Changes between Initial Version and Version 1 of Ticket #15501


Ignore:
Timestamp:
Jun 26, 2024, 11:23:27 AM (18 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #15501

    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash starting ISOLDE

  • Ticket #15501 – Description

    initial v1  
    75007500===== Log before crash end =====
    75017501
    7502 Log:
    7503 UCSF ChimeraX version: 1.5 (2022-11-24) 
    7504 © 2016-2022 Regents of the University of California. All rights reserved. 
    7505 
    7506 > open /home/pinkie/Documents/Charlotte/2024_06/done-brd4-n8.cxs
    7507 
    7508 Opened cryosparc_P9_J412_002_volume_map_sharp.mrc z flip as #17, grid size
    7509 144,144,144, pixel 2.47, shown at level 0.153, step 1, values float32 
    7510 Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #20, grid size
    7511 420,420,420, pixel 0.825, shown at level 0.0707, step 1, values float32 
    7512 Opened cryosparc_P14_J581_003_volume_map_sharp.mrc z flip as #22, grid size
    7513 128,128,128, pixel 3.38, shown at level 0.405, step 1, values float32 
    7514 Opened cryosparc_P9_J659_007_volume_map_sharp.mrc as #1.1, grid size
    7515 480,480,480, pixel 0.825, shown at level 0.264, step 1, values float32 
    7516 Opened cryosparc_P9_J659_007_volume_map.mrc as #1.2, grid size 480,480,480,
    7517 pixel 0.825, shown at level 0.0962, step 1, values float32 
    7518 Log from Wed Jun 26 10:54:46 2024UCSF ChimeraX version: 1.5 (2022-11-24) 
    7519 © 2016-2022 Regents of the University of California. All rights reserved. 
    7520 
    7521 > open
    7522 > /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_30_v2_chimerasession.cxs
    7523 
    7524 Opened cryosparc_P9_J412_002_volume_map_sharp.mrc z flip as #17, grid size
    7525 144,144,144, pixel 2.47, shown at level 0.153, step 1, values float32 
    7526 Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #20, grid size
    7527 420,420,420, pixel 0.825, shown at level 0.0707, step 1, values float32 
    7528 Opened cryosparc_P14_J581_003_volume_map_sharp.mrc z flip as #22, grid size
    7529 128,128,128, pixel 3.38, shown at level 0.255, step 1, values float32 
    7530 Log from Tue Jan 30 11:29:44 2024UCSF ChimeraX version: 1.5 (2022-11-24) 
    7531 © 2016-2022 Regents of the University of California. All rights reserved. 
    7532 How to cite UCSF ChimeraX 
    7533 
    7534 > open
    7535 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J710_006_volume_map_sharp.mrc
    7536 
    7537 Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #1, grid size
    7538 256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32 
    7539 
    7540 > open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v4.pdb
    7541 
    7542 Chain information for fullmodel-v4.pdb #2 
    7543 --- 
    7544 Chain | Description 
    7545 A | No description available 
    7546 B | No description available 
    7547 C | No description available 
    7548 D | No description available 
    7549 E | No description available 
    7550 R | No description available 
    7551  
    7552 
    7553 > volume #1 level 0.204
    7554 
    7555 > show cartoons
    7556 
    7557 > hide atoms
    7558 
    7559 > volume #1 level 0.1434
    7560 
    7561 > transparency 50
    7562 
    7563 > surface dust #1 size 14.8
    7564 
    7565 > select #2/R
    7566 
    7567 1432 atoms, 1452 bonds, 92 residues, 1 model selected 
    7568 
    7569 > isolde start
    7570 
    7571 > set selectionWidth 4
    7572 
    7573 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7574 chains... 
    7575 Chain information for fullmodel-v4.pdb 
    7576 --- 
    7577 Chain | Description 
    7578 2.2/A | No description available 
    7579 2.2/B | No description available 
    7580 2.2/C | No description available 
    7581 2.2/D | No description available 
    7582 2.2/E | No description available 
    7583 2.2/R | No description available 
    7584  
    7585 
    7586 > select clear
    7587 
    7588 > clipper associate #1 toModel #2
    7589 
    7590 Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #2.1.1.1, grid size
    7591 256,256,256, pixel 1.48, shown at step 1, values float32 
    7592 
    7593 > volume #2.1.1.1 level 0.0992
    7594 
    7595 > select #2/R
    7596 
    7597 1432 atoms, 1452 bonds, 92 residues, 1 model selected 
    7598 
    7599 > select clear
    7600 
    7601 > select #2/R:38-108
    7602 
    7603 1106 atoms, 1122 bonds, 71 residues, 1 model selected 
    7604 
    7605 > isolde sim start sel
    7606 
    7607 ISOLDE: started sim 
    7608 
    7609 > isolde sim pause
    7610 
    7611 > isolde sim resume
    7612 
    7613 > isolde sim pause
    7614 
    7615 > isolde sim stop
    7616 
    7617 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7618 chains... 
    7619 ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
    7620 standards. 
    7621 ISOLDE: stopped sim 
    7622 
    7623 > select clear
    7624 
    7625 > hide #!2.1 models
    7626 
    7627 > show #!2.1 models
    7628 
    7629 > open
    7630 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J710_006_volume_map_sharp.mrc
    7631 
    7632 Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #1, grid size
    7633 256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32 
    7634 
    7635 > volume #1 level 0.1585
    7636 
    7637 > save /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb
    7638 
    7639 > open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v4.pdb
    7640 
    7641 Chain information for fullmodel-v4.pdb #3 
    7642 --- 
    7643 Chain | Description 
    7644 A | No description available 
    7645 B | No description available 
    7646 C | No description available 
    7647 D | No description available 
    7648 E | No description available 
    7649 R | No description available 
    7650  
    7651 
    7652 > open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb
    7653 
    7654 Chain information for fullmodel-v5.pdb #4 
    7655 --- 
    7656 Chain | Description 
    7657 A | No description available 
    7658 B | No description available 
    7659 C | No description available 
    7660 D | No description available 
    7661 E | No description available 
    7662 R | No description available 
    7663  
    7664 
    7665 > hide #!2 models
    7666 
    7667 > hide #!2.1 models
    7668 
    7669 > hide #!2.2 models
    7670 
    7671 > hide #2.3 models
    7672 
    7673 > hide #3-4 atoms
    7674 
    7675 > show #3-4 cartoons
    7676 
    7677 > transparency #1.1 50
    7678 
    7679 > hide #3 models
    7680 
    7681 > hide #4 models
    7682 
    7683 > show #4 models
    7684 
    7685 > hide #4 models
    7686 
    7687 > show #4 models
    7688 
    7689 > show #3 models
    7690 
    7691 > hide #3 models
    7692 
    7693 > show #3 models
    7694 
    7695 > hide #3 models
    7696 
    7697 > show #3 models
    7698 
    7699 > hide #3 models
    7700 
    7701 > hide #4 models
    7702 
    7703 > show #4 models
    7704 
    7705 > open 5t35
    7706 
    7707 5t35 title: 
    7708 The PROTAC MZ1 in complex with the second bromodomain of Brd4 and
    7709 pVHL:ElonginC:ElonginB [more info...] 
    7710  
    7711 Chain information for 5t35 #5 
    7712 --- 
    7713 Chain | Description | UniProt 
    7714 A E | Bromodomain-containing protein 4 | BRD4_HUMAN 
    7715 B F | Transcription elongation factor B polypeptide 2 | ELOB_HUMAN 
    7716 C G | Transcription elongation factor B polypeptide 1 | ELOC_HUMAN 
    7717 D H | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    7718  
    7719 Non-standard residues in 5t35 #5 
    7720 --- 
    7721 759 —
    7722 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    7723 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    7724 pyrrolidine-2-carboxamide 
    7725  
    7726 5t35 mmCIF Assemblies 
    7727 --- 
    7728 1| author_defined_assembly 
    7729 2| author_defined_assembly 
    7730  
    7731 
    7732 > select #5/E
    7733 
    7734 910 atoms, 918 bonds, 126 residues, 1 model selected 
    7735 
    7736 > delete sel
    7737 
    7738 > select #5/G
    7739 
    7740 693 atoms, 703 bonds, 1 pseudobond, 92 residues, 2 models selected 
    7741 
    7742 > delete sel
    7743 
    7744 > select #5/F
    7745 
    7746 811 atoms, 826 bonds, 105 residues, 1 model selected 
    7747 
    7748 > delete sel
    7749 
    7750 > select #5/H
    7751 
    7752 1265 atoms, 1294 bonds, 156 residues, 1 model selected 
    7753 
    7754 > delete sel
    7755 
    7756 > ui tool show Matchmaker
    7757 
    7758 > matchmaker #!5 to #4
    7759 
    7760 Parameters 
    7761 --- 
    7762 Chain pairing | bb 
    7763 Alignment algorithm | Needleman-Wunsch 
    7764 Similarity matrix | BLOSUM-62 
    7765 SS fraction | 0.3 
    7766 Gap open (HH/SS/other) | 18/18/6 
    7767 Gap extend | 1 
    7768 SS matrix |  |  | H | S | O 
    7769 ---|---|---|--- 
    7770 H | 6 | -9 | -6 
    7771 S |  | 6 | -6 
    7772 O |  |  | 4 
    7773 Iteration cutoff | 2 
    7774  
    7775 Matchmaker fullmodel-v5.pdb, chain B (#4) with 5t35, chain D (#5), sequence
    7776 alignment score = 792.2 
    7777 RMSD between 149 pruned atom pairs is 0.891 angstroms; (across all 149 pairs:
    7778 0.891) 
    7779  
    7780 
    7781 > matchmaker #!5 to #4
    7782 
    7783 Parameters 
    7784 --- 
    7785 Chain pairing | bb 
    7786 Alignment algorithm | Needleman-Wunsch 
    7787 Similarity matrix | BLOSUM-62 
    7788 SS fraction | 0.3 
    7789 Gap open (HH/SS/other) | 18/18/6 
    7790 Gap extend | 1 
    7791 SS matrix |  |  | H | S | O 
    7792 ---|---|---|--- 
    7793 H | 6 | -9 | -6 
    7794 S |  | 6 | -6 
    7795 O |  |  | 4 
    7796 Iteration cutoff | 2 
    7797  
    7798 Matchmaker fullmodel-v5.pdb, chain B (#4) with 5t35, chain D (#5), sequence
    7799 alignment score = 792.2 
    7800 RMSD between 149 pruned atom pairs is 0.891 angstroms; (across all 149 pairs:
    7801 0.891) 
    7802  
    7803 
    7804 > hide #4#!5 atoms
    7805 
    7806 > select ::name="759"
    7807 
    7808 69 atoms, 75 bonds, 1 residue, 1 model selected 
    7809 
    7810 > show sel atoms
    7811 
    7812 > color sel yellow
    7813 
    7814 > color sel byhetero
    7815 
    7816 > select clear
    7817 
    7818 > select #4/A
    7819 
    7820 1835 atoms, 1858 bonds, 114 residues, 1 model selected 
    7821 
    7822 > color sel #5b42cdff
    7823 
    7824 > select #4/B
    7825 
    7826 2615 atoms, 2648 bonds, 160 residues, 1 model selected 
    7827 
    7828 > color sel #bfbfbfff
    7829 
    7830 > color sel #fafafaff
    7831 
    7832 [Repeated 1 time(s)]
    7833 
    7834 > color sel forest green
    7835 
    7836 > select #4/C
    7837 
    7838 1647 atoms, 1663 bonds, 104 residues, 1 model selected 
    7839 
    7840 > color sel #bdbf40ff
    7841 
    7842 > color sel #bdbf3aff
    7843 
    7844 > color sel #ccce3fff
    7845 
    7846 [Repeated 3 time(s)]
    7847 
    7848 > select #4/D
    7849 
    7850 1522 atoms, 1539 bonds, 97 residues, 1 model selected 
    7851 
    7852 > color sel #54bf40ff
    7853 
    7854 > color sel #9abf93ff
    7855 
    7856 > color sel #b0daa8ff
    7857 
    7858 [Repeated 3 time(s)]
    7859 
    7860 > select #4/E
    7861 
    7862 10756 atoms, 10867 bonds, 658 residues, 1 model selected 
    7863 
    7864 > color sel #40a8bfff
    7865 
    7866 > color sel #4daabfff
    7867 
    7868 > color sel #4293a5ff
    7869 
    7870 [Repeated 3 time(s)]
    7871 
    7872 > select #4/R
    7873 
    7874 1432 atoms, 1452 bonds, 92 residues, 1 model selected 
    7875 
    7876 > color sel #5ebf40ff
    7877 
    7878 > color sel #5abf3aff
    7879 
    7880 > color sel #60cb3eff
    7881 
    7882 [Repeated 3 time(s)]
    7883 
    7884 > select clear
    7885 
    7886 > set bgColor white
    7887 
    7888 > set bgColor #ffffff00
    7889 
    7890 > lighting soft
    7891 
    7892 > show #!1 models
    7893 
    7894 > hide #!1 models
    7895 
    7896 > save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
    7897 > height 803 supersample 3 transparentBackground true
    7898 
    7899 > graphics silhouettes true
    7900 
    7901 > save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
    7902 > height 803 supersample 3
    7903 
    7904 > save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
    7905 > height 803 supersample 3 transparentBackground true
    7906 
    7907 > open 5n4w
    7908 
    7909 5n4w title: 
    7910 Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more
    7911 info...] 
    7912  
    7913 Chain information for 5n4w #6 
    7914 --- 
    7915 Chain | Description | UniProt 
    7916 A | Cullin-2 | CUL2_HUMAN 
    7917 B | Elongin-B | ELOB_HUMAN 
    7918 C | Elongin-C | ELOC_HUMAN 
    7919 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 
    7920 V | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    7921  
    7922 Non-standard residues in 5n4w #6 
    7923 --- 
    7924 ZN — zinc ion 
    7925  
    7926 
    7927 > ui tool show Matchmaker
    7928 
    7929 > matchmaker #!6 to #4
    7930 
    7931 Parameters 
    7932 --- 
    7933 Chain pairing | bb 
    7934 Alignment algorithm | Needleman-Wunsch 
    7935 Similarity matrix | BLOSUM-62 
    7936 SS fraction | 0.3 
    7937 Gap open (HH/SS/other) | 18/18/6 
    7938 Gap extend | 1 
    7939 SS matrix |  |  | H | S | O 
    7940 ---|---|---|--- 
    7941 H | 6 | -9 | -6 
    7942 S |  | 6 | -6 
    7943 O |  |  | 4 
    7944 Iteration cutoff | 2 
    7945  
    7946 Matchmaker fullmodel-v5.pdb, chain E (#4) with 5n4w, chain A (#6), sequence
    7947 alignment score = 3288.4 
    7948 RMSD between 377 pruned atom pairs is 1.063 angstroms; (across all 587 pairs:
    7949 3.224) 
    7950  
    7951 
    7952 > matchmaker #!6 to #4
    7953 
    7954 Parameters 
    7955 --- 
    7956 Chain pairing | bb 
    7957 Alignment algorithm | Needleman-Wunsch 
    7958 Similarity matrix | BLOSUM-62 
    7959 SS fraction | 0.3 
    7960 Gap open (HH/SS/other) | 18/18/6 
    7961 Gap extend | 1 
    7962 SS matrix |  |  | H | S | O 
    7963 ---|---|---|--- 
    7964 H | 6 | -9 | -6 
    7965 S |  | 6 | -6 
    7966 O |  |  | 4 
    7967 Iteration cutoff | 2 
    7968  
    7969 Matchmaker fullmodel-v5.pdb, chain E (#4) with 5n4w, chain A (#6), sequence
    7970 alignment score = 3288.4 
    7971 RMSD between 377 pruned atom pairs is 1.063 angstroms; (across all 587 pairs:
    7972 3.224) 
    7973  
    7974 
    7975 > select add #6
    7976 
    7977 7719 atoms, 7841 bonds, 29 pseudobonds, 970 residues, 3 models selected 
    7978 
    7979 > hide sel atoms
    7980 
    7981 > show sel cartoons
    7982 
    7983 > select clear
    7984 
    7985 > hide #!6 models
    7986 
    7987 > show #3 models
    7988 
    7989 > hide #3 models
    7990 
    7991 > show #3 models
    7992 
    7993 > close #3
    7994 
    7995 > close #2
    7996 
    7997 > show #!1 models
    7998 
    7999 > hide #!1 models
    8000 
    8001 > show #!1 models
    8002 
    8003 > hide #!1 models
    8004 
    8005 > save /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_28__npn-
    8006 > crosslinked-structure__final.cxs includeMaps true
    8007 
    8008 > open
    8009 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map.mrc
    8010 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map_sharp.mrc
    8011 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J647_006_volume_map_sharp.mrc
    8012 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J659_007_volume_map.mrc
    8013 
    8014 Opened cryosparc_P9_J635_008_volume_map.mrc as #2.1, grid size 480,480,480,
    8015 pixel 0.825, shown at level 0.00758, step 2, values float32 
    8016 Opened cryosparc_P9_J635_008_volume_map_sharp.mrc as #2.2, grid size
    8017 480,480,480, pixel 0.825, shown at level 0.0194, step 2, values float32 
    8018 Opened cryosparc_P9_J647_006_volume_map_sharp.mrc as #2.3, grid size
    8019 480,480,480, pixel 0.825, shown at level 0.0203, step 2, values float32 
    8020 Opened cryosparc_P9_J659_007_volume_map.mrc as #2.4, grid size 480,480,480,
    8021 pixel 0.825, shown at level 0.00707, step 2, values float32 
    8022 
    8023 > volume #2.4 level 0.04195
    8024 
    8025 > volume #2.3 level 0.07573
    8026 
    8027 > volume #2.2 level 0.06618
    8028 
    8029 > volume #2.1 level 0.03781
    8030 
    8031 > surface dust #2.1 size 8.25
    8032 
    8033 > surface dust #2.2 size 8.25
    8034 
    8035 > surface dust #2.3 size 8.25
    8036 
    8037 > surface dust #2.4 size 8.25
    8038 
    8039 > volume flip #2.2
    8040 
    8041 Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #3, grid size
    8042 480,480,480, pixel 0.825, shown at step 1, values float32 
    8043 
    8044 > close #2.2
    8045 
    8046 > select add #2.3
    8047 
    8048 2 models selected 
    8049 
    8050 > ui mousemode right "rotate selected models"
    8051 
    8052 > view matrix models
    8053 > #2.3,0.98461,-0.13581,0.11,9.4722,-0.13019,-0.98986,-0.056778,424.6,0.1166,0.041583,-0.99231,332.63
    8054 
    8055 > volume flip #2.3
    8056 
    8057 Opened cryosparc_P9_J647_006_volume_map_sharp.mrc z flip as #7, grid size
    8058 480,480,480, pixel 0.825, shown at step 1, values float32 
    8059 
    8060 > close #2.3
    8061 
    8062 > select add #7
    8063 
    8064 2 models selected 
    8065 
    8066 > ui mousemode right "rotate selected models"
    8067 
    8068 > view matrix models
    8069 > #7,0.94093,0.053579,0.33434,-66.51,-0.17685,0.91978,0.35032,-21.349,-0.28875,-0.38875,0.87493,94.987
    8070 
    8071 > view matrix models
    8072 > #7,0.9958,-0.06531,0.064213,3.5056,-0.016537,-0.81777,-0.5753,480.25,0.090084,0.57182,-0.81542,197.79
    8073 
    8074 > view matrix models
    8075 > #7,-0.94582,-0.18918,-0.2639,470.69,0.14941,-0.97515,0.16355,320.99,-0.28828,0.11526,0.95058,-18.388
    8076 
    8077 > ui mousemode right "translate selected models"
    8078 
    8079 > view matrix models
    8080 > #7,-0.94582,-0.18918,-0.2639,476.46,0.14941,-0.97515,0.16355,320.85,-0.28828,0.11526,0.95058,43.172
    8081 
    8082 > ui mousemode right "translate selected models"
    8083 
    8084 > view matrix models
    8085 > #7,-0.94582,-0.18918,-0.2639,476.75,0.14941,-0.97515,0.16355,319.58,-0.28828,0.11526,0.95058,47.965
    8086 
    8087 > fitmap #3 inMap #1
    8088 
    8089 Fit map cryosparc_P9_J635_008_volume_map_sharp.mrc z flip in map
    8090 cryosparc_P7_J710_006_volume_map_sharp.mrc using 260097 points 
    8091 correlation = 0.7239, correlation about mean = 0.415, overlap = 7246 
    8092 steps = 108, shift = 10.4, angle = 7.23 degrees 
    8093  
    8094 Position of cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#3) relative to
    8095 cryosparc_P7_J710_006_volume_map_sharp.mrc (#1) coordinates: 
    8096 Matrix rotation and translation 
    8097 0.99741254 0.03385855 0.06341789 -25.04544197 
    8098 -0.04024254 0.99394367 0.10225709 -19.05719275 
    8099 -0.05957154 -0.10454460 0.99273444 35.75883607 
    8100 Axis -0.82141607 0.48851388 -0.29432945 
    8101 Axis point 0.00000000 329.56848775 209.41103196 
    8102 Rotation angle (degrees) 7.23164693 
    8103 Shift along axis 0.73814676 
    8104  
    8105 
    8106 > fitmap #7 inMap #1
    8107 
    8108 Fit map cryosparc_P9_J647_006_volume_map_sharp.mrc z flip in map
    8109 cryosparc_P7_J710_006_volume_map_sharp.mrc using 215940 points 
    8110 correlation = 0.7306, correlation about mean = 0.3854, overlap = 6936 
    8111 steps = 208, shift = 9.46, angle = 21.8 degrees 
    8112  
    8113 Position of cryosparc_P9_J647_006_volume_map_sharp.mrc z flip (#7) relative to
    8114 cryosparc_P7_J710_006_volume_map_sharp.mrc (#1) coordinates: 
    8115 Matrix rotation and translation 
    8116 -0.99893793 -0.00322217 0.04596451 381.28217401 
    8117 0.00554917 -0.99870419 0.05058868 376.53393934 
    8118 0.04574195 0.05079001 0.99766132 -20.33401849 
    8119 Axis 0.02293995 0.02535860 0.99941518 
    8120 Axis point 190.46107391 188.94352871 0.00000000 
    8121 Rotation angle (degrees) 179.74857166 
    8122 Shift along axis -2.02715908 
    8123  
    8124 
    8125 > hide #!5 models
    8126 
    8127 > hide #4 models
    8128 
    8129 > show #4 models
    8130 
    8131 > hide #!2 models
    8132 
    8133 > show #!2 models
    8134 
    8135 > hide #!2 models
    8136 
    8137 > show #!3 models
    8138 
    8139 > select clear
    8140 
    8141 > surface dust #3 size 8.25
    8142 
    8143 > surface dust #7 size 8.25
    8144 
    8145 > hide #!3 models
    8146 
    8147 > show #!3 models
    8148 
    8149 > volume #7 level 0.07801
    8150 
    8151 > volume #3 level 0.05626
    8152 
    8153 > select clear
    8154 
    8155 > transparency #3.1 50
    8156 
    8157 > volume #!3 style surface
    8158 
    8159 [Repeated 1 time(s)]
    8160 
    8161 > open 6ttu
    8162 
    8163 6ttu title: 
    8164 Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
    8165 NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...] 
    8166  
    8167 Chain information for 6ttu #8 
    8168 --- 
    8169 Chain | Description | UniProt 
    8170 C | Cullin-1 | CUL1_HUMAN 
    8171 D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 
    8172 I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY | 
    8173 N | NEDD8 | NEDD8_HUMAN 
    8174 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 
    8175 S | S-phase kinase-associated protein 1 | SKP1_HUMAN 
    8176 T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 
    8177 U | Polyubiquitin-C | UBC_HUMAN 
    8178  
    8179 Non-standard residues in 6ttu #8 
    8180 --- 
    8181 ZN — zinc ion 
    8182  
    8183 
    8184 > select add #8
    8185 
    8186 12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected 
    8187 
    8188 > hide sel atoms
    8189 
    8190 > show sel cartoons
    8191 
    8192 > select clear
    8193 
    8194 > select #8/I
    8195 
    8196 58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected 
    8197 
    8198 > delete sel
    8199 
    8200 > select #8/T
    8201 
    8202 3085 atoms, 3146 bonds, 2 pseudobonds, 394 residues, 2 models selected 
    8203 
    8204 > delete sel
    8205 
    8206 > select #8/S
    8207 
    8208 891 atoms, 903 bonds, 3 pseudobonds, 123 residues, 2 models selected 
    8209 
    8210 > delete sel
    8211 
    8212 > ui tool show Matchmaker
    8213 
    8214 Traceback (most recent call last): 
    8215 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8216 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8217 return self._func(self._name, data) 
    8218 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8219 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8220 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8221 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8222 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8223 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8224 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8225  
    8226 Error processing trigger "setting changed": 
    8227 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8228  
    8229 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8230 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8231 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8232  
    8233 See log for complete Python traceback. 
    8234  
    8235 Traceback (most recent call last): 
    8236 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8237 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8238 return self._func(self._name, data) 
    8239 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8240 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8241 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8242 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8243 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8244 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8245 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8246  
    8247 Error processing trigger "setting changed": 
    8248 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8249  
    8250 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8251 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8252 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8253  
    8254 See log for complete Python traceback. 
    8255  
    8256 Traceback (most recent call last): 
    8257 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8258 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8259 return self._func(self._name, data) 
    8260 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8261 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8262 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8263 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8264 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8265 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8266 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8267  
    8268 Error processing trigger "setting changed": 
    8269 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8270  
    8271 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8272 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8273 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8274  
    8275 See log for complete Python traceback. 
    8276  
    8277 Traceback (most recent call last): 
    8278 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8279 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8280 return self._func(self._name, data) 
    8281 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8282 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8283 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8284 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8285 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8286 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8287 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8288  
    8289 Error processing trigger "setting changed": 
    8290 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8291  
    8292 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8293 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8294 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8295  
