Changes between Initial Version and Version 1 of Ticket #10224


Ignore:
Timestamp:
Nov 27, 2023, 10:37:43 AM (2 years ago)
Author:
Eric Pettersen
Comment:

Legend:

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  • Ticket #10224

    • Property Cc Tom Goddard added
    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0

  • Ticket #10224 – Description

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    1697     },
    1698     {
    1699       "rolloutId" : "60356660bbe37970735c5624",
    1700       "factorPackIds" : {
    1701 
    1702       },
    1703       "deploymentId" : 240000027
    1704     }
    1705   ],
    1706   "experiments" : [
    1707 
    1708   ]
    1709 }
    1710 }
    1711 ===== Log before crash start =====
    1712 UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1713 © 2016-2023 Regents of the University of California. All rights reserved. 
    1714 
    1715 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    1716 > UniversityofDundee/Documents/Biology/cryo-
    1717 > EM/CRL2/2023_11_16_mapCRL2/2023_11_21_chimeraxsession.cxs
    1718 
    1719 Opened emd_15829.map as #1, grid size 340,340,340, pixel 1.05, shown at level
    1720 0.904, step 2, values float32 
    1721 Opened cryosparc_P7_J649_008_volume_map_sharp.mrc as #2, grid size
    1722 256,256,256, pixel 1.48, shown at level 0.165, step 1, values float32 
    1723 Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #8, grid size
    1724 256,256,256, pixel 1.48, shown at level 0.178, step 1, values float32 
    1725 Opened emd_10585.map as #11, grid size 320,320,320, pixel 1.06, shown at level
    1726 0.0153, step 2, values float32 
    1727 Opened map series J684_series_000_frame_000.mrc as #12, 41 images, grid size
    1728 128,128,128, pixel 2.96, shown at level 0.00925, step 1, values float32 
    1729 Opened map series J684_series_001_frame_000.mrc as #13, 41 images, grid size
    1730 128,128,128, pixel 2.96, shown at level 0.0119, step 1, values float32 
    1731 Log from Tue Nov 21 10:52:47 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1732 © 2016-2023 Regents of the University of California. All rights reserved. 
    1733 
    1734 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    1735 > UniversityofDundee/Documents/Biology/cryo-
    1736 > EM/CRL2/2023_11_16_mapCRL2/2023_11_16_chimerasession-fittingmodels-
    1737 > preliminary.cxs
    1738 
    1739 Opened emd_15829.map as #1, grid size 340,340,340, pixel 1.05, shown at level
    1740 0.674, step 2, values float32 
    1741 Opened cryosparc_P7_J649_008_volume_map_sharp.mrc as #2, grid size
    1742 256,256,256, pixel 1.48, shown at level 0.12, step 1, values float32 
    1743 Log from Sat Nov 18 13:53:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) 
    1744 © 2016-2023 Regents of the University of California. All rights reserved. 
    1745 How to cite UCSF ChimeraX 
    1746 
    1747 > open /Users/ccrowe/Downloads/emd_15829.map
    1748 
    1749 Opened emd_15829.map as #1, grid size 340,340,340, pixel 1.05, shown at level
    1750 0.319, step 2, values float32 
    1751 
    1752 > open /Users/ccrowe/Downloads/cryosparc_P7_J649_008_volume_map_sharp.mrc
    1753 
    1754 Opened cryosparc_P7_J649_008_volume_map_sharp.mrc as #2, grid size
    1755 256,256,256, pixel 1.48, shown at level 0.0675, step 1, values float32 
    1756 
    1757 > volume #2 level 0.1569
    1758 
    1759 > volume #1 level 1.422
    1760 
    1761 > volume #2 level 0.2462
    1762 
    1763 > fitmap #1 inMap #2
    1764 
    1765 Fit map emd_15829.map in map cryosparc_P7_J649_008_volume_map_sharp.mrc using
    1766 8467 points 
    1767 correlation = 0.2699, correlation about mean = 0.02423, overlap = 792.2 
    1768 steps = 88, shift = 5.5, angle = 8.32 degrees 
    1769  
    1770 Position of emd_15829.map (#1) relative to
    1771 cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) coordinates: 
    1772 Matrix rotation and translation 
    1773 0.98954429 -0.13805513 -0.04174771 37.60417190 
    1774 0.13857643 0.99030278 0.00984807 -22.08426146 
    1775 0.03998330 -0.01553035 0.99907965 -6.71417206 
    1776 Axis -0.08764266 -0.28225251 0.95532836 
    1777 Axis point 184.37562505 256.21425444 0.00000000 
    1778 Rotation angle (degrees) 8.32474228 
    1779 Shift along axis -3.47663053 
    1780  
    1781 
    1782 > select add #1
    1783 
    1784 2 models selected 
    1785 
    1786 > ui mousemode right "translate selected models"
    1787 
    1788 > view matrix models
    1789 > #1,0.98954,-0.13806,-0.041748,35.375,0.13858,0.9903,0.0098481,-2.1466,0.039983,-0.01553,0.99908,24.804
    1790 
    1791 > fitmap #1 inMap #2
    1792 
    1793 Fit map emd_15829.map in map cryosparc_P7_J649_008_volume_map_sharp.mrc using
    1794 8467 points 
    1795 correlation = 0.4314, correlation about mean = 0.0793, overlap = 1491 
    1796 steps = 192, shift = 8.85, angle = 11.7 degrees 
    1797  
    1798 Position of emd_15829.map (#1) relative to
    1799 cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) coordinates: 
    1800 Matrix rotation and translation 
    1801 0.95102599 -0.30734543 0.03299018 64.18837099 
    1802 0.30895288 0.94852311 -0.06965642 -9.87847425 
    1803 -0.00988337 0.07643748 0.99702539 10.52181670 
    1804 Axis 0.23013187 0.06753581 0.97081318 
    1805 Axis point 67.26780029 179.91918163 0.00000000 
    1806 Rotation angle (degrees) 18.50657282 
    1807 Shift along axis 24.31935726 
    1808  
    1809 
    1810 > select clear
    1811 
    1812 > surface dust #1 size 10.5
    1813 
    1814 > surface dust #2 size 14.8
    1815 
    1816 > hide #!1 models
    1817 
    1818 > volume #2 level 0.2409
    1819 
    1820 > volume #2 level 0.2357
    1821 
    1822 > volume #2 level 0.2094
    1823 
    1824 > volume #2 level 0.2041
    1825 
    1826 > volume #2 level 0.1884
    1827 
    1828 > volume #2 level 0.1779
    1829 
    1830 > volume #2 level 0.1674
    1831 
    1832 > volume #2 level 0.1569
    1833 
    1834 > volume #2 level 0.1621
    1835 
    1836 > show #!1 models
    1837 
    1838 > hide #!1 models
    1839 
    1840 > open 5n4w
    1841 
    1842 5n4w title: 
    1843 Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more
    1844 info...] 
    1845  
    1846 Chain information for 5n4w #3 
    1847 --- 
    1848 Chain | Description | UniProt 
    1849 A | Cullin-2 | CUL2_HUMAN 1-745 
    1850 B | Elongin-B | ELOB_HUMAN 1-104 
    1851 C | Elongin-C | ELOC_HUMAN 17-112 
    1852 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-102 
    1853 V | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213 
    1854  
    1855 Non-standard residues in 5n4w #3 
    1856 --- 
    1857 ZN — zinc ion 
    1858  
    1859 
    1860 > select add #3
    1861 
    1862 7719 atoms, 7841 bonds, 29 pseudobonds, 970 residues, 3 models selected 
    1863 
    1864 > ui mousemode right "translate selected models"
    1865 
    1866 > view matrix models #3,1,0,0,67.765,0,1,0,146.24,0,0,1,202.44
    1867 
    1868 > view matrix models #3,1,0,0,86.717,0,1,0,171.74,0,0,1,261.01
    1869 
    1870 > view matrix models #3,1,0,0,139.75,0,1,0,165.25,0,0,1,246.27
    1871 
    1872 > ui mousemode right "rotate selected models"
    1873 
    1874 > view matrix models
    1875 > #3,0.79454,-0.062119,-0.60402,123.9,0.10797,0.99335,0.039873,164.84,0.59753,-0.0969,0.79597,230.62
    1876 
    1877 > ui mousemode right "translate selected models"
    1878 
    1879 > view matrix models
    1880 > #3,0.79454,-0.062119,-0.60402,166.64,0.10797,0.99335,0.039873,161.69,0.59753,-0.0969,0.79597,218.48
    1881 
    1882 > ui mousemode right translate
    1883 
    1884 > fitmap #3 inMap #2
    1885 
    1886 Fit molecule 5n4w (#3) to map cryosparc_P7_J649_008_volume_map_sharp.mrc (#2)
    1887 using 7719 atoms 
    1888 average map value = 0.18, steps = 116 
    1889 shifted from previous position = 3.22 
    1890 rotated from previous position = 10.6 degrees 
    1891 atoms outside contour = 3991, contour level = 0.16211 
    1892  
    1893 Position of 5n4w (#3) relative to cryosparc_P7_J649_008_volume_map_sharp.mrc
    1894 (#2) coordinates: 
    1895 Matrix rotation and translation 
    1896 0.79478450 0.08379181 -0.60107948 162.30251961 
    1897 -0.07692658 0.99634346 0.03717539 161.31478949 
    1898 0.60199660 0.01669257 0.79832415 216.95739215 
    1899 Axis -0.01687306 -0.99105349 -0.13239439 
    1900 Axis point -206.08574593 0.00000000 335.00747620 
    1901 Rotation angle (degrees) 37.37061157 
    1902 Shift along axis -191.33406721 
    1903  
    1904 
    1905 > hide sel atoms
    1906 
    1907 > show sel cartoons
    1908 
    1909 > select /A
    1910 
    1911 5384 atoms, 5468 bonds, 16 pseudobonds, 671 residues, 2 models selected 
    1912 
    1913 > color (#!3 & sel) light sea green
    1914 
    1915 > color (#!3 & sel) #4294a5ff
    1916 
    1917 > select /R
    1918 
    1919 693 atoms, 707 bonds, 6 pseudobonds, 89 residues, 2 models selected 
    1920 
    1921 > color (#!3 & sel) #5ecd3cff
    1922 
    1923 [Repeated 1 time(s)]
    1924 
    1925 > select /V
    1926 
    1927 315 atoms, 319 bonds, 37 residues, 1 model selected 
    1928 
    1929 > color sel #3478f5ff
    1930 
    1931 > color sel #429429ff
    1932 
    1933 > select clear
    1934 
    1935 > transparency #2.1 50
    1936 
    1937 > select /B
    1938 
    1939 627 atoms, 634 bonds, 5 pseudobonds, 82 residues, 2 models selected 
    1940 
    1941 > color (#!3 & sel) #c5c53fff
    1942 
    1943 > select /C
    1944 
    1945 700 atoms, 713 bonds, 2 pseudobonds, 91 residues, 2 models selected 
    1946 
    1947 > color (#!3 & sel) #b1d9aaff
    1948 
    1949 > select #2
    1950 
    1951 2 models selected 
    1952 
    1953 > select clear
    1954 
    1955 > open 5t35
    1956 
    1957 5t35 title: 
    1958 The PROTAC MZ1 in complex with the second bromodomain of Brd4 and
    1959 pVHL:ElonginC:ElonginB [more info...] 
