' has no neighbors to form bonds with according to residue template for
    5952 U /2:1048 
    5953 Atom OP2 has no neighbors to form bonds with according to residue template for
    5954 G /2:1109 
    5955 Atom O6 has no neighbors to form bonds with according to residue template for
    5956 G /2:1109 
    5957 Atom N2 has no neighbors to form bonds with according to residue template for
    5958 G /2:1125 
    5959 Atom O2' has no neighbors to form bonds with according to residue template for
    5960 G /2:1647 
    5961 Atom O2' has no neighbors to form bonds with according to residue template for
    5962 G /2:1678 
    5963 Atom OP2 has no neighbors to form bonds with according to residue template for
    5964 U /2:1706 
    5965 Atom C5' has no neighbors to form bonds with according to residue template for
    5966 U /2:1706 
    5967 Atom N6 has no neighbors to form bonds with according to residue template for
    5968 A /2:1720 
    5969 Atom C5' has no neighbors to form bonds with according to residue template for
    5970 A /2:1744 
    5971 Atom O4' has no neighbors to form bonds with according to residue template for
    5972 A /2:1744 
    5973 Atom OG1 has no neighbors to form bonds with according to residue template for
    5974 THR /C:163 
    5975 Atom O has no neighbors to form bonds with according to residue template for
    5976 PRO /C:178 
    5977 Atom N has no neighbors to form bonds with according to residue template for
    5978 LEU /C:192 
    5979 Atom CB has no neighbors to form bonds with according to residue template for
    5980 LEU /C:192 
    5981 Atom N has no neighbors to form bonds with according to residue template for
    5982 ARG /C:210 
    5983 Atom CG has no neighbors to form bonds with according to residue template for
    5984 ARG /C:210 
    5985 Atom OG1 has no neighbors to form bonds with according to residue template for
    5986 THR /E:81 
    5987 Atom N has no neighbors to form bonds with according to residue template for
    5988 GLU /E:250 
    5989 Atom C has no neighbors to form bonds with according to residue template for
    5990 GLU /E:250 
    5991 Atom CB has no neighbors to form bonds with according to residue template for
    5992 GLU /E:250 
    5993 Atom O has no neighbors to form bonds with according to residue template for
    5994 ARG /G:88 
    5995 Atom O has no neighbors to form bonds with according to residue template for
    5996 ARG /G:183 
    5997 Atom NH2 has no neighbors to form bonds with according to residue template for
    5998 ARG /G:183 
    5999 Atom CD2 has no neighbors to form bonds with according to residue template for
    6000 LEU /G:184 
    6001 Atom C has no neighbors to form bonds with according to residue template for
    6002 ARG /H:96 
    6003 Atom CB has no neighbors to form bonds with according to residue template for
    6004 ARG /H:96 
    6005 Atom NH2 has no neighbors to form bonds with according to residue template for
    6006 ARG /H:96 
    6007 Atom N has no neighbors to form bonds with according to residue template for
    6008 VAL /H:121 
    6009 Atom CG2 has no neighbors to form bonds with according to residue template for
    6010 VAL /H:121 
    6011 Atom CG has no neighbors to form bonds with according to residue template for
    6012 LYS /I:138 
    6013 Atom O has no neighbors to form bonds with according to residue template for
    6014 LYS /J:16 
    6015 Atom NH1 has no neighbors to form bonds with according to residue template for
    6016 ARG /N:104 
    6017 Atom N has no neighbors to form bonds with according to residue template for
    6018 ASN /N:105 
    6019 Atom O has no neighbors to form bonds with according to residue template for
    6020 ASN /N:105 
    6021 Atom CD1 has no neighbors to form bonds with according to residue template for
    6022 ILE /W:14 
    6023 Atom CD1 has no neighbors to form bonds with according to residue template for
    6024 LEU /W:26 
    6025 Atom C has no neighbors to form bonds with according to residue template for
    6026 LYS /W:71 
    6027 Atom O has no neighbors to form bonds with according to residue template for
    6028 ASN /X:79 
    6029 Atom O has no neighbors to form bonds with according to residue template for
    6030 ALA /X:113 
    6031 Atom N has no neighbors to form bonds with according to residue template for
    6032 LYS /b:72 
    6033 Atom O has no neighbors to form bonds with according to residue template for
    6034 LYS /b:72 
    6035 Atom N has no neighbors to form bonds with according to residue template for
    6036 ARG /h:23 
    6037 Atom O has no neighbors to form bonds with according to residue template for
    6038 UNK /o:734 
    6039 Atom C has no neighbors to form bonds with according to residue template for
    6040 ASP /p:360 
    6041 Atom CA has no neighbors to form bonds with according to residue template for
    6042 ASP /p:397 
    6043 Atom N has no neighbors to form bonds with according to residue template for
    6044 ARG /p:677 
    6045 Atom CB has no neighbors to form bonds with according to residue template for
    6046 ARG /p:677 
    6047 Atom N has no neighbors to form bonds with according to residue template for
    6048 LYS /q:113 
    6049  
    6050 Chain information for 0057_6gsm_L.cif #1 
    6051 --- 
    6052 Chain | Description 
    6053 2 | 18S ribosomal RNA 
    6054 C | KLLA0F09812p 
    6055 E | 40S ribosomal protein S4 
    6056 G | 40S ribosomal protein S6 
    6057 H | 40S ribosomal protein S7 
    6058 I | 40S ribosomal protein S8 
    6059 J | KLLA0E23673p 
    6060 L | KLLA0A10483p 
    6061 N | KLLA0F18040p 
    6062 W | 40S ribosomal protein S22 
    6063 X | KLLA0B11231p 
    6064 b | 40S ribosomal protein S27 
    6065 h | 60S ribosomal protein L41-A 
    6066 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    6067 translation initiation factor 3 subunit A,eIF3a 
    6068 p | Eukaryotic translation initiation factor 3 subunit B 
    6069 q | Eukaryotic translation initiation factor 3 subunit C 
    6070  
    6071 
    6072 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L.mrc
    6073 
    6074 Opened 0057_6gsm_L.mrc as #2, grid size 88,112,104, pixel 1, shown at level
    6075 0.147, step 1, values float32 
    6076 
    6077 > fitmap #1 inMap #2
    6078 
    6079 Fit molecule 0057_6gsm_L.cif (#1) to map 0057_6gsm_L.mrc (#2) using 20625
    6080 atoms 
    6081 average map value = 0.0855, steps = 64 
    6082 shifted from previous position = 0.562 
    6083 rotated from previous position = 0.106 degrees 
    6084 atoms outside contour = 19726, contour level = 0.14692 
    6085  
    6086 Position of 0057_6gsm_L.cif (#1) relative to 0057_6gsm_L.mrc (#2) coordinates: 
    6087 Matrix rotation and translation 
    6088 0.99999903 0.00135370 -0.00033389 -0.56069105 
    6089 -0.00135329 0.99999833 0.00122632 -0.32874382 
    6090 0.00033555 -0.00122587 0.99999919 -0.08200758 
    6091 Axis -0.66036488 -0.18027934 -0.72898394 
    6092 Axis point -177.95394095 175.36755179 0.00000000 
    6093 Rotation angle (degrees) 0.10638074 
    6094 Shift along axis 0.48930860 
    6095  
    6096 
    6097 > save /scratch/cs-
    6098 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_L_fitted.cif #1
    6099 
    6100 > close #1
    6101 
    6102 > close #2
    6103 
    6104 > open 6gsm
    6105 
    6106 6gsm title: 
    6107 Structure of a partial yeast 48S preinitiation complex in open conformation.
    6108 [more info...] 
    6109  
    6110 Chain information for 6gsm #1 
    6111 --- 
    6112 Chain | Description | UniProt 
    6113 1 | Met-tRNAi | 
    6114 2 | 18S ribosomal RNA | 
    6115 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    6116 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    6117 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    6118 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    6119 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    6120 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    6121 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    6122 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    6123 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    6124 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    6125 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    6126 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    6127 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    6128 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    6129 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    6130 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    6131 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    6132 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    6133 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    6134 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    6135 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    6136 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    6137 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    6138 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    6139 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    6140 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    6141 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    6142 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    6143 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    6144 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    6145 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    6146 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    6147 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    6148 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    6149 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    6150 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    6151 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    6152 3-265 
    6153 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    6154 90-519 
    6155 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    6156 127-270 
    6157 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    6158 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    6159 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    6160 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    6161 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    6162 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    6163 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    6164  
    6165 Non-standard residues in 6gsm #1 
    6166 --- 
    6167 7NO —
    6168 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    6169 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    6170 GCP — phosphomethylphosphonic acid guanylate ester 
    6171 MG — magnesium ion 
    6172 ZN — zinc ion 
    6173  
    6174 
    6175 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    6176 
    6177 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    6178 level 0.0673, step 2, values float32 
    6179 
    6180 > volume #2 region 203,162,172,250,217,227
    6181 
    6182 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    6183 
    6184 FYI: command is replacing existing command: "selectbox" 
    6185 executed select_box.py 
    6186 
    6187 > selectbox #1 inMap #2
    6188 
    6189 Selected 4594 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    6190 
    6191 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.cif
    6192 > #1 selectedOnly true
    6193 
    6194 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.mrc
    6195 > #2
    6196 
    6197 > close #1
    6198 
    6199 > close #2
    6200 
    6201 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.cif
    6202 
    6203 Summary of feedback from opening /scratch/cs-
    6204 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.cif 
    6205 --- 
    6206 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    6207 near line 35563 
    6208 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    6209 35564 
    6210 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    6211 35565 
    6212 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    6213 35566 
    6214 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    6215 35567 
    6216 172 messages similar to the above omitted 
    6217 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    6218 35816 
    6219 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    6220 35817 
    6221 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    6222 35818 
    6223 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    6224 35819 
    6225 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    6226 35820 
    6227 187 messages similar to the above omitted 
    6228 Atom O5' has no neighbors to form bonds with according to residue template for
    6229 C /1:11 
    6230 Atom N6 has no neighbors to form bonds with according to residue template for
    6231 A /1:28 
    6232 Atom O4' has no neighbors to form bonds with according to residue template for
    6233 A /2:11 
    6234 Atom OP2 has no neighbors to form bonds with according to residue template for
    6235 U /2:12 
    6236 Atom O3' has no neighbors to form bonds with according to residue template for
    6237 A /2:579 
    6238 Atom C2' has no neighbors to form bonds with according to residue template for
    6239 U /2:580 
    6240 Atom O3' has no neighbors to form bonds with according to residue template for
    6241 A /2:906 
    6242 Atom O3' has no neighbors to form bonds with according to residue template for
    6243 A /2:991 
    6244 Atom C8 has no neighbors to form bonds with according to residue template for
    6245 G /2:993 
    6246 Atom OP1 has no neighbors to form bonds with according to residue template for
    6247 A /2:1029 
    6248 Atom O2' has no neighbors to form bonds with according to residue template for
    6249 A /2:1087 
    6250 Atom OP1 has no neighbors to form bonds with according to residue template for
    6251 A /2:1137 
    6252 Atom O5' has no neighbors to form bonds with according to residue template for
    6253 A /2:1137 
    6254 Atom O3' has no neighbors to form bonds with according to residue template for
    6255 A /2:1137 
    6256 Atom O6 has no neighbors to form bonds with according to residue template for
    6257 G /2:1152 
    6258 Atom N6 has no neighbors to form bonds with according to residue template for
    6259 A /2:1156 
    6260 Atom N1 has no neighbors to form bonds with according to residue template for
    6261 A /2:1156 
    6262 Atom N3 has no neighbors to form bonds with according to residue template for
    6263 A /2:1159 
    6264 Atom C2' has no neighbors to form bonds with according to residue template for
    6265 G /2:1187 
    6266 Atom C5' has no neighbors to form bonds with according to residue template for
    6267 C /2:1196 
    6268 Atom OP1 has no neighbors to form bonds with according to residue template for
    6269 G /2:1272 
    6270 Atom O3' has no neighbors to form bonds with according to residue template for
    6271 A /2:1274 
    6272 Atom OP1 has no neighbors to form bonds with according to residue template for
    6273 C /2:1424 
    6274 Atom OP1 has no neighbors to form bonds with according to residue template for
    6275 G /2:1462 
    6276 Atom C6 has no neighbors to form bonds with according to residue template for
    6277 U /2:1577 
    6278 Atom O4' has no neighbors to form bonds with according to residue template for
    6279 C /2:1578 
    6280 Atom OP1 has no neighbors to form bonds with according to residue template for
    6281 C /2:1749 
    6282 Atom OP2 has no neighbors to form bonds with according to residue template for
    6283 C /2:1749 
    6284 Atom OP2 has no neighbors to form bonds with according to residue template for
    6285 A /2:1751 
    6286 Atom O3' has no neighbors to form bonds with according to residue template for
    6287 A /2:1751 
    6288 Atom OP2 has no neighbors to form bonds with according to residue template for
    6289 U /2:1773 
    6290 Atom OP2 has no neighbors to form bonds with according to residue template for
    6291 G /2:1784 
    6292 Atom O6 has no neighbors to form bonds with according to residue template for
    6293 G /2:1784 
    6294 Atom O2' has no neighbors to form bonds with according to residue template for
    6295 A /2:1788 
    6296 Atom OP1 has no neighbors to form bonds with according to residue template for
    6297 C /2:1794 
    6298 Atom OP2 has no neighbors to form bonds with according to residue template for
    6299 C /2:1794 
    6300 Atom N has no neighbors to form bonds with according to residue template for
    6301 ILE /X:68 
    6302 Atom C has no neighbors to form bonds with according to residue template for
    6303 THR /c:19 
    6304 Atom CG2 has no neighbors to form bonds with according to residue template for
    6305 THR /c:19 
    6306 Atom N has no neighbors to form bonds with according to residue template for
    6307 GLY /c:23 
    6308 Atom O has no neighbors to form bonds with according to residue template for
    6309 GLY /c:23 
    6310 Atom CG1 has no neighbors to form bonds with according to residue template for
    6311 VAL /c:25 
    6312 Atom CG2 has no neighbors to form bonds with according to residue template for
    6313 VAL /c:25 
    6314 Atom N has no neighbors to form bonds with according to residue template for
    6315 LEU /h:13 
    6316 Atom O has no neighbors to form bonds with according to residue template for
    6317 ASN /i:55 
    6318 Atom N has no neighbors to form bonds with according to residue template for
    6319 LEU /i:78 
    6320 Atom N has no neighbors to form bonds with according to residue template for
    6321 VAL /j:90 
    6322 Atom N has no neighbors to form bonds with according to residue template for
    6323 ILE /l:180 
    6324 Atom N has no neighbors to form bonds with according to residue template for
    6325 THR /m:41 
    6326 Atom OG1 has no neighbors to form bonds with according to residue template for
    6327 THR /m:41 
    6328 Atom CG2 has no neighbors to form bonds with according to residue template for
    6329 THR /m:41 
    6330 Atom N has no neighbors to form bonds with according to residue template for
    6331 ASP /m:61 
    6332 Atom C has no neighbors to form bonds with according to residue template for
    6333 ASP /m:61 
    6334  
    6335 Chain information for 0057_6gsm_3.cif #1 
    6336 --- 
    6337 Chain | Description 
    6338 1 | Met-tRNAi 
    6339 2 | 18S ribosomal RNA 
    6340 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    6341 C | KLLA0F09812p 
    6342 D | KLLA0D08305p 
    6343 F | KLLA0D10659p 
    6344 O | 40S ribosomal protein S14 
    6345 Q | 40S ribosomal protein S16 
    6346 U | KLLA0F25542p 
    6347 X | KLLA0B11231p 
    6348 a | 40S ribosomal protein S26 
    6349 c | 40S ribosomal protein S28 
    6350 h | 60S ribosomal protein L41-A 
    6351 i | Eukaryotic translation initiation factor 1A 
    6352 j | Eukaryotic translation initiation factor 2 subunit alpha 
    6353 l | Eukaryotic translation initiation factor 2 subunit beta 
    6354 m | Eukaryotic translation initiation factor eIF-1 
    6355  
    6356 
    6357 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3.mrc
    6358 
    6359 Opened 0057_6gsm_3.mrc as #2, grid size 48,56,56, pixel 1, shown at level
    6360 0.147, step 1, values float32 
    6361 
    6362 > fitmap #1 inMap #2
    6363 
    6364 Fit molecule 0057_6gsm_3.cif (#1) to map 0057_6gsm_3.mrc (#2) using 4594 atoms 
    6365 average map value = 0.0782, steps = 56 
    6366 shifted from previous position = 0.482 
    6367 rotated from previous position = 0.264 degrees 
    6368 atoms outside contour = 4481, contour level = 0.14686 
    6369  
    6370 Position of 0057_6gsm_3.cif (#1) relative to 0057_6gsm_3.mrc (#2) coordinates: 
    6371 Matrix rotation and translation 
    6372 0.99999048 0.00086917 -0.00427518 0.27803584 
    6373 -0.00087555 0.99999851 -0.00149093 0.24639436 
    6374 0.00427388 0.00149466 0.99998975 -1.25590328 
    6375 Axis 0.32374789 -0.92703488 -0.18919205 
    6376 Axis point 289.60036558 0.00000000 56.87772451 
    6377 Rotation angle (degrees) 0.26419021 
    6378 Shift along axis 0.09920427 
    6379  
    6380 
    6381 > save /scratch/cs-
    6382 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_3_fitted.cif #1
    6383 
    6384 > close #1
    6385 
    6386 > close #2
    6387 
    6388 > open 6gsm
    6389 
    6390 6gsm title: 
    6391 Structure of a partial yeast 48S preinitiation complex in open conformation.
    6392 [more info...] 