    8296 See log for complete Python traceback. 
    8297  
    8298 
    8299 > hide #!8 models
    8300 
    8301 > hide #!3 models
    8302 
    8303 > show #!8 models
    8304 
    8305 > matchmaker #8/C to #4/E pairing ss
    8306 
    8307 Parameters 
    8308 --- 
    8309 Chain pairing | ss 
    8310 Alignment algorithm | Needleman-Wunsch 
    8311 Similarity matrix | BLOSUM-62 
    8312 SS fraction | 0.3 
    8313 Gap open (HH/SS/other) | 18/18/6 
    8314 Gap extend | 1 
    8315 SS matrix |  |  | H | S | O 
    8316 ---|---|---|--- 
    8317 H | 6 | -9 | -6 
    8318 S |  | 6 | -6 
    8319 O |  |  | 4 
    8320 Iteration cutoff | 2 
    8321  
    8322 Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
    8323 alignment score = 1628.1 
    8324 RMSD between 309 pruned atom pairs is 1.282 angstroms; (across all 619 pairs:
    8325 4.270) 
    8326  
    8327 
    8328 > matchmaker #8/C to #4/E pairing ss
    8329 
    8330 Parameters 
    8331 --- 
    8332 Chain pairing | ss 
    8333 Alignment algorithm | Needleman-Wunsch 
    8334 Similarity matrix | BLOSUM-62 
    8335 SS fraction | 0.3 
    8336 Gap open (HH/SS/other) | 18/18/6 
    8337 Gap extend | 1 
    8338 SS matrix |  |  | H | S | O 
    8339 ---|---|---|--- 
    8340 H | 6 | -9 | -6 
    8341 S |  | 6 | -6 
    8342 O |  |  | 4 
    8343 Iteration cutoff | 2 
    8344  
    8345 Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
    8346 alignment score = 1628.1 
    8347 RMSD between 309 pruned atom pairs is 1.282 angstroms; (across all 619 pairs:
    8348 4.270) 
    8349  
    8350 
    8351 > select #8/C:15-354
    8352 
    8353 2540 atoms, 2582 bonds, 3 pseudobonds, 305 residues, 2 models selected 
    8354 
    8355 > delete sel
    8356 
    8357 > select #8/C:703-776
    8358 
    8359 582 atoms, 587 bonds, 1 pseudobond, 70 residues, 2 models selected 
    8360 
    8361 > delete sel
    8362 
    8363 > ui tool show Matchmaker
    8364 
    8365 > matchmaker #8/C to #4/E pairing ss
    8366 
    8367 Parameters 
    8368 --- 
    8369 Chain pairing | ss 
    8370 Alignment algorithm | Needleman-Wunsch 
    8371 Similarity matrix | BLOSUM-62 
    8372 SS fraction | 0.3 
    8373 Gap open (HH/SS/other) | 18/18/6 
    8374 Gap extend | 1 
    8375 SS matrix |  |  | H | S | O 
    8376 ---|---|---|--- 
    8377 H | 6 | -9 | -6 
    8378 S |  | 6 | -6 
    8379 O |  |  | 4 
    8380 Iteration cutoff | 2 
    8381  
    8382 Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
    8383 alignment score = 1250.8 
    8384 RMSD between 194 pruned atom pairs is 1.196 angstroms; (across all 316 pairs:
    8385 2.691) 
    8386  
    8387 
    8388 > matchmaker #8/C to #4/E pairing ss
    8389 
    8390 Parameters 
    8391 --- 
    8392 Chain pairing | ss 
    8393 Alignment algorithm | Needleman-Wunsch 
    8394 Similarity matrix | BLOSUM-62 
    8395 SS fraction | 0.3 
    8396 Gap open (HH/SS/other) | 18/18/6 
    8397 Gap extend | 1 
    8398 SS matrix |  |  | H | S | O 
    8399 ---|---|---|--- 
    8400 H | 6 | -9 | -6 
    8401 S |  | 6 | -6 
    8402 O |  |  | 4 
    8403 Iteration cutoff | 2 
    8404  
    8405 Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
    8406 alignment score = 1250.8 
    8407 RMSD between 194 pruned atom pairs is 1.196 angstroms; (across all 316 pairs:
    8408 2.691) 
    8409  
    8410 
    8411 > ui tool show Matchmaker
    8412 
    8413 > matchmaker #8/R to #4/R pairing ss
    8414 
    8415 Parameters 
    8416 --- 
    8417 Chain pairing | ss 
    8418 Alignment algorithm | Needleman-Wunsch 
    8419 Similarity matrix | BLOSUM-62 
    8420 SS fraction | 0.3 
    8421 Gap open (HH/SS/other) | 18/18/6 
    8422 Gap extend | 1 
    8423 SS matrix |  |  | H | S | O 
    8424 ---|---|---|--- 
    8425 H | 6 | -9 | -6 
    8426 S |  | 6 | -6 
    8427 O |  |  | 4 
    8428 Iteration cutoff | 2 
    8429  
    8430 Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
    8431 alignment score = 466.8 
    8432 RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
    8433 14.356) 
    8434  
    8435 
    8436 > matchmaker #8/R to #4/R pairing ss
    8437 
    8438 Parameters 
    8439 --- 
    8440 Chain pairing | ss 
    8441 Alignment algorithm | Needleman-Wunsch 
    8442 Similarity matrix | BLOSUM-62 
    8443 SS fraction | 0.3 
    8444 Gap open (HH/SS/other) | 18/18/6 
    8445 Gap extend | 1 
    8446 SS matrix |  |  | H | S | O 
    8447 ---|---|---|--- 
    8448 H | 6 | -9 | -6 
    8449 S |  | 6 | -6 
    8450 O |  |  | 4 
    8451 Iteration cutoff | 2 
    8452  
    8453 Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
    8454 alignment score = 466.8 
    8455 RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
    8456 14.356) 
    8457  
    8458 
    8459 > ui tool show Matchmaker
    8460 
    8461 > select #8/C
    8462 
    8463 2606 atoms, 2650 bonds, 1 pseudobond, 326 residues, 2 models selected 
    8464 
    8465 > delete sel
    8466 
    8467 > close #6
    8468 
    8469 > show #!7 models
    8470 
    8471 > hide #!7 models
    8472 
    8473 > show #!3 models
    8474 
    8475 > hide #!3 models
    8476 
    8477 > show #!3 models
    8478 
    8479 > hide #!3 models
    8480 
    8481 > show #!1 models
    8482 
    8483 > hide #!1 models
    8484 
    8485 > show #!7 models
    8486 
    8487 > hide #!7 models
    8488 
    8489 > show #!5 models
    8490 
    8491 > hide #!5 models
    8492 
    8493 > select add #4
    8494 
    8495 19807 atoms, 20027 bonds, 1225 residues, 1 model selected 
    8496 
    8497 > select add #8
    8498 
    8499 22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected 
    8500 
    8501 > combine sel
    8502 
    8503 Remapping chain ID 'D' in 6ttu #8 to 'F' 
    8504 Remapping chain ID 'R' in 6ttu #8 to 'S' 
    8505 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8506 chains... 
    8507 ISOLDE: Corrected atom nomenclature of 21 residues in model #6 to IUPAC-IUB
    8508 standards. 
    8509 
    8510 > select clear
    8511 
    8512 > clipper associate #3 toModel #6
    8513 
    8514 Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #6.1.1.1, grid
    8515 size 480,480,480, pixel 0.825, shown at step 1, values float32 
    8516 
    8517 > open
    8518 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map_sharp.mrc
    8519 
    8520 Opened cryosparc_P9_J635_008_volume_map_sharp.mrc as #3, grid size
    8521 480,480,480, pixel 0.825, shown at level 0.0194, step 2, values float32 
    8522 
    8523 > volume #3 level 0.09358
    8524 
    8525 > volume flip #3
    8526 
    8527 Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #9, grid size
    8528 480,480,480, pixel 0.825, shown at step 1, values float32 
    8529 
    8530 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    8531 got 3 atomic models, 2 maps. 
    8532 
    8533 > hide #!6.2 models
    8534 
    8535 > show #!6.2 models
    8536 
    8537 > select add #6.2
    8538 
    8539 22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 8 models selected 
    8540 
    8541 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    8542 got 3 atomic models, 2 maps. 
    8543 
    8544 > select add #6.2
    8545 
    8546 22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 8 models selected 
    8547 
    8548 > select add #6
    8549 
    8550 22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 15 models selected 
    8551 
    8552 > close #6
    8553 
    8554 > hide #!9 models
    8555 
    8556 > select add #4
    8557 
    8558 19807 atoms, 20027 bonds, 1225 residues, 1 model selected 
    8559 
    8560 > select add #8
    8561 
    8562 22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected 
    8563 
    8564 > combine sel
    8565 
    8566 Remapping chain ID 'D' in 6ttu #8 to 'F' 
    8567 Remapping chain ID 'R' in 6ttu #8 to 'S' 
    8568 
    8569 > hide #4 models
    8570 
    8571 > select subtract #4
    8572 
    8573 2984 atoms, 3047 bonds, 13 pseudobonds, 380 residues, 3 models selected 
    8574 
    8575 > hide #!8 models
    8576 
    8577 > select subtract #8
    8578 
    8579 Nothing selected 
    8580 
    8581 > select add #6
    8582 
    8583 22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 3 models selected 
    8584 
    8585 > show #!9 models
    8586 
    8587 > fitmap #6 inMap #9
    8588 
    8589 Fit molecule combination (#6) to map
    8590 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) using 22791 atoms 
    8591 average map value = 0.0972, steps = 156 
    8592 shifted from previous position = 11.3 
    8593 rotated from previous position = 6.89 degrees 
    8594 atoms outside contour = 12780, contour level = 0.093576 
    8595  
    8596 Position of combination (#6) relative to
    8597 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) coordinates: 
    8598 Matrix rotation and translation 
    8599 0.99761374 -0.02131244 -0.06567050 24.02263064 
    8600 0.01475408 0.99499981 -0.09878107 25.91855777 
    8601 0.06744740 0.09757645 0.99293992 -32.41202814 
    8602 Axis 0.81831656 -0.55476655 0.15030663 
    8603 Axis point 0.00000000 350.66445652 246.92285576 
    8604 Rotation angle (degrees) 6.89074657 
    8605 Shift along axis 0.40762520 
    8606  
    8607 
    8608 > select clear
    8609 
    8610 > hide #!6 models
    8611 
    8612 > show #!6 models
    8613 
    8614 > ui tool show Matchmaker
    8615 
    8616 > matchmaker #6/R to #4/R pairing ss
    8617 
    8618 Parameters 
    8619 --- 
    8620 Chain pairing | ss 
    8621 Alignment algorithm | Needleman-Wunsch 
    8622 Similarity matrix | BLOSUM-62 
    8623 SS fraction | 0.3 
    8624 Gap open (HH/SS/other) | 18/18/6 
    8625 Gap extend | 1 
    8626 SS matrix |  |  | H | S | O 
    8627 ---|---|---|--- 
    8628 H | 6 | -9 | -6 
    8629 S |  | 6 | -6 
    8630 O |  |  | 4 
    8631 Iteration cutoff | 2 
    8632  
    8633 Matchmaker fullmodel-v5.pdb, chain R (#4) with combination, chain R (#6),
    8634 sequence alignment score = 927 
    8635 RMSD between 89 pruned atom pairs is 0.000 angstroms; (across all 89 pairs:
    8636 0.000) 
    8637  
    8638 
    8639 > matchmaker #6/R to #4/R pairing ss
    8640 
    8641 Parameters 
    8642 --- 
    8643 Chain pairing | ss 
    8644 Alignment algorithm | Needleman-Wunsch 
    8645 Similarity matrix | BLOSUM-62 
    8646 SS fraction | 0.3 
    8647 Gap open (HH/SS/other) | 18/18/6 
    8648 Gap extend | 1 
    8649 SS matrix |  |  | H | S | O 
    8650 ---|---|---|--- 
    8651 H | 6 | -9 | -6 
    8652 S |  | 6 | -6 
    8653 O |  |  | 4 
    8654 Iteration cutoff | 2 
    8655  
    8656 Matchmaker fullmodel-v5.pdb, chain R (#4) with combination, chain R (#6),
    8657 sequence alignment score = 927 
    8658 RMSD between 89 pruned atom pairs is 0.000 angstroms; (across all 89 pairs:
    8659 0.000) 
    8660  
    8661 
    8662 > hide #!6 models
    8663 
    8664 > show #!6 models
    8665 
    8666 > hide #!6 models
    8667 
    8668 > show #!6 models
    8669 
    8670 > hide #!9 models
    8671 
    8672 > show #!9 models
    8673 
    8674 > hide #!9 models
    8675 
    8676 > ui tool show Matchmaker
    8677 
    8678 > close #6
    8679 
    8680 > show #4 models
    8681 
    8682 > show #!8 models
    8683 
    8684 > combine sel
    8685 
    8686 No structures specified 
    8687 
    8688 > select add #4
    8689 
    8690 19807 atoms, 20027 bonds, 1225 residues, 1 model selected 
    8691 
    8692 > select add #8
    8693 
    8694 22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected 
    8695 
    8696 > select subtract #8
    8697 
    8698 19807 atoms, 20027 bonds, 1225 residues, 1 model selected 
    8699 
    8700 > hide #!8 models
    8701 
    8702 > hide #4 models
    8703 
    8704 > show #4 models
    8705 
    8706 > show #!9 models
    8707 
    8708 > select add #9
    8709 
    8710 19807 atoms, 20027 bonds, 1225 residues, 3 models selected 
    8711 
    8712 > fitmap #4 inMap #9
    8713 
    8714 Fit molecule fullmodel-v5.pdb (#4) to map
    8715 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) using 19807 atoms 
    8716 average map value = 0.1121, steps = 152 
    8717 shifted from previous position = 10.8 
    8718 rotated from previous position = 6.89 degrees 
    8719 atoms outside contour = 9792, contour level = 0.093576 
    8720  
    8721 Position of fullmodel-v5.pdb (#4) relative to
    8722 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) coordinates: 
    8723 Matrix rotation and translation 
    8724 0.99762593 -0.02091198 -0.06561397 23.93517264 
    8725 0.01436000 0.99500528 -0.09878407 25.98670381 
    8726 0.06735202 0.09760733 0.99294336 -32.41050705 
    8727 Axis 0.81905399 -0.55453714 0.14710244 
    8728 Axis point 0.00000000 350.60177499 247.72967437 
    8729 Rotation angle (degrees) 6.88570607 
    8730 Shift along axis 0.42594157 
    8731  
    8732 
    8733 > select clear
    8734 
    8735 > hide #!9 models
    8736 
    8737 > show #!8 models
    8738 
    8739 > ui tool show Matchmaker
    8740 
    8741 > matchmaker #8/R to #4/R pairing ss
    8742 
    8743 Parameters 
    8744 --- 
    8745 Chain pairing | ss 
    8746 Alignment algorithm | Needleman-Wunsch 
    8747 Similarity matrix | BLOSUM-62 
    8748 SS fraction | 0.3 
    8749 Gap open (HH/SS/other) | 18/18/6 
    8750 Gap extend | 1 
    8751 SS matrix |  |  | H | S | O 
    8752 ---|---|---|--- 
    8753 H | 6 | -9 | -6 
    8754 S |  | 6 | -6 
    8755 O |  |  | 4 
    8756 Iteration cutoff | 2 
    8757  
    8758 Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
    8759 alignment score = 499.8 
    8760 RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
    8761 14.356) 
    8762  
    8763 Traceback (most recent call last): 
    8764 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8765 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8766 return self._func(self._name, data) 
    8767 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8768 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8769 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8770 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8771 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8772 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8773 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8774  
    8775 Error processing trigger "setting changed": 
    8776 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8777  
    8778 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8779 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8780 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8781  
    8782 See log for complete Python traceback. 
    8783  
    8784 Traceback (most recent call last): 
    8785 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8786 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8787 return self._func(self._name, data) 
    8788 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8789 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8790 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8791 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8792 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8793 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8794 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8795  
    8796 Error processing trigger "setting changed": 
    8797 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8798  
    8799 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8800 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8801 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8802  
    8803 See log for complete Python traceback. 
    8804  
    8805 Traceback (most recent call last): 
    8806 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8807 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8808 return self._func(self._name, data) 
    8809 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8810 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8811 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8812 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8813 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8814 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8815 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8816  
    8817 Error processing trigger "setting changed": 
    8818 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8819  
    8820 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8821 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8822 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8823  
    8824 See log for complete Python traceback. 
    8825  
    8826 Traceback (most recent call last): 
    8827 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8828 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8829 return self._func(self._name, data) 
    8830 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8831 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8832 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8833 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8834 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8835 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8836 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8837  
    8838 Error processing trigger "setting changed": 
    8839 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8840  
    8841 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8842 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8843 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8844  
    8845 See log for complete Python traceback. 
    8846  
    8847 Traceback (most recent call last): 
    8848 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8849 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8850 return self._func(self._name, data) 
    8851 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8852 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8853 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8854 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8855 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8856 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8857 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8858  
    8859 Error processing trigger "setting changed": 
    8860 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8861  
    8862 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8863 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8864 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8865  
    8866 See log for complete Python traceback. 
    8867  
    8868 Traceback (most recent call last): 
    8869 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8870 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8871 return self._func(self._name, data) 
    8872 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8873 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8874 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8875 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8876 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8877 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8878 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8879  
    8880 Error processing trigger "setting changed": 
    8881 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8882  
    8883 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8884 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8885 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8886  
    8887 See log for complete Python traceback. 
    8888  
    8889 Traceback (most recent call last): 
    8890 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8891 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8892 return self._func(self._name, data) 
    8893 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8894 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8895 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8896 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8897 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8898 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8899 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8900  
    8901 Error processing trigger "setting changed": 
    8902 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8903  
    8904 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8905 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8906 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8907  
    8908 See log for complete Python traceback. 
    8909  
    8910 Traceback (most recent call last): 
    8911 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8912 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8913 return self._func(self._name, data) 
    8914 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8915 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8916 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8917 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8918 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8919 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8920 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8921  
    8922 Error processing trigger "setting changed": 
    8923 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8924  
    8925 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8926 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8927 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8928  
    8929 See log for complete Python traceback. 
    8930  
    8931 Traceback (most recent call last): 
    8932 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8933 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8934 return self._func(self._name, data) 
    8935 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8936 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8937 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8938 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8939 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8940 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8941 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8942  
    8943 Error processing trigger "setting changed": 
    8944 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8945  
    8946 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8947 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8948 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8949  
    8950 See log for complete Python traceback. 
    8951  
    8952 Traceback (most recent call last): 
    8953 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8954 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8955 return self._func(self._name, data) 
    8956 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8957 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8958 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8959 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8960 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8961 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8962 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8963  
    8964 Error processing trigger "setting changed": 
    8965 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8966  
    8967 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8968 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8969 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8970  
    8971 See log for complete Python traceback. 
    8972  
    8973 Traceback (most recent call last): 
    8974 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8975 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8976 return self._func(self._name, data) 
    8977 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8978 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    8979 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    8980 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8981 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8982 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8983 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8984  
    8985 Error processing trigger "setting changed": 
    8986 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    8987  
    8988 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8989 packages/chimerax/ui/options/options.py", line 342, in set_value 
    8990 self.__button_group.button(self.values.index(value)).setChecked(True) 
    8991  
    8992 See log for complete Python traceback. 
    8993  
    8994 Traceback (most recent call last): 
    8995 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8996 packages/chimerax/core/triggerset.py", line 134, in invoke 
    8997 return self._func(self._name, data) 
    8998 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8999 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9000 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9001 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9002 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9003 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9004 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9005  
    9006 Error processing trigger "setting changed": 
    9007 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9008  
    9009 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9010 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9011 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9012  
    9013 See log for complete Python traceback. 
    9014  
    9015 Traceback (most recent call last): 
    9016 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9017 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9018 return self._func(self._name, data) 
    9019 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9020 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9021 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9022 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9023 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9024 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9025 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9026  
    9027 Error processing trigger "setting changed": 
    9028 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9029  
    9030 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9031 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9032 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9033  
    9034 See log for complete Python traceback. 
    9035  
    9036 Traceback (most recent call last): 
    9037 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9038 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9039 return self._func(self._name, data) 
    9040 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9041 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9042 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9043 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9044 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9045 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9046 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9047  
    9048 Error processing trigger "setting changed": 
    9049 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9050  
    9051 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9052 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9053 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9054  
    9055 See log for complete Python traceback. 
    9056  
    9057 Traceback (most recent call last): 
    9058 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9059 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9060 return self._func(self._name, data) 
    9061 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9062 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9063 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9064 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9065 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9066 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9067 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9068  
    9069 Error processing trigger "setting changed": 
    9070 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9071  
    9072 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9073 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9074 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9075  
    9076 See log for complete Python traceback. 
    9077  
    9078 Traceback (most recent call last): 
    9079 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9080 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9081 return self._func(self._name, data) 
    9082 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9083 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9084 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9085 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9086 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9087 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9088 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9089  
    9090 Error processing trigger "setting changed": 
    9091 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9092  
    9093 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9094 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9095 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9096  
    9097 See log for complete Python traceback. 
    9098  
    9099 
    9100 > matchmaker #8/R to #4/R pairing ss
    9101 
    9102 Parameters 
    9103 --- 
    9104 Chain pairing | ss 
    9105 Alignment algorithm | Needleman-Wunsch 
    9106 Similarity matrix | BLOSUM-62 
    9107 SS fraction | 0.3 
    9108 Gap open (HH/SS/other) | 18/18/6 
    9109 Gap extend | 1 
    9110 SS matrix |  |  | H | S | O 
    9111 ---|---|---|--- 
    9112 H | 6 | -9 | -6 
    9113 S |  | 6 | -6 
    9114 O |  |  | 4 
    9115 Iteration cutoff | 2 
    9116  
    9117 Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
    9118 alignment score = 499.8 
    9119 RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
    9120 14.356) 
    9121  
    9122 
    9123 > matchmaker #8/R to #4/R pairing ss
    9124 
    9125 Parameters 
    9126 --- 
    9127 Chain pairing | ss 
    9128 Alignment algorithm | Needleman-Wunsch 
    9129 Similarity matrix | BLOSUM-62 
    9130 SS fraction | 0.3 
    9131 Gap open (HH/SS/other) | 18/18/6 
    9132 Gap extend | 1 
    9133 SS matrix |  |  | H | S | O 
    9134 ---|---|---|--- 
    9135 H | 6 | -9 | -6 
    9136 S |  | 6 | -6 
    9137 O |  |  | 4 
    9138 Iteration cutoff | 2 
    9139  
    9140 Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
    9141 alignment score = 499.8 
    9142 RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
    9143 14.356) 
    9144  
    9145 
    9146 > ui tool show Matchmaker
    9147 
    9148 [Repeated 1 time(s)]Traceback (most recent call last): 
    9149 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9150 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9151 return self._func(self._name, data) 
    9152 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9153 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9154 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9155 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9156 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9157 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9158 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9159  
    9160 Error processing trigger "setting changed": 
    9161 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9162  
    9163 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9164 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9165 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9166  
    9167 See log for complete Python traceback. 
    9168  
    9169 Traceback (most recent call last): 
    9170 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9171 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9172 return self._func(self._name, data) 
    9173 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9174 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9175 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9176 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9177 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9178 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9179 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9180  
    9181 Error processing trigger "setting changed": 
    9182 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9183  
    9184 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9185 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9186 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9187  
    9188 See log for complete Python traceback. 
    9189  
    9190 Traceback (most recent call last): 
    9191 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9192 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9193 return self._func(self._name, data) 
    9194 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9195 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9196 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9197 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9198 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9199 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9200 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9201  
    9202 Error processing trigger "setting changed": 
    9203 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9204  
    9205 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9206 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9207 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9208  
    9209 See log for complete Python traceback. 
    9210  
    9211 Traceback (most recent call last): 
    9212 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9213 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9214 return self._func(self._name, data) 
    9215 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9216 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9217 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9218 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9219 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9220 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9221 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9222  
    9223 Error processing trigger "setting changed": 
    9224 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9225  
    9226 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9227 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9228 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9229  
    9230 See log for complete Python traceback. 
    9231  
    9232 Traceback (most recent call last): 
    9233 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9234 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9235 return self._func(self._name, data) 
    9236 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9237 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9238 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9239 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9240 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9241 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9242 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9243  
    9244 Error processing trigger "setting changed": 
    9245 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9246  
    9247 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9248 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9249 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9250  
    9251 See log for complete Python traceback. 
    9252  
    9253 Traceback (most recent call last): 
    9254 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9255 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9256 return self._func(self._name, data) 
    9257 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9258 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9259 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9260 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9261 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9262 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9263 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9264  
    9265 Error processing trigger "setting changed": 
    9266 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9267  
    9268 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9269 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9270 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9271  
    9272 See log for complete Python traceback. 
    9273  
    9274 Traceback (most recent call last): 
    9275 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9276 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9277 return self._func(self._name, data) 
    9278 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9279 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9280 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9281 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9282 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9283 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9284 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9285  
    9286 Error processing trigger "setting changed": 
    9287 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9288  
    9289 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9290 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9291 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9292  
    9293 See log for complete Python traceback. 
    9294  
    9295 Traceback (most recent call last): 
    9296 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9297 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9298 return self._func(self._name, data) 
    9299 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9300 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9301 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9302 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9303 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9304 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9305 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9306  
    9307 Error processing trigger "setting changed": 
    9308 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9309  
    9310 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9311 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9312 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9313  
    9314 See log for complete Python traceback. 
    9315  
    9316 Traceback (most recent call last): 
    9317 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9318 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9319 return self._func(self._name, data) 
    9320 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9321 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9322 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9323 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9324 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9325 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9326 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9327  
    9328 Error processing trigger "setting changed": 
    9329 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9330  
    9331 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9332 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9333 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9334  
