Changes between Initial Version and Version 1 of Ticket #18239


Ignore:
Timestamp:
Jul 22, 2025, 9:22:04 AM (3 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #18239

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

  • Ticket #18239 – Description

    initial v1  
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    1809     "source" : "P",
    1810     "arch" : "arm64e",
    1811     "base" : 6906855424,
    1812     "size" : 51784,
    1813     "uuid" : "647b91fc-96d3-3bbb-af08-970df45257c8",
    1814     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1815     "name" : "libsystem_pthread.dylib"
    1816   },
    1817   {
    1818     "source" : "P",
    1819     "arch" : "arm64e",
    1820     "base" : 6905376768,
    1821     "size" : 529520,
    1822     "uuid" : "f4529d5e-24f3-3bbb-bd3c-984856875fc8",
    1823     "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    1824     "name" : "libsystem_c.dylib"
    1825   },
    1826   {
    1827     "source" : "P",
    1828     "arch" : "arm64e",
    1829     "base" : 6907105280,
    1830     "size" : 31568,
    1831     "uuid" : "519f3220-7499-334a-96d6-ccf3dc28f986",
    1832     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1833     "name" : "libsystem_platform.dylib"
    1834   },
    1835   {
    1836     "source" : "P",
    1837     "arch" : "arm64e",
    1838     "base" : 6973820928,
    1839     "CFBundleShortVersionString" : "6.9",
    1840     "CFBundleIdentifier" : "com.apple.AppKit",
    1841     "size" : 21568640,
    1842     "uuid" : "5d0da1bd-412c-3ed8-84e9-40ca62fe7b42",
    1843     "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    1844     "name" : "AppKit",
    1845     "CFBundleVersion" : "2575.60.5"
    1846   },
    1847   {
    1848     "source" : "P",
    1849     "arch" : "arm64e",
    1850     "base" : 7007809536,
    1851     "CFBundleShortVersionString" : "1.600.0",
    1852     "CFBundleIdentifier" : "com.apple.SkyLight",
    1853     "size" : 5395200,
    1854     "uuid" : "3a386772-a7fe-3359-aac4-1ae9c903cb49",
    1855     "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    1856     "name" : "SkyLight"
    1857   },
    1858   {
    1859     "source" : "P",
    1860     "arch" : "arm64e",
    1861     "base" : 6905073664,
    1862     "size" : 288576,
    1863     "uuid" : "8bf83cda-8db1-3d46-94b0-d811bd77e078",
    1864     "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1865     "name" : "libdispatch.dylib"
    1866   },
    1867   {
    1868     "source" : "P",
    1869     "arch" : "arm64e",
    1870     "base" : 6907334656,
    1871     "CFBundleShortVersionString" : "6.9",
    1872     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    1873     "size" : 5500928,
    1874     "uuid" : "df489a59-b4f6-32b8-9bb4-9b832960aa52",
    1875     "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    1876     "name" : "CoreFoundation",
    1877     "CFBundleVersion" : "3502.1.401"
    1878   },
    1879   {
    1880     "source" : "P",
    1881     "arch" : "arm64e",
    1882     "base" : 7102681088,
    1883     "CFBundleShortVersionString" : "2.1.1",
    1884     "CFBundleIdentifier" : "com.apple.HIToolbox",
    1885     "size" : 3174368,
    1886     "uuid" : "9286e29f-fcee-31d0-acea-2842ea23bedf",
    1887     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    1888     "name" : "HIToolbox"
    1889   },
    1890   {
    1891     "source" : "P",
    1892     "arch" : "arm64e",
    1893     "base" : 6903054336,
    1894     "size" : 636112,
    1895     "uuid" : "9cf0401a-a938-389e-a77d-9e9608076ccf",
    1896     "path" : "\/usr\/lib\/dyld",
    1897     "name" : "dyld"
    1898   },
    1899   {
    1900     "size" : 0,
    1901     "source" : "A",
    1902     "base" : 0,
    1903     "uuid" : "00000000-0000-0000-0000-000000000000"
    1904   },
    1905   {
    1906     "source" : "P",
    1907     "arch" : "arm64e",
    1908     "base" : 6930337792,
    1909     "CFBundleShortVersionString" : "6.9",
    1910     "CFBundleIdentifier" : "com.apple.Foundation",
    1911     "size" : 14586624,
    1912     "uuid" : "e8f6a451-0acc-3e05-b18f-fec6618ce44a",
    1913     "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    1914     "name" : "Foundation",
    1915     "CFBundleVersion" : "3502.1.401"
    1916   },
    1917   {
    1918     "source" : "P",
    1919     "arch" : "arm64e",
    1920     "base" : 8586874880,
    1921     "CFBundleShortVersionString" : "5.4.11",
    1922     "CFBundleIdentifier" : "com.apple.MetalPerformanceShadersGraph",
    1923     "size" : 17877952,
    1924     "uuid" : "d54e0bb3-f77f-3003-bcdf-cd9057c41dce",
    1925     "path" : "\/System\/Library\/Frameworks\/MetalPerformanceShadersGraph.framework\/Versions\/A\/MetalPerformanceShadersGraph",
    1926     "name" : "MetalPerformanceShadersGraph",
    1927     "CFBundleVersion" : "5.4.11"
    1928   }
     74[deleted to fit within ticket limits]
     75
    192976],
    193077  "sharedCache" : {
    … …  
    2103250> hide cartoons
    2104251
    2105 > select #1/XX,23
    2106 
    2107 1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected 
    2108 
    2109 > show sel cartoons
    2110 
    2111 > save sel
    2112 
    2113 Cannot determine format for 'sel' 
    2114 
    2115 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    2116 > VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J194_003_volume_map.mrc
    2117 
    2118 Opened cryosparc_P346_J194_003_volume_map.mrc as #2, grid size 384,384,384,
    2119 pixel 1.19, shown at level 0.252, step 2, values float32 
    2120 
    2121 > select add #1
    2122 
    2123 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2124 selected 
    2125 
    2126 > select subtract #1
    2127 
    2128 Nothing selected 
    2129 
    2130 > select add #1
    2131 
    2132 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2133 selected 
    2134 
    2135 > show sel cartoons
    2136 
    2137 [Repeated 1 time(s)]
    2138 
    2139 > set bgColor white
    2140 
    2141 > lighting simple
    2142 
    2143 > lighting soft
    2144 
    2145 > ui mousemode right zoom
    2146 
    2147 > ui mousemode right "rotate selected models"
    2148 
    2149 > view matrix models
    2150 > #1,0.026961,0.87835,-0.47725,123.11,0.33104,-0.45833,-0.82483,567.07,-0.94323,-0.13575,-0.30313,637.8
    2151 
    2152 > view matrix models
    2153 > #1,-0.56288,0.56327,-0.6049,398.21,-0.26259,-0.81579,-0.51529,734.29,-0.78372,-0.13121,0.6071,344.19
    2154 
    2155 > view matrix models
    2156 > #1,-0.97792,-0.20882,-0.0084945,560.96,0.1812,-0.86744,0.46338,366.38,-0.10413,0.45161,0.88612,-72.908
    2157 
    2158 > ui mousemode right "translate selected models"
    2159 
    2160 > view matrix models
    2161 > #1,-0.97792,-0.20882,-0.0084945,601.58,0.1812,-0.86744,0.46338,344.47,-0.10413,0.45161,0.88612,-74.691
    2162 
    2163 > view matrix models
    2164 > #1,-0.97792,-0.20882,-0.0084945,562.3,0.1812,-0.86744,0.46338,314.21,-0.10413,0.45161,0.88612,-118.43
    2165 
    2166 > fitmap #1 inMap #2
    2167 
    2168 Fit molecule 6sgc (#1) to map cryosparc_P346_J194_003_volume_map.mrc (#2)
    2169 using 218966 atoms 
    2170 average map value = 0.1316, steps = 488 
    2171 shifted from previous position = 34.8 
    2172 rotated from previous position = 8.48 degrees 
    2173 atoms outside contour = 183320, contour level = 0.25215 
    2174  
    2175 Position of 6sgc (#1) relative to cryosparc_P346_J194_003_volume_map.mrc (#2)
    2176 coordinates: 
    2177 Matrix rotation and translation 
    2178 -0.98066463 -0.14575461 -0.13058515 590.89285007 
    2179 0.06111114 -0.86200261 0.50320664 304.88092255 
    2180 -0.18590942 0.48549674 0.85424270 -82.49763079 
    2181 Axis -0.08242257 0.25748142 0.96276157 
    2182 Axis point 283.02756345 179.88973883 0.00000000 
    2183 Rotation angle (degrees) 173.83260911 
    2184 Shift along axis -49.62728285 
    2185  
    2186 
    2187 > select subtract #1
    2188 
    2189 Nothing selected 
    2190 
    2191 Window position QRect(1985,1064 575x259) outside any known screen, using
    2192 primary screen 
    2193 
    2194 > volume #2 step 1
    2195 
    2196 > volume #2 level 0.2106
    2197 
    2198 > select add #1
    2199 
    2200 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2201 selected 
    2202 
    2203 > select subtract #1
    2204 
    2205 Nothing selected 
    2206 
    2207 > select add #1
    2208 
    2209 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2210 selected 
    2211 
    2212 > hide sel cartoons
    2213 
    2214 > select #1/XX,23
    2215 
    2216 1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected 
    2217 
    2218 > show sel cartoons
    2219 
    2220 > select add #1
    2221 
    2222 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2223 selected 
    2224 
    2225 > select subtract #1
    2226 
    2227 Nothing selected 
    2228 
    2229 > color #2 #b2b2b27d models
    2230 
    2231 > color #2 #b2b2b2b7 models
    2232 
    2233 > color #2 #009193ff models
    2234 
    2235 > color #2 #009193a3 models
    2236 
    2237 > color #2 #00919380 models
    2238 
    2239 > ui mousemode right translate
    2240 
    2241 > ui mousemode right zoom
    2242 
    2243 > volume #2 level 0.2487
    2244 
    2245 > clipper associate #2 toModel #1
    2246 
    2247 Opened cryosparc_P346_J194_003_volume_map.mrc as #1.1.1.1, grid size
    2248 384,384,384, pixel 1.19, shown at level 0.312, step 1, values float32 
    2249 6sgc title: 
    2250 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    2251  
    2252 Chain information for 6sgc 
    2253 --- 
    2254 Chain | Description | UniProt 
    2255 1.2/23 1.2/33 | tRNA (Lys3) |   
    2256 1.2/54 | 28S ribosomal RNA |   
    2257 1.2/74 | 5S ribosomal RNA |   
    2258 1.2/84 | 5.8S ribosomal RNA |   
    2259 1.2/A1 | 18S ribosomal RNA |   
    2260 1.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    2261 1.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    2262 1.2/B1 | uS2 |   
    2263 1.2/B2 | uL3 | G1TL06_RABIT 2-403 
    2264 1.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    2265 1.2/C2 | uL4 |   
    2266 1.2/D1 | uS5 |   
    2267 1.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    2268 1.2/E1 | uS5 | G1TNM3_RABIT 1-243 
    2269 1.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    2270 1.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    2271 1.2/F2 | uL30 | G1TUB1_RABIT 1-247 
    2272 1.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    2273 1.2/G2 | eL8 |   
    2274 1.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    2275 1.2/H2 | uL6 | G1TX33_RABIT 1-192 
    2276 1.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    2277 1.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    2278 1.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    2279 1.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    2280 1.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    2281 1.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    2282 1.2/L2 | eL13 |   
    2283 1.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    2284 1.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    2285 1.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    2286 1.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    2287 1.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    2288 1.2/O2 | uL13 |   
    2289 1.2/P1 | uS11 |   
    2290 1.2/P2 | uL22 | G1TVT6_RABIT 1-184 
    2291 1.2/Q1 | uS19 | G1U0Q2_RABIT 1-145 
    2292 1.2/Q2 | eL18 |   
    2293 1.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    2294 1.2/R2 | eL19 |   
    2295 1.2/S1 | eS17 | G1TU13_RABIT 1-135 
    2296 1.2/S2 | eL20 |   
    2297 1.2/T1 | eS13 | G1TPG3_RABIT 1-152 
    2298 1.2/T2 | eL21 | G1SHQ2_RABIT 1-160 
    2299 1.2/U1 | eS19 | G1TN62_RABIT 1-145 
    2300 1.2/U2 | eL22 |   
    2301 1.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    2302 1.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    2303 1.2/W1 | eS21 |   
    2304 1.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    2305 1.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    2306 1.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    2307 1.2/XX | poly-lysine nascent chain |   
    2308 1.2/Y1 | uS12 |   
    2309 1.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    2310 1.2/Z1 | eS24 |   
    2311 1.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    2312 1.2/a1 | eS25 | G1TDB3_RABIT 1-125 
    2313 1.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    2314 1.2/b1 | eS26 |   
    2315 1.2/b2 | eL29 |   
    2316 1.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    2317 1.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    2318 1.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    2319 1.2/d2 | eL31 | G1SHG0_RABIT 1-125 
    2320 1.2/e1 | uS14 | G1U7M4_RABIT 1-56 
    2321 1.2/e2 | eL32 | G1U437_RABIT 1-135 
    2322 1.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    2323 1.2/f2 | eL33 | G1SF08_RABIT 1-110 
    2324 1.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    2325 1.2/g2 | eL34 | G1U945_RABIT 1-116 
    2326 1.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    2327 1.2/h2 | uL29 | G1SIT5_RABIT 1-123 
    2328 1.2/i1 | polyA mRNA |   
    2329 1.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    2330 1.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    2331 1.2/k2 | eL38 | G1U001_RABIT 1-70 
    2332 1.2/l2 | eL39 | G1TTN1_RABIT 1-51 
    2333 1.2/m2 | eL40 |   
    2334 1.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    2335 1.2/o2 | eL42 | G1U344_RABIT 1-106 
    2336 1.2/p2 | eL43 | G1SY53_RABIT 1-92 
    2337 1.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    2338 1.2/s2 | uL10 |   
    2339 1.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    2340  
    2341 Non-standard residues in 6sgc #1.2 
    2342 --- 
    2343 MG — magnesium ion 
    2344 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    2345 ZN — zinc ion 
    2346  
    2347 
    2348 > vop #1 st volume #1 st vop #1 style surface
    2349 
    2350 > transparency #1 50
    2351 
    2352 > volume #1.1.1.1 level 0.1719
    2353 
    2354 > hide atoms
    2355 
    2356 > hide #!1.1 models
    2357 
    2358 > show #!1.1 models
    2359 
    2360 > hide #!1.2 models
    2361 
    2362 > select #1/XX,23
    2363 
    2364 1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected 
    2365 
    2366 > show #!1.2 models
    2367 
    2368 > open 6sgc
    2369 
    2370 6sgc title: 
    2371 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    2372  
    2373 Chain information for 6sgc #2 
    2374 --- 
    2375 Chain | Description | UniProt 
    2376 23 33 | tRNA (Lys3) |   
    2377 54 | 28S ribosomal RNA |   
    2378 74 | 5S ribosomal RNA |   
    2379 84 | 5.8S ribosomal RNA |   
    2380 A1 | 18S ribosomal RNA |   
    2381 A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    2382 B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    2383 B1 | uS2 |   
    2384 B2 | uL3 | G1TL06_RABIT 2-403 
    2385 C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    2386 C2 | uL4 |   
    2387 D1 | uS5 |   
    2388 D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    2389 E1 | uS5 | G1TNM3_RABIT 1-243 
    2390 E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    2391 F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    2392 F2 | uL30 | G1TUB1_RABIT 1-247 
    2393 G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    2394 G2 | eL8 |   
    2395 H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    2396 H2 | uL6 | G1TX33_RABIT 1-192 
    2397 I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    2398 I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    2399 J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    2400 J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    2401 K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    2402 L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    2403 L2 | eL13 |   
    2404 M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    2405 M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    2406 N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    2407 N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    2408 O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    2409 O2 | uL13 |   
    2410 P1 | uS11 |   
    2411 P2 | uL22 | G1TVT6_RABIT 1-184 
    2412 Q1 | uS19 | G1U0Q2_RABIT 1-145 
    2413 Q2 | eL18 |   
    2414 R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    2415 R2 | eL19 |   
    2416 S1 | eS17 | G1TU13_RABIT 1-135 
    2417 S2 | eL20 |   
    2418 T1 | eS13 | G1TPG3_RABIT 1-152 
    2419 T2 | eL21 | G1SHQ2_RABIT 1-160 
    2420 U1 | eS19 | G1TN62_RABIT 1-145 
    2421 U2 | eL22 |   
    2422 V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    2423 V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    2424 W1 | eS21 |   
    2425 W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    2426 X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    2427 X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    2428 XX | poly-lysine nascent chain |   
    2429 Y1 | uS12 |   
    2430 Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    2431 Z1 | eS24 |   
    2432 Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    2433 a1 | eS25 | G1TDB3_RABIT 1-125 
    2434 a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    2435 b1 | eS26 |   
    2436 b2 | eL29 |   
    2437 c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    2438 c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    2439 d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    2440 d2 | eL31 | G1SHG0_RABIT 1-125 
    2441 e1 | uS14 | G1U7M4_RABIT 1-56 
    2442 e2 | eL32 | G1U437_RABIT 1-135 
    2443 f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    2444 f2 | eL33 | G1SF08_RABIT 1-110 
    2445 g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    2446 g2 | eL34 | G1U945_RABIT 1-116 
    2447 h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    2448 h2 | uL29 | G1SIT5_RABIT 1-123 
    2449 i1 | polyA mRNA |   
    2450 i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    2451 j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    2452 k2 | eL38 | G1U001_RABIT 1-70 
    2453 l2 | eL39 | G1TTN1_RABIT 1-51 
    2454 m2 | eL40 |   
    2455 n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    2456 o2 | eL42 | G1U344_RABIT 1-106 
    2457 p2 | eL43 | G1SY53_RABIT 1-92 
    2458 r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    2459 s2 | uL10 |   
