Changes between Initial Version and Version 1 of Ticket #19310


Ignore:
Timestamp:
Nov 7, 2025, 9:51:29 AM (4 weeks ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19310

    • Property Component Unassigned → DICOM
    • Property Owner set to Zach Pearson
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Orthoplanes: 'NoneType' object has no attribute 'image_colors'

  • Ticket #19310 – Description

    initial v1  
    15001500 
    15011501
    1502 > fitmap #1 inMap #2
    1503 
    1504 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1505 (#2) using 8555 atoms 
    1506 average map value = 0.0603, steps = 36 
    1507 shifted from previous position = 0.00222 
    1508 rotated from previous position = 0.00186 degrees 
    1509 atoms outside contour = 6642, contour level = 0.10328 
    1510  
    1511 Position of 5zf6.pdb (#1) relative to
    1512 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1513 Matrix rotation and translation 
    1514 -0.56226149 0.77257686 0.29493559 179.14943502 
    1515 0.55852256 0.09175953 0.82439841 73.23090250 
    1516 0.60984799 0.62825566 -0.48309445 60.26745267 
    1517 Axis -0.45793130 -0.73522087 -0.49974913 
    1518 Axis point 68.44054400 0.00000000 12.84382814 
    1519 Rotation angle (degrees) 167.63364557 
    1520 Shift along axis -165.99762925 
    1521  
    1522 
    1523 > fitmap #1 inMap #2
    1524 
    1525 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1526 (#2) using 8555 atoms 
    1527 average map value = 0.0603, steps = 40 
    1528 shifted from previous position = 0.00382 
    1529 rotated from previous position = 0.0119 degrees 
    1530 atoms outside contour = 6642, contour level = 0.10328 
    1531  
    1532 Position of 5zf6.pdb (#1) relative to
    1533 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1534 Matrix rotation and translation 
    1535 -0.56223213 0.77266158 0.29476960 179.15426710 
    1536 0.55851228 0.09190124 0.82438959 73.22780149 
    1537 0.60988447 0.62813076 -0.48321081 60.26856723 
    1538 Axis -0.45793558 -0.73526530 -0.49967984 
    1539 Axis point 68.44506902 0.00000000 12.85475786 
    1540 Rotation angle (degrees) 167.62632816 
    1541 Shift along axis -165.99796253 
    1542  
    1543 
    1544 > fitmap #1 inMap #2
    1545 
    1546 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1547 (#2) using 8555 atoms 
    1548 average map value = 0.0603, steps = 40 
    1549 shifted from previous position = 0.00189 
    1550 rotated from previous position = 0.0083 degrees 
    1551 atoms outside contour = 6642, contour level = 0.10328 
    1552  
    1553 Position of 5zf6.pdb (#1) relative to
    1554 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1555 Matrix rotation and translation 
    1556 -0.56225259 0.77260149 0.29488805 179.15076237 
    1557 0.55852481 0.09180506 0.82439182 73.22832142 
    1558 0.60985413 0.62821873 -0.48313473 60.26809457 
    1559 Axis -0.45793313 -0.73523542 -0.49972606 
    1560 Axis point 68.44223141 0.00000000 12.84779765 
    1561 Rotation angle (degrees) 167.63175258 
    1562 Shift along axis -165.99666188 
    1563  
    1564 
    1565 > select subtract #1
    1566 
    1567 Nothing selected 
    1568 
    1569 > select #1/A:306
    1570 
    1571 9 atoms, 8 bonds, 1 residue, 1 model selected 
    1572 
    1573 > select #1/A:307
    1574 
    1575 7 atoms, 6 bonds, 1 residue, 1 model selected 
    1576 
    1577 > select #1/A:308
    1578 
    1579 6 atoms, 5 bonds, 1 residue, 1 model selected 
    1580 
    1581 > select #1/A:306
    1582 
    1583 9 atoms, 8 bonds, 1 residue, 1 model selected 
    1584 
    1585 > select #2
    1586 
    1587 2 models selected 
    1588 
    1589 > select subtract #2
    1590 
    1591 Nothing selected 
    1592 
    1593 > select #2
    1594 
    1595 2 models selected 
    1596 
    1597 > select subtract #2
    1598 
    1599 Nothing selected 
    1600 
    1601 > select #2
    1602 
    1603 2 models selected 
    1604 
    1605 > select #2
    1606 
    1607 2 models selected 
    1608 
    1609 > select subtract #2
    1610 
    1611 Nothing selected 
    1612 
    1613 > hide #!2 models
    1614 
    1615 > select sequence 301-306
    1616 
    1617 Nothing selected 
    1618 
    1619 > select sequence 301-306
    1620 
    1621 Nothing selected 
    1622 
    1623 > select sequence 301-306
    1624 
    1625 Nothing selected 
    1626 
    1627 > help help:user/findseq.html
    1628 
    1629 > ui tool show "Show Sequence Viewer"
    1630 
    1631 > select add #3
    1632 
    1633 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1634 
    1635 > ui tool show "Show Sequence Viewer"
    1636 
    1637 > select subtract #3
    1638 
    1639 Nothing selected 
    1640 
    1641 > select add #1
    1642 
    1643 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1644 
    1645 > select subtract #1
    1646 
    1647 Nothing selected 
    1648 
    1649 > select add #3
    1650 
    1651 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1652 
    1653 > select subtract #3
    1654 
    1655 Nothing selected 
    1656 
    1657 > select add #4
    1658 
    1659 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1660 
    1661 > ui tool show "Show Sequence Viewer"
    1662 
    1663 > sequence chain #1/A #1/B #3/A #3/B #4/A #4/B
    1664 
    1665 Alignment identifier is 1 
    1666 
    1667 > select
    1668 > #1/A-B:125-142,164-180,205-212,222-224,237-267,280-301,305-328,332-356,450-462,482-499,534-540,567-593,613-636,653-666
    1669 > #3/A-B:125-142,164-180,205-212,222-224,237-267,280-301,305-328,332-356,450-462,482-499,534-540,567-593,613-636,653-666
    1670 > #4/A-B:125-142,164-180,205-212,222-224,237-267,280-301,305-328,332-356,450-462,482-499,534-540,567-593,613-636,653-666
    1671 
    1672 11616 atoms, 11709 bonds, 1491 residues, 3 models selected 
    1673 
    1674 > show #!2 models
    1675 
    1676 > fitmap #1 inMap #2
    1677 
    1678 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1679 (#2) using 8555 atoms 
    1680 average map value = 0.0603, steps = 40 
    1681 shifted from previous position = 0.0117 
    1682 rotated from previous position = 0.00722 degrees 
    1683 atoms outside contour = 6640, contour level = 0.10328 
    1684  
    1685 Position of 5zf6.pdb (#1) relative to
    1686 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1687 Matrix rotation and translation 
    1688 -0.56224533 0.77263148 0.29482329 179.15688679 
    1689 0.55843537 0.09177590 0.82445565 73.23754273 
    1690 0.60994272 0.62818610 -0.48306532 60.24856479 
    1691 Axis -0.45792677 -0.73522163 -0.49975217 
    1692 Axis point 68.44493944 0.00000000 12.83776309 
    1693 Rotation angle (degrees) 167.62539970 
    1694 Shift along axis -165.99591072 
    1695  
    1696 
    1697 > fitmap #1 inMap #2
    1698 
    1699 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1700 (#2) using 8555 atoms 
    1701 average map value = 0.0603, steps = 40 
    1702 shifted from previous position = 0.00404 
    1703 rotated from previous position = 0.0179 degrees 
    1704 atoms outside contour = 6642, contour level = 0.10328 
    1705  
    1706 Position of 5zf6.pdb (#1) relative to
    1707 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1708 Matrix rotation and translation 
    1709 -0.56227457 0.77250264 0.29510503 179.14987129 
    1710 0.55852816 0.09159555 0.82441285 73.23691669 
    1711 0.60983079 0.62837085 -0.48296633 60.25085966 
    1712 Axis -0.45793476 -0.73516833 -0.49982326 
    1713 Axis point 68.43835304 0.00000000 12.82457642 
    1714 Rotation angle (degrees) 167.64019313 
    1715 Shift along axis -165.99519523 
    1716  
    1717 
    1718 > fitmap #1 inMap #2
    1719 
    1720 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1721 (#2) using 8555 atoms 
    1722 average map value = 0.0603, steps = 40 
    1723 shifted from previous position = 0.00252 
    1724 rotated from previous position = 0.00579 degrees 
    1725 atoms outside contour = 6643, contour level = 0.10328 
    1726  
    1727 Position of 5zf6.pdb (#1) relative to
    1728 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1729 Matrix rotation and translation 
    1730 -0.56226280 0.77254581 0.29501442 179.14915690 
    1731 0.55849019 0.09164317 0.82443328 73.23928513 
    1732 0.60987642 0.62831083 -0.48298680 60.24865553 
    1733 Axis -0.45793277 -0.73518163 -0.49980551 
    1734 Axis point 68.43839047 0.00000000 12.82706773 
    1735 Rotation angle (degrees) 167.63498549 
    1736 Shift along axis -165.99505628 
    1737  
    1738 
    1739 > fitmap #1 inMap #2
    1740 
    1741 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1742 (#2) using 8555 atoms 
    1743 average map value = 0.0603, steps = 44 
    1744 shifted from previous position = 0.0109 
    1745 rotated from previous position = 0.00848 degrees 
    1746 atoms outside contour = 6643, contour level = 0.10328 
    1747  
    1748 Position of 5zf6.pdb (#1) relative to
    1749 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1750 Matrix rotation and translation 
    1751 -0.56228174 0.77250668 0.29508080 179.14693278 
    1752 0.55858918 0.09169034 0.82436097 73.22718572 
    1753 0.60976829 0.62835206 -0.48306968 60.26918749 
    1754 Axis -0.45793423 -0.73520218 -0.49977394 
    1755 Axis point 68.43867717 0.00000000 12.83878493 
    1756 Rotation angle (degrees) 167.64229799 
    1757 Shift along axis -165.99526915 
    1758  
    1759 
    1760 > select add #3
    1761 
    1762 16299 atoms, 16424 bonds, 2168 residues, 3 models selected 
    1763 
    1764 > fitmap #1 inMap #2
    1765 
    1766 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1767 (#2) using 8555 atoms 
    1768 average map value = 0.0603, steps = 48 
    1769 shifted from previous position = 0.00251 
    1770 rotated from previous position = 0.00327 degrees 
    1771 atoms outside contour = 6644, contour level = 0.10328 
    1772  
    1773 Position of 5zf6.pdb (#1) relative to
    1774 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1775 Matrix rotation and translation 
    1776 -0.56227363 0.77253040 0.29503414 179.14739408 
    1777 0.55858437 0.09172832 0.82436000 73.22579110 
    1778 0.60978018 0.62831735 -0.48309982 60.27170015 
    1779 Axis -0.45793523 -0.73521399 -0.49975566 
    1780 Axis point 68.43952822 -0.00000000 12.84303370 
    1781 Rotation angle (degrees) 167.64016407 
    1782 Shift along axis -165.99565204 
    1783  
    1784 
    1785 > fitmap #1 inMap #2
    1786 
    1787 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1788 (#2) using 8555 atoms 
    1789 average map value = 0.0603, steps = 40 
    1790 shifted from previous position = 0.00106 
    1791 rotated from previous position = 0.00975 degrees 
    1792 atoms outside contour = 6643, contour level = 0.10328 
    1793  
    1794 Position of 5zf6.pdb (#1) relative to
    1795 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1796 Matrix rotation and translation 
    1797 -0.56225268 0.77260373 0.29488202 179.15110347 
    1798 0.55852278 0.09180948 0.82439270 73.22831911 
    1799 0.60985591 0.62821532 -0.48313691 60.26806007 
    1800 Axis -0.45793261 -0.73523677 -0.49972454 
    1801 Axis point 68.44249251 0.00000000 12.84809670 
    1802 Rotation angle (degrees) 167.63146412 
    1803 Shift along axis -165.99671418 
    1804  
    1805 
    1806 > select add #4
    1807 
    1808 20982 atoms, 21139 bonds, 2845 residues, 3 models selected 
    1809 
    1810 > select subtract #4
    1811 
    1812 12427 atoms, 12521 bonds, 1671 residues, 2 models selected 
    1813 
    1814 > fitmap #1 inMap #2
    1815 
    1816 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1817 (#2) using 8555 atoms 
    1818 average map value = 0.0603, steps = 40 
    1819 shifted from previous position = 0.0118 
    1820 rotated from previous position = 0.00691 degrees 
    1821 atoms outside contour = 6640, contour level = 0.10328 
    1822  
    1823 Position of 5zf6.pdb (#1) relative to
    1824 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1825 Matrix rotation and translation 
    1826 -0.56224678 0.77262775 0.29483032 179.15681735 
    1827 0.55843723 0.09177153 0.82445488 73.23752923 
    1828 0.60993969 0.62819133 -0.48306235 60.24853618 
    1829 Axis -0.45792659 -0.73522035 -0.49975421 
    1830 Axis point 68.44485428 0.00000000 12.83738565 
    1831 Rotation angle (degrees) 167.62577932 
    1832 Shift along axis -165.99585229 
    1833  
    1834 
    1835 > select add #1
    1836 
    1837 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    1838 
    1839 > select subtract #1
    1840 
    1841 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1842 
    1843 > select add #1
    1844 
    1845 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    1846 
    1847 > view matrix models
    1848 > #1,-0.56225,0.77263,0.29483,231.16,0.55844,0.091772,0.82445,121.3,0.60994,0.62819,-0.48306,94.371,#3,0.32146,-0.80003,-0.50657,136.35,0.63696,-0.21316,0.74085,-39.027,-0.70068,-0.56081,0.44107,322.02
    1849 
    1850 > fitmap #1 inMap #2
    1851 
    1852 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1853 (#2) using 8555 atoms 
    1854 average map value = 0.1101, steps = 252 
    1855 shifted from previous position = 3.7 
    1856 rotated from previous position = 2.65 degrees 
    1857 atoms outside contour = 5173, contour level = 0.10328 
    1858  
    1859 Position of 5zf6.pdb (#1) relative to
    1860 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1861 Matrix rotation and translation 
    1862 -0.53022950 0.78334634 0.32438432 175.25685423 
    1863 0.58887827 0.06499723 0.80560396 67.48236203 
    1864 0.60998283 0.61817787 -0.49575909 63.99041146 
    1865 Axis -0.47681259 -0.72656353 -0.49472739 
    1866 Axis point 66.66494214 0.00000000 15.64059965 
    1867 Rotation angle (degrees) 168.66526300 
    1868 Shift along axis -164.25270661 
    1869  
    1870 
    1871 > view matrix models
    1872 > #1,-0.53023,0.78335,0.32438,227.93,0.58888,0.064997,0.8056,120.21,0.60998,0.61818,-0.49576,94.092,#3,0.32146,-0.80003,-0.50657,136.72,0.63696,-0.21316,0.74085,-35.748,-0.70068,-0.56081,0.44107,323.6
    1873 
    1874 > select subtract #3
    1875 
    1876 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1877 
    1878 > fitmap #1 inMap #2
    1879 
    1880 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1881 (#2) using 8555 atoms 
    1882 average map value = 0.06778, steps = 88 
    1883 shifted from previous position = 4.08 
    1884 rotated from previous position = 2.46 degrees 
    1885 atoms outside contour = 6341, contour level = 0.10328 
    1886  
    1887 Position of 5zf6.pdb (#1) relative to
    1888 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1889 Matrix rotation and translation 
    1890 -0.56182390 0.76213390 0.32172320 177.76957181 
    1891 0.56503217 0.06947264 0.82213879 70.72361557 
    1892 0.60422889 0.64368118 -0.46966157 68.59500191 
    1893 Axis -0.46000085 -0.72820014 -0.50805883 
    1894 Axis point 67.67791239 0.00000000 16.37816490 
    1895 Rotation angle (degrees) 168.81513008 
    1896 Shift along axis -168.12539753 
    1897  
    1898 
    1899 > close #3
    1900 
    1901 > open
    1902 > /Users/madhurikanavalli/Desktop/ImageProcessing/kasiafiles/hPNP_dimer_5zf6_fit_tetramer2.pdb
    1903 
    1904 hPNP_dimer_5zf6_fit_tetramer2.pdb title: 
    1905 Crystal structure of the dimeric human pnpase [more info...] 
    1906  
    1907 Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb #3 
    1908 --- 
    1909 Chain | Description | UniProt 
    1910 A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669 
    1911  
    1912 
    1913 > select add #3
    1914 
    1915 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    1916 
    1917 > select subtract #1
    1918 
    1919 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1920 
    1921 > select subtract #3
    1922 
    1923 Nothing selected 
    1924 
    1925 > select add #3
    1926 
    1927 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1928 
    1929 > view matrix models #3,1,0,0,-29.495,0,1,0,-74.165,0,0,1,7.8615
    1930 
    1931 > view matrix models #3,1,0,0,-30.191,0,1,0,-73.496,0,0,1,19.042
    1932 
    1933 > select add #4
    1934 
    1935 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    1936 
    1937 > view matrix models
    1938 > #4,0.43664,-0.89777,0.05801,169.54,0.24953,0.18281,0.95095,76.564,-0.86434,-0.40075,0.30385,338.08,#3,1,0,0,-33.957,0,1,0,-141.45,0,0,1,73.984
    1939 
    1940 > select subtract #4
    1941 
    1942 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    1943 
    1944 > view matrix models #3,1,0,0,-6.382,0,1,0,-37.244,0,0,1,78.169
    1945 
    1946 > view matrix models #3,1,0,0,7.1074,0,1,0,14.723,0,0,1,79.588
    1947 
    1948 > ui mousemode right "rotate selected models"
    1949 
    1950 > view matrix models
    1951 > #3,-0.39782,0.91744,-0.0062689,97.728,0.85434,0.36795,-0.36705,23.539,-0.33444,-0.15137,-0.93018,435.14
    1952 
    1953 > hide #!4 models
    1954 
    1955 > view matrix models
    1956 > #3,-0.64157,-0.026449,-0.76661,423.28,0.15277,0.97498,-0.16149,13.079,0.7517,-0.22072,-0.62148,203.2
    1957 
    1958 > ui mousemode right "translate selected models"
    1959 
    1960 > view matrix models
    1961 > #3,-0.64157,-0.026449,-0.76661,427.84,0.15277,0.97498,-0.16149,14.341,0.7517,-0.22072,-0.62148,195.08
    1962 
    1963 > fitmap #1 inMap #2
    1964 
    1965 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1966 (#2) using 8555 atoms 
    1967 average map value = 0.06778, steps = 44 
    1968 shifted from previous position = 0.014 
    1969 rotated from previous position = 0.0147 degrees 
    1970 atoms outside contour = 6338, contour level = 0.10328 
    1971  
    1972 Position of 5zf6.pdb (#1) relative to
    1973 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1974 Matrix rotation and translation 
    1975 -0.56177320 0.76214508 0.32178525 177.76212068 
    1976 0.56493063 0.06925504 0.82222693 70.73071438 
    1977 0.60437096 0.64369139 -0.46946473 68.59002634 
    1978 Axis -0.46002220 -0.72812228 -0.50815109 
    1979 Axis point 67.67059892 0.00000000 16.36862818 
    1980 Rotation angle (degrees) 168.81070899 
    1981 Shift along axis -168.12922648 
    1982  
    1983 
    1984 > fitmap #1 inMap #2
    1985 
    1986 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    1987 (#2) using 8555 atoms 
    1988 average map value = 0.06778, steps = 44 
    1989 shifted from previous position = 0.00118 
    1990 rotated from previous position = 0.00555 degrees 
    1991 atoms outside contour = 6338, contour level = 0.10328 
    1992  
    1993 Position of 5zf6.pdb (#1) relative to
    1994 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    1995 Matrix rotation and translation 
    1996 -0.56180042 0.76212365 0.32178849 177.76456401 
    1997 0.56497732 0.06932409 0.82218903 70.72650702 
    1998 0.60430201 0.64370934 -0.46952888 68.59710591 
    1999 Axis -0.46001209 -0.72814803 -0.50812333 
    2000 Axis point 67.67325732 0.00000000 16.37390083 
    2001 Rotation angle (degrees) 168.81400533 
    2002 Shift along axis -168.12900552 
    2003  
    2004 
    2005 > fitmap #1 inMap #2
    2006 
    2007 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2008 (#2) using 8555 atoms 
    2009 average map value = 0.06778, steps = 44 
    2010 shifted from previous position = 0.0011 
    2011 rotated from previous position = 0.00219 degrees 
    2012 atoms outside contour = 6340, contour level = 0.10328 
    2013  
    2014 Position of 5zf6.pdb (#1) relative to
    2015 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2016 Matrix rotation and translation 
    2017 -0.56181677 0.76211115 0.32178954 177.76628394 
    2018 0.56499162 0.06935189 0.82217686 70.72533923 
    2019 0.60427344 0.64372114 -0.46954946 68.59902440 
    2020 Axis -0.46000509 -0.72815841 -0.50811479 
    2021 Axis point 67.67475916 0.00000000 16.37531817 
    2022 Rotation angle (degrees) 168.81535483 
    2023 Shift along axis -168.12882574 
    2024  
    2025 
    2026 > view matrix models
    2027 > #3,-0.64157,-0.026449,-0.76661,428.14,0.15277,0.97498,-0.16149,13.695,0.7517,-0.22072,-0.62148,197.78
    2028 
    2029 > view matrix models
    2030 > #3,-0.64157,-0.026449,-0.76661,429.22,0.15277,0.97498,-0.16149,10.389,0.7517,-0.22072,-0.62148,201.96
    2031 
    2032 > ui mousemode right "rotate selected models"
    2033 
    2034 > view matrix models
    2035 > #3,-0.91507,0.12718,-0.38272,398.89,0.29913,0.85053,-0.43258,43.498,0.2705,-0.51032,-0.81633,372.32
    2036 
    2037 > view matrix models
    2038 > #3,-0.93066,0.25206,-0.26522,362.41,0.34092,0.86054,-0.37847,26.413,0.13284,-0.44264,-0.8868,395.06
    2039 
    2040 > fitmap #1 inMap #2
    2041 
    2042 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2043 (#2) using 8555 atoms 
    2044 average map value = 0.06778, steps = 44 
    2045 shifted from previous position = 0.00109 
    2046 rotated from previous position = 0.0011 degrees 
    2047 atoms outside contour = 6339, contour level = 0.10328 
    2048  
    2049 Position of 5zf6.pdb (#1) relative to
    2050 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2051 Matrix rotation and translation 
    2052 -0.56180508 0.76212041 0.32178802 177.76501259 
    2053 0.56498774 0.06933961 0.82218056 70.72555730 
    2054 0.60428793 0.64371150 -0.46954404 68.59878002 
    2055 Axis -0.46001046 -0.72815376 -0.50811660 
    2056 Axis point 67.67377478 0.00000000 16.37519960 
    2057 Rotation angle (degrees) 168.81464010 
    2058 Shift along axis -168.12902480 
    2059  
    2060 
    2061 > fitmap #1 inMap #2
    2062 
    2063 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2064 (#2) using 8555 atoms 
    2065 average map value = 0.06778, steps = 44 
    2066 shifted from previous position = 0.0013 
    2067 rotated from previous position = 0.00174 degrees 
    2068 atoms outside contour = 6340, contour level = 0.10328 
    2069  
    2070 Position of 5zf6.pdb (#1) relative to
    2071 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2072 Matrix rotation and translation 
    2073 -0.56182107 0.76210821 0.32178898 177.76676058 
    2074 0.56499631 0.06936111 0.82217285 70.72493750 
    2075 0.60426505 0.64372363 -0.46955686 68.59974743 
    2076 Axis -0.46000327 -0.72816181 -0.50811158 
    2077 Axis point 67.67518917 0.00000000 16.37588980 
    2078 Rotation angle (degrees) 168.81572170 
    2079 Shift along axis -168.12881525 
    2080  
    2081 
    2082 > fitmap #1 inMap #2
    2083 
    2084 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2085 (#2) using 8555 atoms 
    2086 average map value = 0.06778, steps = 44 
    2087 shifted from previous position = 0.0015 
    2088 rotated from previous position = 0.00184 degrees 
    2089 atoms outside contour = 6339, contour level = 0.10328 
    2090  
    2091 Position of 5zf6.pdb (#1) relative to
    2092 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2093 Matrix rotation and translation 
    2094 -0.56180367 0.76212182 0.32178714 177.76486802 
    2095 0.56498749 0.06933911 0.82218077 70.72556637 
    2096 0.60428947 0.64370988 -0.46954426 68.59886768 
    2097 Axis -0.46001109 -0.72815353 -0.50811636 
    2098 Axis point 67.67366634 -0.00000000 16.37528860 
    2099 Rotation angle (degrees) 168.81453944 
    2100 Shift along axis -168.12908826 
    2101  
    2102 
    2103 > fitmap #1 inMap #2
    2104 
    2105 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2106 (#2) using 8555 atoms 
    2107 average map value = 0.06778, steps = 44 
    2108 shifted from previous position = 0.00161 
    2109 rotated from previous position = 0.00195 degrees 
    2110 atoms outside contour = 6340, contour level = 0.10328 
    2111  
    2112 Position of 5zf6.pdb (#1) relative to
    2113 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2114 Matrix rotation and translation 
    2115 -0.56182168 0.76210791 0.32178865 177.76684825 
    2116 0.56499718 0.06936289 0.82217211 70.72490535 
    2117 0.60426368 0.64372379 -0.46955839 68.59980313 
    2118 Axis -0.46000301 -0.72816245 -0.50811088 
    2119 Axis point 67.67525750 0.00000000 16.37595603 
    2120 Rotation angle (degrees) 168.81577332 
    2121 Shift along axis -168.12881302 
    2122  
    2123 
    2124 > fitmap #1 inMap #2
    2125 
    2126 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2127 (#2) using 8555 atoms 
    2128 average map value = 0.06778, steps = 44 
    2129 shifted from previous position = 0.0017 
    2130 rotated from previous position = 0.00202 degrees 
    2131 atoms outside contour = 6339, contour level = 0.10328 
    2132  
    2133 Position of 5zf6.pdb (#1) relative to
    2134 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2135 Matrix rotation and translation 
    2136 -0.56180300 0.76212254 0.32178662 177.76481731 
    2137 0.56498709 0.06933868 0.82218108 70.72559720 
    2138 0.60429047 0.64370908 -0.46954407 68.59886938 
    2139 Axis -0.46001136 -0.72815335 -0.50811637 
    2140 Axis point 67.67362036 0.00000000 16.37530466 
    2141 Rotation angle (degrees) 168.81447555 
    2142 Shift along axis -168.12912509 
    2143  
    2144 
    2145 > fitmap #1 inMap #2
    2146 
    2147 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2148 (#2) using 8555 atoms 
    2149 average map value = 0.06778, steps = 44 
    2150 shifted from previous position = 0.00172 
    2151 rotated from previous position = 0.00207 degrees 
    2152 atoms outside contour = 6340, contour level = 0.10328 
    2153  
    2154 Position of 5zf6.pdb (#1) relative to
    2155 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2156 Matrix rotation and translation 
    2157 -0.56182263 0.76210752 0.32178790 177.76699161 
    2158 0.56499677 0.06936407 0.82217229 70.72494421 
    2159 0.60426317 0.64372412 -0.46955859 68.59983213 
    2160 Axis -0.46000248 -0.72816286 -0.50811078 
    2161 Axis point 67.67535296 0.00000000 16.37598872 
    2162 Rotation angle (degrees) 168.81576963 
    2163 Shift along axis -168.12884954 
    2164  
    2165 
    2166 > fitmap #1 inMap #2
    2167 
    2168 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2169 (#2) using 8555 atoms 
    2170 average map value = 0.06778, steps = 44 
    2171 shifted from previous position = 0.00176 
    2172 rotated from previous position = 0.00204 degrees 
    2173 atoms outside contour = 6338, contour level = 0.10328 
    2174  
    2175 Position of 5zf6.pdb (#1) relative to
    2176 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2177 Matrix rotation and translation 
    2178 -0.56180310 0.76212248 0.32178657 177.76482158 
