Changes between Initial Version and Version 1 of Ticket #19800


Ignore:
Timestamp:
Feb 4, 2026, 9:59:38 AM (8 hours ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19800

    • Property Component Unassigned → Graphics
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash in window_size

  • Ticket #19800 – Description

    initial v1  
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    1538     "name" : "_csv.cpython-311-darwin.so"
    1539   },
    1540   {
    1541     "source" : "P",
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    1544     "size" : 737280,
    1545     "uuid" : "3064ecb2-3709-3d94-8d92-ed5e1a3b6f5c",
    1546     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
    1547     "name" : "QtOpenGL.abi3.so"
    1548   },
    1549   {
    1550     "source" : "P",
    1551     "arch" : "arm64",
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    1553     "size" : 49152,
    1554     "uuid" : "41d9a4a9-c948-34f9-b755-29244498ec4d",
    1555     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
    1556     "name" : "QtOpenGLWidgets.abi3.so"
    1557   },
    1558   {
    1559     "source" : "P",
    1560     "arch" : "arm64",
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    1562     "size" : 49152,
    1563     "uuid" : "c0bef4c8-6fde-3bf3-bb63-abf57c774fb2",
    1564     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
    1565     "name" : "QtOpenGLWidgets"
    1566   },
    1567   {
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    1573     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
    1574     "name" : "_ribbons.cpython-311-darwin.so"
    1575   },
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    1581     "uuid" : "a6f965b7-4c4f-3eac-9469-6e23d676fbfe",
    1582     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
    1583     "name" : "_graphics.cpython-311-darwin.so"
    1584   },
    1585   {
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    1589     "size" : 458752,
    1590     "uuid" : "5a3a7577-7503-3a30-8fae-d2dd268c2956",
    1591     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
    1592     "name" : "mmcif.cpython-311-darwin.so"
    1593   },
    1594   {
    1595     "source" : "P",
    1596     "arch" : "arm64",
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    1598     "size" : 442368,
    1599     "uuid" : "301bbc3d-fda9-3083-b4bb-16602d88cb5e",
    1600     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
    1601     "name" : "_mmcif.cpython-311-darwin.so"
    1602   },
    1603   {
    1604     "source" : "P",
    1605     "arch" : "arm64",
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    1607     "size" : 180224,
    1608     "uuid" : "19b3ef1e-a67a-3af0-8d1f-cfd646cde92f",
    1609     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
    1610     "name" : "_pdbio.cpython-311-darwin.so"
    1611   },
    1612   {
    1613     "source" : "P",
    1614     "arch" : "arm64",
    1615     "base" : 5888032768,
    1616     "size" : 3833856,
    1617     "uuid" : "bd3bfa3e-c1d4-3ee2-b082-3b38ca7693ca",
    1618     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
    1619     "name" : "etree.cpython-311-darwin.so"
    1620   },
    1621   {
    1622     "source" : "P",
    1623     "arch" : "arm64",
    1624     "base" : 5522702336,
    1625     "size" : 131072,
    1626     "uuid" : "c9441298-6125-3b5c-8f21-032910e5184d",
    1627     "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    1628     "name" : "_elementpath.cpython-311-darwin.so"
    1629   },
    1630   {
    1631     "source" : "P",
    1632     "arch" : "arm64e",
    1633     "base" : 6654140416,
    1634     "size" : 246944,
    1635     "uuid" : "9fe7c84d-0c2b-363f-bee5-6fd76d67a227",
    1636     "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    1637     "name" : "libsystem_kernel.dylib"
    1638   },
    1639   {
    1640     "source" : "P",
    1641     "arch" : "arm64e",
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    1643     "size" : 51900,
    1644     "uuid" : "e95973b8-824c-361e-adf4-390747c40897",
    1645     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1646     "name" : "libsystem_pthread.dylib"
    1647   },
    1648   {
    1649     "source" : "P",
    1650     "arch" : "arm64e",
    1651     "base" : 6652891136,
    1652     "size" : 532552,
    1653     "uuid" : "9f5bd98b-9367-3594-933b-16f392c2a5f8",
    1654     "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    1655     "name" : "libsystem_c.dylib"
    1656   },
    1657   {
    1658     "source" : "P",
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    1661     "size" : 33728,
    1662     "uuid" : "530fc11d-a495-375d-b2b9-81ae3e701781",
    1663     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1664     "name" : "libsystem_platform.dylib"
    1665   },
    1666   {
    1667     "source" : "P",
    1668     "arch" : "arm64e",
    1669     "base" : 6858883072,
    1670     "CFBundleShortVersionString" : "370.63.7",
    1671     "CFBundleIdentifier" : "com.apple.Metal",
    1672     "size" : 3028608,
    1673     "uuid" : "965ce830-cb1d-324e-b9f2-bcafddca8f8a",
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    1675     "name" : "Metal",
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    1677   },
    1678   {
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    1689   },
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    1694     "CFBundleShortVersionString" : "6.9",
    1695     "CFBundleIdentifier" : "com.apple.AppKit",
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    1697     "uuid" : "3c0949bb-e361-369a-80b7-17440eb09e98",
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    1699     "name" : "AppKit",
    1700     "CFBundleVersion" : "2685.20.119"
    1701   },
    1702   {
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    1707     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    1708     "size" : 5532352,
    1709     "uuid" : "3c4a3add-9e48-33da-82ee-80520e6cbe3b",
    1710     "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    1711     "name" : "CoreFoundation",
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    1713   },
    1714   {
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    1717     "base" : 6866857984,
    1718     "CFBundleShortVersionString" : "2.1.1",
    1719     "CFBundleIdentifier" : "com.apple.HIToolbox",
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    1721     "uuid" : "9ab64c08-0685-3a0d-9a7e-83e7a1e9ebb4",
    1722     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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    1724   },
    1725   {
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    1730     "uuid" : "b50f5a1a-be81-3068-92e1-3554f2be478a",
    1731     "path" : "\/usr\/lib\/dyld",
    1732     "name" : "dyld"
    1733   },
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    1736     "source" : "A",
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    1738     "uuid" : "00000000-0000-0000-0000-000000000000"
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    1743     "base" : 6680145920,
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    1745     "CFBundleIdentifier" : "com.apple.Foundation",
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    1751   },
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    1754     "arch" : "arm64e",
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    1756     "size" : 12575104,
    1757     "uuid" : "c78330dc-67e0-3d3f-96a7-c50956a2dfd8",
    1758     "path" : "\/System\/Library\/Frameworks\/WebKit.framework\/Versions\/A\/Frameworks\/WebCore.framework\/Versions\/A\/Frameworks\/libwebrtc.dylib",
    1759     "name" : "libwebrtc.dylib"
    1760   }
     76[deleted to fit within ticket limits]
     77
    176178],
    176279  "sharedCache" : {
    … …  
    34311748> show #16 models
    34321749
    3433 > save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
    3434 > transparentBackground true
    3435 
    3436 > hide #16 models
    3437 
    3438 > show #19 models
    3439 
    3440 > save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
    3441 > transparentBackground true
    3442 
    3443 > save occupancy_analysis.cxs includeMaps true
    3444 
    3445 > hide #!19 models
    3446 
    3447 > show #!16 models
    3448 
    3449 > hide #!16 models
    3450 
    3451 > show #!19 models
    3452 
    3453 > color #4 #707000 transparency 20
    3454 
    3455 > color #2 #168E78 transparency 20
    3456 
    3457 > color #2 #3D5480 transparency 20
    3458 
    3459 > color #18/3 #6120AC transparency 20
    3460 
    3461 > color #18/1 #b2b2b2 transparency 20
    3462 
    3463 > color #18/2 #C691FF transparency 20
    3464 
    3465 > color #18/A #ABAA00
    3466 
    3467 > color #18/B #ABAA00
    3468 
    3469 > color #18/A #363600
    3470 
    3471 > color #18/K #005A4A
    3472 
    3473 > color #18/L #2CC9A6
    3474 
    3475 > color #18/I #1F2A44
    3476 
    3477 > color #18/J #5B7DBB
    3478 
    3479 > color zone #14 near #18 distance 20
    3480 
    3481 > color #14-16,19 white transparency 20
    3482 
    3483 > color zone #19 near #18 & ~/K,L distance 20
    3484 
    3485 > color zone #16 near #18 & ~/I,J,K,L distance 20
    3486 
    3487 > color zone #15 near #18 & ~/I,J distance 20
    3488 
    3489 > color zone #14 near #18 distance 20
    3490 
    3491 > show #!1 models
    3492 
    3493 > show #!2 models
    3494 
    3495 > show #!3 models
    3496 
    3497 > show #!4 models
    3498 
    3499 > show #1-4 models
    3500 
    3501 > hide #!19 models
    3502 
    3503 > hide all models
    3504 
    3505 > view bottom_overview
    3506 
    3507 > show #1-4 models
    3508 
    3509 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    3510 > transparentBackground true
    3511 
    3512 > show #14 models
    3513 
    3514 > save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
    3515 > 3 transparentBackground true
    3516 
    3517 > hide #14 models
    3518 
    3519 > show #15 models
    3520 
    3521 > save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
    3522 > transparentBackground true
    3523 
    3524 > hide #15 models
    3525 
    3526 > show #16 models
    3527 
    3528 > save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
    3529 > transparentBackground true
    3530 
    3531 > hide #16 models
    3532 
    3533 > show #19 models
    3534 
    3535 > save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
    3536 > transparentBackground true
    3537 
    3538 > Make the figures
    3539 
    3540 Unknown command: Make the figures 
    3541 
    3542 > hide all models
    3543 
    3544 > view bottom_overview
    3545 
    3546 > show #1-4 models
    3547 
    3548 > hide all models
    3549 
    3550 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    3551 > transparentBackground true
    3552 
    3553 > show #14 models
    3554 
    3555 > save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
    3556 > 3 transparentBackground true
    3557 
    3558 > hide #14 models
    3559 
    3560 > show #15 models
    3561 
    3562 > save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
    3563 > transparentBackground true
    3564 
    3565 > hide #15 models
    3566 
    3567 > show #16 models
    3568 
    3569 > save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
    3570 > transparentBackground true
    3571 
    3572 > hide #16 models
    3573 
    3574 > show #19 models
    3575 
    3576 > save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
    3577 > transparentBackground true
    3578 
    3579 > hide all models
    3580 
    3581 > view bottom_overview
    3582 
    3583 > show #1-4 models
    3584 
    3585 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    3586 > transparentBackground true
    3587 
    3588 > hide all models
    3589 
    3590 > color #4 #707000 transparency 50
    3591 
    3592 > color #2 #168E78 transparency 50
    3593 
    3594 > color #2 #3D5480 transparency 50
    3595 
    3596 > hide all models
    3597 
    3598 > view bottom_overview
    3599 
    3600 > show #1-4 models
    3601 
    3602 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    3603 > transparentBackground true
    3604 
    3605 > hide all models
    3606 
    3607 > show #14 models
    3608 
    3609 > save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
    3610 > 3 transparentBackground true
    3611 
    3612 > hide #14 models
    3613 
    3614 > show #15 models
    3615 
    3616 > save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
    3617 > transparentBackground true
    3618 
    3619 > hide #15 models
    3620 
    3621 > show #16 models
    3622 
    3623 > save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
    3624 > transparentBackground true
    3625 
    3626 > hide #16 models
    3627 
    3628 > show #19 models
    3629 
    3630 > save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
    3631 > transparentBackground true
    3632 
    3633 > hide all models
    3634 
    3635 > view side_overview
    3636 
    3637 > show #1-4 models
    3638 
    3639 > save J772_consensus_side.png width 3000 height 3000 supersample 3
    3640 > transparentBackground true
    3641 
    3642 > hide all models
    3643 
    3644 > show #14 models
    3645 
    3646 > save J1930_arm-1-2-3_occupied_side.png width 3000 height 3000 supersample 3
    3647 > transparentBackground true
    3648 
    3649 > hide #14 models
    3650 
    3651 > show #15 models
    3652 
    3653 > save J1932_arm-1-2_occupied_side.png width 3000 height 3000 supersample 3
    3654 > transparentBackground true
    3655 
    3656 > hide #15 models
    3657 
    3658 > show #16 models
    3659 
    3660 > save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
    3661 > transparentBackground true
    3662 
    3663 > hide #16 models
    3664 
    3665 > show #19 models
    3666 
    3667 > save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
    3668 > transparentBackground true
    3669 
    3670 > hide #!19 models
    3671 
    3672 > show #!4 models
    3673 
    3674 > hide #!4 models
    3675 
    3676 > show #8 models
    3677 
    3678 > show #8-16 models
    3679 
    3680 > hide #!14-16 target m
    3681 
    3682 > hide #!10-13 target m
    3683 
    3684 > hide #!9 models
    3685 
    3686 > hide #!8 models
    3687 
    3688 > show #!9 models
    3689 
    3690 > show #!8 models
    3691 
    3692 > hide #!9 models
    3693 
    3694 > show #!9 models
    3695 
    3696 > hide #!8 models
    3697 
    3698 > show #!8 models
    3699 
    3700 > hide #!8 models
    3701 
    3702 > show #!8 models
    3703 
    3704 > volume #8 level 0.0949
    3705 
    3706 > volume #9 level 0.0846
    3707 
    3708 > volume #8 level 0.0846
    3709 
    3710 > volume #11 level 0.0846
    3711 
    3712 > hide #!11 models
    3713 
    3714 > show #!11 models
    3715 
    3716 > hide #!11 models
    3717 
    3718 > show #!11 models
    3719 
    3720 > show #!12 models
    3721 
    3722 > hide #!11 models
    3723 
    3724 > hide #!8 models
    3725 
    3726 > hide #!9 models
    3727 
    3728 > show #!13 models
    3729 
    3730 > hide #!12 models
    3731 
    3732 > show #!11 models
    3733 
    3734 > hide #!11 models
    3735 
    3736 > close #12-13
    3737 
    3738 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1711_volume_map.mrc
    3739 
    3740 Opened cryosparc_P615_J1711_volume_map.mrc as #5, grid size 360,360,360, pixel
    3741 1.27, shown at level 0.0987, step 2, values float32 
    3742 
    3743 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1714_volume_map.mrc
    3744 
    3745 Opened cryosparc_P615_J1714_volume_map.mrc as #6, grid size 360,360,360, pixel
    3746 1.27, shown at level 0.099, step 2, values float32 
    3747 
    3748 > hide #!6 models
    3749 
    3750 > show #!6 models
    3751 
    3752 > volume #5 step 1
    3753 
    3754 > volume #6 step 1
    3755 
    3756 > volume #5 level 0.08297
    3757 
    3758 > show #!18 models
    3759 
    3760 > hide #!5 models
    3761 
    3762 > show #!5 models
    3763 
    3764 > color #5 darkgrey
    3765 
    3766 > color #5 near #18/A,B dist 6
    3767 
    3768 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    3769 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    3770 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    3771 
    3772 > color zone #5 near #18/A,B distance 6
    3773 
    3774 > ui tool show "Side View"
    3775 
    3776 > save test.png width 3000 height 3000 supersample 3 transparentBackground
    3777 > true
    3778 
    3779 [Repeated 1 time(s)]
    3780 
    3781 > hide #!18 models
    3782 
    3783 > show #!6 models
    3784 
    3785 > hide #!5 models
    3786 
    3787 > color #6 darkgrey
    3788 
    3789 > color zone #6 near #18/A,B distance 6
    3790 
    3791 > save J17114_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
    3792 > supersample 3 transparentBackground true
    3793 
    3794 > save J1714_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
    3795 > supersample 3 transparentBackground true
    3796 
    3797 > show #!5 models
    3798 
    3799 > hide #!6 models
    3800 
    3801 > save J1711_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
    3802 > supersample 3 transparentBackground true
    3803 
    3804 > view name diemr_1_close
    3805 
    3806 > view list
    3807 
    3808 Named views: bottom_overview, diemr_1_close, side_overview 
    3809 
    3810 > view side_overview
    3811 
    3812 > show #!1 models
    3813 
    3814 > hide #!5 models
    3815 
    3816 > view #1 m
    3817 
    3818 Expected an integer >= 1 or a keyword 
    3819 
    3820 > show #1 models
    3821 
    3822 > show #!4 models
    3823 
    3824 > show #4 models
    3825 
    3826 > save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
    3827 > transparentBackground true
    3828 
    3829 > turn y 120
    3830 
    3831 > show #!3 models
    3832 
    3833 > hide #!4 models
    3834 
    3835 > show #3 models
    3836 
    3837 > show #2
    3838 
    3839 > hide #!2 models
    3840 
    3841 > show #!2 models
    3842 
    3843 > hide #!3 models
    3844 
    3845 > save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
    3846 > transparentBackground true
    3847 
    3848 > turn y 120
    3849 
    3850 > show #!3 models
    3851 
    3852 > hide #!2 models
    3853 
    3854 > show #!2 models
    3855 
    3856 > turn y 120
    3857 
    3858 [Repeated 1 time(s)]
    3859 
    3860 > hide #!3 models
    3861 
    3862 > save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
    3863 > transparentBackground true
    3864 
    3865 > turn y 120
    3866 
    3867 > show #!3 models
    3868 
    3869 > hide #!2 models
    3870 
    3871 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    3872 > transparentBackground true
    3873 
    3874 > color #3 #168e781b models
    3875 
    3876 > color #3 #168e7800 models
    3877 
    3878 > color #3 #168e7880 models
    3879 
    3880 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    3881 > transparentBackground true
    3882 
    3883 > graphics silhouettes true width 8
    3884 
    3885 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    3886 > transparentBackground true
    3887 
    3888 > graphics silhouettes true width 16
    3889 
    3890 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    3891 > transparentBackground true
    3892 
    3893 > graphics silhouettes true width 32
    3894 
    3895 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    3896 > transparentBackground true
    3897 
    3898 > view list
    3899 
    3900 Named views: bottom_overview, diemr_1_close, side_overview 
    3901 
    3902 > side_overview_P5P1_dimer_2
    3903 
    3904 Unknown command: side_overview_P5P1_dimer_2 
    3905 
    3906 > view name side_overview_P5P1_dimer_2
    3907 
    3908 > turn y 12
    3909 
    3910 [Repeated 1 time(s)]
    3911 
    3912 > turn y -12
    3913 
    3914 [Repeated 1 time(s)]
    3915 
    3916 > turn y 120
    3917 
    3918 > hide #!3 models
    3919 
    3920 > show #!4 models
    3921 
    3922 > save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
    3923 > transparentBackground true
    3924 
    3925 > show #!3 models
    3926 
    3927 > hide #!4 models
    3928 
    3929 > show #!2 models
    3930 
    3931 > hide #!3 models
    3932 
    3933 > show #!4 models
    3934 
    3935 > hide #!2 models
    3936 
    3937 > view list
    3938 
    3939 Named views: bottom_overview, diemr_1_close, side_overview,
    3940 side_overview_P5P1_dimer_2 
    3941 
    3942 > view side_overview
    3943 
    3944 > save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
    3945 > transparentBackground true
    3946 
    3947 > show #!3 models
    3948 
    3949 > hide #!3 models
    3950 
    3951 > show #!2 models
    3952 
    3953 > hide #!4 models
    3954 
    3955 > undo
    3956 
    3957 > redo
    3958 
    3959 > view side_overview
    3960 
    3961 > hide #!4 models
    3962 
    3963 > turn y 120
    3964 
    3965 > view name side_overview_P5P1_dimer_3
    3966 
    3967 > save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
    3968 > transparentBackground true
    3969 
    3970 > graphics silhouettes true width 4
    3971 
    3972 > hide #!2 models
    3973 
    3974 > hide #!1 models
    3975 
    3976 > show #!14 models
    3977 
    3978 > show #!15 models
    3979 
    3980 > hide #!14 models
    3981 
    3982 > show #!16 models
    3983 
    3984 > hide #!15 models
    3985 
    3986 > show #!19 models
    3987 
    3988 > hide #!16 models
    3989 
    3990 > show #!15 models
    3991 
    3992 > hide #!19 models
    3993 
    3994 > show #!19 models
    3995 
    3996 > hide #!15 models
    3997 
    3998 > pwd
    3999 
    4000 Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
    4001 Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy 
    4002 
    4003 > view list
    4004 
    4005 Named views: bottom_overview, diemr_1_close, side_overview,
    4006 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    4007 
    4008 > view diemr_1_close
    4009 
    4010 > turn y 120
    4011 
    4012 > view side_overview_P5P1_dimer_2
    4013 
    4014 > view diemr_1_close
    4015 
    4016 > view name dimer_1_close
    4017 
    4018 > view delete diemer_1_close
    4019 
    4020 > view list
    4021 
    4022 Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
    4023 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    4024 
    4025 > view dimer_1_close
    4026 
    4027 > view dimer_2 close
    4028 
    4029 Expected an objects specifier or a view name or a keyword 
    4030 
    4031 > show #!2 models
    4032 
    4033 > hide #!2 models
    4034 
    4035 > show #!3 models
    4036 
    4037 > hide #!3 models
    4038 
    4039 > show #!3 models
    4040 
    4041 > hide #!3 models
    4042 
    4043 > view list
    4044 
    4045 Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
    4046 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    4047 
    4048 > view side_overview_P5P1_dimer_3
    4049 
    4050 > hide #!19 models
    4051 
    4052 > show #!5 models
    4053 
    4054 > show #!6 models
    4055 
    4056 > hide #!5 models
    4057 
    4058 > show #!8 models
    4059 
    4060 > hide #!6 models
    4061 
    4062 > show #!9 models
    4063 
    4064 > hide #!8 models
    4065 
    4066 > show #!10 models
    4067 
    4068 > hide #!9 models
    4069 
    4070 > show #!11 models
    4071 
    4072 > hide #!10 models
    4073 
    4074 > show #!10 models
    4075 
    4076 > hide #!11 models
    4077 
    4078 > show #!11 models
    4079 
    4080 > hide #!11 models
    4081 
    4082 > show #!11 models
    4083 
    4084 > show #!18 models
    4085 
    4086 > hide #!10 models
    4087 
    4088 > hide #!11 models
    4089 
    4090 > show #!11 models
    4091 
    4092 > show #!10 models
    4093 
    4094 > hide #!11 models
    4095 
    4096 > color #10,11 darkgrey
    4097 
    4098 > show #!11 models
    4099 
    4100 > hide #!10 models
    4101 
    4102 > hide #!11 models
    4103 
    4104 > color zone #11 near #18/J,I distance 6
    4105 
    4106 > show #!11 models
    4107 
    4108 > show #!10 models
    4109 
    4110 > hide #!11 models
    4111 
    4112 > show #!11 models
    4113 
    4114 > hide #!10 models
    4115 
    4116 > color #10,11 darkgrey
    4117 
    4118 > color zone #11 near #18/J,I distance 4
    4119 
    4120 > hide #!18 models
    4121 
    4122 > show #!18 models
    4123 
    4124 > hide #!18 models
    4125 
    4126 > save test.png width 3000 height 3000 supersample 3 transparentBackground
    4127 > true
    4128 
    4129 > view name dimer_3_close
    4130 
    4131 > save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
    4132 > supersample 3 transparentBackground true
    4133 
    4134 > show #!10 models
    4135 
    4136 > hide #!11 models
    4137 
    4138 > show #!11 models
    4139 
    4140 > hide #!10 models
    4141 
    4142 > save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
    4143 > supersample 3 transparentBackground true
    4144 
    4145 > show #!10 models
    4146 
    4147 > hide #!11 models
    4148 
    4149 > save J1843_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
    4150 > supersample 3 transparentBackground true
    4151 
    4152 > hide #!10 models
    4153 
    4154 > show #!8 models
    4155 
    4156 > show #!9 models
    4157 
    4158 > view list
    4159 
    4160 Named views: bottom_overview, diemr_1_close, dimer_1_close, dimer_3_close,
    4161 side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    4162 
    4163 > view side_overview_P5P1_dimer_2
    4164 
    4165 > hide #!9 models
    4166 
    4167 > show #!9 models
    4168 
    4169 > hide #!8 models
    4170 
    4171 > show #!8 models
    4172 
    4173 > hide #!9 models
    4174 
    4175 > show #!9 models
    4176 
    4177 > hide #!8 models
    4178 
    4179 > show #!8 models
    4180 
    4181 > color #8,9 darkgrey
    4182 
    4183 > show #!18 models
    4184 
    4185 > hide #!8 models
    4186 
    4187 > color zone #10 near #18/K,L distance 6
    4188 
    4189 > show #!10 models
    4190 
    4191 > hide #!9 models
    4192 
    4193 > show #!9 models
    4194 
    4195 > hide #!9 models
    4196 
    4197 > show #!8 models
    4198 
    4199 > hide #!10 models
    4200 
    4201 > show #!9 models
    4202 
    4203 > hide #!8 models
    4204 
    4205 > show #!8 models
    4206 
    4207 > color #10,11 darkgrey
    4208 
    4209 > color zone #11 near #18/J,I distance 4
    4210 
    4211 > hide #!9 models
    4212 
    4213 > color zone #8 near #18/K,L distance 6
    4214 
    4215 > hide #!18 models
    4216 
    4217 > show #!9 models
    4218 
    4219 > hide #!8 models
    4220 
    4221 > show #!8 models
    4222 
    4223 > save test.png width 3000 height 3000 supersample 3 transparentBackground
    4224 > true
    4225 
    4226 > view name dimer_2_close
    4227 
    4228 > hide #!9 models
    4229 
    4230 > show #!9 models
    4231 
    4232 > hide #!8 models
    4233 
    4234 > save J1786_class-3D_P5P1-dimer-2-reconstruct.png width 3000 height 3000
    4235 > supersample 3 transparentBackground true
    4236 
    4237 > show #!8 models
    4238 
    4239 > hide #!9 models
    4240 
    4241 > save J1783_class-3D_P5P1-dimer-2-reconstruct.png width 3000 height 3000
    4242 > supersample 3 transparentBackground true
    4243 
    4244 > hide #!8 models
    4245 
    4246 > show #!10 models
    4247 
    4248 > show #!14 models
    4249 
    4250 > hide #!10 models
    4251 
    4252 > show #!15 models
    4253 
    4254 > hide #!14 models
    4255 
    4256 > hide #!15 models
    4257 
    4258 > show #!16 models
    4259 
    4260 > show #!14 models
    4261 
    4262 > hide #!16 models
    4263 
    4264 > show #!16 models
    4265 
    4266 > hide #!14 models
    4267 
    4268 > show #!19 models
    4269 
    4270 > show #17 models
    4271 
    4272 > hide #!16 models
    4273 
    4274 > hide #17 models
    4275 
    4276 > save analysis-cxs i t
    4277 
    4278 Cannot determine format for 'analysis-cxs' 
    4279 
    4280 > save analysis.cxs includeMaps true
    4281 
    4282 ——— End of log from Mon Jan 19 11:45:42 2026 ———
    4283 
    4284 opened ChimeraX session 
    4285 
    4286 > open
    4287 > /Users/lorenz.grundmann/Downloads/fold_herc2_1_1550_3mer/fold_herc2_1_1550_3mer_model_0.cif