    2460 t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    2461  
    2462 Non-standard residues in 6sgc #2 
    2463 --- 
    2464 MG — magnesium ion 
    2465 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    2466 ZN — zinc ion 
    2467  
    2468 
    2469 > hide sel atoms
    2470 
    2471 [Repeated 1 time(s)]
    2472 
    2473 > show sel cartoons
    2474 
    2475 > hide sel atoms
    2476 
    2477 > select add #1.2
    2478 
    2479 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2480 selected 
    2481 
    2482 > select add #1
    2483 
    2484 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 10 models
    2485 selected 
    2486 
    2487 > select add #2
    2488 
    2489 437932 atoms, 469824 bonds, 11698 pseudobonds, 35902 residues, 14 models
    2490 selected 
    2491 
    2492 > select subtract #1
    2493 
    2494 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2495 selected 
    2496 
    2497 > hide sel atoms
    2498 
    2499 > show sel cartoons
    2500 
    2501 > hide #!2 models
    2502 
    2503 > show #!2 models
    2504 
    2505 > ui mousemode right "translate selected models"
    2506 
    2507 > ui mousemode right "rotate selected models"
    2508 
    2509 > view matrix models
    2510 > #2,0.30353,0.95259,-0.020974,-94.412,0.20733,-0.087513,-0.97435,532.35,-0.92999,0.29139,-0.22406,488.97
    2511 
    2512 > view matrix models
    2513 > #2,-0.9081,0.082743,-0.41051,570.36,-0.30149,-0.80952,0.50377,460.01,-0.29063,0.58124,0.76007,-28.529
    2514 
    2515 > ui mousemode right "translate selected models"
    2516 
    2517 > view matrix models
    2518 > #2,-0.9081,0.082743,-0.41051,597.68,-0.30149,-0.80952,0.50377,438.49,-0.29063,0.58124,0.76007,-10.954
    2519 
    2520 > view matrix models
    2521 > #2,-0.9081,0.082743,-0.41051,578.02,-0.30149,-0.80952,0.50377,399.84,-0.29063,0.58124,0.76007,-54.959
    2522 
    2523 Must specify one map, got 0 
    2524 
    2525 > close #1
    2526 
    2527 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    2528 > VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J194_003_volume_map.mrc
    2529 
    2530 Opened cryosparc_P346_J194_003_volume_map.mrc as #1, grid size 384,384,384,
    2531 pixel 1.19, shown at level 0.252, step 2, values float32 
    2532 
    2533 > fitmap #2 inMap #1
    2534 
    2535 Fit molecule 6sgc (#2) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
    2536 using 218966 atoms 
    2537 average map value = 0.1873, steps = 284 
    2538 shifted from previous position = 12.9 
    2539 rotated from previous position = 21.1 degrees 
    2540 atoms outside contour = 165465, contour level = 0.25215 
    2541  
    2542 Position of 6sgc (#2) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
    2543 coordinates: 
    2544 Matrix rotation and translation 
    2545 -0.98229801 -0.13687159 -0.12789363 585.89147373 
    2546 0.03751455 -0.81264194 0.58155459 275.19570461 
    2547 -0.18353003 0.56646204 0.80339124 -94.67478878 
    2548 Axis -0.08217323 0.30291927 0.94946694 
    2549 Axis point 281.77911784 166.78862352 0.00000000 
    2550 Rotation angle (degrees) 174.73089241 
    2551 Shift along axis -54.67309215 
    2552  
    2553 
    2554 > open 6sgc
    2555 
    2556 6sgc title: 
    2557 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    2558  
    2559 Chain information for 6sgc #3 
    2560 --- 
    2561 Chain | Description | UniProt 
    2562 23 33 | tRNA (Lys3) |   
    2563 54 | 28S ribosomal RNA |   
    2564 74 | 5S ribosomal RNA |   
    2565 84 | 5.8S ribosomal RNA |   
    2566 A1 | 18S ribosomal RNA |   
    2567 A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    2568 B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    2569 B1 | uS2 |   
    2570 B2 | uL3 | G1TL06_RABIT 2-403 
    2571 C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    2572 C2 | uL4 |   
    2573 D1 | uS5 |   
    2574 D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    2575 E1 | uS5 | G1TNM3_RABIT 1-243 
    2576 E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    2577 F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    2578 F2 | uL30 | G1TUB1_RABIT 1-247 
    2579 G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    2580 G2 | eL8 |   
    2581 H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    2582 H2 | uL6 | G1TX33_RABIT 1-192 
    2583 I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    2584 I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    2585 J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    2586 J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    2587 K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    2588 L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    2589 L2 | eL13 |   
    2590 M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    2591 M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    2592 N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    2593 N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    2594 O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    2595 O2 | uL13 |   
    2596 P1 | uS11 |   
    2597 P2 | uL22 | G1TVT6_RABIT 1-184 
    2598 Q1 | uS19 | G1U0Q2_RABIT 1-145 
    2599 Q2 | eL18 |   
    2600 R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    2601 R2 | eL19 |   
    2602 S1 | eS17 | G1TU13_RABIT 1-135 
    2603 S2 | eL20 |   
    2604 T1 | eS13 | G1TPG3_RABIT 1-152 
    2605 T2 | eL21 | G1SHQ2_RABIT 1-160 
    2606 U1 | eS19 | G1TN62_RABIT 1-145 
    2607 U2 | eL22 |   
    2608 V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    2609 V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    2610 W1 | eS21 |   
    2611 W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    2612 X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    2613 X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    2614 XX | poly-lysine nascent chain |   
    2615 Y1 | uS12 |   
    2616 Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    2617 Z1 | eS24 |   
    2618 Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    2619 a1 | eS25 | G1TDB3_RABIT 1-125 
    2620 a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    2621 b1 | eS26 |   
    2622 b2 | eL29 |   
    2623 c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    2624 c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    2625 d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    2626 d2 | eL31 | G1SHG0_RABIT 1-125 
    2627 e1 | uS14 | G1U7M4_RABIT 1-56 
    2628 e2 | eL32 | G1U437_RABIT 1-135 
    2629 f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    2630 f2 | eL33 | G1SF08_RABIT 1-110 
    2631 g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    2632 g2 | eL34 | G1U945_RABIT 1-116 
    2633 h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    2634 h2 | uL29 | G1SIT5_RABIT 1-123 
    2635 i1 | polyA mRNA |   
    2636 i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    2637 j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    2638 k2 | eL38 | G1U001_RABIT 1-70 
    2639 l2 | eL39 | G1TTN1_RABIT 1-51 
    2640 m2 | eL40 |   
    2641 n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    2642 o2 | eL42 | G1U344_RABIT 1-106 
    2643 p2 | eL43 | G1SY53_RABIT 1-92 
    2644 r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    2645 s2 | uL10 |   
    2646 t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    2647  
    2648 Non-standard residues in 6sgc #3 
    2649 --- 
    2650 MG — magnesium ion 
    2651 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    2652 ZN — zinc ion 
    2653  
    2654 
    2655 > select subtract #2
    2656 
    2657 Nothing selected 
    2658 
    2659 > select add #3
    2660 
    2661 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2662 selected 
    2663 
    2664 > hide sel atoms
    2665 
    2666 > show sel cartoons
    2667 
    2668 > ui mousemode right "rotate selected models"
    2669 
    2670 > view matrix models
    2671 > #3,-0.96108,-0.064244,-0.26868,586.96,0.1585,-0.92482,-0.34581,612.84,-0.22627,-0.37494,0.89901,193.46
    2672 
    2673 > ui mousemode right "translate selected models"
    2674 
    2675 > view matrix models
    2676 > #3,-0.96108,-0.064244,-0.26868,608.73,0.1585,-0.92482,-0.34581,540.2,-0.22627,-0.37494,0.89901,213.61
    2677 
    2678 > fitmap #3 inMap #1
    2679 
    2680 Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
    2681 using 218966 atoms 
    2682 average map value = 0.06041, steps = 168 
    2683 shifted from previous position = 28.9 
    2684 rotated from previous position = 6.05 degrees 
    2685 atoms outside contour = 201607, contour level = 0.25215 
    2686  
    2687 Position of 6sgc (#3) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
    2688 coordinates: 
    2689 Matrix rotation and translation 
    2690 -0.97980063 -0.08877694 -0.17919092 591.56129031 
    2691 0.14110944 -0.94185710 -0.30494807 535.96571783 
    2692 -0.14169988 -0.32407384 0.93535944 137.77850284 
    2693 Axis -0.08183641 -0.16041873 0.98365067 
    2694 Axis point 285.53422334 296.84958914 0.00000000 
    2695 Rotation angle (degrees) 173.28944637 
    2696 Shift along axis 1.13571978 
    2697  
    2698 
    2699 > ui mousemode right "rotate selected models"
    2700 
    2701 > view matrix models
    2702 > #3,-0.95798,0.046422,-0.28305,575.71,0.027314,-0.96757,-0.25114,557.16,-0.28552,-0.24832,0.92564,154.77
    2703 
    2704 > ui mousemode right "translate selected models"
    2705 
    2706 > view matrix models
    2707 > #3,-0.95798,0.046422,-0.28305,572.66,0.027314,-0.96757,-0.25114,540.9,-0.28552,-0.24832,0.92564,129.09
    2708 
    2709 > fitmap #3 inMap #1
    2710 
    2711 Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
    2712 using 218966 atoms 
    2713 average map value = 0.0663, steps = 100 
    2714 shifted from previous position = 2.69 
    2715 rotated from previous position = 1.43 degrees 
    2716 atoms outside contour = 199648, contour level = 0.25215 
    2717  
    2718 Position of 6sgc (#3) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
    2719 coordinates: 
    2720 Matrix rotation and translation 
    2721 -0.95684098 0.05053273 -0.28618487 574.31564589 
    2722 0.03132374 -0.96109585 -0.27443323 543.89064126 
    2723 -0.28891895 -0.27155334 0.91803302 137.30438044 
    2724 Axis 0.14681952 0.13938622 -0.97929337 
    2725 Axis point 298.80326321 280.28829116 0.00000000 
    2726 Rotation angle (degrees) 179.43805844 
    2727 Shift along axis 25.67033918 
    2728  
    2729 
    2730 > hide #!2 models
    2731 
    2732 > show #!2 models
    2733 
    2734 > hide #!2 models
    2735 
    2736 > show #!2 models
    2737 
    2738 > hide #!2 models
    2739 
    2740 > view matrix models
    2741 > #3,-0.95684,0.050533,-0.28618,590.35,0.031324,-0.9611,-0.27443,581.63,-0.28892,-0.27155,0.91803,167.76
    2742 
    2743 > view matrix models
    2744 > #3,-0.95684,0.050533,-0.28618,569.34,0.031324,-0.9611,-0.27443,545.91,-0.28892,-0.27155,0.91803,122.47
    2745 
    2746 > ui mousemode right "rotate selected models"
    2747 
    2748 > view matrix models
    2749 > #3,-0.98737,-0.085662,-0.13329,574.09,0.10658,-0.98156,-0.1587,500.82,-0.11723,-0.1709,0.97829,33.411
    2750 
    2751 > ui mousemode right "translate selected models"
    2752 
    2753 > view matrix models
    2754 > #3,-0.98737,-0.085662,-0.13329,573.07,0.10658,-0.98156,-0.1587,508.71,-0.11723,-0.1709,0.97829,49.178
    2755 
    2756 > fitmap #3 inMap #1
    2757 
    2758 Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc (#1)
    2759 using 218966 atoms 
    2760 average map value = 0.1316, steps = 724 
    2761 shifted from previous position = 3.53 
    2762 rotated from previous position = 39.4 degrees 
    2763 atoms outside contour = 183320, contour level = 0.25215 
    2764  
    2765 Position of 6sgc (#3) relative to cryosparc_P346_J194_003_volume_map.mrc (#1)
    2766 coordinates: 
    2767 Matrix rotation and translation 
    2768 -0.98066245 -0.14578975 -0.13056231 590.90929382 
    2769 0.06115674 -0.86200822 0.50319150 304.88736380 
    2770 -0.18590595 0.48547624 0.85425511 -82.50217123 
    2771 Axis -0.08241564 0.25747188 0.96276471 
    2772 Axis point 283.03227912 179.89992220 0.00000000 
    2773 Rotation angle (degrees) 173.83021276 
    2774 Shift along axis -49.63042116 
    2775  
    2776 
    2777 > show #!2 models
    2778 
    2779 > matchmaker #3 to #1
    2780 
    2781 No 'to' model specified 
    2782 
    2783 > matchmaker #3 to #2
    2784 
    2785 Computing secondary structure 
    2786 [Repeated 1 time(s)]  Parameters 
    2787 --- 
    2788 Chain pairing | bb 
    2789 Alignment algorithm | Needleman-Wunsch 
    2790 Similarity matrix | BLOSUM-62 
    2791 SS fraction | 0.3 
    2792 Gap open (HH/SS/other) | 18/18/6 
    2793 Gap extend | 1 
    2794 SS matrix |  |  | H | S | O 
    2795 ---|---|---|--- 
    2796 H | 6 | -9 | -6 
    2797 S |  | 6 | -6 
    2798 O |  |  | 4 
    2799 Iteration cutoff | 2 
    2800  
    2801 Matchmaker 6sgc, chain 54 (#2) with 6sgc, chain 54 (#3), sequence alignment
    2802 score = 21821.5 
    2803 RMSD between 3603 pruned atom pairs is 0.000 angstroms; (across all 3603
    2804 pairs: 0.000) 
    2805  
    2806 
    2807 > clipper associate #1 toModel #2
    2808 
    2809 Opened cryosparc_P346_J194_003_volume_map.mrc as #1.1.1.1, grid size
    2810 384,384,384, pixel 1.19, shown at level 0.326, step 1, values float32 
    2811 6sgc title: 
    2812 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    2813  
    2814 Chain information for 6sgc 
    2815 --- 
    2816 Chain | Description | UniProt 
    2817 1.2/23 1.2/33 | tRNA (Lys3) |   
    2818 1.2/54 | 28S ribosomal RNA |   
    2819 1.2/74 | 5S ribosomal RNA |   
    2820 1.2/84 | 5.8S ribosomal RNA |   
    2821 1.2/A1 | 18S ribosomal RNA |   
    2822 1.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    2823 1.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    2824 1.2/B1 | uS2 |   
    2825 1.2/B2 | uL3 | G1TL06_RABIT 2-403 
    2826 1.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    2827 1.2/C2 | uL4 |   
    2828 1.2/D1 | uS5 |   
    2829 1.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    2830 1.2/E1 | uS5 | G1TNM3_RABIT 1-243 
    2831 1.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    2832 1.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    2833 1.2/F2 | uL30 | G1TUB1_RABIT 1-247 
    2834 1.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    2835 1.2/G2 | eL8 |   
    2836 1.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    2837 1.2/H2 | uL6 | G1TX33_RABIT 1-192 
    2838 1.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    2839 1.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    2840 1.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    2841 1.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    2842 1.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    2843 1.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    2844 1.2/L2 | eL13 |   
    2845 1.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    2846 1.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    2847 1.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    2848 1.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    2849 1.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    2850 1.2/O2 | uL13 |   
    2851 1.2/P1 | uS11 |   
    2852 1.2/P2 | uL22 | G1TVT6_RABIT 1-184 
    2853 1.2/Q1 | uS19 | G1U0Q2_RABIT 1-145 
    2854 1.2/Q2 | eL18 |   
    2855 1.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    2856 1.2/R2 | eL19 |   
    2857 1.2/S1 | eS17 | G1TU13_RABIT 1-135 
    2858 1.2/S2 | eL20 |   
    2859 1.2/T1 | eS13 | G1TPG3_RABIT 1-152 
    2860 1.2/T2 | eL21 | G1SHQ2_RABIT 1-160 
    2861 1.2/U1 | eS19 | G1TN62_RABIT 1-145 
    2862 1.2/U2 | eL22 |   
    2863 1.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    2864 1.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    2865 1.2/W1 | eS21 |   
    2866 1.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    2867 1.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    2868 1.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    2869 1.2/XX | poly-lysine nascent chain |   
    2870 1.2/Y1 | uS12 |   
    2871 1.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    2872 1.2/Z1 | eS24 |   
    2873 1.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    2874 1.2/a1 | eS25 | G1TDB3_RABIT 1-125 
    2875 1.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    2876 1.2/b1 | eS26 |   
    2877 1.2/b2 | eL29 |   
    2878 1.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    2879 1.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    2880 1.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    2881 1.2/d2 | eL31 | G1SHG0_RABIT 1-125 
    2882 1.2/e1 | uS14 | G1U7M4_RABIT 1-56 
    2883 1.2/e2 | eL32 | G1U437_RABIT 1-135 
    2884 1.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    2885 1.2/f2 | eL33 | G1SF08_RABIT 1-110 
    2886 1.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    2887 1.2/g2 | eL34 | G1U945_RABIT 1-116 
    2888 1.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    2889 1.2/h2 | uL29 | G1SIT5_RABIT 1-123 
    2890 1.2/i1 | polyA mRNA |   
    2891 1.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    2892 1.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    2893 1.2/k2 | eL38 | G1U001_RABIT 1-70 
    2894 1.2/l2 | eL39 | G1TTN1_RABIT 1-51 
    2895 1.2/m2 | eL40 |   
    2896 1.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    2897 1.2/o2 | eL42 | G1U344_RABIT 1-106 
    2898 1.2/p2 | eL43 | G1SY53_RABIT 1-92 
    2899 1.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    2900 1.2/s2 | uL10 |   
    2901 1.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    2902  
    2903 Non-standard residues in 6sgc #1.2 
    2904 --- 
    2905 MG — magnesium ion 
    2906 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    2907 ZN — zinc ion 
    2908  
    2909 
    2910 > hide sel atoms
    2911 
    2912 > hide sel cartoons
    2913 
    2914 > select #1/XX,23
    2915 
    2916 1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected 
    2917 
    2918 > select #3/XX,23
    2919 
    2920 1736 atoms, 1924 bonds, 72 pseudobonds, 92 residues, 2 models selected 
    2921 
    2922 > show sel cartoons
    2923 
    2924 > vop #1 style surface
    2925 
    2926 > transparency #1 50
    2927 
    2928 > view matrix models
    2929 > #3,-0.9823,-0.13687,-0.12789,629.65,0.037515,-0.81264,0.58155,222.2,-0.18353,0.56646,0.80339,-63.905