    2179 0.56498745 0.06933920 0.82218079 70.72554566 
    2180 0.60429004 0.64370910 -0.46954462 68.59896224 
    2181 Axis -0.46001133 -0.72815354 -0.50811613 
    2182 Axis point 67.67363504 0.00000000 16.37537496 
    2183 Rotation angle (degrees) 168.81449424 
    2184 Shift along axis -168.12912781 
    2185  
    2186 
    2187 > select add #1
    2188 
    2189 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    2190 
    2191 > view matrix models
    2192 > #1,-0.14985,0.98863,0.012626,183.06,0.38156,0.046045,0.9232,139.05,0.91212,0.14316,-0.38412,80.456,#3,-0.71358,-0.03176,-0.69986,455.85,0.2007,0.94783,-0.24765,11.335,0.67121,-0.31718,-0.66998,236.49
    2193 
    2194 > view matrix models
    2195 > #1,0.70687,0.28057,0.64932,108.08,0.4226,-0.90364,-0.069595,177.3,0.56723,0.3236,-0.75732,116.2,#3,0.34115,0.69223,-0.63595,112.39,0.88425,-0.0067957,0.46696,-46.86,0.31892,-0.72165,-0.61442,370.77
    2196 
    2197 > view matrix models
    2198 > #1,0.148,-0.90826,0.39135,209.41,0.70956,0.37316,0.59772,89.53,-0.68892,0.18923,0.6997,243.87,#3,0.63093,0.4315,0.64478,-110.94,0.29194,0.63795,-0.7126,129.47,-0.71882,0.63783,0.27653,139.68
    2199 
    2200 > select add #2
    2201 
    2202 17110 atoms, 17236 bonds, 2348 residues, 4 models selected 
    2203 
    2204 > hide #!3 models
    2205 
    2206 > fitmap #1 inMap #2
    2207 
    2208 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2209 (#2) using 8555 atoms 
    2210 average map value = 0.04801, steps = 284 
    2211 shifted from previous position = 22 
    2212 rotated from previous position = 25 degrees 
    2213 atoms outside contour = 7189, contour level = 0.10328 
    2214  
    2215 Position of 5zf6.pdb (#1) relative to
    2216 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2217 Matrix rotation and translation 
    2218 0.38285300 -0.90468146 0.18701612 126.18295836 
    2219 0.48235861 0.36841712 0.79473202 61.45913081 
    2220 -0.78787927 -0.21405670 0.57743049 239.44909763 
    2221 Axis -0.51134765 0.49416737 0.70308050 
    2222 Axis point 154.24471051 110.10948885 0.00000000 
    2223 Rotation angle (degrees) 80.54050570 
    2224 Shift along axis 134.19972853 
    2225  
    2226 
    2227 > view matrix models
    2228 > #2,0.9936,0.053643,0.099376,30.867,-0.051054,0.99829,-0.028415,60.494,-0.10073,0.023159,0.99464,39.57,#1,0.32798,-0.9004,0.28583,183.34,0.48438,0.42006,0.76742,108.6,-0.81105,-0.11325,0.57391,266.45,#3,0.57112,0.52635,0.62991,-115.99,0.27965,0.5967,-0.75216,145.55,-0.77176,0.60573,0.19359,168.43
    2229 
    2230 > select subtract #3
    2231 
    2232 8555 atoms, 8618 bonds, 1174 residues, 3 models selected 
    2233 
    2234 > view matrix models
    2235 > #2,0.96755,0.032451,0.25059,15.256,-0.015944,0.99758,-0.067624,60.534,-0.25218,0.061434,0.96573,59.216,#1,0.18865,-0.91701,0.35144,199.34,0.52837,0.39643,0.75078,103.64,-0.82779,0.044056,0.5593,262.41
    2236 
    2237 > select subtract #2
    2238 
    2239 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    2240 
    2241 > view matrix models
    2242 > #1,0.64787,-0.38882,0.65504,144.54,0.036303,0.8747,0.4833,147.87,-0.76089,-0.28934,0.58081,260.13
    2243 
    2244 > ui mousemode right "translate selected models"
    2245 
    2246 > view matrix models
    2247 > #1,0.64787,-0.38882,0.65504,135.53,0.036303,0.8747,0.4833,160.4,-0.76089,-0.28934,0.58081,260.02
    2248 
    2249 > ui mousemode right "rotate selected models"
    2250 
    2251 > view matrix models
    2252 > #1,0.23258,-0.84668,0.47859,181.53,0.70575,0.48551,0.51595,108.3,-0.6692,0.21777,0.71046,241.92
    2253 
    2254 > view matrix models
    2255 > #1,0.49293,-0.85966,-0.13421,180.79,0.52373,0.16999,0.83475,116.43,-0.69478,-0.48176,0.53402,258.42
    2256 
    2257 > ui mousemode right "move picked models"
    2258 
    2259 > view matrix models
    2260 > #2,0.96755,0.032451,0.25059,16.908,-0.015944,0.99758,-0.067624,59.82,-0.25218,0.061434,0.96573,63.354
    2261 
    2262 > fitmap #1 inMap #2
    2263 
    2264 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2265 (#2) using 8555 atoms 
    2266 average map value = 0.1297, steps = 808 
    2267 shifted from previous position = 2.33 
    2268 rotated from previous position = 6.32 degrees 
    2269 atoms outside contour = 4645, contour level = 0.10328 
    2270  
    2271 Position of 5zf6.pdb (#1) relative to
    2272 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2273 Matrix rotation and translation 
    2274 0.57319897 -0.77448652 -0.26760710 116.68481785 
    2275 0.55163281 0.12322629 0.82493425 69.43518167 
    2276 -0.60592423 -0.62047232 0.49786536 223.43458404 
    2277 Axis -0.72613777 0.16996245 0.66621070 
    2278 Axis point 0.00000000 179.57744939 122.33493989 
    2279 Rotation angle (degrees) 84.42519184 
    2280 Shift along axis 75.92663194 
    2281  
    2282 
    2283 > select subtract #1
    2284 
    2285 Nothing selected 
    2286 
    2287 > ui tool show "Model Loops"
    2288 
    2289 > ui tool show "Fit to Segments"
    2290 
    2291 Density map not found or not selected 
    2292 [Repeated 3 time(s)]
    2293 
    2294 > select add #2
    2295 
    2296 2 models selected 
    2297 
    2298 > fitmap #1 inMap #2
    2299 
    2300 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2301 (#2) using 8555 atoms 
    2302 average map value = 0.1297, steps = 144 
    2303 shifted from previous position = 0.0143 
    2304 rotated from previous position = 0.0137 degrees 
    2305 atoms outside contour = 4641, contour level = 0.10328 
    2306  
    2307 Position of 5zf6.pdb (#1) relative to
    2308 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2309 Matrix rotation and translation 
    2310 0.57308626 -0.77449802 -0.26781512 116.69540535 
    2311 0.55179062 0.12306769 0.82485238 69.42161691 
    2312 -0.60588715 -0.62048944 0.49788915 223.41907541 
    2313 Axis -0.72609643 0.16983726 0.66628768 
    2314 Axis point 0.00000000 179.54103153 122.34637292 
    2315 Rotation angle (degrees) 84.43231602 
    2316 Shift along axis 75.91963727 
    2317  
    2318 
    2319 > fitmap #1 inMap #2
    2320 
    2321 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2322 (#2) using 8555 atoms 
    2323 average map value = 0.129, steps = 2000 
    2324 shifted from previous position = 0.23 
    2325 rotated from previous position = 0.448 degrees 
    2326 atoms outside contour = 4639, contour level = 0.10328 
    2327  
    2328 Position of 5zf6.pdb (#1) relative to
    2329 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2330 Matrix rotation and translation 
    2331 0.57258795 -0.77437910 -0.26922116 116.75226867 
    2332 0.54793977 0.11719931 0.82826706 69.68325907 
    2333 -0.60984017 -0.62177272 0.49142002 223.76402791 
    2334 Axis -0.72801419 0.17101288 0.66389000 
    2335 Axis point 0.00000000 179.16562442 122.41380851 
    2336 Rotation angle (degrees) 84.80166483 
    2337 Shift along axis 75.47412571 
    2338  
    2339 
    2340 > fitmap #1 inMap #2
    2341 
    2342 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2343 (#2) using 8555 atoms 
    2344 average map value = 0.1277, steps = 2000 
    2345 shifted from previous position = 0.609 
    2346 rotated from previous position = 0.904 degrees 
    2347 atoms outside contour = 4682, contour level = 0.10328 
    2348  
    2349 Position of 5zf6.pdb (#1) relative to
    2350 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2351 Matrix rotation and translation 
    2352 0.57348064 -0.77417828 -0.26789537 116.57776864 
    2353 0.55651791 0.12818804 0.82088709 68.70481792 
    2354 -0.60117198 -0.61985143 0.50435745 223.01355175 
    2355 Axis -0.72422213 0.16752956 0.66890669 
    2356 Axis point 0.00000000 179.52079300 122.52462323 
    2357 Rotation angle (degrees) 84.08729719 
    2358 Shift along axis 76.25714444 
    2359  
    2360 
    2361 > fitmap #1 inMap #2
    2362 
    2363 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2364 (#2) using 8555 atoms 
    2365 average map value = 0.129, steps = 2000 
    2366 shifted from previous position = 0.398 
    2367 rotated from previous position = 0.192 degrees 
    2368 atoms outside contour = 4689, contour level = 0.10328 
    2369  
    2370 Position of 5zf6.pdb (#1) relative to
    2371 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2372 Matrix rotation and translation 
    2373 0.57102733 -0.77539121 -0.26962241 116.96381429 
    2374 0.55768186 0.12537938 0.82053089 68.95823782 
    2375 -0.60242736 -0.61890909 0.50401667 222.89061469 
    2376 Axis -0.72336130 0.16724436 0.66990877 
    2377 Axis point 0.00000000 179.32454376 122.64471433 
    2378 Rotation angle (degrees) 84.24863936 
    2379 Shift along axis 76.24215771 
    2380  
    2381 
    2382 > hide #!1 models
    2383 
    2384 > show #!1 models
    2385 
    2386 > select add #1
    2387 
    2388 8555 atoms, 8618 bonds, 1174 residues, 3 models selected 
    2389 
    2390 > ui tool show "Show Sequence Viewer"
    2391 
    2392 > select subtract #2
    2393 
    2394 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    2395 
    2396 > hide #!2 models
    2397 
    2398 > select subtract #1
    2399 
    2400 Nothing selected 
    2401 
    2402 > select #1/A
    2403 
    2404 4328 atoms, 4357 bonds, 597 residues, 1 model selected 
    2405 
    2406 > select #1/B
    2407 
    2408 4227 atoms, 4261 bonds, 577 residues, 1 model selected 
    2409 
    2410 > ui tool show "Show Sequence Viewer"
    2411 
    2412 [Repeated 1 time(s)]
    2413 
    2414 > select add #1
    2415 
    2416 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    2417 
    2418 > select subtract #1
    2419 
    2420 Nothing selected 
    2421 
    2422 > ui tool show "Show Sequence Viewer"
    2423 
    2424 > sequence chain #1/B
    2425 
    2426 Alignment identifier is 1/B 
    2427 
    2428 > select #1/B:300
    2429 
    2430 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2431 
    2432 > select #1/B:300-304
    2433 
    2434 46 atoms, 47 bonds, 5 residues, 1 model selected 
    2435 
    2436 > select #1/B:299-300
    2437 
    2438 18 atoms, 18 bonds, 2 residues, 1 model selected 
    2439 
    2440 > select #1/B:295-300
    2441 
    2442 50 atoms, 51 bonds, 6 residues, 1 model selected 
    2443 
    2444 > select #1/B:295
    2445 
    2446 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2447 
    2448 > select #1/B:285-295
    2449 
    2450 96 atoms, 97 bonds, 11 residues, 1 model selected 
    2451 
    2452 > select #1/B:285
    2453 
    2454 9 atoms, 8 bonds, 1 residue, 1 model selected 
    2455 
    2456 > select #1/B:280-285
    2457 
    2458 46 atoms, 46 bonds, 6 residues, 1 model selected 
    2459 
    2460 > select #1/B:279
    2461 
    2462 7 atoms, 7 bonds, 1 residue, 1 model selected 
    2463 
    2464 > select #1/B:279-319
    2465 
    2466 343 atoms, 350 bonds, 41 residues, 1 model selected 
    2467 
    2468 > select #1/B:320
    2469 
    2470 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2471 
    2472 > select #1/B:320-322
    2473 
    2474 25 atoms, 24 bonds, 3 residues, 1 model selected 
    2475 
    2476 > select #1/B:277-278
    2477 
    2478 18 atoms, 18 bonds, 2 residues, 1 model selected 
    2479 
    2480 > select #1/B:277-288
    2481 
    2482 100 atoms, 104 bonds, 12 residues, 1 model selected 
    2483 
    2484 > select #1/B:277-278
    2485 
    2486 18 atoms, 18 bonds, 2 residues, 1 model selected 
    2487 
    2488 > select #1/B:277-307
    2489 
    2490 263 atoms, 271 bonds, 31 residues, 1 model selected 
    2491 
    2492 > select #1/B:279-319
    2493 
    2494 343 atoms, 350 bonds, 41 residues, 1 model selected 
    2495 
    2496 > select #1/B:277
    2497 
    2498 11 atoms, 11 bonds, 1 residue, 1 model selected 
    2499 
    2500 > select #1/B:277-335
    2501 
    2502 498 atoms, 510 bonds, 59 residues, 1 model selected 
    2503 
    2504 > select add #2
    2505 
    2506 498 atoms, 510 bonds, 59 residues, 3 models selected 
    2507 
    2508 > show #!2 models
    2509 
    2510 > hide #!2 models
    2511 
    2512 > show #!2 models
    2513 
    2514 > ui tool show "Fit to Segments"
    2515 
    2516 Density map not found or not selected 
    2517 [Repeated 6 time(s)]
    2518 
    2519 > select subtract #2
    2520 
    2521 498 atoms, 510 bonds, 59 residues, 1 model selected 
    2522 
    2523 > fitmap #1 inMap #2
    2524 
    2525 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2526 (#2) using 8555 atoms 
    2527 average map value = 0.1289, steps = 2000 
    2528 shifted from previous position = 0.257 
    2529 rotated from previous position = 0.915 degrees 
    2530 atoms outside contour = 4632, contour level = 0.10328 
    2531  
    2532 Position of 5zf6.pdb (#1) relative to
    2533 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2534 Matrix rotation and translation 
    2535 0.57267166 -0.77461823 -0.26835379 116.74682003 
    2536 0.54692091 0.11716150 0.82894553 69.74141727 
    2537 -0.61067559 -0.62148191 0.49074998 223.83938491 
    2538 Axis -0.72818810 0.17186290 0.66347964 
    2539 Axis point 0.00000000 179.26106398 122.43296113 
    2540 Rotation angle (degrees) 84.81961892 
    2541 Shift along axis 75.48519232 
    2542  
    2543 
    2544 > select add #2
    2545 
    2546 498 atoms, 510 bonds, 59 residues, 3 models selected 
    2547 
    2548 > ui tool show "Fit to Segments"
    2549 
    2550 Simulating map res 4.000, grid 2.000 
    2551 
    2552 > molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false
    2553 
    2554 Opened 5zf6.pdb map 4 as #5, grid size 47,52,63, pixel 2, shown at level
    2555 0.104, step 1, values float32 
    2556 Please select an open structure to fit 
    2557 
    2558 > select subtract #2
    2559 
    2560 498 atoms, 510 bonds, 59 residues, 1 model selected 
    2561 
    2562 > fitmap #1 inMap #2
    2563 
    2564 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2565 (#2) using 8555 atoms 
    2566 average map value = 0.1276, steps = 2000 
    2567 shifted from previous position = 0.642 
    2568 rotated from previous position = 1.03 degrees 
    2569 atoms outside contour = 4675, contour level = 0.10328 
    2570  
    2571 Position of 5zf6.pdb (#1) relative to
    2572 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2573 Matrix rotation and translation 
    2574 0.95624965 0.12601838 -0.26401886 146.56566194 
    2575 0.23327279 0.21618286 0.94807635 145.55677599 
    2576 0.17655140 -0.96818610 0.17732813 184.05932290 
    2577 Axis -0.97312742 -0.22373293 0.05446655 
    2578 Axis point 0.00000000 174.29413134 29.54554523 
    2579 Rotation angle (degrees) 79.92830613 
    2580 Shift along axis -165.16783062 
    2581  
    2582 
    2583 > fitmap #1 inMap #2
    2584 
    2585 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2586 (#2) using 8555 atoms 
    2587 average map value = 0.1291, steps = 2000 
    2588 shifted from previous position = 0.427 
    2589 rotated from previous position = 0.28 degrees 
    2590 atoms outside contour = 4695, contour level = 0.10328 
    2591  
    2592 Position of 5zf6.pdb (#1) relative to
    2593 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2594 Matrix rotation and translation 
    2595 0.95531248 0.12439245 -0.26815027 146.59108838 
    2596 0.23788270 0.21497353 0.94720546 145.90157205 
    2597 0.17547042 -0.96866552 0.17577609 183.80822404 
    2598 Axis -0.97260592 -0.22520729 0.05761416 
    2599 Axis point 0.00000000 174.33443147 29.64460255 
    2600 Rotation angle (degrees) 80.03590204 
    2601 Shift along axis -164.84350294 
    2602  
    2603 
    2604 > fitmap #1 inMap #2
    2605 
    2606 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2607 (#2) using 8555 atoms 
    2608 average map value = 0.129, steps = 2000 
    2609 shifted from previous position = 0.223 
    2610 rotated from previous position = 0.829 degrees 
    2611 atoms outside contour = 4631, contour level = 0.10328 
    2612  
    2613 Position of 5zf6.pdb (#1) relative to
    2614 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2615 Matrix rotation and translation 
    2616 0.95523491 0.12627846 -0.26754441 146.55435334 
    2617 0.23947844 0.20095469 0.94987751 145.96486274 
    2618 0.17371337 -0.97142727 0.16171797 183.59795330 
    2619 Axis -0.97302339 -0.22347009 0.05732887 
    2620 Axis point 0.00000000 172.59699771 30.26934598 
    2621 Rotation angle (degrees) 80.85382484 
    2622 Shift along axis -164.69413167 
    2623  
    2624 
    2625 > select add #1
    2626 
    2627 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    2628 
    2629 > fitmap #1 inMap #2
    2630 
    2631 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2632 (#2) using 8555 atoms 
    2633 average map value = 0.1276, steps = 2000 
    2634 shifted from previous position = 0.578 
    2635 rotated from previous position = 0.903 degrees 
    2636 atoms outside contour = 4673, contour level = 0.10328 
    2637  
    2638 Position of 5zf6.pdb (#1) relative to
    2639 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2640 Matrix rotation and translation 
    2641 0.95643333 0.12570810 -0.26350093 146.62391692 
    2642 0.23300137 0.21516139 0.94837541 145.55544584 
    2643 0.17591370 -0.96845394 0.17649737 184.00030683 
    2644 Axis -0.97326919 -0.22311257 0.05447811 
    2645 Axis point 0.00000000 174.18154237 29.52131391 
    2646 Rotation angle (degrees) 79.97685109 
    2647 Shift along axis -165.15580209 
    2648  
    2649 
    2650 > fitmap #1 inMap #2
    2651 
    2652 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2653 (#2) using 8555 atoms 
    2654 average map value = 0.1291, steps = 2000 
    2655 shifted from previous position = 0.363 
    2656 rotated from previous position = 0.352 degrees 
    2657 atoms outside contour = 4685, contour level = 0.10328 
    2658  
    2659 Position of 5zf6.pdb (#1) relative to
    2660 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2661 Matrix rotation and translation 
    2662 0.95497719 0.12448000 -0.26930149 146.60547981 
    2663 0.23896831 0.21519467 0.94688193 145.87389672 
    2664 0.17582011 -0.96860517 0.17575923 183.82784665 
    2665 Axis -0.97239968 -0.22596660 0.05812015 
    2666 Axis point 0.00000000 174.33808153 29.77706094 
    2667 Rotation angle (degrees) 80.03971295 
    2668 Shift along axis -164.83764797 
    2669  
    2670 
    2671 > volume gaussian #1 sDev 2
    2672 
    2673 [Repeated 1 time(s)]
    2674 
    2675 > hide #!2 models
    2676 
    2677 > select subtract #1
    2678 
    2679 Nothing selected 
    2680 
    2681 > select :260-320
    2682 
    2683 3024 atoms, 3078 bonds, 366 residues, 3 models selected 
    2684 
    2685 > select add #3
    2686 
    2687 10571 atoms, 10670 bonds, 1418 residues, 3 models selected 
    2688 
    2689 > select add #4
    2690 
    2691 18118 atoms, 18262 bonds, 2470 residues, 3 models selected 
    2692 
    2693 > select subtract #4
    2694 
    2695 9563 atoms, 9644 bonds, 1296 residues, 2 models selected 
    2696 
    2697 > select subtract #3
    2698 
    2699 1008 atoms, 1026 bonds, 122 residues, 1 model selected 
    2700 
    2701 > select add #2
    2702 
    2703 1008 atoms, 1026 bonds, 122 residues, 3 models selected 
    2704 
    2705 > show #!2 models
    2706 
    2707 > hide #!1 models
    2708 
    2709 > volume guassian #1 stdev 2
    2710 
    2711 Expected a density maps specifier or a keyword 
    2712 
    2713 > select subtract #2
    2714 
    2715 1008 atoms, 1026 bonds, 122 residues, 1 model selected 
    2716 
    2717 > show #!1 models
    2718 
    2719 > select add #1
    2720 
    2721 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    2722 
    2723 > select subtract #1
    2724 
    2725 Nothing selected 
    2726 
    2727 > hide #!2 models
    2728 
    2729 > select :270-312
    2730 
    2731 2172 atoms, 2226 bonds, 258 residues, 3 models selected 
    2732 
    2733 > select :270-320
    2734 
    2735 2568 atoms, 2622 bonds, 306 residues, 3 models selected 
    2736 
    2737 > select add #2
    2738 
    2739 2568 atoms, 2622 bonds, 306 residues, 5 models selected 
    2740 
    2741 > show #!2 models
    2742 
    2743 > select subtract #2
    2744 
    2745 2568 atoms, 2622 bonds, 306 residues, 3 models selected 
    2746 
    2747 > fitmap #1 inMap #5
    2748 
    2749 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    2750 average map value = 0.6588, steps = 44 
    2751 shifted from previous position = 0.251 
    2752 rotated from previous position = 0.917 degrees 
    2753 atoms outside contour = 0, contour level = 0.10406 
    2754  
    2755 Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates: 
    2756 Matrix rotation and translation 
    2757 0.99999998 -0.00021839 -0.00002624 -0.00561747 
    2758 0.00021838 0.99999996 -0.00015664 -0.02705654 
    2759 0.00002627 0.00015663 0.99999999 -0.00142914 
    2760 Axis 0.58007012 -0.09724114 0.80874150 
    2761 Axis point 124.68665962 -20.99976529 -0.00000000 
    2762 Rotation angle (degrees) 0.01547148 
    2763 Shift along axis -0.00178332 
    2764  
    2765 
    2766 > fitmap #1 inMap #2
    2767 
    2768 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2769 (#2) using 8555 atoms 
    2770 average map value = 0.1297, steps = 192 
    2771 shifted from previous position = 0.223 
    2772 rotated from previous position = 0.497 degrees 
    2773 atoms outside contour = 4641, contour level = 0.10328 
    2774  
    2775 Position of 5zf6.pdb (#1) relative to
    2776 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    2777 Matrix rotation and translation 
    2778 0.95551911 0.12624268 -0.26654456 146.57951723 
    2779 0.23725555 0.20782832 0.94895584 145.98336518 
    2780 0.17519424 -0.96998462 0.16863216 183.82012764 
    2781 Axis -0.97296776 -0.22397652 0.05628729 
    2782 Axis point 0.00000000 173.45562784 29.89819058 
    2783 Rotation angle (degrees) 80.44526139 
    2784 Shift along axis -164.96725473 
    2785  
    2786 
    2787 > fitmap #1 inMap #2 moveWholeMolecules false
    2788 
    2789 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2790 (#2) using 8555 atoms 
    2791 average map value = 0.1297, steps = 116 
    2792 shifted from previous position = 0.00753 
    2793 rotated from previous position = 0.0169 degrees 
    2794 atoms outside contour = 4645, contour level = 0.10328 
    2795  
    2796 
    2797 > fitmap #1 inMap #2 moveWholeMolecules false
    2798 
    2799 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2800 (#2) using 8555 atoms 
    2801 average map value = 0.1297, steps = 340 
    2802 shifted from previous position = 0.00951 
    2803 rotated from previous position = 0.0154 degrees 
    2804 atoms outside contour = 4645, contour level = 0.10328 
    2805  
    2806 
    2807 > fitmap #1 inMap #5 moveWholeMolecules false
    2808 
    2809 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    2810 average map value = 0.6588, steps = 44 
    2811 shifted from previous position = 0.233 
    2812 rotated from previous position = 0.48 degrees 
    2813 atoms outside contour = 0, contour level = 0.10406 
    2814  
    2815 
    2816 > select add #1
    2817 
    2818 10267 atoms, 10366 bonds, 1378 residues, 3 models selected 
    2819 
    2820 > select subtract #1
    2821 
    2822 1712 atoms, 1748 bonds, 204 residues, 2 models selected 
    2823 
    2824 > volume #2 color #b2b2b268
    2825 
    2826 > volume #2 color #b2b2b269
    2827 
    2828 > ui tool show "Show Sequence Viewer"
    2829 
    2830 > sequence chain #1/B
    2831 
    2832 Destroying pre-existing alignment with identifier 1/B 
    2833 Alignment identifier is 1/B 
    2834 
    2835 > select #1/B:268-269
    2836 
    2837 14 atoms, 13 bonds, 2 residues, 1 model selected 
    2838 
    2839 > select #1/B:268-288
    2840 
    2841 174 atoms, 179 bonds, 21 residues, 1 model selected 
    2842 
    2843 > select
    2844 > #1/B:125-142,164-180,207-212,222-224,237-267,280-299,305-328,332-356,450-462,482-499,534-540,567-593,622-636,653-666
    2845 
    2846 1850 atoms, 1864 bonds, 238 residues, 1 model selected 
    2847 
    2848 > select clear
    2849 
    2850 > select #1/B:304
    2851 
    2852 10 atoms, 10 bonds, 1 residue, 1 model selected 
    2853 
    2854 > select #1/B:304-305
    2855 
    2856 18 atoms, 18 bonds, 2 residues, 1 model selected 
    2857 
    2858 > select #1/B:304
    2859 
    2860 10 atoms, 10 bonds, 1 residue, 1 model selected 
    2861 
    2862 > select #1/B:304-322
    2863 
    2864 157 atoms, 157 bonds, 19 residues, 1 model selected 
    2865 
    2866 > select #1/B:331-332
    2867 
    2868 13 atoms, 12 bonds, 2 residues, 1 model selected 
    2869 
    2870 > select #1/B:302-332
    2871 
    2872 262 atoms, 265 bonds, 31 residues, 1 model selected 
    2873 
    2874 > fitmap #1 inMap #2 moveWholeMolecules false
    2875 
    2876 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2877 (#2) using 8555 atoms 
    2878 average map value = 0.1297, steps = 232 
    2879 shifted from previous position = 0.214 
    2880 rotated from previous position = 0.47 degrees 
    2881 atoms outside contour = 4639, contour level = 0.10328 
    2882  
    2883 
    2884 > fitmap #1 inMap #2 moveWholeMolecules false
    2885 
    2886 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2887 (#2) using 8555 atoms 
    2888 average map value = 0.1291, steps = 2000 
    2889 shifted from previous position = 0.0958 
    2890 rotated from previous position = 0.454 degrees 
    2891 atoms outside contour = 4687, contour level = 0.10328 
    2892  
    2893 
    2894 > fitmap #1 inMap #2 moveWholeMolecules false
    2895 
    2896 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2897 (#2) using 8555 atoms 
    2898 average map value = 0.129, steps = 2000 
    2899 shifted from previous position = 0.25 
    2900 rotated from previous position = 0.875 degrees 
    2901 atoms outside contour = 4630, contour level = 0.10328 
    2902  
    2903 
    2904 > fitmap #1 inMap #2 moveWholeMolecules false
    2905 
    2906 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2907 (#2) using 8555 atoms 
    2908 average map value = 0.1277, steps = 2000 
    2909 shifted from previous position = 0.604 
    2910 rotated from previous position = 0.954 degrees 
    2911 atoms outside contour = 4674, contour level = 0.10328 
    2912  
    2913 
    2914 > fitmap #1 inMap #2 moveWholeMolecules false
    2915 
    2916 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2917 (#2) using 8555 atoms 
    2918 average map value = 0.1291, steps = 2000 
    2919 shifted from previous position = 0.392 