    6393  
    6394 Chain information for 6gsm #1 
    6395 --- 
    6396 Chain | Description | UniProt 
    6397 1 | Met-tRNAi | 
    6398 2 | 18S ribosomal RNA | 
    6399 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    6400 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    6401 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    6402 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    6403 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    6404 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    6405 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    6406 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    6407 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    6408 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    6409 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    6410 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    6411 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    6412 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    6413 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    6414 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    6415 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    6416 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    6417 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    6418 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    6419 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    6420 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    6421 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    6422 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    6423 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    6424 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    6425 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    6426 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    6427 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    6428 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    6429 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    6430 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    6431 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    6432 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    6433 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    6434 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    6435 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    6436 3-265 
    6437 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    6438 90-519 
    6439 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    6440 127-270 
    6441 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    6442 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    6443 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    6444 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    6445 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    6446 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    6447 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    6448  
    6449 Non-standard residues in 6gsm #1 
    6450 --- 
    6451 7NO —
    6452 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    6453 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    6454 GCP — phosphomethylphosphonic acid guanylate ester 
    6455 MG — magnesium ion 
    6456 ZN — zinc ion 
    6457  
    6458 
    6459 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    6460 
    6461 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    6462 level 0.0673, step 2, values float32 
    6463 
    6464 > volume #2 region 151,212,105,246,299,232
    6465 
    6466 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    6467 
    6468 FYI: command is replacing existing command: "selectbox" 
    6469 executed select_box.py 
    6470 
    6471 > selectbox #1 inMap #2
    6472 
    6473 Selected 20634 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    6474 
    6475 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.cif
    6476 > #1 selectedOnly true
    6477 
    6478 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.mrc
    6479 > #2
    6480 
    6481 > close #1
    6482 
    6483 > close #2
    6484 
    6485 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.cif
    6486 
    6487 Summary of feedback from opening /scratch/cs-
    6488 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.cif 
    6489 --- 
    6490 warnings | Invalid residue range for struct_conf "HELX7": invalid chain "E",
    6491 near line 51987 
    6492 Invalid residue range for struct_conf "HELX8": invalid chain "E", near line
    6493 51988 
    6494 Invalid residue range for struct_conf "HELX9": invalid chain "E", near line
    6495 51989 
    6496 Invalid residue range for struct_conf "HELX10": invalid chain "E", near line
    6497 51990 
    6498 Invalid residue range for struct_conf "HELX11": invalid chain "E", near line
    6499 51991 
    6500 147 messages similar to the above omitted 
    6501 Invalid sheet range for struct_sheet_range "? 8": invalid chain "E", near line
    6502 52241 
    6503 Invalid sheet range for struct_sheet_range "? 9": invalid chain "E", near line
    6504 52242 
    6505 Invalid sheet range for struct_sheet_range "? 10": invalid chain "E", near
    6506 line 52243 
    6507 Invalid sheet range for struct_sheet_range "? 11": invalid chain "E", near
    6508 line 52244 
    6509 Invalid sheet range for struct_sheet_range "? 12": invalid chain "E", near
    6510 line 52245 
    6511 130 messages similar to the above omitted 
    6512 Atom OP1 has no neighbors to form bonds with according to residue template for
    6513 A /2:11 
    6514 Atom OP2 has no neighbors to form bonds with according to residue template for
    6515 C /2:49 
    6516 Atom OP2 has no neighbors to form bonds with according to residue template for
    6517 U /2:295 
    6518 Atom O5' has no neighbors to form bonds with according to residue template for
    6519 U /2:295 
    6520 Atom OP2 has no neighbors to form bonds with according to residue template for
    6521 A /2:322 
    6522 Atom N7 has no neighbors to form bonds with according to residue template for
    6523 G /2:325 
    6524 Atom C4' has no neighbors to form bonds with according to residue template for
    6525 A /2:327 
    6526 Atom OP1 has no neighbors to form bonds with according to residue template for
    6527 G /2:328 
    6528 Atom OP2 has no neighbors to form bonds with according to residue template for
    6529 G /2:328 
    6530 Atom O4' has no neighbors to form bonds with according to residue template for
    6531 C /2:430 
    6532 Atom OP2 has no neighbors to form bonds with according to residue template for
    6533 G /2:431 
    6534 Atom OP2 has no neighbors to form bonds with according to residue template for
    6535 C /2:432 
    6536 Atom OP2 has no neighbors to form bonds with according to residue template for
    6537 C /2:565 
    6538 Atom O2' has no neighbors to form bonds with according to residue template for
    6539 A /2:629 
    6540 Atom O4 has no neighbors to form bonds with according to residue template for
    6541 U /2:666 
    6542 Atom OP1 has no neighbors to form bonds with according to residue template for
    6543 A /2:707 
    6544 Atom O3' has no neighbors to form bonds with according to residue template for
    6545 G /2:722 
    6546 Atom O2' has no neighbors to form bonds with according to residue template for
    6547 G /2:722 
    6548 Atom OP1 has no neighbors to form bonds with according to residue template for
    6549 U /2:745 
    6550 Atom O4' has no neighbors to form bonds with according to residue template for
    6551 A /2:805 
    6552 Atom O2' has no neighbors to form bonds with according to residue template for
    6553 A /2:978 
    6554 Atom N3 has no neighbors to form bonds with according to residue template for
    6555 A /2:978 
    6556 Atom C4' has no neighbors to form bonds with according to residue template for
    6557 G /2:979 
    6558 Atom O3' has no neighbors to form bonds with according to residue template for
    6559 G /2:979 
    6560 Atom O2' has no neighbors to form bonds with according to residue template for
    6561 G /2:979 
    6562 Atom O3' has no neighbors to form bonds with according to residue template for
    6563 C /2:1021 
    6564 Atom O2' has no neighbors to form bonds with according to residue template for
    6565 C /2:1021 
    6566 Atom OP2 has no neighbors to form bonds with according to residue template for
    6567 C /2:1032 
    6568 Atom C5' has no neighbors to form bonds with according to residue template for
    6569 A /2:1038 
    6570 Atom O4' has no neighbors to form bonds with according to residue template for
    6571 A /2:1038 
    6572 Atom OP2 has no neighbors to form bonds with according to residue template for
    6573 U /2:1088 
    6574 Atom O2' has no neighbors to form bonds with according to residue template for
    6575 A /2:1142 
    6576 Atom C5' has no neighbors to form bonds with according to residue template for
    6577 G /2:1294 
    6578 Atom O3' has no neighbors to form bonds with according to residue template for
    6579 G /2:1294 
    6580 Atom O4' has no neighbors to form bonds with according to residue template for
    6581 A /2:1299 
    6582 Atom OP1 has no neighbors to form bonds with according to residue template for
    6583 A /2:1738 
    6584 Atom O3' has no neighbors to form bonds with according to residue template for
    6585 A /2:1747 
    6586 Atom O2' has no neighbors to form bonds with according to residue template for
    6587 A /2:1747 
    6588 Atom C2 has no neighbors to form bonds with according to residue template for
    6589 A /2:1747 
    6590 Atom OP1 has no neighbors to form bonds with according to residue template for
    6591 A /2:1753 
    6592 Atom N6 has no neighbors to form bonds with according to residue template for
    6593 A /2:1753 
    6594 Atom O3' has no neighbors to form bonds with according to residue template for
    6595 C /2:1770 
    6596 Atom O2' has no neighbors to form bonds with according to residue template for
    6597 C /2:1770 
    6598 Atom O3' has no neighbors to form bonds with according to residue template for
    6599 A /2:1788 
    6600 Atom O2' has no neighbors to form bonds with according to residue template for
    6601 A /2:1788 
    6602 Atom O4' has no neighbors to form bonds with according to residue template for
    6603 G /2:1790 
    6604 Atom CD1 has no neighbors to form bonds with according to residue template for
    6605 LEU /A:59 
    6606 Atom OG1 has no neighbors to form bonds with according to residue template for
    6607 THR /A:108 
    6608 Atom CG2 has no neighbors to form bonds with according to residue template for
    6609 THR /A:108 
    6610 Atom O has no neighbors to form bonds with according to residue template for
    6611 LEU /A:177 
    6612 Atom NH1 has no neighbors to form bonds with according to residue template for
    6613 ARG /C:48 
    6614 Atom N has no neighbors to form bonds with according to residue template for
    6615 VAL /C:91 
    6616 Atom CD1 has no neighbors to form bonds with according to residue template for
    6617 PHE /C:103 
    6618 Atom OG1 has no neighbors to form bonds with according to residue template for
    6619 THR /C:122 
    6620 Atom N has no neighbors to form bonds with according to residue template for
    6621 GLY /C:128 
    6622 Atom OD1 has no neighbors to form bonds with according to residue template for
    6623 ASP /C:250 
    6624 Atom N has no neighbors to form bonds with according to residue template for
    6625 PRO /E:35 
    6626 Atom C has no neighbors to form bonds with according to residue template for
    6627 ASP /E:79 
    6628 Atom O has no neighbors to form bonds with according to residue template for
    6629 HIS /E:142 
    6630 Atom C has no neighbors to form bonds with according to residue template for
    6631 LEU /E:238 
    6632 Atom CA has no neighbors to form bonds with according to residue template for
    6633 GLY /H:145 
    6634 Atom O has no neighbors to form bonds with according to residue template for
    6635 GLY /H:145 
    6636 Atom N has no neighbors to form bonds with according to residue template for
    6637 THR /L:72 
    6638 Atom O has no neighbors to form bonds with according to residue template for
    6639 THR /L:72 
    6640 Atom C has no neighbors to form bonds with according to residue template for
    6641 ARG /L:87 
    6642 Atom OE2 has no neighbors to form bonds with according to residue template for
    6643 GLU /V:64 
    6644 Atom O has no neighbors to form bonds with according to residue template for
    6645 LEU /V:69 
    6646 Atom O has no neighbors to form bonds with according to residue template for
    6647 LYS /Y:52 
    6648 Atom N has no neighbors to form bonds with according to residue template for
    6649 VAL /Y:75 
    6650 Atom CG2 has no neighbors to form bonds with according to residue template for
    6651 VAL /Y:75 
    6652 Atom CE2 has no neighbors to form bonds with according to residue template for
    6653 TYR /Y:76 
    6654 Atom OH has no neighbors to form bonds with according to residue template for
    6655 TYR /Y:76 
    6656 Atom CD1 has no neighbors to form bonds with according to residue template for
    6657 LEU /Y:96 
    6658 Atom N has no neighbors to form bonds with according to residue template for
    6659 TRP /h:5 
    6660 Atom CD has no neighbors to form bonds with according to residue template for
    6661 ARG /i:57 
    6662 Atom NH1 has no neighbors to form bonds with according to residue template for
    6663 ARG /i:57 
    6664  
    6665 Chain information for 0057_6gsm_J.cif #1 
    6666 --- 
    6667 Chain | Description 
    6668 2 | 18S ribosomal RNA 
    6669 A | 40S ribosomal protein S0 
    6670 C | KLLA0F09812p 
    6671 E | 40S ribosomal protein S4 
    6672 H | 40S ribosomal protein S7 
    6673 I | 40S ribosomal protein S8 
    6674 J | KLLA0E23673p 
    6675 L | KLLA0A10483p 
    6676 V | 40S ribosomal protein S21 
    6677 W | 40S ribosomal protein S22 
    6678 X | KLLA0B11231p 
    6679 Y | 40S ribosomal protein S24 
    6680 a | 40S ribosomal protein S26 
    6681 e | 40S ribosomal protein S30 
    6682 h | 60S ribosomal protein L41-A 
    6683 i | Eukaryotic translation initiation factor 1A 
    6684  
    6685 
    6686 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J.mrc
    6687 
    6688 Opened 0057_6gsm_J.mrc as #2, grid size 96,88,128, pixel 1, shown at level
    6689 0.146, step 1, values float32 
    6690 
    6691 > fitmap #1 inMap #2
    6692 
    6693 Fit molecule 0057_6gsm_J.cif (#1) to map 0057_6gsm_J.mrc (#2) using 20634
    6694 atoms 
    6695 average map value = 0.08539, steps = 48 
    6696 shifted from previous position = 0.283 
    6697 rotated from previous position = 0.0807 degrees 
    6698 atoms outside contour = 19712, contour level = 0.14584 
    6699  
    6700 Position of 0057_6gsm_J.cif (#1) relative to 0057_6gsm_J.mrc (#2) coordinates: 
    6701 Matrix rotation and translation 
    6702 0.99999926 0.00084597 0.00087723 -0.52834288 
    6703 -0.00084659 0.99999939 0.00070453 -0.19287997 
    6704 -0.00087663 -0.00070527 0.99999937 0.28359637 
    6705 Axis -0.50068506 0.62287955 -0.60111192 
    6706 Axis point 305.17755694 0.00000000 617.43129214 
    6707 Rotation angle (degrees) 0.08066466 
    6708 Shift along axis -0.02608076 
    6709  
    6710 
    6711 > save /scratch/cs-
    6712 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_J_fitted.cif #1
    6713 
    6714 > close #1
    6715 
    6716 > close #2
    6717 
    6718 > open 6gsm
    6719 
    6720 6gsm title: 
    6721 Structure of a partial yeast 48S preinitiation complex in open conformation.
    6722 [more info...] 