    4288 
    4289 Chain information for fold_herc2_1_1550_3mer_model_0.cif #7 
    4290 --- 
    4291 Chain | Description 
    4292 A B C | . 
    4293  
    4294 Computing secondary structure 
    4295 
    4296 > hide #7 models
    4297 
    4298 > hide #!19 models
    4299 
    4300 > show #!19 models
    4301 
    4302 > open
    4303 > /Users/lorenz.grundmann/Downloads/fold_herc2_1_1550_3mer/fold_herc2_1_1550_3mer_model_0.cif
    4304 
    4305 Chain information for fold_herc2_1_1550_3mer_model_0.cif #12 
    4306 --- 
    4307 Chain | Description 
    4308 A B C | . 
    4309  
    4310 Computing secondary structure 
    4311 
    4312 > hide #!19 models
    4313 
    4314 > view #12 clip false
    4315 
    4316 > color bychain
    4317 
    4318 > open /Users/lorenz.grundmann/Downloads/fold_herc2/fold_herc2_model_0.cif
    4319 
    4320 Chain information for fold_herc2_model_0.cif #13 
    4321 --- 
    4322 Chain | Description 
    4323 A | . 
    4324  
    4325 Computing secondary structure 
    4326 
    4327 > matchmaker #13 to #12/A
    4328 
    4329 Computing secondary structure 
    4330 [Repeated 1 time(s)]  Parameters 
    4331 --- 
    4332 Chain pairing | bb 
    4333 Alignment algorithm | Needleman-Wunsch 
    4334 Similarity matrix | BLOSUM-62 
    4335 SS fraction | 0.3 
    4336 Gap open (HH/SS/other) | 18/18/6 
    4337 Gap extend | 1 
    4338 SS matrix |  |  | H | S | O 
    4339 ---|---|---|--- 
    4340 H | 6 | -9 | -6 
    4341 S |  | 6 | -6 
    4342 O |  |  | 4 
    4343 Iteration cutoff | 2 
    4344  
    4345 Matchmaker fold_herc2_1_1550_3mer_model_0.cif, chain A (#12) with
    4346 fold_herc2_model_0.cif, chain A (#13), sequence alignment score = 7500.8 
    4347 RMSD between 485 pruned atom pairs is 1.091 angstroms; (across all 1500 pairs:
    4348 22.343) 
    4349  
    4350 
    4351 > rainbow #13
    4352 
    4353 > open
    4354 > /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_job_request.json
    4355 
    4356 Opening an AlphaFold PAE file requires first opening the predicted atomic
    4357 model. Did not find an open atomic model from the same directory. If the
    4358 atomic model is already open choose it using menu 
    4359  
    4360 Tools / Structure Prediction / AlphaFold Error Plot 
    4361  
    4362 or use the open command structure option, for example 
    4363  
    4364 open
    4365 /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_job_request.json
    4366 structure #1 
    4367  
    4368 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    4369 need to specify the specific JSON format such as 
    4370  
    4371 open mole_channels.json format mole 
    4372 
    4373 > open
    4374 > /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_model_0.cif
    4375 
    4376 Chain information for fold_19s_base_paaf1_model_0.cif #20 
    4377 --- 
    4378 Chain | Description 
    4379 A | . 
    4380 B | . 
    4381 C | . 
    4382 D | . 
    4383 E | . 
    4384 F | . 
    4385 G | . 
    4386 H | . 
    4387 I | . 
    4388 J | . 
    4389 K | . 
    4390 L | . 
    4391  
    4392 
    4393 > hide #12 models
    4394 
    4395 > hide #13 models
    4396 
    4397 > show #20 cartoons
    4398 
    4399 Computing secondary structure 
    4400 
    4401 > hide #20 atoms
    4402 
    4403 > hide #20 models
    4404 
    4405 > show #20 models
    4406 
    4407 > open
    4408 > /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_full_data_0.json
    4409 
    4410 Opened AlphaFold PAE with values for 4971 residues and atoms 
    4411 
    4412 > color #20/K:856/L lime
    4413 
    4414 > open "/Users/lorenz.grundmann/Downloads/cryosparc_P561_J448_009_volume_map
    4415 > (1).mrc"
    4416 
    4417 Opened cryosparc_P561_J448_009_volume_map (1).mrc as #21, grid size
    4418 360,360,360, pixel 1.27, shown at level 0.0807, step 2, values float32 
    4419 
    4420 > hide #20 models
    4421 
    4422 > view #21 clip false
    4423 
    4424 > open
    4425 > /Users/lorenz.grundmann/Downloads/cryosparc_P561_J254_009_volume_map.mrc
    4426 
    4427 Opened cryosparc_P561_J254_009_volume_map.mrc as #22, grid size 360,360,360,
    4428 pixel 1.27, shown at level 0.0788, step 2, values float32 
    4429 
    4430 > hide #!21 models
    4431 
    4432 > volume #22 level 0.05311
    4433 
    4434 > volume #22 step 1
    4435 
    4436 > volume #22 level 0.08379
    4437 
    4438 > show #!21 models
    4439 
    4440 > hide #!22 models
    4441 
    4442 > volume #21 step 1
    4443 
    4444 > volume #21 level 0.1209
    4445 
    4446 > open
    4447 > /Volumes/Herc/20241024_ZH027_Hek_Herc1_PSMC5_PAAF1/relion/J448/Refine3D/local_sampling_lp-12/run_class001.mrc
    4448 
    4449 Opened run_class001.mrc as #23, grid size 360,360,360, pixel 1.27, shown at
    4450 level 0.00236, step 2, values float32 
    4451 
    4452 > volume #23 level 0.003573
    4453 
    4454 > volume #23 step 1
    4455 
    4456 > hide #!21 models
    4457 
    4458 > volume #23 level 0.003573
    4459 
    4460 > volume #23 level 0.004357
    4461 
    4462 > color #28/1:372-734 light sky blue
    4463 
    4464 > color #28/1:3420-3820 #350CED
    4465 
    4466 > color #28/1:3996-4366 #90CED6
    4467 
    4468 > color #28/1:4447-4840 #d31340ff
    4469 
    4470 > color #28/1:2315-2379 palegreen
    4471 
    4472 > color #28/1:1384-1399 #009193ff
    4473 
    4474 > color #28/1:2747-2799 lime
    4475 
    4476 > color #28/1:2975-3055 #EF6B11
    4477 
    4478 > color #28/1:2075-2186 #F4EB45
    4479 
    4480 > color #28/1:3297-3329 #CE3674
    4481 
    4482 > close
    4483 
    4484 > windowsize 1200 1200
    4485 
    4486 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4487 > model/20260203_franekenmodel_new.pdb
    4488 
    4489 Chain information for 20260203_franekenmodel_new.pdb #1 
    4490 --- 
    4491 Chain | Description 
    4492 1 | No description available 
    4493 2 3 | No description available 
    4494 A C E | No description available 
    4495 B D F | No description available 
    4496  
    4497 
    4498 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4499 > model/20260203_frankenmap.mrc
    4500 
    4501 Opened 20260203_frankenmap.mrc as #2, grid size 360,360,360, pixel 1.27, shown
    4502 at level 0.14, step 2, values float32 
    4503 
    4504 > volume #2 step 1
    4505 
    4506 > fitmap #1 inMap #2
    4507 
    4508 Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
    4509 20260203_frankenmap.mrc (#2) using 193662 atoms 
    4510 average map value = 0.1852, steps = 124 
    4511 shifted from previous position = 2.36 
    4512 rotated from previous position = 2.79 degrees 
    4513 atoms outside contour = 111278, contour level = 0.1401 
    4514  
    4515 Position of 20260203_franekenmodel_new.pdb (#1) relative to
    4516 20260203_frankenmap.mrc (#2) coordinates: 
    4517 Matrix rotation and translation 
    4518 0.99898431 -0.02740180 0.03577001 0.08643429 
    4519 0.02805832 0.99944452 -0.01798280 -3.96522601 
    4520 -0.03525738 0.01896818 0.99919824 4.42656013 
    4521 Axis 0.37938688 0.72925970 0.56942592 
    4522 Axis point 131.06536616 0.00000000 -2.28277335 
    4523 Rotation angle (degrees) 2.79130992 
    4524 Shift along axis -0.33828942 
    4525  
    4526 
    4527 > hide #!1 models
    4528 
    4529 > show #!1 models
    4530 
    4531 > hide #!2 models
    4532 
    4533 > show #!2 models
    4534 
    4535 > hide #!1 models
    4536 
    4537 > show #!1 models
    4538 
    4539 > hide #!2 models
    4540 
    4541 > show cartoons
    4542 
    4543 > hide atoms
    4544 
    4545 > show #!2 models
    4546 
    4547 > fitmap #1 inMap #2
    4548 
    4549 Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
    4550 20260203_frankenmap.mrc (#2) using 193662 atoms 
    4551 average map value = 0.1852, steps = 64 
    4552 shifted from previous position = 0.019 
    4553 rotated from previous position = 0.00619 degrees 
    4554 atoms outside contour = 111364, contour level = 0.1401 
    4555  
    4556 Position of 20260203_franekenmodel_new.pdb (#1) relative to
    4557 20260203_frankenmap.mrc (#2) coordinates: 
    4558 Matrix rotation and translation 
    4559 0.99898711 -0.02743147 0.03566887 0.12837483 
    4560 0.02808688 0.99944331 -0.01800537 -3.96190269 
    4561 -0.03515510 0.01898896 0.99920145 4.41043263 
    4562 Axis 0.38021682 0.72790771 0.57060104 
    4563 Axis point 130.70040370 0.00000000 -3.28257276 
    4564 Rotation angle (degrees) 2.78848325 
    4565 Shift along axis -0.31849179 
    4566  
    4567 
    4568 > close #1
    4569 
    4570 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4571 > model/20260203_franekenmodel_new.pdb
    4572 
    4573 Summary of feedback from opening
    4574 /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4575 model/20260203_franekenmodel_new.pdb 
    4576 --- 
    4577 warnings | Start residue of secondary structure not found: HELIX 114 114 ILE F 298 ILE F 300 1 3 
    4578 Start residue of secondary structure not found: HELIX 115 115 SER F 303 LEU F
    4579 305 1 3 
    4580 Start residue of secondary structure not found: HELIX 116 116 GLU F 322 HIS F
    4581 332 1 11 
    4582 Start residue of secondary structure not found: HELIX 117 117 SER F 333 LYS F
    4583 335 1 3 
    4584 Start residue of secondary structure not found: HELIX 118 118 LEU F 344 GLU F
    4585 349 1 6 
    4586 756 messages similar to the above omitted 
    4587 Ignored bad PDB record found on line 47792 
    4588 RG F 297 190.126 173.141 191.732 1.00 53.47 N 
    4589  
    4590 Chain information for 20260203_franekenmodel_new.pdb 
    4591 --- 
    4592 Chain | Description 
    4593 1.1/1 | No description available 
    4594 1.1/2 | No description available 
    4595 1.1/3 | No description available 
    4596 1.1/A 1.1/E | No description available 
    4597 1.1/B 1.1/F | No description available 
    4598 1.2/F | No description available 
    4599  
    4600 
    4601 > close #1
    4602 
    4603 > close #2
    4604 
    4605 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4606 > model/20260203_franekenmodel_new.pdb
    4607 
    4608 Summary of feedback from opening
    4609 /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4610 model/20260203_franekenmodel_new.pdb 
    4611 --- 
    4612 warnings | End residue of secondary structure not found: HELIX 305 305 VAL 3 2557 ARG 3 2573 1 17 
    4613 Start residue of secondary structure not found: HELIX 306 306 VAL 3 3190 LEU 3
    4614 3197 1 8 
    4615 Start residue of secondary structure not found: HELIX 307 307 SER 3 3203 LEU 3
    4616 3210 1 8 
    4617 Start residue of secondary structure not found: HELIX 308 308 ILE 3 3218 ALA 3
    4618 3229 1 12 
    4619 Start residue of secondary structure not found: HELIX 309 309 LEU 3 3263 ALA 3
    4620 3274 1 12 
    4621 Start residue of secondary structure not found: HELIX 310 310 PRO 3 3278 THR 3
    4622 3297 1 20 
    4623 412 messages similar to the above omitted 
    4624 Ignored bad PDB record found on line 112037 
    4625 566 293.184 107.305 203.880 1.00 92.87 H 
    4626  
    4627 Chain information for 20260203_franekenmodel_new.pdb 
    4628 --- 
    4629 Chain | Description 
    4630 1.1/1 | No description available 
    4631 1.1/2 | No description available 
    4632 1.1/3 | No description available 
    4633 1.2/3 | No description available 
    4634 1.1/A 1.1/C 1.1/E | No description available 
    4635 1.1/B 1.1/D 1.1/F | No description available 
    4636  
    4637 Computing secondary structure 
    4638 
    4639 > hide #!1.2 models
    4640 
    4641 > hide #!1.1 models
    4642 
    4643 > close #1
    4644 
    4645 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4646 > model/20260203_franekenmodel_new.pdb
    4647 
    4648 Chain information for 20260203_franekenmodel_new.pdb #1 
    4649 --- 
    4650 Chain | Description 
    4651 1 | No description available 
    4652 2 3 | No description available 
    4653 A C E | No description available 
    4654 B D F | No description available 
    4655  
    4656 
    4657 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4658 > model/20260203_frankenmap.mrc
    4659 
    4660 Opened 20260203_frankenmap.mrc as #2, grid size 360,360,360, pixel 1.27, shown
    4661 at level 0.14, step 2, values float32 
    4662 
    4663 > fitmap #1 inMap #2
    4664 
    4665 Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
    4666 20260203_frankenmap.mrc (#2) using 193662 atoms 
    4667 average map value = 0.1852, steps = 124 
    4668 shifted from previous position = 2.36 
    4669 rotated from previous position = 2.79 degrees 
    4670 atoms outside contour = 101671, contour level = 0.1401 
    4671  
    4672 Position of 20260203_franekenmodel_new.pdb (#1) relative to
    4673 20260203_frankenmap.mrc (#2) coordinates: 
    4674 Matrix rotation and translation 
    4675 0.99898431 -0.02740180 0.03577001 0.08643429 
    4676 0.02805832 0.99944452 -0.01798280 -3.96522601 
    4677 -0.03525738 0.01896818 0.99919824 4.42656013 
    4678 Axis 0.37938688 0.72925970 0.56942592 
    4679 Axis point 131.06536616 0.00000000 -2.28277335 
    4680 Rotation angle (degrees) 2.79130992 
    4681 Shift along axis -0.33828942 
    4682  
    4683 
    4684 > volume #2 level 0.05999
    4685 
    4686 > volume #2 step 1
    4687 
    4688 > close
    4689 
    4690 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4691 > model/20260203_frankemnmap.mrc
    4692 
    4693 Opened 20260203_frankemnmap.mrc as #1, grid size 360,360,360, pixel 1.27,
    4694 shown at level 0.141, step 2, values float32 
    4695 
    4696 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4697 > model/20260203_frankemnmodel.pdb
    4698 
    4699 Summary of feedback from opening
    4700 /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4701 model/20260203_frankemnmodel.pdb 
    4702 --- 
    4703 warnings | End residue of secondary structure not found: HELIX 142 142 ARG 3 4680 LEU 3 4692 1 13 
    4704 Start residue of secondary structure not found: HELIX 143 143 ASP 3 4696 GLY 3
    4705 4705 1 10 
    4706 Start residue of secondary structure not found: HELIX 144 144 MET 3 4706 TRP 3
    4707 4708 1 3 
    4708 Start residue of secondary structure not found: HELIX 145 145 VAL 3 4712 LEU 3
    4709 4717 1 6 
    4710 Start residue of secondary structure not found: HELIX 146 146 ALA 3 4720 CYS 3
    4711 4728 1 9 
    4712 Start residue of secondary structure not found: HELIX 147 147 VAL 3 4735 LYS 3
    4713 4740 1 6 
    4714 724 messages similar to the above omitted 
    4715 Ignored bad PDB record found on line 55477 
    4716 GLU 34689 256.307 357.171 212.206 1.00 65.82 C 
    4717  
    4718 Chain information for 20260203_frankemnmodel.pdb 
    4719 --- 
    4720 Chain | Description 
    4721 2.1/1 | No description available 
    4722 2.1/3 | No description available 
    4723 2.2/3 | No description available 
    4724 2.1/A | No description available 
    4725 2.1/B | No description available 
    4726 2.1/E 2.1/F 2.1/G | No description available 
    4727  
    4728 
    4729 > volume #1 step 1
    4730 
    4731 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4732 > model/20260203_frankemnmodel.pdb
    4733 
    4734 Chain information for 20260203_frankemnmodel.pdb #3 
    4735 --- 
    4736 Chain | Description 
    4737 1 8 9 | No description available 
    4738 2 5 7 | No description available 
    4739 3 4 6 | No description available 
    4740 A I K | No description available 
    4741 B J L | No description available 
    4742 E F G | No description available 
    4743  
    4744 
    4745 > hide #!1 models
    4746 
    4747 > show #!1 models
    4748 
    4749 > hide #!2 models
    4750 
    4751 Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
    4752 table model. 