    2930 
    2931 > select add #3
    2932 
    2933 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    2934 selected 
    2935 
    2936 > select subtract #3
    2937 
    2938 Nothing selected 
    2939 
    2940 > ui mousemode right translate
    2941 
    2942 > ui mousemode right zoom
    2943 
    2944 > select #3/23
    2945 
    2946 1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected 
    2947 
    2948 > view sel
    2949 
    2950 > select #3/xx
    2951 
    2952 Nothing selected 
    2953 
    2954 > view sel
    2955 
    2956 No objects specified. 
    2957 
    2958 > select #3/XX
    2959 
    2960 100 atoms, 99 bonds, 16 residues, 1 model selected 
    2961 
    2962 > view sel
    2963 
    2964 > hide #!1.2 models
    2965 
    2966 > volume #1.1.1.1 level 0.09475
    2967 
    2968 > volume #1.1.1.1 level 0.1824
    2969 
    2970 > show sel atoms
    2971 
    2972 [Repeated 1 time(s)]
    2973 
    2974 > hide sel atoms
    2975 
    2976 > show sel atoms
    2977 
    2978 > style sel stick
    2979 
    2980 Changed 100 atom styles 
    2981 
    2982 > style sel stick
    2983 
    2984 Changed 100 atom styles 
    2985 
    2986 > hide sel atoms
    2987 
    2988 > select #3/23
    2989 
    2990 1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected 
    2991 
    2992 > show sel atoms
    2993 
    2994 > style sel stick
    2995 
    2996 Changed 1636 atom styles 
    2997 
    2998 > volume #1.1.1.1 level 0.1906
    2999 
    3000 > volume #1.1.1.1 level 0.1842
    3001 
    3002 > volume #1.1.1.1 level 0.2934
    3003 
    3004 > save "/Users/roan.groh/Documents/OneDrive -
    3005 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/tRNA_coding.cxs"
    3006 
    3007 ——— End of log from Wed Jul 16 16:56:30 2025 ———
    3008 
    3009 opened ChimeraX session 
    3010 
    3011 > open 6sgc
    3012 
    3013 6sgc title: 
    3014 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    3015  
    3016 Chain information for 6sgc #2 
    3017 --- 
    3018 Chain | Description | UniProt 
    3019 23 33 | tRNA (Lys3) |   
    3020 54 | 28S ribosomal RNA |   
    3021 74 | 5S ribosomal RNA |   
    3022 84 | 5.8S ribosomal RNA |   
    3023 A1 | 18S ribosomal RNA |   
    3024 A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    3025 B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    3026 B1 | uS2 |   
    3027 B2 | uL3 | G1TL06_RABIT 2-403 
    3028 C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    3029 C2 | uL4 |   
    3030 D1 | uS5 |   
    3031 D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    3032 E1 | uS5 | G1TNM3_RABIT 1-243 
    3033 E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    3034 F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    3035 F2 | uL30 | G1TUB1_RABIT 1-247 
    3036 G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    3037 G2 | eL8 |   
    3038 H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    3039 H2 | uL6 | G1TX33_RABIT 1-192 
    3040 I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    3041 I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    3042 J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    3043 J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    3044 K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    3045 L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    3046 L2 | eL13 |   
    3047 M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    3048 M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    3049 N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    3050 N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    3051 O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    3052 O2 | uL13 |   
    3053 P1 | uS11 |   
    3054 P2 | uL22 | G1TVT6_RABIT 1-184 
    3055 Q1 | uS19 | G1U0Q2_RABIT 1-145 
    3056 Q2 | eL18 |   
    3057 R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    3058 R2 | eL19 |   
    3059 S1 | eS17 | G1TU13_RABIT 1-135 
    3060 S2 | eL20 |   
    3061 T1 | eS13 | G1TPG3_RABIT 1-152 
    3062 T2 | eL21 | G1SHQ2_RABIT 1-160 
    3063 U1 | eS19 | G1TN62_RABIT 1-145 
    3064 U2 | eL22 |   
    3065 V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    3066 V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    3067 W1 | eS21 |   
    3068 W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    3069 X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    3070 X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    3071 XX | poly-lysine nascent chain |   
    3072 Y1 | uS12 |   
    3073 Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    3074 Z1 | eS24 |   
    3075 Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    3076 a1 | eS25 | G1TDB3_RABIT 1-125 
    3077 a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    3078 b1 | eS26 |   
    3079 b2 | eL29 |   
    3080 c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    3081 c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    3082 d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    3083 d2 | eL31 | G1SHG0_RABIT 1-125 
    3084 e1 | uS14 | G1U7M4_RABIT 1-56 
    3085 e2 | eL32 | G1U437_RABIT 1-135 
    3086 f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    3087 f2 | eL33 | G1SF08_RABIT 1-110 
    3088 g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    3089 g2 | eL34 | G1U945_RABIT 1-116 
    3090 h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    3091 h2 | uL29 | G1SIT5_RABIT 1-123 
    3092 i1 | polyA mRNA |   
    3093 i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    3094 j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    3095 k2 | eL38 | G1U001_RABIT 1-70 
    3096 l2 | eL39 | G1TTN1_RABIT 1-51 
    3097 m2 | eL40 |   
    3098 n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    3099 o2 | eL42 | G1U344_RABIT 1-106 
    3100 p2 | eL43 | G1SY53_RABIT 1-92 
    3101 r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    3102 s2 | uL10 |   
    3103 t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    3104  
    3105 Non-standard residues in 6sgc #2 
    3106 --- 
    3107 MG — magnesium ion 
    3108 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    3109 ZN — zinc ion 
    3110  
    3111 
    3112 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    3113 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
    3114 > Refine_tRNA/cryosparc_P618_J54_003_volume_map.mrc
    3115 
    3116 Opened cryosparc_P618_J54_003_volume_map.mrc as #4, grid size 384,384,384,
    3117 pixel 1.19, shown at level 0.29, step 2, values float32 
    3118 
    3119 > volume #4 step 1
    3120 
    3121 > select add #3
    3122 
    3123 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    3124 selected 
    3125 
    3126 > select subtract #3
    3127 
    3128 Nothing selected 
    3129 
    3130 > hide #!3 models
    3131 
    3132 > hide #!2 models
    3133 
    3134 > show #!2 models
    3135 
    3136 > select add #2
    3137 
    3138 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    3139 selected 
    3140 
    3141 > hide sel atoms
    3142 
    3143 > show sel cartoons
    3144 
    3145 > ui mousemode right "rotate selected models"
    3146 
    3147 > view matrix models
    3148 > #2,-0.81877,0.18205,0.5445,254.6,0.57124,0.16331,0.80438,-124.57,0.05751,0.96963,-0.23771,47.766
    3149 
    3150 > view matrix models
    3151 > #2,-0.99925,0.027104,0.027539,488.09,-0.0039227,-0.78019,0.62553,342.85,0.03844,0.62496,0.77971,-129.5
    3152 
    3153 > ui mousemode right "translate selected models"
    3154 
    3155 > view matrix models
    3156 > #2,-0.99925,0.027104,0.027539,531.74,-0.0039227,-0.78019,0.62553,299.63,0.03844,0.62496,0.77971,-123.01
    3157 
    3158 > view matrix models
    3159 > #2,-0.99925,0.027104,0.027539,500.7,-0.0039227,-0.78019,0.62553,258.34,0.03844,0.62496,0.77971,-158.51
    3160 
    3161 > fitmap #2 inMap #4
    3162 
    3163 Fit molecule 6sgc (#2) to map cryosparc_P618_J54_003_volume_map.mrc (#4) using
    3164 218966 atoms 
    3165 average map value = 0.2332, steps = 208 
    3166 shifted from previous position = 10.1 
    3167 rotated from previous position = 14.2 degrees 
    3168 atoms outside contour = 145921, contour level = 0.28985 
    3169  
    3170 Position of 6sgc (#2) relative to cryosparc_P618_J54_003_volume_map.mrc (#4)
    3171 coordinates: 
    3172 Matrix rotation and translation 
    3173 -0.97989020 -0.11868533 -0.16040260 588.93884983 
    3174 0.00560370 -0.81992322 0.57244608 289.42161497 
    3175 -0.19945877 0.56003545 0.80409980 -88.70086500 
    3176 Axis -0.09483113 0.29843296 0.94970776 
    3177 Axis point 284.77379625 168.71493739 0.00000000 
    3178 Rotation angle (degrees) 176.24814645 
    3179 Shift along axis -53.71668938 
    3180  
    3181 
    3182 > show #!3 models
    3183 
    3184 > hide #!3 models
    3185 
    3186 > show #!3 models
    3187 
    3188 > hide #!3 models
    3189 
    3190 > select subtract #2
    3191 
    3192 Nothing selected 
    3193 
    3194 > clipper associate #4 toModel #2
    3195 
    3196 Opened cryosparc_P618_J54_003_volume_map.mrc as #2.1.1.1, grid size
    3197 384,384,384, pixel 1.19, shown at level 0.402, step 1, values float32 
    3198 6sgc title: 
    3199 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    3200  
    3201 Chain information for 6sgc 
    3202 --- 
    3203 Chain | Description | UniProt 
    3204 2.2/23 2.2/33 | tRNA (Lys3) |   
    3205 2.2/54 | 28S ribosomal RNA |   
    3206 2.2/74 | 5S ribosomal RNA |   
    3207 2.2/84 | 5.8S ribosomal RNA |   
    3208 2.2/A1 | 18S ribosomal RNA |   
    3209 2.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    3210 2.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    3211 2.2/B1 | uS2 |   
    3212 2.2/B2 | uL3 | G1TL06_RABIT 2-403 
    3213 2.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    3214 2.2/C2 | uL4 |   
    3215 2.2/D1 | uS5 |   
    3216 2.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    3217 2.2/E1 | uS5 | G1TNM3_RABIT 1-243 
    3218 2.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    3219 2.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    3220 2.2/F2 | uL30 | G1TUB1_RABIT 1-247 
    3221 2.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    3222 2.2/G2 | eL8 |   
    3223 2.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    3224 2.2/H2 | uL6 | G1TX33_RABIT 1-192 
    3225 2.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    3226 2.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    3227 2.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    3228 2.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    3229 2.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    3230 2.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    3231 2.2/L2 | eL13 |   
    3232 2.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    3233 2.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    3234 2.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    3235 2.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    3236 2.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    3237 2.2/O2 | uL13 |   
    3238 2.2/P1 | uS11 |   
    3239 2.2/P2 | uL22 | G1TVT6_RABIT 1-184 
    3240 2.2/Q1 | uS19 | G1U0Q2_RABIT 1-145 
    3241 2.2/Q2 | eL18 |   
    3242 2.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    3243 2.2/R2 | eL19 |   
    3244 2.2/S1 | eS17 | G1TU13_RABIT 1-135 
    3245 2.2/S2 | eL20 |   
    3246 2.2/T1 | eS13 | G1TPG3_RABIT 1-152 
    3247 2.2/T2 | eL21 | G1SHQ2_RABIT 1-160 
    3248 2.2/U1 | eS19 | G1TN62_RABIT 1-145 
    3249 2.2/U2 | eL22 |   
    3250 2.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    3251 2.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    3252 2.2/W1 | eS21 |   
    3253 2.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    3254 2.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    3255 2.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    3256 2.2/XX | poly-lysine nascent chain |   
    3257 2.2/Y1 | uS12 |   
    3258 2.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    3259 2.2/Z1 | eS24 |   
    3260 2.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    3261 2.2/a1 | eS25 | G1TDB3_RABIT 1-125 
    3262 2.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    3263 2.2/b1 | eS26 |   
    3264 2.2/b2 | eL29 |   
    3265 2.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    3266 2.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    3267 2.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    3268 2.2/d2 | eL31 | G1SHG0_RABIT 1-125 
    3269 2.2/e1 | uS14 | G1U7M4_RABIT 1-56 
    3270 2.2/e2 | eL32 | G1U437_RABIT 1-135 
    3271 2.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    3272 2.2/f2 | eL33 | G1SF08_RABIT 1-110 
    3273 2.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    3274 2.2/g2 | eL34 | G1U945_RABIT 1-116 
    3275 2.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    3276 2.2/h2 | uL29 | G1SIT5_RABIT 1-123 
    3277 2.2/i1 | polyA mRNA |   
    3278 2.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    3279 2.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    3280 2.2/k2 | eL38 | G1U001_RABIT 1-70 
    3281 2.2/l2 | eL39 | G1TTN1_RABIT 1-51 
    3282 2.2/m2 | eL40 |   
    3283 2.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    3284 2.2/o2 | eL42 | G1U344_RABIT 1-106 
    3285 2.2/p2 | eL43 | G1SY53_RABIT 1-92 
    3286 2.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    3287 2.2/s2 | uL10 |   
    3288 2.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    3289  
    3290 Non-standard residues in 6sgc #2.2 