    6723  
    6724 Chain information for 6gsm #1 
    6725 --- 
    6726 Chain | Description | UniProt 
    6727 1 | Met-tRNAi | 
    6728 2 | 18S ribosomal RNA | 
    6729 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    6730 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    6731 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    6732 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    6733 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    6734 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    6735 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    6736 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    6737 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    6738 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    6739 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    6740 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    6741 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    6742 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    6743 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    6744 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    6745 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    6746 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    6747 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    6748 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    6749 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    6750 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    6751 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    6752 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    6753 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    6754 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    6755 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    6756 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    6757 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    6758 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    6759 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    6760 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    6761 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    6762 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    6763 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    6764 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    6765 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    6766 3-265 
    6767 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    6768 90-519 
    6769 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    6770 127-270 
    6771 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    6772 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    6773 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    6774 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    6775 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    6776 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    6777 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    6778  
    6779 Non-standard residues in 6gsm #1 
    6780 --- 
    6781 7NO —
    6782 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    6783 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    6784 GCP — phosphomethylphosphonic acid guanylate ester 
    6785 MG — magnesium ion 
    6786 ZN — zinc ion 
    6787  
    6788 
    6789 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    6790 
    6791 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    6792 level 0.0673, step 2, values float32 
    6793 
    6794 > volume #2 region 151,200,212,230,263,315
    6795 
    6796 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    6797 
    6798 FYI: command is replacing existing command: "selectbox" 
    6799 executed select_box.py 
    6800 
    6801 > selectbox #1 inMap #2
    6802 
    6803 Selected 13648 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    6804 
    6805 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_b.cif
    6806 > #1 selectedOnly true
    6807 
    6808 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_b.mrc
    6809 > #2
    6810 
    6811 > close #1
    6812 
    6813 > close #2
    6814 
    6815 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_b.cif
    6816 
    6817 Summary of feedback from opening /scratch/cs-
    6818 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_b.cif 
    6819 --- 
    6820 warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
    6821 near line 44712 
    6822 Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
    6823 44713 
    6824 Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
    6825 44714 
    6826 Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
    6827 44715 
    6828 Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
    6829 44716 
    6830 111 messages similar to the above omitted 
    6831 Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
    6832 line 44969 
    6833 Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
    6834 line 44970 
    6835 Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
    6836 line 44971 
    6837 Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
    6838 line 44972 
    6839 Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
    6840 line 44973 
    6841 189 messages similar to the above omitted 
    6842 Atom OP1 has no neighbors to form bonds with according to residue template for
    6843 G /2:306 
    6844 Atom O2' has no neighbors to form bonds with according to residue template for
    6845 G /2:306 
    6846 Atom OP1 has no neighbors to form bonds with according to residue template for
    6847 C /2:308 
    6848 Atom OP2 has no neighbors to form bonds with according to residue template for
    6849 C /2:308 
    6850 Atom OP1 has no neighbors to form bonds with according to residue template for
    6851 U /2:348 
    6852 Atom O3' has no neighbors to form bonds with according to residue template for
    6853 U /2:348 
    6854 Atom O2 has no neighbors to form bonds with according to residue template for
    6855 U /2:349 
    6856 Atom O4 has no neighbors to form bonds with according to residue template for
    6857 U /2:637 
    6858 Atom O2' has no neighbors to form bonds with according to residue template for
    6859 U /2:639 
    6860 Atom O2' has no neighbors to form bonds with according to residue template for
    6861 U /2:794 
    6862 Atom O2 has no neighbors to form bonds with according to residue template for
    6863 U /2:794 
    6864 Atom OP2 has no neighbors to form bonds with according to residue template for
    6865 U /2:1023 
    6866 Atom C5 has no neighbors to form bonds with according to residue template for
    6867 U /2:1023 
    6868 Atom OP2 has no neighbors to form bonds with according to residue template for
    6869 G /2:1113 
    6870 Atom O3' has no neighbors to form bonds with according to residue template for
    6871 U /2:1302 
    6872 Atom O2' has no neighbors to form bonds with according to residue template for
    6873 U /2:1302 
    6874 Atom OP1 has no neighbors to form bonds with according to residue template for
    6875 U /2:1626 
    6876 Atom C5' has no neighbors to form bonds with according to residue template for
    6877 U /2:1626 
    6878 Atom O3' has no neighbors to form bonds with according to residue template for
    6879 U /2:1626 
    6880 Atom O4' has no neighbors to form bonds with according to residue template for
    6881 G /2:1772 
    6882 Atom OP2 has no neighbors to form bonds with according to residue template for
    6883 G /2:1786 
    6884 Atom N has no neighbors to form bonds with according to residue template for
    6885 THR /A:10 
    6886 Atom NZ has no neighbors to form bonds with according to residue template for
    6887 LYS /A:88 
    6888 Atom ND1 has no neighbors to form bonds with according to residue template for
    6889 HIS /A:92 
    6890 Atom N has no neighbors to form bonds with according to residue template for
    6891 GLY /A:100 
    6892 Atom NH2 has no neighbors to form bonds with according to residue template for
    6893 ARG /A:179 
    6894 Atom OE1 has no neighbors to form bonds with according to residue template for
    6895 GLU /B:122 
    6896 Atom CE has no neighbors to form bonds with according to residue template for
    6897 LYS /B:145 
    6898 Atom N has no neighbors to form bonds with according to residue template for
    6899 LEU /B:172 
    6900 Atom C has no neighbors to form bonds with according to residue template for
    6901 LEU /B:172 
    6902 Atom CB has no neighbors to form bonds with according to residue template for
    6903 LEU /B:172 
    6904 Atom CD1 has no neighbors to form bonds with according to residue template for
    6905 LEU /B:172 
    6906 Atom CE has no neighbors to form bonds with according to residue template for
    6907 MET /C:245 
    6908 Atom OD1 has no neighbors to form bonds with according to residue template for
    6909 ASP /H:87 
    6910 Atom OD2 has no neighbors to form bonds with according to residue template for
    6911 ASP /H:87 
    6912 Atom O has no neighbors to form bonds with according to residue template for
    6913 ARG /H:114 
    6914 Atom O has no neighbors to form bonds with according to residue template for
    6915 HIS /L:104 
    6916 Atom NH1 has no neighbors to form bonds with according to residue template for
    6917 ARG /N:99 
    6918 Atom NH2 has no neighbors to form bonds with according to residue template for
    6919 ARG /N:99 
    6920 Atom CB has no neighbors to form bonds with according to residue template for
    6921 LYS /N:100 
    6922 Atom CE has no neighbors to form bonds with according to residue template for
    6923 LYS /N:100 
    6924 Atom CG has no neighbors to form bonds with according to residue template for
    6925 LYS /N:140 
    6926 Atom N has no neighbors to form bonds with according to residue template for
    6927 ARG /O:133 
    6928 Atom N has no neighbors to form bonds with according to residue template for
    6929 SER /R:96 
    6930 Atom OG has no neighbors to form bonds with according to residue template for
    6931 SER /R:96 
    6932 Atom C has no neighbors to form bonds with according to residue template for
    6933 VAL /V:13 
    6934 Atom N has no neighbors to form bonds with according to residue template for
    6935 VAL /V:39 
    6936 Atom OD1 has no neighbors to form bonds with according to residue template for
    6937 ASP /q:393 
    6938 Atom CG2 has no neighbors to form bonds with according to residue template for
    6939 ILE /q:448 
    6940 Atom NE1 has no neighbors to form bonds with according to residue template for
    6941 TRP /q:456 
    6942 Atom CZ2 has no neighbors to form bonds with according to residue template for
    6943 TRP /q:456 
    6944 Atom OD1 has no neighbors to form bonds with according to residue template for
    6945 ASP /q:484 
    6946 Atom CA has no neighbors to form bonds with according to residue template for
    6947 GLN /q:517 
    6948 Atom CB has no neighbors to form bonds with according to residue template for
    6949 ARG /q:654 
    6950  
    6951 Chain information for 0057_6gsm_b.cif #1 
    6952 --- 
    6953 Chain | Description 
    6954 2 | 18S ribosomal RNA 
    6955 A | 40S ribosomal protein S0 
    6956 B | 40S ribosomal protein S1 
    6957 C | KLLA0F09812p 
    6958 H | 40S ribosomal protein S7 
    6959 L | KLLA0A10483p 
    6960 N | KLLA0F18040p 
    6961 O | 40S ribosomal protein S14 
    6962 R | KLLA0B01474p 
    6963 V | 40S ribosomal protein S21 
    6964 W | 40S ribosomal protein S22 
    6965 X | KLLA0B11231p 
    6966 a | 40S ribosomal protein S26 
    6967 b | 40S ribosomal protein S27 
    6968 h | 60S ribosomal protein L41-A 
    6969 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    6970 translation initiation factor 3 subunit A,eIF3a 
    6971 q | Eukaryotic translation initiation factor 3 subunit C 
    6972  
    6973 
    6974 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_b.mrc
    6975 
    6976 Opened 0057_6gsm_b.mrc as #2, grid size 80,64,104, pixel 1, shown at level
    6977 0.145, step 1, values float32 
    6978 
    6979 > fitmap #1 inMap #2
    6980 
    6981 Fit molecule 0057_6gsm_b.cif (#1) to map 0057_6gsm_b.mrc (#2) using 13648
    6982 atoms 
    6983 average map value = 0.06975, steps = 120 
    6984 shifted from previous position = 0.477 
    6985 rotated from previous position = 0.155 degrees 
    6986 atoms outside contour = 13183, contour level = 0.1446 
    6987  
    6988 Position of 0057_6gsm_b.cif (#1) relative to 0057_6gsm_b.mrc (#2) coordinates: 
    6989 Matrix rotation and translation 
    6990 0.99999867 0.00068419 -0.00147724 0.10063725 
    6991 -0.00068737 0.99999744 -0.00215405 0.39911254 
    6992 0.00147576 0.00215506 0.99999659 -1.14122012 
    6993 Axis 0.79784835 -0.54676044 -0.25395084 
    6994 Axis point 0.00000000 512.00866074 223.23098321 
    6995 Rotation angle (degrees) 0.15472488 
    6996 Shift along axis 0.15188813 
    6997  
    6998 
    6999 > save /scratch/cs-
    7000 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_b_fitted.cif #1
    7001 
    7002 > close #1
    7003 
    7004 > close #2
    7005 
    7006 > open 6gsm
    7007 
    7008 6gsm title: 
    7009 Structure of a partial yeast 48S preinitiation complex in open conformation.
    7010 [more info...] 
    7011  
    7012 Chain information for 6gsm #1 
    7013 --- 
    7014 Chain | Description | UniProt 
    7015 1 | Met-tRNAi | 
    7016 2 | 18S ribosomal RNA | 
    7017 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    7018 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    7019 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    7020 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    7021 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    7022 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    7023 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    7024 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    7025 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    7026 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    7027 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    7028 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    7029 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    7030 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    7031 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    7032 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    7033 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    7034 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    7035 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    7036 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    7037 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    7038 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    7039 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    7040 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    7041 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    7042 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    7043 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    7044 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    7045 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    7046 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    7047 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    7048 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    7049 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    7050 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    7051 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    7052 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    7053 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    7054 3-265 
    7055 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    7056 90-519 
    7057 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    7058 127-270 
    7059 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    7060 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    7061 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    7062 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    7063 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    7064 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    7065 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    7066  
    7067 Non-standard residues in 6gsm #1 
    7068 --- 
    7069 7NO —
    7070 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    7071 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    7072 GCP — phosphomethylphosphonic acid guanylate ester 
    7073 MG — magnesium ion 
    7074 ZN — zinc ion 
    7075  
    7076 
    7077 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    7078 
    7079 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    7080 level 0.0673, step 2, values float32 
    7081 
    7082 > volume #2 region 163,124,197,234,203,268
    7083 
    7084 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    7085 
    7086 FYI: command is replacing existing command: "selectbox" 
    7087 executed select_box.py 
    7088 
    7089 > selectbox #1 inMap #2
    7090 
    7091 Selected 9480 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    7092 
    7093 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.cif
    7094 > #1 selectedOnly true
    7095 
    7096 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.mrc
    7097 > #2
    7098 
    7099 > close #1
    7100 
    7101 > close #2
    7102 
    7103 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.cif
    7104 
    7105 Summary of feedback from opening /scratch/cs-
    7106 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.cif 
    7107 --- 
    7108 warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
    7109 near line 40502 
    7110 Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
    7111 40503 
    7112 Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
    7113 40504 
    7114 Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
    7115 40505 
    7116 Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
    7117 40506 
    7118 134 messages similar to the above omitted 
    7119 Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
    7120 line 40760 
    7121 Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
    7122 line 40761 
    7123 Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
    7124 line 40762 
    7125 Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
    7126 line 40763 
    7127 Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
    7128 line 40764 
    7129 163 messages similar to the above omitted 
    7130 Atom N4 has no neighbors to form bonds with according to residue template for
    7131 C /1:34 
    7132 Atom C5 has no neighbors to form bonds with according to residue template for
    7133 C /1:34 
    7134 Atom O2' has no neighbors to form bonds with according to residue template for
    7135 C /2:882 
    7136 Atom C5 has no neighbors to form bonds with according to residue template for
    7137 U /2:887 
    7138 Atom OP1 has no neighbors to form bonds with according to residue template for
    7139 G /2:900 
    7140 Atom OP2 has no neighbors to form bonds with according to residue template for
    7141 G /2:900 
    7142 Atom O4' has no neighbors to form bonds with according to residue template for
    7143 A /2:905 
    7144 Atom O2' has no neighbors to form bonds with according to residue template for
    7145 U /2:927 
    7146 Atom C5' has no neighbors to form bonds with according to residue template for
    7147 G /2:1166 
    7148 Atom O4' has no neighbors to form bonds with according to residue template for
    7149 G /2:1166 
    7150 Atom OP1 has no neighbors to form bonds with according to residue template for
    7151 U /2:1284 
    7152 Atom O3' has no neighbors to form bonds with according to residue template for
    7153 A /2:1320 
    7154 Atom O4' has no neighbors to form bonds with according to residue template for
    7155 A /2:1325 
    7156 Atom C8 has no neighbors to form bonds with according to residue template for
    7157 A /2:1330 
    7158 Atom O4' has no neighbors to form bonds with according to residue template for
    7159 C /2:1338 
    7160 Atom O3' has no neighbors to form bonds with according to residue template for
    7161 G /2:1532 
    7162 Atom O2' has no neighbors to form bonds with according to residue template for
    7163 G /2:1532 
    7164 Atom C1' has no neighbors to form bonds with according to residue template for
    7165 G /2:1532 
    7166 Atom OP2 has no neighbors to form bonds with according to residue template for
    7167 C /2:1578 
    7168 Atom OP1 has no neighbors to form bonds with according to residue template for
    7169 U /2:1607 
    7170 Atom OP2 has no neighbors to form bonds with according to residue template for
    7171 U /2:1607 
    7172 Atom O5' has no neighbors to form bonds with according to residue template for
    7173 U /2:1607 
    7174 Atom C4' has no neighbors to form bonds with according to residue template for
    7175 A /2:1631 
    7176 Atom O4' has no neighbors to form bonds with according to residue template for
    7177 U /2:1769 
    7178 Atom O3' has no neighbors to form bonds with according to residue template for
    7179 C /2:1782 
    7180 Atom O3' has no neighbors to form bonds with according to residue template for
    7181 G /2:1791 
    7182 Atom O2' has no neighbors to form bonds with according to residue template for
    7183 G /2:1791 
    7184 Atom O has no neighbors to form bonds with according to residue template for
    7185 ILE /A:111 
    7186 Atom CG2 has no neighbors to form bonds with according to residue template for
    7187 ILE /A:111 
    7188 Atom CD2 has no neighbors to form bonds with according to residue template for
    7189 HIS /A:168 
    7190 Atom O has no neighbors to form bonds with according to residue template for
    7191 TYR /A:204 
    7192 Atom O4 has no neighbors to form bonds with according to residue template for
    7193 U /3:30 
    7194 Atom OG1 has no neighbors to form bonds with according to residue template for
    7195 THR /B:46 
    7196 Atom N has no neighbors to form bonds with according to residue template for
    7197 VAL /B:84 