    4753 
    4754 > close #2
    4755 
    4756 > volume #1 level 0.008212
    4757 
    4758 > hide atoms
    4759 
    4760 > show cartoons
    4761 
    4762 > volume #1 level 0.05603
    4763 
    4764 > volume #1 level 0.1278
    4765 
    4766 > volume #1 color #b2b2b281
    4767 
    4768 > volume #1 level 0.2712
    4769 
    4770 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4771 > model/20260203_frankemnmodel.pdb
    4772 
    4773 Chain information for 20260203_frankemnmodel.pdb #2 
    4774 --- 
    4775 Chain | Description 
    4776 1 8 9 | No description available 
    4777 2 5 7 | No description available 
    4778 3 4 6 | No description available 
    4779 A I K | No description available 
    4780 B J L | No description available 
    4781 E F G | No description available 
    4782  
    4783 
    4784 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4785 > model/20260203_frankemnmap.mrc
    4786 
    4787 Opened 20260203_frankemnmap.mrc as #4, grid size 360,360,360, pixel 1.27,
    4788 shown at level 0.141, step 2, values float32 
    4789 
    4790 > hide #!2 models
    4791 
    4792 > hide #!1 models
    4793 
    4794 > close #1-4
    4795 
    4796 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4797 > model/20260203_frankemnmodel.pdb
    4798 
    4799 Chain information for 20260203_frankemnmodel.pdb #1 
    4800 --- 
    4801 Chain | Description 
    4802 1 8 9 | No description available 
    4803 2 5 7 | No description available 
    4804 3 4 6 | No description available 
    4805 A I K | No description available 
    4806 B J L | No description available 
    4807 E F G | No description available 
    4808  
    4809 
    4810 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4811 > model/20260203_frankemnmap.mrc
    4812 
    4813 Opened 20260203_frankemnmap.mrc as #2, grid size 360,360,360, pixel 1.27,
    4814 shown at level 0.141, step 2, values float32 
    4815 
    4816 > volume #2 step 1
    4817 
    4818 > volume #2 level 0.05606
    4819 
    4820 > hide #!1 models
    4821 
    4822 > show #!1 models
    4823 
    4824 > hide H
    4825 
    4826 > style stick
    4827 
    4828 Changed 192903 atom styles 
    4829 
    4830 > hide atoms
    4831 
    4832 > show cartoons
    4833 
    4834 > hide #!2 models
    4835 
    4836 > hide #!1 models
    4837 
    4838 > show #!1 models
    4839 
    4840 > close #1
    4841 
    4842 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    4843 > model/20260203_frankemnmodel.pdb
    4844 
    4845 Chain information for 20260203_frankemnmodel.pdb #1 
    4846 --- 
    4847 Chain | Description 
    4848 1 | No description available 
    4849 2 3 | No description available 
    4850 A C E | No description available 
    4851 B D F | No description available 
    4852  
    4853 
    4854 > show #!2 models
    4855 
    4856 > hide atoms
    4857 
    4858 > show cartoons
    4859 
    4860 > hide #!2 models
    4861 
    4862 > color #1/1 #BBBDBF
    4863 
    4864 > color #1/2 #C691FF
    4865 
    4866 > color #1/2 #6120AC
    4867 
    4868 > color #1/3 #6120AC
    4869 
    4870 > color #1/2 #C691FF
    4871 
    4872 > color #1/1,-3:372-734 light sky blue
    4873 
    4874 > color #1/1,-3:3420-3820 #350CED
    4875 
    4876 > color #1/1,-3:3996-4366 #90CED6
    4877 
    4878 > color #1/1,-3:4447-4840 #d31340ff
    4879 
    4880 > color #1/1,-3:2315-2379 palegreen
    4881 
    4882 > color #1/1,-3:1384-1399 #009193ff
    4883 
    4884 > color #1/1,-3:2747-2799 lime
    4885 
    4886 > color #1/1,-3:2975-3055 #EF6B11
    4887 
    4888 > color #1/1,-3:2030-2190 #F4EB45
    4889 
    4890 > color #1/1,-3:3297-3329 #CE3674
    4891 
    4892 > color #1/1-3:372-734 light sky blue
    4893 
    4894 > color #1/1-3:3420-3820 #350CED
    4895 
    4896 > color #1/1-3:3996-4366 #90CED6
    4897 
    4898 > color #1/1-3:4447-4840 #d31340ff
    4899 
    4900 > color #1/1-3:2315-2379 palegreen
    4901 
    4902 > color #1/1-3:1384-1399 #009193ff
    4903 
    4904 > color #1/1-3:2747-2799 lime
    4905 
    4906 > color #1/1-3:2975-3055 #EF6B11
    4907 
    4908 > color #1/1-3:2030-2190 #F4EB45
    4909 
    4910 > color #1/1-3:3297-3329 #CE3674
    4911 
    4912 > color #1/A #363600
    4913 
    4914 > color #1/B #ABAA00
    4915 
    4916 > color #1/C #005A4A
    4917 
    4918 > color #1/D #2CC9A6
    4919 
    4920 > color #1/E #1F2A44
    4921 
    4922 > color #1/F #5B7DBB
    4923 
    4924 > show #!2 models
    4925 
    4926 > hide #!1 models
    4927 
    4928 > hide #!2 models
    4929 
    4930 > show #!1 models
    4931 
    4932 > combine #1
    4933 
    4934 > hide #!1 models
    4935 
    4936 > show #!2 models
    4937 
    4938 > volume #2 level 0.07655
    4939 
    4940 > color zone #2 near #1 r 6
    4941 
    4942 Expected a keyword 
    4943 
    4944 > color zone #2 near #1 distance 6
    4945 
    4946 > hide #!2 models
    4947 
    4948 > show #!2 models
    4949 
    4950 > lighting soft
    4951 
    4952 > lighting full
    4953 
    4954 > lighting soft
    4955 
    4956 > lighting simple
    4957 
    4958 > lighting soft
    4959 
    4960 > hide #!2 models
    4961 
    4962 > color #1/1 #BBBDBF
    4963 
    4964 > color #1/2 #C691FF
    4965 
    4966 > color #1/3 #6120AC
    4967 
    4968 > color zone #2 near #1 distance 6
    4969 
    4970 > show #!2 models
    4971 
    4972 > hide #!3 models
    4973 
    4974 > hide #!2 models
    4975 
    4976 > show #!2 models
    4977 
    4978 > show #!3 models
    4979 
    4980 > hide #!2 models
    4981 
    4982 > color #1/a-c dark grey
    4983 
    4984 > color zone #2 near #1 distance 6
    4985 
    4986 > show #!2 models
    4987 
    4988 > hide #!3 models
    4989 
    4990 > hide #!2 models
    4991 
    4992 > open
    4993 > /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/20260114_P5P1_new-
    4994 > fit.cif
    4995 
    4996 Summary of feedback from opening
    4997 /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/20260114_P5P1_new-
    4998 fit.cif 
    4999 --- 
    5000 warnings | Unknown polymer entity '1' on line 166 
    5001 Unknown polymer entity '2' on line 6052 
    5002 Unknown polymer entity '3' on line 9979 
    5003 Unknown polymer entity '4' on line 15357 
    5004 Atom H is not in the residue template for LEU /B:137 
    5005 Atom H is not in the residue template for GLU /C:370 
    5006 Missing or incomplete sequence information. Inferred polymer connectivity. 
    5007  
    5008  
    5009 Chain information for 20260114_P5P1_new-fit.cif #4 
    5010 --- 
    5011 Chain | Description 
    5012 A | No description available 
    5013 B | No description available 
    5014 C | No description available 
    5015 D | No description available 
    5016  
    5017 
    5018 > open
    5019 > /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/cryosparc_P615_J1927_014_volume_map.mrc
    5020 
    5021 Opened cryosparc_P615_J1927_014_volume_map.mrc as #5, grid size 360,360,360,
    5022 pixel 1.27, shown at level 0.0844, step 2, values float32 
    5023 
    5024 > hide #!5 models
    5025 
    5026 > hide #!4 models
    5027 
    5028 > show #!4 models
    5029 
    5030 > dssp #4
    5031 
    5032 Computing secondary structure 
    5033 
    5034 > select #4/C,D 1
    5035 
    5036 Expected a keyword 
    5037 
    5038 > changechains #4/C,D 1
    5039 
    5040 Chain IDs of 530 residues changed 
    5041 
    5042 > windowsize 1100 1100
    5043 
    5044 > color #4/1 #BBBDBF
    5045 
    5046 > color #4/A #363600
    5047 
    5048 > color #4/B #ABAA00
    5049 
    5050 > show #!2 models
    5051 
    5052 > hide #!2 models
    5053 
    5054 > show #!5 models
    5055 
    5056 > volume #5 step 1
    5057 
    5058 > volume #5 level 0.2004
    5059 
    5060 > color #5 #ffffb282 models
    5061 
    5062 > color #4/1-3:372-734 light sky blue
    5063 
    5064 > color #4/1-3:3420-3820 #350CED
    5065 
    5066 > color #4/1-3:3996-4366 #90CED6
    5067 
    5068 > color #4/1-3:4447-4840 #d31340ff
    5069 
    5070 > color #4/1-3:2315-2379 palegreen
    5071 
    5072 > color #4/1-3:1384-1399 #009193ff
    5073 
    5074 > color #4/1-3:2747-2799 lime
    5075 
    5076 > color #4/1-3:2975-3055 #EF6B11
    5077 
    5078 > color #4/1-3:2030-2190 #F4EB45
    5079 
    5080 > color #4/1-3:3297-3329 #CE3674
    5081 
    5082 > color #5 near #4 tr 50
    5083 
    5084 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    5085 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    5086 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    5087 
    5088 > color #5 near #4
    5089 
    5090 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    5091 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    5092 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    5093 
    5094 > color zone #5 near #4 trans 50
    5095 
    5096 Expected a keyword 
    5097 
    5098 > color zone #5 near #4
    5099 
    5100 > color zone #5 near #4 r 6
    5101 
    5102 Expected a keyword 
    5103 
    5104 > color zone #5 near #4 distance 6
    5105 
    5106 > transparency #5 50
    5107 
    5108 > lighting soft
    5109 
    5110 > color #4/1-3:372-734 light sky blue
    5111 
    5112 > color #4/1-3:3420-3820 #350CED
    5113 
    5114 > color #4/1-3:3996-4366 #90CED6
    5115 
    5116 > color #4/1-3:4447-4840 #d31340ff
    5117 
    5118 > color #4/1-3:2315-2379 palegreen
    5119 
    5120 > color #4/1-3:1384-1399 #009193ff
    5121 
    5122 > color #4/1-3:2747-2799 lime
    5123 
    5124 > color #4/1-3:2975-3055 #EF6B11
    5125 
    5126 > color #4/1-3:2030-2190 #F4EB45
    5127 
    5128 > color #4/1-3:3297-3329 #CE3674
    5129 
    5130 > show nucleic
    5131 
    5132 > hide protein|solvent|H
    5133 
    5134 > surface hidePatches
    5135 
    5136 > style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5137 
    5138 Changed 385230 atom styles 
    5139 
    5140 > cartoon
    5141 
    5142 > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
    5143 > width 2 thickness 0.4 sides 12 divisions 20
    5144 
    5145 > cartoon style ~(nucleic|strand) xsection round
    5146 
    5147 > cartoon style (nucleic|strand) xsection rectangle
    5148 
    5149 > cartoon style protein modeHelix default arrows false xsection round width 2
    5150 > thickness 1
    5151 
    5152 > cartoon style nucleic xsection round width 1.6 thickness 1.6
    5153 
    5154 > nucleotides stubs radius 0.5
    5155 
    5156 > size stickRadius 0.3
    5157 
    5158 Changed 407138 bond radii 
    5159 
    5160 > hide #!4 models
    5161 
    5162 > show #!4 models
    5163 
    5164 > view name P5P1_front
    5165 
    5166 > select #4/A:373,381,384
    5167 
    5168 50 atoms, 47 bonds, 3 residues, 1 model selected 
    5169 
    5170 > select #B/A:373,381,384
    5171 
    5172 Expected an objects specifier or a keyword 
    5173 
    5174 > select #4/B:373,381,384
    5175 
    5176 45 atoms, 42 bonds, 3 residues, 1 model selected 
    5177 
    5178 > select add #4/A:55,19,21,332,333,350,349
    5179 
    5180 155 atoms, 147 bonds, 10 residues, 1 model selected 
    5181 
    5182 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    5183 
    5184 349 atoms, 334 bonds, 20 residues, 1 model selected 
    5185 
    5186 > show sel
    5187 
    5188 > hide H
    5189 
    5190 > color sel byhetero
    5191 
    5192 > select add #4
    5193 
    5194 17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected 
    5195 
    5196 > select subtract #4
    5197 
    5198 Nothing selected 
    5199 
    5200 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    5201 
    5202 194 atoms, 187 bonds, 10 residues, 1 model selected 
    5203 
    5204 > select #4/A:373,381,384
    5205 
    5206 50 atoms, 47 bonds, 3 residues, 1 model selected 
    5207 
    5208 > select #4/B:373,381,384
    5209 
    5210 45 atoms, 42 bonds, 3 residues, 1 model selected 
    5211 
    5212 > select add #4/A:55,19,21,332,333,350,349
    5213 
    5214 155 atoms, 147 bonds, 10 residues, 1 model selected 
    5215 
    5216 > name sel residues frozen
    5217 
    5218 "sel" is reserved and cannot be redefined 
    5219 
    5220 > name residues sel frozen
    5221 
    5222 "sel frozen": contains extra trailing text 
    5223 
    5224 > name frozen residues sel
    5225 
    5226 > select add #4
    5227 
    5228 17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected 
    5229 
    5230 > select subtract #4
    5231 
    5232 Nothing selected 
    5233 
    5234 > hide resides
    5235 
    5236 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    5237 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    5238 
    5239 > hide residues
    5240 
    5241 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    5242 
    5243 194 atoms, 187 bonds, 10 residues, 1 model selected 
    5244 
    5245 > select #4/A:373,381,384
    5246 
    5247 50 atoms, 47 bonds, 3 residues, 1 model selected 
    5248 
    5249 > select #4/B:373,381,384
    5250 
    5251 45 atoms, 42 bonds, 3 residues, 1 model selected 
    5252 
    5253 > select add #4/A:55,19,21,332,333,350,349
    5254 
    5255 155 atoms, 147 bonds, 10 residues, 1 model selected 
    5256 
    5257 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    5258 
    5259 349 atoms, 334 bonds, 20 residues, 1 model selected 
    5260 
    5261 > select #4/A:373,381,384
    5262 
    5263 50 atoms, 47 bonds, 3 residues, 1 model selected 
    5264 
    5265 > select #4/B:373,381,384
    5266 
    5267 45 atoms, 42 bonds, 3 residues, 1 model selected 
    5268 
    5269 > select add #4/A:55,19,21,332,333,350,349
    5270 
    5271 155 atoms, 147 bonds, 10 residues, 1 model selected 
    5272 
    5273 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    5274 
    5275 349 atoms, 334 bonds, 20 residues, 1 model selected 
    5276 
    5277 > name frozen residues sel
    5278 
    5279 > hide residues
    5280 
    5281 > select add #4
    5282 
    5283 17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected 
    5284 
    5285 > select subtract #4
    5286 
    5287 Nothing selected 
    5288 
    5289 > view list
    5290 
    5291 Named views: P5P1_front, bottom_overview, diemr_1_close, dimer_1_close,
    5292 dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
    5293 side_overview_P5P1_dimer_3 
    5294 
    5295 > view P5P1_front
    5296 
    5297 > cd "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
    5298 > Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1"
    5299 
    5300 Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
    5301 Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1 
    5302 
    5303 > spng overview.png
    5304 
    5305 > save overview.png width 3000 height 3000 supersample 3 transparentBackground
    5306 > true
    5307 
    5308 > show residuesz
    5309 
    5310 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    5311 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    5312 
    5313 > show residues
    5314 
    5315 > hdie H
    5316 
    5317 Unknown command: hdie H 
    5318 
    5319 > hide H
    5320 
    5321 > select #4/A:373,381,384
    5322 
    5323 50 atoms, 47 bonds, 3 residues, 1 model selected 
    5324 
    5325 > select #4/B:373,381,384
    5326 
    5327 45 atoms, 42 bonds, 3 residues, 1 model selected 
    5328 
    5329 > select add #4/1:499,432
    5330 
    5331 88 atoms, 84 bonds, 5 residues, 1 model selected 
    5332 
    5333 > name frozen RLD1-PSMC5 sel
    5334 
    5335 > hide residues
    5336 
    5337 > show RLD1-PSMC5
    5338 
    5339 > hide H
    5340 
    5341 > select add #4
    5342 
    5343 17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected 
    5344 
    5345 > view list
    5346 
    5347 Named views: P5P1_front, bottom_overview, diemr_1_close, dimer_1_close,
    5348 dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
    5349 side_overview_P5P1_dimer_3 
    5350 
    5351 > view P5P1_front
    5352 
    5353 > select subtract #4
    5354 
    5355 Nothing selected 
    5356 
    5357 > ui tool show "Side View"
    5358 
    5359 > view name RLD1-P5-interface
    5360 
    5361 > select add #4/B:373@OE2
    5362 
    5363 1 atom, 1 residue, 1 model selected 
    5364 
    5365 > select add #4
    5366 
    5367 17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 4 models selected 
    5368 
    5369 > select add #5
    5370 
    5371 17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 6 models selected 
    5372 
    5373 > select subtract #5
    5374 
    5375 17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected 
    5376 
    5377 > select subtract #4
    5378 
    5379 Nothing selected 
    5380 
    5381 > hide #!5 models
    5382 
    5383 > select add #4/B:373@OE2
    5384 
    5385 1 atom, 1 residue, 1 model selected 
    5386 
    5387 > select add #4/1:499@NZ
    5388 
    5389 2 atoms, 2 residues, 1 model selected 
    5390 
    5391 > pbond sel color grey radius 0.3 dashes 4
    5392 
    5393 > hide #4.2 models
    5394 
    5395 > close #4.2
    5396 
    5397 > pbond sel color grey radius 0.2 dashes 4
    5398 
    5399 > close #4.2
    5400 
    5401 > pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
    5402 
    5403 > select subtract #4/1:499@NZ
    5404 
    5405 1 atom, 1 residue, 1 model selected 
    5406 
    5407 > select subtract #4/B:373@OE2
    5408 
    5409 Nothing selected 
    5410 
    5411 > select add #4/1:499@NZ
    5412 
    5413 1 atom, 1 residue, 1 model selected 
    5414 
    5415 > select add #4/B:381@OE2
    5416 
    5417 2 atoms, 2 residues, 1 model selected 
    5418 
    5419 > pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
    5420 
    5421 > select add #4/B:384@OE1
    5422 
    5423 3 atoms, 3 residues, 1 model selected 
    5424 
    5425 > select add #4
    5426 
    5427 17636 atoms, 17798 bonds, 3 pseudobonds, 1170 residues, 3 models selected 
    5428 
    5429 > select subtract #4
    5430 
    5431 Nothing selected 
    5432 
    5433 > select #4/B:384@OE1
    5434 
    5435 1 atom, 1 residue, 1 model selected 
    5436 
    5437 > select add #4/1:432@OH
    5438 
    5439 2 atoms, 2 residues, 1 model selected 
    5440 
    5441 > pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
    5442 
    5443 > close #4.2
    5444 
    5445 > pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
    5446 
    5447 > hide #4.2.1 models
    5448 
    5449 > show #4.2.1 models
    5450 
    5451 > select #4/B:381@OE2
    5452 
    5453 1 atom, 1 residue, 1 model selected 
    5454 
    5455 > select add #4/1:499@NZ
    5456 
    5457 2 atoms, 2 residues, 1 model selected 
    5458 
    5459 > pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
    5460 
    5461 > select #4/B:373@OE2
    5462 
    5463 1 atom, 1 residue, 1 model selected 
    5464 
    5465 > select add #4/1:499@NZ
    5466 
    5467 2 atoms, 2 residues, 1 model selected 
    5468 
    5469 > pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
    5470 
    5471 > close #4.2
    5472 
    5473 Cell requested for row 5 is out of bounds for table with 8 rows! Resizing
    5474 table model. 
    5475 
    5476 > pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true reveal
    5477 > true
    5478 
    5479 Cell requested for row 0 is out of bounds for table with 8 rows! Resizing
    5480 table model. 