    2920 rotated from previous position = 0.273 degrees 
    2921 atoms outside contour = 4688, contour level = 0.10328 
    2922  
    2923 
    2924 > ui mousemode right "rotate selected models"
    2925 
    2926 > select add #1
    2927 
    2928 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    2929 
    2930 > view matrix models
    2931 > #1,0.9936,-0.094139,-0.062377,209.56,0.083684,0.24289,0.96644,190.72,-0.075829,-0.96548,0.24921,212.87
    2932 
    2933 > fitmap #1 inMap #2 moveWholeMolecules false
    2934 
    2935 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2936 (#2) using 8555 atoms 
    2937 average map value = 0.1297, steps = 408 
    2938 shifted from previous position = 0.0525 
    2939 rotated from previous position = 7.42 degrees 
    2940 atoms outside contour = 4643, contour level = 0.10328 
    2941  
    2942 
    2943 > ui tool show "Show Sequence Viewer"
    2944 
    2945 > sequence chain #1/B
    2946 
    2947 Alignment identifier is 1/B 
    2948 
    2949 > select :200-320
    2950 
    2951 5772 atoms, 5862 bonds, 726 residues, 3 models selected 
    2952 
    2953 > fitmap #1 inMap #2 moveWholeMolecules false
    2954 
    2955 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2956 (#2) using 8555 atoms 
    2957 average map value = 0.1289, steps = 2000 
    2958 shifted from previous position = 0.251 
    2959 rotated from previous position = 0.502 degrees 
    2960 atoms outside contour = 4632, contour level = 0.10328 
    2961  
    2962 
    2963 > fitmap #1 inMap #5 moveWholeMolecules false
    2964 
    2965 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    2966 average map value = 0.6589, steps = 40 
    2967 shifted from previous position = 0.0131 
    2968 rotated from previous position = 0.0174 degrees 
    2969 atoms outside contour = 0, contour level = 0.10406 
    2970  
    2971 
    2972 > fitmap #1 inMap #5 moveWholeMolecules false
    2973 
    2974 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    2975 average map value = 0.6588, steps = 40 
    2976 shifted from previous position = 0.0121 
    2977 rotated from previous position = 0.00956 degrees 
    2978 atoms outside contour = 0, contour level = 0.10406 
    2979  
    2980 
    2981 > fitmap #1 inMap #5 moveWholeMolecules false
    2982 
    2983 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    2984 average map value = 0.6589, steps = 40 
    2985 shifted from previous position = 0.0371 
    2986 rotated from previous position = 0.0128 degrees 
    2987 atoms outside contour = 0, contour level = 0.10406 
    2988  
    2989 
    2990 > fitmap #4 inMap #2 moveWholeMolecules false
    2991 
    2992 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    2993 (#2) using 8555 atoms 
    2994 average map value = 0.000603, steps = 96 
    2995 shifted from previous position = 1.87 
    2996 rotated from previous position = 3.83 degrees 
    2997 atoms outside contour = 8554, contour level = 0.10328 
    2998  
    2999 
    3000 > fitmap #4 inMap #2 moveWholeMolecules false
    3001 
    3002 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3003 (#2) using 8555 atoms 
    3004 average map value = 0.0006029, steps = 44 
    3005 shifted from previous position = 0.00257 
    3006 rotated from previous position = 0.00598 degrees 
    3007 atoms outside contour = 8554, contour level = 0.10328 
    3008  
    3009 
    3010 > select add #3
    3011 
    3012 12403 atoms, 12526 bonds, 1658 residues, 3 models selected 
    3013 
    3014 > select add #4
    3015 
    3016 19034 atoms, 19190 bonds, 2590 residues, 3 models selected 
    3017 
    3018 > select subtract #4
    3019 
    3020 10479 atoms, 10572 bonds, 1416 residues, 2 models selected 
    3021 
    3022 > select subtract #3
    3023 
    3024 1924 atoms, 1954 bonds, 242 residues, 1 model selected 
    3025 
    3026 > fitmap #4 inMap #2 moveWholeMolecules false
    3027 
    3028 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3029 (#2) using 8555 atoms 
    3030 average map value = 0.0006029, steps = 48 
    3031 shifted from previous position = 0.00238 
    3032 rotated from previous position = 0.0048 degrees 
    3033 atoms outside contour = 8554, contour level = 0.10328 
    3034  
    3035 
    3036 > select add #1
    3037 
    3038 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    3039 
    3040 > select subtract #1
    3041 
    3042 Nothing selected 
    3043 
    3044 > open /Users/madhurikanavalli/Downloads/hPNP_dimer_5zf6_fit_tetramer1.pdb
    3045 
    3046 hPNP_dimer_5zf6_fit_tetramer1.pdb title: 
    3047 Crystal structure of the dimeric human pnpase [more info...] 
    3048  
    3049 Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb #6 
    3050 --- 
    3051 Chain | Description | UniProt 
    3052 A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669 
    3053  
    3054 
    3055 > hide #!1 models
    3056 
    3057 > select add #2
    3058 
    3059 2 models selected 
    3060 
    3061 > select subtract #2
    3062 
    3063 Nothing selected 
    3064 
    3065 > select add #6
    3066 
    3067 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    3068 
    3069 > select add #2
    3070 
    3071 8555 atoms, 8618 bonds, 1174 residues, 3 models selected 
    3072 
    3073 > fitmap #4 inMap #2
    3074 
    3075 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3076 (#2) using 8555 atoms 
    3077 average map value = 0.0006029, steps = 44 
    3078 shifted from previous position = 0.00473 
    3079 rotated from previous position = 0.0042 degrees 
    3080 atoms outside contour = 8554, contour level = 0.10328 
    3081  
    3082 Position of 5zf6.pdb (#4) relative to
    3083 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3084 Matrix rotation and translation 
    3085 0.63645764 -0.77048569 -0.03568582 78.12947023 
    3086 0.21006805 0.12863727 0.96918722 38.53015783 
    3087 -0.74215436 -0.62434307 0.24372659 302.42254591 
    3088 Axis -0.79677289 0.35323770 0.49028163 
    3089 Axis point -0.00000000 196.41371757 173.14599918 
    3090 Rotation angle (degrees) 89.74728167 
    3091 Shift along axis 99.63108047 
    3092  
    3093 
    3094 > fitmap #4 inMap #2
    3095 
    3096 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3097 (#2) using 8555 atoms 
    3098 average map value = 0.0006032, steps = 48 
    3099 shifted from previous position = 0.00496 
    3100 rotated from previous position = 0.0115 degrees 
    3101 atoms outside contour = 8554, contour level = 0.10328 
    3102  
    3103 Position of 5zf6.pdb (#4) relative to
    3104 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3105 Matrix rotation and translation 
    3106 0.63656824 -0.77038796 -0.03582278 78.12779013 
    3107 0.21013537 0.12856732 0.96918191 38.52558497 
    3108 -0.74204044 -0.62447805 0.24372763 302.41095664 
    3109 Axis -0.79683780 0.35311230 0.49026648 
    3110 Axis point 0.00000000 196.39377529 173.12757133 
    3111 Rotation angle (degrees) 89.74608769 
    3112 Shift along axis 99.61063610 
    3113  
    3114 
    3115 > select subtract #2
    3116 
    3117 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    3118 
    3119 > fitmap #4 inMap #2
    3120 
    3121 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3122 (#2) using 8555 atoms 
    3123 average map value = 0.0006032, steps = 48 
    3124 shifted from previous position = 0.0201 
    3125 rotated from previous position = 0.0227 degrees 
    3126 atoms outside contour = 8554, contour level = 0.10328 
    3127  
    3128 Position of 5zf6.pdb (#4) relative to
    3129 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3130 Matrix rotation and translation 
    3131 0.63632725 -0.77059781 -0.03559006 78.13063330 
    3132 0.21006324 0.12869982 0.96917996 38.51852128 
    3133 -0.74226752 -0.62419178 0.24376948 302.43743598 
    3134 Axis -0.79669358 0.35334215 0.49033527 
    3135 Axis point 0.00000000 196.42606613 173.17892989 
    3136 Rotation angle (degrees) 89.74799671 
    3137 Shift along axis 99.65978425 
    3138  
    3139 
    3140 > fitmap #6 inMap #2
    3141 
    3142 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3143 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3144 average map value = 0.1265, steps = 2000 
    3145 shifted from previous position = 26.4 
    3146 rotated from previous position = 14.9 degrees 
    3147 atoms outside contour = 4568, contour level = 0.10328 
    3148  
    3149 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    3150 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3151 Matrix rotation and translation 
    3152 0.99998715 0.00501254 -0.00076596 -38.39780829 
    3153 -0.00499658 0.99979573 0.01958429 -41.08711100 
    3154 0.00086397 -0.01958021 0.99980792 -27.19225070 
    3155 Axis -0.96807371 -0.04028867 -0.24740679 
    3156 Axis point 0.00000000 -832.72852867 1995.56199881 
    3157 Rotation angle (degrees) 1.15906129 
    3158 Shift along axis 45.55480119 
    3159  
    3160 
    3161 > fitmap #6 inMap #5
    3162 
    3163 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3164 using 8555 atoms 
    3165 average map value = 0.6589, steps = 80 
    3166 shifted from previous position = 6.92 
    3167 rotated from previous position = 21.3 degrees 
    3168 atoms outside contour = 0, contour level = 0.10406 
    3169  
    3170 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
    3171 (#5) coordinates: 
    3172 Matrix rotation and translation 
    3173 0.97042337 0.22451382 -0.08872453 -205.64095764 
    3174 -0.06918024 -0.09348358 -0.99321444 243.81703053 
    3175 -0.23128466 0.96997648 -0.07518673 -124.63683134 
    3176 Axis 0.98645360 0.07163285 -0.14757381 
    3177 Axis point 0.00000000 197.87770362 39.67267018 
    3178 Rotation angle (degrees) 95.68869835 
    3179 Shift along axis -166.99682276 
    3180  
    3181 
    3182 > select subtract #6
    3183 
    3184 Nothing selected 
    3185 
    3186 > hide #!6 models
    3187 
    3188 > color #6 #db5f27ff
    3189 
    3190 > color #6 #db7553ff
    3191 
    3192 > color #6 #db9a8cff
    3193 
    3194 > color #6 #db7a33ff
    3195 
    3196 > color #6 #db5b31ff
    3197 
    3198 > color #6 #db4122ff
    3199 
    3200 > show #!6 models
    3201 
    3202 > ui tool show "Show Sequence Viewer"
    3203 
    3204 > sequence chain #6/B
    3205 
    3206 Alignment identifier is 6/B 
    3207 
    3208 > hide #!2 models
    3209 
    3210 > select #6/B:293
    3211 
    3212 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3213 
    3214 > select #6/B:293-363
    3215 
    3216 599 atoms, 609 bonds, 71 residues, 1 model selected 
    3217 
    3218 > select #6/B:270
    3219 
    3220 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3221 
    3222 > select #6/B:270-369
    3223 
    3224 837 atoms, 853 bonds, 100 residues, 1 model selected 
    3225 
    3226 > select add #2
    3227 
    3228 837 atoms, 853 bonds, 100 residues, 3 models selected 
    3229 
    3230 > show #!2 models
    3231 
    3232 > fitmap #6 inMap #5 moveWholeMolecules false
    3233 
    3234 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3235 using 8555 atoms 
    3236 average map value = 0.6589, steps = 40 
    3237 shifted from previous position = 0.0331 
    3238 rotated from previous position = 0.0118 degrees 
    3239 atoms outside contour = 0, contour level = 0.10406 
    3240  
    3241 
    3242 > fitmap #6 inMap #5 moveWholeMolecules false
    3243 
    3244 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3245 using 8555 atoms 
    3246 average map value = 0.6589, steps = 40 
    3247 shifted from previous position = 0.0336 
    3248 rotated from previous position = 0.00485 degrees 
    3249 atoms outside contour = 0, contour level = 0.10406 
    3250  
    3251 
    3252 > fitmap #6 inMap #5 moveWholeMolecules false
    3253 
    3254 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3255 using 8555 atoms 
    3256 average map value = 0.6589, steps = 40 
    3257 shifted from previous position = 0.03 
    3258 rotated from previous position = 0.0369 degrees 
    3259 atoms outside contour = 0, contour level = 0.10406 
    3260  
    3261 
    3262 > fitmap #6 inMap #5 moveWholeMolecules false
    3263 
    3264 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3265 using 8555 atoms 
    3266 average map value = 0.6589, steps = 40 
    3267 shifted from previous position = 0.00753 
    3268 rotated from previous position = 0.00808 degrees 
    3269 atoms outside contour = 0, contour level = 0.10406 
    3270  
    3271 
    3272 > fitmap #6 inMap #5 moveWholeMolecules false
    3273 
    3274 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3275 using 8555 atoms 
    3276 average map value = 0.6588, steps = 44 
    3277 shifted from previous position = 0.0101 
    3278 rotated from previous position = 0.0526 degrees 
    3279 atoms outside contour = 0, contour level = 0.10406 
    3280  
    3281 
    3282 > fitmap #6 inMap #5 moveWholeMolecules false
    3283 
    3284 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3285 using 8555 atoms 
    3286 average map value = 0.6589, steps = 40 
    3287 shifted from previous position = 0.0172 
    3288 rotated from previous position = 0.00948 degrees 
    3289 atoms outside contour = 0, contour level = 0.10406 
    3290  
    3291 
    3292 > fitmap #6 inMap #5 moveWholeMolecules false
    3293 
    3294 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3295 using 8555 atoms 
    3296 average map value = 0.6589, steps = 40 
    3297 shifted from previous position = 0.0295 
    3298 rotated from previous position = 0.0068 degrees 
    3299 atoms outside contour = 0, contour level = 0.10406 
    3300  
    3301 
    3302 > fitmap #6 inMap #5 moveWholeMolecules false
    3303 
    3304 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3305 using 8555 atoms 
    3306 average map value = 0.6589, steps = 40 
    3307 shifted from previous position = 0.0301 
    3308 rotated from previous position = 0.033 degrees 
    3309 atoms outside contour = 0, contour level = 0.10406 
    3310  
    3311 
    3312 > fitmap #6 inMap #5 moveWholeMolecules false
    3313 
    3314 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3315 using 8555 atoms 
    3316 average map value = 0.6589, steps = 40 
    3317 shifted from previous position = 0.00827 
    3318 rotated from previous position = 0.00575 degrees 
    3319 atoms outside contour = 0, contour level = 0.10406 
    3320  
    3321 
    3322 > fitmap #6 inMap #5 moveWholeMolecules false
    3323 
    3324 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3325 using 8555 atoms 
    3326 average map value = 0.6588, steps = 44 
    3327 shifted from previous position = 0.0134 
    3328 rotated from previous position = 0.0519 degrees 
    3329 atoms outside contour = 0, contour level = 0.10406 
    3330  
    3331 
    3332 > fitmap #6 inMap #5 moveWholeMolecules false
    3333 
    3334 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3335 using 8555 atoms 
    3336 average map value = 0.6589, steps = 36 
    3337 shifted from previous position = 0.0421 
    3338 rotated from previous position = 0.0115 degrees 
    3339 atoms outside contour = 0, contour level = 0.10406 
    3340  
    3341 
    3342 > fitmap #6 inMap #5 moveWholeMolecules false
    3343 
    3344 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3345 using 8555 atoms 
    3346 average map value = 0.6589, steps = 40 
    3347 shifted from previous position = 0.033 
    3348 rotated from previous position = 0.048 degrees 
    3349 atoms outside contour = 0, contour level = 0.10406 
    3350  
    3351 
    3352 > fitmap #6 inMap #5 moveWholeMolecules false
    3353 
    3354 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3355 using 8555 atoms 
    3356 average map value = 0.6589, steps = 40 
    3357 shifted from previous position = 0.00797 
    3358 rotated from previous position = 0.0109 degrees 
    3359 atoms outside contour = 0, contour level = 0.10406 
    3360  
    3361 
    3362 > fitmap #6 inMap #5 moveWholeMolecules false
    3363 
    3364 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3365 using 8555 atoms 
    3366 average map value = 0.6588, steps = 44 
    3367 shifted from previous position = 0.0483 
    3368 rotated from previous position = 0.047 degrees 
    3369 atoms outside contour = 0, contour level = 0.10406 
    3370  
    3371 
    3372 > select subtract #2
    3373 
    3374 837 atoms, 853 bonds, 100 residues, 1 model selected 
    3375 
    3376 > fitmap #6 inMap #5 moveWholeMolecules false
    3377 
    3378 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3379 using 8555 atoms 
    3380 average map value = 0.6588, steps = 28 
    3381 shifted from previous position = 0.0141 
    3382 rotated from previous position = 0.00276 degrees 
    3383 atoms outside contour = 0, contour level = 0.10406 
    3384  
    3385 
    3386 > select #6/B:297-300
    3387 
    3388 30 atoms, 30 bonds, 4 residues, 1 model selected 
    3389 
    3390 > select #6/B:235-300
    3391 
    3392 536 atoms, 546 bonds, 66 residues, 1 model selected 
    3393 
    3394 > fitmap #6 inMap #2 moveWholeMolecules false
    3395 
    3396 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3397 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3398 average map value = 0.1275, steps = 2000 
    3399 shifted from previous position = 0.591 
    3400 rotated from previous position = 0.862 degrees 
    3401 atoms outside contour = 4676, contour level = 0.10328 
    3402  
    3403 
    3404 > select #6/B:213
    3405 
    3406 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3407 
    3408 > select #6/B:213-306
    3409 
    3410 747 atoms, 760 bonds, 94 residues, 1 model selected 
    3411 
    3412 > fitmap #6 inMap #2 moveWholeMolecules false
    3413 
    3414 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3415 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3416 average map value = 0.129, steps = 2000 
    3417 shifted from previous position = 0.31 
    3418 rotated from previous position = 0.339 degrees 
    3419 atoms outside contour = 4685, contour level = 0.10328 
    3420  
    3421 
    3422 > fitmap #6 inMap #2 moveWholeMolecules false
    3423 
    3424 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3425 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3426 average map value = 0.129, steps = 2000 
    3427 shifted from previous position = 0.349 
    3428 rotated from previous position = 0.98 degrees 
    3429 atoms outside contour = 4646, contour level = 0.10328 
    3430  
    3431 
    3432 > fitmap #6 inMap #2 moveWholeMolecules false
    3433 
    3434 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3435 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3436 average map value = 0.1277, steps = 2000 
    3437 shifted from previous position = 0.633 
    3438 rotated from previous position = 0.897 degrees 
    3439 atoms outside contour = 4681, contour level = 0.10328 
    3440  
    3441 
    3442 > fitmap #6 inMap #2 moveWholeMolecules false
    3443 
    3444 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3445 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3446 average map value = 0.129, steps = 2000 
    3447 shifted from previous position = 0.41 
    3448 rotated from previous position = 0.127 degrees 
    3449 atoms outside contour = 4685, contour level = 0.10328 
    3450  
    3451 
    3452 > fitmap #6 inMap #2 moveWholeMolecules false
    3453 
    3454 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3455 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3456 average map value = 0.1287, steps = 2000 
    3457 shifted from previous position = 0.256 
    3458 rotated from previous position = 0.952 degrees 
    3459 atoms outside contour = 4632, contour level = 0.10328 
    3460  
    3461 
    3462 > fitmap #6 inMap #2 moveWholeMolecules false
    3463 
    3464 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3465 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3466 average map value = 0.1277, steps = 2000 
    3467 shifted from previous position = 0.662 
    3468 rotated from previous position = 1.12 degrees 
    3469 atoms outside contour = 4683, contour level = 0.10328 
    3470  
    3471 
    3472 > fitmap #6 inMap #2 moveWholeMolecules false
    3473 
    3474 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3475 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3476 average map value = 0.1291, steps = 2000 
    3477 shifted from previous position = 0.449 
    3478 rotated from previous position = 0.373 degrees 
    3479 atoms outside contour = 4684, contour level = 0.10328 
    3480  
    3481 
    3482 > fitmap #6 inMap #2 moveWholeMolecules false
    3483 
    3484 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3485 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3486 average map value = 0.129, steps = 2000 
    3487 shifted from previous position = 0.167 
    3488 rotated from previous position = 0.682 degrees 
    3489 atoms outside contour = 4646, contour level = 0.10328 
    3490  
    3491 
    3492 > select #6/B:182
    3493 
    3494 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3495 
    3496 > select #6/B:182-304
    3497 
    3498 964 atoms, 983 bonds, 123 residues, 1 model selected 
    3499 
    3500 > fitmap #6 inMap #2 moveWholeMolecules false
    3501 
    3502 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3503 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3504 average map value = 0.1275, steps = 2000 
    3505 shifted from previous position = 0.548 
    3506 rotated from previous position = 0.789 degrees 
    3507 atoms outside contour = 4671, contour level = 0.10328 
    3508  
    3509 
    3510 > fitmap #6 inMap #2 moveWholeMolecules false
    3511 
    3512 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3513 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3514 average map value = 0.129, steps = 2000 
    3515 shifted from previous position = 0.33 
    3516 rotated from previous position = 0.366 degrees 
    3517 atoms outside contour = 4685, contour level = 0.10328 
    3518  
    3519 
    3520 > fitmap #6 inMap #5 moveWholeMolecules false
    3521 
    3522 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3523 using 8555 atoms 
    3524 average map value = 0.6589, steps = 44 
    3525 shifted from previous position = 0.3 
    3526 rotated from previous position = 0.943 degrees 
    3527 atoms outside contour = 0, contour level = 0.10406 
    3528  
    3529 
    3530 > fitmap #6 inMap #2 moveWholeMolecules false
    3531 
    3532 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3533 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3534 average map value = 0.1275, steps = 2000 
    3535 shifted from previous position = 0.595 
    3536 rotated from previous position = 0.908 degrees 
    3537 atoms outside contour = 4673, contour level = 0.10328 
    3538  
    3539 
    3540 > select #6/B:290
    3541 
    3542 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3543 
    3544 > select #6/B:290-291
    3545 
    3546 13 atoms, 12 bonds, 2 residues, 1 model selected 
    3547 
    3548 > select #6/B:302
    3549 
    3550 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3551 
    3552 > select #6/B:302-373
    3553 
    3554 597 atoms, 605 bonds, 72 residues, 1 model selected 
    3555 
    3556 > fitmap #6 inMap #2 moveWholeMolecules false
    3557 
    3558 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3559 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3560 average map value = 0.129, steps = 2000 
    3561 shifted from previous position = 0.319 
    3562 rotated from previous position = 0.348 degrees 
    3563 atoms outside contour = 4688, contour level = 0.10328 
    3564  
    3565 
    3566 > fitmap #6 inMap #2 moveWholeMolecules false
    3567 
    3568 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3569 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3570 average map value = 0.129, steps = 2000 
    3571 shifted from previous position = 0.331 
    3572 rotated from previous position = 0.953 degrees 
    3573 atoms outside contour = 4637, contour level = 0.10328 
    3574  
    3575 
    3576 > fitmap #6 inMap #2 moveWholeMolecules false
    3577 
    3578 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3579 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3580 average map value = 0.1278, steps = 2000 
    3581 shifted from previous position = 0.601 
    3582 rotated from previous position = 0.815 degrees 
    3583 atoms outside contour = 4675, contour level = 0.10328 
    3584  
    3585 
    3586 > fitmap #6 inMap #2 moveWholeMolecules false
    3587 
    3588 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3589 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3590 average map value = 0.129, steps = 2000 
    3591 shifted from previous position = 0.403 
    3592 rotated from previous position = 0.116 degrees 
    3593 atoms outside contour = 4686, contour level = 0.10328 
    3594  
    3595 
    3596 > fitmap #6 inMap #2 moveWholeMolecules false
    3597 
    3598 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3599 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3600 average map value = 0.1287, steps = 2000 
    3601 shifted from previous position = 0.254 
    3602 rotated from previous position = 0.971 degrees 
    3603 atoms outside contour = 4636, contour level = 0.10328 
    3604  
    3605 
    3606 > select clear
    3607 
    3608 > show #!4 models
    3609 
    3610 > select add #4
    3611 
    3612 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    3613 
    3614 > view matrix models
    3615 > #4,0.41896,-0.90784,0.01751,172.56,0.15936,0.092502,0.98288,84.02,-0.89391,-0.40899,0.18343,344.93
    3616 
    3617 > ui mousemode right "translate selected models"
    3618 
    3619 > view matrix models
    3620 > #4,0.41896,-0.90784,0.01751,178.41,0.15936,0.092502,0.98288,144.07,-0.89391,-0.40899,0.18343,218.26
    3621 
    3622 > ui mousemode right "rotate selected models"
    3623 
    3624 > view matrix models
    3625 > #4,-0.42775,0.90035,0.079962,224.76,0.60709,0.22062,0.76339,113.04,0.66968,0.37509,-0.64097,107.87
    3626 
    3627 > view matrix models
    3628 > #4,-0.18295,0.98312,0.003384,206.1,0.40212,0.071688,0.91278,126.6,0.89712,0.16835,-0.40844,83.19
    3629 
    3630 > hide #!6 models
    3631 
    3632 > show #!6 models
    3633 
    3634 > fitmap #6 inMap #2
    3635 
    3636 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    3637 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3638 average map value = 0.1277, steps = 2000 