    7198 Atom O has no neighbors to form bonds with according to residue template for
    7199 VAL /B:84 
    7200 Atom SD has no neighbors to form bonds with according to residue template for
    7201 MET /B:103 
    7202 Atom OE1 has no neighbors to form bonds with according to residue template for
    7203 GLN /B:149 
    7204 Atom CA has no neighbors to form bonds with according to residue template for
    7205 VAL /B:150 
    7206 Atom O has no neighbors to form bonds with according to residue template for
    7207 VAL /B:150 
    7208 Atom CG1 has no neighbors to form bonds with according to residue template for
    7209 VAL /F:25 
    7210 Atom CG2 has no neighbors to form bonds with according to residue template for
    7211 VAL /F:25 
    7212 Atom O has no neighbors to form bonds with according to residue template for
    7213 GLU /F:34 
    7214 Atom CD has no neighbors to form bonds with according to residue template for
    7215 ARG /F:104 
    7216 Atom NH1 has no neighbors to form bonds with according to residue template for
    7217 ARG /F:104 
    7218 Atom N has no neighbors to form bonds with according to residue template for
    7219 ASP /F:128 
    7220 Atom C has no neighbors to form bonds with according to residue template for
    7221 ASP /F:128 
    7222 Atom N has no neighbors to form bonds with according to residue template for
    7223 MET /O:46 
    7224 Atom N has no neighbors to form bonds with according to residue template for
    7225 LYS /Q:14 
    7226 Atom CG has no neighbors to form bonds with according to residue template for
    7227 LYS /Q:14 
    7228 Atom CE has no neighbors to form bonds with according to residue template for
    7229 LYS /Q:14 
    7230 Atom C has no neighbors to form bonds with according to residue template for
    7231 ALA /Q:20 
    7232 Atom CB has no neighbors to form bonds with according to residue template for
    7233 ALA /Q:20 
    7234 Atom N has no neighbors to form bonds with according to residue template for
    7235 GLN /Q:40 
    7236 Atom N has no neighbors to form bonds with according to residue template for
    7237 GLN /Q:77 
    7238 Atom N has no neighbors to form bonds with according to residue template for
    7239 LEU /Q:89 
    7240 Atom CD1 has no neighbors to form bonds with according to residue template for
    7241 LEU /Q:105 
    7242 Atom OE1 has no neighbors to form bonds with according to residue template for
    7243 GLU /R:18 
    7244 Atom OE2 has no neighbors to form bonds with according to residue template for
    7245 GLU /R:18 
    7246 Atom OG1 has no neighbors to form bonds with according to residue template for
    7247 THR /R:54 
    7248 Atom OG1 has no neighbors to form bonds with according to residue template for
    7249 THR /R:55 
    7250 Atom CG1 has no neighbors to form bonds with according to residue template for
    7251 ILE /R:61 
    7252 Atom O has no neighbors to form bonds with according to residue template for
    7253 LYS /a:32 
    7254 Atom CG has no neighbors to form bonds with according to residue template for
    7255 LYS /a:32 
    7256 Atom CG has no neighbors to form bonds with according to residue template for
    7257 LYS /a:34 
    7258 Atom N has no neighbors to form bonds with according to residue template for
    7259 ASP /j:18 
    7260 Atom O has no neighbors to form bonds with according to residue template for
    7261 ASP /j:18 
    7262 Atom ND2 has no neighbors to form bonds with according to residue template for
    7263 ASN /j:23 
    7264 Atom CD1 has no neighbors to form bonds with according to residue template for
    7265 ILE /j:63 
    7266 Atom NH1 has no neighbors to form bonds with according to residue template for
    7267 ARG /j:64 
    7268 Atom N has no neighbors to form bonds with according to residue template for
    7269 VAL /o:48 
    7270 Atom NZ has no neighbors to form bonds with according to residue template for
    7271 LYS /o:76 
    7272  
    7273 Chain information for 0057_6gsm_c.cif #1 
    7274 --- 
    7275 Chain | Description 
    7276 1 | Met-tRNAi 
    7277 2 | 18S ribosomal RNA 
    7278 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    7279 A | 40S ribosomal protein S0 
    7280 B | 40S ribosomal protein S1 
    7281 C | KLLA0F09812p 
    7282 D | KLLA0D08305p 
    7283 F | KLLA0D10659p 
    7284 O | 40S ribosomal protein S14 
    7285 Q | 40S ribosomal protein S16 
    7286 R | KLLA0B01474p 
    7287 Z | KLLA0B06182p 
    7288 a | 40S ribosomal protein S26 
    7289 c | 40S ribosomal protein S28 
    7290 g | KLLA0E12277p 
    7291 j | Eukaryotic translation initiation factor 2 subunit alpha 
    7292 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    7293 translation initiation factor 3 subunit A,eIF3a 
    7294  
    7295 
    7296 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c.mrc
    7297 
    7298 Opened 0057_6gsm_c.mrc as #2, grid size 72,80,72, pixel 1, shown at level
    7299 0.137, step 1, values float32 
    7300 
    7301 > fitmap #1 inMap #2
    7302 
    7303 Fit molecule 0057_6gsm_c.cif (#1) to map 0057_6gsm_c.mrc (#2) using 9480 atoms 
    7304 average map value = 0.07507, steps = 48 
    7305 shifted from previous position = 0.58 
    7306 rotated from previous position = 0.323 degrees 
    7307 atoms outside contour = 9159, contour level = 0.13696 
    7308  
    7309 Position of 0057_6gsm_c.cif (#1) relative to 0057_6gsm_c.mrc (#2) coordinates: 
    7310 Matrix rotation and translation 
    7311 0.99999841 -0.00143913 0.00105503 -0.05309246 
    7312 0.00144474 0.99998470 -0.00534025 0.88891144 
    7313 -0.00104733 0.00534177 0.99998518 -1.26219123 
    7314 Axis 0.94846552 0.18667082 0.25606087 
    7315 Axis point 0.00000000 226.81472737 173.06242894 
    7316 Rotation angle (degrees) 0.32264642 
    7317 Shift along axis -0.20762033 
    7318  
    7319 
    7320 > save /scratch/cs-
    7321 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_c_fitted.cif #1
    7322 
    7323 > close #1
    7324 
    7325 > close #2
    7326 
    7327 > open 6gsm
    7328 
    7329 6gsm title: 
    7330 Structure of a partial yeast 48S preinitiation complex in open conformation.
    7331 [more info...] 
    7332  
    7333 Chain information for 6gsm #1 
    7334 --- 
    7335 Chain | Description | UniProt 
    7336 1 | Met-tRNAi | 
    7337 2 | 18S ribosomal RNA | 
    7338 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    7339 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    7340 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    7341 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    7342 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    7343 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    7344 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    7345 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    7346 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    7347 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    7348 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    7349 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    7350 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    7351 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    7352 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    7353 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    7354 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    7355 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    7356 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    7357 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    7358 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    7359 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    7360 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    7361 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    7362 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    7363 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    7364 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    7365 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    7366 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    7367 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    7368 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    7369 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    7370 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    7371 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    7372 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    7373 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    7374 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    7375 3-265 
    7376 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    7377 90-519 
    7378 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    7379 127-270 
    7380 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    7381 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    7382 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    7383 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    7384 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    7385 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    7386 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    7387  
    7388 Non-standard residues in 6gsm #1 
    7389 --- 
    7390 7NO —
    7391 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    7392 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    7393 GCP — phosphomethylphosphonic acid guanylate ester 
    7394 MG — magnesium ion 
    7395 ZN — zinc ion 
    7396  
    7397 
    7398 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    7399 
    7400 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    7401 level 0.0673, step 2, values float32 
    7402 
    7403 > volume #2 region 199,164,139,278,243,210
    7404 
    7405 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    7406 
    7407 FYI: command is replacing existing command: "selectbox" 
    7408 executed select_box.py 
    7409 
    7410 > selectbox #1 inMap #2
    7411 
    7412 Selected 10393 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    7413 
    7414 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.cif
    7415 > #1 selectedOnly true
    7416 
    7417 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.mrc
    7418 > #2
    7419 
    7420 > close #1
    7421 
    7422 > close #2
    7423 
    7424 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.cif
    7425 
    7426 Summary of feedback from opening /scratch/cs-
    7427 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.cif 
    7428 --- 
    7429 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    7430 near line 41478 
    7431 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    7432 41479 
    7433 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    7434 41480 
    7435 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    7436 41481 
    7437 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    7438 41482 
    7439 130 messages similar to the above omitted 
    7440 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    7441 41731 
    7442 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    7443 41732 
    7444 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    7445 41733 
    7446 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    7447 41734 
    7448 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    7449 41735 
    7450 155 messages similar to the above omitted 
    7451 Atom O2 has no neighbors to form bonds with according to residue template for
    7452 C /1:11 
    7453 Atom OP1 has no neighbors to form bonds with according to residue template for
    7454 G /1:12 
    7455 Atom O3' has no neighbors to form bonds with according to residue template for
    7456 G /1:12 
    7457 Atom N2 has no neighbors to form bonds with according to residue template for
    7458 G /1:24 
    7459 Atom N3 has no neighbors to form bonds with according to residue template for
    7460 G /1:24 
    7461 Atom OP2 has no neighbors to form bonds with according to residue template for
    7462 G /1:29 
    7463 Atom O2 has no neighbors to form bonds with according to residue template for
    7464 C /1:69 
    7465 Atom O4' has no neighbors to form bonds with according to residue template for
    7466 U /1:72 
    7467 Atom OP2 has no neighbors to form bonds with according to residue template for
    7468 C /2:4 
    7469 Atom OP2 has no neighbors to form bonds with according to residue template for
    7470 C /2:13 
    7471 Atom N6 has no neighbors to form bonds with according to residue template for
    7472 A /2:540 
    7473 Atom O3' has no neighbors to form bonds with according to residue template for
    7474 A /2:544 
    7475 Atom O2' has no neighbors to form bonds with according to residue template for
    7476 A /2:544 
    7477 Atom OP2 has no neighbors to form bonds with according to residue template for
    7478 A /2:555 
    7479 Atom OP2 has no neighbors to form bonds with according to residue template for
    7480 G /2:556 
    7481 Atom OP2 has no neighbors to form bonds with according to residue template for
    7482 U /2:557 
    7483 Atom OP2 has no neighbors to form bonds with according to residue template for
    7484 C /2:588 
    7485 Atom O5' has no neighbors to form bonds with according to residue template for
    7486 C /2:588 
    7487 Atom OP2 has no neighbors to form bonds with according to residue template for
    7488 U /2:601 
    7489 Atom N7 has no neighbors to form bonds with according to residue template for
    7490 G /2:609 
    7491 Atom O6 has no neighbors to form bonds with according to residue template for
    7492 G /2:609 
    7493 Atom C8 has no neighbors to form bonds with according to residue template for
    7494 G /2:612 
    7495 Atom O4' has no neighbors to form bonds with according to residue template for
    7496 A /2:1085 
    7497 Atom O2' has no neighbors to form bonds with according to residue template for
    7498 A /2:1085 
    7499 Atom O2' has no neighbors to form bonds with according to residue template for
    7500 U /2:1114 
    7501 Atom O2' has no neighbors to form bonds with according to residue template for
    7502 A /2:1142 
    7503 Atom OP1 has no neighbors to form bonds with according to residue template for
    7504 G /2:1149 
    7505 Atom OP2 has no neighbors to form bonds with according to residue template for
    7506 G /2:1149 
    7507 Atom OP2 has no neighbors to form bonds with according to residue template for
    7508 C /2:1158 
    7509 Atom O3' has no neighbors to form bonds with according to residue template for
    7510 G /2:1175 
    7511 Atom O2' has no neighbors to form bonds with according to residue template for
    7512 G /2:1175 
    7513 Atom O2 has no neighbors to form bonds with according to residue template for
    7514 C /2:1176 
    7515 Atom O2 has no neighbors to form bonds with according to residue template for
    7516 U /2:1184 
    7517 Atom C5' has no neighbors to form bonds with according to residue template for
    7518 G /2:1199 
    7519 Atom OP2 has no neighbors to form bonds with according to residue template for
    7520 U /2:1213 
    7521 Atom O2' has no neighbors to form bonds with according to residue template for
    7522 C /2:1214 
    7523 Atom O3' has no neighbors to form bonds with according to residue template for
    7524 C /2:1215 
    7525 Atom N3 has no neighbors to form bonds with according to residue template for
    7526 A /2:1216 
    7527 Atom O4' has no neighbors to form bonds with according to residue template for
    7528 G /2:1264 
    7529 Atom O3' has no neighbors to form bonds with according to residue template for
    7530 G /2:1280 
    7531 Atom O5' has no neighbors to form bonds with according to residue template for
    7532 U /2:1281 
    7533 Atom O2 has no neighbors to form bonds with according to residue template for
    7534 U /2:1281 
    7535 Atom O2 has no neighbors to form bonds with according to residue template for
    7536 U /2:1282 
    7537 Atom N3 has no neighbors to form bonds with according to residue template for
    7538 A /2:1423 
    7539 Atom O4 has no neighbors to form bonds with according to residue template for
    7540 U /2:1435 
    7541 Atom OP2 has no neighbors to form bonds with according to residue template for
    7542 G /2:1436 
    7543 Atom O2' has no neighbors to form bonds with according to residue template for
    7544 G /2:1462 
    7545 Atom OP1 has no neighbors to form bonds with according to residue template for
    7546 A /2:1575 
    7547 Atom O5' has no neighbors to form bonds with according to residue template for
    7548 A /2:1575 
    7549 Atom O2' has no neighbors to form bonds with according to residue template for
    7550 A /2:1575 
    7551 Atom O4' has no neighbors to form bonds with according to residue template for
    7552 C /2:1622 
    7553 Atom OP2 has no neighbors to form bonds with according to residue template for
    7554 C /2:1623 
    7555 Atom O6 has no neighbors to form bonds with according to residue template for
    7556 G /2:1627 
    7557 Atom N1 has no neighbors to form bonds with according to residue template for
    7558 G /2:1627 
    7559 Atom N2 has no neighbors to form bonds with according to residue template for
    7560 G /2:1627 
    7561 Atom OP1 has no neighbors to form bonds with according to residue template for
    7562 U /2:1740 
    7563 Atom OP2 has no neighbors to form bonds with according to residue template for
    7564 U /2:1740 
    7565 Atom C5' has no neighbors to form bonds with according to residue template for
    7566 U /2:1740 
    7567 Atom N3 has no neighbors to form bonds with according to residue template for
    7568 A /2:1780 
    7569 Atom N has no neighbors to form bonds with according to residue template for
    7570 ALA /C:97 
    7571 Atom NH1 has no neighbors to form bonds with according to residue template for
    7572 ARG /J:23 
    7573 Atom NH2 has no neighbors to form bonds with according to residue template for
    7574 ARG /J:23 
    7575 Atom N has no neighbors to form bonds with according to residue template for
    7576 LYS /U:77 
    7577 Atom CD has no neighbors to form bonds with according to residue template for
    7578 LYS /X:39 
    7579 Atom N has no neighbors to form bonds with according to residue template for
    7580 LYS /X:78 
    7581 Atom C has no neighbors to form bonds with according to residue template for
    7582 LYS /X:78 
    7583 Atom N has no neighbors to form bonds with according to residue template for
    7584 LYS /f:90 
    7585 Atom O has no neighbors to form bonds with according to residue template for
    7586 LYS /f:90 
    7587 Atom O has no neighbors to form bonds with according to residue template for
    7588 ILE /l:141 
    7589 Atom CG2 has no neighbors to form bonds with according to residue template for
    7590 ILE /l:141 
    7591 Atom CD has no neighbors to form bonds with according to residue template for
    7592 ARG /l:253 
    7593 Atom CD1 has no neighbors to form bonds with according to residue template for
    7594 ILE /m:54 
    7595 Atom CA has no neighbors to form bonds with according to residue template for
    7596 LEU /m:55 
    7597 Atom O has no neighbors to form bonds with according to residue template for
    7598 LEU /m:55 
    7599 Atom N has no neighbors to form bonds with according to residue template for
    7600 ASN /m:67 
    7601 Atom O has no neighbors to form bonds with according to residue template for
    7602 ASN /m:67 
    7603 Atom N has no neighbors to form bonds with according to residue template for
    7604 TRP /p:315 
    7605 Atom N has no neighbors to form bonds with according to residue template for
    7606 GLY /p:320 
    7607 Atom CG1 has no neighbors to form bonds with according to residue template for
    7608 VAL /p:480 
    7609 Atom CG2 has no neighbors to form bonds with according to residue template for
    7610 VAL /p:480 
    7611  
    7612 Chain information for 0057_6gsm_i.cif #1 
    7613 --- 
    7614 Chain | Description 
    7615 1 | Met-tRNAi 
    7616 2 | 18S ribosomal RNA 
    7617 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    7618 C | KLLA0F09812p 
    7619 D | KLLA0D08305p 
    7620 J | KLLA0E23673p 
    7621 Q | 40S ribosomal protein S16 
    7622 U | KLLA0F25542p 
    7623 X | KLLA0B11231p 
    7624 d | 40S ribosomal protein S29 
    7625 e | 40S ribosomal protein S30 
    7626 f | Ubiquitin-40S ribosomal protein S27a 
    7627 h | 60S ribosomal protein L41-A 
    7628 i | Eukaryotic translation initiation factor 1A 
    7629 j | Eukaryotic translation initiation factor 2 subunit alpha 
    7630 k | Eukaryotic translation initiation factor 2 subunit gamma 
    7631 l | Eukaryotic translation initiation factor 2 subunit beta 
    7632 m | Eukaryotic translation initiation factor eIF-1 
    7633 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    7634 translation initiation factor 3 subunit A,eIF3a 
    7635 p | Eukaryotic translation initiation factor 3 subunit B 
    7636  
    7637 
    7638 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i.mrc
    7639 
    7640 Opened 0057_6gsm_i.mrc as #2, grid size 80,80,72, pixel 1, shown at level
    7641 0.139, step 1, values float32 
    7642 
    7643 > fitmap #1 inMap #2
    7644 
    7645 Fit molecule 0057_6gsm_i.cif (#1) to map 0057_6gsm_i.mrc (#2) using 10393
    7646 atoms 
    7647 average map value = 0.07196, steps = 56 
    7648 shifted from previous position = 0.474 
    7649 rotated from previous position = 0.143 degrees 
    7650 atoms outside contour = 9995, contour level = 0.13898 
    7651  
    7652 Position of 0057_6gsm_i.cif (#1) relative to 0057_6gsm_i.mrc (#2) coordinates: 
    7653 Matrix rotation and translation 
    7654 0.99999692 0.00018283 0.00247368 -0.90601607 
    7655 -0.00018207 0.99999994 -0.00030762 -0.12008924 
    7656 -0.00247373 0.00030717 0.99999689 0.50653629 
    7657 Axis 0.12298613 0.98972007 -0.07299718 
    7658 Axis point 196.43577144 0.00000000 353.21954976 
    7659 Rotation angle (degrees) 0.14320519 
    7660 Shift along axis -0.26725786 
    7661  
    7662 
    7663 > save /scratch/cs-
    7664 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_i_fitted.cif #1
    7665 
    7666 > close #1
    7667 
    7668 > close #2
    7669 
    7670 > open 6gsm
    7671 
    7672 6gsm title: 