    9335 See log for complete Python traceback. 
    9336  
    9337 Traceback (most recent call last): 
    9338 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9339 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9340 return self._func(self._name, data) 
    9341 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9342 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9343 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9344 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9345 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9346 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9347 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9348  
    9349 Error processing trigger "setting changed": 
    9350 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9351  
    9352 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9353 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9354 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9355  
    9356 See log for complete Python traceback. 
    9357  
    9358 Traceback (most recent call last): 
    9359 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9360 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9361 return self._func(self._name, data) 
    9362 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9363 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9364 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9365 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9366 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9367 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9368 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9369  
    9370 Error processing trigger "setting changed": 
    9371 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9372  
    9373 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9374 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9375 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9376  
    9377 See log for complete Python traceback. 
    9378  
    9379 Traceback (most recent call last): 
    9380 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9381 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9382 return self._func(self._name, data) 
    9383 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9384 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9385 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9386 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9387 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9388 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9389 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9390  
    9391 Error processing trigger "setting changed": 
    9392 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9393  
    9394 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9395 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9396 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9397  
    9398 See log for complete Python traceback. 
    9399  
    9400 Traceback (most recent call last): 
    9401 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9402 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9403 return self._func(self._name, data) 
    9404 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9405 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9406 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9407 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9408 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9409 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9410 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9411  
    9412 Error processing trigger "setting changed": 
    9413 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9414  
    9415 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9416 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9417 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9418  
    9419 See log for complete Python traceback. 
    9420  
    9421 Traceback (most recent call last): 
    9422 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9423 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9424 return self._func(self._name, data) 
    9425 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9426 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9427 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9428 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9429 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9430 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9431 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9432  
    9433 Error processing trigger "setting changed": 
    9434 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9435  
    9436 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9437 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9438 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9439  
    9440 See log for complete Python traceback. 
    9441  
    9442 Traceback (most recent call last): 
    9443 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9444 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9445 return self._func(self._name, data) 
    9446 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9447 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9448 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9449 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9450 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9451 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9452 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9453  
    9454 Error processing trigger "setting changed": 
    9455 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9456  
    9457 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9458 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9459 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9460  
    9461 See log for complete Python traceback. 
    9462  
    9463 Traceback (most recent call last): 
    9464 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9465 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9466 return self._func(self._name, data) 
    9467 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9468 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9469 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9470 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9471 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9472 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9473 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9474  
    9475 Error processing trigger "setting changed": 
    9476 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9477  
    9478 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9479 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9480 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9481  
    9482 See log for complete Python traceback. 
    9483  
    9484 Traceback (most recent call last): 
    9485 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9486 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9487 return self._func(self._name, data) 
    9488 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9489 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9490 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9491 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9492 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9493 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9494 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9495  
    9496 Error processing trigger "setting changed": 
    9497 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9498  
    9499 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9500 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9501 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9502  
    9503 See log for complete Python traceback. 
    9504  
    9505 Traceback (most recent call last): 
    9506 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9507 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9508 return self._func(self._name, data) 
    9509 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9510 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9511 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9512 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9513 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9514 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9515 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9516  
    9517 Error processing trigger "setting changed": 
    9518 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9519  
    9520 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9521 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9522 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9523  
    9524 See log for complete Python traceback. 
    9525  
    9526 Traceback (most recent call last): 
    9527 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9528 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9529 return self._func(self._name, data) 
    9530 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9531 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9532 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9533 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9534 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9535 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9536 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9537  
    9538 Error processing trigger "setting changed": 
    9539 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9540  
    9541 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9542 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9543 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9544  
    9545 See log for complete Python traceback. 
    9546  
    9547 Traceback (most recent call last): 
    9548 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9549 packages/chimerax/core/triggerset.py", line 134, in invoke 
    9550 return self._func(self._name, data) 
    9551 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9552 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    9553 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    9554 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9555 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9556 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9557 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9558  
    9559 Error processing trigger "setting changed": 
    9560 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    9561  
    9562 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9563 packages/chimerax/ui/options/options.py", line 342, in set_value 
    9564 self.__button_group.button(self.values.index(value)).setChecked(True) 
    9565  
    9566 See log for complete Python traceback. 
    9567  
    9568 
    9569 > matchmaker #!8 to #4
    9570 
    9571 Parameters 
    9572 --- 
    9573 Chain pairing | bb 
    9574 Alignment algorithm | Needleman-Wunsch 
    9575 Similarity matrix | BLOSUM-62 
    9576 SS fraction | 0.3 
    9577 Gap open (HH/SS/other) | 18/18/6 
    9578 Gap extend | 1 
    9579 SS matrix |  |  | H | S | O 
    9580 ---|---|---|--- 
    9581 H | 6 | -9 | -6 
    9582 S |  | 6 | -6 
    9583 O |  |  | 4 
    9584 Iteration cutoff | 2 
    9585  
    9586 Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
    9587 alignment score = 476.4 
    9588 RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
    9589 14.356) 
    9590  
    9591 
    9592 > matchmaker #!8 to #4
    9593 
    9594 Parameters 
    9595 --- 
    9596 Chain pairing | bb 
    9597 Alignment algorithm | Needleman-Wunsch 
    9598 Similarity matrix | BLOSUM-62 
    9599 SS fraction | 0.3 
    9600 Gap open (HH/SS/other) | 18/18/6 
    9601 Gap extend | 1 
    9602 SS matrix |  |  | H | S | O 
    9603 ---|---|---|--- 
    9604 H | 6 | -9 | -6 
    9605 S |  | 6 | -6 
    9606 O |  |  | 4 
    9607 Iteration cutoff | 2 
    9608  
    9609 Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
    9610 alignment score = 476.4 
    9611 RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
    9612 14.356) 
    9613  
    9614 
    9615 > select add #8
    9616 
    9617 2984 atoms, 3047 bonds, 13 pseudobonds, 380 residues, 3 models selected 
    9618 
    9619 > ui mousemode right "rotate selected models"
    9620 
    9621 > view matrix models
    9622 > #8,0.5203,0.56446,-0.64084,135.43,0.36003,-0.82545,-0.43475,422.57,-0.77438,-0.0045259,-0.6327,409.12
    9623 
    9624 > ui mousemode right "translate selected models"
    9625 
    9626 > view matrix models
    9627 > #8,0.5203,0.56446,-0.64084,121.21,0.36003,-0.82545,-0.43475,360.91,-0.77438,-0.0045259,-0.6327,411.66
    9628 
    9629 > view matrix models
    9630 > #8,0.5203,0.56446,-0.64084,67.915,0.36003,-0.82545,-0.43475,357.48,-0.77438,-0.0045259,-0.6327,425.56
    9631 
    9632 > view matrix models
    9633 > #8,0.5203,0.56446,-0.64084,83.916,0.36003,-0.82545,-0.43475,369.99,-0.77438,-0.0045259,-0.6327,452.45
    9634 
    9635 > view matrix models
    9636 > #8,0.5203,0.56446,-0.64084,75.872,0.36003,-0.82545,-0.43475,367.76,-0.77438,-0.0045259,-0.6327,456.02
    9637 
    9638 > view matrix models
    9639 > #8,0.5203,0.56446,-0.64084,74.881,0.36003,-0.82545,-0.43475,370.35,-0.77438,-0.0045259,-0.6327,456.29
    9640 
    9641 > view matrix models
    9642 > #8,0.5203,0.56446,-0.64084,75.862,0.36003,-0.82545,-0.43475,369.49,-0.77438,-0.0045259,-0.6327,457.55
    9643 
    9644 > ui mousemode right "translate selected models"
    9645 
    9646 > ui mousemode right "rotate selected models"
    9647 
    9648 > view matrix models
    9649 > #8,0.2363,0.60838,-0.75765,130.06,0.41768,-0.76762,-0.48612,357.73,-0.87733,-0.20159,-0.43549,479.62
    9650 
    9651 > ui mousemode right "translate selected models"
    9652 
    9653 > view matrix models
    9654 > #8,0.2363,0.60838,-0.75765,133.58,0.41768,-0.76762,-0.48612,354.6,-0.87733,-0.20159,-0.43549,486.99
    9655 
    9656 > view matrix models
    9657 > #8,0.2363,0.60838,-0.75765,133.86,0.41768,-0.76762,-0.48612,354.1,-0.87733,-0.20159,-0.43549,487.38
    9658 
    9659 > select clear
    9660 
    9661 > select #8/R:19-39
    9662 
    9663 184 atoms, 190 bonds, 21 residues, 1 model selected 
    9664 
    9665 > delete sel
    9666 
    9667 Undo failed, probably because structures have been modified. 
    9668 
    9669 > hide #!8 models
    9670 
    9671 > show #!8 models
    9672 
    9673 > show #!9 models
    9674 
    9675 > hide #!8 models
    9676 
    9677 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9678 chains... 
    9679 Chain information for fullmodel-v5.pdb 
    9680 --- 
    9681 Chain | Description 
    9682 4.2/A | No description available 
    9683 4.2/B | No description available 
    9684 4.2/C | No description available 
    9685 4.2/D | No description available 
    9686 4.2/E | No description available 
    9687 4.2/R | No description available 
    9688  
    9689 
    9690 > clipper associate #9 toModel #4
    9691 
    9692 Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #4.1.1.1, grid
    9693 size 480,480,480, pixel 0.825, shown at step 1, values float32 
    9694 
    9695 > view matrix models #4.2,1,0,0,0.56548,0,1,0,-4.8388,0,0,1,-5.2016
    9696 
    9697 > show #!3 models
    9698 
    9699 > hide #!3 models
    9700 
    9701 > isolde sim start sel
    9702 
    9703 ISOLDE: started sim 
    9704 
    9705 > isolde sim pause
    9706 
    9707 > hide #!4 models
    9708 
    9709 > show #!4 models
    9710 
    9711 > hide #!4.1 models
    9712 
    9713 > show #!4.1 models
    9714 
    9715 > volume #!4.1.1.1 style surface
    9716 
    9717 > fitmap #4.2 inMap #4.1.1.1
    9718 
    9719 Fit molecule fullmodel-v5.pdb (#4.2) to map
    9720 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#4.1.1.1) using 19807 atoms 
    9721 average map value = 0.1316, steps = 140 
    9722 shifted from previous position = 7.11 
    9723 rotated from previous position = 0.0441 degrees 
    9724 atoms outside contour = 15522, contour level = 0.19368 
    9725  
    9726 Position of fullmodel-v5.pdb (#4.2) relative to
    9727 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#4.1.1.1) coordinates: 
    9728 Matrix rotation and translation 
    9729 0.99999973 -0.00058113 0.00045808 0.02446487 
    9730 0.00058103 0.99999981 0.00021172 -0.18611887 
    9731 -0.00045820 -0.00021146 0.99999987 0.13541812 
    9732 Axis -0.27492671 0.59527919 0.75502185 
    9733 Axis point 304.68612802 34.72877780 0.00000000 
    9734 Rotation angle (degrees) 0.04409607 
    9735 Shift along axis -0.01527510 
    9736  
    9737 
    9738 > isolde sim resume
    9739 
    9740 > isolde sim pause
    9741 
    9742 > isolde sim stop
    9743 
    9744 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9745 chains... 
    9746 ISOLDE: Corrected atom nomenclature of 39 residues in model #4.2 to IUPAC-IUB
    9747 standards. 
    9748 ISOLDE: stopped sim 
    9749 
    9750 > isolde sim start sel
    9751 
    9752 ISOLDE: started sim 
    9753 
    9754 > isolde sim stop
    9755 
    9756 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9757 chains... 
    9758 ISOLDE: Corrected atom nomenclature of 50 residues in model #4.2 to IUPAC-IUB
    9759 standards. 
    9760 ISOLDE: stopped sim 
    9761 
    9762 > save /home/pinkie/Documents/Charlotte/2024_01_28/fulmodel-v6-crosslinked.pdb
    9763 > models #4
    9764 
    9765 > hide #!4 models
    9766 
    9767 > show #!4 models
    9768 
    9769 > show #!7 models
    9770 
    9771 > hide #!7 models
    9772 
    9773 > hide #!4 models
    9774 
    9775 > show #!3 models
    9776 
    9777 > volume flip #3
    9778 
    9779 Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #6, grid size
    9780 480,480,480, pixel 0.825, shown at step 1, values float32 
    9781 
    9782 > open /home/pinkie/Documents/Charlotte/2024_01_28/fulmodel-v6-crosslinked.pdb
    9783 
    9784 Chain information for fulmodel-v6-crosslinked.pdb #9 
    9785 --- 
    9786 Chain | Description 
    9787 A | No description available 
    9788 B | No description available 
    9789 C | No description available 
    9790 D | No description available 
    9791 E | No description available 
    9792 R | No description available 
    9793  
    9794 
    9795 > open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb
    9796 
    9797 Chain information for fullmodel-v5.pdb #10 
    9798 --- 
    9799 Chain | Description 
    9800 A | No description available 
    9801 B | No description available 
    9802 C | No description available 
    9803 D | No description available 
    9804 E | No description available 
    9805 R | No description available 
    9806  
    9807 
    9808 > hide #9-10 atoms
    9809 
    9810 > show #9-10 cartoons
    9811 
    9812 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    9813 got 2 atomic models, 1 maps. 
    9814 
    9815 > hide #10 models
    9816 
    9817 > fitmap #9 inMap #6
    9818 
    9819 Fit molecule fulmodel-v6-crosslinked.pdb (#9) to map
    9820 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) using 19807 atoms 
    9821 average map value = 0.1322, steps = 48 
    9822 shifted from previous position = 0.00848 
    9823 rotated from previous position = 0.0222 degrees 
    9824 atoms outside contour = 7877, contour level = 0.093576 
    9825  
    9826 Position of fulmodel-v6-crosslinked.pdb (#9) relative to
    9827 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) coordinates: 
    9828 Matrix rotation and translation 
    9829 0.99999993 -0.00034748 -0.00013386 0.09294722 
    9830 0.00034750 0.99999993 0.00010561 -0.08510450 
    9831 0.00013382 -0.00010566 0.99999999 0.00149379 
    9832 Axis -0.27290890 -0.34577439 0.89775320 
    9833 Axis point 239.58376669 271.68215520 0.00000000 
    9834 Rotation angle (degrees) 0.02217725 
    9835 Shift along axis 0.00540189 
    9836  
    9837 
    9838 > hide #9 models
    9839 
    9840 > show #10 models
    9841 
    9842 > fitmap #10 inMap #6
    9843 
    9844 Fit molecule fullmodel-v5.pdb (#10) to map
    9845 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) using 19807 atoms 
    9846 average map value = 0.1121, steps = 152 
    9847 shifted from previous position = 10.8 
    9848 rotated from previous position = 6.89 degrees 
    9849 atoms outside contour = 9792, contour level = 0.093576 
    9850  
    9851 Position of fullmodel-v5.pdb (#10) relative to
    9852 cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) coordinates: 
    9853 Matrix rotation and translation 
    9854 0.99762593 -0.02091198 -0.06561397 23.93517264 
    9855 0.01436000 0.99500528 -0.09878407 25.98670381 
    9856 0.06735202 0.09760733 0.99294336 -32.41050705 
    9857 Axis 0.81905399 -0.55453714 0.14710244 
    9858 Axis point 0.00000000 350.60177499 247.72967437 
    9859 Rotation angle (degrees) 6.88570607 
    9860 Shift along axis 0.42594157 
    9861  
    9862 
    9863 > show #9 models
    9864 
    9865 > hide #!6 models
    9866 
    9867 > hide #10 models
    9868 
    9869 > show #10 models
    9870 
    9871 > hide #10 models
    9872 
    9873 > show #10 models
    9874 
    9875 > hide #10 models
    9876 
    9877 > show #10 models
    9878 
    9879 > hide #10 models
    9880 
    9881 > show #10 models
    9882 
    9883 > hide #10 models
    9884 
    9885 > show #10 models
    9886 
    9887 > hide #10 models
    9888 
    9889 > show #10 models
    9890 
    9891 > show #!5 models
    9892 
    9893 > show #9-10#!5 cartoons
    9894 
    9895 > hide #!5 models
    9896 
    9897 > show #!5 models
    9898 
    9899 > hide #!5 models
    9900 
    9901 > show #!5 models
    9902 
    9903 > select add #5
    9904 
    9905 23537 atoms, 23790 bonds, 1 pseudobond, 1735 residues, 3 models selected 
    9906 
    9907 > help help:user
    9908 
    9909 > ui mousemode right "translate selected models"
    9910 
    9911 > view matrix models
    9912 > #5,-0.52174,-0.29947,0.79881,191.85,-0.34266,-0.78395,-0.5177,206.15,0.78126,-0.54383,0.3064,152.39,#4.2,1,-0.00058113,0.00045808,-0.80996,0.00058103,1,0.00021172,5.8066,-0.0004582,-0.00021146,1,0.83911
    9913 
    9914 > select subtract #5
    9915 
    9916 19807 atoms, 20027 bonds, 1225 residues, 1 model selected 
    9917 
    9918 > hide #9 models
    9919 
    9920 > hide #10 models
    9921 
    9922 > show #!6 models
    9923 
    9924 > fitmap #5 inMap #6
    9925 
    9926 Fit molecule 5t35 (#5) to map cryosparc_P9_J635_008_volume_map_sharp.mrc z
    9927 flip (#6) using 3730 atoms 
    9928 average map value = 0.08285, steps = 112 
    9929 shifted from previous position = 5.2 
    9930 rotated from previous position = 3.59 degrees 
    9931 atoms outside contour = 2412, contour level = 0.093576 
    9932  
    9933 Position of 5t35 (#5) relative to cryosparc_P9_J635_008_volume_map_sharp.mrc z
    9934 flip (#6) coordinates: 
    9935 Matrix rotation and translation 
    9936 -0.49489741 -0.35355994 0.79377070 195.33404698 
    9937 -0.33737792 -0.76363743 -0.55048525 209.06766347 
    9938 0.80078255 -0.54023443 0.25863887 152.81110365 
    9939 Axis 0.50252548 -0.34374169 0.79329049 
    9940 Axis point 48.43141862 138.03079969 0.00000000 
    9941 Rotation angle (degrees) 179.41561301 
    9942 Shift along axis 147.51865747 
    9943  
    9944 
    9945 > show #9 models
    9946 
    9947 > show #10 models
    9948 
    9949 > hide #!6 models
    9950 
    9951 > hide #!5 models
    9952 
    9953 > select #9/R
    9954 
    9955 1432 atoms, 1452 bonds, 92 residues, 1 model selected 
    9956 
    9957 > select clear
    9958 
    9959 > select #9/R
    9960 
    9961 1432 atoms, 1452 bonds, 92 residues, 1 model selected 
    9962 
    9963 > color sel lime
    9964 
    9965 > select clear
    9966 
    9967 > open
    9968 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J649_006_volume_map_sharp.mrc
    9969 
    9970 Opened cryosparc_P9_J649_006_volume_map_sharp.mrc as #11, grid size
    9971 420,420,420, pixel 0.825, shown at level 0.0268, step 2, values float32 
    9972 
    9973 > volume #11 level 0.09477
    9974 
    9975 > volume #11 level 0.07304
    9976 
    9977 > select add #11
    9978 
    9979 3 models selected 
    9980 
    9981 > ui mousemode right "translate selected models"
    9982 
    9983 > ui mousemode right "rotate selected models"
    9984 
    9985 > view matrix models
    9986 > #11,0.79578,-0.21636,0.56562,-21.157,-0.2012,-0.9754,-0.090028,385.2,0.57118,-0.042161,-0.81974,208.32
    9987 
    9988 > volume flip #11
    9989 
    9990 Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #12, grid size
    9991 420,420,420, pixel 0.825, shown at step 1, values float32 
    9992 
    9993 > select add #12
    9994 
    9995 4 models selected 
    9996 
    9997 > close #11
    9998 
    9999 > ui mousemode right "translate selected models"
    10000 
    10001 > view matrix models
    10002 > #12,0.79578,-0.21636,0.56562,-21.535,-0.2012,-0.9754,-0.090028,420.27,0.57118,-0.042161,-0.81974,256.69
    10003 
    10004 > ui mousemode right "rotate selected models"
    10005 
    10006 > view matrix models
    10007 > #12,-0.97755,0.059009,-0.20229,370.12,-0.055777,-0.99821,-0.021647,387.2,-0.20321,-0.0098776,0.97909,50.616
    10008 
    10009 > ui mousemode right "translate selected models"
    10010 
    10011 > view matrix models
    10012 > #12,-0.97755,0.059009,-0.20229,369.93,-0.055777,-0.99821,-0.021647,388.27,-0.20321,-0.0098776,0.97909,64.412
    10013 
    10014 > view matrix models
    10015 > #12,-0.97755,0.059009,-0.20229,390.8,-0.055777,-0.99821,-0.021647,385.58,-0.20321,-0.0098776,0.97909,68.302
    10016 
    10017 Must specify one map, got 0 
    10018 
    10019 > show #!7 models
    10020 
    10021 > hide #!7 models
    10022 
    10023 > show #!6 models
    10024 
    10025 > hide #!6 models
    10026 
    10027 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    10028 got 2 atomic models, 1 maps. 
    10029 
    10030 > hide #!4.1 models
    10031 
    10032 > hide #!4.2 models
    10033 
    10034 > hide #4.3 models
    10035 
    10036 > close #10
    10037 
    10038 > fitmap #9 inMap #12
    10039 
    10040 Fit molecule fulmodel-v6-crosslinked.pdb (#9) to map
    10041 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#12) using 19807 atoms 
    10042 average map value = 0.1186, steps = 168 
    10043 shifted from previous position = 7.18 
    10044 rotated from previous position = 10.2 degrees 
    10045 atoms outside contour = 7210, contour level = 0.073036 
    10046  
    10047 Position of fulmodel-v6-crosslinked.pdb (#9) relative to
    10048 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#12) coordinates: 
    10049 Matrix rotation and translation 
    10050 -0.99893072 -0.03543972 -0.02968888 383.81872944 
    10051 0.03672114 -0.99836564 -0.04379003 372.34530599 
    10052 -0.02808845 -0.04483342 0.99859951 -6.07997840 
    10053 Axis -0.01445423 -0.02217085 0.99964970 
    10054 Axis point 188.50734431 189.56827757 0.00000000 
    10055 Rotation angle (degrees) 177.93156998 
    10056 Shift along axis -19.88086512 
    10057  
    10058 
    10059 > select clear
    10060 
    10061 > surface dust #12 size 8.25
    10062 
    10063 > volume #12 level 0.04915
    10064 
    10065 > volume #4.1.1.1 level 0.1137
    10066 
    10067 > show #!4.1 models
    10068 
    10069 > show #!4.2 models
    10070 
    10071 > show #4.3 models
    10072 
    10073 > hide #!4.2 models
    10074 
    10075 > hide #4.3 models
    10076 
    10077 > hide #!4.1 models
    10078 
    10079 > show #!6 models
    10080 
    10081 > hide #!6 models
    10082 
    10083 > open 8b3i
    10084 
    10085 Summary of feedback from opening 8b3i fetched from pdb 
    10086 --- 
    10087 warnings | Atom H1 is not in the residue template for MET /N:1 
    10088 Atom H1 is not in the residue template for MET /U:1 
    10089 Atom H1 is not in the residue template for MET /a:1 
    10090 Atom H1 is not in the residue template for MET /d:1 
    10091 note | Fetching compressed mmCIF 8b3i from
    10092 http://files.rcsb.org/download/8b3i.cif 
    10093  
    10094 8b3i title: 