    3639 shifted from previous position = 0.66 
    3640 rotated from previous position = 1.14 degrees 
    3641 atoms outside contour = 4682, contour level = 0.10328 
    3642  
    3643 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    3644 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3645 Matrix rotation and translation 
    3646 0.98050817 -0.05115886 -0.18970108 13.07808380 
    3647 -0.00988416 0.95144047 -0.30767407 32.79012008 
    3648 0.19622954 0.30355198 0.93238949 -110.39635553 
    3649 Axis 0.84418066 -0.53301911 0.05700559 
    3650 Axis point 0.00000000 367.20770125 26.56375354 
    3651 Rotation angle (degrees) 21.22450246 
    3652 Shift along axis -12.73070479 
    3653  
    3654 
    3655 > view matrix models
    3656 > #4,-0.08736,0.99518,0.044597,196.53,0.42306,-0.0034671,0.90609,126.01,0.90188,0.098024,-0.42072,84.082
    3657 
    3658 > ui mousemode right "translate selected models"
    3659 
    3660 > view matrix models
    3661 > #4,-0.08736,0.99518,0.044597,191.27,0.42306,-0.0034671,0.90609,129.79,0.90188,0.098024,-0.42072,71.859
    3662 
    3663 > view matrix models
    3664 > #4,-0.08736,0.99518,0.044597,183.77,0.42306,-0.0034671,0.90609,130.43,0.90188,0.098024,-0.42072,77.917
    3665 
    3666 > fitmap #1 inMap #2
    3667 
    3668 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3669 (#2) using 8555 atoms 
    3670 average map value = 0.1277, steps = 2000 
    3671 shifted from previous position = 0.621 
    3672 rotated from previous position = 1.01 degrees 
    3673 atoms outside contour = 4676, contour level = 0.10328 
    3674  
    3675 Position of 5zf6.pdb (#1) relative to
    3676 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3677 Matrix rotation and translation 
    3678 0.97947769 0.14877998 -0.13597045 146.59186252 
    3679 0.10549263 0.19640199 0.97483206 145.59322335 
    3680 0.17174037 -0.96917014 0.17667618 184.27065038 
    3681 Axis -0.98746437 -0.15630305 -0.02198800 
    3682 Axis point 0.00000000 170.41082713 18.63330543 
    3683 Rotation angle (degrees) 79.84696577 
    3684 Shift along axis -171.56264926 
    3685  
    3686 
    3687 > fitmap #4 inMap #2
    3688 
    3689 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3690 (#2) using 8555 atoms 
    3691 average map value = 0.111, steps = 1076 
    3692 shifted from previous position = 4.65 
    3693 rotated from previous position = 13.2 degrees 
    3694 atoms outside contour = 5073, contour level = 0.10328 
    3695  
    3696 Position of 5zf6.pdb (#4) relative to
    3697 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3698 Matrix rotation and translation 
    3699 -0.36553432 0.89395507 0.25928552 159.59107335 
    3700 0.35313265 -0.12454696 0.92724612 89.23861751 
    3701 0.86120960 0.43050246 -0.27015854 37.52485026 
    3702 Axis -0.52316181 -0.63393602 -0.56958480 
    3703 Axis point 53.81283798 -0.00000000 -6.36388496 
    3704 Rotation angle (degrees) 151.65683196 
    3705 Shift along axis -161.43711324 
    3706  
    3707 
    3708 > fitmap #5 inMap #2
    3709 
    3710 Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
    3711 13249 points 
    3712 correlation = 0.5788, correlation about mean = 0.198, overlap = 733.5 
    3713 steps = 2000, shift = 0.484, angle = 0.682 degrees 
    3714  
    3715 Position of 5zf6.pdb map 4 (#5) relative to
    3716 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3717 Matrix rotation and translation 
    3718 0.95807999 0.12330246 -0.25861017 146.85960897 
    3719 0.23030716 0.20545224 0.95118241 145.69179160 
    3720 0.17041517 -0.97086861 0.16844224 183.83696417 
    3721 Axis -0.97454450 -0.21753027 0.05425498 
    3722 Axis point 0.00000000 173.40314082 29.37698708 
    3723 Rotation angle (degrees) 80.44541010 
    3724 Shift along axis -164.83952771 
    3725  
    3726 
    3727 > select add #1
    3728 
    3729 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    3730 
    3731 > show #!1 models
    3732 
    3733 > hide #!6 models
    3734 
    3735 > select subtract #4
    3736 
    3737 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    3738 
    3739 > fitmap #5 inMap #2
    3740 
    3741 Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
    3742 13249 points 
    3743 correlation = 0.5837, correlation about mean = 0.2048, overlap = 738.4 
    3744 steps = 2000, shift = 0.311, angle = 0.305 degrees 
    3745  
    3746 Position of 5zf6.pdb map 4 (#5) relative to
    3747 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3748 Matrix rotation and translation 
    3749 0.95689175 0.12490398 -0.26221586 146.68598283 
    3750 0.23295357 0.20914731 0.94973155 145.87551846 
    3751 0.17346699 -0.96987442 0.17103451 183.65499502 
    3752 Axis -0.97373187 -0.22100279 0.05480881 
    3753 Axis point 0.00000000 173.59451621 29.35452178 
    3754 Rotation angle (degrees) 80.29724460 
    3755 Shift along axis -165.00580142 
    3756  
    3757 
    3758 > fitmap #5 inMap #2
    3759 
    3760 Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
    3761 13249 points 
    3762 correlation = 0.5802, correlation about mean = 0.2023, overlap = 737.3 
    3763 steps = 2000, shift = 0.297, angle = 0.896 degrees 
    3764  
    3765 Position of 5zf6.pdb map 4 (#5) relative to
    3766 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3767 Matrix rotation and translation 
    3768 0.95523339 0.12648677 -0.26745139 146.55407822 
    3769 0.24029680 0.19565106 0.95077763 145.98961234 
    3770 0.17258794 -0.97248226 0.15649806 183.41632773 
    3771 Axis -0.97319253 -0.22266517 0.05758923 
    3772 Axis point 0.00000000 171.93881899 30.45197129 
    3773 Rotation angle (degrees) 81.15909876 
    3774 Shift along axis -164.56933019 
    3775  
    3776 
    3777 > fitmap #1 inMap #2
    3778 
    3779 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3780 (#2) using 8555 atoms 
    3781 average map value = 0.1291, steps = 2000 
    3782 shifted from previous position = 0.392 
    3783 rotated from previous position = 0.273 degrees 
    3784 atoms outside contour = 4687, contour level = 0.10328 
    3785  
    3786 Position of 5zf6.pdb (#1) relative to
    3787 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3788 Matrix rotation and translation 
    3789 0.97915094 0.14700446 -0.14018954 146.62405858 
    3790 0.11011085 0.19584575 0.97443318 145.92300788 
    3791 0.17070156 -0.96955356 0.17557577 184.05988413 
    3792 Axis -0.98727891 -0.15789008 -0.01873690 
    3793 Axis point 0.00000000 170.57529358 18.76382801 
    3794 Rotation angle (degrees) 79.90468443 
    3795 Shift along axis -171.24734835 
    3796  
    3797 
    3798 > fitmap #3 inMap #2
    3799 
    3800 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) to map
    3801 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    3802 average map value = 0.02577, steps = 116 
    3803 shifted from previous position = 8.58 
    3804 rotated from previous position = 7.99 degrees 
    3805 atoms outside contour = 7667, contour level = 0.10328 
    3806  
    3807 Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) relative to
    3808 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3809 Matrix rotation and translation 
    3810 0.68645478 0.37419295 0.62350577 -153.15730085 
    3811 0.19540344 0.73097981 -0.65382413 67.23553836 
    3812 -0.70042652 0.57065588 0.42866600 94.59887008 
    3813 Axis 0.67568241 0.73056133 -0.09865815 
    3814 Axis point -12.74486076 0.00000000 170.20042114 
    3815 Rotation angle (degrees) 64.97268395 
    3816 Shift along axis -63.69895833 
    3817  
    3818 
    3819 > fitmap #4 inMap #2
    3820 
    3821 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    3822 (#2) using 8555 atoms 
    3823 average map value = 0.111, steps = 628 
    3824 shifted from previous position = 0.0142 
    3825 rotated from previous position = 0.0153 degrees 
    3826 atoms outside contour = 5070, contour level = 0.10328 
    3827  
    3828 Position of 5zf6.pdb (#4) relative to
    3829 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3830 Matrix rotation and translation 
    3831 -0.36562224 0.89396097 0.25914118 159.60672611 
    3832 0.35289438 -0.12448775 0.92734478 89.24870916 
    3833 0.86126995 0.43050734 -0.26995831 37.49952053 
    3834 Axis -0.52308545 -0.63393934 -0.56965124 
    3835 Axis point 53.83227055 0.00000000 -6.37339730 
    3836 Rotation angle (degrees) 151.64648359 
    3837 Shift along axis -161.42787146 
    3838  
    3839 
    3840 > fitmap #5 inMap #2
    3841 
    3842 Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
    3843 13249 points 
    3844 correlation = 0.5788, correlation about mean = 0.198, overlap = 733.5 
    3845 steps = 2000, shift = 0.601, angle = 0.852 degrees 
    3846  
    3847 Position of 5zf6.pdb map 4 (#5) relative to
    3848 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3849 Matrix rotation and translation 
    3850 0.95808182 0.12330121 -0.25860399 146.85969531 
    3851 0.23030239 0.20544566 0.95118499 145.69187618 
    3852 0.17041133 -0.97087016 0.16843719 183.83677193 
    3853 Axis -0.97454577 -0.21752501 0.05425315 
    3854 Axis point 0.00000000 173.40254461 29.37657817 
    3855 Rotation angle (degrees) 80.44569473 
    3856 Shift along axis -164.83939909 
    3857  
    3858 
    3859 > fitmap #5 inMap #2
    3860 
    3861 Fit map 5zf6.pdb map 4 in map cryosparc_P1_J138_004_volume_map_sharp.mrc using
    3862 13249 points 
    3863 correlation = 0.5837, correlation about mean = 0.2048, overlap = 738.4 
    3864 steps = 2000, shift = 0.311, angle = 0.306 degrees 
    3865  
    3866 Position of 5zf6.pdb map 4 (#5) relative to
    3867 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    3868 Matrix rotation and translation 
    3869 0.95689295 0.12490402 -0.26221149 146.68601347 
    3870 0.23294922 0.20914729 0.94973262 145.87546726 
    3871 0.17346624 -0.96987442 0.17103528 183.65508357 
    3872 Axis -0.97373258 -0.22100023 0.05480660 
    3873 Axis point 0.00000000 173.59456162 29.35417238 
    3874 Rotation angle (degrees) 80.29718783 
    3875 Shift along axis -165.00595139 
    3876  
    3877 
    3878 > select add #6
    3879 
    3880 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    3881 
    3882 > show #!5 models
    3883 
    3884 > hide #!5 models
    3885 
    3886 > select add #4
    3887 
    3888 25665 atoms, 25854 bonds, 3522 residues, 3 models selected 
    3889 
    3890 > select subtract #4
    3891 
    3892 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    3893 
    3894 > select subtract #6
    3895 
    3896 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    3897 
    3898 > select add #6
    3899 
    3900 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    3901 
    3902 > select subtract #1
    3903 
    3904 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    3905 
    3906 > fitmap #6 inMap #5
    3907 
    3908 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3909 using 8555 atoms 
    3910 average map value = 0.6588, steps = 48 
    3911 shifted from previous position = 0.493 
    3912 rotated from previous position = 0.363 degrees 
    3913 atoms outside contour = 0, contour level = 0.10406 
    3914  
    3915 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
    3916 (#5) coordinates: 
    3917 Matrix rotation and translation 
    3918 0.97055165 0.22364863 -0.08950306 -205.36240728 
    3919 -0.06949210 -0.09581212 -0.99297075 244.22612919 
    3920 -0.23065202 0.96994914 -0.07744880 -124.28462420 
    3921 Axis 0.98654027 0.07093980 -0.14732906 
    3922 Axis point 0.00000000 197.65683581 39.75508724 
    3923 Rotation angle (degrees) 95.81718147 
    3924 Shift along axis -166.96219566 
    3925  
    3926 
    3927 > fitmap #6 inMap #5
    3928 
    3929 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3930 using 8555 atoms 
    3931 average map value = 0.6589, steps = 40 
    3932 shifted from previous position = 0.019 
    3933 rotated from previous position = 0.00359 degrees 
    3934 atoms outside contour = 0, contour level = 0.10406 
    3935  
    3936 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
    3937 (#5) coordinates: 
    3938 Matrix rotation and translation 
    3939 0.97055020 0.22365652 -0.08949909 -205.37186328 
    3940 -0.06950193 -0.09575101 -0.99297595 244.20964705 
    3941 -0.23065517 0.96995336 -0.07738660 -124.28250667 
    3942 Axis 0.98653885 0.07094293 -0.14733704 
    3943 Axis point 0.00000000 197.65379741 39.75494966 
    3944 Rotation angle (degrees) 95.81367267 
    3945 Shift along axis -166.97095635 
    3946  
    3947 
    3948 > fitmap #6 inMap #5
    3949 
    3950 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    3951 using 8555 atoms 
    3952 average map value = 0.6589, steps = 40 
    3953 shifted from previous position = 0.0306 
    3954 rotated from previous position = 0.00975 degrees 
    3955 atoms outside contour = 0, contour level = 0.10406 
    3956  
    3957 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
    3958 (#5) coordinates: 
    3959 Matrix rotation and translation 
    3960 0.97055232 0.22364004 -0.08951726 -205.34348872 
    3961 -0.06955967 -0.09559197 -0.99298723 244.19422434 
    3962 -0.23062884 0.96997285 -0.07722068 -124.30528679 
    3963 Axis 0.98653781 0.07091938 -0.14735532 
    3964 Axis point 0.00000000 197.66396599 39.75351657 
    3965 Rotation angle (degrees) 95.80425393 
    3966 Shift along axis -166.94396819 
    3967  
    3968 
    3969 > fitmap #1 inMap #5
    3970 
    3971 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    3972 average map value = 0.6588, steps = 48 
    3973 shifted from previous position = 0.161 
    3974 rotated from previous position = 0.509 degrees 
    3975 atoms outside contour = 0, contour level = 0.10406 
    3976  
    3977 Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates: 
    3978 Matrix rotation and translation 
    3979 0.99145298 0.01667906 0.12939396 0.08470249 
    3980 -0.01973646 0.99955465 0.02238229 -0.25108805 
    3981 -0.12896302 -0.02474477 0.99134063 0.07775739 
    3982 Axis -0.17774891 0.97444383 -0.13734824 
    3983 Axis point 0.33249228 0.00000000 -0.26118801 
    3984 Rotation angle (degrees) 7.61791888 
    3985 Shift along axis -0.27040682 
    3986  
    3987 
    3988 > fitmap #1 inMap #5
    3989 
    3990 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    3991 average map value = 0.6589, steps = 40 
    3992 shifted from previous position = 0.0407 
    3993 rotated from previous position = 0.0102 degrees 
    3994 atoms outside contour = 0, contour level = 0.10406 
    3995  
    3996 Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates: 
    3997 Matrix rotation and translation 
    3998 0.99146916 0.01666799 0.12927133 0.06971343 
    3999 -0.01970608 0.99955802 0.02225820 -0.21745944 
    4000 -0.12884319 -0.02461575 0.99135942 0.06043299 
    4001 Axis -0.17698575 0.97458383 -0.13734048 
    4002 Axis point 0.23490649 0.00000000 -0.20536492 
    4003 Rotation angle (degrees) 7.60962745 
    4004 Shift along axis -0.23257063 
    4005  
    4006 
    4007 > fitmap #3 inMap #5
    4008 
    4009 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) to map 5zf6.pdb map 4 (#5)
    4010 using 8555 atoms 
    4011 average map value = 0.1347, steps = 208 
    4012 shifted from previous position = 25.2 
    4013 rotated from previous position = 35.7 degrees 
    4014 atoms outside contour = 6498, contour level = 0.10406 
    4015  
    4016 Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#3) relative to 5zf6.pdb map 4
    4017 (#5) coordinates: 
    4018 Matrix rotation and translation 
    4019 0.77158106 0.62513280 0.11777791 -289.07448145 
    4020 0.63513719 -0.74671117 -0.19754285 78.40770373 
    4021 -0.03554444 0.22722545 -0.97319329 91.27335582 
    4022 Axis 0.94037000 0.33943148 0.02214813 
    4023 Axis point 0.00000000 85.49559070 58.83183688 
    4024 Rotation angle (degrees) 166.94703469 
    4025 Shift along axis -243.20139227 
    4026  
    4027 
    4028 > fitmap #4 inMap #5
    4029 
    4030 Fit molecule 5zf6.pdb (#4) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    4031 average map value = 0.1942, steps = 288 
    4032 shifted from previous position = 83.6 
    4033 rotated from previous position = 22.3 degrees 
    4034 atoms outside contour = 4391, contour level = 0.10406 
    4035  
    4036 Position of 5zf6.pdb (#4) relative to 5zf6.pdb map 4 (#5) coordinates: 
    4037 Matrix rotation and translation 
    4038 0.19636392 0.91428712 0.35428840 -37.79820017 
    4039 -0.65264442 -0.14778711 0.74311118 24.99961702 
    4040 0.73177624 -0.37714458 0.56768433 -77.46490126 
    4041 Axis -0.57073182 -0.19231708 -0.79829777 
    4042 Axis point 29.48192807 18.18756670 0.00000000 
    4043 Rotation angle (degrees) 101.06190229 
    4044 Shift along axis 78.60484018 
    4045  
    4046 
    4047 > show #!6 models
    4048 
    4049 > hide #!4 models
    4050 
    4051 > show #!4 models
    4052 
    4053 > hide #!1 models
    4054 
    4055 > fitmap #6 inMap #5
    4056 
    4057 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map 5zf6.pdb map 4 (#5)
    4058 using 8555 atoms 
    4059 average map value = 0.6589, steps = 40 
    4060 shifted from previous position = 0.025 
    4061 rotated from previous position = 0.006 degrees 
    4062 atoms outside contour = 0, contour level = 0.10406 
    4063  
    4064 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to 5zf6.pdb map 4
    4065 (#5) coordinates: 
    4066 Matrix rotation and translation 
    4067 0.97055420 0.22364475 -0.08948515 -205.36895267 
    4068 -0.06950521 -0.09568124 -0.99298245 244.19933684 
    4069 -0.23063735 0.96996296 -0.07731936 -124.29858846 
    4070 Axis 0.98653982 0.07094047 -0.14733171 
    4071 Axis point 0.00000000 197.65981342 39.75092422 
    4072 Rotation angle (degrees) 95.80961211 
    4073 Shift along axis -166.96791002 
    4074  
    4075 
    4076 > fitmap #6 inMap #2
    4077 
    4078 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4079 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4080 average map value = 0.1297, steps = 224 
    4081 shifted from previous position = 0.231 
    4082 rotated from previous position = 0.288 degrees 
    4083 atoms outside contour = 4645, contour level = 0.10328 
    4084  
    4085 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4086 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4087 Matrix rotation and translation 
    4088 0.98003837 -0.05662787 -0.19057303 14.34462696 
    4089 -0.00335724 0.95372551 -0.30065992 30.04155398 
    4090 0.19878009 0.29529806 0.93449748 -109.97811233 
    4091 Axis 0.83483592 -0.54541761 0.07462310 
    4092 Axis point 0.00000000 373.57563125 19.53424803 
    4093 Rotation angle (degrees) 20.91184972 
    4094 Shift along axis -12.61669073 
    4095  
    4096 
    4097 > select subtract #6
    4098 
    4099 Nothing selected 
    4100 
    4101 > hide #!6 models
    4102 
    4103 > show #!1 models
    4104 
    4105 > fitmap #1 inMap #5
    4106 
    4107 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    4108 average map value = 0.6589, steps = 44 
    4109 shifted from previous position = 0.026 
    4110 rotated from previous position = 0.0331 degrees 
    4111 atoms outside contour = 0, contour level = 0.10406 
    4112  
    4113 Position of 5zf6.pdb (#1) relative to 5zf6.pdb map 4 (#5) coordinates: 
    4114 Matrix rotation and translation 
    4115 0.99146060 0.01666840 0.12933693 0.08477383 
    4116 -0.01963405 0.99957196 0.02168854 -0.22398077 
    4117 -0.12892005 -0.02404274 0.99136349 0.08044059 
    4118 Axis -0.17271744 0.97538220 -0.13710670 
    4119 Axis point 0.38468345 0.00000000 -0.30402781 
    4120 Rotation angle (degrees) 7.60758331 
    4121 Shift along axis -0.24413772 
    4122  
    4123 
    4124 > fitmap #1 inMap #5 moveWholeMolecules false
    4125 
    4126 Fit molecule 5zf6.pdb (#1) to map 5zf6.pdb map 4 (#5) using 8555 atoms 
    4127 average map value = 0.6589, steps = 40 
    4128 shifted from previous position = 0.0313 
    4129 rotated from previous position = 0.0104 degrees 
    4130 atoms outside contour = 0, contour level = 0.10406 
    4131  
    4132 
    4133 > ui tool show "Fit in Map"
    4134 
    4135 > close #5
    4136 
    4137 > select :200-320
    4138 
    4139 7696 atoms, 7816 bonds, 968 residues, 4 models selected 
    4140 
    4141 > select :250-350
    4142 
    4143 6712 atoms, 6840 bonds, 808 residues, 4 models selected 
    4144 
    4145 > select :270-350
    4146 
    4147 5440 atoms, 5560 bonds, 648 residues, 4 models selected 
    4148 
    4149 > fitmap #1 inMap #2 moveWholeMolecules false
    4150 
    4151 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4152 (#2) using 8555 atoms 
    4153 average map value = 0.1289, steps = 2000 
    4154 shifted from previous position = 0.175 
    4155 rotated from previous position = 0.694 degrees 
    4156 atoms outside contour = 4632, contour level = 0.10328 
    4157  
    4158 
    4159 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4160 
    4161 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4162 (#2) using 8555 atoms 
    4163 average map value = 0.1293, steps = 48 
    4164 shifted from previous position = 0.142 
    4165 rotated from previous position = 0 degrees 
    4166 atoms outside contour = 4629, contour level = 0.10328 
    4167  
    4168 
    4169 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4170 
    4171 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4172 (#2) using 8555 atoms 
    4173 average map value = 0.1293, steps = 40 
    4174 shifted from previous position = 0.0151 
    4175 rotated from previous position = 0 degrees 
    4176 atoms outside contour = 4630, contour level = 0.10328 
    4177  
    4178 
    4179 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4180 
    4181 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4182 (#2) using 8555 atoms 
    4183 average map value = 0.1293, steps = 40 
    4184 shifted from previous position = 0.0142 
    4185 rotated from previous position = 0 degrees 
    4186 atoms outside contour = 4629, contour level = 0.10328 
    4187  
    4188 
    4189 > select clear
    4190 
    4191 > select add #2
    4192 
    4193 2 models selected 
    4194 
    4195 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4196 
    4197 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4198 (#2) using 8555 atoms 
    4199 average map value = 0.1293, steps = 40 
    4200 shifted from previous position = 0.0141 
    4201 rotated from previous position = 0 degrees 
    4202 atoms outside contour = 4630, contour level = 0.10328 
    4203  
    4204 
    4205 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4206 
    4207 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4208 (#2) using 8555 atoms 
    4209 average map value = 0.1293, steps = 40 
    4210 shifted from previous position = 0.0156 
    4211 rotated from previous position = 0 degrees 
    4212 atoms outside contour = 4629, contour level = 0.10328 
    4213  
    4214 
    4215 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4216 
    4217 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4218 (#2) using 8555 atoms 
    4219 average map value = 0.1293, steps = 36 
    4220 shifted from previous position = 0.00098 
    4221 rotated from previous position = 0 degrees 
    4222 atoms outside contour = 4629, contour level = 0.10328 
    4223  
    4224 
    4225 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4226 
    4227 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4228 (#2) using 8555 atoms 
    4229 average map value = 0.1293, steps = 36 
    4230 shifted from previous position = 0.000935 
    4231 rotated from previous position = 0 degrees 
    4232 atoms outside contour = 4630, contour level = 0.10328 
    4233  
    4234 
    4235 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4236 
    4237 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4238 (#2) using 8555 atoms 
    4239 average map value = 0.1293, steps = 28 
    4240 shifted from previous position = 0.00984 
    4241 rotated from previous position = 0 degrees 
    4242 atoms outside contour = 4631, contour level = 0.10328 
    4243  
    4244 
    4245 > fitmap #1 inMap #2 moveWholeMolecules false rotate false
    4246 
    4247 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4248 (#2) using 8555 atoms 
    4249 average map value = 0.1293, steps = 40 
    4250 shifted from previous position = 0.00416 
    4251 rotated from previous position = 0 degrees 
    4252 atoms outside contour = 4629, contour level = 0.10328 
    4253  
    4254 
    4255 > fitmap #4 inMap #2 moveWholeMolecules false rotate false
    4256 
    4257 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4258 (#2) using 8555 atoms 
    4259 average map value = 0.111, steps = 40 
    4260 shifted from previous position = 0.012 
    4261 rotated from previous position = 0 degrees 
    4262 atoms outside contour = 5072, contour level = 0.10328 
    4263  
    4264 
    4265 > select subtract #2
    4266 
    4267 Nothing selected 
    4268 
    4269 > fitmap #4 inMap #2 moveWholeMolecules false rotate false
    4270 
    4271 Fit molecule 5zf6.pdb (#4) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4272 (#2) using 8555 atoms 
    4273 average map value = 0.111, steps = 28 
    4274 shifted from previous position = 0.0186 
    4275 rotated from previous position = 0 degrees 
    4276 atoms outside contour = 5074, contour level = 0.10328 
    4277  
    4278 
    4279 > hide /B ribbons
    4280 
    4281 > select clear
    4282 
    4283 > show /B ribbons
    4284 
    4285 > select :301-310
    4286 
    4287 704 atoms, 712 bonds, 80 residues, 4 models selected 
    4288 
    4289 > select :301-3330
    4290 
    4291 20188 atoms, 20216 bonds, 2848 residues, 4 models selected 
    4292 
    4293 > select :301-310
    4294 
    4295 704 atoms, 712 bonds, 80 residues, 4 models selected 
    4296 
    4297 > select :301-350
    4298 
    4299 3360 atoms, 3416 bonds, 400 residues, 4 models selected 
    4300 
    4301 > set bgColor white
    4302 
    4303 > lighting soft
    4304 
    4305 [Repeated 2 time(s)]
    4306 
    4307 > volume #2 color #6d6d6d69
    4308 
    4309 > volume #2 color #b6b6b669
    4310 
    4311 > set bgColor black
    4312 
    4313 > close #4
    4314 
    4315 > open
    4316 > /Users/madhurikanavalli/Desktop/Madhuri/Downloads/hPNP_dimer_5zf6_fit_tetramer2.pdb
    4317 
    4318 hPNP_dimer_5zf6_fit_tetramer2.pdb title: 