    7673 Structure of a partial yeast 48S preinitiation complex in open conformation.
    7674 [more info...] 
    7675  
    7676 Chain information for 6gsm #1 
    7677 --- 
    7678 Chain | Description | UniProt 
    7679 1 | Met-tRNAi | 
    7680 2 | 18S ribosomal RNA | 
    7681 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    7682 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    7683 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    7684 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    7685 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    7686 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    7687 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    7688 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    7689 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    7690 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    7691 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    7692 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    7693 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    7694 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    7695 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    7696 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    7697 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    7698 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    7699 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    7700 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    7701 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    7702 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    7703 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    7704 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    7705 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    7706 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    7707 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    7708 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    7709 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    7710 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    7711 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    7712 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    7713 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    7714 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    7715 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    7716 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    7717 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    7718 3-265 
    7719 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    7720 90-519 
    7721 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    7722 127-270 
    7723 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    7724 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    7725 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    7726 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    7727 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    7728 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    7729 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    7730  
    7731 Non-standard residues in 6gsm #1 
    7732 --- 
    7733 7NO —
    7734 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    7735 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    7736 GCP — phosphomethylphosphonic acid guanylate ester 
    7737 MG — magnesium ion 
    7738 ZN — zinc ion 
    7739  
    7740 
    7741 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    7742 
    7743 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    7744 level 0.0673, step 2, values float32 
    7745 
    7746 > volume #2 region 183,191,137,270,278,248
    7747 
    7748 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    7749 
    7750 FYI: command is replacing existing command: "selectbox" 
    7751 executed select_box.py 
    7752 
    7753 > selectbox #1 inMap #2
    7754 
    7755 Selected 24244 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    7756 
    7757 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.cif
    7758 > #1 selectedOnly true
    7759 
    7760 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.mrc
    7761 > #2
    7762 
    7763 > close #1
    7764 
    7765 > close #2
    7766 
    7767 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.cif
    7768 
    7769 Summary of feedback from opening /scratch/cs-
    7770 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.cif 
    7771 --- 
    7772 warnings | Invalid residue range for struct_conf "HELX32": invalid chain "I",
    7773 near line 55763 
    7774 Invalid residue range for struct_conf "HELX33": invalid chain "I", near line
    7775 55764 
    7776 Invalid residue range for struct_conf "HELX34": invalid chain "I", near line
    7777 55765 
    7778 Invalid residue range for struct_conf "HELX35": invalid chain "I", near line
    7779 55766 
    7780 Invalid residue range for struct_conf "HELX36": invalid chain "I", near line
    7781 55767 
    7782 58 messages similar to the above omitted 
    7783 Invalid sheet range for struct_sheet_range "? 47": invalid chain "I", near
    7784 line 56031 
    7785 Invalid sheet range for struct_sheet_range "? 48": invalid chain "I", near
    7786 line 56032 
    7787 Invalid sheet range for struct_sheet_range "? 79": invalid chain "P", near
    7788 line 56063 
    7789 Invalid sheet range for struct_sheet_range "? 80": invalid chain "P", near
    7790 line 56064 
    7791 Invalid sheet range for struct_sheet_range "? 86": invalid chain "S", near
    7792 line 56070 
    7793 104 messages similar to the above omitted 
    7794 Atom N7 has no neighbors to form bonds with according to residue template for
    7795 G /2:325 
    7796 Atom O6 has no neighbors to form bonds with according to residue template for
    7797 G /2:325 
    7798 Atom O3' has no neighbors to form bonds with according to residue template for
    7799 C /2:338 
    7800 Atom N4 has no neighbors to form bonds with according to residue template for
    7801 C /2:341 
    7802 Atom C5 has no neighbors to form bonds with according to residue template for
    7803 C /2:341 
    7804 Atom O4' has no neighbors to form bonds with according to residue template for
    7805 G /2:391 
    7806 Atom OP1 has no neighbors to form bonds with according to residue template for
    7807 A /2:415 
    7808 Atom O3' has no neighbors to form bonds with according to residue template for
    7809 A /2:459 
    7810 Atom OP2 has no neighbors to form bonds with according to residue template for
    7811 G /2:479 
    7812 Atom O2' has no neighbors to form bonds with according to residue template for
    7813 U /2:481 
    7814 Atom N6 has no neighbors to form bonds with according to residue template for
    7815 A /2:525 
    7816 Atom O2' has no neighbors to form bonds with according to residue template for
    7817 G /2:809 
    7818 Atom O2' has no neighbors to form bonds with according to residue template for
    7819 U /2:888 
    7820 Atom O3' has no neighbors to form bonds with according to residue template for
    7821 A /2:925 
    7822 Atom O2' has no neighbors to form bonds with according to residue template for
    7823 C /2:926 
    7824 Atom O2' has no neighbors to form bonds with according to residue template for
    7825 A /2:928 
    7826 Atom OP1 has no neighbors to form bonds with according to residue template for
    7827 C /2:930 
    7828 Atom OP2 has no neighbors to form bonds with according to residue template for
    7829 C /2:930 
    7830 Atom OP2 has no neighbors to form bonds with according to residue template for
    7831 C /2:936 
    7832 Atom OP2 has no neighbors to form bonds with according to residue template for
    7833 G /2:937 
    7834 Atom OP2 has no neighbors to form bonds with according to residue template for
    7835 A /2:943 
    7836 Atom N7 has no neighbors to form bonds with according to residue template for
    7837 A /2:943 
    7838 Atom C6 has no neighbors to form bonds with according to residue template for
    7839 U /2:964 
    7840 Atom O3' has no neighbors to form bonds with according to residue template for
    7841 G /2:1001 
    7842 Atom O2' has no neighbors to form bonds with according to residue template for
    7843 G /2:1001 
    7844 Atom OP1 has no neighbors to form bonds with according to residue template for
    7845 A /2:1002 
    7846 Atom O2' has no neighbors to form bonds with according to residue template for
    7847 A /2:1002 
    7848 Atom OP2 has no neighbors to form bonds with according to residue template for
    7849 U /2:1016 
    7850 Atom O2' has no neighbors to form bonds with according to residue template for
    7851 U /2:1043 
    7852 Atom O3' has no neighbors to form bonds with according to residue template for
    7853 C /2:1071 
    7854 Atom OP1 has no neighbors to form bonds with according to residue template for
    7855 A /2:1150 
    7856 Atom O6 has no neighbors to form bonds with according to residue template for
    7857 G /2:1290 
    7858 Atom O2' has no neighbors to form bonds with according to residue template for
    7859 A /2:1318 
    7860 Atom OP1 has no neighbors to form bonds with according to residue template for
    7861 U /2:1421 
    7862 Atom O3' has no neighbors to form bonds with according to residue template for
    7863 U /2:1435 
    7864 Atom O2' has no neighbors to form bonds with according to residue template for
    7865 U /2:1435 
    7866 Atom OP1 has no neighbors to form bonds with according to residue template for
    7867 C /2:1623 
    7868 Atom C5' has no neighbors to form bonds with according to residue template for
    7869 C /2:1623 
    7870 Atom O3' has no neighbors to form bonds with according to residue template for
    7871 C /2:1623 
    7872 Atom O2 has no neighbors to form bonds with according to residue template for
    7873 C /2:1635 
    7874 Atom OP2 has no neighbors to form bonds with according to residue template for
    7875 U /2:1667 
    7876 Atom OP1 has no neighbors to form bonds with according to residue template for
    7877 A /3:29 
    7878 Atom O has no neighbors to form bonds with according to residue template for
    7879 LEU /C:159 
    7880 Atom N has no neighbors to form bonds with according to residue template for
    7881 LEU /C:195 
    7882 Atom O has no neighbors to form bonds with according to residue template for
    7883 VAL /C:198 
    7884 Atom CG1 has no neighbors to form bonds with according to residue template for
    7885 VAL /C:198 
    7886 Atom CG2 has no neighbors to form bonds with according to residue template for
    7887 VAL /C:198 
    7888 Atom CE has no neighbors to form bonds with according to residue template for
    7889 MET /D:105 
    7890 Atom N has no neighbors to form bonds with according to residue template for
    7891 TYR /D:120 
    7892 Atom N has no neighbors to form bonds with according to residue template for
    7893 ALA /D:153 
    7894 Atom CB has no neighbors to form bonds with according to residue template for
    7895 ALA /D:153 
    7896 Atom NH1 has no neighbors to form bonds with according to residue template for
    7897 ARG /D:173 
    7898 Atom N has no neighbors to form bonds with according to residue template for
    7899 SER /H:106 
    7900 Atom N has no neighbors to form bonds with according to residue template for
    7901 GLN /H:110 
    7902 Atom O has no neighbors to form bonds with according to residue template for
    7903 GLN /H:110 
    7904 Atom N has no neighbors to form bonds with according to residue template for
    7905 LYS /J:65 
    7906 Atom O has no neighbors to form bonds with according to residue template for
    7907 LEU /J:93 
    7908 Atom N has no neighbors to form bonds with according to residue template for
    7909 ALA /J:177 
    7910 Atom CB has no neighbors to form bonds with according to residue template for
    7911 ALA /J:177 
    7912 Atom N has no neighbors to form bonds with according to residue template for
    7913 PHE /K:54 
    7914 Atom CE1 has no neighbors to form bonds with according to residue template for
    7915 PHE /K:54 
    7916 Atom NE has no neighbors to form bonds with according to residue template for
    7917 ARG /L:116 
    7918 Atom NH2 has no neighbors to form bonds with according to residue template for
    7919 ARG /L:116 
    7920 Atom O has no neighbors to form bonds with according to residue template for
    7921 VAL /L:125 
    7922 Atom C has no neighbors to form bonds with according to residue template for
    7923 SER /L:132 
    7924 Atom N has no neighbors to form bonds with according to residue template for
    7925 ARG /L:136 
    7926 Atom CA has no neighbors to form bonds with according to residue template for
    7927 GLY /L:147 
    7928 Atom O has no neighbors to form bonds with according to residue template for
    7929 GLY /L:147 
    7930 Atom O has no neighbors to form bonds with according to residue template for
    7931 ILE /N:116 
    7932 Atom O has no neighbors to form bonds with according to residue template for
    7933 THR /O:89 
    7934 Atom N has no neighbors to form bonds with according to residue template for
    7935 SER /O:125 
    7936 Atom OG has no neighbors to form bonds with according to residue template for
    7937 SER /O:125 
    7938 Atom N has no neighbors to form bonds with according to residue template for
    7939 GLN /W:39 
    7940 Atom N has no neighbors to form bonds with according to residue template for
    7941 MET /W:41 
    7942 Atom CD1 has no neighbors to form bonds with according to residue template for
    7943 LEU /W:69 
    7944 Atom CD2 has no neighbors to form bonds with according to residue template for
    7945 LEU /W:69 
    7946 Atom O has no neighbors to form bonds with according to residue template for
    7947 ASN /Y:31 
    7948 Atom N has no neighbors to form bonds with according to residue template for
    7949 ASN /a:25 
    7950 Atom C has no neighbors to form bonds with according to residue template for
    7951 ASN /a:25 
    7952 Atom CB has no neighbors to form bonds with according to residue template for
    7953 ASN /a:25 
    7954 Atom ND2 has no neighbors to form bonds with according to residue template for
    7955 ASN /a:25 
    7956 Atom N has no neighbors to form bonds with according to residue template for
    7957 MET /a:39 
    7958 Atom N has no neighbors to form bonds with according to residue template for
    7959 GLN /a:99 
    7960 Atom N has no neighbors to form bonds with according to residue template for
    7961 VAL /e:47 
    7962 Atom CG1 has no neighbors to form bonds with according to residue template for
    7963 VAL /e:47 
    7964 Atom O has no neighbors to form bonds with according to residue template for
    7965 ARG /m:36 
    7966 Atom O has no neighbors to form bonds with according to residue template for
    7967 THR /m:38 
    7968 Atom OG1 has no neighbors to form bonds with according to residue template for
    7969 THR /m:38 
    7970 Atom OE2 has no neighbors to form bonds with according to residue template for
    7971 GLU /m:47 
    7972 Atom OD1 has no neighbors to form bonds with according to residue template for
    7973 ASN /m:67 
    7974 Atom O has no neighbors to form bonds with according to residue template for
    7975 ILE /m:103 
    7976 Atom O has no neighbors to form bonds with according to residue template for
    7977 PRO /p:88 
    7978 Atom N has no neighbors to form bonds with according to residue template for
    7979 ILE /p:116 
    7980 Atom CD1 has no neighbors to form bonds with according to residue template for
    7981 ILE /p:116 
    7982 Atom N has no neighbors to form bonds with according to residue template for
    7983 ASP /p:380 
    7984 Atom N has no neighbors to form bonds with according to residue template for
    7985 GLN /p:444 
    7986 Atom O has no neighbors to form bonds with according to residue template for
    7987 GLN /p:444 
    7988 Atom N has no neighbors to form bonds with according to residue template for
    7989 GLU /p:455 
    7990 Atom CD2 has no neighbors to form bonds with according to residue template for
    7991 LEU /p:468 
    7992 Atom OD1 has no neighbors to form bonds with according to residue template for
    7993 ASN /p:592 
    7994 Atom ND2 has no neighbors to form bonds with according to residue template for
    7995 ASN /p:592 
    7996 Atom N has no neighbors to form bonds with according to residue template for
    7997 VAL /p:595 
    7998 Atom CG1 has no neighbors to form bonds with according to residue template for
    7999 VAL /p:595 
    8000  
    8001 Chain information for 0057_6gsm_X.cif #1 
    8002 --- 
    8003 Chain | Description 
    8004 2 | 18S ribosomal RNA 
    8005 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    8006 B | 40S ribosomal protein S1 
    8007 C | KLLA0F09812p 
    8008 D | KLLA0D08305p 
    8009 E | 40S ribosomal protein S4 
    8010 H | 40S ribosomal protein S7 
    8011 I | 40S ribosomal protein S8 
    8012 J | KLLA0E23673p 
    8013 K | KLLA0B08173p 
    8014 L | KLLA0A10483p 
    8015 N | KLLA0F18040p 
    8016 O | 40S ribosomal protein S14 
    8017 V | 40S ribosomal protein S21 
    8018 W | 40S ribosomal protein S22 
    8019 X | KLLA0B11231p 
    8020 Y | 40S ribosomal protein S24 
    8021 a | 40S ribosomal protein S26 
    8022 b | 40S ribosomal protein S27 
    8023 e | 40S ribosomal protein S30 
    8024 h | 60S ribosomal protein L41-A 
    8025 i | Eukaryotic translation initiation factor 1A 
    8026 l | Eukaryotic translation initiation factor 2 subunit beta 
    8027 m | Eukaryotic translation initiation factor eIF-1 
    8028 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    8029 translation initiation factor 3 subunit A,eIF3a 
    8030 p | Eukaryotic translation initiation factor 3 subunit B 
    8031 q | Eukaryotic translation initiation factor 3 subunit C 
    8032  
    8033 
    8034 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X.mrc
    8035 
    8036 Opened 0057_6gsm_X.mrc as #2, grid size 88,88,112, pixel 1, shown at level
    8037 0.153, step 1, values float32 
    8038 
    8039 > fitmap #1 inMap #2
    8040 
    8041 Fit molecule 0057_6gsm_X.cif (#1) to map 0057_6gsm_X.mrc (#2) using 24244
    8042 atoms 
    8043 average map value = 0.08409, steps = 40 
    8044 shifted from previous position = 0.373 
    8045 rotated from previous position = 0.099 degrees 
    8046 atoms outside contour = 23533, contour level = 0.15287 
    8047  
    8048 Position of 0057_6gsm_X.cif (#1) relative to 0057_6gsm_X.mrc (#2) coordinates: 
    8049 Matrix rotation and translation 
    8050 0.99999908 0.00000025 0.00135501 -0.57857011 
    8051 -0.00000170 0.99999943 0.00107085 -0.40116203 
    8052 -0.00135501 -0.00107086 0.99999851 0.45634782 
    8053 Axis -0.62003964 0.78457028 -0.00056271 
    8054 Axis point 336.35507218 0.00000000 407.19792982 
    8055 Rotation angle (degrees) 0.09895421 
    8056 Shift along axis 0.04373981 
    8057  
    8058 
    8059 > save /scratch/cs-
    8060 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_X_fitted.cif #1
    8061 
    8062 > close #1
    8063 
    8064 > close #2
    8065 
    8066 > open 6gsm
    8067 
    8068 6gsm title: 