    5481 
    5482 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
    5483 > true
    5484 
    5485 > select up
    5486 
    5487 2 atoms, 1 bond, 1 residue, 1 model selected 
    5488 
    5489 > label sel
    5490 
    5491 > close #4.3
    5492 
    5493 > select #4/B:373@OE2
    5494 
    5495 1 atom, 1 residue, 1 model selected 
    5496 
    5497 > select add #4/1:499@NZ
    5498 
    5499 2 atoms, 2 residues, 1 model selected 
    5500 
    5501 > label sel
    5502 
    5503 > select #4/1:499@NZ
    5504 
    5505 1 atom, 1 residue, 1 model selected 
    5506 
    5507 > select add #4/B:381@OE2
    5508 
    5509 2 atoms, 2 residues, 1 model selected 
    5510 
    5511 > label sel
    5512 
    5513 > view list
    5514 
    5515 Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
    5516 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    5517 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    5518 
    5519 > view P5P1_front
    5520 
    5521 > view RLD1-P5-interface
    5522 
    5523 > select subtract #4/1:499@NZ
    5524 
    5525 1 atom, 1 residue, 1 model selected 
    5526 
    5527 > select #4/1:499@NZ
    5528 
    5529 1 atom, 1 residue, 1 model selected 
    5530 
    5531 > select add #4/B:381@OE2
    5532 
    5533 2 atoms, 2 residues, 1 model selected 
    5534 
    5535 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
    5536 > true
    5537 
    5538 > hide #!4.2 models
    5539 
    5540 > hide #4.3 models
    5541 
    5542 > show #4.3 models
    5543 
    5544 > hide #4.3 models
    5545 
    5546 > show #4.3 models
    5547 
    5548 > hide #4.3 models
    5549 
    5550 > close #4.3
    5551 
    5552 > show #!4.2 models
    5553 
    5554 > select #4/B:384@OE1
    5555 
    5556 1 atom, 1 residue, 1 model selected 
    5557 
    5558 > select add #4/1:432@OH
    5559 
    5560 2 atoms, 2 residues, 1 model selected 
    5561 
    5562 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
    5563 > true
    5564 
    5565 > select #4/B:373@OE2
    5566 
    5567 1 atom, 1 residue, 1 model selected 
    5568 
    5569 > select add #4/1:499@NZ
    5570 
    5571 2 atoms, 2 residues, 1 model selected 
    5572 
    5573 > select add #4/B:381@OE2
    5574 
    5575 3 atoms, 3 residues, 1 model selected 
    5576 
    5577 > select add #4/B:381@OE1
    5578 
    5579 4 atoms, 3 residues, 1 model selected 
    5580 
    5581 > select #4/B:381@OE1
    5582 
    5583 1 atom, 1 residue, 1 model selected 
    5584 
    5585 > select #4/B:373@OE2
    5586 
    5587 1 atom, 1 residue, 1 model selected 
    5588 
    5589 > select add #4/B:381@OE2
    5590 
    5591 2 atoms, 2 residues, 1 model selected 
    5592 
    5593 > select add #4/B:384@OE1
    5594 
    5595 3 atoms, 3 residues, 1 model selected 
    5596 
    5597 > select add #4/1:432@OH
    5598 
    5599 4 atoms, 4 residues, 1 model selected 
    5600 
    5601 > label sel name RLD1-P5
    5602 
    5603 Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
    5604 keyword 
    5605 
    5606 > label sel
    5607 
    5608 > show #!2 models
    5609 
    5610 > hide #!2 models
    5611 
    5612 > show #!5 models
    5613 
    5614 > select add #4
    5615 
    5616 17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected 
    5617 
    5618 > select subtract #4
    5619 
    5620 Nothing selected 
    5621 
    5622 > spng RLD1-P5_interaction.png
    5623 
    5624 > save RLD1-P5_interaction.png width 3000 height 3000 supersample 3
    5625 > transparentBackground true
    5626 
    5627 > hide #4.2.1 models
    5628 
    5629 > hide #4.3 models
    5630 
    5631 > spng RLD1-P5_interaction.png
    5632 
    5633 > save RLD1-P5_interaction.png width 3000 height 3000 supersample 3
    5634 > transparentBackground true
    5635 
    5636 > show #4.2.1 models
    5637 
    5638 > show #4.3 models
    5639 
    5640 > spng RLD1-P5_interaction_labelled.png
    5641 
    5642 > save RLD1-P5_interaction_labelled.png width 3000 height 3000 supersample 3
    5643 > transparentBackground true
    5644 
    5645 > hide #!4.2 models
    5646 
    5647 > hide #4.2.1 models
    5648 
    5649 > hide #4.3 models
    5650 
    5651 > show residues
    5652 
    5653 > hide H
    5654 
    5655 > show #4
    5656 
    5657 > color #4 byhetero
    5658 
    5659 > hide H
    5660 
    5661 > select #5
    5662 
    5663 4 models selected 
    5664 
    5665 > select #4/1:674@OD2
    5666 
    5667 1 atom, 1 residue, 1 model selected 
    5668 
    5669 > hide #!5 models
    5670 
    5671 > select add #4/A:41@NE2
    5672 
    5673 2 atoms, 2 residues, 1 model selected 
    5674 
    5675 > select up
    5676 
    5677 29 atoms, 27 bonds, 2 residues, 1 model selected 
    5678 
    5679 > select up
    5680 
    5681 175 atoms, 174 bonds, 13 residues, 1 model selected 
    5682 
    5683 > select down
    5684 
    5685 29 atoms, 27 bonds, 2 residues, 1 model selected 
    5686 
    5687 > select down
    5688 
    5689 2 atoms, 2 residues, 1 model selected 
    5690 
    5691 > pbond sel color grey radius 0.2 dashes 4 reveal true name test
    5692 
    5693 > pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
    5694 
    5695 > select #4/A:50@OE1
    5696 
    5697 1 atom, 1 residue, 1 model selected 
    5698 
    5699 > select add #4/1:691@OD1
    5700 
    5701 2 atoms, 2 residues, 1 model selected 
    5702 
    5703 > pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
    5704 
    5705 > select add #4/A:39@CG2
    5706 
    5707 3 atoms, 3 residues, 1 model selected 
    5708 
    5709 > select add #4/1:674@OD2
    5710 
    5711 4 atoms, 4 residues, 1 model selected 
    5712 
    5713 > pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
    5714 
    5715 Must specify exactly 2 atoms to form pseudobond between; you specified 4 
    5716 
    5717 > select #4/A:19
    5718 
    5719 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5720 
    5721 > select #4/A:39@CG2
    5722 
    5723 1 atom, 1 residue, 1 model selected 
    5724 
    5725 > select add #4/1:674@OD2
    5726 
    5727 2 atoms, 2 residues, 1 model selected 
    5728 
    5729 > pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
    5730 
    5731 > close #4.4
    5732 
    5733 > view list
    5734 
    5735 Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
    5736 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    5737 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    5738 
    5739 > view P5P1_front
    5740 
    5741 > hide #4
    5742 
    5743 > show residues
    5744 
    5745 > hdie H
    5746 
    5747 Unknown command: hdie H 
    5748 
    5749 > hide H
    5750 
    5751 > view P5P1_front
    5752 
    5753 > select add #4
    5754 
    5755 17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected 
    5756 
    5757 > select subtract #4
    5758 
    5759 Nothing selected 
    5760 
    5761 > select #4/1:381@OG
    5762 
    5763 1 atom, 1 residue, 1 model selected 
    5764 
    5765 > select add #4/1:379@OG
    5766 
    5767 2 atoms, 2 residues, 1 model selected 
    5768 
    5769 > select add #4/A:19@OE1
    5770 
    5771 3 atoms, 3 residues, 1 model selected 
    5772 
    5773 > select add #4/A:21@OE2
    5774 
    5775 4 atoms, 4 residues, 1 model selected 
    5776 
    5777 > select add #4/1:413@OH
    5778 
    5779 5 atoms, 5 residues, 1 model selected 
    5780 
    5781 > select add #4/A:55@OE1
    5782 
    5783 6 atoms, 6 residues, 1 model selected 
    5784 
    5785 > select add #4/1:542@NH1
    5786 
    5787 7 atoms, 7 residues, 1 model selected 
    5788 
    5789 > show #4.2.1 models
    5790 
    5791 > hide #4.2.1 models
    5792 
    5793 > show #4.3 models
    5794 
    5795 > hide #4.3 models
    5796 
    5797 > label sel
    5798 
    5799 > show #4.3 models
    5800 
    5801 > select add #4
    5802 
    5803 17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected 
    5804 
    5805 > select subtract #4
    5806 
    5807 Nothing selected 
    5808 
    5809 > show #!5 models
    5810 
    5811 > color zone #5 near #4 distance 6
    5812 
    5813 > combine #4
    5814 
    5815 > color #5/1 #BBBDBF
    5816 
    5817 > hide #4.1 models
    5818 
    5819 > show #4.1 models
    5820 
    5821 > hide #!4 models
    5822 
    5823 > show #!4 models
    5824 
    5825 > hide #!5 models
    5826 
    5827 > show #!5 models
    5828 
    5829 > color #6/1 #BBBDBF
    5830 
    5831 > hide #!5 models
    5832 
    5833 > hide #!4 models
    5834 
    5835 > color #6/1-3:372-734 light sky blue
    5836 
    5837 > color #6/1-3:3420-3820 #350CED
    5838 
    5839 > color #6/1-3:3996-4366 #90CED6
    5840 
    5841 > color #6/1-3:4447-4840 #d31340ff
    5842 
    5843 > color #6/1-3:2315-2379 palegreen
    5844 
    5845 > color #6/1-3:1384-1399 #009193ff
    5846 
    5847 > color #6/1-3:2747-2799 lime
    5848 
    5849 > color #6/1-3:2975-3055 #EF6B11
    5850 
    5851 > color #6/1-3:2030-2190 #F4EB45
    5852 
    5853 > color #6/1-3:3297-3329 #CE3674
    5854 
    5855 > hide #!6 models
    5856 
    5857 > show #!6 models
    5858 
    5859 > hide #!6 models
    5860 
    5861 > show #!6 models
    5862 
    5863 > color #6 bychain
    5864 
    5865 > color #6/1 #BBBDBF
    5866 
    5867 > color #6/1-3:372-734 light sky blue
    5868 
    5869 > color #6/1-3:3420-3820 #350CED
    5870 
    5871 > color #6/1-3:3996-4366 #90CED6
    5872 
    5873 > color #6/1-3:4447-4840 #d31340ff
    5874 
    5875 > color #6/1-3:2315-2379 palegreen
    5876 
    5877 > color #6/1-3:1384-1399 #009193ff
    5878 
    5879 > color #6/1-3:2747-2799 lime
    5880 
    5881 > color #6/1-3:2975-3055 #EF6B11
    5882 
    5883 > color #6/1-3:2030-2190 #F4EB45
    5884 
    5885 > color #6/1-3:3297-3329 #CE3674
    5886 
    5887 > hide #6
    5888 
    5889 > show nucleic
    5890 
    5891 > hide protein|solvent|H
    5892 
    5893 > surface hidePatches
    5894 
    5895 > style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5896 
    5897 Changed 0 atom styles 
    5898 
    5899 > cartoon
    5900 
    5901 > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
    5902 > width 2 thickness 0.4 sides 12 divisions 20
    5903 
    5904 > cartoon style ~(nucleic|strand) xsection round
    5905 
    5906 > cartoon style (nucleic|strand) xsection rectangle
    5907 
    5908 > cartoon style protein modeHelix default arrows false xsection round width 2
    5909 > thickness 1
    5910 
    5911 > cartoon style nucleic xsection round width 1.6 thickness 1.6
    5912 
    5913 > nucleotides stubs radius 0.5
    5914 
    5915 > size stickRadius 0.3
    5916 
    5917 Changed 424936 bond radii 
    5918 
    5919 > color #6 #7b68ee7e
    5920 
    5921 > undo
    5922 
    5923 > transparency #6 50
    5924 
    5925 > transparency #6 50color #6 tr 50
    5926 
    5927 Missing or invalid "percent" argument: Expected a number 
    5928 
    5929 > color #6 transparency 50
    5930 
    5931 > show #!5 models
    5932 
    5933 > show #!4 models
    5934 
    5935 > color zone #5 near #6 distance 6
    5936 
    5937 > transparency #5 50
    5938 
    5939 > hide #!6 models
    5940 
    5941 > show #!6 models
    5942 
    5943 > hide #!6 models
    5944 
    5945 > hide #!5 models
    5946 
    5947 > show #!6 models
    5948 
    5949 > hide #!6 models
    5950 
    5951 > shpw residues
    5952 
    5953 Unknown command: shpw residues 
    5954 
    5955 > show residues
    5956 
    5957 > hide H
    5958 
    5959 > select add #4/1:381@OG
    5960 
    5961 1 atom, 1 residue, 1 model selected 
    5962 
    5963 > select add #4/1:379@OG
    5964 
    5965 2 atoms, 2 residues, 1 model selected 
    5966 
    5967 > select add #4/1:413@OH
    5968 
    5969 3 atoms, 3 residues, 1 model selected 
    5970 
    5971 > select add #4/A:19@OE1
    5972 
    5973 4 atoms, 4 residues, 1 model selected 
    5974 
    5975 > select add #4/A:21@OE1
    5976 
    5977 5 atoms, 5 residues, 1 model selected 
    5978 
    5979 > select add #4/A:55@OE2
    5980 
    5981 6 atoms, 6 residues, 1 model selected 
    5982 
    5983 > select add #4/1:542@NH1
    5984 
    5985 7 atoms, 7 residues, 1 model selected 
    5986 
    5987 > select #4/1:542@NH1
    5988 
    5989 1 atom, 1 residue, 1 model selected 
    5990 
    5991 > select add #4/A:55@OE2
    5992 
    5993 2 atoms, 2 residues, 1 model selected 
    5994 
    5995 > select add #4/A:21@OE1
    5996 
    5997 3 atoms, 3 residues, 1 model selected 
    5998 
    5999 > select add #4/A:19@OE1
    6000 
    6001 4 atoms, 4 residues, 1 model selected 
    6002 
    6003 > select add #4/1:381@OG
    6004 
    6005 5 atoms, 5 residues, 1 model selected 
    6006 
    6007 > select add #4/1:379@OG
    6008 
    6009 6 atoms, 6 residues, 1 model selected 
    6010 
    6011 > select add #4/1:413@OH
    6012 
    6013 7 atoms, 7 residues, 1 model selected 
    6014 
    6015 > select up
    6016 
    6017 112 atoms, 106 bonds, 7 residues, 1 model selected 
    6018 
    6019 > name frozen sel RLD1-P1
    6020 
    6021 Missing or invalid "objects" argument: invalid objects specifier 
    6022 
    6023 > name frozen RLD1-P1 sel
    6024 
    6025 > select add #4
    6026 
    6027 17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected 
    6028 
    6029 > select subtract #4
    6030 
    6031 Nothing selected 
    6032 
    6033 > show #!5 models
    6034 
    6035 > color zone #5 near #6 distance 6
    6036 
    6037 > transparency #5 50
    6038 
    6039 > show #!6 models
    6040 
    6041 > hide #!6 models
    6042 
    6043 > show #!6 models
    6044 
    6045 > hide #!5 models
    6046 
    6047 > color #6/B #ABAA00
    6048 
    6049 > color zone #5 near #6 distance 6
    6050 
    6051 > transparency #5 50
    6052 
    6053 > show #!5 models
    6054 
    6055 > color zone #5 near #6 distance 6
    6056 
    6057 > transparency #5 50
    6058 
    6059 > volume #5 level 0.1811
    6060 
    6061 > transparency #5 50
    6062 
    6063 > color zone #5 near #6 distance 6
    6064 
    6065 > transparency #5 50
    6066 
    6067 > hide #!5 models
    6068 
    6069 > select clear
    6070 
    6071 > select #4/1:381@OG
    6072 
    6073 1 atom, 1 residue, 1 model selected 
    6074 
    6075 > select add #4/A:19@OE1
    6076 
    6077 2 atoms, 2 residues, 1 model selected 
    6078 
    6079 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
    6080 > true
    6081 
    6082 > select #4/1:379@OG
    6083 
    6084 1 atom, 1 residue, 1 model selected 
    6085 
    6086 > select add #4/A:19@OE2
    6087 
    6088 2 atoms, 2 residues, 1 model selected 
    6089 
    6090 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
    6091 > true
    6092 
    6093 > select #4/1:413@OH
    6094 
    6095 1 atom, 1 residue, 1 model selected 
    6096 
    6097 > select add #4/A:21@OE2
    6098 
    6099 2 atoms, 2 residues, 1 model selected 
    6100 
    6101 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
    6102 > true
    6103 
    6104 > select #4/A:55@OE2
    6105 
    6106 1 atom, 1 residue, 1 model selected 
    6107 
    6108 > select add #4/1:542@NH1
    6109 
    6110 2 atoms, 2 residues, 1 model selected 
    6111 
    6112 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
    6113 > true
    6114 
    6115 > show #!5 models
    6116 
    6117 > transparency #5 50
    6118 
    6119 > color zone #5 near #6 distance 6
    6120 
    6121 > transparency #5 50
    6122 
    6123 > volume #5 level 0.2294
    6124 
    6125 > color zone #5 near #6 distance 6
    6126 
    6127 > transparency #5 50
    6128 
    6129 > select add #4
    6130 
    6131 17636 atoms, 17798 bonds, 9 pseudobonds, 1170 residues, 7 models selected 
    6132 
    6133 > select subtract #4
    6134 
    6135 Nothing selected 
    6136 
    6137 > color zone #5 near #6 distance 6
    6138 
    6139 > transparency #5 50
    6140 
    6141 > spng RLD1-P1_interaction_labelled.png
    6142 
    6143 > save RLD1-P1_interaction_labelled.png width 3000 height 3000 supersample 3
    6144 > transparentBackground true
    6145 
    6146 > graphics silhouettes true width 4
    6147 
    6148 > graphics silhouettes true width 8
    6149 
    6150 > spng RLD1-P1_interaction_labelled.png
    6151 
    6152 > save RLD1-P1_interaction_labelled.png width 3000 height 3000 supersample 3
    6153 > transparentBackground true
    6154 
    6155 > graphics silhouettes true width 4
    6156 
    6157 > graphics silhouettes true width 6
    6158 
    6159 > view list
    6160 
    6161 Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
    6162 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    6163 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    6164 
    6165 > view P5P1_front
    6166 
    6167 > spng RLD1-P1_interaction-1_labelled.png
    6168 
    6169 > save RLD1-P1_interaction-1_labelled.png width 3000 height 3000 supersample 3
    6170 > transparentBackground true
    6171 
    6172 > color zone #5 near #6 distance 6
    6173 
    6174 > transparency #5 50
    6175 
    6176 > select #4/1:728
    6177 
    6178 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6179 
    6180 > select resideus
    6181 
    6182 Expected an objects specifier or a keyword 
    6183 
    6184 > select residues
    6185 
    6186 Missing "residues" keyword's argument 
    6187 
    6188 > name list
    6189 
    6190 RLD1-P1 [112 atoms, 212 bonds] 
    6191 RLD1-PSMC5 [88 atoms, 168 bonds] 
    6192 residues [349 atoms, 668 bonds] 
    6193 
    6194 > select residues
    6195 
    6196 Missing "residues" keyword's argument 
    6197 
    6198 > show residues
    6199 
    6200 > hide residues
    6201 
    6202 > name
    6203 
    6204 Missing or invalid "name" argument: Expected a text string 
    6205 
    6206 > select #4/A:373,381,384
    6207 
    6208 50 atoms, 47 bonds, 3 residues, 1 model selected 
    6209 
    6210 > select #4/B:373,381,384
    6211 
    6212 45 atoms, 42 bonds, 3 residues, 1 model selected 
    6213 
    6214 > select add #4/A:55,19,21,332,333,350,349
    6215 
    6216 155 atoms, 147 bonds, 10 residues, 1 model selected 
    6217 
    6218 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    6219 
    6220 349 atoms, 334 bonds, 20 residues, 1 model selected 
    6221 
    6222 > select add #4/1:728
    6223 
    6224 360 atoms, 344 bonds, 21 residues, 1 model selected 
    6225 
    6226 > show sel
    6227 
    6228 > view name RLD1-P1_interaction-1
    6229 
    6230 > select #4/A:19@OE2
    6231 
    6232 1 atom, 1 residue, 1 model selected 
    6233 
    6234 > select add #4/1:728@HG
    6235 
    6236 2 atoms, 2 residues, 1 model selected 
    6237 
    6238 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
    6239 > true
    6240 
    6241 > view list
    6242 
    6243 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
    6244 bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
    6245 side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    6246 
    6247 > view P5P1_front
    6248 
    6249 > show
    6250 
    6251 > hide
    6252 
    6253 > hide #!6 models
    6254 
    6255 > show #!6 models
    6256 
    6257 > hide #!6 models
    6258 
    6259 > show #!6 models
    6260 
    6261 > hide #!4 models
    6262 
    6263 > hide #!5 models
    6264 
    6265 > color #6/B #ABAA00
    6266 
    6267 > color #6/A #363600
    6268 
    6269 > hide #!6 models
    6270 
    6271 > select add #4/1:728
    6272 
    6273 12 atoms, 10 bonds, 2 residues, 1 model selected 
    6274 
    6275 > select #4/A:373,381,384
    6276 
    6277 50 atoms, 47 bonds, 3 residues, 1 model selected 
    6278 
    6279 > select #4/B:373,381,384
    6280 
    6281 45 atoms, 42 bonds, 3 residues, 1 model selected 
    6282 
    6283 > select add #4/A:55,19,21,332,333,350,349
    6284 
    6285 155 atoms, 147 bonds, 10 residues, 1 model selected 
    6286 
    6287 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    6288 
    6289 349 atoms, 334 bonds, 20 residues, 1 model selected 
    6290 
    6291 > show #!6 models
    6292 
    6293 > hide #!6 models
    6294 
    6295 > show #!4 models
    6296 
    6297 > name frozen residues sel
    6298 
    6299 > view list
    6300 
    6301 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
    6302 bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
    6303 side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    6304 
    6305 > view RLD1-P1_interaction-1
    6306 
    6307 > show residues
    6308 
    6309 > hide H
    6310 
    6311 > select add #4
    6312 
    6313 17636 atoms, 17798 bonds, 10 pseudobonds, 1170 residues, 7 models selected 
    6314 
    6315 > select subtract #4
    6316 
    6317 Nothing selected 
    6318 
    6319 > show #!5 models
    6320 
    6321 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    6322 
    6323 194 atoms, 187 bonds, 10 residues, 1 model selected 
    6324 
    6325 > select #4/A:373,381,384
    6326 
    6327 50 atoms, 47 bonds, 3 residues, 1 model selected 
    6328 
    6329 > select #4/B:373,381,384
    6330 
    6331 45 atoms, 42 bonds, 3 residues, 1 model selected 
    6332 
    6333 > select add #4/A:55,19,21,332,333,350,349
    6334 
    6335 155 atoms, 147 bonds, 10 residues, 1 model selected 
    6336 
    6337 > select add #4/1:728
    6338 
    6339 166 atoms, 157 bonds, 11 residues, 1 model selected 
    6340 
    6341 > name frozen residues sel
    6342 
    6343 > show residues
    6344 
    6345 > hide H
    6346 
    6347 > select #4/A:19@OE2
    6348 
    6349 1 atom, 1 residue, 1 model selected 
    6350 
    6351 > select add #4/1:728@OG
    6352 
    6353 2 atoms, 2 residues, 1 model selected 
    6354 
    6355 > pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
    6356 > true
    6357 
    6358 > view list
    6359 
    6360 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
    6361 bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
    6362 side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    6363 
    6364 > view RLD1-P1_interaction-1
    6365 
    6366 > color zone #5 near #6 distance 6
    6367 
    6368 > transparency #5 50
    6369 
    6370 > select add #4
    6371 
    6372 17636 atoms, 17798 bonds, 11 pseudobonds, 1170 residues, 7 models selected 
    6373 
    6374 > select subtract #4
    6375 
    6376 Nothing selected 
    6377 
    6378 > spng RLD1-P1_interaction-1_labelled.png
    6379 
    6380 > save RLD1-P1_interaction-1_labelled.png width 3000 height 3000 supersample 3
    6381 > transparentBackground true
    6382 
    6383 > view RLD1-P1_interaction-1
    6384 
    6385 [Repeated 1 time(s)]
    6386 
    6387 > color zone #5 near #6 distance 6