    4319 Crystal structure of the dimeric human pnpase [more info...] 
    4320  
    4321 Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb #4 
    4322 --- 
    4323 Chain | Description | UniProt 
    4324 A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669 
    4325  
    4326 
    4327 > fitmap #4 inMap #2 moveWholeMolecules false rotate false
    4328 
    4329 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
    4330 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4331 average map value = 0.06485, steps = 92 
    4332 shifted from previous position = 12 
    4333 rotated from previous position = 0 degrees 
    4334 atoms outside contour = 6477, contour level = 0.10328 
    4335  
    4336 
    4337 > close #3
    4338 
    4339 > show #!6 models
    4340 
    4341 > fitmap #6 inMap #2 moveWholeMolecules false rotate false
    4342 
    4343 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4344 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4345 average map value = 0.1297, steps = 40 
    4346 shifted from previous position = 0.0105 
    4347 rotated from previous position = 0 degrees 
    4348 atoms outside contour = 4642, contour level = 0.10328 
    4349  
    4350 
    4351 > fitmap #6 inMap #2 moveWholeMolecules false rotate false
    4352 
    4353 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4354 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4355 average map value = 0.1297, steps = 40 
    4356 shifted from previous position = 0.00663 
    4357 rotated from previous position = 0 degrees 
    4358 atoms outside contour = 4644, contour level = 0.10328 
    4359  
    4360 
    4361 > select add #6
    4362 
    4363 9395 atoms, 9472 bonds, 1274 residues, 2 models selected 
    4364 
    4365 > fitmap #6 inMap #2 moveWholeMolecules false rotate false
    4366 
    4367 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4368 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4369 average map value = 0.1297, steps = 40 
    4370 shifted from previous position = 0.0111 
    4371 rotated from previous position = 0 degrees 
    4372 atoms outside contour = 4642, contour level = 0.10328 
    4373  
    4374 
    4375 > close #4
    4376 
    4377 > open /Users/madhurikanavalli/Downloads/hPNP_dimer_5zf6_fit_tetramer1.pdb
    4378 
    4379 hPNP_dimer_5zf6_fit_tetramer1.pdb title: 
    4380 Crystal structure of the dimeric human pnpase [more info...] 
    4381  
    4382 Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb #3 
    4383 --- 
    4384 Chain | Description | UniProt 
    4385 A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669 
    4386  
    4387 
    4388 > view matrix models
    4389 > #1,0.994,-0.094744,-0.054626,186.44,0.077109,0.25294,0.9644,196.21,-0.077554,-0.96283,0.25873,175.8,#6,0.99794,0.050158,0.040032,-19.038,-0.032417,0.93235,-0.36009,102.59,-0.055385,0.35805,0.93206,-81.741
    4390 
    4391 > undo
    4392 
    4393 > hide #!6 models
    4394 
    4395 > select subtract #6
    4396 
    4397 840 atoms, 854 bonds, 100 residues, 1 model selected 
    4398 
    4399 > hide #!1 models
    4400 
    4401 > select add #1
    4402 
    4403 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4404 
    4405 > select subtract #1
    4406 
    4407 Nothing selected 
    4408 
    4409 > select add #3
    4410 
    4411 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4412 
    4413 > view matrix models #3,1,0,0,1.8097,0,1,0,0.23566,0,0,1,-36.997
    4414 
    4415 > view matrix models #3,1,0,0,35.394,0,1,0,-3.855,0,0,1,-64.467
    4416 
    4417 > view matrix models #3,1,0,0,29.376,0,1,0,4.2566,0,0,1,1.29
    4418 
    4419 > fitmap #3 inMap #2 moveWholeMolecules false rotate false
    4420 
    4421 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    4422 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4423 average map value = 0.0719, steps = 92 
    4424 shifted from previous position = 9.37 
    4425 rotated from previous position = 0 degrees 
    4426 atoms outside contour = 6159, contour level = 0.10328 
    4427  
    4428 
    4429 > view matrix models #3,1,0,0,31.644,0,1,0,5.3303,0,0,1,3.0727
    4430 
    4431 > fitmap #3 inMap #2 moveWholeMolecules false rotate false
    4432 
    4433 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    4434 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4435 average map value = 0.07189, steps = 48 
    4436 shifted from previous position = 3.09 
    4437 rotated from previous position = 0 degrees 
    4438 atoms outside contour = 6159, contour level = 0.10328 
    4439  
    4440 
    4441 > view matrix models #3,1,0,0,34.027,0,1,0,1.7493,0,0,1,4.222
    4442 
    4443 > ui mousemode right "rotate selected models"
    4444 
    4445 > view matrix models
    4446 > #3,0.927,0.099914,0.3615,-47.503,-0.090663,0.99497,-0.042509,27.476,-0.36393,0.0066319,0.9314,81.127
    4447 
    4448 > fitmap #3 inMap #2 moveWholeMolecules false
    4449 
    4450 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    4451 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4452 average map value = 0.1263, steps = 2000 
    4453 shifted from previous position = 3.7 
    4454 rotated from previous position = 7.87 degrees 
    4455 atoms outside contour = 4616, contour level = 0.10328 
    4456  
    4457 
    4458 > fitmap #3 inMap #2 moveWholeMolecules false
    4459 
    4460 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    4461 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4462 average map value = 0.1261, steps = 2000 
    4463 shifted from previous position = 0.241 
    4464 rotated from previous position = 0.799 degrees 
    4465 atoms outside contour = 4569, contour level = 0.10328 
    4466  
    4467 
    4468 > volume #2 color #9c9c9c69
    4469 
    4470 > volume #2 color #8e8e8e69
    4471 
    4472 > volume #2 color #4c4c4c69
    4473 
    4474 > volume #2 color #ffffff69
    4475 
    4476 > volume #2 color #adadad69
    4477 
    4478 > color #3 #c76be1ff
    4479 
    4480 > color #3 #ba49e1ff
    4481 
    4482 > color #3 #e119e0ff
    4483 
    4484 > color #3 #e121bdff
    4485 
    4486 > select subtract #3
    4487 
    4488 Nothing selected 
    4489 
    4490 > fitmap #3 inMap #2
    4491 
    4492 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    4493 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4494 average map value = 0.1249, steps = 2000 
    4495 shifted from previous position = 0.637 
    4496 rotated from previous position = 1.01 degrees 
    4497 atoms outside contour = 4588, contour level = 0.10328 
    4498  
    4499 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
    4500 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4501 Matrix rotation and translation 
    4502 0.99026797 0.07877011 0.11473715 -66.08205858 
    4503 -0.08429553 0.99546348 0.04412174 -36.13256533 
    4504 -0.11074116 -0.05336418 0.99241557 6.84643690 
    4505 Axis -0.33063295 0.76473153 -0.55305292 
    4506 Axis point -27.14208933 0.00000000 601.21610338 
    4507 Rotation angle (degrees) 8.47762549 
    4508 Shift along axis -9.56924816 
    4509  
    4510 
    4511 > hide #!3 models
    4512 
    4513 > show #!1 models
    4514 
    4515 > select add #1
    4516 
    4517 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4518 
    4519 > show #!3 models
    4520 
    4521 > select add #3
    4522 
    4523 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    4524 
    4525 > color #3 #24cbd8ff
    4526 
    4527 > color #3 #b4d827ff
    4528 
    4529 > select subtract #3
    4530 
    4531 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4532 
    4533 > hide #!3 models
    4534 
    4535 > hide #!1 models
    4536 
    4537 > show #!1 models
    4538 
    4539 > color #3 #4264d8ff
    4540 
    4541 > color #1 #6d61d7ff
    4542 
    4543 > select subtract #1
    4544 
    4545 Nothing selected 
    4546 
    4547 > select #1/B
    4548 
    4549 4227 atoms, 4261 bonds, 577 residues, 1 model selected 
    4550 
    4551 > fitmap #1 inMap #2 moveWholeMolecules false
    4552 
    4553 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4554 (#2) using 8555 atoms 
    4555 average map value = 0.1297, steps = 340 
    4556 shifted from previous position = 0.209 
    4557 rotated from previous position = 0.503 degrees 
    4558 atoms outside contour = 4642, contour level = 0.10328 
    4559  
    4560 
    4561 > fitmap #1 inMap #2 moveWholeMolecules false
    4562 
    4563 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4564 (#2) using 8555 atoms 
    4565 average map value = 0.1297, steps = 504 
    4566 shifted from previous position = 0.0115 
    4567 rotated from previous position = 0.0127 degrees 
    4568 atoms outside contour = 4645, contour level = 0.10328 
    4569  
    4570 
    4571 > fitmap #1 inMap #2 moveWholeMolecules false
    4572 
    4573 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4574 (#2) using 8555 atoms 
    4575 average map value = 0.1297, steps = 348 
    4576 shifted from previous position = 0.00671 
    4577 rotated from previous position = 0.0114 degrees 
    4578 atoms outside contour = 4646, contour level = 0.10328 
    4579  
    4580 
    4581 > select add #1
    4582 
    4583 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4584 
    4585 > select subtract #1
    4586 
    4587 Nothing selected 
    4588 
    4589 > color #1 #2322d7ff
    4590 
    4591 > color #1 #304bd7ff
    4592 
    4593 > color #1 #405cd7ff
    4594 
    4595 > select #1/A-B:293
    4596 
    4597 18 atoms, 16 bonds, 2 residues, 1 model selected 
    4598 
    4599 > select #1/A-B:293-367
    4600 
    4601 1256 atoms, 1276 bonds, 150 residues, 1 model selected 
    4602 
    4603 > hide /chain bonds
    4604 
    4605 [Repeated 1 time(s)]
    4606 
    4607 > fitmap #1 inMap #2 moveWholeMolecules false
    4608 
    4609 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4610 (#2) using 8555 atoms 
    4611 average map value = 0.129, steps = 2000 
    4612 shifted from previous position = 0.217 
    4613 rotated from previous position = 0.341 degrees 
    4614 atoms outside contour = 4649, contour level = 0.10328 
    4615  
    4616 
    4617 > fitmap #1 inMap #2 moveWholeMolecules false
    4618 
    4619 Fit molecule 5zf6.pdb (#1) to map cryosparc_P1_J138_004_volume_map_sharp.mrc
    4620 (#2) using 8555 atoms 
    4621 average map value = 0.1275, steps = 2000 
    4622 shifted from previous position = 0.536 
    4623 rotated from previous position = 0.764 degrees 
    4624 atoms outside contour = 4674, contour level = 0.10328 
    4625  
    4626 
    4627 > select add #6
    4628 
    4629 9811 atoms, 9894 bonds, 1324 residues, 2 models selected 
    4630 
    4631 > show #!6 models
    4632 
    4633 > hide #!6 models
    4634 
    4635 > select subtract #6
    4636 
    4637 1256 atoms, 1276 bonds, 150 residues, 1 model selected 
    4638 
    4639 > select add #3
    4640 
    4641 9811 atoms, 9894 bonds, 1324 residues, 2 models selected 
    4642 
    4643 > show #!3 models
    4644 
    4645 > show #!6 models
    4646 
    4647 > select add #6
    4648 
    4649 18366 atoms, 18512 bonds, 2498 residues, 3 models selected 
    4650 
    4651 > hide #!3 models
    4652 
    4653 > select subtract #3
    4654 
    4655 9811 atoms, 9894 bonds, 1324 residues, 2 models selected 
    4656 
    4657 > select add #1
    4658 
    4659 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    4660 
    4661 > view matrix models
    4662 > #1,0.96064,0.23479,0.14849,209.24,-0.19007,0.16566,0.96769,190.25,0.2026,-0.95783,0.20377,213.18,#6,0.92816,0.21046,-0.30695,60.885,-0.29394,0.92042,-0.25774,126.04,0.22828,0.32945,0.91616,-88.788
    4663 
    4664 > undo
    4665 
    4666 > select subtract #1
    4667 
    4668 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4669 
    4670 > hide #!1 models
    4671 
    4672 > view matrix models
    4673 > #6,-0.27804,-0.71665,-0.63961,531.76,-0.24176,0.69664,-0.67546,247.87,0.92965,-0.033174,-0.36695,123.49
    4674 
    4675 > view matrix models
    4676 > #6,-0.80854,-0.29339,-0.51009,522.64,0.17861,0.70359,-0.68779,171.01,0.56068,-0.64722,-0.51647,340.29
    4677 
    4678 > ui mousemode right "translate selected models"
    4679 
    4680 > view matrix models
    4681 > #6,-0.80854,-0.29339,-0.51009,480.38,0.17861,0.70359,-0.68779,178.26,0.56068,-0.64722,-0.51647,288.18
    4682 
    4683 > fitmap #6 inMap #2 moveWholeMolecules false
    4684 
    4685 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4686 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4687 average map value = 0.04021, steps = 244 
    4688 shifted from previous position = 22.5 
    4689 rotated from previous position = 9.8 degrees 
    4690 atoms outside contour = 7262, contour level = 0.10328 
    4691  
    4692 
    4693 > ui mousemode right "rotate selected models"
    4694 
    4695 > view matrix models
    4696 > #6,-0.35639,-0.29895,-0.88522,483.61,-0.004137,0.94793,-0.31846,84.725,0.93433,-0.10983,-0.33907,84.393
    4697 
    4698 > view matrix models
    4699 > #6,-0.25916,-0.51199,-0.81897,494.96,0.10101,0.82892,-0.55017,138.34,0.96054,-0.22531,-0.16311,65.902
    4700 
    4701 > fitmap #6 inMap #2 moveWholeMolecules false
    4702 
    4703 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4704 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4705 average map value = 0.04682, steps = 180 
    4706 shifted from previous position = 9.55 
    4707 rotated from previous position = 14.6 degrees 
    4708 atoms outside contour = 7079, contour level = 0.10328 
    4709  
    4710 
    4711 > fitmap #6 inMap #2
    4712 
    4713 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4714 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4715 average map value = 0.04682, steps = 44 
    4716 shifted from previous position = 0.0919 
    4717 rotated from previous position = 0.204 degrees 
    4718 atoms outside contour = 7090, contour level = 0.10328 
    4719  
    4720 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4721 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4722 Matrix rotation and translation 
    4723 -0.49668241 -0.45211172 -0.74087892 460.77188640 
    4724 0.15262355 0.79481607 -0.58734441 94.44318983 
    4725 0.85440777 -0.40479921 -0.32576827 117.80701656 
    4726 Axis 0.10639077 -0.92976301 0.35245106 
    4727 Axis point 200.17990455 0.00000000 217.14121089 
    4728 Rotation angle (degrees) 120.91843476 
    4729 Shift along axis 2.73329794 
    4730  
    4731 
    4732 > view matrix models
    4733 > #6,-0.52907,-0.0047689,-0.84857,450.01,0.53325,0.77601,-0.33683,33.426,0.6601,-0.6307,-0.40802,241.83
    4734 
    4735 > ui mousemode right "translate selected models"
    4736 
    4737 > view matrix models
    4738 > #6,-0.52907,-0.0047689,-0.84857,424.69,0.53325,0.77601,-0.33683,-64.127,0.6601,-0.6307,-0.40802,233.02
    4739 
    4740 > view matrix models
    4741 > #6,-0.52907,-0.0047689,-0.84857,427.56,0.53325,0.77601,-0.33683,-69.035,0.6601,-0.6307,-0.40802,240.81
    4742 
    4743 > ui mousemode right "rotate selected models"
    4744 
    4745 > view matrix models
    4746 > #6,-0.76339,-0.51264,-0.39298,467.55,-0.13914,0.72461,-0.67496,120.5,0.63077,-0.46058,-0.62449,258.25
    4747 
    4748 > view matrix models
    4749 > #6,-0.86546,-0.26374,-0.42593,444.28,0.16092,0.65879,-0.73491,96.05,0.47442,-0.70458,-0.52772,309.8
    4750 
    4751 > view matrix models
    4752 > #6,-0.28971,-0.90683,-0.30614,446.12,-0.56931,0.42039,-0.70651,254.69,0.76939,-0.030393,-0.63806,157.46
    4753 
    4754 > view matrix models
    4755 > #6,0.071191,-0.22599,-0.97153,396.1,-0.32791,0.91456,-0.23676,25.444,0.94202,0.33543,-0.0089961,-69.223
    4756 
    4757 > view matrix models
    4758 > #6,-0.62244,0.01769,-0.78247,425.02,-0.32291,0.90489,0.27732,-79.49,0.71295,0.42528,-0.55752,64.459
    4759 
    4760 > view matrix models
    4761 > #6,-0.22541,0.34331,-0.91177,325.38,-0.19676,0.90053,0.38772,-122.1,0.95419,0.26679,-0.13544,-32.26
    4762 
    4763 > view matrix models
    4764 > #6,-0.41827,-0.28212,-0.8634,464.59,-0.64872,0.75811,0.066552,44.931,0.63578,0.58794,-0.50012,34.704
    4765 
    4766 > view matrix models
    4767 > #6,-0.25107,0.40226,-0.88043,312.05,-0.2867,0.83785,0.46456,-111.4,0.92454,0.36905,-0.095032,-54.949
    4768 
    4769 > view matrix models
    4770 > #6,-0.76906,0.13581,-0.62458,394.31,-0.1572,0.90696,0.39079,-130.42,0.61954,0.39873,-0.67616,109.21
    4771 
    4772 > view matrix models
    4773 > #6,-0.98343,0.03782,-0.1773,355.7,-0.074325,0.80792,0.58458,-165.32,0.16536,0.58807,-0.79172,171.87
    4774 
    4775 > view matrix models
    4776 > #6,-0.39477,0.68819,-0.60873,225.86,0.36199,0.72545,0.58539,-221.49,0.84446,0.010739,-0.5355,116.29
    4777 
    4778 > view matrix models
    4779 > #6,-0.79966,0.075061,-0.59575,404.81,-0.040684,0.9831,0.17847,-120.08,0.59908,0.16695,-0.78309,178.16
    4780 
    4781 > fitmap #6 inMap #2
    4782 
    4783 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4784 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4785 average map value = -0.0005825, steps = 96 
    4786 shifted from previous position = 3.28 
    4787 rotated from previous position = 3.03 degrees 
    4788 atoms outside contour = 8555, contour level = 0.10328 
    4789  
    4790 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4791 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4792 Matrix rotation and translation 
    4793 -0.92490882 -0.02938852 -0.37905143 356.59797481 
    4794 -0.08084042 0.98941082 0.12054485 -153.92939959 
    4795 0.37149495 0.14213567 -0.91749057 213.28677900 
    4796 Axis 0.02868764 -0.99724791 -0.06836393 
    4797 Axis point 154.19781165 0.00000000 146.42433529 
    4798 Rotation angle (degrees) 157.89477035 
    4799 Shift along axis 149.15460281 
    4800  
    4801 
    4802 > fitmap #6 inMap #2
    4803 
    4804 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4805 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4806 average map value = -0.0005823, steps = 28 
    4807 shifted from previous position = 0.00579 
    4808 rotated from previous position = 0.00269 degrees 
    4809 atoms outside contour = 8555, contour level = 0.10328 
    4810  
    4811 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4812 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4813 Matrix rotation and translation 
    4814 -0.92492308 -0.02936526 -0.37901843 356.58713815 
    4815 -0.08080731 0.98941435 0.12053802 -153.93925469 
    4816 0.37146665 0.14211586 -0.91750510 213.29930744 
    4817 Axis 0.02867275 -0.99724885 -0.06835648 
    4818 Axis point 154.19422266 0.00000000 146.42639014 
    4819 Rotation angle (degrees) 157.89669311 
    4820 Shift along axis 149.15968848 
    4821  
    4822 
    4823 > ui mousemode right "translate selected models"
    4824 
    4825 > view matrix models
    4826 > #6,-0.80444,0.039308,-0.59273,388.5,-0.090985,0.97788,0.18834,-22.775,0.58702,0.20543,-0.78307,177.39
    4827 
    4828 > volume #2 level 0.0888
    4829 
    4830 > volume #2 level 0.09242
    4831 
    4832 > fitmap #6 inMap #2
    4833 
    4834 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4835 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4836 average map value = 0.03454, steps = 280 
    4837 shifted from previous position = 32.1 
    4838 rotated from previous position = 34.8 degrees 
    4839 atoms outside contour = 7410, contour level = 0.092417 
    4840  
    4841 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4842 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4843 Matrix rotation and translation 
    4844 -0.90947492 -0.41561998 0.01074203 352.97733471 
    4845 -0.39427535 0.87038984 0.29490417 -29.46763984 
    4846 -0.13191783 0.26397263 -0.95546645 264.47171436 
    4847 Axis -0.20966712 0.96700906 0.14468300 
    4848 Axis point 178.52191521 0.00000000 127.95705739 
    4849 Rotation angle (degrees) 175.76982332 
    4850 Shift along axis -64.23865431 
    4851  
    4852 
    4853 > view matrix models
    4854 > #6,-0.92581,-0.30774,-0.21947,427.56,-0.3699,0.85706,0.35863,24.591,0.077733,0.41321,-0.90731,235.42
    4855 
    4856 > view matrix models
    4857 > #6,-0.92581,-0.30774,-0.21947,445.36,-0.3699,0.85706,0.35863,22.611,0.077733,0.41321,-0.90731,226.52
    4858 
    4859 > fitmap #6 inMap #2
    4860 
    4861 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4862 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4863 average map value = 0.06286, steps = 200 
    4864 shifted from previous position = 6.44 
    4865 rotated from previous position = 25.2 degrees 
    4866 atoms outside contour = 6186, contour level = 0.092417 
    4867  
    4868 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4869 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4870 Matrix rotation and translation 
    4871 -0.94057101 -0.15322448 -0.30306507 389.01736554 
    4872 -0.21329908 0.96098057 0.17612448 -31.15370261 
    4873 0.26425307 0.23030108 -0.93655311 208.49710154 
    4874 Axis 0.09453969 -0.98998612 -0.10483186 
    4875 Axis point 177.25741183 0.00000000 134.32900383 
    4876 Rotation angle (degrees) 163.34977424 
    4877 Shift along axis 45.76217553 
    4878  
    4879 
    4880 > select subtract #6
    4881 
    4882 Nothing selected 
    4883 
    4884 > ui mousemode right "rotate selected models"
    4885 
    4886 > select add #6
    4887 
    4888 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4889 
    4890 > view matrix models
    4891 > #6,-0.76191,-0.0097647,-0.64761,446.5,-0.20035,0.9544,0.22132,8.908,0.61591,0.29837,-0.72912,128.23
    4892 
    4893 > fitmap #6 inMap #2
    4894 
    4895 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4896 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4897 average map value = 0.111, steps = 324 
    4898 shifted from previous position = 1.84 
    4899 rotated from previous position = 10.5 degrees 
    4900 atoms outside contour = 4725, contour level = 0.092417 
    4901  
    4902 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4903 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4904 Matrix rotation and translation 
    4905 -0.94065942 0.02845456 -0.33815704 363.23421540 
    4906 -0.02966661 0.98576805 0.16547275 -62.67392798 
    4907 0.33805287 0.16568547 -0.92642786 207.49334626 
    4908 Axis 0.00031343 -0.99632647 -0.08563563 
    4909 Axis point 163.06221544 0.00000000 138.31429213 
    4910 Rotation angle (degrees) 160.16262663 
    4911 Shift along axis 44.78871788 
    4912  
    4913 
    4914 > ui mousemode right "translate selected models"
    4915 
    4916 > ui mousemode right "rotate selected models"
    4917 
    4918 > view matrix models
    4919 > #6,-0.64462,0.060699,-0.76209,438.99,-0.16555,0.96211,0.21666,3.6667,0.74636,0.26583,-0.61015,89.225
    4920 
    4921 > fitmap #6 inMap #2
    4922 
    4923 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4924 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4925 average map value = 0.111, steps = 232 
    4926 shifted from previous position = 1.12 
    4927 rotated from previous position = 16.6 degrees 
    4928 atoms outside contour = 4726, contour level = 0.092417 
    4929  
    4930 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4931 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4932 Matrix rotation and translation 
    4933 -0.94065481 0.02863395 -0.33815474 363.19518707 
    4934 -0.02945052 0.98578726 0.16539693 -62.69088648 
    4935 0.33808460 0.16554025 -0.92644224 207.53053559 
    4936 Axis 0.00021116 -0.99633143 -0.08557825 