    8069 Structure of a partial yeast 48S preinitiation complex in open conformation.
    8070 [more info...] 
    8071  
    8072 Chain information for 6gsm #1 
    8073 --- 
    8074 Chain | Description | UniProt 
    8075 1 | Met-tRNAi | 
    8076 2 | 18S ribosomal RNA | 
    8077 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    8078 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    8079 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    8080 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    8081 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    8082 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    8083 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    8084 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    8085 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    8086 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    8087 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    8088 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    8089 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    8090 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    8091 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    8092 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    8093 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    8094 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    8095 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    8096 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    8097 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    8098 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    8099 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    8100 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    8101 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    8102 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    8103 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    8104 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    8105 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    8106 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    8107 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    8108 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    8109 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    8110 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    8111 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    8112 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    8113 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    8114 3-265 
    8115 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    8116 90-519 
    8117 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    8118 127-270 
    8119 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    8120 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    8121 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    8122 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    8123 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    8124 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    8125 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    8126  
    8127 Non-standard residues in 6gsm #1 
    8128 --- 
    8129 7NO —
    8130 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    8131 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    8132 GCP — phosphomethylphosphonic acid guanylate ester 
    8133 MG — magnesium ion 
    8134 ZN — zinc ion 
    8135  
    8136 
    8137 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    8138 
    8139 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    8140 level 0.0673, step 2, values float32 
    8141 
    8142 > volume #2 region 192,109,163,319,204,242
    8143 
    8144 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    8145 
    8146 FYI: command is replacing existing command: "selectbox" 
    8147 executed select_box.py 
    8148 
    8149 > selectbox #1 inMap #2
    8150 
    8151 Selected 18608 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    8152 
    8153 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.cif
    8154 > #1 selectedOnly true
    8155 
    8156 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.mrc
    8157 > #2
    8158 
    8159 > close #1
    8160 
    8161 > close #2
    8162 
    8163 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.cif
    8164 
    8165 Summary of feedback from opening /scratch/cs-
    8166 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.cif 
    8167 --- 
    8168 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    8169 near line 49791 
    8170 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    8171 49792 
    8172 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    8173 49793 
    8174 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    8175 49794 
    8176 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    8177 49795 
    8178 111 messages similar to the above omitted 
    8179 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    8180 50044 
    8181 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    8182 50045 
    8183 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    8184 50046 
    8185 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    8186 50047 
    8187 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    8188 50048 
    8189 131 messages similar to the above omitted 
    8190 Atom OP1 has no neighbors to form bonds with according to residue template for
    8191 U /2:577 
    8192 Atom OP2 has no neighbors to form bonds with according to residue template for
    8193 U /2:577 
    8194 Atom O2' has no neighbors to form bonds with according to residue template for
    8195 U /2:577 
    8196 Atom C5' has no neighbors to form bonds with according to residue template for
    8197 U /2:910 
    8198 Atom OP2 has no neighbors to form bonds with according to residue template for
    8199 A /2:1012 
    8200 Atom O4' has no neighbors to form bonds with according to residue template for
    8201 U /2:1181 
    8202 Atom OP1 has no neighbors to form bonds with according to residue template for
    8203 G /2:1270 
    8204 Atom C5' has no neighbors to form bonds with according to residue template for
    8205 G /2:1270 
    8206 Atom O3' has no neighbors to form bonds with according to residue template for
    8207 A /2:1286 
    8208 Atom O2' has no neighbors to form bonds with according to residue template for
    8209 A /2:1286 
    8210 Atom OP1 has no neighbors to form bonds with according to residue template for
    8211 G /2:1287 
    8212 Atom O2' has no neighbors to form bonds with according to residue template for
    8213 G /2:1287 
    8214 Atom O2' has no neighbors to form bonds with according to residue template for
    8215 U /2:1306 
    8216 Atom OP1 has no neighbors to form bonds with according to residue template for
    8217 C /2:1308 
    8218 Atom OP2 has no neighbors to form bonds with according to residue template for
    8219 C /2:1308 
    8220 Atom O2' has no neighbors to form bonds with according to residue template for
    8221 U /2:1435 
    8222 Atom O2' has no neighbors to form bonds with according to residue template for
    8223 G /2:1436 
    8224 Atom OP2 has no neighbors to form bonds with according to residue template for
    8225 U /2:1526 
    8226 Atom C4' has no neighbors to form bonds with according to residue template for
    8227 U /2:1556 
    8228 Atom O3' has no neighbors to form bonds with according to residue template for
    8229 U /2:1556 
    8230 Atom N4 has no neighbors to form bonds with according to residue template for
    8231 C /2:1589 
    8232 Atom O2' has no neighbors to form bonds with according to residue template for
    8233 G /2:1592 
    8234 Atom OP2 has no neighbors to form bonds with according to residue template for
    8235 U /2:1596 
    8236 Atom O5' has no neighbors to form bonds with according to residue template for
    8237 U /2:1596 
    8238 Atom O4' has no neighbors to form bonds with according to residue template for
    8239 U /2:1602 
    8240 Atom C8 has no neighbors to form bonds with according to residue template for
    8241 G /2:1784 
    8242 Atom CD has no neighbors to form bonds with according to residue template for
    8243 LYS /C:93 
    8244 Atom NZ has no neighbors to form bonds with according to residue template for
    8245 LYS /C:93 
    8246 Atom N has no neighbors to form bonds with according to residue template for
    8247 ARG /D:143 
    8248 Atom C has no neighbors to form bonds with according to residue template for
    8249 ARG /D:143 
    8250 Atom CG1 has no neighbors to form bonds with according to residue template for
    8251 VAL /F:55 
    8252 Atom CB has no neighbors to form bonds with according to residue template for
    8253 ARG /F:94 
    8254 Atom N has no neighbors to form bonds with according to residue template for
    8255 ASN /F:130 
    8256 Atom N has no neighbors to form bonds with according to residue template for
    8257 LEU /F:132 
    8258 Atom NE2 has no neighbors to form bonds with according to residue template for
    8259 GLN /F:133 
    8260 Atom N has no neighbors to form bonds with according to residue template for
    8261 LYS /O:92 
    8262 Atom O has no neighbors to form bonds with according to residue template for
    8263 THR /O:93 
    8264 Atom CB has no neighbors to form bonds with according to residue template for
    8265 VAL /S:52 
    8266 Atom O has no neighbors to form bonds with according to residue template for
    8267 LEU /S:66 
    8268 Atom N has no neighbors to form bonds with according to residue template for
    8269 ALA /S:83 
    8270 Atom CE3 has no neighbors to form bonds with according to residue template for
    8271 TRP /S:84 
    8272 Atom CD1 has no neighbors to form bonds with according to residue template for
    8273 PHE /S:128 
    8274 Atom CB has no neighbors to form bonds with according to residue template for
    8275 PRO /T:31 
    8276 Atom N has no neighbors to form bonds with according to residue template for
    8277 PHE /T:54 
    8278 Atom CB has no neighbors to form bonds with according to residue template for
    8279 ARG /Z:49 
    8280 Atom CD has no neighbors to form bonds with according to residue template for
    8281 ARG /Z:49 
    8282 Atom O has no neighbors to form bonds with according to residue template for
    8283 GLU /Z:84 
    8284 Atom N has no neighbors to form bonds with according to residue template for
    8285 VAL /Z:92 
    8286 Atom CG2 has no neighbors to form bonds with according to residue template for
    8287 VAL /Z:92 
    8288 Atom NH1 has no neighbors to form bonds with according to residue template for
    8289 ARG /a:89 
    8290 Atom OE2 has no neighbors to form bonds with according to residue template for
    8291 GLU /c:31 
    8292 Atom OE1 has no neighbors to form bonds with according to residue template for
    8293 GLU /c:34 
    8294 Atom OE2 has no neighbors to form bonds with according to residue template for
    8295 GLU /c:34 
    8296 Atom N has no neighbors to form bonds with according to residue template for
    8297 TYR /i:28 
    8298 Atom N has no neighbors to form bonds with according to residue template for
    8299 GLU /i:30 
    8300 Atom OE1 has no neighbors to form bonds with according to residue template for
    8301 GLU /i:30 
    8302 Atom O has no neighbors to form bonds with according to residue template for
    8303 SER /i:50 
    8304 Atom N has no neighbors to form bonds with according to residue template for
    8305 GLN /k:175 
    8306 Atom N has no neighbors to form bonds with according to residue template for
    8307 LEU /k:260 
    8308 Atom N has no neighbors to form bonds with according to residue template for
    8309 MET /k:310 
    8310 Atom N has no neighbors to form bonds with according to residue template for
    8311 GLU /k:457 
    8312 Atom N has no neighbors to form bonds with according to residue template for
    8313 ALA /k:477 
    8314 Atom OH has no neighbors to form bonds with according to residue template for
    8315 TYR /l:131 
    8316 Atom ND1 has no neighbors to form bonds with according to residue template for
    8317 HIS /p:145 
    8318 Atom O has no neighbors to form bonds with according to residue template for
    8319 LEU /p:149 
    8320 Atom O has no neighbors to form bonds with according to residue template for
    8321 ASP /q:97 
    8322  
    8323 Chain information for 0057_6gsm_1.cif #1 
    8324 --- 
    8325 Chain | Description 
    8326 1 | Met-tRNAi 
    8327 2 | 18S ribosomal RNA 
    8328 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    8329 B | 40S ribosomal protein S1 
    8330 C | KLLA0F09812p 
    8331 D | KLLA0D08305p 
    8332 F | KLLA0D10659p 
    8333 O | 40S ribosomal protein S14 
    8334 P | KLLA0F07843p 
    8335 Q | 40S ribosomal protein S16 
    8336 S | KLLA0B01562p 
    8337 T | KLLA0A07194p 
    8338 U | KLLA0F25542p 
    8339 Z | KLLA0B06182p 
    8340 a | 40S ribosomal protein S26 
    8341 c | 40S ribosomal protein S28 
    8342 d | 40S ribosomal protein S29 
    8343 i | Eukaryotic translation initiation factor 1A 
    8344 j | Eukaryotic translation initiation factor 2 subunit alpha 
    8345 k | Eukaryotic translation initiation factor 2 subunit gamma 
    8346 l | Eukaryotic translation initiation factor 2 subunit beta 
    8347 m | Eukaryotic translation initiation factor eIF-1 
    8348 p | Eukaryotic translation initiation factor 3 subunit B 
    8349 q | Eukaryotic translation initiation factor 3 subunit C 
    8350  
    8351 
    8352 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1.mrc
    8353 
    8354 Opened 0057_6gsm_1.mrc as #2, grid size 128,96,80, pixel 1, shown at level
    8355 0.126, step 1, values float32 
    8356 
    8357 > fitmap #1 inMap #2
    8358 
    8359 Fit molecule 0057_6gsm_1.cif (#1) to map 0057_6gsm_1.mrc (#2) using 18608
    8360 atoms 
    8361 average map value = 0.0684, steps = 64 
    8362 shifted from previous position = 0.53 
    8363 rotated from previous position = 0.158 degrees 
    8364 atoms outside contour = 17745, contour level = 0.126 
    8365  
    8366 Position of 0057_6gsm_1.cif (#1) relative to 0057_6gsm_1.mrc (#2) coordinates: 
    8367 Matrix rotation and translation 
    8368 0.99999827 0.00173579 0.00066214 -0.84382811 
    8369 -0.00173443 0.99999640 -0.00204519 0.72064419 
    8370 -0.00066568 0.00204403 0.99999769 -0.47427235 
    8371 Axis 0.74010988 0.24032262 -0.62807835 
    8372 Axis point 0.00000000 279.59960222 369.90215785 
    8373 Rotation angle (degrees) 0.15828409 
    8374 Shift along axis -0.15345823 
    8375  
    8376 
    8377 > save /scratch/cs-
    8378 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_1_fitted.cif #1
    8379 
    8380 > close #1
    8381 
    8382 > close #2
    8383 
    8384 > open 6gsm
    8385 
    8386 6gsm title: 
    8387 Structure of a partial yeast 48S preinitiation complex in open conformation.
    8388 [more info...] 