    10095 CRL4CSA-E2-Ub (state 2) [more info...] 
    10096  
    10097 Chain information for 8b3i #10 
    10098 --- 
    10099 Chain | Description | UniProt 
    10100 D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 
    10101 N | NEDD8 | NEDD8_HUMAN 
    10102 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 
    10103 U | Ubiquitin | UBC_HUMAN 
    10104 a | DNA excision repair protein ERCC-8 | ERCC8_HUMAN 
    10105 d | DNA damage-binding protein 1 | DDB1_HUMAN 
    10106 e | Cullin-4A | CUL4A_HUMAN 
    10107  
    10108 Non-standard residues in 8b3i #10 
    10109 --- 
    10110 ZN — zinc ion 
    10111  
    10112 
    10113 > select #10/a
    10114 
    10115 5627 atoms, 5686 bonds, 365 residues, 1 model selected 
    10116 
    10117 > delete sel
    10118 
    10119 > select #10/d
    10120 
    10121 17196 atoms, 17351 bonds, 6 pseudobonds, 1096 residues, 2 models selected 
    10122 
    10123 > delete sel
    10124 
    10125 > ui tool show Matchmaker
    10126 
    10127 > matchmaker #!10 to #9
    10128 
    10129 Parameters 
    10130 --- 
    10131 Chain pairing | bb 
    10132 Alignment algorithm | Needleman-Wunsch 
    10133 Similarity matrix | BLOSUM-62 
    10134 SS fraction | 0.3 
    10135 Gap open (HH/SS/other) | 18/18/6 
    10136 Gap extend | 1 
    10137 SS matrix |  |  | H | S | O 
    10138 ---|---|---|--- 
    10139 H | 6 | -9 | -6 
    10140 S |  | 6 | -6 
    10141 O |  |  | 4 
    10142 Iteration cutoff | 2 
    10143  
    10144 Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
    10145 sequence alignment score = 1216.9 
    10146 RMSD between 161 pruned atom pairs is 1.160 angstroms; (across all 614 pairs:
    10147 19.630) 
    10148  
    10149 
    10150 > matchmaker #!10 to #9
    10151 
    10152 Parameters 
    10153 --- 
    10154 Chain pairing | bb 
    10155 Alignment algorithm | Needleman-Wunsch 
    10156 Similarity matrix | BLOSUM-62 
    10157 SS fraction | 0.3 
    10158 Gap open (HH/SS/other) | 18/18/6 
    10159 Gap extend | 1 
    10160 SS matrix |  |  | H | S | O 
    10161 ---|---|---|--- 
    10162 H | 6 | -9 | -6 
    10163 S |  | 6 | -6 
    10164 O |  |  | 4 
    10165 Iteration cutoff | 2 
    10166  
    10167 Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
    10168 sequence alignment score = 1216.9 
    10169 RMSD between 161 pruned atom pairs is 1.160 angstroms; (across all 614 pairs:
    10170 19.630) 
    10171  
    10172 
    10173 > hide #!12 models
    10174 
    10175 > hide #9 models
    10176 
    10177 > hide #!4 models
    10178 
    10179 > hide #!10 atoms
    10180 
    10181 > show #!10 cartoons
    10182 
    10183 > select #10/E:42-354
    10184 
    10185 Nothing selected 
    10186 
    10187 > select #10/e:42-354
    10188 
    10189 5160 atoms, 5206 bonds, 313 residues, 1 model selected 
    10190 
    10191 > delete sel
    10192 
    10193 > show #9 models
    10194 
    10195 > ui tool show Matchmaker
    10196 
    10197 > matchmaker #!10 to #9
    10198 
    10199 Parameters 
    10200 --- 
    10201 Chain pairing | bb 
    10202 Alignment algorithm | Needleman-Wunsch 
    10203 Similarity matrix | BLOSUM-62 
    10204 SS fraction | 0.3 
    10205 Gap open (HH/SS/other) | 18/18/6 
    10206 Gap extend | 1 
    10207 SS matrix |  |  | H | S | O 
    10208 ---|---|---|--- 
    10209 H | 6 | -9 | -6 
    10210 S |  | 6 | -6 
    10211 O |  |  | 4 
    10212 Iteration cutoff | 2 
    10213  
    10214 Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
    10215 sequence alignment score = 826.6 
    10216 RMSD between 150 pruned atom pairs is 1.050 angstroms; (across all 315 pairs:
    10217 4.185) 
    10218  
    10219 
    10220 > matchmaker #!10 to #9
    10221 
    10222 Parameters 
    10223 --- 
    10224 Chain pairing | bb 
    10225 Alignment algorithm | Needleman-Wunsch 
    10226 Similarity matrix | BLOSUM-62 
    10227 SS fraction | 0.3 
    10228 Gap open (HH/SS/other) | 18/18/6 
    10229 Gap extend | 1 
    10230 SS matrix |  |  | H | S | O 
    10231 ---|---|---|--- 
    10232 H | 6 | -9 | -6 
    10233 S |  | 6 | -6 
    10234 O |  |  | 4 
    10235 Iteration cutoff | 2 
    10236  
    10237 Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
    10238 sequence alignment score = 826.6 
    10239 RMSD between 150 pruned atom pairs is 1.050 angstroms; (across all 315 pairs:
    10240 4.185) 
    10241  
    10242 
    10243 > show #!12 models
    10244 
    10245 > hide #9 models
    10246 
    10247 > show #9 models
    10248 
    10249 > hide #!12 models
    10250 
    10251 > open 6nyo
    10252 
    10253 Summary of feedback from opening 6nyo fetched from pdb 
    10254 --- 
    10255 note | Fetching compressed mmCIF 6nyo from
    10256 http://files.rcsb.org/download/6nyo.cif 
    10257  
    10258 6nyo title: 
    10259 Crystal structure of a human Cdc34-ubiquitin thioester mimetic [more info...] 
    10260  
    10261 Chain information for 6nyo #11 
    10262 --- 
    10263 Chain | Description | UniProt 
    10264 A | Ubiquitin-conjugating enzyme E2 R2 | UB2R2_HUMAN 
    10265 E | Ubiquitin | 
    10266  
    10267 Non-standard residues in 6nyo #11 
    10268 --- 
    10269 EDO — 1,2-ethanediol (ethylene glycol) 
    10270 PO4 — phosphate ion 
    10271 U94 —
    10272 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic
    10273 acid 
    10274  
    10275 
    10276 > ui tool show Matchmaker
    10277 
    10278 > matchmaker #11 to #10
    10279 
    10280 Parameters 
    10281 --- 
    10282 Chain pairing | bb 
    10283 Alignment algorithm | Needleman-Wunsch 
    10284 Similarity matrix | BLOSUM-62 
    10285 SS fraction | 0.3 
    10286 Gap open (HH/SS/other) | 18/18/6 
    10287 Gap extend | 1 
    10288 SS matrix |  |  | H | S | O 
    10289 ---|---|---|--- 
    10290 H | 6 | -9 | -6 
    10291 S |  | 6 | -6 
    10292 O |  |  | 4 
    10293 Iteration cutoff | 2 
    10294  
    10295 Matchmaker 8b3i, chain U (#10) with 6nyo, chain E (#11), sequence alignment
    10296 score = 312.7 
    10297 RMSD between 71 pruned atom pairs is 0.646 angstroms; (across all 76 pairs:
    10298 1.638) 
    10299  
    10300 
    10301 > matchmaker #11 to #10
    10302 
    10303 Parameters 
    10304 --- 
    10305 Chain pairing | bb 
    10306 Alignment algorithm | Needleman-Wunsch 
    10307 Similarity matrix | BLOSUM-62 
    10308 SS fraction | 0.3 
    10309 Gap open (HH/SS/other) | 18/18/6 
    10310 Gap extend | 1 
    10311 SS matrix |  |  | H | S | O 
    10312 ---|---|---|--- 
    10313 H | 6 | -9 | -6 
    10314 S |  | 6 | -6 
    10315 O |  |  | 4 
    10316 Iteration cutoff | 2 
    10317  
    10318 Matchmaker 8b3i, chain U (#10) with 6nyo, chain E (#11), sequence alignment
    10319 score = 312.7 
    10320 RMSD between 71 pruned atom pairs is 0.646 angstroms; (across all 76 pairs:
    10321 1.638) 
    10322  
    10323 
    10324 > show #!12 models
    10325 
    10326 > hide #11 models
    10327 
    10328 > hide #!10 models
    10329 
    10330 > transparency #12.1 50
    10331 
    10332 > volume #12 level 0.1357
    10333 
    10334 > volume #12 level 0.09393
    10335 
    10336 > show #!10 models
    10337 
    10338 > hide #9 models
    10339 
    10340 > volume #12 level 0.07005
    10341 
    10342 > open
    10343 > /home/pinkie/Documents/Charlotte/2024_01_28/OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc
    10344 
    10345 Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc as #13, grid
    10346 size 512,512,512, pixel 0.74, shown at level 0.0183, step 2, values float32 
    10347 
    10348 > volume #13 level 0.08943
    10349 
    10350 > hide #!10 models
    10351 
    10352 > volume #13 level 0.04837
    10353 
    10354 > surface dust #13 size 7.4
    10355 
    10356 > volume #13 level 0.04837
    10357 
    10358 > open
    10359 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J846_005_volume_mask_refine.mrc
    10360 
    10361 Opened cryosparc_P7_J846_005_volume_mask_refine.mrc as #14, grid size
    10362 512,512,512, pixel 0.74, shown at level 0.959, step 2, values float32 
    10363 
    10364 > ui mousemode right "map eraser"
    10365 
    10366 [Repeated 1 time(s)]
    10367 
    10368 Can only have one displayed volume when erasing 
    10369 
    10370 [Repeated 11 time(s)]
    10371 
    10372 > volume erase #13 center 210.44,248.48,205.99 radius 24.248
    10373 
    10374 Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy as #16,
    10375 grid size 512,512,512, pixel 0.74, shown at step 1, values float32 
    10376 
    10377 > volume erase #16 center 141.76,228.51,179.62 radius 24.248
    10378 
    10379 > ui mousemode right "map eraser"
    10380 
    10381 [Repeated 1 time(s)]
    10382 
    10383 > volume gaussian #16
    10384 
    10385 Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy gaussian as
    10386 #17, grid size 512,512,512, pixel 0.74, shown at step 1, values float32 
    10387 
    10388 > volume #17 level 0.02761
    10389 
    10390 > close #17
    10391 
    10392 > volume gaussian #16 sDev 3
    10393 
    10394 Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy gaussian as
    10395 #17, grid size 512,512,512, pixel 0.74, shown at step 1, values float32 
    10396 
    10397 > surface dust #16 size 7.4
    10398 
    10399 > save /home/pinkie/Documents/Charlotte/2024_01_28/J846-edited.mrc models #16
    10400 
    10401 > close #17
    10402 
    10403 > open /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J852_mask.mrc
    10404 
    10405 Opened cryosparc_P7_J852_mask.mrc as #17, grid size 512,512,512, pixel 0.74,
    10406 shown at level 1, step 2, values float32 
    10407 
    10408 > volume #17 level 0.9908
    10409 
    10410 > close #17
    10411 
    10412 > close #16
    10413 
    10414 > close #14
    10415 
    10416 > close #13
    10417 
    10418 > close #1
    10419 
    10420 > volume #7 level 0.07099
    10421 
    10422 > close #3
    10423 
    10424 > volume #12 level 0.04968
    10425 
    10426 > show #9 models
    10427 
    10428 > hide #!12 models
    10429 
    10430 > show #11 models
    10431 
    10432 > select #11/E
    10433 
    10434 705 atoms, 628 bonds, 161 residues, 1 model selected 
    10435 
    10436 > color sel yellow
    10437 
    10438 > select clear
    10439 
    10440 > show #!12 models
    10441 
    10442 > hide #!12 models
    10443 
    10444 > hide #9 models
    10445 
    10446 > show #!8 models
    10447 
    10448 > show #9 models
    10449 
    10450 > hide #9 models
    10451 
    10452 > hide #11 models
    10453 
    10454 > view
    10455 
    10456 > show #11 models
    10457 
    10458 > ui mousemode right translate
    10459 
    10460 > ui mousemode right select
    10461 
    10462 > select clear
    10463 
    10464 > select #11/E:34
    10465 
    10466 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10467 
    10468 > show sel atoms
    10469 
    10470 > color sel orange
    10471 
    10472 > select clear
    10473 
    10474 > hide #!8 models
    10475 
    10476 > show #!8 models
    10477 
    10478 > ui tool show Matchmaker
    10479 
    10480 > matchmaker #!8 to #11
    10481 
    10482 Parameters 
    10483 --- 
    10484 Chain pairing | bb 
    10485 Alignment algorithm | Needleman-Wunsch 
    10486 Similarity matrix | BLOSUM-62 
    10487 SS fraction | 0.3 
    10488 Gap open (HH/SS/other) | 18/18/6 
    10489 Gap extend | 1 
    10490 SS matrix |  |  | H | S | O 
    10491 ---|---|---|--- 
    10492 H | 6 | -9 | -6 
    10493 S |  | 6 | -6 
    10494 O |  |  | 4 
    10495 Iteration cutoff | 2 
    10496  
    10497 Matchmaker 6nyo, chain E (#11) with 6ttu, chain U (#8), sequence alignment
    10498 score = 340 
    10499 RMSD between 70 pruned atom pairs is 0.714 angstroms; (across all 75 pairs:
    10500 1.524) 
    10501  
    10502 
    10503 > matchmaker #!8 to #11
    10504 
    10505 Parameters 
    10506 --- 
    10507 Chain pairing | bb 
    10508 Alignment algorithm | Needleman-Wunsch 
    10509 Similarity matrix | BLOSUM-62 
    10510 SS fraction | 0.3 
    10511 Gap open (HH/SS/other) | 18/18/6 
    10512 Gap extend | 1 
    10513 SS matrix |  |  | H | S | O 
    10514 ---|---|---|--- 
    10515 H | 6 | -9 | -6 
    10516 S |  | 6 | -6 
    10517 O |  |  | 4 
    10518 Iteration cutoff | 2 
    10519  
    10520 Matchmaker 6nyo, chain E (#11) with 6ttu, chain U (#8), sequence alignment
    10521 score = 340 
    10522 RMSD between 70 pruned atom pairs is 0.714 angstroms; (across all 75 pairs:
    10523 1.524) 
    10524  
    10525 
    10526 > show #9 models
    10527 
    10528 Drag select of 27 residues, 1 atoms, 4 bonds 
    10529 
    10530 > select clear
    10531 
    10532 > ui mousemode right translate
    10533 
    10534 > select sequence YGH
    10535 
    10536 92 atoms, 94 bonds, 6 residues, 2 models selected 
    10537 
    10538 > color (#9 & sel) orange red
    10539 
    10540 > select clear
    10541 
    10542 > hide #11 models
    10543 
    10544 > open 6ttu
    10545 
    10546 6ttu title: 
    10547 Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
    10548 NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...] 
    10549  
    10550 Chain information for 6ttu #1 
    10551 --- 
    10552 Chain | Description | UniProt 
    10553 C | Cullin-1 | CUL1_HUMAN 
    10554 D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 
    10555 I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY | 
    10556 N | NEDD8 | NEDD8_HUMAN 
    10557 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 
    10558 S | S-phase kinase-associated protein 1 | SKP1_HUMAN 
    10559 T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 
    10560 U | Polyubiquitin-C | UBC_HUMAN 
    10561  
    10562 Non-standard residues in 6ttu #1 
    10563 --- 
    10564 ZN — zinc ion 
    10565  
    10566 
    10567 > hide #!8 models
    10568 
    10569 > show #!10 models
    10570 
    10571 > hide #!1 models
    10572 
    10573 > show #11 models
    10574 
    10575 > select sequence YGH
    10576 
    10577 92 atoms, 94 bonds, 6 residues, 2 models selected 
    10578 
    10579 > select sequence YGH
    10580 
    10581 92 atoms, 94 bonds, 6 residues, 2 models selected 
    10582 
    10583 > select sequence YGH
    10584 
    10585 92 atoms, 94 bonds, 6 residues, 2 models selected 
    10586 
    10587 > select sequence YGH
    10588 
    10589 92 atoms, 94 bonds, 6 residues, 2 models selected 
    10590 
    10591 > select sequence YGH
    10592 
    10593 92 atoms, 94 bonds, 6 residues, 2 models selected 
    10594 
    10595 > select sequence YGH
    10596 
    10597 92 atoms, 94 bonds, 6 residues, 2 models selected 
    10598 
    10599 > select clear
    10600 
    10601 > show #!12 models
    10602 
    10603 > open
    10604 > /home/pinkie/Documents/Charlotte/2024_01_28/UBE2R1AF-P49427-F1-model_v4.pdb
    10605 
    10606 UBE2R1AF-P49427-F1-model_v4.pdb title: 
    10607 Alphafold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1
    10608 (P49427) [more info...] 
    10609  
    10610 Chain information for UBE2R1AF-P49427-F1-model_v4.pdb #3 
    10611 --- 
    10612 Chain | Description | UniProt 
    10613 A | ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    10614  
    10615 
    10616 > ui tool show Matchmaker
    10617 
    10618 > matchmaker #3 to #11
    10619 
    10620 Parameters 
    10621 --- 
    10622 Chain pairing | bb 
    10623 Alignment algorithm | Needleman-Wunsch 
    10624 Similarity matrix | BLOSUM-62 
    10625 SS fraction | 0.3 
    10626 Gap open (HH/SS/other) | 18/18/6 
    10627 Gap extend | 1 
    10628 SS matrix |  |  | H | S | O 
    10629 ---|---|---|--- 
    10630 H | 6 | -9 | -6 
    10631 S |  | 6 | -6 
    10632 O |  |  | 4 
    10633 Iteration cutoff | 2 
    10634  
    10635 Matchmaker 6nyo, chain A (#11) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
    10636 (#3), sequence alignment score = 920.3 
    10637 RMSD between 162 pruned atom pairs is 1.029 angstroms; (across all 188 pairs:
    10638 1.823) 
    10639  
    10640 
    10641 > matchmaker #3 to #11
    10642 
    10643 Parameters 
    10644 --- 
    10645 Chain pairing | bb 
    10646 Alignment algorithm | Needleman-Wunsch 
    10647 Similarity matrix | BLOSUM-62 
    10648 SS fraction | 0.3 
    10649 Gap open (HH/SS/other) | 18/18/6 
    10650 Gap extend | 1 
    10651 SS matrix |  |  | H | S | O 
    10652 ---|---|---|--- 
    10653 H | 6 | -9 | -6 
    10654 S |  | 6 | -6 
    10655 O |  |  | 4 
    10656 Iteration cutoff | 2 
    10657  
    10658 Matchmaker 6nyo, chain A (#11) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
    10659 (#3), sequence alignment score = 920.3 
    10660 RMSD between 162 pruned atom pairs is 1.029 angstroms; (across all 188 pairs:
    10661 1.823) 
    10662  
    10663 
    10664 > volume #12 level 0.02057
    10665 
    10666 > volume #12 level 0.04386
    10667 
    10668 > hide #!10 models
    10669 
    10670 > hide #!12 models
    10671 
    10672 > hide #11 models
    10673 
    10674 > select #9/R
    10675 
    10676 1432 atoms, 1452 bonds, 92 residues, 1 model selected 
    10677 
    10678 > delete sel
    10679 
    10680 > show #11 models
    10681 
    10682 > hide #11 models
    10683 
    10684 > show #!8 models
    10685 
    10686 > hide #!8 models
    10687 
    10688 > show #!8 models
    10689 
    10690 > hide #!8 models
    10691 
    10692 > show #!1 models
    10693 
    10694 > show #!8 models
    10695 
    10696 > ui tool show Matchmaker
    10697 
    10698 > matchmaker #!1 to #8
    10699 
    10700 Parameters 
    10701 --- 
    10702 Chain pairing | bb 
    10703 Alignment algorithm | Needleman-Wunsch 
    10704 Similarity matrix | BLOSUM-62 
    10705 SS fraction | 0.3 
    10706 Gap open (HH/SS/other) | 18/18/6 
    10707 Gap extend | 1 
    10708 SS matrix |  |  | H | S | O 
    10709 ---|---|---|--- 
    10710 H | 6 | -9 | -6 
    10711 S |  | 6 | -6 
    10712 O |  |  | 4 
    10713 Iteration cutoff | 2 
    10714  
    10715 Matchmaker 6ttu, chain D (#8) with 6ttu, chain D (#1), sequence alignment
    10716 score = 782.4 
    10717 RMSD between 146 pruned atom pairs is 0.000 angstroms; (across all 146 pairs:
    10718 0.000) 
    10719  
    10720 
    10721 > select add #1
    10722 
    10723 12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected 
    10724 
    10725 > show sel cartoons
    10726 
    10727 > hide sel atoms
    10728 
    10729 > select clear
    10730 
    10731 > select #1/I
    10732 
    10733 58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected 
    10734 
    10735 > delete sel
    10736 
    10737 > select #1/T
    10738 
    10739 3085 atoms, 3146 bonds, 2 pseudobonds, 394 residues, 2 models selected 
    10740 
    10741 > delete sel
    10742 
    10743 > select #1/S
    10744 
    10745 891 atoms, 903 bonds, 3 pseudobonds, 123 residues, 2 models selected 
    10746 
    10747 > delete sel
    10748 
    10749 > select #1/C
    10750 
    10751 5728 atoms, 5820 bonds, 6 pseudobonds, 701 residues, 2 models selected 
    10752 
    10753 > delete sel
    10754 
    10755 > show #11 models
    10756 
    10757 > hide #11 models
    10758 
    10759 > show #11 models
    10760 
    10761 > hide #11 models
    10762 
    10763 > show #11 models
    10764 
    10765 > hide #11 models
    10766 
    10767 > show #11 models
    10768 
    10769 > hide #11 models
    10770 
    10771 > show #11 models
    10772 
    10773 > hide #11 models
    10774 
    10775 Traceback (most recent call last): 
    10776 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10777 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10778 return self._func(self._name, data) 
    10779 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10780 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10781 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10782 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10783 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10784 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10785 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10786  
    10787 Error processing trigger "setting changed": 
    10788 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10789  
    10790 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10791 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10792 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10793  
    10794 See log for complete Python traceback. 
    10795  
    10796 Traceback (most recent call last): 
    10797 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10798 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10799 return self._func(self._name, data) 
    10800 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10801 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10802 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10803 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10804 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10805 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10806 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10807  
    10808 Error processing trigger "setting changed": 
    10809 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10810  
    10811 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10812 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10813 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10814  
    10815 See log for complete Python traceback. 
    10816  
    10817 Traceback (most recent call last): 
    10818 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10819 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10820 return self._func(self._name, data) 
    10821 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10822 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10823 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10824 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10825 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10826 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10827 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10828  
    10829 Error processing trigger "setting changed": 
    10830 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10831  
    10832 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10833 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10834 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10835  
    10836 See log for complete Python traceback. 
    10837  
    10838 Traceback (most recent call last): 
    10839 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10840 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10841 return self._func(self._name, data) 
    10842 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10843 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10844 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10845 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10846 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10847 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10848 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10849  
    10850 Error processing trigger "setting changed": 
    10851 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10852  
    10853 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10854 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10855 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10856  
    10857 See log for complete Python traceback. 
    10858  
    10859 Traceback (most recent call last): 
    10860 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10861 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10862 return self._func(self._name, data) 
    10863 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10864 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10865 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10866 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10867 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10868 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10869 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10870  
    10871 Error processing trigger "setting changed": 
    10872 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10873  
    10874 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10875 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10876 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10877  
    10878 See log for complete Python traceback. 
    10879  
    10880 Traceback (most recent call last): 
    10881 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10882 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10883 return self._func(self._name, data) 
    10884 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10885 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10886 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10887 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10888 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10889 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10890 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10891  
    10892 Error processing trigger "setting changed": 
    10893 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10894  
    10895 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10896 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10897 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10898  
    10899 See log for complete Python traceback. 
    10900  
    10901 Traceback (most recent call last): 
    10902 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10903 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10904 return self._func(self._name, data) 
    10905 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10906 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10907 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10908 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10909 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10910 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10911 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10912  
    10913 Error processing trigger "setting changed": 
    10914 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10915  
    10916 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10917 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10918 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10919  
    10920 See log for complete Python traceback. 
    10921  
    10922 Traceback (most recent call last): 
    10923 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10924 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10925 return self._func(self._name, data) 
    10926 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10927 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10928 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10929 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10930 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10931 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10932 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10933  
    10934 Error processing trigger "setting changed": 
    10935 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10936  
    10937 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10938 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10939 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10940  
    10941 See log for complete Python traceback. 
    10942  
    10943 Traceback (most recent call last): 
    10944 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10945 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10946 return self._func(self._name, data) 
    10947 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10948 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10949 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10950 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10951 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10952 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10953 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10954  
    10955 Error processing trigger "setting changed": 
    10956 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10957  
    10958 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10959 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10960 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10961  
    10962 See log for complete Python traceback. 
    10963  
    10964 Traceback (most recent call last): 
    10965 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10966 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10967 return self._func(self._name, data) 
    10968 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10969 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10970 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10971 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10972 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10973 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10974 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10975  
    10976 Error processing trigger "setting changed": 
    10977 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10978  
    10979 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10980 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10981 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10982  
    10983 See log for complete Python traceback. 
    10984  
    10985 Traceback (most recent call last): 
    10986 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10987 packages/chimerax/core/triggerset.py", line 134, in invoke 
    10988 return self._func(self._name, data) 
    10989 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10990 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    10991 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    10992 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10993 packages/chimerax/ui/options/options.py", line 342, in set_value 
    10994 self.__button_group.button(self.values.index(value)).setChecked(True) 
    10995 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10996  
    10997 Error processing trigger "setting changed": 
    10998 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    10999  
    11000 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11001 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11002 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11003  
    11004 See log for complete Python traceback. 
    11005  
    11006 Traceback (most recent call last): 
    11007 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11008 packages/chimerax/core/triggerset.py", line 134, in invoke 
    11009 return self._func(self._name, data) 
    11010 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11011 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    11012 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    11013 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11014 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11015 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11016 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11017  
    11018 Error processing trigger "setting changed": 
    11019 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11020  
    11021 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11022 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11023 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11024  
    11025 See log for complete Python traceback. 
    11026  
    11027 Traceback (most recent call last): 
    11028 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11029 packages/chimerax/core/triggerset.py", line 134, in invoke 
    11030 return self._func(self._name, data) 
    11031 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11032 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    11033 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    11034 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11035 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11036 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11037 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11038  
    11039 Error processing trigger "setting changed": 
    11040 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11041  
    11042 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11043 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11044 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11045  
    11046 See log for complete Python traceback. 
    11047  
    11048 Traceback (most recent call last): 
    11049 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11050 packages/chimerax/core/triggerset.py", line 134, in invoke 
    11051 return self._func(self._name, data) 
    11052 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11053 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    11054 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    11055 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11056 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11057 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11058 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11059  
    11060 Error processing trigger "setting changed": 
    11061 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11062  
    11063 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11064 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11065 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11066  
    11067 See log for complete Python traceback. 
    11068  
    11069 Traceback (most recent call last): 
    11070 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11071 packages/chimerax/core/triggerset.py", line 134, in invoke 
    11072 return self._func(self._name, data) 
    11073 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11074 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    11075 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    11076 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11077 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11078 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11079 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11080  
    11081 Error processing trigger "setting changed": 
    11082 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11083  
    11084 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11085 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11086 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11087  
    11088 See log for complete Python traceback. 
    11089  
    11090 Traceback (most recent call last): 
    11091 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11092 packages/chimerax/core/triggerset.py", line 134, in invoke 
    11093 return self._func(self._name, data) 
    11094 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11095 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    11096 data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute()) 
    11097 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11098 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11099 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11100 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11101  
    11102 Error processing trigger "setting changed": 
    11103 AttributeError: 'NoneType' object has no attribute 'setChecked' 
    11104  
    11105 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    11106 packages/chimerax/ui/options/options.py", line 342, in set_value 
    11107 self.__button_group.button(self.values.index(value)).setChecked(True) 
    11108  
    11109 See log for complete Python traceback. 
    11110  
    11111 
    11112 > matchmaker #3 to #1/D pairing bs
    11113 
    11114 Parameters 
    11115 --- 
    11116 Chain pairing | bs 
    11117 Alignment algorithm | Needleman-Wunsch 
    11118 Similarity matrix | BLOSUM-62 
    11119 SS fraction | 0.3 
    11120 Gap open (HH/SS/other) | 18/18/6 
    11121 Gap extend | 1 
    11122 SS matrix |  |  | H | S | O 
    11123 ---|---|---|--- 
    11124 H | 6 | -9 | -6 
    11125 S |  | 6 | -6 
    11126 O |  |  | 4 
    11127 Iteration cutoff | 2 
    11128  
    11129 Matchmaker 6ttu, chain D (#1) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
    11130 (#3), sequence alignment score = 338.9 
    11131 RMSD between 135 pruned atom pairs is 0.960 angstroms; (across all 145 pairs:
    11132 1.521) 
    11133  
    11134 
    11135 > select #1/D
    11136 
    11137 1135 atoms, 1171 bonds, 146 residues, 1 model selected 
    11138 
    11139 > delete sel
    11140 
    11141 > hide #!8 models
    11142 
    11143 > select add #9
    11144 
    11145 18375 atoms, 18575 bonds, 1133 residues, 1 model selected 
    11146 
    11147 > select add #3
    11148 
    11149 20262 atoms, 20513 bonds, 1369 residues, 2 models selected 
    11150 
    11151 > select add #1
    11152 
    11153 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 5 models selected 
    11154 
    11155 > save /home/pinkie/Documents/Charlotte/2024_01_28/full-model-7.pdb
    11156 > selectedOnly true
    11157 
    11158 > select clear
    11159 
    11160 > select add #1
    11161 
    11162 1849 atoms, 1876 bonds, 13 pseudobonds, 234 residues, 3 models selected 
    11163 
    11164 > select add #3
    11165 
    11166 3736 atoms, 3814 bonds, 13 pseudobonds, 470 residues, 4 models selected 
    11167 
    11168 > select add #9
    11169 
    11170 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 5 models selected 
    11171 
    11172 > combine sel
    11173 
    11174 Remapping chain ID 'A' in fulmodel-v6-crosslinked.pdb #9 to 'F' 
    11175 
    11176 > save /home/pinkie/Documents/Charlotte/2024_01_28/full-model-7.pdb models #13
    11177 
    11178 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11179 chains... 