    3291 --- 
    3292 MG — magnesium ion 
    3293 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    3294 ZN — zinc ion 
    3295  
    3296 
    3297 > show #!3 models
    3298 
    3299 > hide #!3 models
    3300 
    3301 > vop #2 style surface
    3302 
    3303 > transparency #2 50
    3304 
    3305 > volume #2.1.1.1 level 0.1905
    3306 
    3307 > show #!3 models
    3308 
    3309 > hide #!2.2 models
    3310 
    3311 > volume #2.1.1.1 level 0.3129
    3312 
    3313 > hide #!1 models
    3314 
    3315 > volume #2.1.1.1 level 0.2558
    3316 
    3317 > show #!1 models
    3318 
    3319 > hide #!2 models
    3320 
    3321 > show #!2 models
    3322 
    3323 > hide #!1 models
    3324 
    3325 > select add #2.2
    3326 
    3327 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    3328 selected 
    3329 
    3330 > select subtract #2.2
    3331 
    3332 Nothing selected 
    3333 
    3334 > select add #3
    3335 
    3336 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    3337 selected 
    3338 
    3339 > view matrix models
    3340 > #3,-0.9823,-0.13687,-0.12789,587.59,0.037515,-0.81264,0.58155,274.91,-0.18353,0.56646,0.80339,-95.128
    3341 
    3342 > view matrix models
    3343 > #3,-0.9823,-0.13687,-0.12789,588.14,0.037515,-0.81264,0.58155,275.91,-0.18353,0.56646,0.80339,-92.203
    3344 
    3345 > view matrix models
    3346 > #3,-0.9823,-0.13687,-0.12789,587.24,0.037515,-0.81264,0.58155,277.52,-0.18353,0.56646,0.80339,-93.442
    3347 
    3348 > view matrix models
    3349 > #3,-0.9823,-0.13687,-0.12789,587.68,0.037515,-0.81264,0.58155,277.73,-0.18353,0.56646,0.80339,-93.749
    3350 
    3351 > view matrix models
    3352 > #3,-0.9823,-0.13687,-0.12789,587.75,0.037515,-0.81264,0.58155,277.72,-0.18353,0.56646,0.80339,-93.851
    3353 
    3354 > volume #2.1.1.1 level 0.3499
    3355 
    3356 > open from emdb:10181
    3357 
    3358 'from' has no suffix 
    3359 
    3360 > open emdb:10181
    3361 
    3362 Summary of feedback from opening 10181 fetched from emdb 
    3363 --- 
    3364 notes | Fetching compressed map 10181 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10181/map/emd_10181.map.gz 
    3365 Fetching map header 10181 from
    3366 ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10181/header/emd-10181.xml 
    3367  
    3368 Opened emdb 10181 as #4, grid size 512,512,512, pixel 1.09, shown at level
    3369 0.05, step 2, values float32, fit PDB 6sgc 
    3370 
    3371 > hide #!2 models
    3372 
    3373 > select subtract #3
    3374 
    3375 Nothing selected 
    3376 
    3377 > hide #!3 models
    3378 
    3379 > volume #4 step 1
    3380 
    3381 > open 6sgc
    3382 
    3383 6sgc title: 
    3384 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    3385  
    3386 Chain information for 6sgc #5 
    3387 --- 
    3388 Chain | Description | UniProt 
    3389 23 33 | tRNA (Lys3) |   
    3390 54 | 28S ribosomal RNA |   
    3391 74 | 5S ribosomal RNA |   
    3392 84 | 5.8S ribosomal RNA |   
    3393 A1 | 18S ribosomal RNA |   
    3394 A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    3395 B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    3396 B1 | uS2 |   
    3397 B2 | uL3 | G1TL06_RABIT 2-403 
    3398 C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    3399 C2 | uL4 |   
    3400 D1 | uS5 |   
    3401 D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    3402 E1 | uS5 | G1TNM3_RABIT 1-243 
    3403 E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    3404 F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    3405 F2 | uL30 | G1TUB1_RABIT 1-247 
    3406 G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    3407 G2 | eL8 |   
    3408 H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    3409 H2 | uL6 | G1TX33_RABIT 1-192 
    3410 I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    3411 I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    3412 J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    3413 J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    3414 K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    3415 L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    3416 L2 | eL13 |   
    3417 M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    3418 M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    3419 N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    3420 N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    3421 O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    3422 O2 | uL13 |   
    3423 P1 | uS11 |   
    3424 P2 | uL22 | G1TVT6_RABIT 1-184 
    3425 Q1 | uS19 | G1U0Q2_RABIT 1-145 
    3426 Q2 | eL18 |   
    3427 R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    3428 R2 | eL19 |   
    3429 S1 | eS17 | G1TU13_RABIT 1-135 
    3430 S2 | eL20 |   
    3431 T1 | eS13 | G1TPG3_RABIT 1-152 
    3432 T2 | eL21 | G1SHQ2_RABIT 1-160 
    3433 U1 | eS19 | G1TN62_RABIT 1-145 
    3434 U2 | eL22 |   
    3435 V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    3436 V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    3437 W1 | eS21 |   
    3438 W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    3439 X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    3440 X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    3441 XX | poly-lysine nascent chain |   
    3442 Y1 | uS12 |   
    3443 Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    3444 Z1 | eS24 |   
    3445 Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    3446 a1 | eS25 | G1TDB3_RABIT 1-125 
    3447 a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    3448 b1 | eS26 |   
    3449 b2 | eL29 |   
    3450 c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    3451 c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    3452 d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    3453 d2 | eL31 | G1SHG0_RABIT 1-125 
    3454 e1 | uS14 | G1U7M4_RABIT 1-56 
    3455 e2 | eL32 | G1U437_RABIT 1-135 
    3456 f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    3457 f2 | eL33 | G1SF08_RABIT 1-110 
    3458 g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    3459 g2 | eL34 | G1U945_RABIT 1-116 
    3460 h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    3461 h2 | uL29 | G1SIT5_RABIT 1-123 
    3462 i1 | polyA mRNA |   
    3463 i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    3464 j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    3465 k2 | eL38 | G1U001_RABIT 1-70 
    3466 l2 | eL39 | G1TTN1_RABIT 1-51 
    3467 m2 | eL40 |   
    3468 n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    3469 o2 | eL42 | G1U344_RABIT 1-106 
    3470 p2 | eL43 | G1SY53_RABIT 1-92 
    3471 r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    3472 s2 | uL10 |   
    3473 t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    3474  
    3475 Non-standard residues in 6sgc #5 
    3476 --- 
    3477 MG — magnesium ion 
    3478 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    3479 ZN — zinc ion 
    3480  
    3481 
    3482 > hide #!5 atoms
    3483 
    3484 > show #!5 cartoons
    3485 
    3486 > clipper associate #4 toModel #5
    3487 
    3488 Opened emdb 10181 as #4.1.1.1, grid size 512,512,512, pixel 1.09, shown at
    3489 level 0.0864, step 1, values float32 
    3490 6sgc title: 
    3491 Rabbit 80S ribosome stalled on a poly(A) tail [more info...] 
    3492  
    3493 Chain information for 6sgc 
    3494 --- 
    3495 Chain | Description | UniProt 
    3496 4.2/23 4.2/33 | tRNA (Lys3) |   
    3497 4.2/54 | 28S ribosomal RNA |   
    3498 4.2/74 | 5S ribosomal RNA |   
    3499 4.2/84 | 5.8S ribosomal RNA |   
    3500 4.2/A1 | 18S ribosomal RNA |   
    3501 4.2/A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    3502 4.2/B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    3503 4.2/B1 | uS2 |   
    3504 4.2/B2 | uL3 | G1TL06_RABIT 2-403 
    3505 4.2/C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    3506 4.2/C2 | uL4 |   
    3507 4.2/D1 | uS5 |   
    3508 4.2/D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    3509 4.2/E1 | uS5 | G1TNM3_RABIT 1-243 
    3510 4.2/E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    3511 4.2/F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    3512 4.2/F2 | uL30 | G1TUB1_RABIT 1-247 
    3513 4.2/G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    3514 4.2/G2 | eL8 |   
    3515 4.2/H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    3516 4.2/H2 | uL6 | G1TX33_RABIT 1-192 
    3517 4.2/I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    3518 4.2/I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    3519 4.2/J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    3520 4.2/J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    3521 4.2/K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    3522 4.2/L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    3523 4.2/L2 | eL13 |   
    3524 4.2/M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    3525 4.2/M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    3526 4.2/N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    3527 4.2/N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    3528 4.2/O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    3529 4.2/O2 | uL13 |   
    3530 4.2/P1 | uS11 |   
    3531 4.2/P2 | uL22 | G1TVT6_RABIT 1-184 
    3532 4.2/Q1 | uS19 | G1U0Q2_RABIT 1-145 
    3533 4.2/Q2 | eL18 |   
    3534 4.2/R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    3535 4.2/R2 | eL19 |   
    3536 4.2/S1 | eS17 | G1TU13_RABIT 1-135 
    3537 4.2/S2 | eL20 |   
    3538 4.2/T1 | eS13 | G1TPG3_RABIT 1-152 
    3539 4.2/T2 | eL21 | G1SHQ2_RABIT 1-160 
    3540 4.2/U1 | eS19 | G1TN62_RABIT 1-145 
    3541 4.2/U2 | eL22 |   
    3542 4.2/V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    3543 4.2/V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    3544 4.2/W1 | eS21 |   
    3545 4.2/W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    3546 4.2/X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    3547 4.2/X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    3548 4.2/XX | poly-lysine nascent chain |   
    3549 4.2/Y1 | uS12 |   
    3550 4.2/Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    3551 4.2/Z1 | eS24 |   
    3552 4.2/Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    3553 4.2/a1 | eS25 | G1TDB3_RABIT 1-125 
    3554 4.2/a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    3555 4.2/b1 | eS26 |   
    3556 4.2/b2 | eL29 |   
    3557 4.2/c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    3558 4.2/c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    3559 4.2/d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    3560 4.2/d2 | eL31 | G1SHG0_RABIT 1-125 
    3561 4.2/e1 | uS14 | G1U7M4_RABIT 1-56 
    3562 4.2/e2 | eL32 | G1U437_RABIT 1-135 
    3563 4.2/f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    3564 4.2/f2 | eL33 | G1SF08_RABIT 1-110 
    3565 4.2/g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    3566 4.2/g2 | eL34 | G1U945_RABIT 1-116 
    3567 4.2/h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    3568 4.2/h2 | uL29 | G1SIT5_RABIT 1-123 
    3569 4.2/i1 | polyA mRNA |   
    3570 4.2/i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    3571 4.2/j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    3572 4.2/k2 | eL38 | G1U001_RABIT 1-70 
    3573 4.2/l2 | eL39 | G1TTN1_RABIT 1-51 
    3574 4.2/m2 | eL40 |   
    3575 4.2/n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    3576 4.2/o2 | eL42 | G1U344_RABIT 1-106 
    3577 4.2/p2 | eL43 | G1SY53_RABIT 1-92 
    3578 4.2/r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    3579 4.2/s2 | uL10 |   
    3580 4.2/t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    3581  
    3582 Non-standard residues in 6sgc #4.2 
    3583 --- 
    3584 MG — magnesium ion 
    3585 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    3586 ZN — zinc ion 
    3587  
    3588 
    3589 > vop #4 style surface
    3590 
    3591 > transparency #4 50
    3592 
    3593 > hide #!4.2 models
    3594 
    3595 > hide #!4 models
    3596 
    3597 > show #!1 models
    3598 
    3599 > show #!3 models
    3600 
    3601 > view #3 clip false
    3602 
    3603 > show #!2 models
    3604 
    3605 > hide #!1 models
    3606 
    3607 > show #!1.2 models
    3608 
    3609 > hide #!1.2 models
    3610 
    3611 > hide #!1 models
    3612 
    3613 > hide #!3 models
    3614 
    3615 > volume #2.1.1.1 color #00f900
    3616 
    3617 > volume #2.1.1.1 color #00f90080
    3618 
    3619 > volume #2.1.1.1 color #76d6ff
    3620 
    3621 > volume #2.1.1.1 color #76d6ff7e
    3622 
    3623 > volume #2.1.1.1 level 0.4425
    3624 
    3625 > volume #2.1.1.1 level 0.4209
    3626 
    3627 > show #!1 models
    3628 
    3629 > volume #1.1.1.1 color #ffd479
    3630 
    3631 > volume #1.1.1.1 color #ffd47980
    3632 
    3633 > hide #!2 models
    3634 
    3635 > rename #2 "Germ - Data manager (6sgc)"
    3636 
    3637 > rename #1 "Dehyd - Data manager (6sgc)"
    3638 
    3639 > volume #1.1.1.1 level 0.3165
    3640 
    3641 > open /Users/roan.groh/Downloads/cryosparc_P618_J123_003_volume_map.mrc
    3642 
    3643 Opened cryosparc_P618_J123_003_volume_map.mrc as #5, grid size 384,384,384,
    3644 pixel 1.19, shown at level 0.274, step 2, values float32 
    3645 
    3646 > hide #!1 models
    3647 
    3648 > volume #5 step 1
    3649 
    3650 > open /Users/roan.groh/Downloads/cryosparc_P346_J294_005_volume_map.mrc
    3651 
    3652 Opened cryosparc_P346_J294_005_volume_map.mrc as #6, grid size 384,384,384,