    1960  
    1961 Chain information for 5t35 #4 
    1962 --- 
    1963 Chain | Description | UniProt 
    1964 A E | Bromodomain-containing protein 4 | BRD4_HUMAN 333-460 
    1965 B F | Transcription elongation factor B polypeptide 2 | ELOB_HUMAN 1-104 
    1966 C G | Transcription elongation factor B polypeptide 1 | ELOC_HUMAN 17-112 
    1967 D H | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213 
    1968  
    1969 Non-standard residues in 5t35 #4 
    1970 --- 
    1971 759 —
    1972 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
    1973 butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
    1974 pyrrolidine-2-carboxamide 
    1975  
    1976 5t35 mmCIF Assemblies 
    1977 --- 
    1978 1| author_defined_assembly 
    1979 2| author_defined_assembly 
    1980  
    1981 
    1982 > select #4/E
    1983 
    1984 910 atoms, 918 bonds, 126 residues, 1 model selected 
    1985 
    1986 > delete sel
    1987 
    1988 > select #4/G
    1989 
    1990 693 atoms, 703 bonds, 1 pseudobond, 92 residues, 2 models selected 
    1991 
    1992 > delete sel
    1993 
    1994 > select #4/F
    1995 
    1996 811 atoms, 826 bonds, 105 residues, 1 model selected 
    1997 
    1998 > delete sel
    1999 
    2000 > select #4/H
    2001 
    2002 1265 atoms, 1294 bonds, 156 residues, 1 model selected 
    2003 
    2004 > delete sel
    2005 
    2006 > ui mousemode right "translate selected models"
    2007 
    2008 > select add #4
    2009 
    2010 3730 atoms, 3763 bonds, 1 pseudobond, 510 residues, 2 models selected 
    2011 
    2012 > view matrix models #4,1,0,0,-5.3699,0,1,0,134.86,0,0,1,94.837
    2013 
    2014 > view matrix models #4,1,0,0,2.1659,0,1,0,-62.339,0,0,1,-18.94
    2015 
    2016 > view matrix models #4,1,0,0,2.3333,0,1,0,-67.77,0,0,1,-18.915
    2017 
    2018 > view matrix models #4,1,0,0,2.5358,0,1,0,-69.072,0,0,1,-31.691
    2019 
    2020 > ui mousemode right "translate selected models"
    2021 
    2022 > view matrix models #4,1,0,0,1.5607,0,1,0,-14.072,0,0,1,-88.646
    2023 
    2024 > view matrix models #4,1,0,0,-5.8062,0,1,0,211.25,0,0,1,194
    2025 
    2026 > view matrix models #4,1,0,0,172.88,0,1,0,205.94,0,0,1,213.38
    2027 
    2028 > ui mousemode right translate
    2029 
    2030 > ui mousemode right "translate selected models"
    2031 
    2032 > view matrix models #4,1,0,0,170.43,0,1,0,219.02,0,0,1,201.75
    2033 
    2034 > ui mousemode right "rotate selected models"
    2035 
    2036 > view matrix models
    2037 > #4,-0.87652,0.14211,-0.4599,186.86,0.47965,0.33829,-0.80963,203.87,0.040523,-0.93025,-0.36468,185.16
    2038 
    2039 > view matrix models
    2040 > #4,-0.82238,-0.48607,0.29569,170.12,0.079795,-0.61313,-0.78595,185.13,0.56332,-0.62275,0.54301,185.81
    2041 
    2042 > view matrix models
    2043 > #4,-0.42813,-0.10102,0.89806,174.29,-0.57519,-0.73601,-0.357,185.14,0.69704,-0.66939,0.257,184.85
    2044 
    2045 > ui mousemode right "translate selected models"
    2046 
    2047 > view matrix models
    2048 > #4,-0.42813,-0.10102,0.89806,169.91,-0.57519,-0.73601,-0.357,201.7,0.69704,-0.66939,0.257,150.37
    2049 
    2050 > view matrix models
    2051 > #4,-0.42813,-0.10102,0.89806,196.15,-0.57519,-0.73601,-0.357,202.85,0.69704,-0.66939,0.257,152.15
    2052 
    2053 > fitmap #4 inMap #2
    2054 
    2055 Fit molecule 5t35 (#4) to map cryosparc_P7_J649_008_volume_map_sharp.mrc (#2)
    2056 using 3730 atoms 
    2057 average map value = 0.215, steps = 108 
    2058 shifted from previous position = 3.82 
    2059 rotated from previous position = 14.6 degrees 
    2060 atoms outside contour = 1669, contour level = 0.16211 
    2061  
    2062 Position of 5t35 (#4) relative to cryosparc_P7_J649_008_volume_map_sharp.mrc
    2063 (#2) coordinates: 
    2064 Matrix rotation and translation 
    2065 -0.47918317 -0.26739413 0.83599275 190.99987496 
    2066 -0.36232349 -0.80726251 -0.46588511 200.32242340 
    2067 0.79944054 -0.52614411 0.28994343 151.75878688 
    2068 Axis -0.50966766 0.30915673 -0.80290784 
    2069 Axis point 51.91965946 127.33615507 0.00000000 
    2070 Rotation angle (degrees) 176.61092812 
    2071 Shift along axis -157.26375277 
    2072  
    2073 
    2074 > select clear
    2075 
    2076 > ui mousemode right "translate selected models"
    2077 
    2078 > select add #4
    2079 
    2080 3730 atoms, 3763 bonds, 1 pseudobond, 510 residues, 2 models selected 
    2081 
    2082 > show sel cartoons
    2083 
    2084 > hide sel atoms
    2085 
    2086 > select clear
    2087 
    2088 > select #4/A
    2089 
    2090 893 atoms, 908 bonds, 119 residues, 1 model selected 
    2091 
    2092 > color sel #590df2ff
    2093 
    2094 > select #4/D
    2095 
    2096 1305 atoms, 1322 bonds, 171 residues, 1 model selected 
    2097 
    2098 > color sel #429429ff
    2099 
    2100 > select clear
    2101 
    2102 > select #4/B
    2103 
    2104 831 atoms, 830 bonds, 121 residues, 1 model selected 
    2105 
    2106 > color sel #c5c53fff
    2107 
    2108 > select clear
    2109 
    2110 > select #4/C
    2111 
    2112 701 atoms, 703 bonds, 1 pseudobond, 99 residues, 2 models selected 
    2113 
    2114 > ui tool show "Color Actions"
    2115 
    2116 > color (#!4 & sel) #b1d9aaff
    2117 
    2118 > select clear
    2119 
    2120 > volume #2 level 0.2199
    2121 
    2122 > volume #2 level 0.3092
    2123 
    2124 > volume #2 level 0.4143
    2125 
    2126 > volume #2 level 0.2987
    2127 
    2128 > volume #2 level 0.2567
    2129 
    2130 > volume #2 level 0.2199
    2131 
    2132 > volume #2 level 0.1201
    2133 
    2134 > volume #2 level 0.1621
    2135 
    2136 > volume #2 level 0.2567
    2137 
    2138 > volume #2 level 0.4195
    2139 
    2140 > volume #2 level 0.3092
    2141 
    2142 > volume #2 level 0.304
    2143 
    2144 > volume #2 level 0.2199
    2145 
    2146 > volume #2 level 0.2567
    2147 
    2148 > hide #!3 models
    2149 
    2150 > hide #!1 models
    2151 
    2152 > show #!1 models
    2153 
    2154 > hide #!1 models
    2155 
    2156 > volume #2 level 0.3145
    2157 
    2158 > volume #2 level 0.2882
    2159 
    2160 > volume #2 level 0.388
    2161 
    2162 > volume #2 level 0.698
    2163 
    2164 > volume #2 level 0.5509
    2165 
    2166 > volume #2 level 0.4038
    2167 
    2168 > volume #2 level 0.2567
    2169 
    2170 > volume #2 level 0.1726
    2171 
    2172 > volume #2 level 0.2567
    2173 
    2174 > volume #2 level 0.1989
    2175 
    2176 > volume #2 level 0.2567
    2177 
    2178 > volume #2 level 0.4143
    2179 
    2180 > volume #2 level 0.2882
    2181 
    2182 > show #!3 models
    2183 
    2184 > hide #!4 models
    2185 
    2186 > show #!4 models
    2187 
    2188 > hide #!4 models
    2189 
    2190 > show #!4 models
    2191 
    2192 > hide #!4 models
    2193 
    2194 > show #!4 models
    2195 
    2196 > hide #!4 models
    2197 
    2198 > show #!4 models
    2199 
    2200 > hide #!4 models
    2201 
    2202 > show #!4 models
    2203 
    2204 > hide #!4 models
    2205 
    2206 > show #!4 models
    2207 
    2208 > hide #!4 models
    2209 
    2210 > show #!4 models
    2211 
    2212 > volume #2 level 0.1884
    2213 
    2214 > open 4wqo
    2215 
    2216 Summary of feedback from opening 4wqo fetched from pdb 
    2217 --- 
    2218 note | Fetching compressed mmCIF 4wqo from
    2219 http://files.rcsb.org/download/4wqo.cif 
    2220  
    2221 4wqo title: 