    11180 ISOLDE: Corrected atom nomenclature of 58 residues in model #13 to IUPAC-IUB
    11181 standards. 
    11182 
    11183 > select clear
    11184 
    11185 > show #!12 models
    11186 
    11187 > hide #!12 models
    11188 
    11189 > clipper associate #12 toModel #13
    11190 
    11191 Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #13.1.1.1, grid
    11192 size 420,420,420, pixel 0.825, shown at step 1, values float32 
    11193 
    11194 > show #!7 models
    11195 
    11196 > hide #!7 models
    11197 
    11198 > select add #13.2
    11199 
    11200 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 8 models selected 
    11201 
    11202 > fitmap #13.2 inMap #13.1.1.1
    11203 
    11204 Fit molecule combination (#13.2) to map
    11205 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
    11206 atoms 
    11207 average map value = 0.05014, steps = 396 
    11208 shifted from previous position = 23.4 
    11209 rotated from previous position = 24.1 degrees 
    11210 atoms outside contour = 19566, contour level = 0.05014 
    11211  
    11212 Position of combination (#13.2) relative to
    11213 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates: 
    11214 Matrix rotation and translation 
    11215 0.92317061 -0.20312451 0.32633796 -11.17355132 
    11216 0.24869275 0.96296817 -0.10413559 -33.51889854 
    11217 -0.29310057 0.17729280 0.93949950 15.03016877 
    11218 Axis 0.34458025 0.75843906 0.55320398 
    11219 Axis point 84.24190480 0.00000000 31.94318234 
    11220 Rotation angle (degrees) 24.10210987 
    11221 Shift along axis -20.95747771 
    11222  
    11223 
    11224 > hide #9 models
    11225 
    11226 > hide #3 models
    11227 
    11228 > hide #!1 models
    11229 
    11230 > volume #!13.1.1.1 style surface
    11231 
    11232 > select add #13.1
    11233 
    11234 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 13 models selected 
    11235 
    11236 > select add #13.2
    11237 
    11238 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 13 models selected 
    11239 
    11240 > ui mousemode right "translate selected models"
    11241 
    11242 > ui mousemode right "rotate selected models"
    11243 
    11244 > view matrix models
    11245 > #13.1,-0.98269,-0.1026,-0.15424,429.7,0.10866,-0.99358,-0.031368,347.81,-0.15003,-0.047586,0.98753,39.267,#13.2,-0.8875,0.073459,-0.45492,441.8,-0.13759,-0.98442,0.10946,379.43,-0.43979,0.15973,0.88378,57.381
    11246 
    11247 > select add #13
    11248 
    11249 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 15 models selected 
    11250 
    11251 > select subtract #13.3
    11252 
    11253 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 14 models selected 
    11254 
    11255 > hide #!13 models
    11256 
    11257 > show #!13 models
    11258 
    11259 > view matrix models
    11260 > #13,0.81208,0.54878,0.19838,-100.24,-0.5225,0.8352,-0.17155,164.87,-0.25983,0.035658,0.96499,51.139
    11261 
    11262 > select clear
    11263 
    11264 > select add #13.1
    11265 
    11266 5 models selected 
    11267 
    11268 > view matrix models
    11269 > #13.1,0.83139,-0.40689,-0.37845,195.35,0.35956,0.91317,-0.19191,-14.667,0.42368,0.023477,0.90551,-63.182
    11270 
    11271 > ui mousemode right "translate selected models"
    11272 
    11273 > view matrix models
    11274 > #13.1,0.83139,-0.40689,-0.37845,187.29,0.35956,0.91317,-0.19191,-11.823,0.42368,0.023477,0.90551,-54.397
    11275 
    11276 > fitmap #13.2 inMap #13.1.1.1
    11277 
    11278 Fit molecule combination (#13.2) to map
    11279 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
    11280 atoms 
    11281 average map value = 0.1116, steps = 280 
    11282 shifted from previous position = 5.36 
    11283 rotated from previous position = 24.3 degrees 
    11284 atoms outside contour = 8152, contour level = 0.05014 
    11285  
    11286 Position of combination (#13.2) relative to
    11287 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates: 
    11288 Matrix rotation and translation 
    11289 -0.75913436 0.36618451 -0.53816720 379.62642684 
    11290 -0.25697956 -0.92820081 -0.26908132 464.97537207 
    11291 -0.59806064 -0.06597091 0.79873106 150.13087714 
    11292 Axis 0.30860342 0.09100135 -0.94682769 
    11293 Axis point 255.69788645 206.24934727 0.00000000 
    11294 Rotation angle (degrees) 160.78705671 
    11295 Shift along axis 17.31932933 
    11296  
    11297 
    11298 > select clear
    11299 
    11300 > surface dust #13.1.1.1 size 8.25
    11301 
    11302 > view matrix models
    11303 > #13.2,-0.75913,0.36618,-0.53817,398.64,-0.25698,-0.9282,-0.26908,469.57,-0.59806,-0.065971,0.79873,125.43
    11304 
    11305 > view matrix models
    11306 > #13.2,-0.75913,0.36618,-0.53817,381.57,-0.25698,-0.9282,-0.26908,467.93,-0.59806,-0.065971,0.79873,146.56
    11307 
    11308 > fitmap #13.2 inMap #13.1.1.1
    11309 
    11310 Fit molecule combination (#13.2) to map
    11311 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
    11312 atoms 
    11313 average map value = 0.1336, steps = 120 
    11314 shifted from previous position = 5.13 
    11315 rotated from previous position = 0.544 degrees 
    11316 atoms outside contour = 12403, contour level = 0.05014 
    11317  
    11318 Position of combination (#13.2) relative to
    11319 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates: 
    11320 Matrix rotation and translation 
    11321 -0.75493092 0.36668844 -0.54370847 379.59746213 
    11322 -0.25313255 -0.92775240 -0.27422507 464.92394264 
    11323 -0.60498200 -0.06939067 0.79320975 153.04464514 
    11324 Axis 0.31240962 0.09345325 -0.94533947 
    11325 Axis point 256.39528686 206.66536567 0.00000000 
    11326 Rotation angle (degrees) 160.86289101 
    11327 Shift along axis 17.35941085 
    11328  
    11329 
    11330 > select clear
    11331 
    11332 > volume #!13.1.1.1 style mesh
    11333 
    11334 > isolde sim start sel
    11335 
    11336 ISOLDE: stopped sim 
    11337 
    11338 > select clear
    11339 
    11340 [Repeated 1 time(s)]Fetching CCD MET_LL from http://ligand-
    11341 expo.rcsb.org/reports/M/MET_LL/MET_LL.cif 
    11342 Fetching CCD MET_LEO2 from http://ligand-
    11343 expo.rcsb.org/reports/M/MET_LEO2/MET_LEO2.cif 
    11344 Fetching CCD MET_LFZW from http://ligand-
    11345 expo.rcsb.org/reports/M/MET_LFZW/MET_LFZW.cif 
    11346 Fetching CCD FME from http://ligand-expo.rcsb.org/reports/F/FME/FME.cif 
    11347 Fetching CCD AME from http://ligand-expo.rcsb.org/reports/A/AME/AME.cif 
    11348 Fetching CCD ALA_LL from http://ligand-
    11349 expo.rcsb.org/reports/A/ALA_LL/ALA_LL.cif 
    11350 Fetching CCD SER_LL_DHG from http://ligand-
    11351 expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif 
    11352 Fetching CCD SER_LL from http://ligand-
    11353 expo.rcsb.org/reports/S/SER_LL/SER_LL.cif 
    11354 Fetching CCD ALA_LEO2 from http://ligand-
    11355 expo.rcsb.org/reports/A/ALA_LEO2/ALA_LEO2.cif 
    11356 Fetching CCD SER_LSN3_DHG from http://ligand-
    11357 expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif 
    11358 Fetching CCD ALA_LFZW from http://ligand-
    11359 expo.rcsb.org/reports/A/ALA_LFZW/ALA_LFZW.cif 
    11360 Fetching CCD PRO_LL from http://ligand-
    11361 expo.rcsb.org/reports/P/PRO_LL/PRO_LL.cif 
    11362 Fetching CCD CYS_LL_DHG from http://ligand-
    11363 expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif 
    11364 Fetching CCD THR_LL_DHG1 from http://ligand-
    11365 expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif 
    11366 Fetching CCD SER_LEO2_DHG from http://ligand-
    11367 expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif 
    11368 Fetching CCD CYS_LL from http://ligand-
    11369 expo.rcsb.org/reports/C/CYS_LL/CYS_LL.cif 
    11370 Fetching CCD THR_LL from http://ligand-
    11371 expo.rcsb.org/reports/T/THR_LL/THR_LL.cif 
    11372 Fetching CCD VAL_LL from http://ligand-
    11373 expo.rcsb.org/reports/V/VAL_LL/VAL_LL.cif 
    11374 Fetching CCD SER_LEO2 from http://ligand-
    11375 expo.rcsb.org/reports/S/SER_LEO2/SER_LEO2.cif 
    11376 Fetching CCD CYS_LSN3_DHG from http://ligand-
    11377 expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif 
    11378 Fetching CCD THR_LSN3_DHG1 from http://ligand-
    11379 expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif 
    11380 Fetching CCD SER_LFZW_DHG from http://ligand-
    11381 expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif 
    11382 Fetching CCD SER_LFZW from http://ligand-
    11383 expo.rcsb.org/reports/S/SER_LFZW/SER_LFZW.cif 
    11384 Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif 
    11385 Fetching CCD ASP_LL_DHD2 from http://ligand-
    11386 expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif 
    11387 Fetching CCD ASN_LL from http://ligand-
    11388 expo.rcsb.org/reports/A/ASN_LL/ASN_LL.cif 
    11389 Fetching CCD ASP_LL from http://ligand-
    11390 expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif 
    11391 Fetching CCD PRO_LEO2 from http://ligand-
    11392 expo.rcsb.org/reports/P/PRO_LEO2/PRO_LEO2.cif 
    11393 Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif 
    11394 Fetching CCD CYS_LEO2_DHG from http://ligand-
    11395 expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif 
    11396 Fetching CCD ASP_LSN3_DHD2 from http://ligand-
    11397 expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif 
    11398 Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif 
    11399 Fetching CCD THR_LEO2_DHG1 from http://ligand-
    11400 expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif 
    11401 Fetching CCD ILE_LL from http://ligand-
    11402 expo.rcsb.org/reports/I/ILE_LL/ILE_LL.cif 
    11403 Fetching CCD LEU_LL from http://ligand-
    11404 expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif 
    11405 Fetching CCD CYS_LEO2 from http://ligand-
    11406 expo.rcsb.org/reports/C/CYS_LEO2/CYS_LEO2.cif 
    11407 Fetching CCD THR_LEO2 from http://ligand-
    11408 expo.rcsb.org/reports/T/THR_LEO2/THR_LEO2.cif 
    11409 Fetching CCD VAL_LEO2 from http://ligand-
    11410 expo.rcsb.org/reports/V/VAL_LEO2/VAL_LEO2.cif 
    11411 Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif 
    11412 Fetching CCD PRO_LFZW from http://ligand-
    11413 expo.rcsb.org/reports/P/PRO_LFZW/PRO_LFZW.cif 
    11414 Fetching CCD THR_LFZW_DHG1 from http://ligand-
    11415 expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif 
    11416 Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif 
    11417 Fetching CCD CYS_LFZW from http://ligand-
    11418 expo.rcsb.org/reports/C/CYS_LFZW/CYS_LFZW.cif 
    11419 Fetching CCD THR_LFZW from http://ligand-
    11420 expo.rcsb.org/reports/T/THR_LFZW/THR_LFZW.cif 
    11421 Fetching CCD VAL_LFZW from http://ligand-
    11422 expo.rcsb.org/reports/V/VAL_LFZW/VAL_LFZW.cif 
    11423 Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif 
    11424 Fetching CCD ARG_LL from http://ligand-
    11425 expo.rcsb.org/reports/A/ARG_LL/ARG_LL.cif 
    11426 Fetching CCD ARG_LL_DHH22 from http://ligand-
    11427 expo.rcsb.org/reports/A/ARG_LL_DHH22/ARG_LL_DHH22.cif 
    11428 Fetching CCD ARG_LEO2 from http://ligand-
    11429 expo.rcsb.org/reports/A/ARG_LEO2/ARG_LEO2.cif 
    11430 Fetching CCD NMM from http://ligand-expo.rcsb.org/reports/N/NMM/NMM.cif 
    11431 Fetching CCD ARG_LFZW from http://ligand-
    11432 expo.rcsb.org/reports/A/ARG_LFZW/ARG_LFZW.cif 
    11433 Fetching CCD 2MR from http://ligand-expo.rcsb.org/reports/2/2MR/2MR.cif 
    11434 Fetching CCD DA2 from http://ligand-expo.rcsb.org/reports/D/DA2/DA2.cif 
    11435 Fetching CCD AAG from http://ligand-expo.rcsb.org/reports/A/AAG/AAG.cif 
    11436 Fetching CCD N7P from http://ligand-expo.rcsb.org/reports/N/N7P/N7P.cif 
    11437 Fetching CCD LEU_LEO2 from http://ligand-
    11438 expo.rcsb.org/reports/L/LEU_LEO2/LEU_LEO2.cif 
    11439 Fetching CCD LEU_LFZW from http://ligand-
    11440 expo.rcsb.org/reports/L/LEU_LFZW/LEU_LFZW.cif 
    11441 Fetching CCD PHE_LL from http://ligand-
    11442 expo.rcsb.org/reports/P/PHE_LL/PHE_LL.cif 
    11443 Fetching CCD LAY from http://ligand-expo.rcsb.org/reports/L/LAY/LAY.cif 
    11444 Fetching CCD ILE_LEO2 from http://ligand-
    11445 expo.rcsb.org/reports/I/ILE_LEO2/ILE_LEO2.cif 
    11446 Fetching CCD ILE_LFZW from http://ligand-
    11447 expo.rcsb.org/reports/I/ILE_LFZW/ILE_LFZW.cif 
    11448 
    11449 > fitmap #13.2 inMap #13.1.1.1
    11450 
    11451 Fit molecule combination (#13.2) to map
    11452 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
    11453 atoms 
    11454 average map value = 0.07731, steps = 320 
    11455 shifted from previous position = 20.7 
    11456 rotated from previous position = 33.8 degrees 
    11457 atoms outside contour = 11736, contour level = 0.05014 
    11458  
    11459 Position of combination (#13.2) relative to
    11460 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates: 
    11461 Matrix rotation and translation 
    11462 -0.97583225 -0.05210471 -0.21221809 418.79073088 
    11463 0.06601319 -0.99607381 -0.05898489 373.10247849 
    11464 -0.20831149 -0.07156855 0.97544055 32.30370160 
    11465 Axis -0.10587804 -0.03286985 0.99383571 
    11466 Axis point 205.54590673 193.31244448 0.00000000 
    11467 Rotation angle (degrees) 176.59317612 
    11468 Shift along axis -24.49999338 
    11469  
    11470 
    11471 > isolde sim start sel
    11472 
    11473 ISOLDE: stopped sim 
    11474 
    11475 > select #13.2/F
    11476 
    11477 1835 atoms, 1858 bonds, 114 residues, 1 model selected 
    11478 
    11479 > select #13.2/B
    11480 
    11481 2615 atoms, 2648 bonds, 160 residues, 1 model selected 
    11482 
    11483 > select #13.2/A
    11484 
    11485 1887 atoms, 1938 bonds, 236 residues, 1 model selected 
    11486 Please select a single atom! 
    11487 
    11488 > select clear
    11489 
    11490 [Repeated 2 time(s)]Please select a single atom! 
    11491 
    11492 > isolde shorthand
    11493    
    11494    
    11495     Initialising ISOLDE-specific command aliases:
    11496     Alias       Equivalent full command
    11497     -------------------------------------------------
    11498     st  isolde step {arguments}
    11499     aw  isolde add water {arguments}
    11500     awsf        isolde add water {arguments} sim false
    11501     al  isolde add ligand {arguments}
    11502     aa  isolde add aa $1 sel {arguments}
    11503     ht  isolde mod his sel {arguments}
    11504     so  setattr sel atoms occupancy {arguments}
    11505     ab  isolde adjust bfactors {arguments}
    11506     ss  isolde sim start sel
    11507     rt  isolde release torsions sel {arguments}
    11508     rd  isolde release distances sel {arguments}
    11509     ra  rd; rt
    11510     pf  isolde pepflip sel
    11511     cf  isolde cisflip sel
    11512     cbb color bfactor {arguments}
    11513     cbo color byattr occupancy {arguments}
    11514     cbc color {arguments} bychain; color {arguments} byhet
    11515     cs  clipper set contourSensitivity {arguments}
    11516    
    11517 
    11518  
    11519 
    11520 > addh
    11521 
    11522 Summary of feedback from adding hydrogens to multiple structures 
    11523 --- 
    11524 warnings | Not adding hydrogens to 5t35 #5/A LYS 349 CB because it is missing
    11525 heavy-atom bond partners 
    11526 Not adding hydrogens to 5t35 #5/A LYS 362 CD because it is missing heavy-atom
    11527 bond partners 
    11528 Not adding hydrogens to 5t35 #5/A LYS 367 CB because it is missing heavy-atom
    11529 bond partners 
    11530 Not adding hydrogens to 5t35 #5/A LYS 395 CB because it is missing heavy-atom
    11531 bond partners 
    11532 Not adding hydrogens to 5t35 #5/A ARG 413 CB because it is missing heavy-atom
    11533 bond partners 
    11534 33 messages similar to the above omitted 
    11535 notes | Termini for 5t35 (#5) chain A determined from SEQRES records 
    11536 Termini for 5t35 (#5) chain B determined from SEQRES records 
    11537 Termini for 5t35 (#5) chain C determined from SEQRES records 
    11538 Termini for 5t35 (#5) chain D determined from SEQRES records 
    11539 Chain-initial residues that are actual N termini: 5t35 #5/B MET 1, 5t35 #5/C
    11540 MET 16 
    11541 Chain-initial residues that are not actual N termini: 5t35 #5/A LYS 349, 5t35
    11542 #5/C ASN 58, 5t35 #5/D PRO 61 
    11543 Chain-final residues that are actual C termini: 5t35 #5/B LYS 104, 5t35 #5/C
    11544 CYS 112 
    11545 Chain-final residues that are not actual C termini: 5t35 #5/A ASP 459, 5t35
    11546 #5/C SER 47, 5t35 #5/D GLN 209 
    11547 579 hydrogen bonds 
    11548 Adding 'H' to 5t35 #5/A LYS 349 
    11549 Adding 'H' to 5t35 #5/C ASN 58 
    11550 5t35 #5/A ASP 459 is not terminus, removing H atom from 'C' 
    11551 5t35 #5/D GLN 209 is not terminus, removing H atom from 'C' 
    11552 Termini for 6ttu (#8) chain N determined from SEQRES records 
    11553 Termini for 6ttu (#8) chain R determined from SEQRES records 
    11554 Termini for 6ttu (#8) chain D determined from SEQRES records 
    11555 Termini for 6ttu (#8) chain U determined from SEQRES records 
    11556 Chain-initial residues that are actual N termini: 6ttu #8/N SER 0, 6ttu #8/U
    11557 MET 1 
    11558 Chain-initial residues that are not actual N termini: 6ttu #8/R ASP 40, 6ttu
    11559 #8/R GLU 67, 6ttu #8/D ALA 2 
    11560 Chain-final residues that are actual C termini: 6ttu #8/N GLY 76, 6ttu #8/D
    11561 MET 147 
    11562 Chain-final residues that are not actual C termini: 6ttu #8/R ASN 59, 6ttu
    11563 #8/R GLN 104, 6ttu #8/U GLY 75 
    11564 Missing OXT added to C-terminal residue 6ttu #8/N GLY 76 
    11565 Missing OXT added to C-terminal residue 6ttu #8/D MET 147 
    11566 224 hydrogen bonds 
    11567 Adding 'H' to 6ttu #8/R ASP 40 
    11568 Adding 'H' to 6ttu #8/R GLU 67 
    11569 Adding 'H' to 6ttu #8/D ALA 2 
    11570 6ttu #8/R GLN 104 is not terminus, removing H atom from 'C' 
    11571 6ttu #8/U GLY 75 is not terminus, removing H atom from 'C' 
    11572 Termini for fullmodel-v5.pdb (#4.2) chain A determined from SEQRES records 
    11573 Termini for fullmodel-v5.pdb (#4.2) chain B determined from SEQRES records 
    11574 Termini for fullmodel-v5.pdb (#4.2) chain C determined from SEQRES records 
    11575 Termini for fullmodel-v5.pdb (#4.2) chain D determined from SEQRES records 
    11576 Termini for fullmodel-v5.pdb (#4.2) chain E determined from SEQRES records 
    11577 1 messages similar to the above omitted 
    11578 Chain-initial residues that are actual N termini: fullmodel-v5.pdb #4.2/B MET
    11579 54, fullmodel-v5.pdb #4.2/C MET 1, fullmodel-v5.pdb #4.2/D ALA 16,
    11580 fullmodel-v5.pdb #4.2/E MET 1 
    11581 Chain-initial residues that are not actual N termini: fullmodel-v5.pdb #4.2/A
    11582 SER 347, fullmodel-v5.pdb #4.2/R LYS 20 
    11583 Chain-final residues that are actual C termini: fullmodel-v5.pdb #4.2/A GLU
    11584 460, fullmodel-v5.pdb #4.2/B ASP 213, fullmodel-v5.pdb #4.2/C LYS 104,
    11585 fullmodel-v5.pdb #4.2/D CYS 112 
    11586 Chain-final residues that are not actual C termini: fullmodel-v5.pdb #4.2/E
    11587 GLN 658, fullmodel-v5.pdb #4.2/R HIS 108 
    11588 1466 hydrogen bonds 
    11589 fullmodel-v5.pdb #4.2/E GLN 658 is not terminus, removing H atom from 'C' 
    11590 Termini for fulmodel-v6-crosslinked.pdb (#9) chain A determined from SEQRES
    11591 records 
    11592 Termini for fulmodel-v6-crosslinked.pdb (#9) chain B determined from SEQRES
    11593 records 
    11594 Termini for fulmodel-v6-crosslinked.pdb (#9) chain C determined from SEQRES
    11595 records 
    11596 Termini for fulmodel-v6-crosslinked.pdb (#9) chain D determined from SEQRES
    11597 records 
    11598 Termini for fulmodel-v6-crosslinked.pdb (#9) chain E determined from SEQRES
    11599 records 
    11600 Chain-initial residues that are actual N termini: fulmodel-v6-crosslinked.pdb
    11601 #9/B MET 54, fulmodel-v6-crosslinked.pdb #9/C MET 1,
    11602 fulmodel-v6-crosslinked.pdb #9/D ALA 16, fulmodel-v6-crosslinked.pdb #9/E MET
    11603 1 
    11604 Chain-initial residues that are not actual N termini:
    11605 fulmodel-v6-crosslinked.pdb #9/A SER 347 
    11606 Chain-final residues that are actual C termini: fulmodel-v6-crosslinked.pdb
    11607 #9/A GLU 460, fulmodel-v6-crosslinked.pdb #9/B ASP 213,
    11608 fulmodel-v6-crosslinked.pdb #9/C LYS 104, fulmodel-v6-crosslinked.pdb #9/D CYS
    11609 112 
    11610 Chain-final residues that are not actual C termini:
    11611 fulmodel-v6-crosslinked.pdb #9/E GLN 658 
    11612 1353 hydrogen bonds 
    11613 fulmodel-v6-crosslinked.pdb #9/E GLN 658 is not terminus, removing H atom from
    11614 'C' 
    11615 Termini for 8b3i (#10) chain D determined from SEQRES records 
    11616 Termini for 8b3i (#10) chain N determined from SEQRES records 
    11617 Termini for 8b3i (#10) chain R determined from SEQRES records 
    11618 Termini for 8b3i (#10) chain U determined from SEQRES records 
    11619 Termini for 8b3i (#10) chain e determined from SEQRES records 
    11620 Chain-initial residues that are actual N termini: 8b3i #10/N MET 1, 8b3i #10/U
    11621 MET 1 
    11622 Chain-initial residues that are not actual N termini: 8b3i #10/D ALA 2, 8b3i
    11623 #10/R LYS 19, 8b3i #10/R GLU 67, 8b3i #10/e PRO 355, 8b3i #10/e ARG 692 
    11624 Chain-final residues that are actual C termini: 8b3i #10/D MET 147, 8b3i #10/N
    11625 GLY 76, 8b3i #10/U GLY 76, 8b3i #10/e ALA 759 
    11626 Chain-final residues that are not actual C termini: 8b3i #10/R ASN 59, 8b3i
    11627 #10/R GLN 104, 8b3i #10/e ILE 672 
    11628 Missing OXT added to C-terminal residue 8b3i #10/D MET 147 
    11629 Missing OXT added to C-terminal residue 8b3i #10/N GLY 76 
    11630 Missing OXT added to C-terminal residue 8b3i #10/U GLY 76 
    11631 500 hydrogen bonds 
    11632 Adding 'H' to 8b3i #10/D ALA 2 
    11633 Adding 'H' to 8b3i #10/R LYS 19 
    11634 Adding 'H' to 8b3i #10/R GLU 67 
    11635 Adding 'H' to 8b3i #10/e ARG 692 
    11636 8b3i #10/R GLN 104 is not terminus, removing H atom from 'C' 
    11637 Termini for 6nyo (#11) chain A determined from SEQRES records 
    11638 Termini for 6nyo (#11) chain E determined from SEQRES records 
    11639 Chain-initial residues that are actual N termini: 
    11640 Chain-initial residues that are not actual N termini: 6nyo #11/A GLN 5, 6nyo
    11641 #11/E SER -1 
    11642 Chain-final residues that are actual C termini: 6nyo #11/E GLY 76 
    11643 Chain-final residues that are not actual C termini: 6nyo #11/A ILE 192 
    11644 1134 hydrogen bonds 
    11645 Adding 'H' to 6nyo #11/A GLN 5 
    11646 Adding 'H' to 6nyo #11/E SER -1 
    11647 6nyo #11/A ILE 192 is not terminus, removing H atom from 'C' 
    11648 Termini for 6ttu (#1) chain N determined from SEQRES records 
    11649 Termini for 6ttu (#1) chain R determined from SEQRES records 
    11650 Termini for 6ttu (#1) chain U determined from SEQRES records 
    11651 Chain-initial residues that are actual N termini: 6ttu #1/N SER 0, 6ttu #1/U
    11652 MET 1 
    11653 Chain-initial residues that are not actual N termini: 6ttu #1/R LYS 19, 6ttu
    11654 #1/R GLU 67 
    11655 Chain-final residues that are actual C termini: 6ttu #1/N GLY 76 
    11656 Chain-final residues that are not actual C termini: 6ttu #1/R ASN 59, 6ttu
    11657 #1/R GLN 104, 6ttu #1/U GLY 75 
    11658 Missing OXT added to C-terminal residue 6ttu #1/N GLY 76 
    11659 126 hydrogen bonds 
    11660 Adding 'H' to 6ttu #1/R LYS 19 
    11661 Adding 'H' to 6ttu #1/R GLU 67 
    11662 6ttu #1/R GLN 104 is not terminus, removing H atom from 'C' 
    11663 6ttu #1/U GLY 75 is not terminus, removing H atom from 'C' 
    11664 Termini for UBE2R1AF-P49427-F1-model_v4.pdb (#3) chain A determined from
    11665 SEQRES records 
    11666 Chain-initial residues that are actual N termini:
    11667 UBE2R1AF-P49427-F1-model_v4.pdb #3/A MET 1 
    11668 Chain-initial residues that are not actual N termini: 
    11669 Chain-final residues that are actual C termini:
    11670 UBE2R1AF-P49427-F1-model_v4.pdb #3/A SER 236 
    11671 Chain-final residues that are not actual C termini: 
    11672 177 hydrogen bonds 
    11673 Termini for combination (#13.2) chain N determined from SEQRES records 
    11674 Termini for combination (#13.2) chain R determined from SEQRES records 
    11675 Termini for combination (#13.2) chain U determined from SEQRES records 
    11676 Termini for combination (#13.2) chain A determined from SEQRES records 
    11677 Termini for combination (#13.2) chain F determined from SEQRES records 
    11678 4 messages similar to the above omitted 
    11679 Chain-initial residues that are actual N termini: combination #13.2/N SER 0,
    11680 combination #13.2/U MET 1, combination #13.2/A MET 1, combination #13.2/B MET
    11681 54, combination #13.2/C MET 1, combination #13.2/D ALA 16, combination #13.2/E
    11682 MET 1 
    11683 Chain-initial residues that are not actual N termini: combination #13.2/R LYS
    11684 19, combination #13.2/R GLU 67, combination #13.2/F SER 347 
    11685 Chain-final residues that are actual C termini: combination #13.2/N GLY 76,
    11686 combination #13.2/A SER 236, combination #13.2/F GLU 460, combination #13.2/B
    11687 ASP 213, combination #13.2/C LYS 104, combination #13.2/D CYS 112 
    11688 Chain-final residues that are not actual C termini: combination #13.2/R ASN
    11689 59, combination #13.2/R GLN 104, combination #13.2/U GLY 75, combination
    11690 #13.2/E GLN 658 
    11691 Missing OXT added to C-terminal residue combination #13.2/N GLY 76 
    11692 1674 hydrogen bonds 
    11693 Adding 'H' to combination #13.2/R LYS 19 
    11694 Adding 'H' to combination #13.2/R GLU 67 
    11695 combination #13.2/R GLN 104 is not terminus, removing H atom from 'C' 
    11696 combination #13.2/U GLY 75 is not terminus, removing H atom from 'C' 
    11697 combination #13.2/E GLN 658 is not terminus, removing H atom from 'C' 
    11698 16651 hydrogens added 
    11699  
    11700 
    11701 > select clear
    11702 
    11703 > isolde sim start sel
    11704 
    11705 ISOLDE: started sim 
    11706 
    11707 > select clear
    11708 
    11709 > dhide sideonly
    11710 
    11711 Unknown command: dhide sideonly 
    11712 
    11713 > dhide sideonly
    11714 
    11715 Unknown command: dhide sideonly 
    11716 
    11717 > hide sideonly
    11718 
    11719 > isolde sim stop
    11720 
    11721 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11722 chains... 