    4937 Axis point 163.04229456 0.00000000 138.32992186 
    4938 Rotation angle (degrees) 160.16182981 
    4939 Shift along axis 44.77749212 
    4940  
    4941 
    4942 > view matrix models
    4943 > #6,-0.88604,0.038516,-0.462,420.9,-0.03934,0.9867,0.15771,-9.4885,0.46193,0.15791,-0.87275,210.25
    4944 
    4945 > fitmap #6 inMap #2
    4946 
    4947 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4948 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4949 average map value = 0.111, steps = 192 
    4950 shifted from previous position = 0.498 
    4951 rotated from previous position = 8.14 degrees 
    4952 atoms outside contour = 4728, contour level = 0.092417 
    4953  
    4954 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    4955 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    4956 Matrix rotation and translation 
    4957 -0.94066665 0.02855601 -0.33812838 363.20627610 
    4958 -0.02957366 0.98576223 0.16552410 -62.69813440 
    4959 0.33804090 0.16570270 -0.92642915 207.49987033 
    4960 Axis 0.00026316 -0.99632498 -0.08565318 
    4961 Axis point 163.05029791 0.00000000 138.31495884 
    4962 Rotation angle (degrees) 160.16383770 
    4963 Shift along axis 44.79027516 
    4964  
    4965 
    4966 > view matrix models
    4967 > #6,-0.72409,0.17019,-0.66837,412.13,-0.025472,0.96182,0.2725,-30.744,0.68923,0.21434,-0.69211,125.17
    4968 
    4969 > fitmap #6 inMap #2 moveWholeMolecules false
    4970 
    4971 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4972 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4973 average map value = 0.111, steps = 776 
    4974 shifted from previous position = 0.661 
    4975 rotated from previous position = 9.75 degrees 
    4976 atoms outside contour = 4722, contour level = 0.092417 
    4977  
    4978 
    4979 > select subtract #6
    4980 
    4981 Nothing selected 
    4982 
    4983 > select add #6
    4984 
    4985 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    4986 
    4987 > view matrix models
    4988 > #6,-0.76187,-0.15221,-0.6296,471.01,-0.29458,0.94708,0.12751,45.668,0.57687,0.28261,-0.76639,145.88
    4989 
    4990 > ui mousemode right "translate selected models"
    4991 
    4992 > view matrix models
    4993 > #6,-0.76187,-0.15221,-0.6296,471.34,-0.29458,0.94708,0.12751,43.678,0.57687,0.28261,-0.76639,146.42
    4994 
    4995 > fitmap #6 inMap #2 moveWholeMolecules false
    4996 
    4997 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    4998 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    4999 average map value = 0.06236, steps = 84 
    5000 shifted from previous position = 2.22 
    5001 rotated from previous position = 3.59 degrees 
    5002 atoms outside contour = 6255, contour level = 0.092417 
    5003  
    5004 
    5005 > select subtract #6
    5006 
    5007 Nothing selected 
    5008 
    5009 > ui mousemode right "rotate selected models"
    5010 
    5011 > select add #6
    5012 
    5013 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5014 
    5015 > view matrix models
    5016 > #6,-0.6777,0.059786,-0.73291,439.37,-0.22546,0.93179,0.28449,3.074,0.69992,0.35804,-0.61799,81.912
    5017 
    5018 > ui mousemode right "translate selected models"
    5019 
    5020 > view matrix models
    5021 > #6,-0.6777,0.059786,-0.73291,439.44,-0.22546,0.93179,0.28449,2.7263,0.69992,0.35804,-0.61799,83.451
    5022 
    5023 > fitmap #6 inMap #2
    5024 
    5025 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5026 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5027 average map value = 0.111, steps = 920 
    5028 shifted from previous position = 3.95 
    5029 rotated from previous position = 10.1 degrees 
    5030 atoms outside contour = 4722, contour level = 0.092417 
    5031  
    5032 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    5033 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5034 Matrix rotation and translation 
    5035 -0.88994782 0.04420559 -0.45391491 374.83079362 
    5036 -0.05717949 0.97662253 0.20721711 -63.35120865 
    5037 0.45246368 0.21036704 -0.86661544 168.59587277 
    5038 Axis 0.00345373 -0.99379614 -0.11116337 
    5039 Axis point 166.22449866 0.00000000 133.32450793 
    5040 Rotation angle (degrees) 152.86952298 
    5041 Shift along axis 45.51106552 
    5042  
    5043 
    5044 > select subtract #6
    5045 
    5046 Nothing selected 
    5047 
    5048 > hide #!2 models
    5049 
    5050 > undo
    5051 
    5052 > fitmap #6 inMap #2
    5053 
    5054 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5055 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5056 average map value = 0.111, steps = 116 
    5057 shifted from previous position = 0.00709 
    5058 rotated from previous position = 0.00318 degrees 
    5059 atoms outside contour = 4727, contour level = 0.092417 
    5060  
    5061 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    5062 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5063 Matrix rotation and translation 
    5064 -0.88993311 0.04424511 -0.45393989 374.82642072 
    5065 -0.05716226 0.97661562 0.20725443 -63.36706439 
    5066 0.45249479 0.21039081 -0.86659343 168.57997819 
    5067 Axis 0.00343866 -0.99379426 -0.11118072 
    5068 Axis point 166.22292888 0.00000000 133.32090242 
    5069 Rotation angle (degrees) 152.86765033 
    5070 Shift along axis 45.51987962 
    5071  
    5072 
    5073 > fitmap #6 inMap #2
    5074 
    5075 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5076 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5077 average map value = 0.111, steps = 568 
    5078 shifted from previous position = 0.0114 
    5079 rotated from previous position = 0.0123 degrees 
    5080 atoms outside contour = 4724, contour level = 0.092417 
    5081  
    5082 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    5083 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5084 Matrix rotation and translation 
    5085 -0.88993442 0.04404381 -0.45395691 374.86893906 
    5086 -0.05737351 0.97660900 0.20722726 -63.32915866 
    5087 0.45246548 0.21046377 -0.86659101 168.55952594 
    5088 Axis 0.00354848 -0.99379250 -0.11119295 
    5089 Axis point 166.24336123 0.00000000 133.31298230 
    5090 Rotation angle (degrees) 152.86799669 
    5091 Shift along axis 45.52362736 
    5092  
    5093 
    5094 > select add #6
    5095 
    5096 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5097 
    5098 > fitmap #6 inMap #2
    5099 
    5100 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5101 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5102 average map value = 0.111, steps = 180 
    5103 shifted from previous position = 0.0152 
    5104 rotated from previous position = 0.00465 degrees 
    5105 atoms outside contour = 4732, contour level = 0.092417 
    5106  
    5107 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) relative to
    5108 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5109 Matrix rotation and translation 
    5110 -0.88993786 0.04410294 -0.45394442 374.85142718 
    5111 -0.05729523 0.97661769 0.20720798 -63.34867632 
    5112 0.45246863 0.21041107 -0.86660217 168.58221982 
    5113 Axis 0.00351189 -0.99379482 -0.11117335 
    5114 Axis point 166.23335059 0.00000000 133.32210930 
    5115 Rotation angle (degrees) 152.86836781 
    5116 Shift along axis 45.53017211 
    5117  
    5118 
    5119 > select :605-635
    5120 
    5121 1296 atoms, 1317 bonds, 171 residues, 3 models selected 
    5122 
    5123 > fitmap #6 inMap #2 moveWholeMolecules false
    5124 
    5125 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5126 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5127 average map value = 0.111, steps = 344 
    5128 shifted from previous position = 0.0176 
    5129 rotated from previous position = 0.0105 degrees 
    5130 atoms outside contour = 4729, contour level = 0.092417 
    5131  
    5132 
    5133 > fitmap #6 inMap #2 moveWholeMolecules false
    5134 
    5135 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5136 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5137 average map value = 0.111, steps = 196 
    5138 shifted from previous position = 0.0146 
    5139 rotated from previous position = 0.00622 degrees 
    5140 atoms outside contour = 4723, contour level = 0.092417 
    5141  
    5142 
    5143 > fitmap #6 inMap #2 moveWholeMolecules false
    5144 
    5145 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5146 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5147 average map value = 0.111, steps = 180 
    5148 shifted from previous position = 0.0248 
    5149 rotated from previous position = 0.0219 degrees 
    5150 atoms outside contour = 4722, contour level = 0.092417 
    5151  
    5152 
    5153 > fitmap #6 inMap #2 moveWholeMolecules false
    5154 
    5155 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5156 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5157 average map value = 0.111, steps = 548 
    5158 shifted from previous position = 0.0148 
    5159 rotated from previous position = 0.00714 degrees 
    5160 atoms outside contour = 4725, contour level = 0.092417 
    5161  
    5162 
    5163 > fitmap #6 inMap #2 moveWholeMolecules false
    5164 
    5165 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5166 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5167 average map value = 0.111, steps = 312 
    5168 shifted from previous position = 0.0297 
    5169 rotated from previous position = 0.0316 degrees 
    5170 atoms outside contour = 4729, contour level = 0.092417 
    5171  
    5172 
    5173 > fitmap #6 inMap #2 moveWholeMolecules false
    5174 
    5175 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5176 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5177 average map value = 0.111, steps = 128 
    5178 shifted from previous position = 0.00953 
    5179 rotated from previous position = 0.0083 degrees 
    5180 atoms outside contour = 4725, contour level = 0.092417 
    5181  
    5182 
    5183 > fitmap #6 inMap #2 moveWholeMolecules false
    5184 
    5185 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5186 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5187 average map value = 0.111, steps = 208 
    5188 shifted from previous position = 0.0222 
    5189 rotated from previous position = 0.0184 degrees 
    5190 atoms outside contour = 4724, contour level = 0.092417 
    5191  
    5192 
    5193 > fitmap #6 inMap #2 moveWholeMolecules false
    5194 
    5195 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5196 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5197 average map value = 0.111, steps = 220 
    5198 shifted from previous position = 0.0138 
    5199 rotated from previous position = 0.00774 degrees 
    5200 atoms outside contour = 4725, contour level = 0.092417 
    5201  
    5202 
    5203 > fitmap #6 inMap #2 moveWholeMolecules false
    5204 
    5205 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5206 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5207 average map value = 0.111, steps = 1912 
    5208 shifted from previous position = 0.0151 
    5209 rotated from previous position = 0.00815 degrees 
    5210 atoms outside contour = 4724, contour level = 0.092417 
    5211  
    5212 
    5213 > fitmap #6 inMap #2 moveWholeMolecules false
    5214 
    5215 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5216 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5217 average map value = 0.111, steps = 388 
    5218 shifted from previous position = 0.0217 
    5219 rotated from previous position = 0.0192 degrees 
    5220 atoms outside contour = 4728, contour level = 0.092417 
    5221  
    5222 
    5223 > view matrix models
    5224 > #1,0.994,-0.094744,-0.054626,207.02,0.077109,0.25294,0.9644,190.31,-0.077554,-0.96283,0.25873,213.32,#6,-0.74953,0.12709,-0.64965,417.13,-0.073566,0.95933,0.27255,-21.057,0.65787,0.25208,-0.7097,128.14,#3,0.92765,0.095145,0.36114,-49.146,-0.092392,0.99541,-0.024925,24.061,-0.36185,-0.010244,0.93218,84.812
    5225 
    5226 > fitmap #6 inMap #2 moveWholeMolecules false
    5227 
    5228 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#6) to map
    5229 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5230 average map value = 0.111, steps = 448 
    5231 shifted from previous position = 2.71 
    5232 rotated from previous position = 0.0121 degrees 
    5233 atoms outside contour = 4721, contour level = 0.092417 
    5234  
    5235 
    5236 > select add #6
    5237 
    5238 9419 atoms, 9496 bonds, 1288 residues, 3 models selected 
    5239 
    5240 > select add #3
    5241 
    5242 17542 atoms, 17675 bonds, 2405 residues, 3 models selected 
    5243 
    5244 > select subtract #6
    5245 
    5246 8987 atoms, 9057 bonds, 1231 residues, 2 models selected 
    5247 
    5248 > hide #!6 models
    5249 
    5250 > hide #!2 models
    5251 
    5252 > select add #1
    5253 
    5254 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    5255 
    5256 > select subtract #1
    5257 
    5258 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5259 
    5260 > select subtract #3
    5261 
    5262 Nothing selected 
    5263 
    5264 > show #!3 models
    5265 
    5266 > show #!1 models
    5267 
    5268 > hide #!1 models
    5269 
    5270 > show #!6 models
    5271 
    5272 > select add #6
    5273 
    5274 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5275 
    5276 > select add #3
    5277 
    5278 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    5279 
    5280 > open
    5281 > /Users/madhurikanavalli/Desktop/ImageProcessing/kasiafiles/hPNP_dimer_5zf6_fit_tetramer2.pdb
    5282 
    5283 hPNP_dimer_5zf6_fit_tetramer2.pdb title: 
    5284 Crystal structure of the dimeric human pnpase [more info...] 
    5285  
    5286 Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb #4 
    5287 --- 
    5288 Chain | Description | UniProt 
    5289 A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669 
    5290  
    5291 
    5292 > hide #!6 models
    5293 
    5294 > select subtract #6
    5295 
    5296 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5297 
    5298 > show #!2 models
    5299 
    5300 > select add #2
    5301 
    5302 8555 atoms, 8618 bonds, 1174 residues, 3 models selected 
    5303 
    5304 > select add #4
    5305 
    5306 17110 atoms, 17236 bonds, 2348 residues, 4 models selected 
    5307 
    5308 > ui tool show "Fit in Map"
    5309 
    5310 > fitmap #3 inMap #2
    5311 
    5312 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5313 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5314 average map value = 0.1262, steps = 2000 
    5315 shifted from previous position = 2.56 
    5316 rotated from previous position = 0.165 degrees 
    5317 atoms outside contour = 4321, contour level = 0.092417 
    5318  
    5319 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
    5320 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5321 Matrix rotation and translation 
    5322 0.99008565 0.08020231 0.11531698 -66.56585309 
    5323 -0.08547902 0.99547290 0.04155783 -35.70187256 
    5324 -0.11146190 -0.05100299 0.99245904 6.18707679 
    5325 Axis -0.31300845 0.76688716 -0.56027654 
    5326 Axis point -35.49371356 -0.00000000 601.36159142 
    5327 Rotation angle (degrees) 8.50274218 
    5328 Shift along axis -10.01010685 
    5329  
    5330 
    5331 > fitmap #3 inMap #2
    5332 
    5333 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5334 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5335 average map value = 0.1265, steps = 2000 
    5336 shifted from previous position = 0.239 
    5337 rotated from previous position = 0.818 degrees 
    5338 atoms outside contour = 4303, contour level = 0.092417 
    5339  
    5340 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
    5341 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5342 Matrix rotation and translation 
    5343 0.99012491 0.07955173 0.11543040 -66.35338000 
    5344 -0.08323899 0.99615079 0.02747518 -33.39555135 
    5345 -0.11280039 -0.03681217 0.99293552 3.37679073 
    5346 Axis -0.22351799 0.79352600 -0.56600018 
    5347 Axis point -75.44975106 0.00000000 594.67655370 
    5348 Rotation angle (degrees) 8.26825993 
    5349 Shift along axis -13.58032821 
    5350  
    5351 
    5352 > fitmap #4 inMap #2
    5353 
    5354 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
    5355 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5356 average map value = 0.1106, steps = 296 
    5357 shifted from previous position = 11.4 
    5358 rotated from previous position = 15 degrees 
    5359 atoms outside contour = 4757, contour level = 0.092417 
    5360  
    5361 Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) relative to
    5362 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5363 Matrix rotation and translation 
    5364 0.99975115 0.02225007 0.00160437 -42.37113273 
    5365 -0.02229050 0.99922195 0.03253675 -39.86667288 
    5366 -0.00087917 -0.03256442 0.99946925 -26.34167349 
    5367 Axis -0.82491227 0.03146955 -0.56438411 
    5368 Axis point 0.00000000 12.03996179 1272.54105826 
    5369 Rotation angle (degrees) 2.26144694 
    5370 Shift along axis 48.56470264 
    5371  
    5372 
    5373 > select subtract #4
    5374 
    5375 8555 atoms, 8618 bonds, 1174 residues, 3 models selected 
    5376 
    5377 > select subtract #3
    5378 
    5379 2 models selected 
    5380 
    5381 > select subtract #2
    5382 
    5383 Nothing selected 
    5384 
    5385 > ui mousemode right "rotate selected models"
    5386 
    5387 > select add #3
    5388 
    5389 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5390 
    5391 > view matrix models
    5392 > #3,0.88251,0.23211,0.40903,-75.275,-0.21961,0.97246,-0.078009,62.282,-0.41588,-0.020986,0.90918,100.45
    5393 
    5394 > ui mousemode right "translate selected models"
    5395 
    5396 > view matrix models
    5397 > #3,0.88251,0.23211,0.40903,-75.557,-0.21961,0.97246,-0.078009,61.908,-0.41588,-0.020986,0.90918,99.178
    5398 
    5399 > fitmap #3 inMap #2
    5400 
    5401 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5402 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5403 average map value = 0.127, steps = 272 
    5404 shifted from previous position = 1.55 
    5405 rotated from previous position = 8.41 degrees 
    5406 atoms outside contour = 4288, contour level = 0.092417 
    5407  
    5408 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
    5409 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5410 Matrix rotation and translation 
    5411 0.98988621 0.08222609 0.11560346 -66.94222621 
    5412 -0.08667313 0.99565733 0.03397417 -34.07262077 
    5413 -0.11230787 -0.04365027 0.99271426 4.88957146 
    5414 Axis -0.26393700 0.77493934 -0.57428763 
    5415 Axis point -54.45818067 0.00000000 600.65902030 
    5416 Rotation angle (degrees) 8.45607029 
    5417 Shift along axis -11.54370437 
    5418  
    5419 
    5420 > select subtract #3
    5421 
    5422 Nothing selected 
    5423 
    5424 > select add #4
    5425 
    5426 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5427 
    5428 > view matrix models
    5429 > #4,0.96636,0.045793,0.25307,-32.02,-0.038117,0.99865,-0.035156,22.745,-0.25434,0.024327,0.96681,48.2
    5430 
    5431 > ui mousemode right "rotate selected models"
    5432 
    5433 > view matrix models
    5434 > #4,0.98649,-0.13285,0.095881,19.07,0.13318,0.99109,0.0030574,-13.022,-0.095433,0.009753,0.99539,17.369
    5435 
    5436 > fitmap #3 inMap #2 moveWholeMolecules false
    5437 
    5438 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5439 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5440 average map value = 0.1267, steps = 2000 
    5441 shifted from previous position = 0.231 
    5442 rotated from previous position = 0.209 degrees 
    5443 atoms outside contour = 4265, contour level = 0.092417 
    5444  
    5445 
    5446 > fitmap #3 inMap #2 moveWholeMolecules false
    5447 
    5448 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5449 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5450 average map value = 0.1257, steps = 2000 
    5451 shifted from previous position = 0.153 
    5452 rotated from previous position = 0.802 degrees 
    5453 atoms outside contour = 4316, contour level = 0.092417 
    5454  
    5455 
    5456 > select subtract #4
    5457 
    5458 Nothing selected 
    5459 
    5460 > select add #4
    5461 
    5462 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    5463 
    5464 > view matrix models
    5465 > #4,0.98865,0.077128,0.12895,-24.965,-0.061721,0.99092,-0.11949,40.165,-0.13699,0.11017,0.98443,7.9262
    5466 
    5467 > fitmap #3 inMap #2 moveWholeMolecules false
    5468 
    5469 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5470 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5471 average map value = 0.1256, steps = 2000 
    5472 shifted from previous position = 0.447 
    5473 rotated from previous position = 0.959 degrees 
    5474 atoms outside contour = 4316, contour level = 0.092417 
    5475  
    5476 
    5477 > fitmap #3 inMap #2 moveWholeMolecules false
    5478 
    5479 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5480 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5481 average map value = 0.1267, steps = 2000 
    5482 shifted from previous position = 0.369 
    5483 rotated from previous position = 0.333 degrees 
    5484 atoms outside contour = 4261, contour level = 0.092417 
    5485  
    5486 
    5487 > fitmap #4 inMap #2
    5488 
    5489 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
    5490 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5491 average map value = 0.1106, steps = 464 
    5492 shifted from previous position = 2.2 
    5493 rotated from previous position = 8.71 degrees 
    5494 atoms outside contour = 4757, contour level = 0.092417 
    5495  
    5496 Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) relative to
    5497 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) coordinates: 
    5498 Matrix rotation and translation 
    5499 0.99975184 0.02221316 0.00168369 -42.37411242 
    5500 -0.02225622 0.99922206 0.03255658 -39.87679425 
    5501 -0.00095919 -0.03258598 0.99946848 -26.32053100 
    5502 Axis -0.82544529 0.03348892 -0.56348786 
    5503 Axis point 0.00000000 9.69649265 1274.93904155 
    5504 Rotation angle (degrees) 2.26142362 
    5505 Shift along axis 48.47338052 
    5506  
    5507 
    5508 > select subtract #4
    5509 
    5510 Nothing selected 
    5511 
    5512 > ui tool show "Fit to Segments"
    5513 
    5514 > select #1/A-B:293
    5515 
    5516 18 atoms, 16 bonds, 2 residues, 1 model selected 
    5517 
    5518 > select #1/A-B:293-367
    5519 
    5520 1256 atoms, 1276 bonds, 150 residues, 1 model selected 
    5521 
    5522 > select add #4
    5523 
    5524 9811 atoms, 9894 bonds, 1324 residues, 2 models selected 
    5525 
    5526 > select subtract #4
    5527 
    5528 1256 atoms, 1276 bonds, 150 residues, 1 model selected 
    5529 
    5530 > select :605-635
    5531 
    5532 1728 atoms, 1756 bonds, 228 residues, 4 models selected 
    5533 
    5534 > fitmap #4 inMap #2 moveWholeMolecules false
    5535 
    5536 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
    5537 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5538 average map value = 0.1106, steps = 776 
    5539 shifted from previous position = 0.00595 
    5540 rotated from previous position = 0.00471 degrees 
    5541 atoms outside contour = 4758, contour level = 0.092417 
    5542  