    2222 Structure of VHL-EloB-EloC-Cul2 [more info...] 
    2223  
    2224 Chain information for 4wqo #5 
    2225 --- 
    2226 Chain | Description | UniProt 
    2227 A | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 1-213 
    2228 B | Transcription elongation factor B polypeptide 2 | ELOB_HUMAN 1-118 
    2229 C | Transcription elongation factor B polypeptide 1 | ELOC_HUMAN 17-112 
    2230 D | Cullin-2 | CUL2_HUMAN 1-163 
    2231  
    2232 
    2233 > select add #5
    2234 
    2235 3902 atoms, 3993 bonds, 1 pseudobond, 489 residues, 2 models selected 
    2236 
    2237 > ui mousemode right "translate selected models"
    2238 
    2239 > view matrix models #5,1,0,0,180.02,0,1,0,177.54,0,0,1,282.36
    2240 
    2241 > ui mousemode right translate
    2242 
    2243 > ui mousemode right "rotate selected models"
    2244 
    2245 > view matrix models
    2246 > #5,-0.092227,-0.96275,0.25417,126.56,-0.93133,-0.006911,-0.36411,100,0.35231,-0.2703,-0.896,199.81
    2247 
    2248 > view matrix models
    2249 > #5,0.16376,-0.64354,-0.74769,87.296,0.41354,-0.64333,0.64429,238.26,-0.89564,-0.41471,0.16078,180.97
    2250 
    2251 > ui mousemode right "translate selected models"
    2252 
    2253 > view matrix models
    2254 > #5,0.16376,-0.64354,-0.74769,111.47,0.41354,-0.64333,0.64429,266.25,-0.89564,-0.41471,0.16078,190.29
    2255 
    2256 > view matrix models
    2257 > #5,0.16376,-0.64354,-0.74769,123.34,0.41354,-0.64333,0.64429,258.18,-0.89564,-0.41471,0.16078,186.92
    2258 
    2259 > ui mousemode right "rotate selected models"
    2260 
    2261 > view matrix models
    2262 > #5,0.7722,-0.13503,-0.62087,167.87,0.44116,-0.58928,0.67685,261.68,-0.45727,-0.79656,-0.39547,183.32
    2263 
    2264 > view matrix models
    2265 > #5,0.72947,-0.079516,-0.67938,162.03,0.5206,-0.5797,0.62684,263.82,-0.44368,-0.81094,-0.38147,184.92
    2266 
    2267 > view matrix models
    2268 > #5,0.70928,-0.056381,-0.70267,159.51,0.5528,-0.57404,0.60407,264.56,-0.43741,-0.81689,-0.37599,185.61
    2269 
    2270 > ui mousemode right "translate selected models"
    2271 
    2272 > view matrix models
    2273 > #5,0.70928,-0.056381,-0.70267,202.01,0.5528,-0.57404,0.60407,256.45,-0.43741,-0.81689,-0.37599,174.15
    2274 
    2275 > view matrix models
    2276 > #5,0.70928,-0.056381,-0.70267,194.92,0.5528,-0.57404,0.60407,251.32,-0.43741,-0.81689,-0.37599,113.88
    2277 
    2278 > fitmap #5 inMap #2
    2279 
    2280 Fit molecule 4wqo (#5) to map cryosparc_P7_J649_008_volume_map_sharp.mrc (#2)
    2281 using 3902 atoms 
    2282 average map value = 0.2249, steps = 96 
    2283 shifted from previous position = 7.16 
    2284 rotated from previous position = 20.3 degrees 
    2285 atoms outside contour = 1821, contour level = 0.18838 
    2286  
    2287 Position of 4wqo (#5) relative to cryosparc_P7_J649_008_volume_map_sharp.mrc
    2288 (#2) coordinates: 
    2289 Matrix rotation and translation 
    2290 0.61111157 -0.06427886 -0.78893022 179.81366838 
    2291 0.74581173 -0.28711959 0.60110499 262.91204689 
    2292 -0.26515567 -0.95573562 -0.12752218 141.29348770 
    2293 Axis -0.85004254 -0.28598345 0.44231340 
    2294 Axis point 0.00000000 183.63820774 34.59377662 
    2295 Rotation angle (degrees) 113.68856996 
    2296 Shift along axis -165.54175955 
    2297  
    2298 
    2299 > select clear
    2300 
    2301 > select ::name="759"
    2302 
    2303 69 atoms, 75 bonds, 1 residue, 1 model selected 
    2304 
    2305 > color sel yellow
    2306 
    2307 > color sel byhetero
    2308 
    2309 > show sel atoms
    2310 
    2311 > select clear
    2312 
    2313 > select #5/D
    2314 
    2315 1168 atoms, 1197 bonds, 1 pseudobond, 141 residues, 2 models selected 
    2316 
    2317 > color (#!5 & sel) #3e8a9aff
    2318 
    2319 > select clear
    2320 
    2321 > select #5/A
    2322 
    2323 1197 atoms, 1228 bonds, 148 residues, 1 model selected 
    2324 
    2325 > color sel #409028ff
    2326 
    2327 > select clear
    2328 
    2329 > select #3/B
    2330 
    2331 627 atoms, 634 bonds, 5 pseudobonds, 82 residues, 2 models selected 
    2332 
    2333 > color (#!3 & sel) #c0c03dff
    2334 
    2335 > select #5/B
    2336 
    2337 798 atoms, 813 bonds, 104 residues, 1 model selected 
    2338 
    2339 > color sel #c0c03dff
    2340 
    2341 > select #5/C
    2342 
    2343 739 atoms, 755 bonds, 96 residues, 1 model selected 
    2344 
    2345 > color sel #91b28bff
    2346 
    2347 > select clear
    2348 
    2349 > volume #2 level 0.1201
    2350 
    2351 > open /Users/ccrowe/Downloads/AF-Q13617-F1-model_v4.pdb
    2352 
    2353 AF-Q13617-F1-model_v4.pdb title: 
    2354 Alphafold monomer V2.0 prediction for cullin-2 (Q13617) [more info...] 
    2355  
    2356 Chain information for AF-Q13617-F1-model_v4.pdb #6 
    2357 --- 
    2358 Chain | Description | UniProt 
    2359 A | cullin-2 | CUL2_HUMAN 1-745 
    2360  
    2361 
    2362 > select add #6
    2363 
    2364 6101 atoms, 6220 bonds, 745 residues, 1 model selected 
    2365 
    2366 > color sel #39808fff
    2367 
    2368 > ui mousemode right "translate selected models"
    2369 
    2370 > view matrix models #6,1,0,0,17.593,0,1,0,199.75,0,0,1,200.97
    2371 
    2372 > view matrix models #6,1,0,0,156.95,0,1,0,177.05,0,0,1,231.02
    2373 
    2374 > ui mousemode right translate
    2375 
    2376 > ui mousemode right "rotate selected models"
    2377 
    2378 > view matrix models
    2379 > #6,-0.17819,-0.97355,-0.14301,180.77,0.48079,-0.21295,0.85058,183.71,-0.85854,0.082807,0.50602,240.32
    2380 
    2381 > ui mousemode right "translate selected models"
    2382 
    2383 > view matrix models
    2384 > #6,-0.17819,-0.97355,-0.14301,182.97,0.48079,-0.21295,0.85058,171.99,-0.85854,0.082807,0.50602,209.51
    2385 
    2386 > fitmap #6 inMap #2
    2387 
    2388 Fit molecule AF-Q13617-F1-model_v4.pdb (#6) to map
    2389 cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) using 6101 atoms 
    2390 average map value = 0.1704, steps = 248 
    2391 shifted from previous position = 16.5 
    2392 rotated from previous position = 17.7 degrees 
    2393 atoms outside contour = 2691, contour level = 0.12007 
    2394  
    2395 Position of AF-Q13617-F1-model_v4.pdb (#6) relative to
    2396 cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) coordinates: 
    2397 Matrix rotation and translation 
    2398 -0.08107301 -0.98653713 0.14202696 193.35932442 
    2399 0.46251136 0.08898798 0.88213626 175.29744761 
    2400 -0.88289887 0.13720652 0.44907010 221.70078625 
    2401 Axis -0.38700209 0.53246422 0.75280225 
    2402 Axis point 115.16845768 142.52512290 0.00000000 
    2403 Rotation angle (degrees) 105.75398941 
    2404 Shift along axis 185.40600949 
    2405  
    2406 
    2407 > select clear
    2408 
    2409 > hide #!3 models
    2410 
    2411 > show #!3 models
    2412 
    2413 > show #!1 models
    2414 
    2415 > hide #!2 models
    2416 
    2417 > volume #1 level 0.884
    2418 
    2419 > open 6ttu
    2420 
    2421 6ttu title: 
    2422 Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
    2423 NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...] 
    2424  
    2425 Chain information for 6ttu #7 
    2426 --- 
    2427 Chain | Description | UniProt 
    2428 C | Cullin-1 | CUL1_HUMAN 1-776 
    2429 D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147 
    2430 I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY | 
    2431 N | NEDD8 | NEDD8_HUMAN 1-76 
    2432 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108 
    2433 S | S-phase kinase-associated protein 1 | SKP1_HUMAN 1-145 
    2434 T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 1-605 
    2435 U | Polyubiquitin-C | UBC_HUMAN 1-76 
    2436  
    2437 Non-standard residues in 6ttu #7 
    2438 --- 
    2439 ZN — zinc ion 
    2440  
    2441 
    2442 > ui tool show Matchmaker
    2443 
    2444 > matchmaker #!7 to #3/A pairing bs
    2445 
    2446 Parameters 
    2447 --- 
    2448 Chain pairing | bs 
    2449 Alignment algorithm | Needleman-Wunsch 
    2450 Similarity matrix | BLOSUM-62 
    2451 SS fraction | 0.3 
    2452 Gap open (HH/SS/other) | 18/18/6 
    2453 Gap extend | 1 
    2454 SS matrix |  |  | H | S | O 
    2455 ---|---|---|--- 
    2456 H | 6 | -9 | -6 
    2457 S |  | 6 | -6 
    2458 O |  |  | 4 
    2459 Iteration cutoff | 2 
    2460  
    2461 Matchmaker 5n4w, chain A (#3) with 6ttu, chain C (#7), sequence alignment
    2462 score = 1558.4 
    2463 RMSD between 318 pruned atom pairs is 1.340 angstroms; (across all 640 pairs:
    2464 9.463) 
    2465  
    2466 
    2467 > select add #7
    2468 
    2469 12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected 
    2470 
    2471 > hide sel atoms
    2472 
    2473 > show sel cartoons
    2474 
    2475 > color (#!7 & sel) orange
    2476 
    2477 > select clear
    2478 
    2479 > volume #1 level 1.015
    2480 
    2481 [Repeated 1 time(s)]
    2482 
    2483 > volume #1 level 0.6739
    2484 
    2485 > save "/Users/ccrowe/OneDrive - University of Dundee/Documents/Biology/cryo-
    2486 > EM/CRL2/2023_11_16_mapCRL2/2023_11_16_chimerasession-fittingmodels-
    2487 > preliminary.cxs"
    2488 
    2489 ——— End of log from Sat Nov 18 13:53:42 2023 ———
    2490 
    2491 opened ChimeraX session 
    2492 
    2493 > save /Users/ccrowe/Library/CloudStorage/OneDrive-
    2494 > UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2/AF-
    2495 > cul2-docked-chimera.pdb models #6
    2496 
    2497 > hide #!7 models
    2498 
    2499 > hide #!1 models
    2500 
    2501 > show #!2 models
    2502 
    2503 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    2504 > UniversityofDundee/Documents/Biology/cryo-
    2505 > EM/CRL2/2023_11_16_mapCRL2/DockInMap_1/placed_model.pdb
    2506 
    2507 Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
    2508 UniversityofDundee/Documents/Biology/cryo-
    2509 EM/CRL2/2023_11_16_mapCRL2/DockInMap_1/placed_model.pdb 
    2510 --- 
    2511 warning | Ignored bad PDB record found on line 6108 
    2512  
    2513 Chain information for placed_model.pdb #8 
    2514 --- 
    2515 Chain | Description 
    2516 A | No description available 
    2517  
    2518 
    2519 > volume #2 level 0.2567
    2520 
    2521 > close #8
    2522 
    2523 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    2524 > UniversityofDundee/Documents/Biology/cryo-
    2525 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J710_006_volume_map_sharp.mrc
    2526 
    2527 Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #8, grid size
    2528 256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32 
    2529 
    2530 > volume #8 level 0.1539
    2531 
    2532 > surface dust #2 size 14.8
    2533 
    2534 > surface dust #8 size 14.8
    2535 
    2536 > volume #8 level 0.2007
    2537 
    2538 > hide #!8 models
    2539 
    2540 > show #!8 models
    2541 
    2542 > hide #!8 models
    2543 
    2544 > show #!8 models
    2545 
    2546 > hide #!8 models
    2547 
    2548 > show #!8 models
    2549 
    2550 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    2551 > UniversityofDundee/Documents/Biology/cryo-
    2552 > EM/CRL2/2023_11_16_mapCRL2/DockInMap_3/placed_model.pdb
    2553 
    2554 Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
    2555 UniversityofDundee/Documents/Biology/cryo-
    2556 EM/CRL2/2023_11_16_mapCRL2/DockInMap_3/placed_model.pdb 
    2557 --- 
    2558 warning | Ignored bad PDB record found on line 6108 
    2559  
    2560 Chain information for placed_model.pdb #9 
    2561 --- 