    11723 ISOLDE: stopped sim 
    11724 
    11725 > hide sideonly
    11726 
    11727 > hide ~@CA
    11728 
    11729 > select clear
    11730 
    11731 > select #13.2/N
    11732 
    11733 1249 atoms, 1254 bonds, 77 residues, 1 model selected 
    11734 
    11735 > color (#!13.2 & sel) cyan
    11736 
    11737 > select clear
    11738 
    11739 [Repeated 1 time(s)]
    11740 
    11741 > delete sel
    11742 
    11743 > select #13.2/A:180-218
    11744 
    11745 579 atoms, 586 bonds, 39 residues, 1 model selected 
    11746 
    11747 > delete sel
    11748 
    11749 > isolde sim start sel
    11750 
    11751 ISOLDE: started sim 
    11752 
    11753 > select clear
    11754 
    11755 [Repeated 1 time(s)]
    11756 
    11757 > ui mousemode right "isolde tug atom"
    11758 
    11759 > ui mousemode right "isolde tug residue"
    11760 
    11761 > ui mousemode right "isolde tug atom"
    11762 
    11763 [Repeated 1 time(s)]
    11764 
    11765 > isolde sim resume
    11766 
    11767 > select #13.2/R:19-37
    11768 
    11769 345 atoms, 351 bonds, 17 pseudobonds, 19 residues, 2 models selected 
    11770 
    11771 > delete sel
    11772 
    11773 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11774 chains... 
    11775 ISOLDE: stopped sim 
    11776 
    11777 > hide ~@CA
    11778 
    11779 > ui mousemode right translate
    11780 
    11781 > isolde sim start sel
    11782 
    11783 ISOLDE: started sim 
    11784 
    11785 > ui mousemode right translate
    11786 
    11787 > isolde sim pause
    11788 
    11789 > select clear
    11790 
    11791 > select add #13
    11792 
    11793 24624 atoms, 24886 bonds, 1169 pseudobonds, 1527 residues, 21 models selected 
    11794 
    11795 > isolde sim resume
    11796 
    11797 > isolde sim pause
    11798 
    11799 > select clear
    11800 
    11801 > isolde sim stop
    11802 
    11803 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11804 chains... 
    11805 ISOLDE: Corrected atom nomenclature of 56 residues in model #13.2 to IUPAC-IUB
    11806 standards. 
    11807 ISOLDE: stopped sim 
    11808 
    11809 > save /home/pinkie/Documents/Charlotte/2024_01_28/full-model-9-isoldeatt1.pdb
    11810 > models #13
    11811 
    11812 > open /home/pinkie/Documents/Charlotte/2024_01_28/full-model-9-isoldeatt1.pdb
    11813 
    11814 full-model-9-isoldeatt1.pdb title: 
    11815 Alphafold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1
    11816 (P49427) [more info...] 
    11817  
    11818 Chain information for full-model-9-isoldeatt1.pdb #12 
    11819 --- 
    11820 Chain | Description | UniProt 
    11821 A | ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    11822 B | No description available | 
    11823 C | No description available | 
    11824 D | No description available | 
    11825 E | No description available | 
    11826 F | No description available | 
    11827 N | No description available | 
    11828 R | No description available | 
    11829 U | No description available | 
    11830  
    11831 Non-standard residues in full-model-9-isoldeatt1.pdb #12 
    11832 --- 
    11833 ZN — (ZN) 
    11834  
    11835 
    11836 > select add #12
    11837 
    11838 24624 atoms, 24886 bonds, 13 pseudobonds, 1527 residues, 3 models selected 
    11839 
    11840 > hide sel atoms
    11841 
    11842 > show sel cartoons
    11843 
    11844 > select clear
    11845 
    11846 > hide #!13 models
    11847 
    11848 > hide #!13.1 models
    11849 
    11850 > hide #!13.2 models
    11851 
    11852 > hide #13.3 models
    11853 
    11854 > show #11 models
    11855 
    11856 > hide #11 models
    11857 
    11858 > show #9 models
    11859 
    11860 > hide #9 models
    11861 
    11862 > open /home/pinkie/Documents/Charlotte/2024_01_28/full-model-7.pdb
    11863 
    11864 full-model-7.pdb title: 
    11865 Alphafold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1
    11866 (P49427) [more info...] 
    11867  
    11868 Chain information for full-model-7.pdb #14 
    11869 --- 
    11870 Chain | Description | UniProt 
    11871 A | ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    11872 B | No description available | 
    11873 C | No description available | 
    11874 D | No description available | 
    11875 E | No description available | 
    11876 F | No description available | 
    11877 N | No description available | 
    11878 R | No description available | 
    11879 U | No description available | 
    11880  
    11881 Non-standard residues in full-model-7.pdb #14 
    11882 --- 
    11883 ZN — (ZN) 
    11884  
    11885 
    11886 > select add #14
    11887 
    11888 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 3 models selected 
    11889 
    11890 > ui mousemode right "rotate selected models"
    11891 
    11892 > view matrix models
    11893 > #14,-0.76775,-0.61838,0.16783,439.68,0.61794,-0.78383,-0.061302,262.94,0.16946,0.056645,0.98391,-41.6
    11894 
    11895 > ui mousemode right "translate selected models"
    11896 
    11897 > view matrix models
    11898 > #14,-0.76775,-0.61838,0.16783,414.71,0.61794,-0.78383,-0.061302,236.59,0.16946,0.056645,0.98391,-67.689
    11899 
    11900 > show #!13.1 models
    11901 
    11902 > ui mousemode right "translate selected atoms"
    11903 
    11904 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    11905 got 2 atomic models, 0 maps. 
    11906 
    11907 > hide #!12 models
    11908 
    11909 > show #!13.2 models
    11910 
    11911 > hide #!13.2 models
    11912 
    11913 > show #13.3 models
    11914 
    11915 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    11916 got 1 atomic models, 0 maps. 
    11917 
    11918 > hide #13.3 models
    11919 
    11920 > open
    11921 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J659_007_volume_map.mrc
    11922 
    11923 Opened cryosparc_P9_J659_007_volume_map.mrc as #15, grid size 480,480,480,
    11924 pixel 0.825, shown at level 0.00707, step 2, values float32 
    11925 
    11926 > close #15
    11927 
    11928 > select clear
    11929 
    11930 > select add #14
    11931 
    11932 22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 3 models selected 
    11933 
    11934 > hide sel atoms
    11935 
    11936 > show sel cartoons
    11937 
    11938 > select clear
    11939 
    11940 > select #13.2/A:177-236
    11941 
    11942 51 atoms, 50 bonds, 3 residues, 1 model selected 
    11943 
    11944 > delete sel
    11945 
    11946 > select #14/A:177-236
    11947 
    11948 465 atoms, 473 bonds, 60 residues, 1 model selected 
    11949 
    11950 > delete sel
    11951 
    11952 > select #14/R:19-37
    11953 
    11954 170 atoms, 176 bonds, 19 residues, 1 model selected 
    11955 
    11956 > delete sel
    11957 
    11958 > open 7ojx
    11959 
    11960 Summary of feedback from opening 7ojx fetched from pdb 
    11961 --- 
    11962 notes | Fetching compressed mmCIF 7ojx from
    11963 http://files.rcsb.org/download/7ojx.cif 
    11964 Fetching CCD ME7 from http://ligand-expo.rcsb.org/reports/M/ME7/ME7.cif 
    11965  
    11966 7ojx title: 
    11967 E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for
    11968 K48-linked Ub chain synthesis [more info...] 
    11969  
    11970 Chain information for 7ojx #15 
    11971 --- 
    11972 Chain | Description | UniProt 
    11973 A | E3 ubiquitin-protein ligase RNF38 | RNF38_HUMAN 
    11974 B | Ubiquitin-conjugating enzyme E2 K | UBE2K_HUMAN 
    11975 C | Polyubiquitin-B | UBB_HUMAN 
    11976 D | Polyubiquitin-B | UBB_HUMAN 
    11977 E | Polyubiquitin-B | UBB_HUMAN 
    11978  
    11979 Non-standard residues in 7ojx #15 
    11980 --- 
    11981 ME7 — 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) 
    11982 ZN — zinc ion 
    11983  
    11984 
    11985 > matchmaker #!15 to #14/A pairing bs
    11986 
    11987 Parameters 
    11988 --- 
    11989 Chain pairing | bs 
    11990 Alignment algorithm | Needleman-Wunsch 
    11991 Similarity matrix | BLOSUM-62 
    11992 SS fraction | 0.3 
    11993 Gap open (HH/SS/other) | 18/18/6 
    11994 Gap extend | 1 
    11995 SS matrix |  |  | H | S | O 
    11996 ---|---|---|--- 
    11997 H | 6 | -9 | -6 
    11998 S |  | 6 | -6 
    11999 O |  |  | 4 
    12000 Iteration cutoff | 2 
    12001  
    12002 Matchmaker full-model-7.pdb, chain A (#14) with 7ojx, chain B (#15), sequence
    12003 alignment score = 298.9 
    12004 RMSD between 112 pruned atom pairs is 0.940 angstroms; (across all 157 pairs:
    12005 7.065) 
    12006  
    12007 
    12008 > select add #15
    12009 
    12010 3731 atoms, 3746 bonds, 9 pseudobonds, 541 residues, 3 models selected 
    12011 
    12012 > hide sel atoms
    12013 
    12014 > show sel cartoons
    12015 
    12016 > select clear
    12017 
    12018 > select #15/A
    12019 
    12020 529 atoms, 534 bonds, 8 pseudobonds, 75 residues, 2 models selected 
    12021 
    12022 > delete sel
    12023 
    12024 > hide #!14 models
    12025 
    12026 > show #!14 models
    12027 
    12028 > hide #!15 models
    12029 
    12030 > select clear
    12031 
    12032 > ui mousemode right select
    12033 
    12034 > select clear
    12035 
    12036 > select #14/A:93
    12037 
    12038 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12039 
    12040 > show sel atoms
    12041 
    12042 > hide sel atoms
    12043 
    12044 > show sel atoms
    12045 
    12046 > style sel stick
    12047 
    12048 Changed 6 atom styles 
    12049 
    12050 > color sel lime
    12051 
    12052 > select clear
    12053 
    12054 Drag select of 16 residues 
    12055 
    12056 > select clear
    12057 
    12058 > select #14/A:138
    12059 
    12060 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12061 
    12062 > style sel stick
    12063 
    12064 Changed 6 atom styles 
    12065 
    12066 > show sel atoms
    12067 
    12068 > color sel forest green
    12069 
    12070 > select clear
    12071 
    12072 > show #!15 models
    12073 
    12074 > ui mousemode right translate
    12075 
    12076 > ui mousemode right select
    12077 
    12078 > select #15/D:47
    12079 
    12080 4 atoms, 3 bonds, 1 residue, 1 model selected 
    12081 
    12082 > select #15/D:48
    12083 
    12084 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12085 
    12086 > show sel atoms
    12087 
    12088 > show sel cartoons
    12089 
    12090 > style sel stick
    12091 
    12092 Changed 6 atom styles 
    12093 
    12094 > color sel forest green
    12095 
    12096 > select clear
    12097 
    12098 Drag select of 2 residues 
    12099 
    12100 > select clear
    12101 
    12102 > select #15/B
    12103 
    12104 1562 atoms, 1566 bonds, 1 pseudobond, 228 residues, 2 models selected 
    12105 
    12106 > delete sel
    12107 
    12108 > ui mousemode right translate
    12109 
    12110 > select #15/C
    12111 
    12112 561 atoms, 564 bonds, 79 residues, 1 model selected 
    12113 
    12114 > delete sel
    12115 
    12116 > save /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_29.cxs includeMaps
    12117 > true
    12118 
    12119 > select ::name="PO4"
    12120 
    12121 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12122 
    12123 > select add #11
    12124 
    12125 5302 atoms, 5029 bonds, 590 residues, 1 model selected 
    12126 
    12127 > select subtract #11
    12128 
    12129 Nothing selected 
    12130 
    12131 > select ::name="U94"
    12132 
    12133 49 atoms, 50 bonds, 1 residue, 1 model selected 
    12134 
    12135 > select add #11
    12136 
    12137 5302 atoms, 5029 bonds, 590 residues, 1 model selected 
    12138 
    12139 > select subtract #11
    12140 
    12141 Nothing selected 
    12142 
    12143 > select ::name="EDO"
    12144 
    12145 30 atoms, 27 bonds, 3 residues, 1 model selected 
    12146 
    12147 > select add #11
    12148 
    12149 5302 atoms, 5029 bonds, 590 residues, 1 model selected 
    12150 
    12151 > select subtract #11
    12152 
    12153 Nothing selected 
    12154 
    12155 > open
    12156 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J412_002_volume_map_sharp.mrc
    12157 
    12158 Opened cryosparc_P9_J412_002_volume_map_sharp.mrc as #16, grid size
    12159 144,144,144, pixel 2.47, shown at level 0.0775, step 1, values float32 
    12160 
    12161 > volume flip #16
    12162 
    12163 Opened cryosparc_P9_J412_002_volume_map_sharp.mrc z flip as #17, grid size
    12164 144,144,144, pixel 2.47, shown at step 1, values float32 
    12165 
    12166 > volume #17 level 0.1448
    12167 
    12168 > select add #17
    12169 
    12170 2 models selected 
    12171 
    12172 > ui mousemode right "translate selected models"
    12173 
    12174 > ui mousemode right "rotate selected models"
    12175 
    12176 > view matrix models
    12177 > #17,0.9922,0.0044226,0.12458,-22.95,1.9255e-05,0.99937,-0.03563,6.8457,-0.12466,0.035355,0.99157,17.52
    12178 
    12179 > ui mousemode right "translate selected models"
    12180 
    12181 > view matrix models
    12182 > #17,0.9922,0.0044226,0.12458,-22.362,1.9255e-05,0.99937,-0.03563,11.357,-0.12466,0.035355,0.99157,10.34
    12183 
    12184 > view matrix models
    12185 > #17,0.9922,0.0044226,0.12458,-22.105,1.9255e-05,0.99937,-0.03563,16.904,-0.12466,0.035355,0.99157,11.29
    12186 
    12187 > ui mousemode right "rotate selected models"
    12188 
    12189 > view matrix models
    12190 > #17,0.71959,0.6866,0.10379,-85.778,-0.69179,0.72177,0.021512,174.71,-0.060147,-0.087284,0.99437,20.189
    12191 
    12192 > ui mousemode right "translate selected models"
    12193 
    12194 > view matrix models
    12195 > #17,0.71959,0.6866,0.10379,-85.787,-0.69179,0.72177,0.021512,174.94,-0.060147,-0.087284,0.99437,24.387
    12196 
    12197 > select clear
    12198 
    12199 > hide #!13 models
    12200 
    12201 > hide #!13.1 models
    12202 
    12203 > hide #!14 models
    12204 
    12205 > show #!14 models
    12206 
    12207 > hide #!17 models
    12208 
    12209 > select add #14
    12210 
    12211 21476 atoms, 21738 bonds, 13 pseudobonds, 1524 residues, 3 models selected 
    12212 
    12213 > select add #15
    12214 
    12215 22555 atoms, 22818 bonds, 13 pseudobonds, 1683 residues, 4 models selected 
    12216 
    12217 > combine sel
    12218 
    12219 Remapping chain ID 'D' in 7ojx #15 to 'G' 
    12220 Remapping chain ID 'E' in 7ojx #15 to 'H' 
    12221 
    12222 > show #!17 models
    12223 
    12224 > hide #!14 models
    12225 
    12226 > hide #!15 models
    12227 
    12228 > select subtract #14
    12229 
    12230 1079 atoms, 1080 bonds, 159 residues, 1 model selected 
    12231 
    12232 > select subtract #15
    12233 
    12234 Nothing selected 
    12235 
    12236 > fitmap #18 inMap #17
    12237 
    12238 Fit molecule combination (#18) to map
    12239 cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) using 22555 atoms 
    12240 average map value = 0.447, steps = 112 
    12241 shifted from previous position = 9.21 
    12242 rotated from previous position = 19.6 degrees 
    12243 atoms outside contour = 3053, contour level = 0.14484 
    12244  
    12245 Position of combination (#18) relative to
    12246 cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates: 
    12247 Matrix rotation and translation 
    12248 -0.97806640 -0.06230326 -0.19875723 422.48504677 
    12249 0.06581407 -0.99777016 -0.01109996 366.20147167 
    12250 -0.19762247 -0.02393752 0.97998590 23.12448917 
    12251 Axis -0.09969844 -0.00881272 0.99497867 
    12252 Axis point 206.47417814 190.00859521 0.00000000 
    12253 Rotation angle (degrees) 176.30863292 
    12254 Shift along axis -22.33995844 
    12255  
    12256 
    12257 > select clear
    12258 
    12259 > surface dust #17 size 24.7
    12260 
    12261 > volume #17 level 0.2526
    12262 
    12263 > volume #17 level 0.1448
    12264 
    12265 > volume #17 level 0.1493
    12266 
    12267 > volume #17 level 0.1987
    12268 
    12269 > volume #17 level 0.1269
    12270 
    12271 > open
    12272 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J649_006_volume_map_sharp.mrc
    12273 
    12274 Opened cryosparc_P9_J649_006_volume_map_sharp.mrc as #19, grid size
    12275 420,420,420, pixel 0.825, shown at level 0.0268, step 2, values float32 
    12276 
    12277 > volume #19 level 0.05665
    12278 
    12279 > volume flip #19
    12280 
    12281 Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #20, grid size
    12282 420,420,420, pixel 0.825, shown at step 1, values float32 
    12283 
    12284 > fitmap #20 inMap #17
    12285 
    12286 Fit map cryosparc_P9_J649_006_volume_map_sharp.mrc z flip in map
    12287 cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 287605 points 
    12288 correlation = 0.9078, correlation about mean = 0.6488, overlap = 2.095e+04 
    12289 steps = 188, shift = 14, angle = 44 degrees 
    12290  
    12291 Position of cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#20) relative
    12292 to cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates: 
    12293 Matrix rotation and translation 
    12294 0.99999751 -0.00223074 -0.00003978 5.13478599 
    12295 0.00223068 0.99999658 -0.00136232 4.84445548 
    12296 0.00004281 0.00136223 0.99999907 3.01854380 
    12297 Axis 0.52112337 -0.01579715 0.85333515 
    12298 Axis point -2206.70833640 1095.32414338 0.00000000 
    12299 Rotation angle (degrees) 0.14977758 
    12300 Shift along axis 5.17515790 
    12301  
    12302 
    12303 > surface dust #17 size 24.7
    12304 
    12305 > surface dust #20 size 8.25
    12306 
    12307 > open
    12308 > /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P14_J581_003_volume_map_sharp.mrc
    12309 
    12310 Opened cryosparc_P14_J581_003_volume_map_sharp.mrc as #21, grid size
    12311 128,128,128, pixel 3.38, shown at level 0.0872, step 1, values float32 
    12312 
    12313 > surface dust #21 size 33.8
    12314 
    12315 > volume #21 level 0.3273
    12316 
    12317 > fitmap #21 inMap #17
    12318 
    12319 Fit map cryosparc_P14_J581_003_volume_map_sharp.mrc in map
    12320 cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 6517 points 
    12321 correlation = 0.4039, correlation about mean = -0.01045, overlap = 553.7 
    12322 steps = 436, shift = 15.8, angle = 37.9 degrees 
    12323  
    12324 Position of cryosparc_P14_J581_003_volume_map_sharp.mrc (#21) relative to
    12325 cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates: 
    12326 Matrix rotation and translation 
    12327 0.98601219 -0.14446284 -0.08312907 19.61215113 
    12328 0.11673704 0.95455998 -0.27420378 36.87216779 
    12329 0.11896395 0.26066403 0.95807194 -57.49708785 
    12330 Axis 0.85087384 -0.32149189 0.41551976 
    12331 Axis point 0.00000000 202.82855623 78.51350943 
    12332 Rotation angle (degrees) 18.31886274 
    12333 Shift along axis -19.05781241 
    12334  
    12335 
    12336 > select add #21
    12337 
    12338 4 models selected 
    12339 
    12340 > ui mousemode right "translate selected models"
    12341 
    12342 > view matrix models
    12343 > #21,0.80202,0.57851,-0.14864,-91.371,-0.5953,0.79452,-0.1198,180.05,0.048799,0.18457,0.98161,-96.697
    12344 
    12345 > ui mousemode right "rotate selected models"
    12346 
    12347 > view matrix models
    12348 > #21,0.80229,0.52541,0.28334,-180.65,-0.57975,0.7989,0.16015,110.76,-0.14221,-0.29275,0.94555,52.725
    12349 
    12350 > volume flip #21
    12351 
    12352 Opened cryosparc_P14_J581_003_volume_map_sharp.mrc z flip as #22, grid size
    12353 128,128,128, pixel 3.38, shown at step 1, values float32 
    12354 
    12355 > fitmap #22 inMap #17
    12356 
    12357 Fit map cryosparc_P14_J581_003_volume_map_sharp.mrc z flip in map
    12358 cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 6517 points 
    12359 correlation = 0.6482, correlation about mean = 0.2156, overlap = 1441 
    12360 steps = 164, shift = 21.6, angle = 36.5 degrees 
    12361  
    12362 Position of cryosparc_P14_J581_003_volume_map_sharp.mrc z flip (#22) relative