    6388 
    6389 > transparency #5 50
    6390 
    6391 > spng RLD1-P1_interaction-2_labelled.png
    6392 
    6393 > save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
    6394 > transparentBackground true
    6395 
    6396 > transparency #5 50
    6397 
    6398 > color zone #5 near #6 distance 6
    6399 
    6400 > transparency #5 50
    6401 
    6402 > color zone #5 near #6 distance 6
    6403 
    6404 > transparency #5 50
    6405 
    6406 > spng RLD1-P1_interaction-2_labelled.png
    6407 
    6408 > save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
    6409 > transparentBackground true
    6410 
    6411 > hide #4.3 models
    6412 
    6413 > hide #4.4.1 models
    6414 
    6415 > color zone #5 near #6 distance 6
    6416 
    6417 > transparency #5 50
    6418 
    6419 > spng RLD1-P1_interaction-2.png
    6420 
    6421 > save RLD1-P1_interaction-2.png width 3000 height 3000 supersample 3
    6422 > transparentBackground true
    6423 
    6424 > view list
    6425 
    6426 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
    6427 bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
    6428 side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    6429 
    6430 > view name RLD1-P1_interaction-2
    6431 
    6432 > view RLD1-P1_interaction-1
    6433 
    6434 > transparency #5 50
    6435 
    6436 > color zone #5 near #6 distance 6
    6437 
    6438 > transparency #5 50
    6439 
    6440 > spng RLD1-P1_interaction-1.png
    6441 
    6442 > save RLD1-P1_interaction-1.png width 3000 height 3000 supersample 3
    6443 > transparentBackground true
    6444 
    6445 > view list
    6446 
    6447 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    6448 RLD1-P5-interface, bottom_overview, diemr_1_close, dimer_1_close,
    6449 dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
    6450 side_overview_P5P1_dimer_3 
    6451 
    6452 > view RLD1-P1_interaction-2
    6453 
    6454 > view name RLD1-P1_interaction-1
    6455 
    6456 > color zone #5 near #6 distance 6
    6457 
    6458 > transparency #5 50
    6459 
    6460 > spng RLD1-P1_interaction-2.png
    6461 
    6462 > save RLD1-P1_interaction-2.png width 3000 height 3000 supersample 3
    6463 > transparentBackground true
    6464 
    6465 > show #4.4.1 models
    6466 
    6467 > show #4.3 models
    6468 
    6469 > spng RLD1-P1_interaction-2_labelled.png
    6470 
    6471 > save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
    6472 > transparentBackground true
    6473 
    6474 > color zone #5 near #6 distance 6
    6475 
    6476 > transparency #5 50
    6477 
    6478 > spng RLD1-P1_interaction-2_labelled.png
    6479 
    6480 > save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
    6481 > transparentBackground true
    6482 
    6483 > view list
    6484 
    6485 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    6486 RLD1-P5-interface, bottom_overview, diemr_1_close, dimer_1_close,
    6487 dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
    6488 side_overview_P5P1_dimer_3 
    6489 
    6490 > view P5P1_front
    6491 
    6492 > volume #5 level 0.1714
    6493 
    6494 > hide #!5 models
    6495 
    6496 > show #!5 models
    6497 
    6498 > volume #5 level 0.2488
    6499 
    6500 > volume #5 level 0.2004
    6501 
    6502 > select #5
    6503 
    6504 4 models selected 
    6505 
    6506 > hide #!5 models
    6507 
    6508 > select #4/A:349@NE2
    6509 
    6510 1 atom, 1 residue, 1 model selected 
    6511 
    6512 > select add #4/1:2176@OH
    6513 
    6514 2 atoms, 2 residues, 1 model selected 
    6515 
    6516 > select up
    6517 
    6518 38 atoms, 37 bonds, 2 residues, 1 model selected 
    6519 
    6520 > name frozen SPRY-P1_1
    6521 
    6522 Missing or invalid "objects" argument: empty atom specifier 
    6523 
    6524 > name frozen SPRY-P1_1 sel
    6525 
    6526 > hide residues
    6527 
    6528 > show SPRY-P1_1
    6529 
    6530 > hide H
    6531 
    6532 > hide residues
    6533 
    6534 > name list
    6535 
    6536 RLD1-P1 [112 atoms, 212 bonds] 
    6537 RLD1-PSMC5 [88 atoms, 168 bonds] 
    6538 SPRY-P1_1 [38 atoms, 74 bonds] 
    6539 residues [166 atoms, 314 bonds] 
    6540 
    6541 > hide al
    6542 
    6543 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    6544 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    6545 
    6546 > hide al
    6547 
    6548 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    6549 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    6550 
    6551 > hide all
    6552 
    6553 > show residues
    6554 
    6555 > hide residues
    6556 
    6557 > select #4/B:373,381,384
    6558 
    6559 45 atoms, 42 bonds, 3 residues, 1 model selected 
    6560 
    6561 > select add #4/A:55,19,21,332,333,350,349
    6562 
    6563 155 atoms, 147 bonds, 10 residues, 1 model selected 
    6564 
    6565 > select add #4/1:728
    6566 
    6567 166 atoms, 157 bonds, 11 residues, 1 model selected 
    6568 
    6569 > select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
    6570 
    6571 360 atoms, 344 bonds, 21 residues, 1 model selected 
    6572 
    6573 > name frozen residues sel
    6574 
    6575 > show residues
    6576 
    6577 > hide residues
    6578 
    6579 > show SPRY-P1_1
    6580 
    6581 > hide H
    6582 
    6583 > show #!5 models
    6584 
    6585 > select add #4
    6586 
    6587 17636 atoms, 17798 bonds, 11 pseudobonds, 1170 residues, 7 models selected 
    6588 
    6589 > select subtract #4
    6590 
    6591 Nothing selected 
    6592 
    6593 > hide #!5 models
    6594 
    6595 > select #4/A:349@NE2
    6596 
    6597 1 atom, 1 residue, 1 model selected 
    6598 
    6599 > select add #4/1:2176@OH
    6600 
    6601 2 atoms, 2 residues, 1 model selected 
    6602 
    6603 > pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-1 showDist
    6604 > true
    6605 
    6606 > label sel
    6607 
    6608 > show #!5 models
    6609 
    6610 > color zone #5 near #6 distance 6
    6611 
    6612 > transparency #5 50
    6613 
    6614 > spng SPRY-P1_1_labelled.png
    6615 
    6616 > save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
    6617 > transparentBackground true
    6618 
    6619 > select add #4
    6620 
    6621 17636 atoms, 17798 bonds, 12 pseudobonds, 1170 residues, 9 models selected 
    6622 
    6623 > select subtract #4
    6624 
    6625 Nothing selected 
    6626 
    6627 > color zone #5 near #6 distance 6
    6628 
    6629 > transparency #5 50
    6630 
    6631 > spng SPRY-P1_1_labelled.png
    6632 
    6633 > save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
    6634 > transparentBackground true
    6635 
    6636 > hide #4.4.1 models
    6637 
    6638 > hide #4.3 models
    6639 
    6640 > spng SPRY-P1_1.png
    6641 
    6642 > save SPRY-P1_1.png width 3000 height 3000 supersample 3
    6643 > transparentBackground true
    6644 
    6645 > color zone #5 near #6 distance 6
    6646 
    6647 > transparency #5 50
    6648 
    6649 > color zone #5 near #6 distance 6
    6650 
    6651 > transparency #5 50
    6652 
    6653 > spng SPRY-P1_1.png
    6654 
    6655 > save SPRY-P1_1.png width 3000 height 3000 supersample 3
    6656 > transparentBackground true
    6657 
    6658 > show #4.4.1 models
    6659 
    6660 > hide #4.4.1 models
    6661 
    6662 > show #4.3 models
    6663 
    6664 > color zone #5 near #6 distance 6
    6665 
    6666 > transparency #5 50
    6667 
    6668 > spng SPRY-P1_1_labelled.png
    6669 
    6670 > save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
    6671 > transparentBackground true
    6672 
    6673 > hide #4.3 models
    6674 
    6675 > hide #4.5.1 models
    6676 
    6677 > spng SPRY-P1_1.png
    6678 
    6679 > save SPRY-P1_1.png width 3000 height 3000 supersample 3
    6680 > transparentBackground true
    6681 
    6682 > view name SPRY-P1_1
    6683 
    6684 > show residues
    6685 
    6686 > hide H
    6687 
    6688 > name list
    6689 
    6690 RLD1-P1 [112 atoms, 212 bonds] 
    6691 RLD1-PSMC5 [88 atoms, 168 bonds] 
    6692 SPRY-P1_1 [38 atoms, 74 bonds] 
    6693 residues [360 atoms, 688 bonds] 
    6694 
    6695 > hide SPRY-P1_1
    6696 
    6697 > volume #5 level 0.1811
    6698 
    6699 > color zone #5 near #6 distance 6
    6700 
    6701 > transparency #5 50
    6702 
    6703 > hide #!5 models
    6704 
    6705 > hide SPRY-P1_2
    6706 
    6707 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    6708 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    6709 
    6710 > view name SPRY-P1_2
    6711 
    6712 > show #!5 models
    6713 
    6714 > select #4/A:332@NH1
    6715 
    6716 1 atom, 1 residue, 1 model selected 
    6717 
    6718 > select add #4/1:2123@OE1
    6719 
    6720 2 atoms, 2 residues, 1 model selected 
    6721 
    6722 > pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
    6723 > true
    6724 
    6725 > select #4/1:2123@OE2
    6726 
    6727 1 atom, 1 residue, 1 model selected 
    6728 
    6729 > select add #4/A:333@OD1
    6730 
    6731 2 atoms, 2 residues, 1 model selected 
    6732 
    6733 > select #4/1:2103@NH2
    6734 
    6735 1 atom, 1 residue, 1 model selected 
    6736 
    6737 > select add #4/A:333@OD2
    6738 
    6739 2 atoms, 2 residues, 1 model selected 
    6740 
    6741 > pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
    6742 > true
    6743 
    6744 > select #4/1:2112@NH1
    6745 
    6746 1 atom, 1 residue, 1 model selected 
    6747 
    6748 > select add #4/A:350@OD1
    6749 
    6750 2 atoms, 2 residues, 1 model selected 
    6751 
    6752 > pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
    6753 > true
    6754 
    6755 > select #4/1:2103@NH1
    6756 
    6757 1 atom, 1 residue, 1 model selected 
    6758 
    6759 > select add #4/A:350@OD1
    6760 
    6761 2 atoms, 2 residues, 1 model selected 
    6762 
    6763 > pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
    6764 > true
    6765 
    6766 > hide #!5 models
    6767 
    6768 > select add #4/1:2112@NH1
    6769 
    6770 3 atoms, 3 residues, 1 model selected 
    6771 
    6772 > select add #4/A:333@OD2
    6773 
    6774 4 atoms, 4 residues, 1 model selected 
    6775 
    6776 > select add #4/1:2123@OE2
    6777 
    6778 5 atoms, 5 residues, 1 model selected 
    6779 
    6780 > select add #4/A:332@NH1
    6781 
    6782 6 atoms, 6 residues, 1 model selected 
    6783 
    6784 > select up
    6785 
    6786 111 atoms, 106 bonds, 6 residues, 1 model selected 
    6787 
    6788 > name frozen SPRY-P1_12 sel
    6789 
    6790 > name frozen SPRY-P1_2 sel
    6791 
    6792 > name remove SPRY-P1_2
    6793 
    6794 > name remove SPRY-P1_12
    6795 
    6796 > name frozen SPRY-P1_2 sel
    6797 
    6798 > show #!5 models
    6799 
    6800 > volume #5 level 0.1908
    6801 
    6802 > color zone #5 near #6 distance 6
    6803 
    6804 > transparency #5 50
    6805 
    6806 > select add #4
    6807 
    6808 17636 atoms, 17798 bonds, 16 pseudobonds, 1170 residues, 11 models selected 
    6809 
    6810 > select subtract #4
    6811 
    6812 Nothing selected 
    6813 
    6814 > spng SPRY-P1_2_labelled.png
    6815 
    6816 > save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
    6817 > transparentBackground true
    6818 
    6819 > select #4/1:2103@NH2
    6820 
    6821 1 atom, 1 residue, 1 model selected 
    6822 
    6823 > select #4/A:350@OD1
    6824 
    6825 1 atom, 1 residue, 1 model selected 
    6826 
    6827 > select add #4/1:2103@NH2
    6828 
    6829 2 atoms, 2 residues, 1 model selected 
    6830 
    6831 > select add #5
    6832 
    6833 2 atoms, 2 residues, 5 models selected 
    6834 
    6835 > select subtract #5
    6836 
    6837 2 atoms, 2 residues, 1 model selected 
    6838 
    6839 > hide #!5 models
    6840 
    6841 > select add #4/1:2112@NH1
    6842 
    6843 3 atoms, 3 residues, 1 model selected 
    6844 
    6845 > select add #4/1:2112@NH2
    6846 
    6847 4 atoms, 3 residues, 1 model selected 
    6848 
    6849 > select add #4/A:333@OD2
    6850 
    6851 5 atoms, 4 residues, 1 model selected 
    6852 
    6853 > select add #4/1:2123@OE1
    6854 
    6855 6 atoms, 5 residues, 1 model selected 
    6856 
    6857 > select add #4/A:332@NH1
    6858 
    6859 7 atoms, 6 residues, 1 model selected 
    6860 
    6861 > label sel
    6862 
    6863 > show #4.3 models
    6864 
    6865 > hide #4.3 models
    6866 
    6867 > show #4.3 models
    6868 
    6869 > hide #!4.6 models
    6870 
    6871 > show #!4.6 models
    6872 
    6873 > hide #4.3 models
    6874 
    6875 > show #4.3 models
    6876 
    6877 > hide #4.3 models
    6878 
    6879 > show #4.3 models
    6880 
    6881 > hide #!4.6 models
    6882 
    6883 > show #!4.6 models
    6884 
    6885 > show #!5 models
    6886 
    6887 > color zone #5 near #6 distance 6
    6888 
    6889 > transparency #5 50
    6890 
    6891 > spng SPRY-P1_2_labelled.png
    6892 
    6893 > save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
    6894 > transparentBackground true
    6895 
    6896 > select add #4
    6897 
    6898 17636 atoms, 17798 bonds, 16 pseudobonds, 1170 residues, 11 models selected 
    6899 
    6900 > select subtract #4
    6901 
    6902 Nothing selected 
    6903 
    6904 > spng SPRY-P1_2_labelled.png
    6905 
    6906 > save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
    6907 > transparentBackground true
    6908 
    6909 > hide #!4.6 models
    6910 
    6911 > show #!4.6 models
    6912 
    6913 > hide #4.6.1 models
    6914 
    6915 > hide #4.3 models
    6916 
    6917 > spng SPRY-P1_2.png
    6918 
    6919 > save SPRY-P1_2.png width 3000 height 3000 supersample 3
    6920 > transparentBackground true
    6921 
    6922 > save 20260203_interactions.cxs
    6923 
    6924 > view list
    6925 
    6926 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    6927 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    6928 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    6929 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    6930 
    6931 > view P5P1_front
    6932 
    6933 > volume #5 level 0.2294
    6934 
    6935 > show #!2 models
    6936 
    6937 > hide #!2 models
    6938 
    6939 > show #!2 models
    6940 
    6941 > hide #!5 models
    6942 
    6943 > show #!3 models
    6944 
    6945 > hide #!3 models
    6946 
    6947 > hide #!2 models
    6948 
    6949 > show #!2 models
    6950 
    6951 > show #!1 models
    6952 
    6953 > hide #!2 models
    6954 
    6955 > show #!3 models
    6956 
    6957 > hide #!1 models
    6958 
    6959 > hide #!3 models
    6960 
    6961 > show #!3 models
    6962 
    6963 > show #!1 models
    6964 
    6965 > hide #!3 models
    6966 
    6967 > hide #!1 models
    6968 
    6969 > show #!1 models
    6970 
    6971 > hide #!4 models
    6972 
    6973 > show #!3 models
    6974 
    6975 > hide #!1 models
    6976 
    6977 > show #!2 models
    6978 
    6979 > view list
    6980 
    6981 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    6982 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    6983 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    6984 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    6985 
    6986 > view P5P1_front
    6987 
    6988 > vop copy #2
    6989 
    6990 Opened 20260203_frankemnmap.mrc copy as #7, grid size 360,360,360, pixel 1.27,
    6991 shown at step 1, values float32 
    6992 
    6993 > hide #!3 models
    6994 
    6995 > show #!3 models
    6996 
    6997 > color zone #7 near #3 distance 6
    6998 
    6999 > hide #!7 models
    7000 
    7001 > show #!7 models
    7002 
    7003 > hide #!4.6 models
    7004 
    7005 > hide #!7 models
    7006 
    7007 > show #!7 models
    7008 
    7009 > hide #4.1 models
    7010 
    7011 > hide #!3 models
    7012 
    7013 > movie record
    7014 
    7015 > turn y 2 180
    7016 
    7017 > wait 180
    7018 
    7019 > movie encode /Users/lorenz.grundmann/Desktop/movie1.mp4
    7020 
    7021 Movie saved to /Users/lorenz.grundmann/Desktop/movie1.mp4 
    7022  
    7023 
    7024 > view #7 clip false
    7025 
    7026 > save /Users/lorenz.grundmann/Desktop/image1.png supersample 3
    7027 
    7028 > movie record
    7029 
    7030 > turn y 2 180
    7031 
    7032 > wait 180
    7033 
    7034 > movie encode /Users/lorenz.grundmann/Desktop/movie2.mp4
    7035 
    7036 Movie saved to /Users/lorenz.grundmann/Desktop/movie2.mp4 
    7037  
    7038 
    7039 > view list
    7040 
    7041 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7042 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7043 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7044 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7045 
    7046 > view bottom_overview
    7047 
    7048 > spng bottom.png
    7049 
    7050 > save bottom.png width 3000 height 3000 supersample 3 transparentBackground
    7051 > true
    7052 
    7053 > view side_overview_P5P1_dimer_2
    7054 
    7055 > view side_overview_P5P1_dimer_3
    7056 
    7057 > view side_overview
    7058 
    7059 > spng side.png
    7060 
    7061 > save side.png width 3000 height 3000 supersample 3 transparentBackground
    7062 > true
    7063 
    7064 > movie record
    7065 
    7066 > turn y 2 180
    7067 
    7068 > wait 180
    7069 
    7070 > movie encode /Users/lorenz.grundmann/Desktop/movie3.mp4
    7071 
    7072 Movie saved to /Users/lorenz.grundmann/Desktop/movie3.mp4 
    7073  
    7074 
    7075 > hide #!7 models
    7076 
    7077 > show #!3 models
    7078 
    7079 > graphics silhouettes true width 4
    7080 
    7081 > view list
    7082 
    7083 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7084 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7085 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7086 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7087 
    7088 > view P5P1_front
    7089 
    7090 > hide #!4.2 models
    7091 
    7092 > show #!4.2 models
    7093 
    7094 > hide #!4.2 models
    7095 
    7096 > show #!4.2 models
    7097 
    7098 > show #4.1 models
    7099 
    7100 > hide #!4 models
    7101 
    7102 > mathc #3 to #4
    7103 
    7104 Unknown command: mathc #3 to #4 
    7105 
    7106 > matchmaker #3 to #4
    7107 
    7108 Computing secondary structure 
    7109 [Repeated 1 time(s)]  Parameters 
    7110 --- 
    7111 Chain pairing | bb 
    7112 Alignment algorithm | Needleman-Wunsch 
    7113 Similarity matrix | BLOSUM-62 
    7114 SS fraction | 0.3 
    7115 Gap open (HH/SS/other) | 18/18/6 
    7116 Gap extend | 1 
    7117 SS matrix |  |  | H | S | O 
    7118 ---|---|---|--- 
    7119 H | 6 | -9 | -6 
    7120 S |  | 6 | -6 
    7121 O |  |  | 4 
    7122 Iteration cutoff | 2 
    7123  
    7124 Matchmaker 20260114_P5P1_new-fit.cif, chain A (#4) with copy of
    7125 20260203_frankemnmodel.pdb, chain A (#3), sequence alignment score = 2024.9 
    7126 RMSD between 392 pruned atom pairs is 0.320 angstroms; (across all 392 pairs:
    7127 0.320) 
    7128  
    7129 
    7130 > hide #4.1 models
    7131 
    7132 > show #4.1 models
    7133 
    7134 > hide #!3 models
    7135 
    7136 > show #!3 models
    7137 
    7138 > hide #4.1 models
    7139 
    7140 > show #4.1 models
    7141 
    7142 > hide #!4 models
    7143 
    7144 > view list
    7145 
    7146 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7147 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7148 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7149 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7150 
    7151 > view side_overview
    7152 
    7153 > hide #3/2 cartoons
    7154 
    7155 > hide #3/C-f
    7156 
    7157 > hide #3/C-F
    7158 
    7159 > hide #3/C-F cartoons
    7160 
    7161 > hide #3/3:370-738
    7162 
    7163 > hide #3/3:370-738 cartoons
    7164 
    7165 > color #3/1-3:3996-4366 #0437FF
    7166 
    7167 > undo
    7168 
    7169 > color #3/1-3:3420-3820 #0437FF
    7170 
    7171 [Repeated 1 time(s)]
    7172 
    7173 > show #!2 models
    7174 
    7175 > hide #!2 models
    7176 
    7177 > show #!7 models
    7178 
    7179 > hide #!3 models
    7180 
    7181 > show #!3 models
    7182 
    7183 > hide #!7 models
    7184 
    7185 > show #!7 models
    7186 
    7187 > hide #!3 models
    7188 
    7189 > show #!2 models
    7190 
    7191 > hide #!2 models
    7192 
    7193 > show #!3 models
    7194 
    7195 > color zone #7 near #3 distance 6
    7196 
    7197 > hide #!7 models
    7198 
    7199 > show #!2 models
    7200 
    7201 > hide #!3 models
    7202 
    7203 > view list
    7204 
    7205 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7206 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7207 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7208 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7209 
    7210 > view side_overview
    7211 
    7212 > side.png
    7213 
    7214 Unknown command: side.png 
    7215 
    7216 > spng side.png
    7217 
    7218 > save side.png width 3000 height 3000 supersample 3 transparentBackground
    7219 > true
    7220 
    7221 > view bottom_overview
    7222 
    7223 > spng bottom.png
    7224 
    7225 > save bottom.png width 3000 height 3000 supersample 3 transparentBackground
    7226 > true
    7227 
    7228 > hide #!2 models
    7229 
    7230 > color #1/A #363600
    7231 
    7232 > color #1/B #ABAA00
    7233 
    7234 > color #1/E #005A4A
    7235 
    7236 > color #1/F #2CC9A6
    7237 
    7238 > color #1/C #1F2A44
    7239 
    7240 > color #1/D #5B7DBB
    7241 
    7242 > show #!1 models
    7243 
    7244 > color #3/A #363600
    7245 
    7246 > color #3/B #ABAA00
    7247 
    7248 > color #3/E #005A4A
    7249 
    7250 > color #3/F #2CC9A6
    7251 
    7252 > color #3/C #3F2A44
    7253 
    7254 > color #3/D #5B7DBB
    7255 
    7256 > show #!3 models
    7257 
    7258 > hide #!3 models
    7259 
    7260 > show #!2 models
    7261 
    7262 > hide #!1 models
    7263 
    7264 > color zone #2 near #1 distance 6
    7265 
    7266 > view list
    7267 
    7268 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7269 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7270 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7271 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7272 
    7273 > view bottom_overview
    7274 
    7275 > spng bottom.png
    7276 
    7277 > save bottom.png width 3000 height 3000 supersample 3 transparentBackground
    7278 > true
    7279 
    7280 Cell requested for row 0 is out of bounds for table with 17 rows! Resizing
    7281 table model. 