    3653 pixel 1.19, shown at level 0.181, step 2, values float32 
    3654 
    3655 > hide #!5 models
    3656 
    3657 > volume #6 step 1
    3658 
    3659 > show #!5 models
    3660 
    3661 > hide #!6 models
    3662 
    3663 > lighting full
    3664 
    3665 > hide #!5 models
    3666 
    3667 > show #!1 models
    3668 
    3669 > show #!3 models
    3670 
    3671 > volume #1.1.1.1 level 0.27
    3672 
    3673 > volume #1.1.1.1 level 0.2003
    3674 
    3675 > volume #2.1.1.1 level 0.4396
    3676 
    3677 > volume #1.1.1.1 level 0.2502
    3678 
    3679 > volume #1.1.1.1 level 0.3153
    3680 
    3681 > fitmap #3/23 inMap #1.1.1.1 moveWholeMolecules false
    3682 
    3683 Fit molecule 6sgc (#3) to map cryosparc_P346_J194_003_volume_map.mrc
    3684 (#1.1.1.1) using 1636 atoms 
    3685 average map value = 0.221, steps = 2000 
    3686 shifted from previous position = 15.6 
    3687 rotated from previous position = 27.1 degrees 
    3688 atoms outside contour = 1591, contour level = 0.31528 
    3689  
    3690 
    3691 > show #!3 models
    3692 
    3693 > volume #1.1.1.1 level 0.209
    3694 
    3695 > show #!1 models
    3696 
    3697 > select #3/23
    3698 
    3699 1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected 
    3700 
    3701 > ui mousemode right "move picked models"
    3702 
    3703 > ui mousemode right "translate selected models"
    3704 
    3705 > view matrix models
    3706 > #3,-0.9823,-0.13687,-0.12789,585.26,0.037515,-0.81264,0.58155,277.28,-0.18353,0.56646,0.80339,-92.021
    3707 
    3708 > view matrix models
    3709 > #3,-0.9823,-0.13687,-0.12789,585.12,0.037515,-0.81264,0.58155,277.52,-0.18353,0.56646,0.80339,-92.179
    3710 
    3711 > view matrix models
    3712 > #3,-0.9823,-0.13687,-0.12789,585.13,0.037515,-0.81264,0.58155,277.36,-0.18353,0.56646,0.80339,-91.634
    3713 
    3714 > view matrix models
    3715 > #3,-0.9823,-0.13687,-0.12789,586.96,0.037515,-0.81264,0.58155,276.15,-0.18353,0.56646,0.80339,-92.288
    3716 
    3717 > volume #1.1.1.1 level 0.2732
    3718 
    3719 > volume #1.1.1.1 level 0.2898
    3720 
    3721 > hide #!3 models
    3722 
    3723 > volume #1.1.1.1 level 0.3255
    3724 
    3725 > volume #1.1.1.1 level 0.3775
    3726 
    3727 > show #!3 models
    3728 
    3729 > volume #1.1.1.1 level 0.3157
    3730 
    3731 > ui tool show "Side View"
    3732 
    3733 > volume #1.1.1.1 level 0.362
    3734 
    3735 > hide #!3 models
    3736 
    3737 > show #!3 models
    3738 
    3739 > show #3
    3740 
    3741 > combine #3
    3742 
    3743 > vop copy #1.1.1.1
    3744 
    3745 Opened cryosparc_P346_J194_003_volume_map.mrc copy as #8, grid size
    3746 384,384,384, pixel 1.19, shown at step 1, values float32 
    3747 
    3748 > hide #!4.1 models
    3749 
    3750 > hide #!7 models
    3751 
    3752 > show #!7 models
    3753 
    3754 > hide #!8 models
    3755 
    3756 > hide #!7 models
    3757 
    3758 > hide #4.3 models
    3759 
    3760 > hide #!1 models
    3761 
    3762 > hide all
    3763 
    3764 > hide #!3 models
    3765 
    3766 > show #!7 models
    3767 
    3768 > show #!8 models
    3769 
    3770 > show #7 cartoons
    3771 
    3772 >
    3773 
    3774 Incomplete command: clipper 
    3775 
    3776 > clipper associate #8 toModel #7
    3777 
    3778 Opened cryosparc_P346_J194_003_volume_map.mrc copy as #7.1.1.1, grid size
    3779 384,384,384, pixel 1.19, shown at level 0.321, step 1, values float32 
    3780 
    3781 > volume #7.1.1.1 style surface
    3782 
    3783 > volume #7.1.1.1 color #00ffff2e
    3784 
    3785 > graphics silhouettes true
    3786 
    3787 > graphics silhouettes false
    3788 
    3789 > hide #!7 models
    3790 
    3791 > show #!7 models
    3792 
    3793 > fitmap #7.2 inMap #7.1.1.1
    3794 
    3795 Fit molecule copy of 6sgc (#7.2) to map cryosparc_P346_J194_003_volume_map.mrc
    3796 copy (#7.1.1.1) using 218966 atoms 
    3797 average map value = 0.4603, steps = 68 
    3798 shifted from previous position = 2.05 
    3799 rotated from previous position = 0.26 degrees 
    3800 atoms outside contour = 218565, contour level = 0.32099 
    3801  
    3802 Position of copy of 6sgc (#7.2) relative to
    3803 cryosparc_P346_J194_003_volume_map.mrc copy (#7.1.1.1) coordinates: 
    3804 Matrix rotation and translation 
    3805 0.99999709 0.00222344 -0.00093537 -0.87117785 
    3806 -0.00222702 0.99999010 -0.00385125 0.52470336 
    3807 0.00092680 0.00385332 0.99999215 -2.77644893 
    3808 Axis 0.84755359 -0.20485167 -0.48958013 
    3809 Axis point 0.00000000 655.62973529 161.86802583 
    3810 Rotation angle (degrees) 0.26042055 
    3811 Shift along axis 0.51343796 
    3812  
    3813 Must specify one map, got 0 
    3814 
    3815 > fitmap #7/23 inMap #7 moveWholeMolecules false
    3816 
    3817 Fit molecule copy of 6sgc (#7.2) to map cryosparc_P346_J194_003_volume_map.mrc
    3818 copy (#7.1.1.1) using 1636 atoms 
    3819 average map value = 0.2437, steps = 2000 
    3820 shifted from previous position = 17.4 
    3821 rotated from previous position = 24.6 degrees 
    3822 atoms outside contour = 1604, contour level = 0.32099 
    3823  
    3824 
    3825 > fitmap #7/i1 inMap #7 moveWholeMolecules false
    3826 
    3827 Fit molecule copy of 6sgc (#7.2) to map cryosparc_P346_J194_003_volume_map.mrc
    3828 copy (#7.1.1.1) using 220 atoms 
    3829 average map value = 0.4058, steps = 48 
    3830 shifted from previous position = 2.11 
    3831 rotated from previous position = 5.88 degrees 
    3832 atoms outside contour = 155, contour level = 0.32099 
    3833  
    3834 
    3835 > select #7/23
    3836 
    3837 1636 atoms, 1824 bonds, 72 pseudobonds, 76 residues, 2 models selected 
    3838 
    3839 > view matrix models
    3840 > #7.2,1,0.0022234,-0.00093537,0.84805,-0.002227,0.99999,-0.0038512,-0.88697,0.0009268,0.0038533,0.99999,-2.4048
    3841 
    3842 > undo
    3843 
    3844 > view matrix models
    3845 > #7.2,1,0.0022234,-0.00093537,-0.40992,-0.002227,0.99999,-0.0038512,0.12743,0.0009268,0.0038533,0.99999,-2.6681
    3846 
    3847 > view matrix models
    3848 > #7.2,1,0.0022234,-0.00093537,0.16347,-0.002227,0.99999,-0.0038512,-0.57566,0.0009268,0.0038533,0.99999,-2.4359
    3849 
    3850 > undo
    3851 
    3852 > hide #!7.1 models
    3853 
    3854 > show #!7.1 models
    3855 
    3856 > hide #!7.2 models
    3857 
    3858 > volume #7.1.1.1 level 0.2887
    3859 
    3860 > show #!7.2 models
    3861 
    3862 > vop copy #1.1.1.1
    3863 
    3864 Opened cryosparc_P346_J194_003_volume_map.mrc copy as #8, grid size
    3865 384,384,384, pixel 1.19, shown at step 1, values float32 
    3866 
    3867 > combine §3
    3868 
    3869 Expected a keyword 
    3870 
    3871 > hide #!7 models
    3872 
    3873 > select ~sel & ##selected
    3874 
    3875 217330 atoms, 233088 bonds, 5777 pseudobonds, 17875 residues, 4 models
    3876 selected 
    3877 
    3878 > combine #3
    3879 
    3880 > hide #!9 models
    3881 
    3882 > show #!9 models
    3883 
    3884 > show #9 cartoons
    3885 
    3886 > hide #!9 models
    3887 
    3888 > show #!9 models
    3889 
    3890 > hide #!8 models
    3891 
    3892 > log metadata #9
    3893 
    3894 No models had metadata
    3895 
    3896 > log chains #9
    3897 
    3898 Chain information for copy of 6sgc #9 
    3899 --- 
    3900 Chain | Description | UniProt 
    3901 23 33 | tRNA (Lys3) |   
    3902 54 | 28S ribosomal RNA |   
    3903 74 | 5S ribosomal RNA |   
    3904 84 | 5.8S ribosomal RNA |   
    3905 A1 | 18S ribosomal RNA |   
    3906 A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257 
    3907 B | Ribosomal protein | G1SKZ8_RABIT 1-217 
    3908 B1 | uS2 |   
    3909 B2 | uL3 | G1TL06_RABIT 2-403 
    3910 C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 
    3911 C2 | uL4 |   
    3912 D1 | uS5 |   
    3913 D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297 
    3914 E1 | uS5 | G1TNM3_RABIT 1-243 
    3915 E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 
    3916 F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263 
    3917 F2 | uL30 | G1TUB1_RABIT 1-247 
    3918 G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204 
    3919 G2 | eL8 |   
    3920 H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 
    3921 H2 | uL6 | G1TX33_RABIT 1-192 
    3922 I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194 
    3923 I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 
    3924 J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 
    3925 J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178 
    3926 K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 
    3927 L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165 
    3928 L2 | eL13 |   
    3929 M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158 
    3930 M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218 
    3931 N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 
    3932 N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204 
    3933 O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151 
    3934 O2 | uL13 |   
    3935 P1 | uS11 |   
    3936 P2 | uL22 | G1TVT6_RABIT 1-184 
    3937 Q1 | uS19 | G1U0Q2_RABIT 1-145 
    3938 Q2 | eL18 |   
    3939 R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146 
    3940 R2 | eL19 |   
    3941 S1 | eS17 | G1TU13_RABIT 1-135 
    3942 S2 | eL20 |   
    3943 T1 | eS13 | G1TPG3_RABIT 1-152 
    3944 T2 | eL21 | G1SHQ2_RABIT 1-160 
    3945 U1 | eS19 | G1TN62_RABIT 1-145 
    3946 U2 | eL22 |   
    3947 V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119 
    3948 V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140 
    3949 W1 | eS21 |   
    3950 W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157 
    3951 X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130 
    3952 X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156 
    3953 XX | poly-lysine nascent chain |   
    3954 Y1 | uS12 |   
    3955 Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145 
    3956 Z1 | eS24 |   
    3957 Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 
    3958 a1 | eS25 | G1TDB3_RABIT 1-125 
    3959 a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148 
    3960 b1 | eS26 |   
    3961 b2 | eL29 |   
    3962 c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 
    3963 c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115 
    3964 d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69 
    3965 d2 | eL31 | G1SHG0_RABIT 1-125 
    3966 e1 | uS14 | G1U7M4_RABIT 1-56 
    3967 e2 | eL32 | G1U437_RABIT 1-135 
    3968 f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132 
    3969 f2 | eL33 | G1SF08_RABIT 1-110 
    3970 g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156 
    3971 g2 | eL34 | G1U945_RABIT 1-116 
    3972 h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317 
    3973 h2 | uL29 | G1SIT5_RABIT 1-123 
    3974 i1 | polyA mRNA |   
    3975 i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 
    3976 j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97 
    3977 k2 | eL38 | G1U001_RABIT 1-70 
    3978 l2 | eL39 | G1TTN1_RABIT 1-51 
    3979 m2 | eL40 |   
    3980 n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 
    3981 o2 | eL42 | G1U344_RABIT 1-106 
    3982 p2 | eL43 | G1SY53_RABIT 1-92 
    3983 r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137 
    3984 s2 | uL10 |   
    3985 t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165 
    3986  
    3987 
    3988 > color #9 darkgrey
    3989 
    3990 > select #9/54,74,84,A1
    3991 
    3992 119522 atoms, 133395 bonds, 5630 pseudobonds, 5835 residues, 4 models selected 
    3993 
    3994 > color sel white
    3995 
    3996 > show #!8 models
    3997 
    3998 > hide #!9 models
    3999 
    4000 > color zone #9 ear #9 d 6
    4001 
    4002 Expected a keyword 
    4003 
    4004 > color zone #9 near #9 distance 6
    4005 
    4006 color zone: No surfaces specified. 
    4007 
    4008 > color zone #8 near #9 distance 6
    4009 
    4010 > color #8 white
    4011 
    4012 > graphics silhouettes true
    4013 
    4014 > color #8 ivory
    4015 
    4016 > color #8 floral white
    4017 
    4018 > select up
    4019 
    4020 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    4021 selected 
    4022 
    4023 > select up
    4024 
    4025 218966 atoms, 234912 bonds, 5849 pseudobonds, 17951 residues, 4 models
    4026 selected 
    4027 
    4028 > color #8 antique white
    4029 
    4030 > color zone #8 near #9 distance
    4031 
    4032 Missing "distance" keyword's argument 
    4033 
    4034 > color zone #8 near #9 distance 6
    4035 
    4036 > lighting full
    4037 
    4038 > lighting soft
    4039 
    4040 > volume #8 level 0.362
    4041 
    4042 > volume #8 level 0.3406
    4043 
    4044 > volume #8 level 0.3121
    4045 
    4046 > vop copy #8
    4047 
    4048 Opened cryosparc_P346_J194_003_volume_map.mrc copy as #10, grid size
    4049 384,384,384, pixel 1.19, shown at step 1, values float32 
    4050 
    4051 > color #8 #275c70
    4052 
    4053 > show #!8 models
    4054 
    4055 > hide #!8 models
    4056 
    4057 > show #!8 models
    4058 
    4059 > hide #!10 models
    4060 
    4061 > show #!10 models
    4062 
    4063 > select subtract #9
    4064 
    4065 Nothing selected 
    4066 
    4067 > open 8b2l
    4068 
    4069 Summary of feedback from opening 8b2l fetched from pdb 
    4070 --- 
    4071 warning | Atom H1 is not in the residue template for UNK /l3:1 
    4072  
    4073 8b2l title: 