    12363 to cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates: 
    12364 Matrix rotation and translation 
    12365 0.93922058 0.34326503 -0.00581154 -100.97458873 
    12366 -0.33951902 0.92619472 -0.16398211 87.22555980 
    12367 -0.05090671 0.15598850 0.98644617 -55.53042614 
    12368 Axis 0.42358526 0.05969814 -0.90388697 
    12369 Axis point 180.41192944 341.68760540 0.00000000 
    12370 Rotation angle (degrees) 22.19087245 
    12371 Shift along axis 12.62908512 
    12372  
    12373 
    12374 > select add #22
    12375 
    12376 4 models selected 
    12377 
    12378 > select subtract #21
    12379 
    12380 2 models selected 
    12381 
    12382 > ui mousemode right "translate selected models"
    12383 
    12384 > ui mousemode right "rotate selected models"
    12385 
    12386 > view matrix models
    12387 > #22,-0.55164,0.82005,0.15235,94.206,0.83403,0.54034,0.11145,-132.93,0.0090744,0.18855,-0.98202,315.23
    12388 
    12389 > ui mousemode right "translate selected models"
    12390 
    12391 > view matrix models
    12392 > #22,-0.55164,0.82005,0.15235,95.398,0.83403,0.54034,0.11145,-131.11,0.0090744,0.18855,-0.98202,328.09
    12393 
    12394 > fitmap #22 inMap #17
    12395 
    12396 Fit map cryosparc_P14_J581_003_volume_map_sharp.mrc z flip in map
    12397 cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 6517 points 
    12398 correlation = 0.9521, correlation about mean = 0.7986, overlap = 2739 
    12399 steps = 168, shift = 10.8, angle = 18.3 degrees 
    12400  
    12401 Position of cryosparc_P14_J581_003_volume_map_sharp.mrc z flip (#22) relative
    12402 to cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates: 
    12403 Matrix rotation and translation 
    12404 -0.99979594 0.02007438 -0.00224759 390.44908315 
    12405 0.01996422 0.99894363 0.04138837 -50.61062770 
    12406 0.00307606 0.04133505 -0.99914059 376.77240244 
    12407 Axis -0.01001209 -0.99973588 -0.02068651 
    12408 Axis point 195.22657357 0.00000000 189.17004184 
    12409 Rotation angle (degrees) 179.84744828 
    12410 Shift along axis 38.89394229 
    12411  
    12412 
    12413 > select clear
    12414 
    12415 > volume #22 level 0.1832
    12416 
    12417 > volume #22 level 0.2252
    12418 
    12419 > volume #22 level 0.2552
    12420 
    12421 > select #18/H
    12422 
    12423 478 atoms, 481 bonds, 74 residues, 1 model selected 
    12424 
    12425 > delete sel
    12426 
    12427 > show #!19 models
    12428 
    12429 > show #!20 models
    12430 
    12431 > hide #!19 models
    12432 
    12433 > volume #19 level 0.1077
    12434 
    12435 > volume #20 level 0.08004
    12436 
    12437 > volume #19 level 0.09923
    12438 
    12439 > volume #20 level 0.07069
    12440 
    12441 > hide #!18 models
    12442 
    12443 > show #!18 models
    12444 
    12445 > hide #!20 models
    12446 
    12447 > save /home/pinkie/Documents/Charlotte/2024_01_28/with-Ubacceptor.pdb models
    12448 > #18
    12449 
    12450 > select #18/G
    12451 
    12452 601 atoms, 598 bonds, 85 residues, 1 model selected 
    12453 
    12454 > delete sel
    12455 
    12456 > save /home/pinkie/Documents/Charlotte/2024_01_28/without-Ubacceptor.pdb
    12457 
    12458 > show #!22 models
    12459 
    12460 > hide #!22 models
    12461 
    12462 > show #!22 models
    12463 
    12464 > hide #!22 models
    12465 
    12466 > select #18/B
    12467 
    12468 2615 atoms, 2648 bonds, 160 residues, 1 model selected 
    12469 
    12470 > color sel forest green
    12471 
    12472 > select clear
    12473 
    12474 > select #18/C
    12475 
    12476 1647 atoms, 1663 bonds, 104 residues, 1 model selected 
    12477 
    12478 > color sel #ccce3fff
    12479 
    12480 > select #18/D
    12481 
    12482 1522 atoms, 1539 bonds, 97 residues, 1 model selected 
    12483 
    12484 > color sel #b0daa8ff
    12485 
    12486 > select #18/E
    12487 
    12488 10756 atoms, 10867 bonds, 658 residues, 1 model selected 
    12489 
    12490 > color sel #4293a5ff
    12491 
    12492 > select #18/F
    12493 
    12494 1835 atoms, 1858 bonds, 114 residues, 1 model selected 
    12495 
    12496 > color sel #5b42cdff
    12497 
    12498 > select #18/N
    12499 
    12500 605 atoms, 610 bonds, 77 residues, 1 model selected 
    12501 
    12502 > color sel cyan
    12503 
    12504 > select clear
    12505 
    12506 > select #18/R
    12507 
    12508 499 atoms, 508 bonds, 13 pseudobonds, 63 residues, 3 models selected 
    12509 
    12510 > color (#!18 & sel) #60cb3eff
    12511 
    12512 > select #18/A
    12513 
    12514 1422 atoms, 1464 bonds, 176 residues, 1 model selected 
    12515 
    12516 > color sel #e01b24ff
    12517 
    12518 > color sel #c01c28ff
    12519 
    12520 > select clear
    12521 
    12522 > ui mousemode right select
    12523 
    12524 > select clear
    12525 
    12526 [Repeated 2 time(s)]
    12527 
    12528 > color sel orange
    12529 
    12530 > select clear
    12531 
    12532 Drag select of 2 atoms, 2 bonds 
    12533 
    12534 > color sel orange
    12535 
    12536 > select clear
    12537 
    12538 [Repeated 1 time(s)]
    12539 
    12540 > ui mousemode right select
    12541 
    12542 Drag select of 1 atoms, 1 residues 
    12543 
    12544 > color sel magenta
    12545 
    12546 > select clear
    12547 
    12548 > select sequence GELPER
    12549 
    12550 Nothing selected 
    12551 
    12552 > ui tool show "Show Sequence Viewer"
    12553 
    12554 > sequence chain #18/A
    12555 
    12556 Alignment identifier is 18/A 
    12557 
    12558 > select #18/A:107
    12559 
    12560 4 atoms, 3 bonds, 1 residue, 1 model selected 
    12561 
    12562 > select #18/A:107-119
    12563 
    12564 107 atoms, 110 bonds, 13 residues, 1 model selected 
    12565 
    12566 > select #18/A:102
    12567 
    12568 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12569 
    12570 > select #18/A:102-113
    12571 
    12572 92 atoms, 93 bonds, 12 residues, 1 model selected 
    12573 
    12574 > color sel gray
    12575 
    12576 > select clear
    12577 
    12578 Drag select of 3 residues 
    12579 
    12580 > select clear
    12581 
    12582 > ui mousemode right translate
    12583 
    12584 > select #18/A:98
    12585 
    12586 10 atoms, 10 bonds, 1 residue, 1 model selected 
    12587 
    12588 > select #18/A:98-99
    12589 
    12590 17 atoms, 18 bonds, 2 residues, 1 model selected 
    12591 
    12592 > select #18/A:91
    12593 
    12594 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12595 
    12596 > select #18/A:91-102
    12597 
    12598 90 atoms, 92 bonds, 12 residues, 1 model selected 
    12599 
    12600 > select clear
    12601 
    12602 > select #18/A:91-102
    12603 
    12604 90 atoms, 92 bonds, 12 residues, 1 model selected 
    12605 
    12606 > select clear
    12607 
    12608 > ui mousemode right select
    12609 
    12610 > select #18/A:91-102
    12611 
    12612 90 atoms, 92 bonds, 12 residues, 1 model selected 
    12613 
    12614 > select clear
    12615 
    12616 > select #18/A:96
    12617 
    12618 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12619 
    12620 > select #18/A:97
    12621 
    12622 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12623 
    12624 > select #18/A:96
    12625 
    12626 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12627 
    12628 > select #18/A:97
    12629 
    12630 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12631 
    12632 > select #18/A:99
    12633 
    12634 7 atoms, 7 bonds, 1 residue, 1 model selected 
    12635 
    12636 > select #18/A:101
    12637 
    12638 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12639 
    12640 > select clear
    12641 
    12642 [Repeated 1 time(s)]
    12643 
    12644 > ui mousemode right select
    12645 
    12646 > select #18/A:8-22,95-97,120-132,142-153,160-176
    12647 
    12648 478 atoms, 477 bonds, 60 residues, 1 model selected 
    12649 
    12650 > select #18/A:91-92
    12651 
    12652 15 atoms, 14 bonds, 2 residues, 1 model selected 
    12653 
    12654 > select #18/A:91-118
    12655 
    12656 219 atoms, 226 bonds, 28 residues, 1 model selected 
    12657 
    12658 > select #18/A:91
    12659 
    12660 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12661 
    12662 > select #18/A:91-94
    12663 
    12664 29 atoms, 28 bonds, 4 residues, 1 model selected 
    12665 
    12666 > select #18/A:98
    12667 
    12668 10 atoms, 10 bonds, 1 residue, 1 model selected 
    12669 
    12670 > select #18/A:98-104
    12671 
    12672 54 atoms, 57 bonds, 7 residues, 1 model selected 
    12673 
    12674 > select #18/A:95
    12675 
    12676 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12677 
    12678 > select #18/A:95-105
    12679 
    12680 85 atoms, 88 bonds, 11 residues, 1 model selected 
    12681 
    12682 > color sel gray
    12683 
    12684 > select #18/A:107
    12685 
    12686 4 atoms, 3 bonds, 1 residue, 1 model selected 
    12687 
    12688 > select #18/A:107-119
    12689 
    12690 107 atoms, 110 bonds, 13 residues, 1 model selected 
    12691 
    12692 > color sel gray
    12693 
    12694 > select clear
    12695 
    12696 > ui mousemode right translate
    12697 
    12698 > save
    12699 > /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_29_chimeramodelling.cxs
    12700 > includeMaps true
    12701 
    12702 > ui mousemode right select
    12703 
    12704 > select #18/F:456
    12705 
    12706 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12707 
    12708 > show sel atoms
    12709 
    12710 > style sel stick
    12711 
    12712 Changed 22 atom styles 
    12713 
    12714 > color sel hot pink
    12715 
    12716 > select clear
    12717 
    12718 [Repeated 2 time(s)]
    12719 
    12720 > save
    12721 > /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_30_chimerasession.cxs
    12722 > includeMaps true
    12723 
    12724 > close #4
    12725 
    12726 > close #13
    12727 
    12728 > show #!15 models
    12729 
    12730 > hide #!15 models
    12731 
    12732 > show #!15 models
    12733 
    12734 > hide #!15 models
    12735 
    12736 > show #!17 models
    12737 
    12738 > hide #!17 models
    12739 
    12740 > close #16
    12741 
    12742 > show #!19 models
    12743 
    12744 > hide #!19 models
    12745 
    12746 > show #!20 models
    12747 
    12748 > hide #!20 models
    12749 
    12750 > close #19
    12751 
    12752 > show #!21 models
    12753 
    12754 > hide #!21 models
    12755 
    12756 > show #!22 models
    12757 
    12758 > hide #!22 models
    12759 
    12760 > close #21
    12761 
    12762 > hide #!18 models
    12763 
    12764 > show #!18 models
    12765 
    12766 > show #!1 models
    12767 
    12768 > hide #!1 models
    12769 
    12770 > show #!1 models
    12771 
    12772 > close #1
    12773 
    12774 > show #!2.1 models
    12775 
    12776 > hide #!2.1 models
    12777 
    12778 > show #!2.4 models
    12779 
    12780 > hide #!2.4 models
    12781 
    12782 > close #2
    12783 
    12784 > show #3 models
    12785 
    12786 > hide #3 models
    12787 
    12788 > show #3 models
    12789 
    12790 > hide #3 models
    12791 
    12792 > close #3
    12793 
    12794 > show #!5 models
    12795 
    12796 > hide #!5 models
    12797 
    12798 > show #!5 models
    12799 
    12800 > hide #!5 models
    12801 
    12802 > close #5
    12803 
    12804 > show #!6 models
    12805 
    12806 > hide #!6 models
    12807 
    12808 > close #6
    12809 
    12810 > close #7
    12811 
    12812 > show #!8 models
    12813 
    12814 > hide #!8 models
    12815 
    12816 > close #8
    12817 
    12818 > show #9 models
    12819 
    12820 > hide #9 models
    12821 
    12822 > close #9
    12823 
    12824 > show #!10 models
    12825 
    12826 > hide #!10 models
    12827 
    12828 > close #10
    12829 
    12830 > show #11 models
    12831 
    12832 > hide #11 models
    12833 
    12834 > show #!12 models
    12835 
    12836 Drag select of 60 residues 
    12837 
    12838 > ui mousemode right translate
    12839 
    12840 > select clear
    12841 
    12842 > show #!14 models
    12843 
    12844 > hide #!12 models
    12845 
    12846 > hide #!14 models
    12847 
    12848 > show #!14 models
    12849 
    12850 > hide #!14 models
    12851 
    12852 > show #!14 models
    12853 
    12854 > hide #!14 models
    12855 
    12856 > show #!14 models
    12857 
    12858 > hide #!14 models
    12859 
    12860 > show #!14 models
    12861 
    12862 > hide #!14 models
    12863 
    12864 > show #!15 models
    12865 
    12866 > hide #!15 models
    12867 
    12868 > show #!15 models
    12869 
    12870 > hide #!15 models
    12871 
    12872 > show #!17 models
    12873 
    12874 > hide #!17 models
    12875 
    12876 > show #!20 models
    12877 
    12878 > hide #!18 models
    12879 
    12880 > show #!17 models
    12881 
    12882 > transparency #17.1#20.1 50
    12883 
    12884 > show #!18 models
    12885 
    12886 > volume #17 level 0.1533
    12887 
    12888 > show #!15 models
    12889 
    12890 > hide #!15 models
    12891 
    12892 > hide #!17 models
    12893 
    12894 > show #!17 models
    12895 
    12896 > show #!22 models
    12897 
    12898 > hide #!22 models
    12899 
    12900 > save
    12901 > /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_30_v2_chimerasession.cxs
    12902 > includeMaps true
    12903 
    12904 ——— End of log from Tue Jan 30 11:29:44 2024 ———
    12905 
    12906 opened ChimeraX session 
    12907 
    12908 > hide #!18 models
    12909 
    12910 > hide #!20 models
    12911 
    12912 > show #!20 models
    12913 
    12914 > hide #!17 models
    12915 
    12916 > show #!17 models
    12917 
    12918 > show #!14 models
    12919 
    12920 > show #!12 models
    12921 
    12922 > show #11 models
    12923 
    12924 > hide #11 models
    12925 
    12926 > hide #!12 models
    12927 
    12928 > hide #!14 models
    12929 
    12930 > show #!22 models
    12931 
    12932 > hide #!22 models
    12933 
    12934 > show #!22 models
    12935 
    12936 > show #!18 models
    12937 
    12938 > hide #!18 models
    12939 
    12940 > show #!18 models
    12941 
    12942 > lighting soft
    12943 
    12944 > transparency 0
    12945 
    12946 > transparency 50
    12947 
    12948 > volume #22 level 0.3822
    12949 
    12950 > volume #22 level 0.2552
    12951 
    12952 > volume #22 level 0.4046
    12953 
    12954 > hide #!22 models
    12955 
    12956 > show #!14 models
    12957 
    12958 > hide #!14 models
    12959 
    12960 > show #!14 models
    12961 
    12962 > hide #!14 models
    12963 
    12964 > show #!12 models
    12965 
    12966 > hide #!12 models
    12967 
    12968 > show #!12 models
    12969 
    12970 > hide #!12 models
    12971 
    12972 > hide #!18 models
    12973 
    12974 > show #!18 models
    12975 
    12976 > open
    12977 > /home/pinkie/Documents/Charlotte/2024_06/cryosparc_P9_J659_007_volume_map_sharp.mrc
    12978 > /home/pinkie/Documents/Charlotte/2024_06/cryosparc_P9_J659_007_volume_map.mrc
    12979 
    12980 Opened cryosparc_P9_J659_007_volume_map_sharp.mrc as #1.1, grid size
    12981 480,480,480, pixel 0.825, shown at level 0.0225, step 2, values float32 
    12982 Opened cryosparc_P9_J659_007_volume_map.mrc as #1.2, grid size 480,480,480,
    12983 pixel 0.825, shown at level 0.00707, step 2, values float32 
    12984 
    12985 > hide #!18 models
    12986 
    12987 > volume #1.2 level 0.01906
    12988 
    12989 > volume #1.1 level 0.05696
    12990 
    12991 > select add #1.1
    12992 
    12993 4 models selected 
    12994 
    12995 > select add #1.2
    12996 
    12997 8 models selected 
    12998 
    12999 > ui mousemode right "translate selected models"
    13000 
    13001 > ui mousemode right "rotate selected models"
    13002 
    13003 > view matrix models
    13004 > #1.1,-0.73945,-0.66601,-0.098215,503.62,0.63499,-0.73846,0.22688,164.46,-0.22363,0.1054,0.96896,31.101,#1.2,-0.73945,-0.66601,-0.098215,503.62,0.63499,-0.73846,0.22688,164.46,-0.22363,0.1054,0.96896,31.101
    13005 
    13006 > ui mousemode right "translate selected models"
    13007 
    13008 > view matrix models
    13009 > #1.1,-0.73945,-0.66601,-0.098215,500.05,0.63499,-0.73846,0.22688,152.07,-0.22363,0.1054,0.96896,5.6966,#1.2,-0.73945,-0.66601,-0.098215,500.05,0.63499,-0.73846,0.22688,152.07,-0.22363,0.1054,0.96896,5.6966
    13010 
    13011 > view matrix models
    13012 > #1.1,-0.73945,-0.66601,-0.098215,476.35,0.63499,-0.73846,0.22688,165.36,-0.22363,0.1054,0.96896,2.2825,#1.2,-0.73945,-0.66601,-0.098215,476.35,0.63499,-0.73846,0.22688,165.36,-0.22363,0.1054,0.96896,2.2825
    13013 
    13014 > fitmap #1.1 inMap #20
    13015 
    13016 Fit map cryosparc_P9_J659_007_volume_map_sharp.mrc in map
    13017 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip using 36781 points 
    13018 correlation = 0.9171, correlation about mean = 0.7903, overlap = 799.1 
    13019 steps = 252, shift = 7.76, angle = 15 degrees 
    13020  
    13021 Position of cryosparc_P9_J659_007_volume_map_sharp.mrc (#1.1) relative to
    13022 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#20) coordinates: 
    13023 Matrix rotation and translation 
    13024 -0.99948342 0.01340843 -0.02920822 373.96402547 
    13025 -0.01366728 -0.99986892 0.00868053 372.14706467 
    13026 -0.02908800 0.00907524 0.99953566 -21.05899600 
    13027 Axis 0.01457641 -0.00443965 -0.99988390 
    13028 Axis point 188.08875457 184.85549199 0.00000000 
    13029 Rotation angle (degrees) 179.22422433 
    13030 Shift along axis 24.85540421 
    13031  
    13032 
    13033 > fitmap #1.2 inMap #20
    13034 
    13035 Fit map cryosparc_P9_J659_007_volume_map.mrc in map
    13036 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip using 78730 points 
    13037 correlation = 0.8962, correlation about mean = 0.818, overlap = 608.1 
    13038 steps = 240, shift = 9.04, angle = 15.1 degrees 
    13039  
    13040 Position of cryosparc_P9_J659_007_volume_map.mrc (#1.2) relative to
    13041 cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#20) coordinates: 
    13042 Matrix rotation and translation 
    13043 -0.99955306 0.01397128 -0.02642920 373.41485214 
    13044 -0.01420867 -0.99986019 0.00881572 372.23852295 
    13045 -0.02630234 0.00918730 0.99961182 -21.62260651 
    13046 Axis 0.01318482 -0.00450140 -0.99990294 
    13047 Axis point 187.87678898 184.85341547 0.00000000 
    13048 Rotation angle (degrees) 179.19259892 
    13049 Shift along axis 24.86831902 
    13050  
    13051 
    13052 > select subtract #1.2
    13053 
    13054 4 models selected 
    13055 
    13056 > select subtract #1.1
    13057 
    13058 Nothing selected 
    13059 
    13060 > hide #!20 models
    13061 
    13062 > show #!20 models
    13063 
    13064 > hide #!20 models
    13065 
    13066 > hide #!1.2 models
    13067 
    13068 > show #!1.2 models
    13069 
    13070 > hide #!1.2 models
    13071 
    13072 > show #!1.2 models
    13073 
    13074 > show #!18 models
    13075 
    13076 > hide #!1.2 models
    13077 
    13078 > show #!1.2 models
    13079 
    13080 > hide #!1.2 models
    13081 
    13082 > surface dust #1.1 size 8.25
    13083 
    13084 > show #!1.2 models
    13085 
    13086 > volume #1.2 step 1
    13087 
    13088 > volume #1.1 step 1
    13089 
    13090 > transparency #1.1.1 50
    13091 
    13092 > open 8rx0
    13093 
    13094 Summary of feedback from opening 8rx0 fetched from pdb 
    13095 --- 
    13096 warnings | Atom H1 is not in the residue template for MET /B:54 
    13097 Atom H1 is not in the residue template for MET /C:1 
    13098 Atom H1 is not in the residue template for ALA /D:16 
    13099 Atom H1 is not in the residue template for MET /E:1 
    13100 note | Fetching compressed mmCIF 8rx0 from
    13101 http://files.rcsb.org/download/8rx0.cif 
    13102  
    13103 8rx0 title: 