    5543 
    5544 > fitmap #4 inMap #2 moveWholeMolecules false
    5545 
    5546 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
    5547 cryosparc_P1_J138_004_volume_map_sharp.mrc (#2) using 8555 atoms 
    5548 average map value = 0.1106, steps = 384 
    5549 shifted from previous position = 0.0135 
    5550 rotated from previous position = 0.0157 degrees 
    5551 atoms outside contour = 4757, contour level = 0.092417 
    5552  
    5553 
    5554 > cd /Users/madhurikanavalli/Desktop/test
    5555 
    5556 Current working directory is: /Users/madhurikanavalli/Desktop/test 
    5557 
    5558 > save /Users/madhurikanavalli/Desktop/test/dimerfit_Kasia.cxs
    5559 
    5560 ——— End of log from Fri Aug 30 15:18:41 2024 ———
    5561 
    5562 > view name session-start
    5563 
    5564 opened ChimeraX session 
    5565 
    5566 > open /Users/madhurikanavalli/Downloads/cryosparc_P1_J482_004_volume_map.mrc
    5567 
    5568 Opened cryosparc_P1_J482_004_volume_map.mrc as #2, grid size 352,352,352,
    5569 pixel 0.846, shown at level 0.0477, step 2, values float32 
    5570 
    5571 > volume #2 level 0.1132
    5572 
    5573 > set bgColor white
    5574 
    5575 > volume #2 level 0.1025
    5576 
    5577 > volume #2 level 0.1001
    5578 
    5579 > volume #2 level 0.08461
    5580 
    5581 > select add #4
    5582 
    5583 9851 atoms, 9935 bonds, 1345 residues, 4 models selected 
    5584 
    5585 > select subtract #4
    5586 
    5587 1296 atoms, 1317 bonds, 171 residues, 3 models selected 
    5588 
    5589 > select add #3
    5590 
    5591 9419 atoms, 9496 bonds, 1288 residues, 3 models selected 
    5592 
    5593 > select subtract #3
    5594 
    5595 864 atoms, 878 bonds, 114 residues, 2 models selected 
    5596 
    5597 > select add #3
    5598 
    5599 9419 atoms, 9496 bonds, 1288 residues, 3 models selected 
    5600 
    5601 > select add #6
    5602 
    5603 17542 atoms, 17675 bonds, 2405 residues, 3 models selected 
    5604 
    5605 > view matrix models
    5606 > #1,0.994,-0.094744,-0.054626,190.68,0.077109,0.25294,0.9644,136.09,-0.077554,-0.96283,0.25873,179.49,#6,-0.74953,0.12709,-0.64965,400.79,-0.073566,0.95933,0.27255,-75.279,0.65787,0.25208,-0.7097,94.31,#3,0.92681,0.10093,0.36172,-64.082,-0.094651,0.99489,-0.035082,-27.656,-0.36341,-0.0017227,0.93163,49.036
    5607 
    5608 > view matrix models
    5609 > #1,0.994,-0.094744,-0.054626,189.74,0.077109,0.25294,0.9644,121.52,-0.077554,-0.96283,0.25873,187.27,#6,-0.74953,0.12709,-0.64965,399.84,-0.073566,0.95933,0.27255,-89.852,0.65787,0.25208,-0.7097,102.09,#3,0.92681,0.10093,0.36172,-65.027,-0.094651,0.99489,-0.035082,-42.229,-0.36341,-0.0017227,0.93163,56.814
    5610 
    5611 > view matrix models
    5612 > #1,0.994,-0.094744,-0.054626,191.44,0.077109,0.25294,0.9644,104.17,-0.077554,-0.96283,0.25873,210.37,#6,-0.74953,0.12709,-0.64965,401.54,-0.073566,0.95933,0.27255,-107.2,0.65787,0.25208,-0.7097,125.19,#3,0.92681,0.10093,0.36172,-63.324,-0.094651,0.99489,-0.035082,-59.577,-0.36341,-0.0017227,0.93163,79.914
    5613 
    5614 > view matrix models
    5615 > #1,0.994,-0.094744,-0.054626,189.26,0.077109,0.25294,0.9644,133.92,-0.077554,-0.96283,0.25873,174.38,#6,-0.74953,0.12709,-0.64965,399.36,-0.073566,0.95933,0.27255,-77.452,0.65787,0.25208,-0.7097,89.203,#3,0.92681,0.10093,0.36172,-65.504,-0.094651,0.99489,-0.035082,-29.83,-0.36341,-0.0017227,0.93163,43.928
    5616 
    5617 > view matrix models
    5618 > #1,0.994,-0.094744,-0.054626,160.99,0.077109,0.25294,0.9644,160.74,-0.077554,-0.96283,0.25873,187.51,#6,-0.74953,0.12709,-0.64965,371.09,-0.073566,0.95933,0.27255,-50.634,0.65787,0.25208,-0.7097,102.33,#3,0.92681,0.10093,0.36172,-93.774,-0.094651,0.99489,-0.035082,-3.0112,-0.36341,-0.0017227,0.93163,57.056
    5619 
    5620 > view matrix models
    5621 > #1,0.994,-0.094744,-0.054626,162.53,0.077109,0.25294,0.9644,159.38,-0.077554,-0.96283,0.25873,186.26,#6,-0.74953,0.12709,-0.64965,372.63,-0.073566,0.95933,0.27255,-51.991,0.65787,0.25208,-0.7097,101.08,#3,0.92681,0.10093,0.36172,-92.239,-0.094651,0.99489,-0.035082,-4.368,-0.36341,-0.0017227,0.93163,55.803
    5622 
    5623 > ui mousemode right "rotate selected models"
    5624 
    5625 > view matrix models
    5626 > #1,0.92939,-0.058623,-0.36441,164.52,0.36859,0.096106,0.92461,157.81,-0.019182,-0.99364,0.11093,186.66,#6,-0.76215,-0.18968,-0.61899,435.59,-0.22171,0.97477,-0.025711,12.579,0.60825,0.11764,-0.78498,147.92,#3,0.94763,-0.1971,0.25131,-14.75,0.152,0.97036,0.18786,-90.399,-0.28088,-0.13982,0.9495,64.215
    5627 
    5628 > view matrix models
    5629 > #1,0.96327,-0.086547,0.2542,161.13,-0.18677,0.46424,0.86579,161.41,-0.19294,-0.88147,0.43103,186.05,#6,-0.68636,0.42515,-0.59005,291.88,0.0013985,0.8121,0.58352,-77.28,0.72726,0.39968,-0.55798,37.696,#3,0.82694,0.39195,0.40316,-139.78,-0.26967,0.90562,-0.32731,105.56,-0.4934,0.16195,0.85459,63.291
    5630 
    5631 Desktop color scheme is dark 
    5632 
    5633 > lighting full
    5634 
    5635 > view matrix models
    5636 > #1,0.92599,0.2946,-0.23612,163.44,0.14324,0.30452,0.94167,158.98,0.34932,-0.9058,0.23979,183.4,#6,-0.94666,-0.068404,-0.31488,406.44,-0.15974,0.9483,0.27424,-33.373,0.27984,0.30991,-0.90865,188.22,#3,0.99828,0.01072,-0.057691,0.50116,-0.0147,0.99751,-0.069014,-12.047,0.056808,0.069743,0.99595,-46.681
    5637 
    5638 > ui mousemode right "translate selected models"
    5639 
    5640 > view matrix models
    5641 > #1,0.92599,0.2946,-0.23612,161.4,0.14324,0.30452,0.94167,143.18,0.34932,-0.9058,0.23979,186.35,#6,-0.94666,-0.068404,-0.31488,404.41,-0.15974,0.9483,0.27424,-49.176,0.27984,0.30991,-0.90865,191.17,#3,0.99828,0.01072,-0.057691,-1.5331,-0.0147,0.99751,-0.069014,-27.85,0.056808,0.069743,0.99595,-43.732
    5642 
    5643 > show #!6 models
    5644 
    5645 > hide #!6 models
    5646 
    5647 > select add #4
    5648 
    5649 26097 atoms, 26293 bonds, 3579 residues, 4 models selected 
    5650 
    5651 > select subtract #3
    5652 
    5653 17542 atoms, 17675 bonds, 2405 residues, 3 models selected 
    5654 
    5655 > view matrix models
    5656 > #1,0.92599,0.2946,-0.23612,159.75,0.14324,0.30452,0.94167,90.273,0.34932,-0.9058,0.23979,167.09,#6,-0.94666,-0.068404,-0.31488,402.75,-0.15974,0.9483,0.27424,-102.08,0.27984,0.30991,-0.90865,171.91,#4,0.96635,0.045752,0.25314,-33.638,-0.038077,0.99866,-0.035137,-30.414,-0.25441,0.024315,0.96679,26.911
    5657 
    5658 > ui mousemode right "rotate selected models"
    5659 
    5660 > view matrix models
    5661 > #1,0.61907,0.58221,-0.52704,153.93,0.26992,0.47248,0.83899,79.331,0.73749,-0.66166,0.13535,146.15,#6,-0.9085,-0.41347,0.060664,407.35,-0.37329,0.86818,0.32698,-61.974,-0.18786,0.27441,-0.94308,255.17,#4,0.96004,-0.20089,-0.19484,74.965,0.18128,0.97681,-0.11393,-56.416,0.2132,0.074054,0.9742,-70.527
    5662 
    5663 > view matrix models
    5664 > #1,0.6268,0.5183,-0.58179,160.01,0.301,0.52764,0.79435,76.265,0.71869,-0.67302,0.17472,146.07,#6,-0.88524,-0.46514,-0.002032,427.41,-0.43651,0.82923,0.34904,-47.779,-0.16067,0.30987,-0.9371,241.9,#4,0.95184,-0.26949,-0.14617,82.582,0.24844,0.95738,-0.14729,-60.738,0.17964,0.10388,0.97823,-70.376
    5665 
    5666 > ui mousemode right "translate selected models"
    5667 
    5668 > view matrix models
    5669 > #1,0.6268,0.5183,-0.58179,139.9,0.301,0.52764,0.79435,59.265,0.71869,-0.67302,0.17472,146.39,#6,-0.88524,-0.46514,-0.002032,407.3,-0.43651,0.82923,0.34904,-64.778,-0.16067,0.30987,-0.9371,242.23,#4,0.95184,-0.26949,-0.14617,62.471,0.24844,0.95738,-0.14729,-77.738,0.17964,0.10388,0.97823,-70.05
    5670 
    5671 > ui mousemode right "rotate selected models"
    5672 
    5673 > view matrix models
    5674 > #1,0.56833,0.70828,-0.41874,122.46,0.33149,0.26869,0.90439,73.602,0.75307,-0.6528,-0.082087,152.32,#6,-0.92587,-0.31765,0.2046,341.15,-0.29507,0.9461,0.13355,-72.727,-0.23599,0.063284,-0.96969,316.14,#4,0.9477,-0.072153,-0.31091,49.129,0.10669,0.98969,0.09553,-90.672,0.30081,-0.1237,0.94563,-45.794
    5675 
    5676 > view matrix models
    5677 > #1,0.54644,0.67075,-0.50149,128.07,0.28728,0.41234,0.86455,65.478,0.78668,-0.61649,0.032625,145.6,#6,-0.89812,-0.40253,0.17703,361.73,-0.34868,0.89718,0.27108,-78.956,-0.26794,0.18173,-0.94614,289.19,#4,0.93818,-0.1649,-0.30435,67.269,0.15659,0.98631,-0.051703,-79.126,0.30871,0.00084819,0.95115,-71.212
    5678 
    5679 > ui mousemode right "translate selected models"
    5680 
    5681 > view matrix models
    5682 > #1,0.54644,0.67075,-0.50149,108.49,0.28728,0.41234,0.86455,68.46,0.78668,-0.61649,0.032625,139.36,#6,-0.89812,-0.40253,0.17703,342.14,-0.34868,0.89718,0.27108,-75.973,-0.26794,0.18173,-0.94614,282.95,#4,0.93818,-0.1649,-0.30435,47.685,0.15659,0.98631,-0.051703,-76.143,0.30871,0.00084819,0.95115,-77.451
    5683 
    5684 > view matrix models
    5685 > #1,0.54644,0.67075,-0.50149,111.2,0.28728,0.41234,0.86455,87.267,0.78668,-0.61649,0.032625,138.22,#6,-0.89812,-0.40253,0.17703,344.86,-0.34868,0.89718,0.27108,-57.167,-0.26794,0.18173,-0.94614,281.81,#4,0.93818,-0.1649,-0.30435,50.401,0.15659,0.98631,-0.051703,-57.337,0.30871,0.00084819,0.95115,-78.588
    5686 
    5687 > select subtract #4
    5688 
    5689 8987 atoms, 9057 bonds, 1231 residues, 2 models selected 
    5690 
    5691 > select add #3
    5692 
    5693 17542 atoms, 17675 bonds, 2405 residues, 3 models selected 
    5694 
    5695 > view matrix models
    5696 > #1,0.54644,0.67075,-0.50149,93.636,0.28728,0.41234,0.86455,86.962,0.78668,-0.61649,0.032625,135.05,#6,-0.89812,-0.40253,0.17703,327.29,-0.34868,0.89718,0.27108,-57.471,-0.26794,0.18173,-0.94614,278.64,#3,0.99828,0.01072,-0.057691,-19.1,-0.0147,0.99751,-0.069014,-28.154,0.056808,0.069743,0.99595,-46.902
    5697 
    5698 > transparency 50
    5699 
    5700 > ui tool show "Fit in Map"
    5701 
    5702 > fitmap #3 inMap #2
    5703 
    5704 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5705 cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms 
    5706 average map value = 0.1145, steps = 1280 
    5707 shifted from previous position = 3.75 
    5708 rotated from previous position = 12.3 degrees 
    5709 atoms outside contour = 4232, contour level = 0.084608 
    5710  
    5711 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
    5712 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    5713 Matrix rotation and translation 
    5714 0.99192569 0.06320433 0.10994826 -62.72498723 
    5715 -0.06914256 0.99629928 0.05105907 -41.19333953 
    5716 -0.10631421 -0.05824891 0.99262497 10.91865642 
    5717 Axis -0.39589431 0.78326468 -0.47933718 
    5718 Axis point 2.83869525 0.00000000 616.31281519 
    5719 Rotation angle (degrees) 7.93513801 
    5720 Shift along axis -12.66654047 
    5721  
    5722 
    5723 > view matrix models
    5724 > #1,0.54644,0.67075,-0.50149,93.206,0.28728,0.41234,0.86455,84.978,0.78668,-0.61649,0.032625,131.42,#6,-0.89812,-0.40253,0.17703,326.86,-0.34868,0.89718,0.27108,-59.456,-0.26794,0.18173,-0.94614,275.01,#3,0.99193,0.063204,0.10995,-63.155,-0.069143,0.9963,0.051059,-43.178,-0.10631,-0.058249,0.99262,7.289
    5725 
    5726 > view matrix models
    5727 > #1,0.54644,0.67075,-0.50149,92.22,0.28728,0.41234,0.86455,84.636,0.78668,-0.61649,0.032625,131.84,#6,-0.89812,-0.40253,0.17703,325.88,-0.34868,0.89718,0.27108,-59.798,-0.26794,0.18173,-0.94614,275.43,#3,0.99193,0.063204,0.10995,-64.141,-0.069143,0.9963,0.051059,-43.52,-0.10631,-0.058249,0.99262,7.7078
    5728 
    5729 > select subtract #3
    5730 
    5731 8987 atoms, 9057 bonds, 1231 residues, 2 models selected 
    5732 
    5733 > view matrix models
    5734 > #1,0.54644,0.67075,-0.50149,94.529,0.28728,0.41234,0.86455,85.746,0.78668,-0.61649,0.032625,118.28,#6,-0.89812,-0.40253,0.17703,328.18,-0.34868,0.89718,0.27108,-58.687,-0.26794,0.18173,-0.94614,261.87
    5735 
    5736 > view matrix models
    5737 > #1,0.54644,0.67075,-0.50149,96.546,0.28728,0.41234,0.86455,85.767,0.78668,-0.61649,0.032625,105.23,#6,-0.89812,-0.40253,0.17703,330.2,-0.34868,0.89718,0.27108,-58.666,-0.26794,0.18173,-0.94614,248.82
    5738 
    5739 > ui mousemode right "rotate selected models"
    5740 
    5741 > view matrix models
    5742 > #1,0.54644,0.67075,-0.50149,96.546,0.28728,0.41234,0.86455,85.767,0.78668,-0.61649,0.032625,105.23,#6,-0.89812,-0.40253,0.17703,330.2,-0.34868,0.89718,0.27108,-58.666,-0.26794,0.18173,-0.94614,248.82
    5743 
    5744 > ui mousemode right "rotate selected models"
    5745 
    5746 > select add #3
    5747 
    5748 17542 atoms, 17675 bonds, 2405 residues, 3 models selected 
    5749 
    5750 > view matrix models
    5751 > #1,0.42372,0.78352,-0.45449,107.25,0.26163,0.3745,0.88955,88.23,0.86718,-0.49583,-0.04631,97.495,#6,-0.85867,-0.37985,0.3441,306.29,-0.30263,0.91759,0.25776,-67.573,-0.41366,0.1172,-0.90286,276.9,#3,0.99096,0.12353,-0.052365,-41.689,-0.12099,0.99143,0.049217,-32.923,0.057996,-0.042437,0.99741,-25.732
    5752 
    5753 > view matrix models
    5754 > #1,0.48037,0.80395,-0.35057,97.566,0.14733,0.32006,0.93587,99.935,0.8646,-0.50122,0.035301,95.294,#6,-0.90139,-0.26766,0.34038,283.39,-0.17286,0.94315,0.28389,-90.096,-0.39701,0.19706,-0.89641,254.77,#3,0.97189,0.23512,-0.012238,-68.434,-0.23532,0.97172,-0.019439,5.7376,0.0073212,0.021773,0.99974,-29.674
    5755 
    5756 > fitmap #3 inMap #2
    5757 
    5758 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5759 cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms 
    5760 average map value = 0.1145, steps = 1020 
    5761 shifted from previous position = 4.13 
    5762 rotated from previous position = 12.7 degrees 
    5763 atoms outside contour = 4240, contour level = 0.084608 
    5764  
    5765 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
    5766 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    5767 Matrix rotation and translation 
    5768 0.99191155 0.06335532 0.10998890 -62.76825757 
    5769 -0.06928609 0.99629434 0.05096082 -41.15660376 
    5770 -0.10635268 -0.05816933 0.99262552 10.90286608 
    5771 Axis -0.39506002 0.78317416 -0.48017268 
    5772 Axis point 2.56900071 0.00000000 616.37826305 
    5773 Rotation angle (degrees) 7.93898321 
    5774 Shift along axis -12.67081790 
    5775  
    5776 
    5777 > fitmap #4 inMap #2
    5778 
    5779 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) to map
    5780 cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms 
    5781 average map value = 0.1047, steps = 804 
    5782 shifted from previous position = 5.34 
    5783 rotated from previous position = 20.5 degrees 
    5784 atoms outside contour = 4422, contour level = 0.084608 
    5785  
    5786 Position of hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) relative to
    5787 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    5788 Matrix rotation and translation 
    5789 0.99999092 0.00412006 0.00108643 -39.00797240 
    5790 -0.00412304 0.99998770 0.00275780 -38.99266428 
    5791 -0.00107505 -0.00276225 0.99999561 -27.76974191 
    5792 Axis -0.54366522 0.21288185 -0.81185556 
    5793 Axis point -11301.91372520 4764.89551107 0.00000000 
    5794 Rotation angle (degrees) 0.29087494 
    5795 Shift along axis 35.45146656 
    5796  
    5797 
    5798 > view matrix models
    5799 > #1,0.50877,0.851,-0.13021,86.529,-0.0070294,0.15535,0.98783,117.65,0.86087,-0.50167,0.08502,94.082,#6,-0.92059,-0.046384,0.38776,226.11,0.053879,0.96834,0.24375,-116.88,-0.38679,0.24528,-0.88895,241.01,#3,0.94978,0.28585,0.12733,-102.22,-0.28518,0.95818,-0.023838,20.523,-0.12882,-0.013672,0.99157,6.4689
    5800 
    5801 > view matrix models
    5802 > #1,0.41106,0.90215,0.13096,88.402,-0.17226,-0.0642,0.98296,139.1,0.89519,-0.42661,0.12901,87.865,#6,-0.83536,0.19218,0.51502,146.98,0.31322,0.93634,0.15865,-129.07,-0.45175,0.29384,-0.84237,231.83,#3,0.84686,0.53103,0.029017,-110.99,-0.52691,0.84518,-0.089589,99.508,-0.0721,0.06058,0.99556,-18.965
    5803 
    5804 > view matrix models
    5805 > #1,0.55394,0.75066,-0.36008,90.156,0.13096,0.34855,0.9281,101.72,0.82219,-0.56127,0.09477,98.841,#6,-0.93074,-0.26307,0.25401,292.43,-0.17738,0.9322,0.31551,-89.483,-0.31979,0.2486,-0.91429,235.23,#3,0.97925,0.042796,0.19808,-74.97,-0.048572,0.99852,0.024389,-39.72,-0.19674,-0.033504,0.97988,24.918
    5806 
    5807 > view matrix models
    5808 > #1,0.5673,0.82189,-0.051582,77.636,0.043048,0.032954,0.99853,113.04,0.82238,-0.56869,-0.016686,102.58,#6,-0.93958,0.041873,0.33975,209.96,0.086342,0.98939,0.11684,-115.11,-0.33126,0.13911,-0.93323,265.4,#3,0.91484,0.35307,0.196,-123.47,-0.3723,0.92541,0.070709,22.647,-0.15642,-0.13766,0.97805,38.388
    5809 
    5810 > view matrix models
    5811 > #1,0.49291,0.78746,-0.37005,96.979,0.077493,0.38389,0.92012,107.63,0.86662,-0.48221,0.1282,91.779,#6,-0.90459,-0.28436,0.31758,289.78,-0.15616,0.91426,0.37381,-92.017,-0.39665,0.28855,-0.87144,229.77,#3,0.99105,0.040677,0.12712,-61.789,-0.035989,0.99859,-0.038956,-28.701,-0.12853,0.034033,0.99112,-2.7827
    5812 
    5813 > fitmap #3 inMap #2
    5814 
    5815 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) to map
    5816 cryosparc_P1_J482_004_volume_map.mrc (#2) using 8555 atoms 
    5817 average map value = 0.1145, steps = 1148 
    5818 shifted from previous position = 0.0468 
    5819 rotated from previous position = 5.6 degrees 
    5820 atoms outside contour = 4238, contour level = 0.084608 
    5821  
    5822 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) relative to
    5823 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    5824 Matrix rotation and translation 
    5825 0.99191901 0.06352370 0.10982442 -62.76919098 
    5826 -0.06945569 0.99627767 0.05105578 -41.13025537 
    5827 -0.10617237 -0.05827113 0.99263885 10.89172991 
    5828 Axis -0.39581462 0.78200954 -0.48144768 
    5829 Axis point 2.83716672 0.00000000 617.02824957 
    5830 Rotation angle (degrees) 7.93812928 
    5831 Shift along axis -12.56308662 
    5832  
    5833 
    5834 > hide #!4 models
    5835 
    5836 > split #3
    5837 
    5838 Split hPNP_dimer_5zf6_fit_tetramer1.pdb (#3) into 2 models 
    5839 Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb A #3.1 
    5840 --- 
    5841 Chain | Description 
    5842 A | No description available 
    5843  
    5844 Chain information for hPNP_dimer_5zf6_fit_tetramer1.pdb B #3.2 
    5845 --- 
    5846 Chain | Description 
    5847 B | No description available 
    5848  
    5849 
    5850 > select add #3.2
    5851 
    5852 13214 atoms, 13318 bonds, 1808 residues, 3 models selected 
    5853 
    5854 > select subtract #3.2
    5855 
    5856 8987 atoms, 9057 bonds, 1231 residues, 2 models selected 
    5857 
    5858 > select add #3.1
    5859 
    5860 13315 atoms, 13414 bonds, 1828 residues, 3 models selected 
    5861 
    5862 > view matrix models
    5863 > #1,0.63866,0.76924,-0.019308,72.947,-0.11384,0.11928,0.98631,131.14,0.76102,-0.62772,0.16375,104.77,#6,-0.96168,0.087149,0.25996,211.37,0.16026,0.94797,0.27507,-124.61,-0.22246,0.30619,-0.92561,212.03,#3.1,0.87837,0.37425,0.29732,-138.47,-0.38698,0.92193,-0.017224,45.309,-0.28055,-0.099926,0.95462,58.624
    5864 
    5865 > ui mousemode right "translate selected models"
    5866 
    5867 > view matrix models
    5868 > #1,0.63866,0.76924,-0.019308,72.084,-0.11384,0.11928,0.98631,125.49,0.76102,-0.62772,0.16375,100.68,#6,-0.96168,0.087149,0.25996,210.51,0.16026,0.94797,0.27507,-130.26,-0.22246,0.30619,-0.92561,207.94,#3.1,0.87837,0.37425,0.29732,-139.33,-0.38698,0.92193,-0.017224,39.653,-0.28055,-0.099926,0.95462,54.532
    5869 
    5870 > view matrix models
    5871 > #1,0.63866,0.76924,-0.019308,72.54,-0.11384,0.11928,0.98631,126.82,0.76102,-0.62772,0.16375,102,#6,-0.96168,0.087149,0.25996,210.96,0.16026,0.94797,0.27507,-128.93,-0.22246,0.30619,-0.92561,209.26,#3.1,0.87837,0.37425,0.29732,-138.87,-0.38698,0.92193,-0.017224,40.985,-0.28055,-0.099926,0.95462,55.849
    5872 
    5873 > ui mousemode right "rotate selected models"
    5874 
    5875 > view matrix models
    5876 > #1,0.72286,0.68885,-0.054338,64.422,-0.094506,0.17646,0.97976,124.12,0.6845,-0.7031,0.19266,111.02,#6,-0.98739,0.06889,0.14254,227.23,0.11061,0.94433,0.30983,-125.74,-0.11326,0.32169,-0.94005,195.53,#3.1,0.86215,0.31108,0.39992,-145.84,-0.33042,0.94358,-0.021645,27.528,-0.38409,-0.11348,0.9163,85.446
    5877 
    5878 > view matrix models
    5879 > #1,0.49021,0.82777,-0.27293,94.401,-0.20452,0.41364,0.88717,136.23,0.84727,-0.37908,0.37207,84.985,#6,-0.91222,-0.18982,0.36306,263.96,0.048035,0.83052,0.55491,-111.5,-0.40687,0.52364,-0.74851,162.13,#3.1,0.98015,0.16795,0.1053,-79.273,-0.14126,0.96443,-0.22342,31.317,-0.13908,0.20411,0.96902,-29.133
    5880 
    5881 > fitmap #3.1 inMap #2
    5882 
    5883 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) to map
    5884 cryosparc_P1_J482_004_volume_map.mrc (#2) using 4328 atoms 
    5885 average map value = 0.1678, steps = 136 
    5886 shifted from previous position = 3.69 
    5887 rotated from previous position = 14.6 degrees 
    5888 atoms outside contour = 1115, contour level = 0.084608 
    5889  
    5890 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) relative to
    5891 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    5892 Matrix rotation and translation 
    5893 0.99674815 0.00855406 -0.08012447 -16.33333536 
    5894 -0.03149945 0.95659060 -0.28972780 24.97205938 
    5895 0.07416797 0.29130952 0.95374937 -82.05312532 
    5896 Axis 0.96436593 -0.25608401 -0.06647806 
    5897 Axis point 0.00000000 289.92437323 27.99933406 
    5898 Rotation angle (degrees) 17.53291000 
    5899 Shift along axis -16.69152470 
    5900  
    5901 
    5902 > volume #2 color #d783ff
    5903 
    5904 > transparency 50
    5905 
    5906 > volume #2 level 0.1528
    5907 
    5908 > fitmap #3.1 inMap #2
    5909 
    5910 Fit molecule hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) to map
    5911 cryosparc_P1_J482_004_volume_map.mrc (#2) using 4328 atoms 
    5912 average map value = 0.1678, steps = 48 
    5913 shifted from previous position = 0.00201 
    5914 rotated from previous position = 0.0151 degrees 
    5915 atoms outside contour = 2432, contour level = 0.15284 
    5916  
    5917 Position of hPNP_dimer_5zf6_fit_tetramer1.pdb A (#3.1) relative to
    5918 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    5919 Matrix rotation and translation 
    5920 0.99676224 0.00853600 -0.07995103 -16.36893175 
    5921 -0.03144631 0.95653366 -0.28992148 25.01195907 
    5922 0.07400108 0.29149695 0.95370506 -82.04786196 
    5923 Axis 0.96455693 -0.25540226 -0.06632955 
    5924 Axis point 0.00000000 289.73990669 28.09020522 
    5925 Rotation angle (degrees) 17.54119628 
    5926 Shift along axis -16.73467989 
    5927  
    5928 Must specify one map, got 0 
    5929 
    5930 > correlation #3.1 #1
    5931 
    5932 Unknown command: correlation #3.1 #1 
    5933 
    5934 > correlation
    5935 
    5936 Unknown command: correlation 
    5937 
    5938 > crossfade correlation #3.1 #1
    5939 
    5940 Expected an integer >= 1 or a keyword 
    5941 
    5942 > crosscorrelation #3.1 #1
    5943 
    5944 Unknown command: crosscorrelation #3.1 #1 
    5945 
    5946 > crosscorrelation #3.1 #1
    5947 
    5948 Unknown command: measure crosscorrelation #3.1 #1 
    5949 
    5950 > volume #2 level 0.09062
    5951 
    5952 Must specify one map, got 0 
    5953 Must specify one map, got 0 
    5954 
    5955 > save
    5956 > /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramer_02_withouttickoncopymaps.cxs
    5957 > includeMaps true
    5958 
    5959 > combine #3.1 #3.2
    5960 
    5961 Cell requested for row 6 is out of bounds for table with 9 rows! Resizing
    5962 table model. 