    8389  
    8390 Chain information for 6gsm #1 
    8391 --- 
    8392 Chain | Description | UniProt 
    8393 1 | Met-tRNAi | 
    8394 2 | 18S ribosomal RNA | 
    8395 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    8396 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    8397 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    8398 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    8399 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    8400 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    8401 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    8402 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    8403 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    8404 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    8405 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    8406 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    8407 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    8408 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    8409 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    8410 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    8411 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    8412 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    8413 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    8414 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    8415 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    8416 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    8417 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    8418 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    8419 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    8420 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    8421 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    8422 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    8423 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    8424 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    8425 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    8426 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    8427 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    8428 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    8429 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    8430 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    8431 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    8432 3-265 
    8433 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    8434 90-519 
    8435 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    8436 127-270 
    8437 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    8438 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    8439 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    8440 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    8441 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    8442 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    8443 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    8444  
    8445 Non-standard residues in 6gsm #1 
    8446 --- 
    8447 7NO —
    8448 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    8449 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    8450 GCP — phosphomethylphosphonic acid guanylate ester 
    8451 MG — magnesium ion 
    8452 ZN — zinc ion 
    8453  
    8454 
    8455 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    8456 
    8457 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    8458 level 0.0673, step 2, values float32 
    8459 
    8460 > volume #2 region 164,80,175,251,151,246
    8461 
    8462 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    8463 
    8464 FYI: command is replacing existing command: "selectbox" 
    8465 executed select_box.py 
    8466 
    8467 > selectbox #1 inMap #2
    8468 
    8469 Selected 6379 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    8470 
    8471 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.cif
    8472 > #1 selectedOnly true
    8473 
    8474 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.mrc
    8475 > #2
    8476 
    8477 > close #1
    8478 
    8479 > close #2
    8480 
    8481 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.cif
    8482 
    8483 Summary of feedback from opening /scratch/cs-
    8484 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.cif 
    8485 --- 
    8486 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    8487 near line 37310 
    8488 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    8489 37311 
    8490 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    8491 37312 
    8492 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    8493 37313 
    8494 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    8495 37314 
    8496 197 messages similar to the above omitted 
    8497 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    8498 37563 
    8499 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    8500 37564 
    8501 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    8502 37565 
    8503 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    8504 37566 
    8505 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    8506 37567 
    8507 227 messages similar to the above omitted 
    8508 Atom O3' has no neighbors to form bonds with according to residue template for
    8509 G /1:43 
    8510 Atom O3' has no neighbors to form bonds with according to residue template for
    8511 A /1:44 
    8512 Atom O3' has no neighbors to form bonds with according to residue template for
    8513 H2U /1:47 
    8514 Atom O3' has no neighbors to form bonds with according to residue template for
    8515 G /2:1166 
    8516 Atom O3' has no neighbors to form bonds with according to residue template for
    8517 G /2:1169 
    8518 Atom O2' has no neighbors to form bonds with according to residue template for
    8519 G /2:1348 
    8520 Atom N2 has no neighbors to form bonds with according to residue template for
    8521 G /2:1357 
    8522 Atom N3 has no neighbors to form bonds with according to residue template for
    8523 G /2:1357 
    8524 Atom O2 has no neighbors to form bonds with according to residue template for
    8525 C /2:1358 
    8526 Atom O3' has no neighbors to form bonds with according to residue template for
    8527 C /2:1364 
    8528 Atom O2 has no neighbors to form bonds with according to residue template for
    8529 C /2:1365 
    8530 Atom O2' has no neighbors to form bonds with according to residue template for
    8531 G /2:1367 
    8532 Atom O2 has no neighbors to form bonds with according to residue template for
    8533 C /2:1377 
    8534 Atom OP1 has no neighbors to form bonds with according to residue template for
    8535 C /2:1465 
    8536 Atom OP2 has no neighbors to form bonds with according to residue template for
    8537 C /2:1483 
    8538 Atom O4' has no neighbors to form bonds with according to residue template for
    8539 U /2:1542 
    8540 Atom O3' has no neighbors to form bonds with according to residue template for
    8541 U /2:1564 
    8542 Atom OD1 has no neighbors to form bonds with according to residue template for
    8543 ASP /F:62 
    8544 Atom N has no neighbors to form bonds with according to residue template for
    8545 ARG /F:145 
    8546 Atom CD2 has no neighbors to form bonds with according to residue template for
    8547 LEU /Q:28 
    8548 Atom O has no neighbors to form bonds with according to residue template for
    8549 ASP /Q:120 
    8550 Atom NH1 has no neighbors to form bonds with according to residue template for
    8551 ARG /S:41 
    8552 Atom N has no neighbors to form bonds with according to residue template for
    8553 ARG /S:68 
    8554 Atom N has no neighbors to form bonds with according to residue template for
    8555 VAL /S:70 
    8556 Atom N has no neighbors to form bonds with according to residue template for
    8557 ARG /S:143 
    8558 Atom CG1 has no neighbors to form bonds with according to residue template for
    8559 VAL /T:34 
    8560 Atom N has no neighbors to form bonds with according to residue template for
    8561 THR /T:39 
    8562 Atom N has no neighbors to form bonds with according to residue template for
    8563 GLN /T:70 
    8564 Atom O has no neighbors to form bonds with according to residue template for
    8565 GLN /T:70 
    8566 Atom CD2 has no neighbors to form bonds with according to residue template for
    8567 LEU /T:76 
    8568 Atom OD1 has no neighbors to form bonds with according to residue template for
    8569 ASP /T:95 
    8570 Atom N has no neighbors to form bonds with according to residue template for
    8571 VAL /T:114 
    8572 Atom OG has no neighbors to form bonds with according to residue template for
    8573 SER /T:125 
    8574 Atom CG2 has no neighbors to form bonds with according to residue template for
    8575 ILE /c:53 
    8576 Atom CD1 has no neighbors to form bonds with according to residue template for
    8577 ILE /c:53 
    8578 Atom N has no neighbors to form bonds with according to residue template for
    8579 ILE /j:27 
    8580 Atom O has no neighbors to form bonds with according to residue template for
    8581 ILE /j:27 
    8582 Atom CG has no neighbors to form bonds with according to residue template for
    8583 LYS /j:67 
    8584 Atom CG1 has no neighbors to form bonds with according to residue template for
    8585 VAL /j:73 
    8586 Atom CG2 has no neighbors to form bonds with according to residue template for
    8587 VAL /j:73 
    8588 Atom O has no neighbors to form bonds with according to residue template for
    8589 ASP /j:84 
    8590  
    8591 Chain information for 0057_6gsm_Z.cif #1 
    8592 --- 
    8593 Chain | Description 
    8594 1 | Met-tRNAi 
    8595 2 | 18S ribosomal RNA 
    8596 F | KLLA0D10659p 
    8597 Q | 40S ribosomal protein S16 
    8598 S | KLLA0B01562p 
    8599 T | KLLA0A07194p 
    8600 Z | KLLA0B06182p 
    8601 c | 40S ribosomal protein S28 
    8602 j | Eukaryotic translation initiation factor 2 subunit alpha 
    8603  
    8604 
    8605 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z.mrc
    8606 
    8607 Opened 0057_6gsm_Z.mrc as #2, grid size 88,72,72, pixel 1, shown at level
    8608 0.12, step 1, values float32 
    8609 
    8610 > fitmap #1 inMap #2
    8611 
    8612 Fit molecule 0057_6gsm_Z.cif (#1) to map 0057_6gsm_Z.mrc (#2) using 6379 atoms 
    8613 average map value = 0.07059, steps = 52 
    8614 shifted from previous position = 0.758 
    8615 rotated from previous position = 0.382 degrees 
    8616 atoms outside contour = 6034, contour level = 0.1198 
    8617  
    8618 Position of 0057_6gsm_Z.cif (#1) relative to 0057_6gsm_Z.mrc (#2) coordinates: 
    8619 Matrix rotation and translation 
    8620 0.99999732 -0.00041871 0.00227831 -0.60321734 
    8621 0.00043294 0.99998038 -0.00624984 1.37470602 
    8622 -0.00227564 0.00625081 0.99997787 -1.05746611 
    8623 Axis 0.93767464 0.34159226 0.06388265 
    8624 Axis point 0.00000000 168.30919662 228.37113330 
    8625 Rotation angle (degrees) 0.38192337 
    8626 Shift along axis -0.16358642 
    8627  
    8628 
    8629 > save /scratch/cs-
    8630 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_Z_fitted.cif #1
    8631 
    8632 > close #1
    8633 
    8634 > close #2
    8635 
    8636 > open 6gsm
    8637 
    8638 6gsm title: 
    8639 Structure of a partial yeast 48S preinitiation complex in open conformation.
    8640 [more info...] 
    8641  
    8642 Chain information for 6gsm #1 
    8643 --- 
    8644 Chain | Description | UniProt 
    8645 1 | Met-tRNAi | 
    8646 2 | 18S ribosomal RNA | 
    8647 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    8648 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    8649 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    8650 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    8651 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    8652 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    8653 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    8654 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    8655 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    8656 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    8657 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    8658 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    8659 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    8660 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    8661 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    8662 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    8663 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    8664 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    8665 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    8666 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    8667 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    8668 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    8669 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    8670 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    8671 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    8672 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    8673 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    8674 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    8675 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    8676 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    8677 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    8678 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    8679 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    8680 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    8681 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    8682 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    8683 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    8684 3-265 
    8685 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    8686 90-519 
    8687 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    8688 127-270 
    8689 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    8690 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    8691 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    8692 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    8693 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    8694 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    8695 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    8696  
    8697 Non-standard residues in 6gsm #1 
    8698 --- 
    8699 7NO —
    8700 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    8701 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    8702 GCP — phosphomethylphosphonic acid guanylate ester 
    8703 MG — magnesium ion 
    8704 ZN — zinc ion 
    8705  
    8706 
    8707 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    8708 
    8709 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    8710 level 0.0673, step 2, values float32 
    8711 
    8712 > volume #2 region 136,215,208,223,310,311
    8713 
    8714 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    8715 
    8716 FYI: command is replacing existing command: "selectbox" 
    8717 executed select_box.py 
    8718 
    8719 > selectbox #1 inMap #2
    8720 
    8721 Selected 14921 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    8722 
    8723 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.cif
    8724 > #1 selectedOnly true
    8725 
    8726 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.mrc
    8727 > #2
    8728 
    8729 > close #1
    8730 
    8731 > close #2
    8732 
    8733 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.cif
    8734 
    8735 Summary of feedback from opening /scratch/cs-
    8736 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.cif 
    8737 --- 
    8738 warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
    8739 near line 46024 
    8740 Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
    8741 46025 
    8742 Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
    8743 46026 
    8744 Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
    8745 46027 
    8746 Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
    8747 46028 
    8748 132 messages similar to the above omitted 
    8749 Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
    8750 line 46281 
    8751 Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
    8752 line 46282 
    8753 Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
    8754 line 46283 
    8755 Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
    8756 line 46284 
    8757 Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
    8758 line 46285 
    8759 179 messages similar to the above omitted 
    8760 Atom O3' has no neighbors to form bonds with according to residue template for
    8761 C /2:14 
    8762 Atom O2 has no neighbors to form bonds with according to residue template for
    8763 C /2:14 
    8764 Atom OP1 has no neighbors to form bonds with according to residue template for
    8765 U /2:15 
    8766 Atom O2' has no neighbors to form bonds with according to residue template for
    8767 G /2:213 
    8768 Atom O3' has no neighbors to form bonds with according to residue template for
    8769 C /2:307 
    8770 Atom O2' has no neighbors to form bonds with according to residue template for
    8771 G /2:370 
    8772 Atom N2 has no neighbors to form bonds with according to residue template for
    8773 G /2:370 
    8774 Atom OP1 has no neighbors to form bonds with according to residue template for
    8775 G /2:371 
    8776 Atom O3' has no neighbors to form bonds with according to residue template for
    8777 G /2:372 
    8778 Atom O3' has no neighbors to form bonds with according to residue template for
    8779 U /2:628 
    8780 Atom OP1 has no neighbors to form bonds with according to residue template for
    8781 U /2:718 
    8782 Atom N6 has no neighbors to form bonds with according to residue template for
    8783 A /2:728 
    8784 Atom OP1 has no neighbors to form bonds with according to residue template for
    8785 U /2:793 
    8786 Atom C6 has no neighbors to form bonds with according to residue template for
    8787 U /2:840 
    8788 Atom N4 has no neighbors to form bonds with according to residue template for
    8789 C /2:841 
    8790 Atom N7 has no neighbors to form bonds with according to residue template for
    8791 G /2:877 
    8792 Atom O6 has no neighbors to form bonds with according to residue template for
    8793 G /2:877 
    8794 Atom N2 has no neighbors to form bonds with according to residue template for
    8795 G /2:935 
    8796 Atom OP2 has no neighbors to form bonds with according to residue template for
    8797 G /2:941 
    8798 Atom C1' has no neighbors to form bonds with according to residue template for
    8799 C /2:942 
    8800 Atom OP2 has no neighbors to form bonds with according to residue template for
    8801 G /2:947 
    8802 Atom O5' has no neighbors to form bonds with according to residue template for
    8803 G /2:947 
    8804 Atom O3' has no neighbors to form bonds with according to residue template for
    8805 U /2:1060 
    8806 Atom C8 has no neighbors to form bonds with according to residue template for
    8807 G /2:1296 
    8808 Atom O has no neighbors to form bonds with according to residue template for
    8809 ILE /A:133 
    8810 Atom CG2 has no neighbors to form bonds with according to residue template for
    8811 ILE /A:133 
    8812 Atom N has no neighbors to form bonds with according to residue template for
    8813 ALA /A:145 
    8814 Atom O has no neighbors to form bonds with according to residue template for
    8815 ALA /A:145 
    8816 Atom CA has no neighbors to form bonds with according to residue template for
    8817 VAL /A:181 
    8818 Atom O has no neighbors to form bonds with according to residue template for
    8819 VAL /A:181 
    8820 Atom NE has no neighbors to form bonds with according to residue template for
    8821 ARG /A:185 
    8822 Atom CB has no neighbors to form bonds with according to residue template for
    8823 ARG /C:173 
    8824 Atom O has no neighbors to form bonds with according to residue template for
    8825 VAL /C:221 
    8826 Atom N has no neighbors to form bonds with according to residue template for
    8827 TYR /C:251 
    8828 Atom C has no neighbors to form bonds with according to residue template for
    8829 TYR /C:251 
    8830 Atom N has no neighbors to form bonds with according to residue template for
    8831 ARG /E:233 
    8832 Atom CB has no neighbors to form bonds with according to residue template for
    8833 ARG /E:233 
    8834 Atom N has no neighbors to form bonds with according to residue template for
    8835 LYS /L:46 
    8836 Atom CG1 has no neighbors to form bonds with according to residue template for
    8837 VAL /L:125 
    8838 Atom CG has no neighbors to form bonds with according to residue template for
    8839 GLU /V:2 
    8840 Atom OE1 has no neighbors to form bonds with according to residue template for
    8841 GLU /V:2 
    8842 Atom C has no neighbors to form bonds with according to residue template for
    8843 ALA /X:25 
    8844 Atom CB has no neighbors to form bonds with according to residue template for
    8845 ALA /X:25 
    8846 Atom NH1 has no neighbors to form bonds with according to residue template for
    8847 ARG /a:15 
    8848 Atom O has no neighbors to form bonds with according to residue template for
    8849 PHE /q:254 
    8850 Atom O has no neighbors to form bonds with according to residue template for
    8851 PHE /q:255 
    8852 Atom O has no neighbors to form bonds with according to residue template for
    8853 VAL /q:270 
    8854 Atom OE2 has no neighbors to form bonds with according to residue template for
    8855 GLU /q:281 
    8856 Atom OE2 has no neighbors to form bonds with according to residue template for
    8857 GLU /q:287 
    8858 Atom NH1 has no neighbors to form bonds with according to residue template for
    8859 ARG /q:303 
    8860 Atom N has no neighbors to form bonds with according to residue template for
    8861 GLN /q:334 
    8862 Atom CB has no neighbors to form bonds with according to residue template for
    8863 GLN /q:334 
    8864 Atom NE2 has no neighbors to form bonds with according to residue template for
    8865 GLN /q:334 
    8866 Atom N has no neighbors to form bonds with according to residue template for
    8867 THR /q:335 
    8868 Atom N has no neighbors to form bonds with according to residue template for
    8869 LYS /q:443 
    8870 Atom CG has no neighbors to form bonds with according to residue template for
    8871 LYS /q:443 
    8872 Atom CE has no neighbors to form bonds with according to residue template for
    8873 LYS /q:443 
    8874 Atom CD2 has no neighbors to form bonds with according to residue template for
    8875 LEU /q:486 
    8876 Atom CG2 has no neighbors to form bonds with according to residue template for
    8877 THR /q:488 
    8878 Atom CG2 has no neighbors to form bonds with according to residue template for
    8879 ILE /q:560 
    8880 Atom CD1 has no neighbors to form bonds with according to residue template for
    8881 LEU /q:576 
    8882 Atom N has no neighbors to form bonds with according to residue template for
    8883 GLN /q:583 
    8884 Atom O has no neighbors to form bonds with according to residue template for
    8885 SER /q:592 
    8886 Atom OG has no neighbors to form bonds with according to residue template for
    8887 SER /q:592 
    8888 Atom CA has no neighbors to form bonds with according to residue template for
    8889 SER /q:593 
    8890 Atom OG has no neighbors to form bonds with according to residue template for
    8891 SER /q:593 
    8892 Atom N has no neighbors to form bonds with according to residue template for
    8893 THR /q:634 
    8894 Atom C has no neighbors to form bonds with according to residue template for
    8895 THR /q:634 
    8896 Atom N has no neighbors to form bonds with according to residue template for
    8897 ARG /q:654 
    8898  
    8899 Chain information for 0057_6gsm_H.cif #1 
    8900 --- 
    8901 Chain | Description 
    8902 2 | 18S ribosomal RNA 
    8903 A | 40S ribosomal protein S0 
    8904 B | 40S ribosomal protein S1 
    8905 C | KLLA0F09812p 
    8906 E | 40S ribosomal protein S4 
    8907 H | 40S ribosomal protein S7 
    8908 L | KLLA0A10483p 
    8909 N | KLLA0F18040p 
    8910 R | KLLA0B01474p 
    8911 V | 40S ribosomal protein S21 
    8912 W | 40S ribosomal protein S22 
    8913 X | KLLA0B11231p 
    8914 a | 40S ribosomal protein S26 
    8915 b | 40S ribosomal protein S27 
    8916 q | Eukaryotic translation initiation factor 3 subunit C 
    8917  
    8918 
    8919 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H.mrc
    8920 
    8921 Opened 0057_6gsm_H.mrc as #2, grid size 88,96,104, pixel 1, shown at level
    8922 0.137, step 1, values float32 
    8923 
    8924 > fitmap #1 inMap #2
    8925 
    8926 Fit molecule 0057_6gsm_H.cif (#1) to map 0057_6gsm_H.mrc (#2) using 14921
    8927 atoms 
    8928 average map value = 0.07261, steps = 80 
    8929 shifted from previous position = 0.499 
    8930 rotated from previous position = 0.179 degrees 
    8931 atoms outside contour = 14137, contour level = 0.1369 
    8932  
    8933 Position of 0057_6gsm_H.cif (#1) relative to 0057_6gsm_H.mrc (#2) coordinates: 
    8934 Matrix rotation and translation 
    8935 0.99999531 -0.00126111 -0.00279203 0.90794240 
    8936 0.00125934 0.99999900 -0.00063652 -0.43925796 
    8937 0.00279283 0.00063300 0.99999590 -1.02865610 
    8938 Axis 0.20288211 -0.89252153 0.40279544 
    8939 Axis point 392.13097233 0.00000000 312.76567637 
    8940 Rotation angle (degrees) 0.17926176 
    8941 Shift along axis 0.16191447 
    8942  
    8943 
    8944 > save /scratch/cs-
    8945 > bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_H_fitted.cif #1
    8946 
    8947 > close #1
    8948 
    8949 > close #2
    8950 
    8951 > open 6gsm
    8952 
    8953 6gsm title: 