    4074 Cryo-EM structure of the plant 80S ribosome [more info...] 
    4075  
    4076 Chain information for 8b2l #11 
    4077 --- 
    4078 Chain | Description | UniProt 
    4079 A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264 
    4080 A3 | 25S rRNA |   
    4081 B1 | mRNA |   
    4082 B3 | 5.8S rRNA |   
    4083 C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144 
    4084 C3 | 5S rRNA |   
    4085 D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149 
    4086 D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206 
    4087 E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143 
    4088 E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134 
    4089 F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261 
    4090 F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204 
    4091 G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83 
    4092 G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187 
    4093 H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133 
    4094 H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214 
    4095 I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107 
    4096 I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178 
    4097 J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127 
    4098 J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164 
    4099 K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86 
    4100 K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127 
    4101 L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65 
    4102 L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164 
    4103 M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62 
    4104 M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135 
    4105 N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156 
    4106 N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143 
    4107 O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191 
    4108 O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61 
    4109 P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224 
    4110 P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113 
    4111 Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329 
    4112 Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120 
    4113 R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122 
    4114 R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133 
    4115 S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150 
    4116 S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112 
    4117 T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142 
    4118 T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120 
    4119 U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152 
    4120 U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110 
    4121 V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56 
    4122 V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95 
    4123 W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151 
    4124 W2 i2 | tRNA |   
    4125 W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69 
    4126 X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159 
    4127 X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51 
    4128 Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152 
    4129 Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128 
    4130 Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336 
    4131 Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105 
    4132 a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248 
    4133 a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92 
    4134 b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197 
    4135 b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230 
    4136 c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280 
    4137 c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258 
    4138 d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210 
    4139 d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206 
    4140 e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130 
    4141 e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140 
    4142 f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150 
    4143 f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148 
    4144 g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221 
    4145 h1 | 18S rRNA |   
    4146 h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301 
    4147 j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175 
    4148 k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249 
    4149 k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154 
    4150 l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208 
    4151 l3 | nascent chain |   
    4152 m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146 
    4153 n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123 
    4154 o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260 
    4155 p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25 
    4156 q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242 
    4157 r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389 
    4158 s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405 
    4159 t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181 
    4160 u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194 
    4161  
    4162 Non-standard residues in 8b2l #11 
    4163 --- 
    4164 B8N —
    4165 (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
    4166 acid 
    4167 K — potassium ion 
    4168 MG — magnesium ion 
    4169 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    4170 SPM — spermine 
    4171 UY1 — 2'-O-methylpseudouridine-5'-monophosphate 
    4172 ZN — zinc ion 
    4173  
    4174 
    4175 > select add #11
    4176 
    4177 361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
    4178 selected 
    4179 
    4180 > show sel cartoons
    4181 
    4182 > show sel atoms
    4183 
    4184 > show sel cartoons
    4185 
    4186 > hide #!8 models
    4187 
    4188 > show #!8 models
    4189 
    4190 > hide #!10 models
    4191 
    4192 > hide #!7.1 models
    4193 
    4194 > hide #!7.2 models
    4195 
    4196 > hide #7.3 models
    4197 
    4198 > hide sel atoms
    4199 
    4200 > ui mousemode right "translate selected models"
    4201 
    4202 > ui mousemode right "rotate selected models"
    4203 
    4204 > view matrix models
    4205 > #11,0.60126,-0.076592,-0.79537,252.21,0.71674,-0.38832,0.57922,-33.46,-0.35322,-0.91834,-0.17859,457.44
    4206 
    4207 > hide #!8 models
    4208 
    4209 > view matrix models
    4210 > #11,0.056689,-0.99181,0.11448,338.95,-0.96828,-0.026667,0.24845,323.63,-0.24336,-0.12493,-0.96186,456.85
    4211 
    4212 > show #!8 models
    4213 
    4214 > ui mousemode right "translate selected models"
    4215 
    4216 > view matrix models
    4217 > #11,0.056689,-0.99181,0.11448,399.17,-0.96828,-0.026667,0.24845,320.3,-0.24336,-0.12493,-0.96186,453.26
    4218 
    4219 > fitmap #11 inMap #8
    4220 
    4221 Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
    4222 (#8) using 361205 atoms 
    4223 average map value = 0.06739, steps = 240 
    4224 shifted from previous position = 39.7 
    4225 rotated from previous position = 4.86 degrees 
    4226 atoms outside contour = 330015, contour level = 0.3121 
    4227  
    4228 Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
    4229 (#8) coordinates: 
    4230 Matrix rotation and translation 
    4231 0.06022402 -0.99764011 0.03297469 417.16316133 
    4232 -0.97223587 -0.05114300 0.22834591 352.74769363 
    4233 -0.22612061 -0.04581109 -0.97302151 469.44404474 
    4234 Axis -0.72514653 0.68530827 0.06719433 
    4235 Axis point 0.00000000 404.49814120 229.53471827 
    4236 Rotation angle (degrees) 169.10349249 
    4237 Shift along axis -29.21952756 
    4238  
    4239 
    4240 > ui mousemode right "rotate selected models"
    4241 
    4242 > view matrix models
    4243 > #11,0.051847,-0.98827,-0.14366,452.05,-0.99743,-0.058364,0.041531,395.9,-0.049428,0.14113,-0.98876,404.64
    4244 
    4245 > view matrix models
    4246 > #11,0.0016974,-0.99619,0.087193,418.5,-0.96519,-0.024437,-0.2604,442.84,0.26154,-0.083715,-0.96156,371.58
    4247 
    4248 > ui mousemode right "translate selected models"
    4249 
    4250 > view matrix models
    4251 > #11,0.0016974,-0.99619,0.087193,404.44,-0.96519,-0.024437,-0.2604,459.37,0.26154,-0.083715,-0.96156,387.72
    4252 
    4253 > fitmap #11 inMap #8
    4254 
    4255 Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
    4256 (#8) using 361205 atoms 
    4257 average map value = 0.1799, steps = 372 
    4258 shifted from previous position = 9.02 
    4259 rotated from previous position = 25.5 degrees 
    4260 atoms outside contour = 272505, contour level = 0.3121 
    4261  
    4262 Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
    4263 (#8) coordinates: 
    4264 Matrix rotation and translation 
    4265 -0.23335507 -0.95789171 -0.16729893 500.38333037 
    4266 -0.81858975 0.28637810 -0.49789401 417.93470463 
    4267 0.52483928 0.02076310 -0.85094810 295.49305506 
    4268 Axis 0.59203979 -0.79006603 0.15901122 
    4269 Axis point 363.94927998 0.00000000 261.72253033 
    4270 Rotation angle (degrees) 154.02202909 
    4271 Shift along axis 13.03753919 
    4272  
    4273 
    4274 > log metadata #11
    4275 
    4276 Metadata for 8b2l #11 
    4277 --- 
    4278 Title | Cryo-EM structure of the plant 80S ribosome 
    4279 Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y 
    4280 Non-standard residues | B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid 
    4281 K — potassium ion 
    4282 MG — magnesium ion 
    4283 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    4284 SPM — spermine 
    4285 UY1 — 2'-O-methylpseudouridine-5'-monophosphate 
    4286 ZN — zinc ion 
    4287 Sources (natural) | Nicotiana tabacum (common tobacco) 
    4288 Nicotiana tabacum 
    4289 CryoEM Map | EMDB 15806 — open map 
    4290 Experimental method | Electron microscopy 
    4291 Resolution | 2.20Å 
    4292  
    4293 > log chains #11
    4294 
    4295 Chain information for 8b2l #11 
    4296 --- 
    4297 Chain | Description | UniProt 
    4298 A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264 
    4299 A3 | 25S rRNA |   
    4300 B1 | mRNA |   
    4301 B3 | 5.8S rRNA |   
    4302 C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144 
    4303 C3 | 5S rRNA |   
    4304 D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149 
    4305 D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206 
    4306 E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143 
    4307 E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134 
    4308 F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261 
    4309 F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204 
    4310 G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83 
    4311 G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187 
    4312 H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133 
    4313 H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214 
    4314 I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107 
    4315 I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178 
    4316 J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127 
    4317 J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164 
    4318 K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86 
    4319 K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127 
    4320 L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65 
    4321 L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164 
    4322 M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62 
    4323 M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135 
    4324 N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156 
    4325 N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143 
    4326 O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191 
    4327 O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61 
    4328 P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224 
    4329 P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113 
    4330 Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329 
    4331 Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120 
    4332 R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122 
    4333 R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133 
    4334 S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150 
    4335 S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112 
    4336 T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142 
    4337 T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120 
    4338 U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152 
    4339 U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110 
    4340 V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56 
    4341 V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95 
    4342 W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151 
    4343 W2 i2 | tRNA |   
    4344 W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69 
    4345 X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159 
    4346 X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51 
    4347 Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152 
    4348 Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128 
    4349 Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336 
    4350 Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105 
    4351 a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248 
    4352 a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92 
    4353 b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197 
    4354 b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230 
    4355 c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280 
    4356 c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258 
    4357 d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210 
    4358 d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206 
    4359 e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130 
    4360 e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140 
    4361 f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150 
    4362 f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148 
    4363 g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221 
    4364 h1 | 18S rRNA |   
    4365 h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301 
    4366 j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175 
    4367 k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249 
    4368 k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154 
    4369 l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208 
    4370 l3 | nascent chain |   
    4371 m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146 
    4372 n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123 
    4373 o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260 
    4374 p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25 
    4375 q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242 
    4376 r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389 
    4377 s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405 
    4378 t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181 
    4379 u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194 
    4380  
    4381 
    4382 > select #8/A3,B3,C3
    4383 
    4384 Nothing selected 
    4385 
    4386 > select #11/A3,B3,C3
    4387 
    4388 116098 atoms, 121178 bonds, 4063 pseudobonds, 7254 residues, 4 models selected 
    4389 
    4390 > select #11/A3,B3,C3,h1
    4391 
    4392 170652 atoms, 177684 bonds, 6097 pseudobonds, 11038 residues, 4 models
    4393 selected 
    4394 
    4395 > color sel #6F92A0
    4396 
    4397 > select add #11
    4398 
    4399 361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
    4400 selected 
    4401 
    4402 > select subtract #11
    4403 
    4404 Nothing selected 
    4405 
    4406 > select add #11
    4407 
    4408 361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
    4409 selected 
    4410 
    4411 > color sel #275C70
    4412 
    4413 > select #11/A3,B3,C3,h1
    4414 
    4415 170652 atoms, 177684 bonds, 6097 pseudobonds, 11038 residues, 4 models
    4416 selected 
    4417 
    4418 > color sel #6F92A0
    4419 
    4420 > color sel #B7C9CF
    4421 
    4422 > color zone #8 near #11 distance 6
    4423 
    4424 > hide #!11 models
    4425 
    4426 > view matrix models
    4427 > #11,-0.23336,-0.95789,-0.1673,514.07,-0.81859,0.28638,-0.49789,398.8,0.52484,0.020763,-0.85095,303.2
    4428 
    4429 > ui mousemode right zoom
    4430 
    4431 > color zone #8 near #11 distance 6.5
    4432 
    4433 > show #!11 models
    4434 
    4435 > undo
    4436 
    4437 > show #!11 models
    4438 
    4439 > color zone #8 near #11 distance 6.5
    4440 
    4441 > color zone #8 near #11 distance 10
    4442 
    4443 > color zone #10 near #11 distance 10
    4444 
    4445 > show #!10 models
    4446 
    4447 > hide #!8 models
    4448 
    4449 > hide #!11 models
    4450 
    4451 > show #!11 models
    4452 
    4453 > hide #!11 models
    4454 
    4455 > show #!11 models
    4456 
    4457 > view #10 clip false
    4458 
    4459 > show #!8 models
    4460 
    4461 > hide #!10 models
    4462 
    4463 > color zone #10 near #11 distance 6
    4464 
    4465 > color zone #8 near #11 distance 6
    4466 
    4467 > color zone #8 near #11 distance 10
    4468 
    4469 > color zone #8 near #11 distance 6
    4470 
    4471 > hide #!11 models
    4472 
    4473 > view #8 clip false
    4474 
    4475 > volume #8 level 0.2836
    4476 
    4477 > volume #8 level 0.2622
    4478 
    4479 > show #!9 models
    4480 
    4481 > hide #!9 models
    4482 
    4483 > show #!11 models
    4484 
    4485 > log metadata #11
    4486 
    4487 Metadata for 8b2l #11 
    4488 --- 
    4489 Title | Cryo-EM structure of the plant 80S ribosome 
    4490 Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y 
    4491 Non-standard residues | B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid 
    4492 K — potassium ion 
    4493 MG — magnesium ion 
    4494 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    4495 SPM — spermine 
    4496 UY1 — 2'-O-methylpseudouridine-5'-monophosphate 
    4497 ZN — zinc ion 
    4498 Sources (natural) | Nicotiana tabacum (common tobacco) 
    4499 Nicotiana tabacum 
    4500 CryoEM Map | EMDB 15806 — open map 
    4501 Experimental method | Electron microscopy 
    4502 Resolution | 2.20Å 
    4503  
    4504 > log chains #11
    4505 
    4506 Chain information for 8b2l #11 
    4507 --- 
    4508 Chain | Description | UniProt 
    4509 A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264 
    4510 A3 | 25S rRNA |   
    4511 B1 | mRNA |   
    4512 B3 | 5.8S rRNA |   