    7282 
    7283 > show #!1 models
    7284 
    7285 > hide #!2 models
    7286 
    7287 > show #!2 models
    7288 
    7289 > hide #!1 models
    7290 
    7291 > view side_overview
    7292 
    7293 > spng side.png
    7294 
    7295 > save side.png width 3000 height 3000 supersample 3 transparentBackground
    7296 > true
    7297 
    7298 > hide #!2 models
    7299 
    7300 > show #!1 models
    7301 
    7302 > show #!7 models
    7303 
    7304 > hide #!7 models
    7305 
    7306 > hide #!1 models
    7307 
    7308 > show #!1 models
    7309 
    7310 > show #!3 models
    7311 
    7312 > hide #!1 models
    7313 
    7314 > view list
    7315 
    7316 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7317 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7318 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7319 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7320 
    7321 > view side_overview
    7322 
    7323 > view list
    7324 
    7325 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7326 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7327 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7328 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7329 
    7330 > view side_overview
    7331 
    7332 > hide #2 cartoons
    7333 
    7334 > hide #3/2 cartoons
    7335 
    7336 > hide #3/3 cartoons
    7337 
    7338 > view list
    7339 
    7340 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7341 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7342 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7343 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7344 
    7345 > view side_overview
    7346 
    7347 [Repeated 1 time(s)]
    7348 
    7349 > spng protomer_P5P1.png
    7350 
    7351 > save protomer_P5P1.png width 3000 height 3000 supersample 3
    7352 > transparentBackground true
    7353 
    7354 > turn z 180
    7355 
    7356 [Repeated 3 time(s)]
    7357 
    7358 > turn y 180
    7359 
    7360 > spng protomer_P5P1_180.png
    7361 
    7362 > save protomer_P5P1_180.png width 3000 height 3000 supersample 3
    7363 > transparentBackground true
    7364 
    7365 > view list
    7366 
    7367 Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
    7368 RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
    7369 dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
    7370 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    7371 
    7372 > view side_overview
    7373 
    7374 > view side_overview_P5P1_dimer_3
    7375 
    7376 > view side_overview
    7377 
    7378 > shpw #3/3 cartoon
    7379 
    7380 Unknown command: shpw #3/3 cartoon 
    7381 
    7382 > show #3/3 cartoons
    7383 
    7384 > spng protomer_2_P5P1_180.png
    7385 
    7386 > save protomer_2_P5P1_180.png width 3000 height 3000 supersample 3
    7387 > transparentBackground true
    7388 
    7389 > save 20260203_interactions.cxs includeMaps true
    7390 
    7391 ——— End of log from Tue Feb 3 16:26:41 2026 ———
    7392 
    7393 > view name session-start
    7394 
    7395 opened ChimeraX session 
    7396 
    7397 > windowsize 1100 1000
    7398 
    7399 > windowsize 1000 1000
    7400 
    7401 > windowsize 9000 9000
    7402 
    7403 
    7404 ===== Log before crash end =====
    7405 
    7406 Log:
    7407 UCSF ChimeraX version: 1.10.1 (2025-07-24) 
    7408 © 2016-2025 Regents of the University of California. All rights reserved. 
    7409 
    7410 > open "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
    7411 > Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1/20260203_interactions.cxs"
    7412 
    7413 Opened 20260203_frankemnmap.mrc as #2, grid size 360,360,360, pixel 1.27,
    7414 shown at level 0.0765, step 1, values float32 
    7415 Opened cryosparc_P615_J1927_014_volume_map.mrc as #5, grid size 360,360,360,
    7416 pixel 1.27, shown at level 0.229, step 1, values float32 
    7417 Opened 20260203_frankemnmap.mrc copy as #7, grid size 360,360,360, pixel 1.27,
    7418 shown at level 0.0765, step 1, values float32 
    7419 Log from Tue Feb 3 16:26:41 2026UCSF ChimeraX version: 1.9 (2024-12-11) 
    7420 © 2016-2024 Regents of the University of California. All rights reserved. 
    7421 
    7422 > open "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
    7423 > Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy/analysis.cxs"
    7424 
    7425 Opened cryosparc_P615_J1783_volume_map.mrc as #8, grid size 360,360,360, pixel
    7426 1.27, shown at level 0.0846, step 1, values float32 
    7427 Opened cryosparc_P615_J1786_volume_map.mrc as #9, grid size 360,360,360, pixel
    7428 1.27, shown at level 0.0846, step 1, values float32 
    7429 Opened cryosparc_P615_J1843_volume_map.mrc as #10, grid size 360,360,360,
    7430 pixel 1.27, shown at level 0.0846, step 1, values float32 
    7431 Opened cryosparc_P615_J1846_volume_map.mrc as #11, grid size 360,360,360,
    7432 pixel 1.27, shown at level 0.0846, step 1, values float32 
    7433 Opened cryosparc_P615_J1930_volume_map.mrc as #14, grid size 360,360,360,
    7434 pixel 1.27, shown at level 0.09, step 1, values float32 
    7435 Opened cryosparc_P615_J1932_volume_map.mrc as #15, grid size 360,360,360,
    7436 pixel 1.27, shown at level 0.09, step 1, values float32 
    7437 Opened cryosparc_P615_J1934_volume_map.mrc as #16, grid size 360,360,360,
    7438 pixel 1.27, shown at level 0.09, step 1, values float32 
    7439 Opened cryosparc_P615_J1936_volume_map.mrc as #19, grid size 360,360,360,
    7440 pixel 1.27, shown at level 0.09, step 1, values float32 
    7441 Opened cryosparc_P615_J772_011_volume_map.mrc as #1, grid size 360,360,360,
    7442 pixel 1.27, shown at level 0.099, step 1, values float32 
    7443 Opened cryosparc_P615_J528_mask.mrc as #2, grid size 240,240,240, pixel 1.9,
    7444 shown at level 0.5, step 1, values float32 
    7445 Opened cryosparc_P615_J526_mask (1).mrc as #3, grid size 240,240,240, pixel
    7446 1.9, shown at level 0.5, step 1, values float32 
    7447 Opened cryosparc_P615_J453_mask (1).mrc as #4, grid size 360,360,360, pixel
    7448 1.27, shown at level 0.5, step 2, values float32 
    7449 Opened cryosparc_P615_J1711_volume_map.mrc as #5, grid size 360,360,360, pixel
    7450 1.27, shown at level 0.083, step 1, values float32 
    7451 Opened cryosparc_P615_J1714_volume_map.mrc as #6, grid size 360,360,360, pixel
    7452 1.27, shown at level 0.099, step 1, values float32 
    7453 Log from Mon Jan 19 11:45:42 2026 Startup Messages 
    7454 --- 
    7455 warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 
    7456 Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
    7457 that from NMRSTAR bundle 
    7458  
    7459 UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    7460 © 2016-2023 Regents of the University of California. All rights reserved. 
    7461 How to cite UCSF ChimeraX 
    7462 
    7463 > open
    7464 > /Volumes/Herc/20241024_ZH027_Hek_Herc1_PSMC5_PAAF1/relion/J448/Refine3D/lp-12/run_class001.mrc
    7465 
    7466 Opened run_class001.mrc as #1, grid size 360,360,360, pixel 1.27, shown at
    7467 level 0.00123, step 2, values float32 
    7468 
    7469 > volume #1 level 0.00391
    7470 
    7471 > volume #1 step 1
    7472 
    7473 > volume #1 level 0.004416
    7474 
    7475 > open
    7476 > /Users/lorenz.grundmann/Downloads/cryosparc_P713_J541_002_volume_map.mrc
    7477 
    7478 Opened cryosparc_P713_J541_002_volume_map.mrc as #2, grid size 256,256,256,
    7479 pixel 0.951, shown at level 0.0567, step 1, values float32 
    7480 
    7481 > hide #!1 models
    7482 
    7483 > view #2 clip false
    7484 
    7485 > volume #2 level 0.1409
    7486 
    7487 > open
    7488 > /Users/lorenz.grundmann/Downloads/fold_herc1_zinc/fold_herc1_zinc_model_0.cif
    7489 
    7490 Summary of feedback from opening
    7491 /Users/lorenz.grundmann/Downloads/fold_herc1_zinc/fold_herc1_zinc_model_0.cif 
    7492 --- 
    7493 note | Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 
    7494  
    7495 Chain information for fold_herc1_zinc_model_0.cif #3 
    7496 --- 
    7497 Chain | Description 
    7498 A | . 
    7499  
    7500 
    7501 > hide #!2 models
    7502 
    7503 > select /A:372-739
    7504 
    7505 2719 atoms, 2772 bonds, 368 residues, 1 model selected 
    7506 
    7507 > show sequence sel
    7508 
    7509 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    7510 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    7511 
    7512 > ui tool show "Show Sequence Viewer"
    7513 
    7514 > sequence chain /A
    7515 
    7516 Alignment identifier is 3/A 
    7517 No active region 
    7518 
    7519 > select /A:739
    7520 
    7521 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7522 
    7523 > select /A:420-739
    7524 
    7525 2348 atoms, 2392 bonds, 320 residues, 1 model selected 
    7526 
    7527 > select /A:372-739
    7528 
    7529 2719 atoms, 2772 bonds, 368 residues, 1 model selected 
    7530 
    7531 > select /A:1987-2027
    7532 
    7533 336 atoms, 339 bonds, 41 residues, 1 model selected 
    7534 
    7535 > select /A:2027-2358
    7536 
    7537 2603 atoms, 2653 bonds, 332 residues, 1 model selected 
    7538 
    7539 > select /A:2027-2193
    7540 
    7541 1304 atoms, 1335 bonds, 167 residues, 1 model selected 
    7542 
    7543 > open
    7544 > /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class001.mrc
    7545 
    7546 Opened run_it025_class001.mrc as #4, grid size 360,360,360, pixel 1.27, shown
    7547 at level 2.54e-06, step 2, values float32 
    7548 
    7549 > open
    7550 > /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class002.mrc
    7551 
    7552 Opened run_it025_class002.mrc as #5, grid size 360,360,360, pixel 1.27, shown
    7553 at level 2.38e-06, step 2, values float32 
    7554 
    7555 > open
    7556 > /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class003.mrc
    7557 
    7558 Opened run_it025_class003.mrc as #6, grid size 360,360,360, pixel 1.27, shown
    7559 at level 8.79e-07, step 2, values float32 
    7560 
    7561 > hide #3 models
    7562 
    7563 > view #5 clip false
    7564 
    7565 > volume #4 level 0.006078
    7566 
    7567 > volume #5 level 0.005325
    7568 
    7569 > volume #6 level 0.004012
    7570 
    7571 > open
    7572 > /Volumes/Herc/20230421_Herc_WT/model_building/model_finalisation/RLD1_PCNA/phenix/RealSpaceRefine_2/20250108_RLDs-
    7573 > fitted_real_space_refined_002.cif
    7574 
    7575 Summary of feedback from opening
    7576 /Volumes/Herc/20230421_Herc_WT/model_building/model_finalisation/RLD1_PCNA/phenix/RealSpaceRefine_2/20250108_RLDs-
    7577 fitted_real_space_refined_002.cif 
    7578 --- 
    7579 warnings | Skipping chem_comp category: Missing column 'type' near line 510 
    7580 Missing entity information. Treating each chain as a separate entity. 
    7581 Invalid residue range for struct_conf "1": invalid chain "1", near line 138 
    7582 Invalid residue range for struct_conf "2": invalid chain "1", near line 139 
    7583 Invalid residue range for struct_conf "3": invalid chain "1", near line 140 
    7584 Invalid residue range for struct_conf "4": invalid chain "1", near line 141 
    7585 Invalid residue range for struct_conf "5": invalid chain "1", near line 142 
    7586 31 messages similar to the above omitted 
    7587 Invalid sheet range for struct_sheet_range "1 1": invalid chain "1", near line
    7588 392 
    7589 Invalid sheet range for struct_sheet_range "2 1": invalid chain "1", near line
    7590 393 
    7591 Invalid sheet range for struct_sheet_range "3 1": invalid chain "1", near line
    7592 394 
    7593 Invalid sheet range for struct_sheet_range "4 1": invalid chain "1", near line
    7594 395 
    7595 Invalid sheet range for struct_sheet_range "5 1": invalid chain "1", near line
    7596 396 
    7597 112 messages similar to the above omitted 
    7598 Atom H1 is not in the residue template for VAL /1:512 
    7599 Atom H1 is not in the residue template for GLY /1:633 
    7600 Atom H1 is not in the residue template for THR /1:665 
    7601 Atom H1 is not in the residue template for SER /1:675 
    7602 Atom H3 is not in the residue template for PRO /1:705 
    7603 Atom H is not in the residue template for LYS /1:1384 
    7604 Atom H1 is not in the residue template for VAL /2:512 
    7605 Atom H1 is not in the residue template for GLY /2:633 
    7606 Atom H1 is not in the residue template for THR /2:665 
    7607 Too many hydrogens missing from residue template(s) to warn about 
    7608 Missing or incomplete sequence information. Inferred polymer connectivity. 
    7609  
    7610  
    7611 Chain information for 20250108_RLDs-fitted_real_space_refined_002.cif #7 
    7612 --- 
    7613 Chain | Description 
    7614 1 2 | No description available 
    7615 3 | No description available 
    7616 Ba Bb Bc | No description available 
    7617  
    7618 
    7619 > hide #!6 models
    7620 
    7621 > show sequence #7/1
    7622 
    7623 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    7624 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    7625 
    7626 > sequence chain #7/1
    7627 
    7628 Alignment identifier is 7/1 
    7629 
    7630 > select #7/1:1399
    7631 
    7632 24 atoms, 23 bonds, 1 residue, 1 model selected 
    7633 
    7634 > select #7/1
    7635 
    7636 5120 atoms, 5166 bonds, 7 pseudobonds, 344 residues, 2 models selected 
    7637 
    7638 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1783_volume_map.mrc
    7639 
    7640 Opened cryosparc_P615_J1783_volume_map.mrc as #8, grid size 360,360,360, pixel
    7641 1.27, shown at level 0.101, step 2, values float32 
    7642 
    7643 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1786_volume_map.mrc
    7644 
    7645 Opened cryosparc_P615_J1786_volume_map.mrc as #9, grid size 360,360,360, pixel
    7646 1.27, shown at level 0.0998, step 2, values float32 
    7647 
    7648 > hide #!7 models
    7649 
    7650 > volume #8 level 0.07925
    7651 
    7652 > volume #9 level 0.08883
    7653 
    7654 > volume #9 step 1
    7655 
    7656 > volume #8 step 1
    7657 
    7658 > volume #9 level 0.09891
    7659 
    7660 > volume #9 level 0.08782
    7661 
    7662 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1843_volume_map.mrc
    7663 
    7664 Opened cryosparc_P615_J1843_volume_map.mrc as #10, grid size 360,360,360,
    7665 pixel 1.27, shown at level 0.0985, step 2, values float32 
    7666 
    7667 > hide #!8 models
    7668 
    7669 > hide #!9 models
    7670 
    7671 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1846_volume_map.mrc
    7672 
    7673 Opened cryosparc_P615_J1846_volume_map.mrc as #11, grid size 360,360,360,
    7674 pixel 1.27, shown at level 0.103, step 2, values float32 
    7675 
    7676 > hide #!10 models
    7677 
    7678 > show #!10 models
    7679 
    7680 > hide #!11 models
    7681 
    7682 > show #!11 models
    7683 
    7684 > hide #!11 models
    7685 
    7686 > volume #11 step 1
    7687 
    7688 > volume #10 step 1
    7689 
    7690 > show #!11 models
    7691 
    7692 > hide #!11 models
    7693 
    7694 > show #!11 models
    7695 
    7696 > volume #10 level 0.07064
    7697 
    7698 > volume #10 level 0.09529
    7699 
    7700 > show #!8 models
    7701 
    7702 > show #!9 models
    7703 
    7704 > hide #!10 models
    7705 
    7706 > show #!10 models
    7707 
    7708 > show #!11 models
    7709 
    7710 > hide #!11 models
    7711 
    7712 > show #!11 models
    7713 
    7714 > hide #!10 models
    7715 
    7716 > hide #!11 models
    7717 
    7718 > volume #9 level 0.09589
    7719 
    7720 > volume #8 level 0.08615
    7721 
    7722 > volume #9 level 0.06767
    7723 
    7724 > volume #10 level 0.0835
    7725 
    7726 > volume #9 level 0.08178
    7727 
    7728 > show #!11 models
    7729 
    7730 > hide #!10 models
    7731 
    7732 > hide #!9 models
    7733 
    7734 > show #!10 models
    7735 
    7736 > volume #10 level 0.08457
    7737 
    7738 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1873_volume_map.mrc
    7739 
    7740 Opened cryosparc_P615_J1873_volume_map.mrc as #12, grid size 360,360,360,
    7741 pixel 1.27, shown at level 0.099, step 2, values float32 
    7742 
    7743 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1876_volume_map.mrc
    7744 
    7745 Opened cryosparc_P615_J1876_volume_map.mrc as #13, grid size 360,360,360,
    7746 pixel 1.27, shown at level 0.102, step 2, values float32 
    7747 
    7748 > volume #12 step 1
    7749 
    7750 > volume #13 step 1
    7751 
    7752 > volume #13 level 0.1007
    7753 
    7754 > show #!10 models
    7755 
    7756 > hide #!10 models
    7757 
    7758 > show #!10 models
    7759 
    7760 > hide #!10 models
    7761 
    7762 > show #!9 models
    7763 
    7764 > hide #!9 models
    7765 
    7766 > show #!9 models
    7767 
    7768 > hide #!9 models
    7769 
    7770 > show #!9 models
    7771 
    7772 > show #!8 models
    7773 
    7774 > hide #!9 models
    7775 
    7776 > hide #!8 models
    7777 
    7778 > show #!10 models
    7779 
    7780 > hide #!10 models
    7781 
    7782 > show #!9 models
    7783 
    7784 > show #!8 models
    7785 
    7786 > hide #!12 models
    7787 
    7788 > hide #!13 models
    7789 
    7790 > hide #!8 models
    7791 
    7792 > hide #!9 models
    7793 
    7794 > show #!10 models
    7795 
    7796 > show #!11 models
    7797 
    7798 > show #!13 models
    7799 
    7800 > hide #!13 models
    7801 
    7802 > show #!12 models
    7803 
    7804 > hide #!11 models
    7805 
    7806 > show #!9 models
    7807 
    7808 > hide #!10 models
    7809 
    7810 > hide #!9 models
    7811 
    7812 > show #!13 models
    7813 
    7814 > show #!10 models
    7815 
    7816 > show #!11 models
    7817 
    7818 > hide #!12 models
    7819 
    7820 > hide #!13 models
    7821 
    7822 > hide #!10 models
    7823 
    7824 > hide #!11 models
    7825 
    7826 > show #!9 models
    7827 
    7828 > show #!8 models
    7829 
    7830 > hide #!9 models
    7831 
    7832 > show #!9 models
    7833 
    7834 > hide #!8 models
    7835 
    7836 > show #!8 models
    7837 
    7838 > hide #!8 models
    7839 
    7840 > show #!8 models
    7841 
    7842 > hide #!8 models
    7843 
    7844 > show #!8 models
    7845 
    7846 > hide #!8 models
    7847 
    7848 > volume #9 level 0.09286
    7849 
    7850 > show #!8 models
    7851 
    7852 > hide #!9 models
    7853 
    7854 > show #!9 models
    7855 
    7856 > hide #!8 models
    7857 
    7858 > show #!8 models
    7859 
    7860 > hide #!8 models
    7861 
    7862 > show #!8 models
    7863 
    7864 > hide #!9 models
    7865 
    7866 > show #!9 models
    7867 
    7868 > hide #!8 models
    7869 
    7870 > show #!8 models
    7871 
    7872 > show #!10 models
    7873 
    7874 > hide #!9 models
    7875 
    7876 > hide #!8 models
    7877 
    7878 > show #!11 models
    7879 
    7880 > hide #!10 models
    7881 
    7882 > hide #!11 models
    7883 
    7884 > show #!8 models
    7885 
    7886 > show #!10 models
    7887 
    7888 > hide #!10 models
    7889 
    7890 > show #!10 models
    7891 
    7892 > hide #!8 models
    7893 
    7894 > show #!8 models
    7895 
    7896 > hide #!8 models
    7897 
    7898 > show #!8 models
    7899 
    7900 > show #!9 models
    7901 
    7902 > hide #!8 models
    7903 
    7904 > hide #!10 models
    7905 
    7906 > show #!10 models
    7907 
    7908 > hide #!10 models
    7909 
    7910 > show #!10 models
    7911 
    7912 > show #!8 models
    7913 
    7914 > hide #!9 models
    7915 
    7916 > show #!11 models
    7917 
    7918 > hide #!10 models
    7919 
    7920 > show #!10 models
    7921 
    7922 > hide #!11 models
    7923 
    7924 > show #!13 models
    7925 
    7926 > hide #!10 models
    7927 
    7928 > hide #!8 models
    7929 
    7930 > show #!10 models
    7931 
    7932 > close #12-13
    7933 
    7934 > show #!9 models
    7935 
    7936 > volume #9 level 0.09488
    7937 
    7938 > show #!8 models
    7939 
    7940 > volume #8 level 0.07039
    7941 
    7942 > hide #!9 models
    7943 
    7944 > hide #!10 models
    7945 
    7946 > show #!11 models
    7947 
    7948 > hide #!8 models
    7949 
    7950 > show #!8 models
    7951 
    7952 > hide #!8 models
    7953 
    7954 > show #!8 models
    7955 
    7956 > show #!7 models
    7957 
    7958 > hide #!7 models
    7959 
    7960 > show #!9 models
    7961 
    7962 > hide #!11 models
    7963 
    7964 > hide #!9 models
    7965 
    7966 > show #!9 models
    7967 
    7968 > hide #!8 models
    7969 
    7970 > show #!8 models
    7971 
    7972 > hide #!9 models
    7973 
    7974 > show #!9 models
    7975 
    7976 > hide #!8 models
    7977 
    7978 > show #!8 models
    7979 
    7980 > hide #!8 models
    7981 
    7982 > show #!8 models
    7983 
    7984 > hide #!8 models
    7985 
    7986 > show #!8 models
    7987 
    7988 > hide #!8 models
    7989 
    7990 > show #!8 models
    7991 
    7992 > hide #!8 models
    7993 
    7994 > show #!8 models
    7995 
    7996 > hide #!8 models
    7997 
    7998 > show #!8 models
    7999 
    8000 > hide #!8 models
    8001 
    8002 > show #!8 models
    8003 
    8004 > hide #!8 models
    8005 
    8006 > show #!8 models
    8007 
    8008 > hide #!8 models
    8009 
    8010 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1873_volume_map.mrc
    8011 
    8012 Opened cryosparc_P615_J1873_volume_map.mrc as #12, grid size 360,360,360,
    8013 pixel 1.27, shown at level 0.099, step 2, values float32 
    8014 
    8015 > hide #!9 models
    8016 
    8017 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1876_volume_map.mrc
    8018 
    8019 Opened cryosparc_P615_J1876_volume_map.mrc as #13, grid size 360,360,360,
    8020 pixel 1.27, shown at level 0.102, step 2, values float32 
    8021 
    8022 > volume #12 level 0.06835
    8023 
    8024 > volume #12 level 0.0958
    8025 
    8026 > volume #13 level 0.09404
    8027 
    8028 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1930_volume_map.mrc
    8029 
    8030 Opened cryosparc_P615_J1930_volume_map.mrc as #14, grid size 360,360,360,
    8031 pixel 1.27, shown at level 0.105, step 2, values float32 
    8032 
    8033 > hide #!12 models
    8034 
    8035 > hide #!13 models
    8036 
    8037 > volume #14 level 0.08558
    8038 
    8039 > volume #14 step 1
    8040 
    8041 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1932_volume_map.mrc
    8042 
    8043 Opened cryosparc_P615_J1932_volume_map.mrc as #15, grid size 360,360,360,
    8044 pixel 1.27, shown at level 0.0999, step 2, values float32 
    8045 
    8046 > hide #!14 models
    8047 
    8048 > volume #15 level 0.07598
    8049 
    8050 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1934_volume_map.mrc
    8051 
    8052 Opened cryosparc_P615_J1934_volume_map.mrc as #16, grid size 360,360,360,
    8053 pixel 1.27, shown at level 0.0991, step 2, values float32 
    8054 
    8055 > hide #!15 models
    8056 
    8057 > volume #16 level 0.08652
    8058 
    8059 > show #!15 models
    8060 
    8061 > show #!14 models
    8062 
    8063 > show #!13 models
    8064 
    8065 > hide #!14 models
    8066 
    8067 > hide #!15 models
    8068 
    8069 > hide #!16 models
    8070 
    8071 > show #!14 models
    8072 
    8073 > hide #!13 models
    8074 
    8075 > set bgColor white
    8076 
    8077 > hide #!14 models
    8078 
    8079 > color #14-16 darkgrey
    8080 
    8081 > show #!14 models
    8082 
    8083 > show #!15 models
    8084 
    8085 > show #!16 models
    8086 
    8087 > hide #!15 models
    8088 
    8089 > hide #!14 models
    8090 
    8091 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    8092 > model/20250505_P5P1-SPRY-RLD1_isolde_clean.pdb
    8093 
    8094 Chain information for 20250505_P5P1-SPRY-RLD1_isolde_clean.pdb #17 
    8095 --- 
    8096 Chain | Description 
    8097 1 | No description available 
    8098 A | No description available 
    8099 B | No description available 
    8100  
    8101 
    8102 > hide #!16 models
    8103 
    8104 > show #!16 models
    8105 
    8106 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    8107 > model/20250902_composite_chain-fix.pdb
    8108 
    8109 Chain information for 20250902_composite_chain-fix.pdb #18 
    8110 --- 
    8111 Chain | Description 
    8112 1 2 3 | No description available 
    8113 A I K | No description available 
    8114 B J L | No description available 
    8115  
    8116 
    8117 > hide #!16 models
    8118 
    8119 > show #17#!18 cartoons
    8120 
    8121 > hide #17#!18 atoms
    8122 
    8123 > show #!14 models
    8124 
    8125 > show #!15 models
    8126 
    8127 > hide #!15 models
    8128 
    8129 > hide #!14 models
    8130 
    8131 > show #!15 models
    8132 
    8133 > show #!16 models
    8134 
    8135 > hide #!15 models
    8136 
    8137 > hide #!16 models
    8138 
    8139 > select #18/1:3783
    8140 
    8141 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8142 
    8143 > select up
    8144 
    8145 98 atoms, 97 bonds, 6 residues, 1 model selected 
    8146 
    8147 > select up
    8148 
    8149 7957 atoms, 8046 bonds, 538 residues, 1 model selected 
    8150 
    8151 > select up
    8152 
    8153 8105 atoms, 8193 bonds, 547 residues, 1 model selected 
    8154 
    8155 > select up
    8156 
    8157 10637 atoms, 10758 bonds, 717 residues, 1 model selected 
    8158 
    8159 > select up
    8160 
    8161 10868 atoms, 10992 bonds, 732 residues, 1 model selected 
    8162 
    8163 > select up
    8164 
    8165 14205 atoms, 14374 bonds, 943 residues, 1 model selected 
    8166 
    8167 > select up
    8168 
    8169 14286 atoms, 14455 bonds, 948 residues, 1 model selected 
    8170 
    8171 > select up
    8172 
    8173 21639 atoms, 21880 bonds, 1408 residues, 1 model selected 
    8174 
    8175 > select #18/!