    13104 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
    13105 C223S)-Ub [more info...] 
    13106  
    13107 Chain information for 8rx0 #2 
    13108 --- 
    13109 Chain | Description | UniProt 
    13110 A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN 
    13111 B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    13112 C | Elongin-B | ELOB_HUMAN 
    13113 D | Elongin-C | L7N190_MYOLU 
    13114 E | Cullin-2 | CUL2_HUMAN 
    13115 G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    13116 N | NEDD8 | NEDD8_HUMAN 
    13117 R | RBX1 | 
    13118 U | Ubiquitin | UBC_HUMAN 
    13119  
    13120 Non-standard residues in 8rx0 #2 
    13121 --- 
    13122 759 —
    13123 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    13124 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    13125 pyrrolidine-2-carboxamide 
    13126 ZN — zinc ion 
    13127  
    13128 
    13129 > hide #!18 models
    13130 
    13131 > select add #2
    13132 
    13133 21370 atoms, 21642 bonds, 13 pseudobonds, 1548 residues, 3 models selected 
    13134 
    13135 > fitmap #2 inMap #1.1
    13136 
    13137 Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map_sharp.mrc
    13138 (#1.1) using 21370 atoms 
    13139 average map value = 0.1073, steps = 68 
    13140 shifted from previous position = 0.808 
    13141 rotated from previous position = 1.01 degrees 
    13142 atoms outside contour = 8594, contour level = 0.056956 
    13143  
    13144 Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map_sharp.mrc
    13145 (#1.1) coordinates: 
    13146 Matrix rotation and translation 
    13147 -0.73092142 0.68081307 0.04740703 197.96935832 
    13148 -0.67616473 -0.73184263 0.08489771 441.44230993 
    13149 0.09249396 0.02999859 0.99526124 3.71445652 
    13150 Axis -0.04040157 -0.03318055 -0.99863245 
    13151 Axis point 185.35205193 182.02538297 0.00000000 
    13152 Rotation angle (degrees) 137.20181648 
    13153 Shift along axis -26.35494835 
    13154  
    13155 
    13156 > select clear
    13157 
    13158 > style #!2 stick
    13159 
    13160 Changed 21370 atom styles 
    13161 
    13162 > show #!2 cartoons
    13163 
    13164 > volume #1.1 level 0.1472
    13165 
    13166 > view
    13167 
    13168 > show #!2 atoms
    13169 
    13170 > select ::name="759"
    13171 
    13172 69 atoms, 75 bonds, 1 residue, 1 model selected 
    13173 
    13174 > color sel yellow
    13175 
    13176 > select clear
    13177 
    13178 > volume #1.1 level 0.1021
    13179 
    13180 > hide #!2 models
    13181 
    13182 > transparency #1.1.1 0
    13183 
    13184 > show #!1.2 models
    13185 
    13186 > volume #1.2 level 0.1935
    13187 
    13188 > volume #1.2 level 0.02577
    13189 
    13190 > show #!2 models
    13191 
    13192 > hide #!2 models
    13193 
    13194 > show #!2 models
    13195 
    13196 > hide #!2 models
    13197 
    13198 > volume #1.2 level 0.05149
    13199 
    13200 > volume #1.2 level 0.03919
    13201 
    13202 > volume #1.2 level 0.1141
    13203 
    13204 > show #!2 models
    13205 
    13206 > transparency #1.2.1 50
    13207 
    13208 > select sidechain only
    13209 
    13210 Expected a keyword 
    13211 
    13212 > select sidechain
    13213 
    13214 69673 atoms, 64004 bonds, 6516 residues, 6 models selected 
    13215 
    13216 > select solvent
    13217 
    13218 976 atoms, 638 bonds, 338 residues, 3 models selected 
    13219 
    13220 > delete sel
    13221 
    13222 > select #2/A:sidechain
    13223 
    13224 Nothing selected 
    13225 
    13226 > select #2/A sidechain
    13227 
    13228 Expected a keyword 
    13229 
    13230 > select #2/A sidechain
    13231 
    13232 Expected a keyword 
    13233 
    13234 > select #2 sidechain
    13235 
    13236 Expected a keyword 
    13237 
    13238 > select sidechain
    13239 
    13240 69673 atoms, 64004 bonds, 6516 residues, 6 models selected 
    13241 
    13242 > select sidechain #2
    13243 
    13244 Expected a keyword 
    13245 
    13246 > select sidechain
    13247 
    13248 69673 atoms, 64004 bonds, 6516 residues, 6 models selected 
    13249 
    13250 > select #2
    13251 
    13252 21362 atoms, 21642 bonds, 13 pseudobonds, 1540 residues, 3 models selected 
    13253 
    13254 > select #2/A
    13255 
    13256 885 atoms, 908 bonds, 111 residues, 1 model selected 
    13257 
    13258 > select #2/Asidechain
    13259 
    13260 Nothing selected 
    13261 
    13262 > select #2/A sidechain
    13263 
    13264 Expected a keyword 
    13265 
    13266 > select #2/A sidechains
    13267 
    13268 Expected a keyword 
    13269 
    13270 > select #2/A sidechain
    13271 
    13272 Expected a keyword 
    13273 
    13274 > select #2/A-sidechain
    13275 
    13276 20787 atoms, 21061 bonds, 13 pseudobonds, 1465 residues, 3 models selected 
    13277 
    13278 > select #2/A sidechain
    13279 
    13280 Expected a keyword 
    13281 
    13282 > select #2/A@sidechain
    13283 
    13284 Nothing selected 
    13285 
    13286 > select #2/A:Ca
    13287 
    13288 Nothing selected 
    13289 
    13290 > select Ca
    13291 
    13292 Nothing selected 
    13293 
    13294 > select @Ca
    13295 
    13296 6517 atoms, 6517 residues, 6 models selected 
    13297 
    13298 > select @sidechain
    13299 
    13300 Nothing selected 
    13301 
    13302 > select @Cb
    13303 
    13304 6225 atoms, 6225 residues, 6 models selected 
    13305 
    13306 > select
    13307 
    13308 94351 atoms, 95475 bonds, 52 pseudobonds, 6534 residues, 25 models selected 
    13309 
    13310 > select #2/A@Ca
    13311 
    13312 111 atoms, 111 residues, 1 model selected 
    13313 
    13314 > hide sel atoms
    13315 
    13316 > show sel atoms
    13317 
    13318 > hide sel cartoons
    13319 
    13320 > show sel cartoons
    13321 
    13322 > hide sel cartoons
    13323 
    13324 > show sel cartoons
    13325 
    13326 > select #2/A@Ca
    13327 
    13328 111 atoms, 111 residues, 1 model selected 
    13329 
    13330 > view matrix models
    13331 > #2,0.99998,-0.0028888,-0.0047606,2.4594,0.0029684,0.99985,0.016795,-1.2113,0.0047114,-0.016809,0.99985,-2.2479
    13332 
    13333 > undo
    13334 
    13335 > select clear
    13336 
    13337 > select #2/A sideonly
    13338 
    13339 Expected a keyword 
    13340 
    13341 > select #2/A :sideonly
    13342 
    13343 Nothing selected 
    13344 
    13345 > select #2/A :sidechain
    13346 
    13347 Nothing selected 
    13348 
    13349 > select #2/A & sidechain
    13350 
    13351 552 atoms, 459 bonds, 111 residues, 1 model selected 
    13352 
    13353 > select #2/A & sideonly
    13354 
    13355 441 atoms, 351 bonds, 108 residues, 1 model selected 
    13356 
    13357 > hide sel cartoons
    13358 
    13359 > select #2/A & sidechain
    13360 
    13361 552 atoms, 459 bonds, 111 residues, 1 model selected 
    13362 
    13363 > select #2/A & sideonly
    13364 
    13365 441 atoms, 351 bonds, 108 residues, 1 model selected 
    13366 
    13367 > select #2/A & sidechain
    13368 
    13369 552 atoms, 459 bonds, 111 residues, 1 model selected 
    13370 
    13371 > delete sel
    13372 
    13373 Undo failed, probably because structures have been modified. 
    13374 
    13375 > show #!2 cartoons
    13376 
    13377 [Repeated 1 time(s)]
    13378 
    13379 > hide #!2 atoms
    13380 
    13381 [Repeated 1 time(s)]
    13382 
    13383 > show #!2 cartoons
    13384 
    13385 > hide #!2 surfaces
    13386 
    13387 > hide #!2 cartoons
    13388 
    13389 > show #!2 cartoons
    13390 
    13391 > show #!2 atoms
    13392 
    13393 > open 8rx0
    13394 
    13395 Summary of feedback from opening 8rx0 fetched from pdb 
    13396 --- 
    13397 warnings | Atom H1 is not in the residue template for MET /B:54 
    13398 Atom H1 is not in the residue template for MET /C:1 
    13399 Atom H1 is not in the residue template for ALA /D:16 
    13400 Atom H1 is not in the residue template for MET /E:1 
    13401  
    13402 8rx0 title: 
    13403 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
    13404 C223S)-Ub [more info...] 
    13405  
    13406 Chain information for 8rx0 #3 
    13407 --- 
    13408 Chain | Description | UniProt 
    13409 A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN 
    13410 B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    13411 C | Elongin-B | ELOB_HUMAN 
    13412 D | Elongin-C | L7N190_MYOLU 
    13413 E | Cullin-2 | CUL2_HUMAN 
    13414 G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    13415 N | NEDD8 | NEDD8_HUMAN 
    13416 R | RBX1 | 
    13417 U | Ubiquitin | UBC_HUMAN 
    13418  
    13419 Non-standard residues in 8rx0 #3 
    13420 --- 
    13421 759 —
    13422 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    13423 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    13424 pyrrolidine-2-carboxamide 
    13425 ZN — zinc ion 
    13426  
    13427 
    13428 > show #!2-3 cartoons
    13429 
    13430 > hide #!2-3 atoms
    13431 
    13432 > hide #!2-3 surfaces
    13433 
    13434 > close #2
    13435 
    13436 > select add #3
    13437 
    13438 21370 atoms, 21642 bonds, 13 pseudobonds, 1548 residues, 3 models selected 
    13439 
    13440 > fitmap #3 inMap #1.2
    13441 
    13442 Fit molecule 8rx0 (#3) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13443 using 21370 atoms 
    13444 average map value = 0.09099, steps = 80 
    13445 shifted from previous position = 0.965 
    13446 rotated from previous position = 0.797 degrees 
    13447 atoms outside contour = 14570, contour level = 0.1141 
    13448  
    13449 Position of 8rx0 (#3) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13450 coordinates: 
    13451 Matrix rotation and translation 
    13452 -0.73601744 0.67550999 0.04432354 200.70850250 
    13453 -0.67100751 -0.73664288 0.08429815 441.51062032 
    13454 0.08959486 0.03230348 0.99545428 3.91215108 
    13455 Axis -0.03856367 -0.03357706 -0.99869186 
    13456 Axis point 185.81581942 181.92454516 0.00000000 
    13457 Rotation angle (degrees) 137.61254970 
    13458 Shift along axis -26.47171863 
    13459  
    13460 
    13461 > select clear
    13462 
    13463 > select #2/A & sidechain
    13464 
    13465 Nothing selected 
    13466 
    13467 > show #!3 atoms
    13468 
    13469 > style #!3 stick
    13470 
    13471 Changed 21370 atom styles 
    13472 
    13473 > select #2/A & sidechain
    13474 
    13475 Nothing selected 
    13476 
    13477 > select #3/A & sidechain
    13478 
    13479 552 atoms, 459 bonds, 111 residues, 1 model selected 
    13480 
    13481 > hide sel
    13482 
    13483 > remove sel
    13484 
    13485 Unknown command: remove sel 
    13486 
    13487 > hide sel
    13488 
    13489 > color bfactor sel
    13490 
    13491 552 atoms, 111 residues, atom bfactor range 38.1 to 137 
    13492 
    13493 > select clear
    13494 
    13495 > show #!3 atoms
    13496 
    13497 > select #3/A:349-350 & sidechain
    13498 
    13499 6 atoms, 4 bonds, 2 residues, 1 model selected 
    13500 
    13501 > delete sel
    13502 
    13503 > select #3/A & sidechain
    13504 
    13505 546 atoms, 455 bonds, 109 residues, 1 model selected 
    13506 
    13507 > delete sel
    13508 
    13509 > show #!3 atoms
    13510 
    13511 > hide #!3 atoms
    13512 
    13513 > show #!3 atoms
    13514 
    13515 > hide #!3 atoms
    13516 
    13517 > show #!3 atoms
    13518 
    13519 > ui mousemode right select
    13520 
    13521 Drag select of 3 residues 
    13522 
    13523 > delete sel
    13524 
    13525 Undo failed, probably because structures have been modified. 
    13526 
    13527 > open 8rx0
    13528 
    13529 Summary of feedback from opening 8rx0 fetched from pdb 
    13530 --- 
    13531 warnings | Atom H1 is not in the residue template for MET /B:54 
    13532 Atom H1 is not in the residue template for MET /C:1 
    13533 Atom H1 is not in the residue template for ALA /D:16 
    13534 Atom H1 is not in the residue template for MET /E:1 
    13535  
    13536 8rx0 title: 
    13537 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
    13538 C223S)-Ub [more info...] 
    13539  
    13540 Chain information for 8rx0 #2 
    13541 --- 
    13542 Chain | Description | UniProt 
    13543 A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN 
    13544 B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    13545 C | Elongin-B | ELOB_HUMAN 
    13546 D | Elongin-C | L7N190_MYOLU 
    13547 E | Cullin-2 | CUL2_HUMAN 
    13548 G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    13549 N | NEDD8 | NEDD8_HUMAN 
    13550 R | RBX1 | 
    13551 U | Ubiquitin | UBC_HUMAN 
    13552  
    13553 Non-standard residues in 8rx0 #2 
    13554 --- 
    13555 759 —
    13556 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    13557 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    13558 pyrrolidine-2-carboxamide 
    13559 ZN — zinc ion 
    13560  
    13561 
    13562 > close #3
    13563 
    13564 > fitmap #2 inMap #1.2
    13565 
    13566 Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13567 using 21370 atoms 
    13568 average map value = 0.09099, steps = 80 
    13569 shifted from previous position = 0.965 
    13570 rotated from previous position = 0.797 degrees 
    13571 atoms outside contour = 14570, contour level = 0.1141 
    13572  
    13573 Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13574 coordinates: 
    13575 Matrix rotation and translation 
    13576 -0.73601744 0.67550999 0.04432354 200.70850250 
    13577 -0.67100751 -0.73664288 0.08429815 441.51062032 
    13578 0.08959486 0.03230348 0.99545428 3.91215108 
    13579 Axis -0.03856367 -0.03357706 -0.99869186 
    13580 Axis point 185.81581942 181.92454516 0.00000000 
    13581 Rotation angle (degrees) 137.61254970 
    13582 Shift along axis -26.47171863 
    13583  
    13584 
    13585 > show #!2 cartoons
    13586 
    13587 > hide #!2 atoms
    13588 
    13589 > show #!2 atoms
    13590 
    13591 > style #!2 stick
    13592 
    13593 Changed 21370 atom styles 
    13594 
    13595 > color bfactor #!2
    13596 
    13597 21370 atoms, 1548 residues, atom bfactor range 29 to 137 
    13598 
    13599 > select clear
    13600 
    13601 > ui mousemode right translate
    13602 
    13603 > select #2/A & sidechain
    13604 
    13605 552 atoms, 459 bonds, 111 residues, 1 model selected 
    13606 
    13607 > delete sel
    13608 
    13609 > select clear
    13610 
    13611 > select #2/A:457-459
    13612 
    13613 9 atoms, 5 bonds, 3 residues, 1 model selected 
    13614 
    13615 > delete sel
    13616 
    13617 > show #!2 cartoons
    13618 
    13619 > hide #!2 cartoons
    13620 
    13621 > show #!2 cartoons
    13622 
    13623 > hide #!2 cartoons
    13624 
    13625 > show #!2 cartoons
    13626 
    13627 > hide #!2 atoms
    13628 
    13629 > show #!2 atoms
    13630 
    13631 > close #2
    13632 
    13633 > open 8rx0
    13634 
    13635 Summary of feedback from opening 8rx0 fetched from pdb 
    13636 --- 
    13637 warnings | Atom H1 is not in the residue template for MET /B:54 
    13638 Atom H1 is not in the residue template for MET /C:1 
    13639 Atom H1 is not in the residue template for ALA /D:16 
    13640 Atom H1 is not in the residue template for MET /E:1 
    13641  
    13642 8rx0 title: 
    13643 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
    13644 C223S)-Ub [more info...] 
    13645  
    13646 Chain information for 8rx0 #2 
    13647 --- 
    13648 Chain | Description | UniProt 
    13649 A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN 
    13650 B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    13651 C | Elongin-B | ELOB_HUMAN 
    13652 D | Elongin-C | L7N190_MYOLU 
    13653 E | Cullin-2 | CUL2_HUMAN 
    13654 G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    13655 N | NEDD8 | NEDD8_HUMAN 
    13656 R | RBX1 | 
    13657 U | Ubiquitin | UBC_HUMAN 
    13658  
    13659 Non-standard residues in 8rx0 #2 
    13660 --- 
    13661 759 —
    13662 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    13663 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    13664 pyrrolidine-2-carboxamide 
    13665 ZN — zinc ion 
    13666  
    13667 
    13668 > fitmap #2 inMap #1.2
    13669 
    13670 Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13671 using 21370 atoms 
    13672 average map value = 0.09099, steps = 80 
    13673 shifted from previous position = 0.965 
    13674 rotated from previous position = 0.797 degrees 
    13675 atoms outside contour = 14570, contour level = 0.1141 
    13676  
    13677 Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13678 coordinates: 
    13679 Matrix rotation and translation 
    13680 -0.73601744 0.67550999 0.04432354 200.70850250 
    13681 -0.67100751 -0.73664288 0.08429815 441.51062032 
    13682 0.08959486 0.03230348 0.99545428 3.91215108 
    13683 Axis -0.03856367 -0.03357706 -0.99869186 
    13684 Axis point 185.81581942 181.92454516 0.00000000 
    13685 Rotation angle (degrees) 137.61254970 
    13686 Shift along axis -26.47171863 
    13687  
    13688 
    13689 > fitmap #2 inMap #1.2
    13690 
    13691 Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13692 using 21370 atoms 
    13693 average map value = 0.09099, steps = 64 
    13694 shifted from previous position = 0.0123 
    13695 rotated from previous position = 0.00696 degrees 
    13696 atoms outside contour = 14571, contour level = 0.1141 
    13697  
    13698 Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13699 coordinates: 
    13700 Matrix rotation and translation 
    13701 -0.73598978 0.67553655 0.04437792 200.68940166 
    13702 -0.67102310 -0.73661694 0.08440070 441.48695869 
    13703 0.08970529 0.03233944 0.99544317 3.87523220 
    13704 Axis -0.03861172 -0.03361746 -0.99868864 
    13705 Axis point 185.80643210 181.91519277 0.00000000 
    13706 Rotation angle (degrees) 137.61074426 
    13707 Shift along axis -26.46078590 
    13708  
    13709 
    13710 > hide #!2 atoms
    13711 
    13712 > show #!2 atoms
    13713 
    13714 > style #!2 stick
    13715 
    13716 Changed 21370 atom styles 
    13717 
    13718 > show #!2 cartoons
    13719 
    13720 > select #2/A:457-459
    13721 
    13722 23 atoms, 23 bonds, 3 residues, 1 model selected 
    13723 
    13724 > delete sel
    13725 
    13726 > select #2/A & sidechain
    13727 
    13728 538 atoms, 448 bonds, 108 residues, 1 model selected 
    13729 
    13730 > delete sel
    13731 
    13732 > select #2/A:349-350
    13733 
    13734 6 atoms, 3 bonds, 2 residues, 1 model selected 
    13735 
    13736 > delete sel
    13737 
    13738 > close #2
    13739 
    13740 > open 8rx0
    13741 
    13742 Summary of feedback from opening 8rx0 fetched from pdb 
    13743 --- 
    13744 warnings | Atom H1 is not in the residue template for MET /B:54 
    13745 Atom H1 is not in the residue template for MET /C:1 
    13746 Atom H1 is not in the residue template for ALA /D:16 
    13747 Atom H1 is not in the residue template for MET /E:1 
    13748  
    13749 8rx0 title: 
    13750 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
    13751 C223S)-Ub [more info...] 
    13752  
    13753 Chain information for 8rx0 #2 
    13754 --- 
    13755 Chain | Description | UniProt 
    13756 A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN 
    13757 B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    13758 C | Elongin-B | ELOB_HUMAN 
    13759 D | Elongin-C | L7N190_MYOLU 
    13760 E | Cullin-2 | CUL2_HUMAN 
    13761 G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    13762 N | NEDD8 | NEDD8_HUMAN 
    13763 R | RBX1 | 
    13764 U | Ubiquitin | UBC_HUMAN 
    13765  
    13766 Non-standard residues in 8rx0 #2 
    13767 --- 
    13768 759 —
    13769 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    13770 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    13771 pyrrolidine-2-carboxamide 
    13772 ZN — zinc ion 
    13773  
    13774 
    13775 > fitmap #2 inMap #1.2
    13776 
    13777 Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13778 using 21370 atoms 
    13779 average map value = 0.09099, steps = 80 
    13780 shifted from previous position = 0.965 
    13781 rotated from previous position = 0.797 degrees 
    13782 atoms outside contour = 14570, contour level = 0.1141 
    13783  
    13784 Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
    13785 coordinates: 
    13786 Matrix rotation and translation 
    13787 -0.73601744 0.67550999 0.04432354 200.70850250 
    13788 -0.67100751 -0.73664288 0.08429815 441.51062032 
    13789 0.08959486 0.03230348 0.99545428 3.91215108 
    13790 Axis -0.03856367 -0.03357706 -0.99869186 
    13791 Axis point 185.81581942 181.92454516 0.00000000 
    13792 Rotation angle (degrees) 137.61254970 
    13793 Shift along axis -26.47171863 
    13794  
    13795 
    13796 > hide #!2 atoms
    13797 
    13798 > style #!2 stick
    13799 
    13800 Changed 21370 atom styles 
    13801 
    13802 > show #!2 atoms
    13803 
    13804 > show #!2 cartoons
    13805 
    13806 > volume #1.2 level 0.07162
    13807 
    13808 > volume #1.2 level 0.09621
    13809 
    13810 > volume #1.1 level 0.09081
    13811 
    13812 > volume #1.1 level 0.07953
    13813 
    13814 > select #2/A:456
    13815 
    13816 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13817 
    13818 > select #2/G:138
    13819 
    13820 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13821 
    13822 > select #2/G:93
    13823 
    13824 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13825 
    13826 > select #2/A & sidechain
    13827 
    13828 552 atoms, 459 bonds, 111 residues, 1 model selected 
    13829 
    13830 > delete sel
    13831 
    13832 > color bfactor #!2
    13833 
    13834 20818 atoms, 1548 residues, atom bfactor range 29 to 124 
    13835 
    13836 > select #2/N & sidechain
    13837 
    13838 374 atoms, 300 bonds, 77 residues, 1 model selected 
    13839 
    13840 > delete sel
    13841 
    13842 > volume #1.1 level 0.1171
    13843 
    13844 > volume #1.1 level 0.08329
    13845 
    13846 Drag select of 4 residues 
    13847 
    13848 > delete sel
    13849 
    13850 > close #2
    13851 
    13852 > open 8rx0
    13853 
    13854 Summary of feedback from opening 8rx0 fetched from pdb 
    13855 --- 
    13856 warnings | Atom H1 is not in the residue template for MET /B:54 
    13857 Atom H1 is not in the residue template for MET /C:1 
    13858 Atom H1 is not in the residue template for ALA /D:16 
    13859 Atom H1 is not in the residue template for MET /E:1 
    13860  
    13861 8rx0 title: 
    13862 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
    13863 C223S)-Ub [more info...] 
    13864  
    13865 Chain information for 8rx0 #2 
    13866 --- 
    13867 Chain | Description | UniProt 
    13868 A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN 
    13869 B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 
    13870 C | Elongin-B | ELOB_HUMAN 
    13871 D | Elongin-C | L7N190_MYOLU 
    13872 E | Cullin-2 | CUL2_HUMAN 
    13873 G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN 
    13874 N | NEDD8 | NEDD8_HUMAN 
    13875 R | RBX1 | 
    13876 U | Ubiquitin | UBC_HUMAN 
    13877  
    13878 Non-standard residues in 8rx0 #2 
    13879 --- 
    13880 759 —
    13881 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    13882 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    13883 pyrrolidine-2-carboxamide 
    13884 ZN — zinc ion 
    13885  
    13886 
    13887 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    13888 got 1 atomic models, 0 maps. 
    13889 
    13890 > hide #!1 models
    13891 
    13892 > show #!1.1 models
    13893 
    13894 > fitmap #2 inMap #1.1
    13895 
    13896 Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map_sharp.mrc
    13897 (#1.1) using 21370 atoms 
    13898 average map value = 0.1073, steps = 68 
    13899 shifted from previous position = 0.808 
    13900 rotated from previous position = 1.01 degrees 
    13901 atoms outside contour = 11206, contour level = 0.08329 
    13902  
    13903 Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map_sharp.mrc
    13904 (#1.1) coordinates: 
    13905 Matrix rotation and translation 
    13906 -0.73092142 0.68081307 0.04740703 197.96935832 
    13907 -0.67616473 -0.73184263 0.08489771 441.44230993 
    13908 0.09249396 0.02999859 0.99526124 3.71445652 
    13909 Axis -0.04040157 -0.03318055 -0.99863245 
    13910 Axis point 185.35205193 182.02538297 0.00000000 
    13911 Rotation angle (degrees) 137.20181648 
    13912 Shift along axis -26.35494835 
    13913  
    13914 
    13915 > select clear
    13916 
    13917 > hide #!2 atoms
    13918 
    13919 > show #!2 atoms
    13920 
    13921 > style #!2 stick
    13922 
    13923 Changed 21370 atom styles 
    13924 
    13925 > show #!2 cartoons
    13926 
    13927 > color bfactor #!2
    13928 
    13929 21370 atoms, 1548 residues, atom bfactor range 29 to 137 
    13930 Drag select of 9 atoms, 4 residues, 7 bonds 
    13931 
    13932 > select clear
    13933 
    13934 Drag select of 4 atoms, 3 residues, 2 bonds 
    13935 
    13936 > delete sel
    13937 
    13938 Drag select of 10 atoms, 3 residues, 9 bonds 
    13939 
    13940 > delete sel
    13941 
    13942 Drag select of 10 atoms, 4 residues, 8 bonds 
    13943 
    13944 > delete sel
    13945 
    13946 > select #2/A:406
    13947 
    13948 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13949 
    13950 > select #2/A:407
    13951 
    13952 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13953 
    13954 > select #2/A:405
    13955 
    13956 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13957 
    13958 > select #2/A:405-412
    13959 
    13960 35 atoms, 34 bonds, 1 pseudobond, 4 residues, 2 models selected 
    13961 
    13962 > delete sel
    13963 
    13964 > select #2/A & sidechain
    13965 
    13966 484 atoms, 404 bonds, 97 residues, 1 model selected 
    13967 
    13968 > delete sel
    13969 
    13970 > select #2/N & sidechain
    13971 
    13972 374 atoms, 300 bonds, 77 residues, 1 model selected 
    13973 
    13974 > delete sel
    13975 
    13976 > volume #1.1 level 0.07953
    13977 
    13978 > volume #1.1 level 0.1247
    13979 
    13980 > volume #1.1 level 0.2639
    13981 
    13982 > save /home/pinkie/Documents/Charlotte/2024_06/done-brd4-n8.cxs includeMaps
    13983 > true
    13984 
    13985 ——— End of log from Wed Jun 26 10:54:46 2024 ———
    13986 
    13987 opened ChimeraX session 
    13988 
     7502[deleted to fit within ticket limits]
    139897503
    139907504