    4513 C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144 
    4514 C3 | 5S rRNA |   
    4515 D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149 
    4516 D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206 
    4517 E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143 
    4518 E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134 
    4519 F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261 
    4520 F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204 
    4521 G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83 
    4522 G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187 
    4523 H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133 
    4524 H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214 
    4525 I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107 
    4526 I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178 
    4527 J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127 
    4528 J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164 
    4529 K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86 
    4530 K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127 
    4531 L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65 
    4532 L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164 
    4533 M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62 
    4534 M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135 
    4535 N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156 
    4536 N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143 
    4537 O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191 
    4538 O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61 
    4539 P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224 
    4540 P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113 
    4541 Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329 
    4542 Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120 
    4543 R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122 
    4544 R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133 
    4545 S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150 
    4546 S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112 
    4547 T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142 
    4548 T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120 
    4549 U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152 
    4550 U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110 
    4551 V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56 
    4552 V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95 
    4553 W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151 
    4554 W2 i2 | tRNA |   
    4555 W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69 
    4556 X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159 
    4557 X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51 
    4558 Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152 
    4559 Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128 
    4560 Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336 
    4561 Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105 
    4562 a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248 
    4563 a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92 
    4564 b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197 
    4565 b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230 
    4566 c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280 
    4567 c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258 
    4568 d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210 
    4569 d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206 
    4570 e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130 
    4571 e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140 
    4572 f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150 
    4573 f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148 
    4574 g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221 
    4575 h1 | 18S rRNA |   
    4576 h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301 
    4577 j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175 
    4578 k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249 
    4579 k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154 
    4580 l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208 
    4581 l3 | nascent chain |   
    4582 m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146 
    4583 n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123 
    4584 o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260 
    4585 p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25 
    4586 q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242 
    4587 r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389 
    4588 s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405 
    4589 t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181 
    4590 u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194 
    4591  
    4592 
    4593 > select #10/i2,W2
    4594 
    4595 Nothing selected 
    4596 
    4597 > select #11/i2,W2
    4598 
    4599 4923 atoms, 5289 bonds, 154 pseudobonds, 172 residues, 2 models selected 
    4600 
    4601 > color sel red
    4602 
    4603 > fitmap #11/i2,W2 inMap #8
    4604 
    4605 Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
    4606 (#8) using 4923 atoms 
    4607 average map value = 0.1344, steps = 180 
    4608 shifted from previous position = 15.6 
    4609 rotated from previous position = 16.9 degrees 
    4610 atoms outside contour = 4146, contour level = 0.26224 
    4611  
    4612 Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
    4613 (#8) coordinates: 
    4614 Matrix rotation and translation 
    4615 -0.12860039 -0.94295209 -0.30708850 501.64792121 
    4616 -0.66615166 0.31153354 -0.67763476 409.30420991 
    4617 0.73464546 0.11742342 -0.66821241 202.11741168 
    4618 Axis 0.59360052 -0.77777179 0.20666271 
    4619 Axis point 358.16523541 0.00000000 276.25974704 
    4620 Rotation angle (degrees) 137.95675880 
    4621 Shift along axis 21.20332999 
    4622  
    4623 
    4624 > undo
    4625 
    4626 > fitmap #11 inMap #8
    4627 
    4628 Fit molecule 8b2l (#11) to map cryosparc_P346_J194_003_volume_map.mrc copy
    4629 (#8) using 361205 atoms 
    4630 average map value = 0.1342, steps = 2000 
    4631 shifted from previous position = 5.68 
    4632 rotated from previous position = 13.2 degrees 
    4633 atoms outside contour = 281306, contour level = 0.26224 
    4634  
    4635 Position of 8b2l (#11) relative to cryosparc_P346_J194_003_volume_map.mrc copy
    4636 (#8) coordinates: 
    4637 Matrix rotation and translation 
    4638 -0.27913453 -0.92113472 -0.27128358 523.17175455 
    4639 -0.75920050 0.38468328 -0.52500802 389.74495037 
    4640 0.58796136 0.05941076 -0.80670431 266.33210522 
    4641 Axis 0.55569039 -0.81700686 0.15397399 
    4642 Axis point 348.17040360 0.00000000 259.58545552 
    4643 Rotation angle (degrees) 148.27456620 
    4644 Shift along axis 13.30543373 
    4645  
    4646 
    4647 > select #11/i2,W2
    4648 
    4649 4923 atoms, 5289 bonds, 154 pseudobonds, 172 residues, 2 models selected 
    4650 
    4651 > color sel red
    4652 
    4653 > color zone #8 near #11 distance 6
    4654 
    4655 > hide #!11 models
    4656 
    4657 > volume #8 level 0.2373
    4658 
    4659 > volume #8 level 0.21
    4660 
    4661 > volume #8 level 0.2
    4662 
    4663 > volume #8 level 0.22
    4664 
    4665 > volume #8 level 0.23
    4666 
    4667 > open /Users/roan.groh/Downloads/cryosparc_P346_J178_006_volume_map.mrc
    4668 
    4669 Opened cryosparc_P346_J178_006_volume_map.mrc as #12, grid size 384,384,384,
    4670 pixel 1.19, shown at level 0.177, step 2, values float32 
    4671 
    4672 > hide #!8 models
    4673 
    4674 > select add #11
    4675 
    4676 361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
    4677 selected 
    4678 
    4679 > volume #10 level 0.3228
    4680 
    4681 > volume #12 step 1
    4682 
    4683 > volume #12 level 0.1391
    4684 
    4685 > open
    4686 > /Users/roan.groh/Downloads/cryosparc_P346_J179_class_01_00143_volume.mrc
    4687 
    4688 Opened cryosparc_P346_J179_class_01_00143_volume.mrc as #13, grid size
    4689 160,160,160, pixel 2.85, shown at level 0.733, step 1, values float32 
    4690 
    4691 > hide #!12 models
    4692 
    4693 > volume #13 level 0.2886
    4694 
    4695 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4696 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P347_2023_Seedling/Seedling_Precessing/J179_3D_Classes/cryosparc_P347_J179_class_02_00023_volume.mrc
    4697 
    4698 Opened cryosparc_P347_J179_class_02_00023_volume.mrc as #14, grid size
    4699 96,96,96, pixel 4.76, shown at level 1.07, step 1, values float32 
    4700 
    4701 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4702 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P347_2023_Seedling/Seedling_Precessing/J179_3D_Classes/cryosparc_P347_J179_class_03_00023_volume.mrc
    4703 
    4704 Opened cryosparc_P347_J179_class_03_00023_volume.mrc as #15, grid size
    4705 96,96,96, pixel 4.76, shown at level 1.11, step 1, values float32 
    4706 
    4707 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4708 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P347_2023_Seedling/Seedling_Precessing/J179_3D_Classes/cryosparc_P347_J179_class_04_00023_volume.mrc
    4709 
    4710 Opened cryosparc_P347_J179_class_04_00023_volume.mrc as #16, grid size
    4711 96,96,96, pixel 4.76, shown at level 1.07, step 1, values float32 
    4712 
    4713 > volume #14 level 0.5403
    4714 
    4715 > volume #15 level 0.5556
    4716 
    4717 > volume #16 level 0.4912
    4718 
    4719 > hide #!14 models
    4720 
    4721 > hide #!16 models
    4722 
    4723 > hide #!13 models
    4724 
    4725 > show #!13 models
    4726 
    4727 > show #!11 models
    4728 
    4729 > hide #!13 models
    4730 
    4731 > show #!14 models
    4732 
    4733 > hide #!14 models
    4734 
    4735 > hide #!15 models
    4736 
    4737 > hide #!11 models
    4738 
    4739 > show #!10 models
    4740 
    4741 > hide #!10 models
    4742 
    4743 > select subtract #11
    4744 
    4745 Nothing selected 
    4746 
    4747 > open
    4748 > /Users/roan.groh/Downloads/cryosparc_P346_J307_class_04_00021_volume.mrc
    4749 
    4750 Opened cryosparc_P346_J307_class_04_00021_volume.mrc as #17, grid size
    4751 160,160,160, pixel 2.85, shown at level 0.768, step 1, values float32 
    4752 
    4753 > open
    4754 > /Users/roan.groh/Downloads/cryosparc_P346_J307_class_03_00021_volume.mrc
    4755 
    4756 Opened cryosparc_P346_J307_class_03_00021_volume.mrc as #18, grid size
    4757 160,160,160, pixel 2.85, shown at level 0.813, step 1, values float32 
    4758 
    4759 > volume #18 level 0.4537
    4760 
    4761 > volume #17 level 0.5378
    4762 
    4763 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4764 > VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J193_004_volume_map.mrc
    4765 
    4766 Opened cryosparc_P346_J193_004_volume_map.mrc as #19, grid size 384,384,384,
    4767 pixel 1.19, shown at level 0.232, step 2, values float32 
    4768 
    4769 > hide #!17 models
    4770 
    4771 > volume #19 step 1
    4772 
    4773 > hide #!18 models
    4774 
    4775 > show #!18 models
    4776 
    4777 > hide #!19 models
    4778 
    4779 > show #!19 models
    4780 
    4781 > hide #!18 models
    4782 
    4783 > hide #!19 models
    4784 
    4785 > show #!17 models
    4786 
    4787 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4788 > VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C/Dehydrated/cryosparc_P346_J194_003_volume_map.mrc
    4789 
    4790 Opened cryosparc_P346_J194_003_volume_map.mrc as #20, grid size 384,384,384,
    4791 pixel 1.19, shown at level 0.252, step 2, values float32 
    4792 
    4793 > hide #!17 models
    4794 
    4795 > hide #!20 models
    4796 
    4797 > open /Users/roan.groh/Downloads/cryosparc_P618_J132_004_volume_map.mrc
    4798 
    4799 Opened cryosparc_P618_J132_004_volume_map.mrc as #21, grid size 384,384,384,
    4800 pixel 1.19, shown at level 0.25, step 2, values float32 
    4801 
    4802 > volume #21 step 1
    4803 
    4804 > volume #21 level 0.2683
    4805 
    4806 > hide #!21 models
    4807 
    4808 > open /Users/roan.groh/Downloads/cryosparc_P346_J303_004_volume_map.mrc
    4809 
    4810 Opened cryosparc_P346_J303_004_volume_map.mrc as #22, grid size 384,384,384,
    4811 pixel 1.19, shown at level 0.226, step 2, values float32 
    4812 
    4813 > volume #22 step 1
    4814 
    4815 > show #!21 models
    4816 
    4817 > fitmap #22 inMap #21
    4818 
    4819 Fit map cryosparc_P346_J303_004_volume_map.mrc in map
    4820 cryosparc_P618_J132_004_volume_map.mrc using 565890 points 
    4821 correlation = 0.964, correlation about mean = 0.8482, overlap = 1.185e+05 
    4822 steps = 68, shift = 0.907, angle = 0.718 degrees 
    4823  
    4824 Position of cryosparc_P346_J303_004_volume_map.mrc (#22) relative to
    4825 cryosparc_P618_J132_004_volume_map.mrc (#21) coordinates: 
    4826 Matrix rotation and translation 
    4827 0.99999627 -0.00182036 -0.00203511 0.38077697 
    4828 0.00179533 0.99992355 -0.01223441 2.39881311 
    4829 0.00205723 0.01223071 0.99992309 -3.97164844 
    4830 Axis 0.97598286 -0.16325517 0.14424010 
    4831 Axis point 0.00000000 318.90662639 186.16711104 
    4832 Rotation angle (degrees) 0.71813988 
    4833 Shift along axis -0.59285781 
    4834  
    4835 
    4836 > show #!12 models
    4837 
    4838 > hide #!21 models
    4839 
    4840 > hide #!22 models
    4841 
    4842 > close #12
    4843 
    4844 > show #!18 models
    4845 
    4846 > close #1.3#2.3#4.3#7.3#1-11,13-22#1.1-2#2.1-2#4.1-2#7.1-2
    4847 
    4848 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4849 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J51-53_NU-
    4850 > Refine_empty/cryosparc_P618_J51_003_volume_map.mrc
    4851 
    4852 Opened cryosparc_P618_J51_003_volume_map.mrc as #1, grid size 384,384,384,
    4853 pixel 1.19, shown at level 0.254, step 2, values float32 
    4854 
    4855 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4856 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J51-53_NU-
    4857 > Refine_empty/cryosparc_P618_J52_004_volume_map.mrc
    4858 
    4859 Opened cryosparc_P618_J52_004_volume_map.mrc as #2, grid size 384,384,384,
    4860 pixel 1.19, shown at level 0.273, step 2, values float32 
    4861 
    4862 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    4863 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J51-53_NU-
    4864 > Refine_empty/cryosparc_P618_J53_003_volume_map.mrc
    4865 
    4866 Opened cryosparc_P618_J53_003_volume_map.mrc as #3, grid size 384,384,384,
    4867 pixel 1.19, shown at level 0.275, step 2, values float32 
    4868 
    4869 > volume #1 step 1
    4870 
    4871 > volume #2 step 1
    4872 
    4873 > volume #3 step 1
    4874 
    4875 > fitmap #2 inMap #1
    4876 
    4877 Fit map cryosparc_P618_J52_004_volume_map.mrc in map
    4878 cryosparc_P618_J51_003_volume_map.mrc using 567130 points 
    4879 correlation = 0.9217, correlation about mean = 0.7276, overlap = 1.16e+05 
    4880 steps = 64, shift = 1.4, angle = 1.66 degrees 
    4881  
    4882 Position of cryosparc_P618_J52_004_volume_map.mrc (#2) relative to
    4883 cryosparc_P618_J51_003_volume_map.mrc (#1) coordinates: 
    4884 Matrix rotation and translation 
    4885 0.99999197 0.00353107 -0.00189288 -0.16361357 
    4886 -0.00358405 0.99957996 -0.02875854 7.11086549 
    4887 0.00179053 0.02876509 0.99958460 -7.88726609 
    4888 Axis 0.99043913 -0.06342073 -0.12250774 
    4889 Axis point 0.00000000 276.21517511 244.00569150 
    4890 Rotation angle (degrees) 1.66407218 
    4891 Shift along axis 0.35322557 
    4892  
    4893 
    4894 > fitmap #3 inMap #1
    4895 
    4896 Fit map cryosparc_P618_J53_003_volume_map.mrc in map
    4897 cryosparc_P618_J51_003_volume_map.mrc using 565425 points 
    4898 correlation = 0.915, correlation about mean = 0.7278, overlap = 1.122e+05 
    4899 steps = 80, shift = 1.36, angle = 1.68 degrees 
    4900  
    4901 Position of cryosparc_P618_J53_003_volume_map.mrc (#3) relative to
    4902 cryosparc_P618_J51_003_volume_map.mrc (#1) coordinates: 
    4903 Matrix rotation and translation 
    4904 0.99998937 0.00398957 -0.00231164 -0.16580550 
    4905 -0.00405496 0.99957087 -0.02901086 7.24709610 
    4906 0.00219491 0.02901992 0.99957642 -8.03134002 
    4907 Axis 0.98761026 -0.07669586 -0.13690770 
    4908 Axis point 0.00000000 278.56071744 246.69042691 
    4909 Rotation angle (degrees) 1.68355743 
    4910 Shift along axis 0.37997882 
    4911  
    4912 
    4913 > vop gaussian #1,2,3 sdev 1
    4914 
    4915 Opened cryosparc_P618_J51_003_volume_map.mrc gaussian as #4, grid size
    4916 384,384,384, pixel 1.19, shown at step 1, values float32 
    4917 Opened cryosparc_P618_J52_004_volume_map.mrc gaussian as #5, grid size
    4918 384,384,384, pixel 1.19, shown at step 1, values float32 
    4919 Opened cryosparc_P618_J53_003_volume_map.mrc gaussian as #6, grid size
    4920 384,384,384, pixel 1.19, shown at step 1, values float32 
    4921 
    4922 > open emdb:15872
    4923 
    4924 Opened emdb 15872 as #7, grid size 348,348,348, pixel 1.72, shown at level
    4925 0.0016, step 2, values float32 
    4926 
    4927 > open emdb:15874
    4928 
    4929 Opened emdb 15874 as #8, grid size 348,348,348, pixel 1.72, shown at level
    4930 0.0032, step 2, values float32 
    4931 
    4932 > open emdb:15876
    4933 
    4934 Opened emdb 15876 as #9, grid size 348,348,348, pixel 1.72, shown at level
    4935 0.0016, step 2, values float32 
    4936 
    4937 > open emdb:15877
    4938 
    4939 Opened emdb 15877 as #10, grid size 348,348,348, pixel 1.72, shown at level
    4940 0.0035, step 2, values float32 
    4941 
    4942 > open emdb:15878
    4943 
    4944 Summary of feedback from opening 15878 fetched from emdb 
    4945 --- 
    4946 note | Fetching map header 15878 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-15878/header/emd-15878.xml 
    4947  
    4948 Opened emdb 15878 as #11, grid size 348,348,348, pixel 1.72, shown at level
    4949 0.0028, step 2, values float32 
    4950 
    4951 > select add #7
    4952 
    4953 2 models selected 
    4954 
    4955 > select add #8
    4956 
    4957 4 models selected 
    4958 
    4959 > select add #9
    4960 
    4961 6 models selected 
    4962 
    4963 > select add #10
    4964 
    4965 8 models selected 
    4966 
    4967 > select add #11
    4968 
    4969 10 models selected 
    4970 
    4971 > ui mousemode right "rotate selected models"
    4972 
    4973 > view matrix models