    8176 
    8177 Expected an objects specifier or a keyword 
    8178 
    8179 > select #18/1
    8180 
    8181 54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected 
    8182 
    8183 > intersect dimer 1, 2 occpued, dimer 3 empty
    8184 
    8185 Unknown command: intersect dimer 1, 2 occpued, dimer 3 empty 
    8186 
    8187 > color sel #d31340ff
    8188 
    8189 > show #!16 models
    8190 
    8191 > color sel #b2b2b2
    8192 
    8193 > color sel #F6921E
    8194 
    8195 > select up
    8196 
    8197 193662 atoms, 195518 bonds, 105 pseudobonds, 12558 residues, 2 models selected 
    8198 
    8199 > select up
    8200 
    8201 193662 atoms, 195518 bonds, 105 pseudobonds, 12558 residues, 2 models selected 
    8202 
    8203 > select #18/1:3561
    8204 
    8205 19 atoms, 18 bonds, 1 residue, 1 model selected 
    8206 
    8207 > solor #18/1 #663399
    8208 
    8209 Unknown command: solor #18/1 #663399 
    8210 
    8211 > color #18/1 #663399
    8212 
    8213 > select /A:2027-2193
    8214 
    8215 1304 atoms, 1335 bonds, 167 residues, 1 model selected 
    8216 
    8217 > select #18/1
    8218 
    8219 54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected 
    8220 
    8221 > color sel #b2b2b2
    8222 
    8223 > select #18/3
    8224 
    8225 54175 atoms, 54694 bonds, 35 pseudobonds, 3516 residues, 2 models selected 
    8226 
    8227 > color sel #6120AC
    8228 
    8229 > select #18/2:3560
    8230 
    8231 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8232 
    8233 > select #18/2
    8234 
    8235 54175 atoms, 54709 bonds, 35 pseudobonds, 3516 residues, 2 models selected 
    8236 
    8237 > color sel #C691FF
    8238 
    8239 > hide #!16 models
    8240 
    8241 > hide #17 models
    8242 
    8243 > select #18/A,B
    8244 
    8245 10283 atoms, 10366 bonds, 669 residues, 1 model selected 
    8246 
    8247 > color sel #abd9e533
    8248 
    8249 > color sel #abd9e533 transparency 0
    8250 
    8251 > select #18/B
    8252 
    8253 4397 atoms, 4428 bonds, 277 residues, 1 model selected 
    8254 
    8255 > color sel cyan
    8256 
    8257 > color sel light blue
    8258 
    8259 > color sel blue
    8260 
    8261 > color sel sky blue
    8262 
    8263 > color sel powder blue
    8264 
    8265 > color sel steel blue
    8266 
    8267 > select #18/l,K
    8268 
    8269 10283 atoms, 10366 bonds, 669 residues, 1 model selected 
    8270 
    8271 > color sel #ffb1fd33
    8272 
    8273 > color sel #ffb1fd33 transparency 0
    8274 
    8275 > select #18/L:278
    8276 
    8277 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8278 
    8279 > color #18/L orchid
    8280 
    8281 > color #18/I,J sea green
    8282 
    8283 > select #18/1:192
    8284 
    8285 16 atoms, 15 bonds, 1 residue, 1 model selected 
    8286 
    8287 > select #18/I:378
    8288 
    8289 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8290 
    8291 > color #18/I light green
    8292 
    8293 > select up
    8294 
    8295 93 atoms, 93 bonds, 6 residues, 1 model selected 
    8296 
    8297 > select up
    8298 
    8299 5886 atoms, 5938 bonds, 392 residues, 1 model selected 
    8300 
    8301 > color #18/1 #b2b2b2 transparency 80
    8302 
    8303 > color #18/2 #C691FF transparency 80
    8304 
    8305 > color #18/3 #6120AC transparency 80
    8306 
    8307 > show #!14 models
    8308 
    8309 > color zone #14 near #18 distance 8
    8310 
    8311 > hide #!18 models
    8312 
    8313 > color #14-16 white transparency 80
    8314 
    8315 > color zone #14 near #18 distance 8
    8316 
    8317 > color #14-16 white transparency 100
    8318 
    8319 > color zone #14 near #18 distance 8
    8320 
    8321 > color zone #14 near #18 distance 10
    8322 
    8323 [Repeated 1 time(s)]
    8324 
    8325 > color zone #14 near #18 distance 12
    8326 
    8327 > color zone #14 near #18 distance 14
    8328 
    8329 > color zone #14 near #18 distance 20
    8330 
    8331 > show #!18 models
    8332 
    8333 > hide #!14 models
    8334 
    8335 > show sel atoms
    8336 
    8337 > hide sel atoms
    8338 
    8339 [Repeated 1 time(s)]
    8340 
    8341 > show #18
    8342 
    8343 > select #18/A,B,C
    8344 
    8345 10379 atoms, 10461 bonds, 670 residues, 1 model selected 
    8346 
    8347 > select #18/A,H,D
    8348 
    8349 6078 atoms, 6128 bonds, 394 residues, 1 model selected 
    8350 
    8351 > delete sel]
    8352 
    8353 Missing or invalid "atoms" argument: only initial part "sel" of atom specifier
    8354 valid 
    8355 
    8356 > delete sel
    8357 
    8358 > undo
    8359 
    8360 Undo failed, probably because structures have been modified. 
    8361 
    8362 > close #18
    8363 
    8364 > open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
    8365 > model/20250902_composite_chain-fix.pdb
    8366 
    8367 Chain information for 20250902_composite_chain-fix.pdb #18 
    8368 --- 
    8369 Chain | Description 
    8370 1 2 3 | No description available 
    8371 A I K | No description available 
    8372 B J L | No description available 
    8373  
    8374 
    8375 > color #18/1 #663399
    8376 
    8377 > select /A:2027-2193
    8378 
    8379 1304 atoms, 1335 bonds, 167 residues, 1 model selected 
    8380 
    8381 > select #18/1
    8382 
    8383 54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected 
    8384 
    8385 > color sel #b2b2b2
    8386 
    8387 > select #18/3
    8388 
    8389 54175 atoms, 54694 bonds, 35 pseudobonds, 3516 residues, 2 models selected 
    8390 
    8391 > color sel #6120AC
    8392 
    8393 > select #18/2
    8394 
    8395 54175 atoms, 54709 bonds, 35 pseudobonds, 3516 residues, 2 models selected 
    8396 
    8397 > color sel #C691FF
    8398 
    8399 > select #18/A,B
    8400 
    8401 10283 atoms, 10366 bonds, 669 residues, 1 model selected 
    8402 
    8403 > color sel #abd9e533
    8404 
    8405 > color sel #abd9e533 transparency 0
    8406 
    8407 > select #18/B
    8408 
    8409 4397 atoms, 4428 bonds, 277 residues, 1 model selected 
    8410 
    8411 > color sel cyan
    8412 
    8413 > color sel light blue
    8414 
    8415 > color sel blue
    8416 
    8417 > color sel sky blue
    8418 
    8419 > color sel powder blue
    8420 
    8421 > color sel steel blue
    8422 
    8423 > select #18/l,K
    8424 
    8425 10283 atoms, 10366 bonds, 669 residues, 1 model selected 
    8426 
    8427 > color sel #ffb1fd33
    8428 
    8429 > color sel #ffb1fd33 transparency 0
    8430 
    8431 > color #18/L orchid
    8432 
    8433 > color #18/I,J sea green
    8434 
    8435 > color #18/I light green
    8436 
    8437 > color #18/1 #b2b2b2 transparency 80
    8438 
    8439 > color #18/2 #C691FF transparency 80
    8440 
    8441 > color #18/3 #6120AC transparency 80
    8442 
    8443 > select #18/C,D,H
    8444 
    8445 288 atoms, 285 bonds, 3 residues, 1 model selected 
    8446 
    8447 > delete sel
    8448 
    8449 > show #!14 models
    8450 
    8451 > show #!15 models
    8452 
    8453 > hide #!14 models
    8454 
    8455 > hide #!15 models
    8456 
    8457 > show #!14 models
    8458 
    8459 > hide #!14 models
    8460 
    8461 > show #!15 models
    8462 
    8463 > hide #!18 models
    8464 
    8465 > show #!18 models
    8466 
    8467 > color #14-16 white transparecny 80
    8468 
    8469 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    8470 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    8471 
    8472 > color #14-16 white transparency 80
    8473 
    8474 > color #14-16 white transparency 100
    8475 
    8476 > color #14-16 white transparency 80
    8477 
    8478 > show #!14 models
    8479 
    8480 > hide #!15 models
    8481 
    8482 > color zone #14 near #18 distance 20
    8483 
    8484 > hide #!18 models
    8485 
    8486 > show #!15 models
    8487 
    8488 > hide #!14 models
    8489 
    8490 > show #!18 models
    8491 
    8492 > color zone #14 near #18 & ~/I,J distance 20
    8493 
    8494 > color zone #14 near #18 distance 20
    8495 
    8496 > color zone #15 near #18 & ~/I,J distance 20
    8497 
    8498 > show #!16 models
    8499 
    8500 > hide #!15 models
    8501 
    8502 > color zone #15 near #18 & ~/K,L distance 20
    8503 
    8504 > color #14-16 white transparency 80
    8505 
    8506 > color zone #14 near #18 distance 20
    8507 
    8508 > color zone #15 near #18 & ~/I,J distance 20
    8509 
    8510 > color zone #16 near #18 & ~/K,L distance 20
    8511 
    8512 > hide #!18 models
    8513 
    8514 > color #16 white transparency 80
    8515 
    8516 > color zone #16 near #18 & ~/I,J,K,L distance 20
    8517 
    8518 > show #!15 models
    8519 
    8520 > show #!14 models
    8521 
    8522 > hide #!14 models
    8523 
    8524 > show #!14 models
    8525 
    8526 > hide #!15 models
    8527 
    8528 > hide #!16 models
    8529 
    8530 > hide #!14 models
    8531 
    8532 > show #!14 models
    8533 
    8534 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1936_volume_map.mrc
    8535 
    8536 Opened cryosparc_P615_J1936_volume_map.mrc as #19, grid size 360,360,360,
    8537 pixel 1.27, shown at level 0.104, step 2, values float32 
    8538 
    8539 > hide #!14 models
    8540 
    8541 > show #!14 models
    8542 
    8543 > volume #19 step 1
    8544 
    8545 > volume #16 step 1
    8546 
    8547 > volume #15 step 1
    8548 
    8549 > volume #13 step 1
    8550 
    8551 > volume #19 level 0.08332
    8552 
    8553 > hide #!14 models
    8554 
    8555 > show #!18 models
    8556 
    8557 > color zone #19 near #18 & ~/K,L distance 20
    8558 
    8559 > hide #!19 models
    8560 
    8561 > show #!19 models
    8562 
    8563 > hide #!18 models
    8564 
    8565 > show #!18 models
    8566 
    8567 > hide #!18 models
    8568 
    8569 > volume #19 level 0.1091
    8570 
    8571 > volume #19 level 0.0865
    8572 
    8573 > color #19 white transparency 80
    8574 
    8575 > color zone #19 near #18 & ~/K,L distance 20
    8576 
    8577 > color #19 white transparency 100
    8578 
    8579 > color zone #19 near #18 & ~/K,L distance 20
    8580 
    8581 > graphics silhouettes true width 4
    8582 
    8583 > graphics silhouettes true width 2
    8584 
    8585 > volume #19 level 0.1
    8586 
    8587 > volume #16 level 0.1
    8588 
    8589 > show #!16 models
    8590 
    8591 > hide #!19 models
    8592 
    8593 > show #!15 models
    8594 
    8595 > hide #!16 models
    8596 
    8597 > volume #15 level 0.1
    8598 
    8599 > volume #14 level 0.1
    8600 
    8601 > show #!14 models
    8602 
    8603 > hide #!15 models
    8604 
    8605 > volume #14 level 0.09
    8606 
    8607 > show #!15 models
    8608 
    8609 > hide #!14 models
    8610 
    8611 > volume #15 level 0.9
    8612 
    8613 > volume #15 level 0.09
    8614 
    8615 > show #!16 models
    8616 
    8617 > hide #!15 models
    8618 
    8619 > volume #16 level 0.09
    8620 
    8621 > volume #19 level 0.09
    8622 
    8623 > show #!19 models
    8624 
    8625 > hide #!16 models
    8626 
    8627 > show #!16 models
    8628 
    8629 > hide #!16 models
    8630 
    8631 > show #!16 models
    8632 
    8633 > hide #!16 models
    8634 
    8635 > show #!16 models
    8636 
    8637 > hide #!16 models
    8638 
    8639 > show #!16 models
    8640 
    8641 > hide #!19 models
    8642 
    8643 > show #!19 models
    8644 
    8645 > hide #!19 models
    8646 
    8647 > show #!19 models
    8648 
    8649 > hide #!19 models
    8650 
    8651 > show #!19 models
    8652 
    8653 > hide #!19 models
    8654 
    8655 > show #!19 models
    8656 
    8657 > hide #!16 models
    8658 
    8659 > show #!16 models
    8660 
    8661 > hide #!19 models
    8662 
    8663 > show #!15 models
    8664 
    8665 > hide #!15 models
    8666 
    8667 > show #!15 models
    8668 
    8669 > hide #!15 models
    8670 
    8671 > show #!15 models
    8672 
    8673 > hide #!15 models
    8674 
    8675 > show #!15 models
    8676 
    8677 > hide #!15 models
    8678 
    8679 > show #!15 models
    8680 
    8681 > hide #!15 models
    8682 
    8683 > show #!15 models
    8684 
    8685 > show #!19 models
    8686 
    8687 > show #!18 models
    8688 
    8689 > hide #!19 models
    8690 
    8691 > hide #!16 models
    8692 
    8693 > hide #!15 models
    8694 
    8695 > show #!18 cartoons
    8696 
    8697 > hide #!18 atoms
    8698 
    8699 > color #18/A ABAA00
    8700 
    8701 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    8702 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    8703 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    8704 
    8705 > color #18/A #ABAA00
    8706 
    8707 > color #18/B #ABAA00
    8708 
    8709 > color #18/A #363600
    8710 
    8711 > color #18/K 005A4A
    8712 
    8713 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    8714 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    8715 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    8716 
    8717 > color #18/K #005A4A
    8718 
    8719 > color #18/L #2CC9A6
    8720 
    8721 > color #18/I #1F2A44
    8722 
    8723 > color #18/J #5B7DBB
    8724 
    8725 > color #14-16,19 white transparency 80
    8726 
    8727 > color zone #19 near #18 & ~/K,L distance 20
    8728 
    8729 > color zone #16 near #18 & ~/I,J,K,L distance 20
    8730 
    8731 > color zone #15 near #18 & ~/I,J distance 20
    8732 
    8733 > color zone #14 near #18 distance 20
    8734 
    8735 > show #!19 models
    8736 
    8737 > hide #!19 models
    8738 
    8739 > show #!19 models
    8740 
    8741 > hide #!18 models
    8742 
    8743 > show #!16 models
    8744 
    8745 > hide #!19 models
    8746 
    8747 > show #!15 models
    8748 
    8749 > hide #!16 models
    8750 
    8751 > show #!14 models
    8752 
    8753 > hide #!15 models
    8754 
    8755 > show #!15 models
    8756 
    8757 > hide #!14 models
    8758 
    8759 > show #!16 models
    8760 
    8761 > hide #!15 models
    8762 
    8763 > show #!19 models
    8764 
    8765 > hide #!19 models
    8766 
    8767 > show #!15 models
    8768 
    8769 > hide #!15 models
    8770 
    8771 > hide #!16 models
    8772 
    8773 > show #!14 models
    8774 
    8775 > view name bottom_overview
    8776 
    8777 > close #3#1-2,4-7
    8778 
    8779 > open
    8780 > /Users/lorenz.grundmann/Downloads/cryosparc_P615_J772_011_volume_map.mrc
    8781 
    8782 Opened cryosparc_P615_J772_011_volume_map.mrc as #1, grid size 360,360,360,
    8783 pixel 1.27, shown at level 0.099, step 2, values float32 
    8784 
    8785 > hide #!14 models
    8786 
    8787 > volume #1 step 1
    8788 
    8789 > color #1 darkgrey
    8790 
    8791 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J528_mask.mrc
    8792 
    8793 Opened cryosparc_P615_J528_mask.mrc as #2, grid size 240,240,240, pixel 1.9,
    8794 shown at level 5e-05, step 1, values float32 
    8795 
    8796 > volume #2 level 0.3808
    8797 
    8798 > open "/Users/lorenz.grundmann/Downloads/cryosparc_P615_J526_mask (1).mrc"
    8799 
    8800 Opened cryosparc_P615_J526_mask (1).mrc as #3, grid size 240,240,240, pixel
    8801 1.9, shown at level 5e-05, step 1, values float32 
    8802 
    8803 > open "/Users/lorenz.grundmann/Downloads/cryosparc_P615_J453_mask (1).mrc"
    8804 
    8805 Opened cryosparc_P615_J453_mask (1).mrc as #4, grid size 360,360,360, pixel
    8806 1.27, shown at level 5e-05, step 2, values float32 
    8807 
    8808 > hide #!2 models
    8809 
    8810 > hide #!3 models
    8811 
    8812 > hide #!4 models
    8813 
    8814 > show #!18 models
    8815 
    8816 > hide #!1 models
    8817 
    8818 > show #!2 models
    8819 
    8820 > hide #!2 models
    8821 
    8822 > show #!2 models
    8823 
    8824 > hide #!2 models
    8825 
    8826 > show #!1 models
    8827 
    8828 > hide #!1 models
    8829 
    8830 > show #!2 models
    8831 
    8832 > hide #!2 models
    8833 
    8834 > show #!3 models
    8835 
    8836 > hide #!3 models
    8837 
    8838 > show #!4 models
    8839 
    8840 > show #!1 models
    8841 
    8842 > hide #!4 models
    8843 
    8844 > show #!16 models
    8845 
    8846 > hide #!16 models
    8847 
    8848 > show #!4 models
    8849 
    8850 > hide #!4 models
    8851 
    8852 > show #!4 models
    8853 
    8854 > hide #!1 models
    8855 
    8856 > volume #2 level 0.5
    8857 
    8858 > volume #3 level 0.5
    8859 
    8860 > volume #4 level 0.5
    8861 
    8862 > color #4 #707000 transparency 80
    8863 
    8864 > show #!2 models
    8865 
    8866 > hide #!4 models
    8867 
    8868 > color #2 #168E78 transparency 80
    8869 
    8870 > show #!4 models
    8871 
    8872 > hide #!4 models
    8873 
    8874 > show #!3 models
    8875 
    8876 > hide #!2 models
    8877 
    8878 > color #3 #168E78 transparency 80
    8879 
    8880 > color #2 #3D5480 transparency 80
    8881 
    8882 > show #!2 models
    8883 
    8884 > show #!4 models
    8885 
    8886 > hide #!18 models
    8887 
    8888 > show #!1 models
    8889 
    8890 > view name side_overview
    8891 
    8892 > turn x 90
    8893 
    8894 [Repeated 3 time(s)]
    8895 
    8896 > turn x -90
    8897 
    8898 > turn z -45
    8899 
    8900 > turn z -120
    8901 
    8902 [Repeated 2 time(s)]
    8903 
    8904 > turn z 120
    8905 
    8906 > view name bottom_overview
    8907 
    8908 > show #!15 models
    8909 
    8910 > hide #!15 models
    8911 
    8912 > show #!15 models
    8913 
    8914 > hide #!15 models
    8915 
    8916 > cd "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
    8917 > Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy"
    8918 
    8919 Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
    8920 Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy 
    8921 
    8922 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    8923 > transparentBackground true
    8924 
    8925 > view list
    8926 
    8927 Named views: bottom_overview, side_overview 
    8928 
    8929 > view side_overview
    8930 
    8931 > save J772_consensus_side.png width 3000 height 3000 supersample 3
    8932 > transparentBackground true
    8933 
    8934 > graphics silhouettes true width 4
    8935 
    8936 > view bottom_overview
    8937 
    8938 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    8939 > transparentBackground true
    8940 
    8941 > view side_overview
    8942 
    8943 > save J772_consensus_side.png width 3000 height 3000 supersample 3
    8944 > transparentBackground true
    8945 
    8946 > lighting full
    8947 
    8948 > lighting soft
    8949 
    8950 > save J772_consensus_side.png width 3000 height 3000 supersample 3
    8951 > transparentBackground true
    8952 
    8953 > view bottom_overview
    8954 
    8955 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    8956 > transparentBackground true
    8957 
    8958 > hide #!1 models
    8959 
    8960 > hide #!2 models
    8961 
    8962 > hide #!3 models
    8963 
    8964 > hide #!4 models
    8965 
    8966 > show #!14 models
    8967 
    8968 > show #!2 models
    8969 
    8970 > hide #!2 models
    8971 
    8972 > hide all models
    8973 
    8974 > shoe #14 model
    8975 
    8976 Unknown command: shoe #14 model 
    8977 
    8978 > view bottom overview
    8979 
    8980 Expected an objects specifier or a view name or a keyword 
    8981 
    8982 > view bottom_overview
    8983 
    8984 > show #14 models
    8985 
    8986 > save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