    2562 Chain | Description 
    2563 A | No description available 
    2564  
    2565 
    2566 > hide #9 models
    2567 
    2568 > show #9 models
    2569 
    2570 > hide #9 models
    2571 
    2572 > show #9 models
    2573 
    2574 > hide #9 models
    2575 
    2576 > show #9 models
    2577 
    2578 > hide #9 models
    2579 
    2580 > show #9 models
    2581 
    2582 > hide #9 models
    2583 
    2584 > show #9 models
    2585 
    2586 > hide #9 models
    2587 
    2588 > show #9 models
    2589 
    2590 > hide #9 models
    2591 
    2592 > show #9 models
    2593 
    2594 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    2595 > UniversityofDundee/Documents/Biology/cryo-
    2596 > EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model.pdb
    2597 
    2598 Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
    2599 UniversityofDundee/Documents/Biology/cryo-
    2600 EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model.pdb 
    2601 --- 
    2602 warnings | Ignored bad PDB record found on line 1 
    2603  
    2604  
    2605 Ignored bad PDB record found on line 2 
    2606 REMARK MODEL FROM PHENIX.MAP_TO_MODEL 
    2607  
    2608 Ignored bad PDB record found on line 3 
    2609 REMARK MAP FILE: /Users/ccrowe/Library/CloudStorage/OneDrive-
    2610 UniversityofDundee/Documents/Biology/cryo-
    2611 EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J710_006_volume_map_sharp.mrc 
    2612  
    2613 Ignored bad PDB record found on line 4 
    2614  
    2615  
    2616 Ignored bad PDB record found on line 90 
    2617  
    2618 Chain information for map_to_model.pdb #10 
    2619 --- 
    2620 Chain | Description 
    2621 U | No description available 
    2622  
    2623 
    2624 > hide #!10 models
    2625 
    2626 > show #!10 models
    2627 
    2628 > hide #!10 models
    2629 
    2630 > show #!10 models
    2631 
    2632 > color #10 #d783ffff
    2633 
    2634 > select add #10
    2635 
    2636 84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2637 
    2638 > select subtract #10
    2639 
    2640 Nothing selected 
    2641 
    2642 > hide #9 models
    2643 
    2644 > hide #!8 models
    2645 
    2646 > select add #10
    2647 
    2648 84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2649 
    2650 > select subtract #10
    2651 
    2652 Nothing selected 
    2653 
    2654 > select add #10
    2655 
    2656 84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2657 
    2658 > select subtract #10
    2659 
    2660 Nothing selected 
    2661 
    2662 > select add #10
    2663 
    2664 84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2665 
    2666 > select subtract #10
    2667 
    2668 Nothing selected 
    2669 
    2670 > select add #10
    2671 
    2672 84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2673 
    2674 > close #10
    2675 
    2676 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    2677 > UniversityofDundee/Documents/Biology/cryo-
    2678 > EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model_0/model_PROTEIN.pdb
    2679 
    2680 Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
    2681 UniversityofDundee/Documents/Biology/cryo-
    2682 EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model_0/model_PROTEIN.pdb 
    2683 --- 
    2684 warning | Ignored bad PDB record found on line 87 
    2685  
    2686 Chain information for model_PROTEIN.pdb #10 
    2687 --- 
    2688 Chain | Description 
    2689 U | No description available 
    2690  
    2691 
    2692 > hide #!10 models
    2693 
    2694 > show #!10 models
    2695 
    2696 > hide #!10 models
    2697 
    2698 > show #!10 models
    2699 
    2700 > select add #10
    2701 
    2702 84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2703 
    2704 > close #10
    2705 
    2706 > show #!8 models
    2707 
    2708 > transparency #2.1#8.1 0
    2709 
    2710 > transparency #2.1#8.1 50
    2711 
    2712 > color #8 #8efa00ff models
    2713 
    2714 > transparency #2.1#8.1 0
    2715 
    2716 > transparency #2.1#8.1 50
    2717 
    2718 > color #8 #ff2600ff models
    2719 
    2720 > transparency #2.1#8.1 0
    2721 
    2722 > transparency #2.1#8.1 50
    2723 
    2724 > hide #6 models
    2725 
    2726 > show #6 models
    2727 
    2728 > hide #6 models
    2729 
    2730 > hide #!3 models
    2731 
    2732 > show #!3 models
    2733 
    2734 > hide #!3 models
    2735 
    2736 > show #!3 models
    2737 
    2738 > show #!1 models
    2739 
    2740 > transparency 0
    2741 
    2742 > transparency 50
    2743 
    2744 > volume #2 level 0.1864
    2745 
    2746 > volume #8 level 0.1461
    2747 
    2748 > volume #1 level 0.9037
    2749 
    2750 > volume #2 level 0.2026
    2751 
    2752 > volume #8 level 0.1851
    2753 
    2754 > open 8bei
    2755 
    2756 Fetching url http://files.rcsb.org/download/8bei.cif failed: 
    2757 HTTP Error 404: Not Found 
    2758 
    2759 > open 8b3i
    2760 
    2761 Summary of feedback from opening 8b3i fetched from pdb 
    2762 --- 
    2763 warnings | Atom H1 is not in the residue template for MET /N:1 
    2764 Atom H1 is not in the residue template for MET /U:1 
    2765 Atom H1 is not in the residue template for MET /a:1 
    2766 Atom H1 is not in the residue template for MET /d:1 
    2767  
    2768 8b3i title: 
    2769 CRL4CSA-E2-Ub (state 2) [more info...] 
    2770  
    2771 Chain information for 8b3i #10 
    2772 --- 
    2773 Chain | Description | UniProt 
    2774 D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147 
    2775 N | NEDD8 | NEDD8_HUMAN 1-76 
    2776 R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108 
    2777 U | Ubiquitin | UBC_HUMAN 1-76 
    2778 a | DNA excision repair protein ERCC-8 | ERCC8_HUMAN 1-396 
    2779 d | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 
    2780 e | Cullin-4A | CUL4A_HUMAN 1-759 
    2781  
    2782 Non-standard residues in 8b3i #10 
    2783 --- 
    2784 ZN — zinc ion 
    2785  
    2786 
    2787 > select add #10
    2788 
    2789 40377 atoms, 40760 bonds, 21 pseudobonds, 2540 residues, 3 models selected 
    2790 
    2791 > hide sel atoms
    2792 
    2793 > show sel cartoons
    2794 
    2795 > ui mousemode right "rotate selected models"
    2796 
    2797 > view matrix models
    2798 > #10,0.99993,0.010671,0.005056,-2.7845,-0.011717,0.94982,0.31259,-45.787,-0.0014665,-0.31263,0.94987,64.421
    2799 
    2800 > ui mousemode right "translate selected models"
    2801 
    2802 > view matrix models
    2803 > #10,0.99993,0.010671,0.005056,-3.3622,-0.011717,0.94982,0.31259,-29.739,-0.0014665,-0.31263,0.94987,85.229
    2804 
    2805 > view matrix models
    2806 > #10,0.99993,0.010671,0.005056,2.5399,-0.011717,0.94982,0.31259,-31.225,-0.0014665,-0.31263,0.94987,80.291
    2807 
    2808 > view matrix models
    2809 > #10,0.99993,0.010671,0.005056,2.5336,-0.011717,0.94982,0.31259,-36.105,-0.0014665,-0.31263,0.94987,81.646
    2810 
    2811 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
    2812 got 4 atomic models, 3 maps. 
    2813 
    2814 > hide #!8 models
    2815 
    2816 > hide #!5 models
    2817 
    2818 > hide #!4 models
    2819 
    2820 > hide #!3 models
    2821 
    2822 > hide #!2 models
    2823 
    2824 > fitmap #10 inMap #1
    2825 
    2826 Fit molecule 8b3i (#10) to map emd_15829.map (#1) using 40377 atoms 
    2827 average map value = 1.297, steps = 256 
    2828 shifted from previous position = 17.3 
    2829 rotated from previous position = 29.2 degrees 
    2830 atoms outside contour = 17017, contour level = 0.90374 
    2831  
    2832 Position of 8b3i (#10) relative to emd_15829.map (#1) coordinates: 
    2833 Matrix rotation and translation 
    2834 0.99999997 -0.00023490 0.00007996 0.02149465 
    2835 0.00023488 0.99999994 0.00024868 -0.07820052 
    2836 -0.00008002 -0.00024866 0.99999997 0.06914071 
    2837 Axis -0.70786977 0.22770737 0.66863274 
    2838 Axis point 0.00000000 242.49058258 326.60984678 
    2839 Rotation angle (degrees) 0.02012788 
    2840 Shift along axis 0.01320749 
    2841  
    2842 
    2843 > select clear
    2844 
    2845 > show #6 models
    2846 
    2847 > show #!3 models
    2848 
    2849 > hide #!3 models
    2850 
    2851 > show #!3 models
    2852 
    2853 > hide #!3 models
    2854 
    2855 > show #!3 models
    2856 
    2857 > hide #!3 models
    2858 
    2859 > show #!3 models
    2860 
    2861 > hide #!3 models
    2862 
    2863 > show #!2 models
    2864 
    2865 > hide #!2 models
    2866 
    2867 > show #!2 models
    2868 
    2869 > hide #!2 models
    2870 
    2871 > show #9 models
    2872 
    2873 > hide #9 models
    2874 
    2875 > show #9 models
    2876 
    2877 > hide #9 models
    2878 
    2879 > show #9 models
    2880 
    2881 > hide #9 models
    2882 
    2883 > show #9 models
    2884 
    2885 > hide #9 models
    2886 
    2887 > show #9 models
    2888 
    2889 > hide #9 models
    2890 
    2891 > show #9 models
    2892 
    2893 > hide #9 models
    2894 
    2895 > show #9 models
    2896 
    2897 > hide #9 models
    2898 
    2899 > show #!8 models
    2900 
    2901 > hide #!10 models
    2902 
    2903 > show #!10 models
    2904 
    2905 > hide #6 models
    2906 
    2907 > show #6 models
    2908 
    2909 > hide #6 models
    2910 
    2911 > show #!3 models
    2912 
    2913 > hide #!3 models
    2914 
    2915 > show #6 models
    2916 
    2917 > hide #!10 models
    2918 
    2919 > show #!10 models
    2920 
    2921 > hide #!10 models
    2922 
    2923 > show #!10 models
    2924 
    2925 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    2926 > UniversityofDundee/Documents/Biology/cryo-
    2927 > EM/CRL2/2023_11_16_mapCRL2/emd_10585.map
    2928 
    2929 Opened emd_10585.map as #11, grid size 320,320,320, pixel 1.06, shown at level
    2930 0.000884, step 2, values float32 
    2931 
    2932 > volume #2 level 0.1647
    2933 
    2934 > volume #11 color #ff9300
    2935 
    2936 > transparency 0
    2937 
    2938 > transparency 50
    2939 
    2940 > volume #11 level 0.01017
    2941 
    2942 > fitmap #11 inMap #8
    2943 
    2944 Fit map emd_10585.map in map cryosparc_P7_J710_006_volume_map_sharp.mrc using
    2945 13478 points 
    2946 correlation = 0.2383, correlation about mean = 0.01468, overlap = 11.76 
    2947 steps = 180, shift = 10.8, angle = 11.3 degrees 
    2948  
    2949 Position of emd_10585.map (#11) relative to
    2950 cryosparc_P7_J710_006_volume_map_sharp.mrc (#8) coordinates: 
    2951 Matrix rotation and translation 
    2952 0.98403384 0.07388692 -0.16192012 28.38530521 
    2953 -0.08713715 0.99326921 -0.07631113 32.01277931 
    2954 0.15519188 0.08920200 0.98384881 -35.82899321 
    2955 Axis 0.42192631 -0.80838238 -0.41048279 
    2956 Axis point 244.25883800 0.00000000 149.12121744 
    2957 Rotation angle (degrees) 11.31131831 
    2958 Shift along axis 0.80512552 
    2959  
    2960 
    2961 > select add #11
    2962 
    2963 2 models selected 
    2964 
    2965 > ui mousemode right "rotate selected models"
    2966 
    2967 > view matrix models
    2968 > #11,-0.1087,0.9264,0.36051,-22.476,0.81709,0.28981,-0.49836,71.941,-0.56616,0.2404,-0.78846,376.31
    2969 
    2970 > ui mousemode right "translate selected models"
    2971 
    2972 > view matrix models
    2973 > #11,-0.1087,0.9264,0.36051,-27.473,0.81709,0.28981,-0.49836,90.516,-0.56616,0.2404,-0.78846,400.2
    2974 
    2975 > fitmap #11 inMap #8
    2976 
    2977 Fit map emd_10585.map in map cryosparc_P7_J710_006_volume_map_sharp.mrc using