    5963 
    5964 > select add #5
    5965 
    5966 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    5967 
    5968 > select subtract #4.1
    5969 
    5970 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    5971 
    5972 > hide #4.1 models
    5973 
    5974 > show #4.1 models
    5975 
    5976 > select subtract #4.1
    5977 
    5978 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    5979 
    5980 > select add #4
    5981 
    5982 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    5983 
    5984 > hide #!4 models
    5985 
    5986 > hide #4.1 models
    5987 
    5988 > show #!4 models
    5989 
    5990 > hide #!4 models
    5991 
    5992 > select subtract #5
    5993 
    5994 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    5995 
    5996 > hide #5 models
    5997 
    5998 > show #5 models
    5999 
    6000 > select add #5
    6001 
    6002 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6003 
    6004 > select subtract #5
    6005 
    6006 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    6007 
    6008 > select add #5
    6009 
    6010 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6011 
    6012 > select subtract #5
    6013 
    6014 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    6015 
    6016 > select add #5
    6017 
    6018 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6019 
    6020 > select subtract #5
    6021 
    6022 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    6023 
    6024 > select add #5
    6025 
    6026 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6027 
    6028 > hide #3.2 models
    6029 
    6030 > select subtract #5
    6031 
    6032 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    6033 
    6034 > select add #5
    6035 
    6036 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6037 
    6038 > select subtract #5
    6039 
    6040 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    6041 
    6042 > select add #5
    6043 
    6044 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6045 
    6046 > combine #3.1 #3.2
    6047 
    6048 > save /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/9kjr_ChainA.pdb
    6049 > models #7 relModel #7
    6050 
    6051 > save
    6052 > /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramer_02_withouttickoncopymaps.cxs
    6053 > includeMaps true
    6054 
    6055 ——— End of log from Wed Nov 5 22:22:09 2025 ———
    6056 
    6057 > view name session-start
    6058 
    6059 opened ChimeraX session 
    6060 
    6061 > show #!4 models
    6062 
    6063 > split #420
    6064 
    6065 > split #4
    6066 
    6067 Split hPNP_dimer_5zf6_fit_tetramer2.pdb (#4) into 2 models 
    6068 Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb A #4.1 
    6069 --- 
    6070 Chain | Description 
    6071 A | No description available 
    6072  
    6073 Chain information for hPNP_dimer_5zf6_fit_tetramer2.pdb B #4.2 
    6074 --- 
    6075 Chain | Description 
    6076 B | No description available 
    6077  
    6078 
    6079 > ui tool show "Fit in Map"
    6080 
    6081 > fitmap #4.1 inMap #2
    6082 
    6083 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb A (#4.1) to map
    6084 cryosparc_P1_J482_004_volume_map.mrc (#2) using 4328 atoms 
    6085 average map value = 0.1511, steps = 156 
    6086 shifted from previous position = 8.94 
    6087 rotated from previous position = 22.3 degrees 
    6088 atoms outside contour = 1422, contour level = 0.090619 
    6089  
    6090 Position of hPNP_dimer_5zf6_fit_tetramer2.pdb A (#4.1) relative to
    6091 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6092 Matrix rotation and translation 
    6093 0.98383867 0.06125938 0.16825207 -71.95682366 
    6094 -0.00104748 0.94160854 -0.33670796 23.75307981 
    6095 -0.17905411 0.33109007 0.92645507 -46.53042246 
    6096 Axis 0.88416501 0.45983359 -0.08249432 
    6097 Axis point 0.00000000 176.40808408 106.68048095 
    6098 Rotation angle (degrees) 22.18778127 
    6099 Shift along axis -48.86074587 
    6100  
    6101 
    6102 > fitmap #4.2 inMap #2
    6103 
    6104 Fit molecule hPNP_dimer_5zf6_fit_tetramer2.pdb B (#4.2) to map
    6105 cryosparc_P1_J482_004_volume_map.mrc (#2) using 4227 atoms 
    6106 average map value = 0.1559, steps = 64 
    6107 shifted from previous position = 0.136 
    6108 rotated from previous position = 0.638 degrees 
    6109 atoms outside contour = 1298, contour level = 0.090619 
    6110  
    6111 Position of hPNP_dimer_5zf6_fit_tetramer2.pdb B (#4.2) relative to
    6112 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6113 Matrix rotation and translation 
    6114 0.99994145 0.01081390 0.00039510 -39.96225052 
    6115 -0.01081776 0.99987385 0.01163050 -39.04984188 
    6116 -0.00026928 -0.01163409 0.99993229 -26.51523205 
    6117 Axis -0.73218070 0.02090926 -0.68078942 
    6118 Axis point 0.00000000 421.54756264 3445.69864868 
    6119 Rotation angle (degrees) 0.91030714 
    6120 Shift along axis 46.49437443 
    6121  
    6122 
    6123 > combine #4..1 #4.2
    6124 
    6125 Expected a keyword 
    6126 
    6127 > combine #4.1 #4.2
    6128 
    6129 > select add #7
    6130 
    6131 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6132 
    6133 > select subtract #7
    6134 
    6135 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    6136 
    6137 > select add #7
    6138 
    6139 30425 atoms, 30650 bonds, 4176 residues, 5 models selected 
    6140 
    6141 > select subtract #7
    6142 
    6143 21870 atoms, 22032 bonds, 3002 residues, 4 models selected 
    6144 
    6145 > select subtract #6
    6146 
    6147 13315 atoms, 13414 bonds, 1828 residues, 3 models selected 
    6148 
    6149 > select subtract #5
    6150 
    6151 4760 atoms, 4796 bonds, 654 residues, 2 models selected 
    6152 
    6153 > select add #1
    6154 
    6155 12883 atoms, 12975 bonds, 1771 residues, 2 models selected 
    6156 
    6157 > select add #3
    6158 
    6159 17110 atoms, 17236 bonds, 2348 residues, 4 models selected 
    6160 
    6161 > select subtract #3
    6162 
    6163 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6164 
    6165 > select subtract #1
    6166 
    6167 Nothing selected 
    6168 
    6169 > select add #5
    6170 
    6171 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6172 
    6173 > select add #8
    6174 
    6175 17110 atoms, 17236 bonds, 2348 residues, 2 models selected 
    6176 
    6177 > combine #5 #8
    6178 
    6179 Remapping chain ID 'A' in combination #8 to 'C' 
    6180 Remapping chain ID 'B' in combination #8 to 'D' 
    6181 
    6182 > select subtract #8
    6183 
    6184 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6185 
    6186 > select subtract #5
    6187 
    6188 Nothing selected 
    6189 
    6190 > select add #7
    6191 
    6192 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6193 
    6194 > select subtract #7
    6195 
    6196 Nothing selected 
    6197 
    6198 > select add #7
    6199 
    6200 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6201 
    6202 > select subtract #7
    6203 
    6204 Nothing selected 
    6205 
    6206 > select add #9
    6207 
    6208 17110 atoms, 17236 bonds, 2348 residues, 1 model selected 
    6209 
    6210 > select subtract #9
    6211 
    6212 Nothing selected 
    6213 
    6214 > close #1
    6215 
    6216 > close #3
    6217 
    6218 > close #4
    6219 
    6220 > hide #5 models
    6221 
    6222 > close #5
    6223 
    6224 > show #!6 models
    6225 
    6226 > hide #!6 models
    6227 
    6228 > close #6
    6229 
    6230 > hide #7 models
    6231 
    6232 > show #7 models
    6233 
    6234 > select add #7
    6235 
    6236 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6237 
    6238 > select subtract #7
    6239 
    6240 Nothing selected 
    6241 
    6242 > select add #7
    6243 
    6244 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6245 
    6246 > select subtract #7
    6247 
    6248 Nothing selected 
    6249 
    6250 > close #7
    6251 
    6252 > select add #8
    6253 
    6254 8555 atoms, 8618 bonds, 1174 residues, 1 model selected 
    6255 
    6256 > select subtract #8
    6257 
    6258 Nothing selected 
    6259 
    6260 > close #8
    6261 
    6262 > select add #9
    6263 
    6264 17110 atoms, 17236 bonds, 2348 residues, 1 model selected 
    6265 
    6266 > select subtract #9
    6267 
    6268 Nothing selected 
    6269 
    6270 > save
    6271 > /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramerfit_J482_goodone.pdb
    6272 > relModel #2
    6273 
    6274 > save
    6275 > /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/tetramerfit_J482_good02.pdb
    6276 > relModel #9
    6277 
    6278 > save
    6279 > /Users/madhurikanavalli/Desktop/2025/Cryosparc/Q387R/Tetramer_goodmodel_01_05Nov25.cxs
    6280 > includeMaps true
    6281 
    6282 ——— End of log from Wed Nov 5 23:47:55 2025 ———
    6283 
    6284 > view name session-start
    6285 
    6286 opened ChimeraX session 
    6287 
    6288 > hide #9 models
    6289 
    6290 > ui tool show "Fit Loops"
    6291 
    6292 > show #9 models
    6293 
    6294 > ui tool show "Fit Loops"
    6295 
    6296 No selected amino-acid residues or missing-structure pseudobonds in
    6297 combination #9 
    6298 
    6299 > open
    6300 > /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_0.cif
    6301 > /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_1.cif
    6302 > /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_2.cif
    6303 > /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_3.cif
    6304 > /Users/madhurikanavalli/Downloads/fold_s1domain/fold_s1domain_model_4.cif
    6305 
    6306 Chain information for fold_s1domain_model_0.cif #1 
    6307 --- 
    6308 Chain | Description 
    6309 A | . 
    6310  
    6311 Chain information for fold_s1domain_model_1.cif #3 
    6312 --- 
    6313 Chain | Description 
    6314 A | . 
    6315  
    6316 Chain information for fold_s1domain_model_2.cif #4 
    6317 --- 
    6318 Chain | Description 
    6319 A | . 
    6320  
    6321 Chain information for fold_s1domain_model_3.cif #5 
    6322 --- 
    6323 Chain | Description 
    6324 A | . 
    6325  
    6326 Chain information for fold_s1domain_model_4.cif #6 
    6327 --- 
    6328 Chain | Description 
    6329 A | . 
    6330  
    6331 Computing secondary structure 
    6332 [Repeated 4 time(s)]
    6333 
    6334 > hide #9 models
    6335 
    6336 > tile
    6337 
    6338 6 models tiled 
    6339 
    6340 > hide #!2 models
    6341 
    6342 > show #!2 models
    6343 
    6344 > color #3 #7a81ffff
    6345 
    6346 > color #3 #0433ffff
    6347 
    6348 > select add #3
    6349 
    6350 522 atoms, 529 bonds, 65 residues, 1 model selected 
    6351 
    6352 > view matrix models #3,1,0,0,167.58,0,1,0,54.796,0,0,1,204.78
    6353 
    6354 > view matrix models #3,1,0,0,165.39,0,1,0,115.67,0,0,1,225.25
    6355 
    6356 > ui mousemode right "move picked models"
    6357 
    6358 > view matrix models #2,1,0,0,-2.0304,0,1,0,-3.9698,0,0,1,-16.281
    6359 
    6360 > view matrix models #2,1,0,0,-2.6783,0,1,0,2.0885,0,0,1,-17.199
    6361 
    6362 > ui mousemode right "rotate selected models"
    6363 
    6364 > view matrix models
    6365 > #3,0.32589,0.91906,-0.22164,161.57,-0.87579,0.20518,-0.43692,116.43,-0.35608,0.3365,0.87177,223.66
    6366 
    6367 > view matrix models
    6368 > #3,0.56547,-0.7859,-0.25021,166.9,0.82291,0.55799,0.10713,118.68,0.055423,-0.26647,0.96225,226.17
    6369 
    6370 > ui mousemode right "translate selected models"
    6371 
    6372 > view matrix models
    6373 > #3,0.56547,-0.7859,-0.25021,163.29,0.82291,0.55799,0.10713,131.17,0.055423,-0.26647,0.96225,208.64
    6374 
    6375 > view matrix models
    6376 > #3,0.29541,0.69457,0.65597,155.91,-0.92197,0.38722,0.0051959,144.72,-0.2504,-0.60633,0.75477,209.92
    6377 
    6378 > view matrix models
    6379 > #3,0.79695,-0.604,0.0075442,161.41,0.52088,0.6935,0.49774,151.3,-0.30587,-0.39275,0.86729,210.32
    6380 
    6381 > view matrix models
    6382 > #3,0.46843,-0.85689,-0.21519,160.99,0.82693,0.33948,0.44827,160.63,-0.31106,-0.38793,0.86761,210.1
    6383 
    6384 > view matrix models
    6385 > #3,-0.34505,0.91726,0.19892,154.61,-0.88742,-0.24981,-0.38741,149.7,-0.30566,-0.3102,0.90019,211.43
    6386 
    6387 > view matrix models
    6388 > #3,0.66119,0.61943,0.42324,159.05,-0.59559,0.77644,-0.20593,116.72,-0.45618,-0.11592,0.8823,203.44
    6389 
    6390 > ui tool show "Fit in Map"
    6391 
    6392 > fitmap #1 inMap #2
    6393 
    6394 Fit molecule fold_s1domain_model_0.cif (#1) to map
    6395 cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms 
    6396 average map value = 0.0003632, steps = 356 
    6397 shifted from previous position = 4.22 
    6398 rotated from previous position = 14.5 degrees 
    6399 atoms outside contour = 522, contour level = 0.090619 
    6400  
    6401 Position of fold_s1domain_model_0.cif (#1) relative to
    6402 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6403 Matrix rotation and translation 
    6404 0.97213948 0.21632806 0.09026078 182.36500636 
    6405 -0.20718521 0.97309809 -0.10076905 2.02323771 
    6406 -0.10963177 0.07926087 0.99080704 169.96457072 
    6407 Axis 0.35881954 0.39840796 -0.84410878 
    6408 Axis point 279.68301149 -935.07624490 0.00000000 
    6409 Rotation angle (degrees) 14.52865421 
    6410 Shift along axis -77.22638618 
    6411  
    6412 
    6413 > fitmap #1 inMap #2
    6414 
    6415 Fit molecule fold_s1domain_model_0.cif (#1) to map
    6416 cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms 
    6417 average map value = 0.000365, steps = 100 
    6418 shifted from previous position = 0.137 
    6419 rotated from previous position = 0.599 degrees 
    6420 atoms outside contour = 522, contour level = 0.090619 
    6421  
    6422 Position of fold_s1domain_model_0.cif (#1) relative to
    6423 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6424 Matrix rotation and translation 
    6425 0.97288387 0.20994836 0.09704977 182.50082645 
    6426 -0.19979031 0.97422533 -0.10473222 2.03411083 
    6427 -0.11653670 0.08250268 0.98975376 169.89241874 
    6428 Axis 0.37555154 0.42840695 -0.82184459 
    6429 Axis point 284.35086060 -958.13936528 0.00000000 
    6430 Rotation angle (degrees) 14.43490420 
    6431 Shift along axis -70.21527182 
    6432  
    6433 
    6434 > fitmap #3 inMap #2
    6435 
    6436 Fit molecule fold_s1domain_model_1.cif (#3) to map
    6437 cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms 
    6438 average map value = 0.07067, steps = 164 
    6439 shifted from previous position = 8.32 
    6440 rotated from previous position = 39.5 degrees 
    6441 atoms outside contour = 363, contour level = 0.090619 
    6442  
    6443 Position of fold_s1domain_model_1.cif (#3) relative to
    6444 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6445 Matrix rotation and translation 
    6446 0.92043171 -0.33817014 -0.19607755 159.00664102 
    6447 0.31899036 0.93970634 -0.12327665 125.40584612 
    6448 0.22594381 0.05092090 0.97280854 218.61730845 
    6449 Axis 0.21769478 -0.52740033 0.82125385 
    6450 Axis point -542.84900192 502.64006802 0.00000000 
    6451 Rotation angle (degrees) 23.58417039 
    6452 Shift along axis 148.01613600 
    6453  
    6454 
    6455 > fitmap #4 inMap #2
    6456 
    6457 Fit molecule fold_s1domain_model_2.cif (#4) to map
    6458 cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms 
    6459 average map value = -0.001537, steps = 80 
    6460 shifted from previous position = 0.947 
    6461 rotated from previous position = 11.5 degrees 
    6462 atoms outside contour = 522, contour level = 0.090619 
    6463  
    6464 Position of fold_s1domain_model_2.cif (#4) relative to
    6465 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6466 Matrix rotation and translation 
    6467 0.98137074 -0.01475330 -0.19155629 124.31223336 
    6468 0.00382580 0.99835020 -0.05729090 166.97625539 
    6469 0.19208549 0.05549076 0.97980811 25.02135082 
    6470 Axis 0.28173775 -0.95836828 0.04641208 
    6471 Axis point -72.08236990 0.00000000 838.11125119 
    6472 Rotation angle (degrees) 11.54594279 
    6473 Shift along axis -123.84000488 
    6474  
    6475 
    6476 > volume #2 level 0.07472
    6477 
    6478 > view matrix models
    6479 > #3,-0.67188,0.62554,0.39658,156.11,-0.55661,-0.77969,0.28683,98.367,0.48863,-0.028029,0.87204,213.25
    6480 
    6481 > style sel ball
    6482 
    6483 Changed 522 atom styles 
    6484 
    6485 > style sel sphere
    6486 
    6487 Changed 522 atom styles 
    6488 
    6489 > show sel surfaces
    6490 
    6491 > view matrix models
    6492 > #3,-0.76709,0.51052,0.38851,156.55,-0.43671,-0.85915,0.26672,89.922,0.46996,0.034932,0.882,210.08
    6493 
    6494 > ui mousemode right "rotate selected models"
    6495 
    6496 > view matrix models
    6497 > #3,-0.7899,0.60735,-0.084731,156.46,-0.59625,-0.72837,0.33758,88.914,0.14331,0.31717,0.93748,208.03
    6498 
    6499 > view matrix models
    6500 > #3,-0.66024,0.41001,0.62926,157.09,-0.37315,-0.90619,0.19893,90.332,0.6518,-0.10346,0.7513,211.23
    6501 
    6502 > view matrix models
    6503 > #3,0.35613,-0.51243,-0.7814,164.32,-0.36034,0.69624,-0.62081,86.3,0.86216,0.50267,0.063305,210.69
    6504 
    6505 > view matrix models
    6506 > #3,0.22649,-0.61697,-0.75369,164.12,-0.74129,0.39275,-0.54427,85.701,0.63181,0.68198,-0.3684,209.58
    6507 
    6508 > view matrix models
    6509 > #3,0.4365,-0.66898,-0.60161,164.96,-0.60804,0.27351,-0.74531,86.654,0.66314,0.69112,-0.28738,209.62
    6510 
    6511 > hide sel surfaces
    6512 
    6513 > view matrix models
    6514 > #3,0.19536,-0.53018,-0.82507,164.33,-0.68664,0.52674,-0.50106,85.416,0.70026,0.66442,-0.26114,209.74
    6515 
    6516 > view matrix models
    6517 > #3,0.35707,-0.66519,-0.65576,164.84,-0.63986,0.33727,-0.69053,86.324,0.6805,0.66617,-0.3052,209.76
    6518 
    6519 > view matrix models
    6520 > #3,0.3911,-0.62689,-0.67384,164.84,-0.65268,0.32728,-0.6833,86.311,0.64888,0.70704,-0.28116,209.53
    6521 
    6522 > view matrix models
    6523 > #3,0.50296,-0.58623,-0.63512,164.94,-0.61625,0.27201,-0.73908,86.63,0.60603,0.76312,-0.22446,209.2
    6524 
    6525 > ui mousemode right "translate selected models"
    6526 
    6527 > view matrix models
    6528 > #3,0.50296,-0.58623,-0.63512,159.63,-0.61625,0.27201,-0.73908,149.03,0.60603,0.76312,-0.22446,209.13
    6529 
    6530 > view matrix models
    6531 > #3,0.50296,-0.58623,-0.63512,160.92,-0.61625,0.27201,-0.73908,148.39,0.60603,0.76312,-0.22446,217.66
    6532 
    6533 > view matrix models
    6534 > #3,0.50296,-0.58623,-0.63512,160.7,-0.61625,0.27201,-0.73908,148.47,0.60603,0.76312,-0.22446,216.16
    6535 
    6536 > view matrix models
    6537 > #3,-0.45496,0.52695,-0.71787,152.27,-0.45166,0.55821,0.696,166.64,0.76747,0.64088,-0.015958,206.6
    6538 
    6539 > fitmap #4 inMap #2
    6540 
    6541 Fit molecule fold_s1domain_model_2.cif (#4) to map
    6542 cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms 
    6543 average map value = -0.0004006, steps = 88 
    6544 shifted from previous position = 1.25 
    6545 rotated from previous position = 6.05 degrees 
    6546 atoms outside contour = 522, contour level = 0.074721 
    6547  
    6548 Position of fold_s1domain_model_2.cif (#4) relative to
    6549 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6550 Matrix rotation and translation 
    6551 0.99147668 0.01049450 -0.12986092 116.82021270 
    6552 -0.00708136 0.99961796 0.02671695 137.03591507 
    6553 0.13009169 -0.02556964 0.99117221 26.84154122 
    6554 Axis -0.19675787 -0.97821877 -0.06613911 
    6555 Axis point -80.51316555 0.00000000 664.24143651 
    6556 Rotation angle (degrees) 7.63549261 
    6557 Shift along axis -158.81167600 
    6558  
    6559 
    6560 > fitmap #3 inMap #2
    6561 
    6562 Fit molecule fold_s1domain_model_1.cif (#3) to map
    6563 cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms 
    6564 average map value = 0.07284, steps = 144 
    6565 shifted from previous position = 9.14 
    6566 rotated from previous position = 32.2 degrees 
    6567 atoms outside contour = 318, contour level = 0.074721 
    6568  
    6569 Position of fold_s1domain_model_1.cif (#3) relative to
    6570 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6571 Matrix rotation and translation 
    6572 -0.51872333 0.27009097 -0.81115779 162.49967762 
    6573 -0.72798453 0.35795974 0.58472501 168.27559607 
    6574 0.44829078 0.89382084 0.01093998 212.26586284 
    6575 Axis 0.18888415 -0.76963145 -0.60991001 
    6576 Axis point 77.24806995 0.00000000 108.85630195 
    6577 Rotation angle (degrees) 125.09345631 
    6578 Shift along axis -228.27965129 
    6579  
    6580 
    6581 > view matrix models
    6582 > #3,0.87466,-0.27955,-0.396,157.61,-0.41844,-0.023029,-0.90795,126.96,0.2447,0.95985,-0.13712,199.83
    6583 
    6584 > view matrix models
    6585 > #3,0.7064,-0.4253,0.56579,157.56,0.3865,-0.43789,-0.81171,108.84,0.59297,0.79207,-0.14495,197.91
    6586 
    6587 > fitmap #3 inMap #2
    6588 
    6589 Fit molecule fold_s1domain_model_1.cif (#3) to map
    6590 cryosparc_P1_J482_004_volume_map.mrc (#2) using 522 atoms 
    6591 average map value = 0.057, steps = 140 
    6592 shifted from previous position = 8.64 
    6593 rotated from previous position = 40 degrees 
    6594 atoms outside contour = 355, contour level = 0.074721 
    6595  
    6596 Position of fold_s1domain_model_1.cif (#3) relative to
    6597 cryosparc_P1_J482_004_volume_map.mrc (#2) coordinates: 
    6598 Matrix rotation and translation 
    6599 -0.87064244 -0.19188813 -0.45294667 134.31464498 
    6600 -0.49130252 0.29321200 0.82015154 169.18135869 
    6601 -0.02456795 0.93659258 -0.34955793 220.00413042 
    6602 Axis 0.21746043 -0.80002225 -0.55917382 
    6603 Axis point 82.32214637 0.00000000 66.57043206 
    6604 Rotation angle (degrees) 164.47081111 
    6605 Shift along axis -229.16128017 
    6606  
    6607 
    6608 > view matrix models
    6609 > #3,0.95229,0.22388,0.20741,154.09,-0.28611,0.41832,0.86206,83.875,0.10624,-0.88028,0.46241,224.1
    6610 
    6611 > open Q8TCS8 fromDatabase alphafold_pae format pae
    6612 
    6613 Fetching an AlphaFold database PAE file requires specifying the structure to
    6614 associate. For example "open P29474 from alphafold_pae structure #1" 
    6615 
    6616 > open /Users/madhurikanavalli/Downloads/AF-Q8TCS8-F1-model_v6.pdb
    6617 
    6618 AF-Q8TCS8-F1-model_v6.pdb title: 
    6619 Alphafold monomer V2.0 prediction for polyribonucleotide
    6620 nucleotidyltransferase 1, mitochondrial (Q8TCS8) [more info...] 
    6621  
    6622 Chain information for AF-Q8TCS8-F1-model_v6.pdb #7 
    6623 --- 
    6624 Chain | Description | UniProt 
    6625 A | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 1-783 
    6626  
    6627 Computing secondary structure 
    6628 
    6629 > hide #!3 models
    6630 
    6631 > select subtract #3
    6632 
    6633 1 model selected 
    6634 
    6635 > hide #6 models
    6636 
    6637 > hide #!2 models
    6638 
    6639 > show #!2 models
    6640 
    6641 > hide #1 models
    6642 
    6643 > close #1
    6644 
    6645 > close #6
    6646 
    6647 > close #5
    6648 
    6649 > close #4
    6650 
    6651 > select add #7
    6652 
    6653 6032 atoms, 6129 bonds, 783 residues, 1 model selected 
    6654 
    6655 > view matrix models
    6656 > #7,0.93203,-0.33526,0.13754,27.703,-0.3055,-0.5228,0.79584,135.27,-0.19491,-0.78376,-0.58968,172.48
    6657 
    6658 > view matrix models
    6659 > #7,0.99383,0.081244,-0.075482,18.858,0.10523,-0.47615,0.87304,113.59,0.034988,-0.8756,-0.48177,159.02
    6660 
    6661 > ui mousemode right "rotate selected models"
    6662 
    6663 > ui mousemode right "move picked models"
    6664 
    6665 > view matrix models
    6666 > #7,0.99383,0.081244,-0.075482,17.188,0.10523,-0.47615,0.87304,122.02,0.034988,-0.8756,-0.48177,152.46
    6667 
    6668 > ui mousemode right "translate selected atoms"
    6669 
    6670 > ui mousemode right "move picked models"
    6671 
    6672 > view matrix models
    6673 > #2,-0.96007,-0.2796,-0.0089378,326.83,0.13649,-0.44028,-0.88742,273.98,0.24419,-0.85321,0.46087,83.166
    6674 
    6675 > ui mousemode right "translate selected models"
    6676 
    6677 > view matrix models
    6678 > #7,-0.88144,0.35786,-0.30822,1.7984,0.34471,0.93357,0.098144,71.119,0.32287,-0.019738,-0.94624,110.86
    6679 
    6680 > view matrix models
    6681 > #7,-0.099404,0.88065,-0.46322,0.9821,0.94473,0.22969,0.23394,71.545,0.31242,-0.41436,-0.85481,105.94
    6682 
    6683 > ui mousemode right "rotate selected models"
    6684 
    6685 > view matrix models
    6686 > #7,-0.76785,-0.43102,-0.47394,-6.4138,-0.52462,0.84765,0.079073,63.133,0.36766,0.30936,-0.877,107.93
    6687 
    6688 > view matrix models
    6689 > #7,-0.33896,-0.93514,-0.10302,5.3628,-0.91127,0.35356,-0.21114,50.667,0.23387,0.022309,-0.97201,103.39
    6690 
    6691 > view matrix models
    6692 > #7,0.12187,-0.96241,-0.24272,2.542,-0.96457,-0.05719,-0.25755,47.564,0.23399,0.2655,-0.93528,105.4
    6693 
    6694 > view matrix models
    6695 > #7,-0.20108,-0.97283,-0.11478,5.3796,-0.68218,0.22315,-0.6963,35.543,0.70299,-0.061709,-0.70852,113.32
     1502[deleted to fit within ticket limits]
    66961503
    66971504> fitmap #7 inMap #2