    8987 > 3 transparentBackground true
    8988 
    8989 > show #!15 models
    8990 
    8991 > hide #!14 models
    8992 
    8993 > show #!14 models
    8994 
    8995 > hide #!15 models
    8996 
    8997 > hide #14 models
    8998 
    8999 > show #15 models
    9000 
    9001 > save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
    9002 > transparentBackground true
    9003 
    9004 > hide #15 models
    9005 
    9006 > show #16 models
    9007 
    9008 > save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
    9009 > transparentBackground true
    9010 
    9011 > show #!19 models
    9012 
    9013 > hide #!19 models
    9014 
    9015 > hide #16 models
    9016 
    9017 > show #19 models
    9018 
    9019 > save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
    9020 > transparentBackground true
    9021 
    9022 > hide all models
    9023 
    9024 > view side_overview
    9025 
    9026 > show #14 models
    9027 
    9028 > save J1930_arm-1-2-3_occupied_side.png width 3000 height 3000 supersample 3
    9029 > transparentBackground true
    9030 
    9031 > hide #14 models
    9032 
    9033 > show #15 models
    9034 
    9035 > save J1932_arm-1-2_occupied_side.png width 3000 height 3000 supersample 3
    9036 > transparentBackground true
    9037 
    9038 > hide #15 models
    9039 
    9040 > show #16 models
    9041 
    9042 > save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
    9043 > transparentBackground true
    9044 
    9045 > hide #16 models
    9046 
    9047 > show #19 models
    9048 
    9049 > save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
    9050 > transparentBackground true
    9051 
    9052 > save occupancy_analysis.cxs includeMaps true
    9053 
    9054 > hide #!19 models
    9055 
    9056 > show #!16 models
    9057 
    9058 > hide #!16 models
    9059 
    9060 > show #!19 models
    9061 
    9062 > color #4 #707000 transparency 20
    9063 
    9064 > color #2 #168E78 transparency 20
    9065 
    9066 > color #2 #3D5480 transparency 20
    9067 
    9068 > color #18/3 #6120AC transparency 20
    9069 
    9070 > color #18/1 #b2b2b2 transparency 20
    9071 
    9072 > color #18/2 #C691FF transparency 20
    9073 
    9074 > color #18/A #ABAA00
    9075 
    9076 > color #18/B #ABAA00
    9077 
    9078 > color #18/A #363600
    9079 
    9080 > color #18/K #005A4A
    9081 
    9082 > color #18/L #2CC9A6
    9083 
    9084 > color #18/I #1F2A44
    9085 
    9086 > color #18/J #5B7DBB
    9087 
    9088 > color zone #14 near #18 distance 20
    9089 
    9090 > color #14-16,19 white transparency 20
    9091 
    9092 > color zone #19 near #18 & ~/K,L distance 20
    9093 
    9094 > color zone #16 near #18 & ~/I,J,K,L distance 20
    9095 
    9096 > color zone #15 near #18 & ~/I,J distance 20
    9097 
    9098 > color zone #14 near #18 distance 20
    9099 
    9100 > show #!1 models
    9101 
    9102 > show #!2 models
    9103 
    9104 > show #!3 models
    9105 
    9106 > show #!4 models
    9107 
    9108 > show #1-4 models
    9109 
    9110 > hide #!19 models
    9111 
    9112 > hide all models
    9113 
    9114 > view bottom_overview
    9115 
    9116 > show #1-4 models
    9117 
    9118 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    9119 > transparentBackground true
    9120 
    9121 > show #14 models
    9122 
    9123 > save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
    9124 > 3 transparentBackground true
    9125 
    9126 > hide #14 models
    9127 
    9128 > show #15 models
    9129 
    9130 > save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
    9131 > transparentBackground true
    9132 
    9133 > hide #15 models
    9134 
    9135 > show #16 models
    9136 
    9137 > save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
    9138 > transparentBackground true
    9139 
    9140 > hide #16 models
    9141 
    9142 > show #19 models
    9143 
    9144 > save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
    9145 > transparentBackground true
    9146 
    9147 > Make the figures
    9148 
    9149 Unknown command: Make the figures 
    9150 
    9151 > hide all models
    9152 
    9153 > view bottom_overview
    9154 
    9155 > show #1-4 models
    9156 
    9157 > hide all models
    9158 
    9159 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    9160 > transparentBackground true
    9161 
    9162 > show #14 models
    9163 
    9164 > save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
    9165 > 3 transparentBackground true
    9166 
    9167 > hide #14 models
    9168 
    9169 > show #15 models
    9170 
    9171 > save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
    9172 > transparentBackground true
    9173 
    9174 > hide #15 models
    9175 
    9176 > show #16 models
    9177 
    9178 > save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
    9179 > transparentBackground true
    9180 
    9181 > hide #16 models
    9182 
    9183 > show #19 models
    9184 
    9185 > save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
    9186 > transparentBackground true
    9187 
    9188 > hide all models
    9189 
    9190 > view bottom_overview
    9191 
    9192 > show #1-4 models
    9193 
    9194 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    9195 > transparentBackground true
    9196 
    9197 > hide all models
    9198 
    9199 > color #4 #707000 transparency 50
    9200 
    9201 > color #2 #168E78 transparency 50
    9202 
    9203 > color #2 #3D5480 transparency 50
    9204 
    9205 > hide all models
    9206 
    9207 > view bottom_overview
    9208 
    9209 > show #1-4 models
    9210 
    9211 > save J772_consensus_bottom.png width 3000 height 3000 supersample 3
    9212 > transparentBackground true
    9213 
    9214 > hide all models
    9215 
    9216 > show #14 models
    9217 
    9218 > save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
    9219 > 3 transparentBackground true
    9220 
    9221 > hide #14 models
    9222 
    9223 > show #15 models
    9224 
    9225 > save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
    9226 > transparentBackground true
    9227 
    9228 > hide #15 models
    9229 
    9230 > show #16 models
    9231 
    9232 > save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
    9233 > transparentBackground true
    9234 
    9235 > hide #16 models
    9236 
    9237 > show #19 models
    9238 
    9239 > save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
    9240 > transparentBackground true
    9241 
    9242 > hide all models
    9243 
    9244 > view side_overview
    9245 
    9246 > show #1-4 models
    9247 
    9248 > save J772_consensus_side.png width 3000 height 3000 supersample 3
    9249 > transparentBackground true
    9250 
    9251 > hide all models
    9252 
    9253 > show #14 models
    9254 
    9255 > save J1930_arm-1-2-3_occupied_side.png width 3000 height 3000 supersample 3
    9256 > transparentBackground true
    9257 
    9258 > hide #14 models
    9259 
    9260 > show #15 models
    9261 
    9262 > save J1932_arm-1-2_occupied_side.png width 3000 height 3000 supersample 3
    9263 > transparentBackground true
    9264 
    9265 > hide #15 models
    9266 
    9267 > show #16 models
    9268 
    9269 > save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
    9270 > transparentBackground true
    9271 
    9272 > hide #16 models
    9273 
    9274 > show #19 models
    9275 
    9276 > save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
    9277 > transparentBackground true
    9278 
    9279 > hide #!19 models
    9280 
    9281 > show #!4 models
    9282 
    9283 > hide #!4 models
    9284 
    9285 > show #8 models
    9286 
    9287 > show #8-16 models
    9288 
    9289 > hide #!14-16 target m
    9290 
    9291 > hide #!10-13 target m
    9292 
    9293 > hide #!9 models
    9294 
    9295 > hide #!8 models
    9296 
    9297 > show #!9 models
    9298 
    9299 > show #!8 models
    9300 
    9301 > hide #!9 models
    9302 
    9303 > show #!9 models
    9304 
    9305 > hide #!8 models
    9306 
    9307 > show #!8 models
    9308 
    9309 > hide #!8 models
    9310 
    9311 > show #!8 models
    9312 
    9313 > volume #8 level 0.0949
    9314 
    9315 > volume #9 level 0.0846
    9316 
    9317 > volume #8 level 0.0846
    9318 
    9319 > volume #11 level 0.0846
    9320 
    9321 > hide #!11 models
    9322 
    9323 > show #!11 models
    9324 
    9325 > hide #!11 models
    9326 
    9327 > show #!11 models
    9328 
    9329 > show #!12 models
    9330 
    9331 > hide #!11 models
    9332 
    9333 > hide #!8 models
    9334 
    9335 > hide #!9 models
    9336 
    9337 > show #!13 models
    9338 
    9339 > hide #!12 models
    9340 
    9341 > show #!11 models
    9342 
    9343 > hide #!11 models
    9344 
    9345 > close #12-13
    9346 
    9347 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1711_volume_map.mrc
    9348 
    9349 Opened cryosparc_P615_J1711_volume_map.mrc as #5, grid size 360,360,360, pixel
    9350 1.27, shown at level 0.0987, step 2, values float32 
    9351 
    9352 > open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1714_volume_map.mrc
    9353 
    9354 Opened cryosparc_P615_J1714_volume_map.mrc as #6, grid size 360,360,360, pixel
    9355 1.27, shown at level 0.099, step 2, values float32 
    9356 
    9357 > hide #!6 models
    9358 
    9359 > show #!6 models
    9360 
    9361 > volume #5 step 1
    9362 
    9363 > volume #6 step 1
    9364 
    9365 > volume #5 level 0.08297
    9366 
    9367 > show #!18 models
    9368 
    9369 > hide #!5 models
    9370 
    9371 > show #!5 models
    9372 
    9373 > color #5 darkgrey
    9374 
    9375 > color #5 near #18/A,B dist 6
    9376 
    9377 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    9378 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    9379 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    9380 
    9381 > color zone #5 near #18/A,B distance 6
    9382 
    9383 > ui tool show "Side View"
    9384 
    9385 > save test.png width 3000 height 3000 supersample 3 transparentBackground
    9386 > true
    9387 
    9388 [Repeated 1 time(s)]
    9389 
    9390 > hide #!18 models
    9391 
    9392 > show #!6 models
    9393 
    9394 > hide #!5 models
    9395 
    9396 > color #6 darkgrey
    9397 
    9398 > color zone #6 near #18/A,B distance 6
    9399 
    9400 > save J17114_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
    9401 > supersample 3 transparentBackground true
    9402 
    9403 > save J1714_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
    9404 > supersample 3 transparentBackground true
    9405 
    9406 > show #!5 models
    9407 
    9408 > hide #!6 models
    9409 
    9410 > save J1711_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
    9411 > supersample 3 transparentBackground true
    9412 
    9413 > view name diemr_1_close
    9414 
    9415 > view list
    9416 
    9417 Named views: bottom_overview, diemr_1_close, side_overview 
    9418 
    9419 > view side_overview
    9420 
    9421 > show #!1 models
    9422 
    9423 > hide #!5 models
    9424 
    9425 > view #1 m
    9426 
    9427 Expected an integer >= 1 or a keyword 
    9428 
    9429 > show #1 models
    9430 
    9431 > show #!4 models
    9432 
    9433 > show #4 models
    9434 
    9435 > save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
    9436 > transparentBackground true
    9437 
    9438 > turn y 120
    9439 
    9440 > show #!3 models
    9441 
    9442 > hide #!4 models
    9443 
    9444 > show #3 models
    9445 
    9446 > show #2
    9447 
    9448 > hide #!2 models
    9449 
    9450 > show #!2 models
    9451 
    9452 > hide #!3 models
    9453 
    9454 > save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
    9455 > transparentBackground true
    9456 
    9457 > turn y 120
    9458 
    9459 > show #!3 models
    9460 
    9461 > hide #!2 models
    9462 
    9463 > show #!2 models
    9464 
    9465 > turn y 120
    9466 
    9467 [Repeated 1 time(s)]
    9468 
    9469 > hide #!3 models
    9470 
    9471 > save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
    9472 > transparentBackground true
    9473 
    9474 > turn y 120
    9475 
    9476 > show #!3 models
    9477 
    9478 > hide #!2 models
    9479 
    9480 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    9481 > transparentBackground true
    9482 
    9483 > color #3 #168e781b models
    9484 
    9485 > color #3 #168e7800 models
    9486 
    9487 > color #3 #168e7880 models
    9488 
    9489 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    9490 > transparentBackground true
    9491 
    9492 > graphics silhouettes true width 8
    9493 
    9494 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    9495 > transparentBackground true
    9496 
    9497 > graphics silhouettes true width 16
    9498 
    9499 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    9500 > transparentBackground true
    9501 
    9502 > graphics silhouettes true width 32
    9503 
    9504 > save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
    9505 > transparentBackground true
    9506 
    9507 > view list
    9508 
    9509 Named views: bottom_overview, diemr_1_close, side_overview 
    9510 
    9511 > side_overview_P5P1_dimer_2
    9512 
    9513 Unknown command: side_overview_P5P1_dimer_2 
    9514 
    9515 > view name side_overview_P5P1_dimer_2
    9516 
    9517 > turn y 12
    9518 
    9519 [Repeated 1 time(s)]
    9520 
    9521 > turn y -12
    9522 
    9523 [Repeated 1 time(s)]
    9524 
    9525 > turn y 120
    9526 
    9527 > hide #!3 models
    9528 
    9529 > show #!4 models
    9530 
    9531 > save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
    9532 > transparentBackground true
    9533 
    9534 > show #!3 models
    9535 
    9536 > hide #!4 models
    9537 
    9538 > show #!2 models
    9539 
    9540 > hide #!3 models
    9541 
    9542 > show #!4 models
    9543 
    9544 > hide #!2 models
    9545 
    9546 > view list
    9547 
    9548 Named views: bottom_overview, diemr_1_close, side_overview,
    9549 side_overview_P5P1_dimer_2 
    9550 
    9551 > view side_overview
    9552 
    9553 > save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
    9554 > transparentBackground true
    9555 
    9556 > show #!3 models
    9557 
    9558 > hide #!3 models
    9559 
    9560 > show #!2 models
    9561 
    9562 > hide #!4 models
    9563 
    9564 > undo
    9565 
    9566 > redo
    9567 
    9568 > view side_overview
    9569 
    9570 > hide #!4 models
    9571 
    9572 > turn y 120
    9573 
    9574 > view name side_overview_P5P1_dimer_3
    9575 
    9576 > save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
    9577 > transparentBackground true
    9578 
    9579 > graphics silhouettes true width 4
    9580 
    9581 > hide #!2 models
    9582 
    9583 > hide #!1 models
    9584 
    9585 > show #!14 models
    9586 
    9587 > show #!15 models
    9588 
    9589 > hide #!14 models
    9590 
    9591 > show #!16 models
    9592 
    9593 > hide #!15 models
    9594 
    9595 > show #!19 models
    9596 
    9597 > hide #!16 models
    9598 
    9599 > show #!15 models
    9600 
    9601 > hide #!19 models
    9602 
    9603 > show #!19 models
    9604 
    9605 > hide #!15 models
    9606 
    9607 > pwd
    9608 
    9609 Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
    9610 Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy 
    9611 
    9612 > view list
    9613 
    9614 Named views: bottom_overview, diemr_1_close, side_overview,
    9615 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    9616 
    9617 > view diemr_1_close
    9618 
    9619 > turn y 120
    9620 
    9621 > view side_overview_P5P1_dimer_2
    9622 
    9623 > view diemr_1_close
    9624 
    9625 > view name dimer_1_close
    9626 
    9627 > view delete diemer_1_close
    9628 
    9629 > view list
    9630 
    9631 Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
    9632 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    9633 
    9634 > view dimer_1_close
    9635 
    9636 > view dimer_2 close
    9637 
    9638 Expected an objects specifier or a view name or a keyword 
    9639 
    9640 > show #!2 models
    9641 
    9642 > hide #!2 models
    9643 
    9644 > show #!3 models
    9645 
    9646 > hide #!3 models
    9647 
    9648 > show #!3 models
    9649 
    9650 > hide #!3 models
    9651 
    9652 > view list
    9653 
    9654 Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
    9655 side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    9656 
    9657 > view side_overview_P5P1_dimer_3
    9658 
    9659 > hide #!19 models
    9660 
    9661 > show #!5 models
    9662 
    9663 > show #!6 models
    9664 
    9665 > hide #!5 models
    9666 
    9667 > show #!8 models
    9668 
    9669 > hide #!6 models
    9670 
    9671 > show #!9 models
    9672 
    9673 > hide #!8 models
    9674 
    9675 > show #!10 models
    9676 
    9677 > hide #!9 models
    9678 
    9679 > show #!11 models
    9680 
    9681 > hide #!10 models
    9682 
    9683 > show #!10 models
    9684 
    9685 > hide #!11 models
    9686 
    9687 > show #!11 models
    9688 
    9689 > hide #!11 models
    9690 
    9691 > show #!11 models
    9692 
    9693 > show #!18 models
    9694 
    9695 > hide #!10 models
    9696 
    9697 > hide #!11 models
    9698 
    9699 > show #!11 models
    9700 
    9701 > show #!10 models
    9702 
    9703 > hide #!11 models
    9704 
    9705 > color #10,11 darkgrey
    9706 
    9707 > show #!11 models
    9708 
    9709 > hide #!10 models
    9710 
    9711 > hide #!11 models
    9712 
    9713 > color zone #11 near #18/J,I distance 6
    9714 
    9715 > show #!11 models
    9716 
    9717 > show #!10 models
    9718 
    9719 > hide #!11 models
    9720 
    9721 > show #!11 models
    9722 
    9723 > hide #!10 models
    9724 
    9725 > color #10,11 darkgrey
    9726 
    9727 > color zone #11 near #18/J,I distance 4
    9728 
    9729 > hide #!18 models
    9730 
    9731 > show #!18 models
    9732 
    9733 > hide #!18 models
    9734 
    9735 > save test.png width 3000 height 3000 supersample 3 transparentBackground
    9736 > true
    9737 
    9738 > view name dimer_3_close
    9739 
    9740 > save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
    9741 > supersample 3 transparentBackground true
    9742 
    9743 > show #!10 models
    9744 
    9745 > hide #!11 models
    9746 
    9747 > show #!11 models
    9748 
    9749 > hide #!10 models
    9750 
    9751 > save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
    9752 > supersample 3 transparentBackground true
    9753 
    9754 > show #!10 models
    9755 
    9756 > hide #!11 models
    9757 
    9758 > save J1843_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
    9759 > supersample 3 transparentBackground true
    9760 
    9761 > hide #!10 models
    9762 
    9763 > show #!8 models
    9764 
    9765 > show #!9 models
    9766 
    9767 > view list
    9768 
    9769 Named views: bottom_overview, diemr_1_close, dimer_1_close, dimer_3_close,
    9770 side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3 
    9771 
    9772 > view side_overview_P5P1_dimer_2
    9773 
    9774 > hide #!9 models
    9775 
    9776 > show #!9 models
    9777 
    9778 > hide #!8 models
     1750[deleted to fit within ticket limits]
     1751
    97791752
    97801753> show #!8 models