    2978 13478 points 
    2979 correlation = 0.4738, correlation about mean = 0.1259, overlap = 30.17 
    2980 steps = 372, shift = 5.18, angle = 30 degrees 
    2981  
    2982 Position of emd_10585.map (#11) relative to
    2983 cryosparc_P7_J710_006_volume_map_sharp.mrc (#8) coordinates: 
    2984 Matrix rotation and translation 
    2985 -0.55622647 0.82178426 0.12362336 113.90601365 
    2986 0.71361529 0.54855645 -0.43570522 50.69802278 
    2987 -0.42587008 -0.15413125 -0.89155944 462.06282433 
    2988 Axis 0.44919643 0.87660980 -0.17256253 
    2989 Axis point 86.58312572 0.00000000 226.23073896 
    2990 Rotation angle (degrees) 161.73456499 
    2991 Shift along axis 15.87382737 
    2992  
    2993 
    2994 > select clear
    2995 
    2996 > volume #11 level 0.01189
    2997 
    2998 > hide #!2 models
    2999 
    3000 > hide #6 models
    3001 
    3002 > hide #!8 models
    3003 
    3004 > hide #!10 models
    3005 
    3006 > hide #!1 models
    3007 
    3008 > show #!2 models
    3009 
    3010 > hide #!2 models
    3011 
    3012 > show #!2 models
    3013 
    3014 > hide #!2 models
    3015 
    3016 > show #!2 models
    3017 
    3018 > hide #!2 models
    3019 
    3020 > show #!8 models
    3021 
    3022 > hide #!8 models
    3023 
    3024 > show #!8 models
    3025 
    3026 > hide #!8 models
    3027 
    3028 > show #!8 models
    3029 
    3030 > hide #!8 models
    3031 
    3032 > show #!8 models
    3033 
    3034 > volume #8 level 0.2397
    3035 
    3036 > volume #11 level 0.01286
    3037 
    3038 > volume #11 level 0.01629
    3039 
    3040 > volume #8 level 0.2085
    3041 
    3042 > volume #11 level 0.01531
    3043 
    3044 > show #!7 models
    3045 
    3046 > hide #!8 models
    3047 
    3048 > show #!10 models
    3049 
    3050 > hide #!10 models
    3051 
    3052 > show #!10 models
    3053 
    3054 > hide #!10 models
    3055 
    3056 > show #!10 models
    3057 
    3058 > hide #!10 models
    3059 
    3060 > show #!10 models
    3061 
    3062 > hide #!10 models
    3063 
    3064 > show #!10 models
    3065 
    3066 > hide #!10 models
    3067 
    3068 > show #!10 models
    3069 
    3070 > hide #!10 models
    3071 
    3072 > show #!8 models
    3073 
    3074 > hide #!11 models
    3075 
    3076 > show #!11 models
    3077 
    3078 > hide #!11 models
    3079 
    3080 > show #!11 models
    3081 
    3082 > hide #!11 models
    3083 
    3084 > show #!1 models
    3085 
    3086 > show #!10 models
    3087 
    3088 > hide #!10 models
    3089 
    3090 > show #!10 models
    3091 
    3092 > hide #!10 models
    3093 
    3094 > show #!11 models
    3095 
    3096 > hide #!11 models
    3097 
    3098 > show #!11 models
    3099 
    3100 > show #!10 models
    3101 
    3102 > hide #!10 models
    3103 
    3104 > show #!10 models
    3105 
    3106 > hide #!10 models
    3107 
    3108 > hide #!11 models
    3109 
    3110 > hide #!8 models
    3111 
    3112 > show #!8 models
    3113 
    3114 > show #6 models
    3115 
    3116 > show #!5 models
    3117 
    3118 > hide #!5 models
    3119 
    3120 > show #!3 models
    3121 
    3122 > hide #!3 models
    3123 
    3124 > show #!3 models
    3125 
    3126 > hide #!3 models
    3127 
    3128 > show #!3 models
    3129 
    3130 > hide #!3 models
    3131 
    3132 > show #!3 models
    3133 
    3134 > hide #!3 models
    3135 
    3136 > show #!3 models
    3137 
    3138 > hide #!3 models
    3139 
    3140 > show #!3 models
    3141 
    3142 > hide #!3 models
    3143 
    3144 > show #!3 models
    3145 
    3146 > hide #!3 models
    3147 
    3148 > show #!3 models
    3149 
    3150 > hide #!3 models
    3151 
    3152 > show #!3 models
    3153 
    3154 > hide #!3 models
    3155 
    3156 > show #!3 models
    3157 
    3158 > hide #!3 models
    3159 
    3160 > show #!3 models
    3161 
    3162 > hide #!3 models
    3163 
    3164 > show #!3 models
    3165 
    3166 > hide #!3 models
    3167 
    3168 > show #!3 models
    3169 
    3170 > hide #!3 models
    3171 
    3172 > show #!3 models
    3173 
    3174 > hide #!3 models
    3175 
    3176 > show #!3 models
    3177 
    3178 > hide #!7 models
    3179 
    3180 > hide #!3 models
    3181 
    3182 > ui tool show "Show Sequence Viewer"
    3183 
    3184 > sequence chain #6/A #9/A
    3185 
    3186 Alignment identifier is 1 
    3187 
    3188 > select
    3189 > #6/A:10-25,32-46,54-104,106-116,120-124,139-172,178-192,201-229,232-253,256-272,275-287,291-303,308-328,332-357,362-376,387-399,408-424,428-444,451-465,467-496,531-547,557-559,579-589,596-603,607-619,656-658,662-691,696-707,715-727
    3190 > #9/A:10-25,32-46,54-104,106-116,120-124,139-172,178-192,201-229,232-253,256-272,275-287,291-303,308-328,332-357,362-376,387-399,408-424,428-444,451-465,467-496,531-547,557-559,579-589,596-603,607-619,656-658,662-691,696-707,715-727
    3191 
    3192 8398 atoms, 8498 bonds, 1010 residues, 2 models selected 
    3193 
    3194 > view matrix models
    3195 > #6,-0.081073,-0.98654,0.14203,193.19,0.46251,0.088988,0.88214,174.98,-0.8829,0.13721,0.44907,219.29,#9,1,0,0,-0.1681,0,1,0,-0.31576,0,0,1,-2.4148
    3196 
    3197 > select clear
    3198 
    3199 > show #!10 models
    3200 
    3201 > hide #!10 models
    3202 
    3203 > show #!10 models
    3204 
    3205 > hide #!10 models
    3206 
    3207 > show #!10 models
    3208 
    3209 > hide #!10 models
    3210 
    3211 > show #!10 models
    3212 
    3213 > save /Users/ccrowe/Library/CloudStorage/OneDrive-
    3214 > UniversityofDundee/Documents/Biology/cryo-
    3215 > EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model_0/2023_11_20.cxs
    3216 > includeMaps true
    3217 
    3218 > select add #8
    3219 
    3220 2 models selected 
    3221 
    3222 > vop gaussian #8 sdev 4.44
    3223 
    3224 Opened cryosparc_P7_J710_006_volume_map_sharp.mrc gaussian as #12, grid size
    3225 256,256,256, pixel 1.48, shown at step 1, values float32 
    3226 
    3227 > volume #12 level 0.07218
    3228 
    3229 > volume #12 level 0.08236
    3230 
    3231 > volume #12 step 4
    3232 
    3233 > volume #12 step 16
    3234 
    3235 > volume #12 step 1
    3236 
    3237 > volume #12 level 0.0271
    3238 
    3239 > hide #!12 models
    3240 
    3241 > show #!8 models
    3242 
    3243 > select subtract #8
    3244 
    3245 Nothing selected 
    3246 
    3247 > close #12
    3248 
    3249 > toolshed show
    3250 
    3251 Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl 
    3252 [Repeated 2 time(s)]
    3253 
    3254 > toolshed show
    3255 
    3256 Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl 
    3257 [Repeated 1 time(s)]
    3258 
    3259 > hide #!10 models
    3260 
    3261 > show #!10 models
    3262 
    3263 > hide #!1 models
    3264 
    3265 > hide #!10 models
    3266 
    3267 > hide #!1 models
    3268 
    3269 > show #!11 models
    3270 
    3271 > hide #!11 models
    3272 
    3273 > show #!11 models
    3274 
    3275 > hide #!11 models
    3276 
    3277 > volume #8 level 0.1175
    3278 
    3279 > volume #!8 style surface
    3280 
    3281 > transparency #8.1 0
    3282 
    3283 > transparency #8.1 50
    3284 
    3285 > show #!2 models
    3286 
    3287 > hide #!8 models
    3288 
    3289 > show #!8 models
    3290 
    3291 > hide #!8 models
    3292 
    3293 > show #!8 models
    3294 
    3295 > hide #!2 models
    3296 
    3297 > show #!2 models
    3298 
    3299 > hide #!2 models
    3300 
    3301 > show #!2 models
    3302 
    3303 > hide #!8 models
    3304 
    3305 > show #!8 models
    3306 
    3307 > hide #!2 models
    3308 
    3309 > show #!2 models
    3310 
    3311 > hide #!2 models
    3312 
    3313 > volume #8 level 0.1782
    3314 
    3315 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3316 > UniversityofDundee/Documents/Biology/cryo-
    3317 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_000.mrc
    3318 
    3319 Opened J684_series_000_frame_000.mrc as #12, grid size 128,128,128, pixel
    3320 2.96, shown at level 0.000154, step 1, values float32 
    3321 
    3322 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3323 > UniversityofDundee/Documents/Biology/cryo-
    3324 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_001.mrc
    3325 
    3326 Opened J684_series_000_frame_001.mrc as #13, grid size 128,128,128, pixel
    3327 2.96, shown at level 0.000181, step 1, values float32 
    3328 
    3329 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3330 > UniversityofDundee/Documents/Biology/cryo-
    3331 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_002.mrc
    3332 
    3333 Opened J684_series_000_frame_002.mrc as #14, grid size 128,128,128, pixel
    3334 2.96, shown at level 2.51e-06, step 1, values float32 
    3335 
    3336 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3337 > UniversityofDundee/Documents/Biology/cryo-
    3338 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_003.mrc
    3339 
    3340 Opened J684_series_000_frame_003.mrc as #15, grid size 128,128,128, pixel
    3341 2.96, shown at level 2.19e-05, step 1, values float32 
    3342 
    3343 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3344 > UniversityofDundee/Documents/Biology/cryo-
    3345 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_004.mrc
    3346 
    3347 Opened J684_series_000_frame_004.mrc as #16, grid size 128,128,128, pixel
    3348 2.96, shown at level 4.29e-05, step 1, values float32 
    3349 
    3350 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3351 > UniversityofDundee/Documents/Biology/cryo-
    3352 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_005.mrc
    3353 
    3354 Opened J684_series_000_frame_005.mrc as #17, grid size 128,128,128, pixel
    3355 2.96, shown at level 9.98e-05, step 1, values float32 
    3356 
    3357 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3358 > UniversityofDundee/Documents/Biology/cryo-
    3359 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_006.mrc
    3360 
    3361 Opened J684_series_000_frame_006.mrc as #18, grid size 128,128,128, pixel
    3362 2.96, shown at level 0.000141, step 1, values float32 
    3363 
    3364 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3365 > UniversityofDundee/Documents/Biology/cryo-
    3366 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_007.mrc
    3367 
    3368 Opened J684_series_000_frame_007.mrc as #19, grid size 128,128,128, pixel
    3369 2.96, shown at level 0.000188, step 1, values float32 
    3370 
    3371 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3372 > UniversityofDundee/Documents/Biology/cryo-
    3373 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_008.mrc
    3374 
    3375 Opened J684_series_000_frame_008.mrc as #20, grid size 128,128,128, pixel
    3376 2.96, shown at level 0.000132, step 1, values float32 
    3377 
    3378 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3379 > UniversityofDundee/Documents/Biology/cryo-
    3380 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_009.mrc
    3381 
    3382 Opened J684_series_000_frame_009.mrc as #21, grid size 128,128,128, pixel
    3383 2.96, shown at level 3.05e-05, step 1, values float32 
    3384 
    3385 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3386 > UniversityofDundee/Documents/Biology/cryo-
    3387 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_010.mrc
    3388 
    3389 Opened J684_series_000_frame_010.mrc as #22, grid size 128,128,128, pixel
    3390 2.96, shown at level 0.000104, step 1, values float32 