    8954 Structure of a partial yeast 48S preinitiation complex in open conformation.
    8955 [more info...] 
    8956  
    8957 Chain information for 6gsm #1 
    8958 --- 
    8959 Chain | Description | UniProt 
    8960 1 | Met-tRNAi | 
    8961 2 | 18S ribosomal RNA | 
    8962 3 | mRNA (5'-R(P*AP*AP*U)-3') | 
    8963 A | 40S ribosomal protein S0 | RSSA_KLULA 2-209 
    8964 B | 40S ribosomal protein S1 | RS3A_KLULA 3-233 
    8965 C | KLLA0F09812p | Q6CKL3_KLULA 39-255 
    8966 D | KLLA0D08305p | Q6CRK7_KLULA 3-225 
    8967 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261 
    8968 F | KLLA0D10659p | Q6CRA3_KLULA 22-227 
    8969 G | 40S ribosomal protein S6 | RS6_KLULA 1-226 
    8970 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187 
    8971 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201 
    8972 J | KLLA0E23673p | Q6CM18_KLULA 2-183 
    8973 K | KLLA0B08173p | Q6CVZ5_KLULA 1-96 
    8974 L | KLLA0A10483p | Q6CX80_KLULA 2-156 
    8975 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134 
    8976 N | KLLA0F18040p | Q6CJK0_KLULA 2-151 
    8977 O | 40S ribosomal protein S14 | RS14_KLULA 11-137 
    8978 P | KLLA0F07843p | Q6CKV4_KLULA 13-131 
    8979 Q | 40S ribosomal protein S16 | RS16_KLULA 3-143 
    8980 R | KLLA0B01474p | Q6CWU3_KLULA 2-126 
    8981 S | KLLA0B01562p | Q6CWT9_KLULA 2-146 
    8982 T | KLLA0A07194p | Q6CXM0_KLULA 2-144 
    8983 U | KLLA0F25542p | Q6CIM1_KLULA 15-120 
    8984 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 
    8985 W | 40S ribosomal protein S22 | RS22_KLULA 2-130 
    8986 X | KLLA0B11231p | F2Z602_KLULA 2-145 
    8987 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135 
    8988 Z | KLLA0B06182p | Q6CW78_KLULA 36-105 
    8989 a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99 
    8990 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82 
    8991 c | 40S ribosomal protein S28 | RS28_KLULA 6-67 
    8992 d | 40S ribosomal protein S29 | RS29_KLULA 4-56 
    8993 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61 
    8994 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150 
    8995 g | KLLA0E12277p | Q6CNI7_KLULA 3-326 
    8996 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    8997 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 21-115 
    8998 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
    8999 3-265 
    9000 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
    9001 90-519 
    9002 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
    9003 127-270 
    9004 m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 13-108 
    9005 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    9006 translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST 5-492 
    9007 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 77-737 
    9008 q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794 
    9009 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST 48-96 
    9010 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST 1-342 
    9011  
    9012 Non-standard residues in 6gsm #1 
    9013 --- 
    9014 7NO —
    9015 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
    9016 (2~{S})-2-azanyl-4-methylsulfanyl-butanoate 
    9017 GCP — phosphomethylphosphonic acid guanylate ester 
    9018 MG — magnesium ion 
    9019 ZN — zinc ion 
    9020  
    9021 
    9022 > open /scratch/cs-bioinfo/tngu/6k_data/Maps_Resampled/0057_6gsm_Sampled.mrc
    9023 
    9024 Opened 0057_6gsm_Sampled.mrc as #2, grid size 404,404,404, pixel 1, shown at
    9025 level 0.0673, step 2, values float32 
    9026 
    9027 > volume #2 region 208,140,133,327,211,220
    9028 
    9029 > open /scratch/cs-bioinfo/tngu/6k_data/select_box.py
    9030 
    9031 FYI: command is replacing existing command: "selectbox" 
    9032 executed select_box.py 
    9033 
    9034 > selectbox #1 inMap #2
    9035 
    9036 Selected 11892 atoms in map 0057_6gsm_Sampled.mrc #2 bounds 
    9037 
    9038 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.cif
    9039 > #1 selectedOnly true
    9040 
    9041 > save /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.mrc
    9042 > #2
    9043 
    9044 > close #1
    9045 
    9046 > close #2
    9047 
    9048 > open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.cif
    9049 
    9050 Summary of feedback from opening /scratch/cs-
    9051 bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.cif 
    9052 --- 
    9053 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    9054 near line 42944 
    9055 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    9056 42945 
    9057 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    9058 42946 
    9059 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    9060 42947 
    9061 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    9062 42948 
    9063 140 messages similar to the above omitted 
    9064 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    9065 43197 
    9066 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    9067 43198 
    9068 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    9069 43199 
    9070 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    9071 43200 
    9072 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    9073 43201 
    9074 168 messages similar to the above omitted 
    9075 Atom O3' has no neighbors to form bonds with according to residue template for
    9076 G /1:19 
    9077 Atom OP1 has no neighbors to form bonds with according to residue template for
    9078 U /2:562 
    9079 Atom OP2 has no neighbors to form bonds with according to residue template for
    9080 U /2:562 
    9081 Atom C5' has no neighbors to form bonds with according to residue template for
    9082 U /2:1003 
    9083 Atom C8 has no neighbors to form bonds with according to residue template for
    9084 A /2:1151 
    9085 Atom O4' has no neighbors to form bonds with according to residue template for
    9086 C /2:1191 
    9087 Atom OP1 has no neighbors to form bonds with according to residue template for
    9088 A /2:1193 
    9089 Atom OP2 has no neighbors to form bonds with according to residue template for
    9090 A /2:1193 
    9091 Atom OP2 has no neighbors to form bonds with according to residue template for
    9092 A /2:1207 
    9093 Atom O6 has no neighbors to form bonds with according to residue template for
    9094 G /2:1217 
    9095 Atom N1 has no neighbors to form bonds with according to residue template for
    9096 G /2:1217 
    9097 Atom N2 has no neighbors to form bonds with according to residue template for
    9098 G /2:1217 
    9099 Atom OP1 has no neighbors to form bonds with according to residue template for
    9100 A /2:1243 
    9101 Atom OP2 has no neighbors to form bonds with according to residue template for
    9102 G /2:1269 
    9103 Atom OP1 has no neighbors to form bonds with according to residue template for
    9104 C /2:1273 
    9105 Atom O5' has no neighbors to form bonds with according to residue template for
    9106 C /2:1273 
    9107 Atom OP1 has no neighbors to form bonds with according to residue template for
    9108 A /2:1425 
    9109 Atom N7 has no neighbors to form bonds with according to residue template for
    9110 G /2:1446 
    9111 Atom O2' has no neighbors to form bonds with according to residue template for
    9112 G /2:1540 
    9113 Atom C6 has no neighbors to form bonds with according to residue template for
    9114 U /2:1542 
    9115 Atom O3' has no neighbors to form bonds with according to residue template for
    9116 A /2:1553 
    9117 Atom O2' has no neighbors to form bonds with according to residue template for
    9118 A /2:1553 
    9119 Atom OP1 has no neighbors to form bonds with according to residue template for
    9120 A /2:1554 
    9121 Atom O2' has no neighbors to form bonds with according to residue template for
    9122 A /2:1554 
    9123 Atom O2' has no neighbors to form bonds with according to residue template for
    9124 A /2:1567 
    9125 Atom O4' has no neighbors to form bonds with according to residue template for
    9126 U /2:1577 
    9127 Atom O2 has no neighbors to form bonds with according to residue template for
    9128 C /2:1617 
    9129 Atom O2' has no neighbors to form bonds with according to residue template for
    9130 U /2:1626 
    9131 Atom O2 has no neighbors to form bonds with according to residue template for
    9132 U /2:1626 
    9133 Atom O3' has no neighbors to form bonds with according to residue template for
    9134 U /2:1768 
    9135 Atom O3' has no neighbors to form bonds with according to residue template for
    9136 G /2:1776 
    9137 Atom O3' has no neighbors to form bonds with according to residue template for
    9138 G /2:1790 
    9139 Atom O2' has no neighbors to form bonds with according to residue template for
    9140 G /2:1790 
    9141 Atom C1' has no neighbors to form bonds with according to residue template for
    9142 G /2:1790 
    9143 Atom N has no neighbors to form bonds with according to residue template for
    9144 GLU /F:183 
    9145 Atom OE1 has no neighbors to form bonds with according to residue template for
    9146 GLU /F:218 
    9147 Atom OE2 has no neighbors to form bonds with according to residue template for
    9148 GLU /F:218 
    9149 Atom C has no neighbors to form bonds with according to residue template for
    9150 LYS /P:59 
    9151 Atom CG has no neighbors to form bonds with according to residue template for
    9152 LYS /P:64 
    9153 Atom CE has no neighbors to form bonds with according to residue template for
    9154 LYS /P:64 
    9155 Atom N has no neighbors to form bonds with according to residue template for
    9156 VAL /P:86 
    9157 Atom CG2 has no neighbors to form bonds with according to residue template for
    9158 VAL /P:86 
    9159 Atom O has no neighbors to form bonds with according to residue template for
    9160 PRO /a:2 
    9161 Atom OD1 has no neighbors to form bonds with according to residue template for
    9162 ASP /i:90 
    9163 Atom O has no neighbors to form bonds with according to residue template for
    9164 LYS /j:35 
    9165 Atom O has no neighbors to form bonds with according to residue template for
    9166 ILE /j:46 
    9167 Atom CD1 has no neighbors to form bonds with according to residue template for
    9168 ILE /j:46 
    9169 Atom O has no neighbors to form bonds with according to residue template for
    9170 ILE /j:95 
    9171 Atom CG2 has no neighbors to form bonds with according to residue template for
    9172 ILE /j:96 
    9173 Atom O has no neighbors to form bonds with according to residue template for
    9174 LYS /j:106 
    9175 Atom SG has no neighbors to form bonds with according to residue template for
    9176 CYS /j:262 
    9177 Atom N has no neighbors to form bonds with according to residue template for
    9178 ASN /j:263 
    9179 Atom O has no neighbors to form bonds with according to residue template for
    9180 LYS /p:142 
    9181 Atom CG has no neighbors to form bonds with according to residue template for
    9182 GLU /p:290 
    9183 Atom OE1 has no neighbors to form bonds with according to residue template for
    9184 GLU /p:290 
    9185 Atom N has no neighbors to form bonds with according to residue template for
    9186 ILE /p:292 
    9187 Atom N has no neighbors to form bonds with according to residue template for
    9188 HIS /p:310 
    9189 Atom CE1 has no neighbors to form bonds with according to residue template for
    9190 HIS /p:310 
    9191  
    9192 Chain information for 0057_6gsm_l.cif #1 
    9193 --- 
    9194 Chain | Description 
    9195 1 | Met-tRNAi 
    9196 2 | 18S ribosomal RNA 
    9197 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    9198 F | KLLA0D10659p 
    9199 P | KLLA0F07843p 
    9200 Q | 40S ribosomal protein S16 
    9201 S | KLLA0B01562p 
    9202 c | 40S ribosomal protein S28 
    9203 e | 40S ribosomal protein S30 
    9204 f | Ubiquitin-40S ribosomal protein S27a 
    9205 h | 60S ribosomal protein L41-A 
    9206 i | Eukaryotic translation initiation factor 1A 
    9207 j | Eukaryotic translation initiation factor 2 subunit alpha 
    9208 k | Eukaryotic translation initiation factor 2 subunit gamma 
    9209 l | Eukaryotic translation initiation factor 2 subunit beta 
    9210 m | Eukaryotic translation initiation factor eIF-1 
    9211 p | Eukaryotic translation initiation factor 3 subunit B 
    9212 q | Eukaryotic translation initiation factor 3 subunit C 
    9213  
     2438[deleted to fit within ticket limits]
     2439
    92142440
    92152441> open /scratch/cs-bioinfo/tngu/6k_data/Box_Chains/0057_6gsm/0057_6gsm_l.mrc