    3391 
    3392 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3393 > UniversityofDundee/Documents/Biology/cryo-
    3394 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_011.mrc
    3395 
    3396 Opened J684_series_000_frame_011.mrc as #23, grid size 128,128,128, pixel
    3397 2.96, shown at level 0.00013, step 1, values float32 
    3398 
    3399 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3400 > UniversityofDundee/Documents/Biology/cryo-
    3401 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_012.mrc
    3402 
    3403 Opened J684_series_000_frame_012.mrc as #24, grid size 128,128,128, pixel
    3404 2.96, shown at level 0.00012, step 1, values float32 
    3405 
    3406 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3407 > UniversityofDundee/Documents/Biology/cryo-
    3408 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_013.mrc
    3409 
    3410 Opened J684_series_000_frame_013.mrc as #25, grid size 128,128,128, pixel
    3411 2.96, shown at level 5.42e-05, step 1, values float32 
    3412 
    3413 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3414 > UniversityofDundee/Documents/Biology/cryo-
    3415 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_014.mrc
    3416 
    3417 Opened J684_series_000_frame_014.mrc as #26, grid size 128,128,128, pixel
    3418 2.96, shown at level 0.000165, step 1, values float32 
    3419 
    3420 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3421 > UniversityofDundee/Documents/Biology/cryo-
    3422 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_015.mrc
    3423 
    3424 Opened J684_series_000_frame_015.mrc as #27, grid size 128,128,128, pixel
    3425 2.96, shown at level 0.000171, step 1, values float32 
    3426 
    3427 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3428 > UniversityofDundee/Documents/Biology/cryo-
    3429 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_016.mrc
    3430 
    3431 Opened J684_series_000_frame_016.mrc as #28, grid size 128,128,128, pixel
    3432 2.96, shown at level 2.93e-05, step 1, values float32 
    3433 
    3434 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3435 > UniversityofDundee/Documents/Biology/cryo-
    3436 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_017.mrc
    3437 
    3438 Opened J684_series_000_frame_017.mrc as #29, grid size 128,128,128, pixel
    3439 2.96, shown at level 0.00017, step 1, values float32 
    3440 
    3441 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3442 > UniversityofDundee/Documents/Biology/cryo-
    3443 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_018.mrc
    3444 
    3445 Opened J684_series_000_frame_018.mrc as #30, grid size 128,128,128, pixel
    3446 2.96, shown at level 0.000176, step 1, values float32 
    3447 
    3448 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3449 > UniversityofDundee/Documents/Biology/cryo-
    3450 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_019.mrc
    3451 
    3452 Opened J684_series_000_frame_019.mrc as #31, grid size 128,128,128, pixel
    3453 2.96, shown at level 6.17e-05, step 1, values float32 
    3454 
    3455 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3456 > UniversityofDundee/Documents/Biology/cryo-
    3457 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_020.mrc
    3458 
    3459 Opened J684_series_000_frame_020.mrc as #32, grid size 128,128,128, pixel
    3460 2.96, shown at level 0.000205, step 1, values float32 
    3461 
    3462 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3463 > UniversityofDundee/Documents/Biology/cryo-
    3464 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_021.mrc
    3465 
    3466 Opened J684_series_000_frame_021.mrc as #33, grid size 128,128,128, pixel
    3467 2.96, shown at level 6.87e-05, step 1, values float32 
    3468 
    3469 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3470 > UniversityofDundee/Documents/Biology/cryo-
    3471 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_022.mrc
    3472 
    3473 Opened J684_series_000_frame_022.mrc as #34, grid size 128,128,128, pixel
    3474 2.96, shown at level 9.07e-05, step 1, values float32 
    3475 
    3476 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3477 > UniversityofDundee/Documents/Biology/cryo-
    3478 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_023.mrc
    3479 
    3480 Opened J684_series_000_frame_023.mrc as #35, grid size 128,128,128, pixel
    3481 2.96, shown at level 9.5e-05, step 1, values float32 
    3482 
    3483 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3484 > UniversityofDundee/Documents/Biology/cryo-
    3485 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_024.mrc
    3486 
    3487 Opened J684_series_000_frame_024.mrc as #36, grid size 128,128,128, pixel
    3488 2.96, shown at level 0.000158, step 1, values float32 
    3489 
    3490 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3491 > UniversityofDundee/Documents/Biology/cryo-
    3492 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_025.mrc
    3493 
    3494 Opened J684_series_000_frame_025.mrc as #37, grid size 128,128,128, pixel
    3495 2.96, shown at level 6.33e-05, step 1, values float32 
    3496 
    3497 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3498 > UniversityofDundee/Documents/Biology/cryo-
    3499 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_026.mrc
    3500 
    3501 Opened J684_series_000_frame_026.mrc as #38, grid size 128,128,128, pixel
    3502 2.96, shown at level 0.000131, step 1, values float32 
    3503 
    3504 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3505 > UniversityofDundee/Documents/Biology/cryo-
    3506 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_027.mrc
    3507 
    3508 Opened J684_series_000_frame_027.mrc as #39, grid size 128,128,128, pixel
    3509 2.96, shown at level 7.92e-05, step 1, values float32 
    3510 
    3511 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3512 > UniversityofDundee/Documents/Biology/cryo-
    3513 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_028.mrc
    3514 
    3515 Opened J684_series_000_frame_028.mrc as #40, grid size 128,128,128, pixel
    3516 2.96, shown at level 0.000171, step 1, values float32 
    3517 
    3518 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3519 > UniversityofDundee/Documents/Biology/cryo-
    3520 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_029.mrc
    3521 
    3522 Opened J684_series_000_frame_029.mrc as #41, grid size 128,128,128, pixel
    3523 2.96, shown at level 8.69e-05, step 1, values float32 
    3524 
    3525 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3526 > UniversityofDundee/Documents/Biology/cryo-
    3527 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_030.mrc
    3528 
    3529 Opened J684_series_000_frame_030.mrc as #42, grid size 128,128,128, pixel
    3530 2.96, shown at level 0.000128, step 1, values float32 
    3531 
    3532 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3533 > UniversityofDundee/Documents/Biology/cryo-
    3534 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_031.mrc
    3535 
    3536 Opened J684_series_000_frame_031.mrc as #43, grid size 128,128,128, pixel
    3537 2.96, shown at level 0.000183, step 1, values float32 
    3538 
    3539 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3540 > UniversityofDundee/Documents/Biology/cryo-
    3541 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_032.mrc
    3542 
    3543 Opened J684_series_000_frame_032.mrc as #44, grid size 128,128,128, pixel
    3544 2.96, shown at level 9.78e-05, step 1, values float32 
    3545 
    3546 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3547 > UniversityofDundee/Documents/Biology/cryo-
    3548 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_033.mrc
    3549 
    3550 Opened J684_series_000_frame_033.mrc as #45, grid size 128,128,128, pixel
    3551 2.96, shown at level 7.4e-05, step 1, values float32 
    3552 
    3553 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3554 > UniversityofDundee/Documents/Biology/cryo-
    3555 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_034.mrc
    3556 
    3557 Opened J684_series_000_frame_034.mrc as #46, grid size 128,128,128, pixel
    3558 2.96, shown at level 8.13e-05, step 1, values float32 
    3559 
    3560 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3561 > UniversityofDundee/Documents/Biology/cryo-
    3562 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_035.mrc
    3563 
    3564 Opened J684_series_000_frame_035.mrc as #47, grid size 128,128,128, pixel
    3565 2.96, shown at level 0.000108, step 1, values float32 
    3566 
    3567 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3568 > UniversityofDundee/Documents/Biology/cryo-
    3569 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_036.mrc
    3570 
    3571 Opened J684_series_000_frame_036.mrc as #48, grid size 128,128,128, pixel
    3572 2.96, shown at level 8.72e-05, step 1, values float32 
    3573 
    3574 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3575 > UniversityofDundee/Documents/Biology/cryo-
    3576 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_037.mrc
    3577 
    3578 Opened J684_series_000_frame_037.mrc as #49, grid size 128,128,128, pixel
    3579 2.96, shown at level 9.87e-05, step 1, values float32 
    3580 
    3581 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3582 > UniversityofDundee/Documents/Biology/cryo-
    3583 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_038.mrc
    3584 
    3585 Opened J684_series_000_frame_038.mrc as #50, grid size 128,128,128, pixel
    3586 2.96, shown at level 0.000132, step 1, values float32 
    3587 
    3588 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3589 > UniversityofDundee/Documents/Biology/cryo-
    3590 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_039.mrc
    3591 
    3592 Opened J684_series_000_frame_039.mrc as #51, grid size 128,128,128, pixel
    3593 2.96, shown at level 0.000167, step 1, values float32 
    3594 
    3595 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3596 > UniversityofDundee/Documents/Biology/cryo-
    3597 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_040.mrc
    3598 
    3599 Opened J684_series_000_frame_040.mrc as #52, grid size 128,128,128, pixel
    3600 2.96, shown at level 0.000203, step 1, values float32 
    3601 
    3602 > close #12
    3603 
    3604 > close #13-23
    3605 
    3606 > close #24-38
    3607 
    3608 > close #39-52
    3609 
    3610 > ui tool show "Volume Viewer"
    3611 
    3612 > hide #6 models
    3613 
    3614 > open /Users/ccrowe/Library/CloudStorage/OneDrive-
    3615 > UniversityofDundee/Documents/Biology/cryo-
    3616 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_000.mrc
    3617 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3618 > UniversityofDundee/Documents/Biology/cryo-
    3619 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_001.mrc
    3620 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3621 > UniversityofDundee/Documents/Biology/cryo-
    3622 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_002.mrc
    3623 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3624 > UniversityofDundee/Documents/Biology/cryo-
    3625 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_003.mrc
    3626 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3627 > UniversityofDundee/Documents/Biology/cryo-
    3628 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_004.mrc
    3629 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3630 > UniversityofDundee/Documents/Biology/cryo-
    3631 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_005.mrc
    3632 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3633 > UniversityofDundee/Documents/Biology/cryo-
    3634 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_006.mrc
    3635 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3636 > UniversityofDundee/Documents/Biology/cryo-
    3637 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_007.mrc
    3638 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3639 > UniversityofDundee/Documents/Biology/cryo-
    3640 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_008.mrc
    3641 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3642 > UniversityofDundee/Documents/Biology/cryo-
    3643 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_009.mrc
    3644 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3645 > UniversityofDundee/Documents/Biology/cryo-
    3646 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_010.mrc
    3647 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3648 > UniversityofDundee/Documents/Biology/cryo-
    3649 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_011.mrc
    3650 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3651 > UniversityofDundee/Documents/Biology/cryo-
    3652 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_012.mrc
    3653 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3654 > UniversityofDundee/Documents/Biology/cryo-
    3655 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_013.mrc
    3656 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3657 > UniversityofDundee/Documents/Biology/cryo-
    3658 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_014.mrc
    3659 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3660 > UniversityofDundee/Documents/Biology/cryo-
    3661 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_015.mrc
    3662 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3663 > UniversityofDundee/Documents/Biology/cryo-
    3664 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_016.mrc
    3665 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3666 > UniversityofDundee/Documents/Biology/cryo-
    3667 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_017.mrc
    3668 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3669 > UniversityofDundee/Documents/Biology/cryo-
    3670 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_018.mrc
    3671 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3672 > UniversityofDundee/Documents/Biology/cryo-
    3673 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_019.mrc
    3674 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3675 > UniversityofDundee/Documents/Biology/cryo-
    3676 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_020.mrc
    3677 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3678 > UniversityofDundee/Documents/Biology/cryo-
    3679 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_021.mrc
    3680 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3681 > UniversityofDundee/Documents/Biology/cryo-
    3682 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_022.mrc
    3683 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3684 > UniversityofDundee/Documents/Biology/cryo-
    3685 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_023.mrc
    3686 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3687 > UniversityofDundee/Documents/Biology/cryo-
    3688 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_024.mrc
    3689 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3690 > UniversityofDundee/Documents/Biology/cryo-
    3691 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_025.mrc
    3692 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3693 > UniversityofDundee/Documents/Biology/cryo-
    3694 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_026.mrc
    3695 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3696 > UniversityofDundee/Documents/Biology/cryo-
    3697 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_027.mrc
    3698 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3699 > UniversityofDundee/Documents/Biology/cryo-
    3700 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_028.mrc
    3701 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3702 > UniversityofDundee/Documents/Biology/cryo-
    3703 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_029.mrc
    3704 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3705 > UniversityofDundee/Documents/Biology/cryo-
    3706 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_030.mrc
    3707 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3708 > UniversityofDundee/Documents/Biology/cryo-
    3709 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_031.mrc
    3710 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3711 > UniversityofDundee/Documents/Biology/cryo-
    3712 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_032.mrc
    3713 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3714 > UniversityofDundee/Documents/Biology/cryo-
    3715 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_033.mrc
    3716 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3717 > UniversityofDundee/Documents/Biology/cryo-
    3718 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_034.mrc
    3719 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3720 > UniversityofDundee/Documents/Biology/cryo-
    3721 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_035.mrc
    3722 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3723 > UniversityofDundee/Documents/Biology/cryo-
    3724 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_036.mrc
    3725 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3726 > UniversityofDundee/Documents/Biology/cryo-
    3727 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_037.mrc
    3728 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3729 > UniversityofDundee/Documents/Biology/cryo-
    3730 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_038.mrc
    3731 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3732 > UniversityofDundee/Documents/Biology/cryo-
    3733 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_039.mrc
    3734 > /Users/ccrowe/Library/CloudStorage/OneDrive-
    3735 > UniversityofDundee/Documents/Biology/cryo-
    3736 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_040.mrc
    3737 
    3738 Opened J684_series_000_frame_000.mrc as #12.1, grid size 128,128,128, pixel
    3739 2.96, shown at level 0.000154, step 1, values float32 
    3740 Opened J684_series_000_frame_001.mrc as #12.2, grid size 128,128,128, pixel
    3741 2.96, shown at level 0.000181, step 1, values float32 
    3742 Opened J684_series_000_frame_002.mrc as #12.3, grid size 128,128,128, pixel
    3743 2.96, shown at level 2.51e-06, step 1, values float32 
    3744 Opened J684_series_000_frame_003.mrc as #12.4, grid size 128,128,128, pixel
    3745 2.96, shown at level 2.19e-05, step 1, values float32 
    3746 Opened J684_series_000_frame_004.mrc as #12.5, grid size 128,128,128, pixel
    3747 2.96, shown at level 4.29e-05, step 1, values float32 
    3748 Opened J684_series_000_frame_005.mrc as #12.6, grid size 128,128,128, pixel
    3749 2.96, shown at level 9.98e-05, step 1, values float32 
    3750 Opened J684_series_000_frame_006.mrc as #12.7, grid size 128,128,128, pixel
    3751 2.96, shown at level 0.000141, step 1, values float32 
    3752 Opened J684_series_000_frame_007.mrc as #12.8, grid size 128,128,128, pixel
    3753 2.96, shown at level 0.000188, step 1, values float32 
    3754 Opened J684_series_000_frame_008.mrc as #12.9, grid size 128,128,128, pixel
    3755 2.96, shown at level 0.000132, step 1, values float32 
    3756 Opened J684_series_000_frame_009.mrc as #12.10, grid size 128,128,128, pixel
    3757 2.96, shown at level 3.05e-05, step 1, values float32 
    3758 Opened J684_series_000_frame_010.mrc as #12.11, grid size 128,128,128, pixel
    3759 2.96, shown at level 0.000104, step 1, values float32 
    3760 Opened J684_series_000_frame_011.mrc as #12.12, grid size 128,128,128, pixel
    3761 2.96, shown at level 0.00013, step 1, values float32 
    3762 Opened J684_series_000_frame_012.mrc as #12.13, grid size 128,128,128, pixel
    3763 2.96, shown at level 0.00012, step 1, values float32 
    3764 Opened J684_series_000_frame_013.mrc as #12.14, grid size 128,128,128, pixel
    3765 2.96, shown at level 5.42e-05, step 1, values float32 
    3766 Opened J684_series_000_frame_014.mrc as #12.15, grid size 128,128,128, pixel
    3767 2.96, shown at level 0.000165, step 1, values float32 
    3768 Opened J684_series_000_frame_015.mrc as #12.16, grid size 128,128,128, pixel
    3769 2.96, shown at level 0.000171, step 1, values float32 
    3770 Opened J684_series_000_frame_016.mrc as #12.17, grid size 128,128,128, pixel
    3771 2.96, shown at level 2.93e-05, step 1, values float32 
    3772 Opened J684_series_000_frame_017.mrc as #12.18, grid size 128,128,128, pixel
    3773 2.96, shown at level 0.00017, step 1, values float32 
    3774 Opened J684_series_000_frame_018.mrc as #12.19, grid size 128,128,128, pixel
    3775 2.96, shown at level 0.000176, step 1, values float32 
    3776 Opened J684_series_000_frame_019.mrc as #12.20, grid size 128,128,128, pixel
    3777 2.96, shown at level 6.17e-05, step 1, values float32 
    3778 Opened J684_series_000_frame_020.mrc as #12.21, grid size 128,128,128, pixel
    3779 2.96, shown at level 0.000205, step 1, values float32 
    3780 Opened J684_series_000_frame_021.mrc as #12.22, grid size 128,128,128, pixel
    3781 2.96, shown at level 6.87e-05, step 1, values float32 
    3782 Opened J684_series_000_frame_022.mrc as #12.23, grid size 128,128,128, pixel
    3783 2.96, shown at level 9.07e-05, step 1, values float32 
    3784 Opened J684_series_000_frame_023.mrc as #12.24, grid size 128,128,128, pixel
    3785 2.96, shown at level 9.5e-05, step 1, values float32 
    3786 Opened J684_series_000_frame_024.mrc as #12.25, grid size 128,128,128, pixel
    3787 2.96, shown at level 0.000158, step 1, values float32 
    3788 Opened J684_series_000_frame_025.mrc as #12.26, grid size 128,128,128, pixel
    3789 2.96, shown at level 6.33e-05, step 1, values float32 
    3790 Opened J684_series_000_frame_026.mrc as #12.27, grid size 128,128,128, pixel
    3791 2.96, shown at level 0.000131, step 1, values float32 
    3792 Opened J684_series_000_frame_027.mrc as #12.28, grid size 128,128,128, pixel
    3793 2.96, shown at level 7.92e-05, step 1, values float32 
    3794 Opened J684_series_000_frame_028.mrc as #12.29, grid size 128,128,128, pixel
    3795 2.96, shown at level 0.000171, step 1, values float32 
    3796 Opened J684_series_000_frame_029.mrc as #12.30, grid size 128,128,128, pixel
    3797 2.96, shown at level 8.69e-05, step 1, values float32 
    3798 Opened J684_series_000_frame_030.mrc as #12.31, grid size 128,128,128, pixel
    3799 2.96, shown at level 0.000128, step 1, values float32 
    3800 Opened J684_series_000_frame_031.mrc as #12.32, grid size 128,128,128, pixel
    3801 2.96, shown at level 0.000183, step 1, values float32 
    3802 Opened J684_series_000_frame_032.mrc as #12.33, grid size 128,128,128, pixel
    3803 2.96, shown at level 9.78e-05, step 1, values float32 
    3804 Opened J684_series_000_frame_033.mrc as #12.34, grid size 128,128,128, pixel
    3805 2.96, shown at level 7.4e-05, step 1, values float32 
    3806 Opened J684_series_000_frame_034.mrc as #12.35, grid size 128,128,128, pixel
    3807 2.96, shown at level 8.13e-05, step 1, values float32 
    3808 Opened J684_series_000_frame_035.mrc as #12.36, grid size 128,128,128, pixel
    3809 2.96, shown at level 0.000108, step 1, values float32 
    3810 Opened J684_series_000_frame_036.mrc as #12.37, grid size 128,128,128, pixel
    3811 2.96, shown at level 8.72e-05, step 1, values float32 
    3812 Opened J684_series_000_frame_037.mrc as #12.38, grid size 128,128,128, pixel
    3813 2.96, shown at level 9.87e-05, step 1, values float32 
    3814 Opened J684_series_000_frame_038.mrc as #12.39, grid size 128,128,128, pixel
    3815 2.96, shown at level 0.000132, step 1, values float32 
    3816 Opened J684_series_000_frame_039.mrc as #12.40, grid size 128,128,128, pixel
    3817 2.96, shown at level 0.000167, step 1, values float32 
    3818 Opened J684_series_000_frame_040.mrc as #12.41, grid size 128,128,128, pixel
    3819 2.96, shown at level 0.000203, step 1, values float32 
    3820 
    3821 > volume #12.1 level 0.004131
    3822 
    3823 > close #12
    3824 
    3825 > cd /Users/ccrowe/Library/CloudStorage/OneDrive-
    3826 > UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2/
    3827 
    3828 Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
    3829 UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2 
    3830 
    3831 > pwd
    3832 
    3833 Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
    3834 UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2 
    3835 
    3836 > open *.mrc vseries true
    3837 
    3838 Cannot make series from volumes with different sizes: 
    3839 5t35map.mrc 256 256 256 
    3840 cryosparc_P13_J404_004_volume_map_sharp.mrc 324 324 324 
    3841 cryosparc_P7_J649_008_volume_map_sharp.mrc 256 256 256 
    3842 cryosparc_P7_J710_006_volume_map_sharp.mrc 256 256 256 
    3843 ctermcullin.mrc 256 256 256 
    3844 cullinmap.mrc 256 256 256 
    3845 
    3846 > open *.mrc vseries true
    3847 
    3848 Cannot make series from volumes with different sizes: 
    3849 5t35map.mrc 256 256 256 
    3850 cryosparc_P13_J404_004_volume_map_sharp.mrc 324 324 324 
    3851 cryosparc_P7_J649_008_volume_map_sharp.mrc 256 256 256 
    3852 cryosparc_P7_J710_006_volume_map_sharp.mrc 256 256 256 
    3853 ctermcullin.mrc 256 256 256 
    3854 cullinmap.mrc 256 256 256 
    3855 
    3856 > cd /Users/ccrowe/Library/CloudStorage/OneDrive-
    3857 > UniversityofDundee/Documents/Biology/cryo-
    3858 > EM/CRL2/2023_11_16_mapCRL2//Users/ccrowe/Library/CloudStorage/OneDrive-
    3859 > UniversityofDundee/Documents/Biology/cryo-
    3860 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000
    3861 
    3862 Expected name of a folder to open/read; a name of 'browse' will bring up a
    3863 file browser or a keyword 
    3864 
    3865 > cd /Users/ccrowe/Library/CloudStorage/OneDrive-
    3866 > UniversityofDundee/Documents/Biology/cryo-
    3867 > EM/CRL2/2023_11_16_mapCRL2//Users/ccrowe/Library/CloudStorage/OneDrive-
    3868 > UniversityofDundee/Documents/Biology/cryo-
    3869 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/
    3870 
    3871 Expected name of a folder to open/read; a name of 'browse' will bring up a
    3872 file browser or a keyword 
    3873 
    3874 > cd /Users/ccrowe/Library/CloudStorage/OneDrive-
    3875 > UniversityofDundee/Documents/Biology/cryo-
    3876 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/
    3877 
    3878 Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
    3879 UniversityofDundee/Documents/Biology/cryo-
    3880 EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000 
    3881 
    3882 > pwd
    3883 
    3884 Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
    3885 UniversityofDundee/Documents/Biology/cryo-
    3886 EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000 
    3887 
    3888 > open *.mrc vseries true
    3889 
    3890 Opened map series J684_series_000_frame_000.mrc as #12, 41 images, grid size
    3891 128,128,128, pixel 2.96, shown at level 0.000154, step 1, values float32 
    3892 
    3893 > volume #12.1 level 0.004131
    3894 
    3895 > volume #12.20 level 0.009246
    3896 
    3897 > cd /Users/ccrowe/Library/CloudStorage/OneDrive-
    3898 > UniversityofDundee/Documents/Biology/cryo-
    3899 > EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_001/
    3900 
    3901 Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
    3902 UniversityofDundee/Documents/Biology/cryo-
    3903 EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_001 
    3904 
    3905 > pwd
    3906 
    3907 Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
    3908 UniversityofDundee/Documents/Biology/cryo-
    3909 EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_001 
    3910 
    3911 > open *.mrc vseries true
    3912 
    3913 Opened map series J684_series_001_frame_000.mrc as #13, 41 images, grid size
    3914 128,128,128, pixel 2.96, shown at level 0.000195, step 1, values float32 
    3915 
    3916 > volume #13.15 level 0.01189
    3917 
    3918 > hide #!12 models
    3919 
    3920 > hide #!13 models
    3921 
    3922 > show #!12 models
    3923 
    3924 > save /Users/ccrowe/Library/CloudStorage/OneDrive-
    3925 > UniversityofDundee/Documents/Biology/cryo-
    3926 > EM/CRL2/2023_11_16_mapCRL2/2023_11_21_chimeraxsession.cxs includeMaps true
    3927 
    3928 ——— End of log from Tue Nov 21 10:52:47 2023 ———
    3929 
    3930 opened ChimeraX session 
    3931 
    3932 > show #!13 models
    3933 
    3934 > hide #!13 models
    3935 
    3936 > show #!13 models
    3937 
    3938 > hide #!13 models
    3939 
    3940 > hide #!12 models
    3941 
    3942 > show #!10 models
    3943 
    3944 > hide #!10 models
    3945 
    3946 > show #9 models
    3947 
    3948 > hide #9 models
    3949 
    3950 > show #!12 models
    3951 
    3952 > volume #12.5 level 0.08829
    3953 
    3954 > show #!13 models
    3955 
    3956 > volume #13.7 level 0.06315
    3957 
    3958 > volume #12.7 level 0.07226
    3959 
    3960 > hide #!12 models
    3961 
    3962 > hide #!13 models
    3963 
    3964 > show #!12 models
    3965 
    3966 > show #!13 models
    3967 
    3968 > hide #!13 models
    3969 
    3970 > hide #!12 models
    3971 
    3972 > show #!8 models
    3973 
    3974 > volume #8 level 0.1157
    3975 
    3976 > show #!4 models
    3977 
    3978 > hide #!4 models
    3979 
    3980 > show #!5 models
    3981 
    3982 > hide #!5 models
    3983 
    3984 > show #9 models
    3985 
    3986 > show #6 models
    3987 
    3988 > hide #6 models
    3989 
    3990 > hide #!8 models
    3991 
    3992 > show #!8 models
    3993 
    3994 > hide #9 models
    3995 
    3996 > open /Users/ccrowe/Downloads/cryosparc_P14_J395_003_volume_map_sharp.mrc
    3997 
    3998 Opened cryosparc_P14_J395_003_volume_map_sharp.mrc as #14, grid size
    3999 128,128,128, pixel 3.38, shown at level 0.124, step 1, values float32 
    4000 
    4001 > open /Users/ccrowe/Downloads/cryosparc_P14_J396_003_volume_map_sharp.mrc
    4002 
    4003 Opened cryosparc_P14_J396_003_volume_map_sharp.mrc as #15, grid size
    4004 128,128,128, pixel 3.38, shown at level 0.152, step 1, values float32 
    4005 
    4006 > volume #14 level 0.2547
    4007 
    4008 > volume #15 level 0.4279
    4009 
    4010 > volume #14 level 0.3449
    4011 
    4012 > surface dust #14 size 33.8
    4013 
    4014 > surface dust #15 size 33.8
    4015 
    4016 > open /Users/ccrowe/Downloads/cryosparc_P14_J427_003_volume_map_sharp.mrc
    4017 
    4018 Opened cryosparc_P14_J427_003_volume_map_sharp.mrc as #16, grid size
    4019 128,128,128, pixel 3.38, shown at level 0.134, step 1, values float32 
    4020 
    4021 > volume #16 level 0.1674
    4022 
    4023 > surface dust #14 size 33.8
    4024 
    4025 > surface dust #16 size 33.8
    4026 
    4027 > volume #16 level 0.3324
    4028 
    4029 > volume #16 level 0.6514
    4030 
    4031 > volume #16 level 0.3104
    4032 
    4033 > show #!8 models
    4034 
    4035 > ui mousemode right "rotate selected models"
    4036 
    4037 > select add #14
    4038 
    4039 2 models selected 
    4040 
    4041 > view matrix models
    4042 > #14,-0.83202,-0.54997,0.072621,494.21,0.52167,-0.82021,-0.23477,322.91,0.18868,-0.15745,0.96933,-0.68575
    4043 
    4044 > view matrix models
    4045 > #14,-0.86702,-0.49747,0.028397,501.16,0.49797,-0.86303,0.084876,262.05,-0.017716,0.08773,0.99599,-13.576
    4046 
    4047 > volume #14 flipNormals
    4048 
    4049 Missing "flipNormals" keyword's argument 
    4050 
    4051 > volume flip #14
    4052 
    4053 Opened cryosparc_P14_J395_003_volume_map_sharp.mrc z flip as #17, grid size
    4054 128,128,128, pixel 3.38, shown at step 1, values float32 
    4055 
    4056 > show #!14 models
    4057 
    4058 > hide #!14 models
    4059 
    4060 > select subtract #14
    4061 
    4062 Nothing selected 
    4063 
    4064 > select add #17
    4065 
    4066 2 models selected 
    4067 
    4068 > ui mousemode right "rotate selected models"
    4069 
    4070 > view matrix models
    4071 > #17,0.98445,-0.096336,0.14692,-6.4957,-0.081978,-0.99152,-0.10084,450.89,0.15539,0.087225,-0.98399,338.63
    4072 
    4073 > ui mousemode right "translate selected models"
    4074 
    4075 > view matrix models
    4076 > #17,0.98445,-0.096336,0.14692,-8.2028,-0.081978,-0.99152,-0.10084,441.44,0.15539,0.087225,-0.98399,350.39
    4077 
    4078 > ui mousemode right rotate
    4079 
    4080 > ui mousemode right "translate selected models"
    4081 
    4082 > view matrix models
    4083 > #17,0.98445,-0.096336,0.14692,-38.071,-0.081978,-0.99152,-0.10084,445.18,0.15539,0.087225,-0.98399,346.35
    4084 
    4085 > fitmap #17 inMap #8
    4086 
    4087 Fit map cryosparc_P14_J395_003_volume_map_sharp.mrc z flip in map
    4088 cryosparc_P7_J710_006_volume_map_sharp.mrc using 6377 points 
    4089 correlation = 0.6796, correlation about mean = 0.4352, overlap = 909.3 
    4090 steps = 92, shift = 6.71, angle = 11.6 degrees 
    4091  
    4092 Position of cryosparc_P14_J395_003_volume_map_sharp.mrc z flip (#17) relative
    4093 to cryosparc_P7_J710_006_volume_map_sharp.mrc (#8) coordinates: 
    4094 Matrix rotation and translation 
    4095 0.99965078 -0.00283677 -0.02627309 -20.41884302 
    4096 -0.00432054 -0.99838806 -0.05659173 418.32860816 
    4097 -0.02607021 0.05668549 -0.99805165 396.56551922 
    4098 Axis 0.99991262 -0.00179092 -0.01309749 
    4099 Axis point 0.00000000 203.53018816 204.07754379 
    4100 Rotation angle (degrees) 176.75282512 
    4101 Shift along axis -26.36026434 
    4102  
    4103 
    4104 > select clear
    4105 
    4106 > hide #!17 models
    4107 
    4108 > show #!17 models
    4109 
    4110 > show #6 models
    4111 
    4112 > hide #6 models
    4113 
    4114 > show #6 models
    4115 
    4116 > hide #6 models
    4117 
    4118 > surface dust #8 size 14.8
    4119 
    4120 > surface dust #17 size 33.8
    4121 
    4122 > volume #17 level 0.2747
    4123 
    4124 > transparency #8.1#17.1 0
    4125 
    4126 > transparency #8.1#17.1 50
    4127 
    4128 > volume #17 level 0.776
    4129 
    4130 > volume #17 level 0.9565
    4131 
    4132 > volume #8 level 0.1548
    4133 
    4134 > volume #17 level 0.2647
    4135 
    4136 > show #!3 models
    4137 
    4138 > hide #!3 models
    4139 
    4140 > show #!7 models
    4141 
    4142 > hide #!7 models
    4143 
    4144 > show #9 models
     668
     669[deleted to fit within ticket limits]
    4145670
    4146671> show #!7 models