    4974 > #7,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#8,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#9,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#10,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82,#11,0.31276,0.36012,0.87892,-161.5,-0.013121,0.92689,-0.3751,137.14,-0.94974,0.10579,0.29462,463.82
    4975 
    4976 > ui mousemode right "translate selected models"
    4977 
    4978 > view matrix models
    4979 > #7,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#8,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#9,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#10,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61,#11,0.31276,0.36012,0.87892,-191.64,-0.013121,0.92689,-0.3751,144.39,-0.94974,0.10579,0.29462,438.61
    4980 
    4981 > view matrix models
    4982 > #7,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#8,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#9,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#10,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79,#11,0.31276,0.36012,0.87892,-228.9,-0.013121,0.92689,-0.3751,54.675,-0.94974,0.10579,0.29462,367.79
    4983 
    4984 > ui mousemode right "rotate selected models"
    4985 
    4986 > view matrix models
    4987 > #7,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#8,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#9,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#10,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06,#11,0.29548,0.60492,0.73943,-255.8,0.51289,0.55254,-0.65699,92.009,-0.806,0.57338,-0.14699,315.06
    4988 
    4989 > ui mousemode right "translate selected models"
    4990 
    4991 > view matrix models
    4992 > #7,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#8,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#9,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#10,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83,#11,0.29548,0.60492,0.73943,-240.22,0.51289,0.55254,-0.65699,76.699,-0.806,0.57338,-0.14699,347.83
    4993 
    4994 > ui mousemode right "rotate selected models"
    4995 
    4996 > view matrix models
    4997 > #7,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#8,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#9,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#10,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04,#11,0.14188,0.79936,0.58386,-206.13,0.38462,0.49896,-0.7766,166.93,-0.9121,0.33475,-0.23666,478.04
    4998 
    4999 > view matrix models
    5000 > #7,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#8,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#9,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#10,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17,#11,0.14904,0.81149,0.56504,-206.35,0.37226,0.48334,-0.79234,180.02,-0.91608,0.32844,-0.23005,479.17
    5001 
    5002 > view matrix models
    5003 > #7,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#8,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#9,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#10,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32,#11,0.15305,0.75889,0.63298,-211.92,0.19617,0.60445,-0.77211,190.76,-0.96855,0.24235,-0.056359,469.32
    5004 
    5005 > select up
    5006 
    5007 22 models selected 
    5008 
    5009 > select down
    5010 
    5011 10 models selected 
    5012 
    5013 > fitmap #7,8,9,10,11 inMap #4
    5014 
    5015 Multiple maps for #7,8,9,10,11 
    5016 
    5017 > fitmap #7 inMap #4
    5018 
    5019 Fit map emdb 15872 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
    5020 38975 points 
    5021 correlation = 0.8713, correlation about mean = 0.511, overlap = 19.12 
    5022 steps = 172, shift = 4.18, angle = 7.74 degrees 
    5023  
    5024 Position of emdb 15872 (#7) relative to cryosparc_P618_J51_003_volume_map.mrc
    5025 gaussian (#4) coordinates: 
    5026 Matrix rotation and translation 
    5027 0.15095486 0.67609126 0.72118878 -213.36408338 
    5028 0.27171285 0.67307181 -0.68785644 124.03261421 
    5029 -0.95046556 0.29979153 -0.08209922 450.44819691 
    5030 Axis 0.49798722 0.84287369 -0.20389378 
    5031 Axis point 81.43122461 0.00000000 327.11961880 
    5032 Rotation angle (degrees) 97.41390561 
    5033 Shift along axis -93.55234397 
    5034  
    5035 
    5036 > fitmap #8 inMap #4
    5037 
    5038 Fit map emdb 15874 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
    5039 50573 points 
    5040 correlation = 0.7901, correlation about mean = 0.3651, overlap = 35.33 
    5041 steps = 200, shift = 4.27, angle = 7.64 degrees 
    5042  
    5043 Position of emdb 15874 (#8) relative to cryosparc_P618_J51_003_volume_map.mrc
    5044 gaussian (#4) coordinates: 
    5045 Matrix rotation and translation 
    5046 0.15020079 0.67788455 0.71966122 -213.34327430 
    5047 0.27224301 0.67141791 -0.68926174 124.63013964 
    5048 -0.95043332 0.29945039 -0.08370183 450.86237576 
    5049 Axis 0.49865603 0.84231061 -0.20458493 
    5050 Axis point 81.05473272 0.00000000 327.27308365 
    5051 Rotation angle (degrees) 97.52978432 
    5052 Shift along axis -93.64727139 
    5053  
    5054 
    5055 > fitmap #9 inMap #4
    5056 
    5057 Fit map emdb 15876 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
    5058 44004 points 
    5059 correlation = 0.8182, correlation about mean = 0.4956, overlap = 19.16 
    5060 steps = 184, shift = 4.33, angle = 7.69 degrees 
    5061  
    5062 Position of emdb 15876 (#9) relative to cryosparc_P618_J51_003_volume_map.mrc
    5063 gaussian (#4) coordinates: 
    5064 Matrix rotation and translation 
    5065 0.15136149 0.67763961 0.71964872 -213.65395858 
    5066 0.27349619 0.67090509 -0.68926498 124.40829276 
    5067 -0.94988923 0.30114936 -0.08378266 450.26873802 
    5068 Axis 0.49949568 0.84199810 -0.20382166 
    5069 Axis point 80.75562073 0.00000000 327.05187886 
    5070 Rotation angle (degrees) 97.51339860 
    5071 Shift along axis -93.74220317 
    5072  
    5073 
    5074 > fitmap #10 inMap #4
    5075 
    5076 Fit map emdb 15877 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
    5077 64603 points 
    5078 correlation = 0.8209, correlation about mean = 0.4433, overlap = 54.96 
    5079 steps = 168, shift = 4.15, angle = 7.71 degrees 
    5080  
    5081 Position of emdb 15877 (#10) relative to cryosparc_P618_J51_003_volume_map.mrc
    5082 gaussian (#4) coordinates: 
    5083 Matrix rotation and translation 
    5084 0.14997351 0.67720895 0.72034436 -213.18207749 
    5085 0.27290595 0.67192385 -0.68850613 124.19979355 
    5086 -0.95027907 0.29984395 -0.08404357 450.86662304 
    5087 Axis 0.49847553 0.84258090 -0.20391069 
    5088 Axis point 81.25347257 0.00000000 327.08689769 
    5089 Rotation angle (degrees) 97.53160719 
    5090 Shift along axis -93.55420115 
    5091  
    5092 
    5093 > fitmap #11 inMap #4
    5094 
    5095 Fit map emdb 15878 in map cryosparc_P618_J51_003_volume_map.mrc gaussian using
    5096 72752 points 
    5097 correlation = 0.8284, correlation about mean = 0.5131, overlap = 54.45 
    5098 steps = 180, shift = 4.14, angle = 7.7 degrees 
    5099  
    5100 Position of emdb 15878 (#11) relative to cryosparc_P618_J51_003_volume_map.mrc
    5101 gaussian (#4) coordinates: 
    5102 Matrix rotation and translation 
    5103 0.14995666 0.67663978 0.72088253 -213.16999021 
    5104 0.27127382 0.67298649 -0.68811315 124.23930647 
    5105 -0.95074893 0.29874370 -0.08263585 451.02348959 
    5106 Axis 0.49764139 0.84295205 -0.20441352 
    5107 Axis point 81.56457018 0.00000000 327.30602168 
    5108 Rotation angle (degrees) 97.46071355 
    5109 Shift along axis -93.54973197 
    5110  
    5111 
    5112 > rename #7 "Classic_emdb 15872"
    5113 
    5114 > rename #8 "Rot-1_emdb 15874"
    5115 
    5116 > rename #9 "Rot-2_emdb 15876"
    5117 
    5118 > rename #10 "Translocation_emdb 15877"
    5119 
    5120 > rename #11 "Post_emdb 15878"
    5121 
    5122 > select subtract #7
    5123 
    5124 8 models selected 
    5125 
    5126 > select subtract #8
    5127 
    5128 6 models selected 
    5129 
    5130 > select subtract #9
    5131 
    5132 4 models selected 
    5133 
    5134 > select subtract #10
    5135 
    5136 2 models selected 
    5137 
    5138 > select subtract #11
    5139 
    5140 Nothing selected 
    5141 
    5142 > hide #!11 models
    5143 
    5144 > hide #!10 models
    5145 
    5146 > hide #!9 models
    5147 
    5148 > hide #!8 models
    5149 
    5150 > hide #!5 models
    5151 
    5152 > hide #!6 models
    5153 
    5154 > volume #7 step 1
    5155 
    5156 > volume #4 level 0.1213
    5157 
    5158 > hide #!7 models
    5159 
    5160 > show #!8 models
    5161 
    5162 > hide #!8 models
    5163 
    5164 > show #!9 models
    5165 
    5166 > volume #8 step 1
    5167 
    5168 > volume #9 step 1
    5169 
    5170 > volume #10 step 1
    5171 
    5172 > hide #!9 models
    5173 
    5174 > show #!8 models
    5175 
    5176 > hide #!8 models
    5177 
    5178 > show #!7 models
    5179 
    5180 > hide #!4 models
    5181 
    5182 > show #!5 models
    5183 
    5184 > volume #5 level 0.1308
    5185 
    5186 > hide #!7 models
    5187 
    5188 > show #!8 models
    5189 
    5190 > hide #!8 models
    5191 
    5192 > show #!8 models
    5193 
    5194 > hide #!8 models
    5195 
    5196 > show #!9 models
    5197 
    5198 > hide #!9 models
    5199 
    5200 > show #!8 models
    5201 
    5202 > hide #!8 models
    5203 
    5204 > show #!7 models
    5205 
    5206 > hide #!5 models
    5207 
    5208 > hide #!7 models
    5209 
    5210 > show #!4 models
    5211 
    5212 > show #!5 models
    5213 
    5214 > hide #!5 models
    5215 
    5216 > show #!5 models
    5217 
    5218 > ui mousemode right zoom
    5219 
    5220 > show #!8 models
    5221 
    5222 > hide #!4 models
    5223 
    5224 > show #!9 models
    5225 
    5226 > hide #!9 models
    5227 
    5228 > show #!9 models
    5229 
    5230 > hide #!8 models
    5231 
    5232 > hide #!9 models
    5233 
    5234 > show #!8 models
    5235 
    5236 > show #!9 models
    5237 
    5238 > hide #!8 models
    5239 
    5240 > hide #!9 models
    5241 
    5242 > show #!6 models
    5243 
    5244 > hide #!5 models
    5245 
    5246 > volume #6 level 0.129
    5247 
    5248 > show #!9 models
    5249 
    5250 > hide #!9 models
    5251 
    5252 > show #!8 models
    5253 
    5254 > hide #!8 models
    5255 
    5256 > show #!8 models
    5257 
    5258 > show #!9 models
    5259 
    5260 > hide #!9 models
    5261 
    5262 > show #!9 models
    5263 
    5264 > hide #!6 models
    5265 
    5266 > show #!6 models
    5267 
    5268 > hide #!6 models
    5269 
    5270 > show #!6 models
    5271 
    5272 > show #!7 models
    5273 
    5274 > hide #!7 models
    5275 
    5276 > hide #!6 models
    5277 
    5278 > show #!6 models
    5279 
    5280 > hide #!6 models
    5281 
    5282 > show #!6 models
    5283 
    5284 > show #!7 models
    5285 
    5286 > hide #!8 models
    5287 
    5288 > hide #!9 models
    5289 
    5290 > hide #!7 models
    5291 
    5292 > show #!7 models
    5293 
    5294 > hide #!7 models
    5295 
    5296 > show #!7 models
    5297 
    5298 > hide #!6 models
    5299 
    5300 > show #!6 models
    5301 
    5302 > show #!4 models
    5303 
    5304 > hide #!7 models
    5305 
    5306 > show #!5 models
    5307 
    5308 > vop morph #4,5,6
    5309 
    5310 Map positions are not the same, cryosparc_P618_J52_004_volume_map.mrc gaussian
    5311 #5 and cryosparc_P618_J51_003_volume_map.mrc gaussian #4. Use the "volume
    5312 resample" command to make a copy of one map with the same grid as the other
    5313 map. 
    5314 
    5315 > hide #!5 models
    5316 
    5317 > vop morph #4,6
    5318 
    5319 Map positions are not the same, cryosparc_P618_J53_003_volume_map.mrc gaussian
    5320 #6 and cryosparc_P618_J51_003_volume_map.mrc gaussian #4. Use the "volume
    5321 resample" command to make a copy of one map with the same grid as the other
    5322 map. 
    5323 
    5324 > morph #4,6
    5325 
    5326 Require at least 2 structures for morph 
    5327 
    5328 > morph #4 to #6
    5329 
    5330 Expected a keyword 
    5331 
    5332 > morph #4 i #6
    5333 
    5334 Expected a keyword 
    5335 
    5336 > show #!5 models
    5337 
    5338 > hide #!4 models
    5339 
    5340 > hide #!5 models
    5341 
    5342 > show #!5 models
    5343 
    5344 > hide #!5 models
    5345 
    5346 > show #!5 models
    5347 
    5348 > hide #!5 models
    5349 
    5350 > show #!5 models
    5351 
    5352 > hide #!5 models
    5353 
    5354 > show #!4 models
    5355 
    5356 > hide #!4 models
    5357 
    5358 > show #!4 models
    5359 
    5360 > show #!5 models
    5361 
    5362 > hide #!6 models
    5363 
    5364 > hide #!5 models
    5365 
    5366 > show #!5 models
    5367 
    5368 > hide #!5 models
    5369 
    5370 > show #!5 models
    5371 
    5372 > hide #!5 models
    5373 
    5374 > show #!6 models
    5375 
    5376 > hide #!6 models
    5377 
    5378 > show #!5 models
    5379 
    5380 > show #!6 models
    5381 
    5382 > hide #!4 models
    5383 
    5384 > hide #!5 models
    5385 
    5386 > hide #!6 models
    5387 
    5388 > open
    5389 > /Users/roan.groh/Downloads/cryosparc_P346_J309_class_03_00033_volume.mrc
    5390 
    5391 Opened cryosparc_P346_J309_class_03_00033_volume.mrc as #12, grid size
    5392 96,96,96, pixel 4.76, shown at level 1.42, step 1, values float32 
    5393 
    5394 > open
    5395 > /Users/roan.groh/Downloads/cryosparc_P346_J309_class_02_00033_volume.mrc
    5396 
    5397 Opened cryosparc_P346_J309_class_02_00033_volume.mrc as #13, grid size
    5398 96,96,96, pixel 4.76, shown at level 1.43, step 1, values float32 
    5399 
    5400 > volume #12 level 0.7386
    5401 
    5402 > volume #13 level 0.8024
    5403 
    5404 > show #!8 models
    5405 
    5406 > hide #!8 models
    5407 
    5408 > show #!9 models
    5409 
    5410 > hide #!9 models
    5411 
    5412 > fitmap #12 inMap #4
    5413 
    5414 Fit map cryosparc_P346_J309_class_03_00033_volume.mrc in map
    5415 cryosparc_P618_J51_003_volume_map.mrc gaussian using 29135 points 
    5416 correlation = 0.8015, correlation about mean = 0.371, overlap = 5382 
    5417 steps = 88, shift = 1.25, angle = 2.64 degrees 
    5418  
    5419 Position of cryosparc_P346_J309_class_03_00033_volume.mrc (#12) relative to
    5420 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    5421 Matrix rotation and translation 
    5422 0.99920994 -0.03526362 -0.01832944 12.26451505 
    5423 0.03482934 0.99911706 -0.02349520 -1.83755016 
    5424 0.01914178 0.02283823 0.99955591 -10.37051771 
    5425 Axis 0.50362718 -0.40729824 0.76188438 
    5426 Axis point 73.30020115 360.09138746 0.00000000 
    5427 Rotation angle (degrees) 2.63652104 
    5428 Shift along axis -0.97596136 
    5429  
    5430 
    5431 > fitmap #13 inMap #4
    5432 
    5433 Fit map cryosparc_P346_J309_class_02_00033_volume.mrc in map
    5434 cryosparc_P618_J51_003_volume_map.mrc gaussian using 27035 points 
    5435 correlation = 0.8395, correlation about mean = 0.4145, overlap = 5679 
    5436 steps = 88, shift = 1.48, angle = 2.79 degrees 
    5437  
    5438 Position of cryosparc_P346_J309_class_02_00033_volume.mrc (#13) relative to
    5439 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    5440 Matrix rotation and translation 
    5441 0.99937018 -0.03014382 -0.01872407 11.03286845 
    5442 0.02950256 0.99899885 -0.03362888 1.34497510 
    5443 0.01971903 0.03305529 0.99925898 -13.18398277 
    5444 Axis 0.68480190 -0.39478501 0.61252849 
    5445 Axis point 0.00000000 379.73346370 16.34908402 
    5446 Rotation angle (degrees) 2.79075805 
    5447 Shift along axis -1.05121174 
    5448  
    5449 
    5450 > hide #!13 models
    5451 
    5452 > show #!13 models
    5453 
    5454 > hide #!13 models
    5455 
    5456 > hide #!12 models
    5457 
    5458 > show #!13 models
    5459 
    5460 > show #!12 models
    5461 
    5462 > hide #!12 models
    5463 
    5464 > show #!12 models
    5465 
    5466 > hide #!12 models
    5467 
    5468 > show #!12 models
    5469 
    5470 > hide #!12 models
    5471 
    5472 > show #!12 models
    5473 
    5474 > show #!8 models
    5475 
    5476 > hide #!13 models
    5477 
    5478 > hide #!12 models
    5479 
    5480 > show #!9 models
    5481 
    5482 > hide #!9 models
    5483 
    5484 > vop gaussian #7,8,9,10,11 sdev 1
    5485 
    5486 Opened Classic_emdb 15872 gaussian as #14, grid size 348,348,348, pixel 1.72,
    5487 shown at step 1, values float32 
    5488 Opened Rot-1_emdb 15874 gaussian as #15, grid size 348,348,348, pixel 1.72,
    5489 shown at step 1, values float32 
    5490 Opened Rot-2_emdb 15876 gaussian as #16, grid size 348,348,348, pixel 1.72,
    5491 shown at step 1, values float32 
    5492 Opened Translocation_emdb 15877 gaussian as #17, grid size 348,348,348, pixel
    5493 1.72, shown at step 1, values float32 
    5494 Opened Post_emdb 15878 gaussian as #18, grid size 348,348,348, pixel 1.72,
    5495 shown at step 1, values float32 
    5496 
    5497 > show #!8 models
    5498 
    5499 > hide #!8 models
    5500 
    5501 > hide #!14 models
    5502 
    5503 > hide #!15 models
    5504 
    5505 > hide #!16 models
    5506 
    5507 > hide #!17 models
    5508 
    5509 > hide #!18 models
    5510 
    5511 > show #!12 models
    5512 
    5513 > show #!13 models
    5514 
    5515 > hide #!13 models
    5516 
    5517 > show #!13 models
    5518 
    5519 > hide #!13 models
    5520 
    5521 > show #!13 models
    5522 
    5523 > hide #!13 models
    5524 
    5525 > show #!13 models
    5526 
    5527 > hide #!13 models
    5528 
    5529 > hide #!12 models
    5530 
    5531 > show #!15 models
    5532 
    5533 > show #!13 models
    5534 
    5535 > hide #!13 models
    5536 
    5537 > hide #!15 models
    5538 
    5539 > show #!14 models
    5540 
    5541 > show #!13 models
    5542 
    5543 > hide #!13 models
    5544 
    5545 > show #!13 models
    5546 
    5547 > show #!18 models
    5548 
    5549 > hide #!14 models
    5550 
    5551 > hide #!13 models
    5552 
    5553 > show #!13 models
    5554 
    5555 > show #!12 models
    5556 
    5557 > hide #!13 models
    5558 
    5559 > show #!14 models
    5560 
    5561 > hide #!18 models
    5562 
    5563 > hide #!14 models
    5564 
    5565 > show #!18 models
    5566 
    5567 > hide #!18 models
    5568 
    5569 > show #!13 models
    5570 
    5571 > show #!11 models
    5572 
    5573 > hide #!11 models
    5574 
    5575 > hide #!12 models
    5576 
    5577 > show #!18 models
    5578 
    5579 > show #!14 models
    5580 
    5581 > hide #!18 models
    5582 
    5583 > hide #!14 models
    5584 
    5585 > show #!14 models
    5586 
    5587 > hide #!14 models
    5588 
    5589 > show #!12 models
    5590 
    5591 > hide #!12 models
    5592 
    5593 > show #!12 models
    5594 
    5595 > hide #!13 models
    5596 
    5597 > show #!14 models
    5598 
    5599 > color #12 #ffffb281 models
    5600 
    5601 > color #12 #ffffb280 models
    5602 
    5603 > color #13 #b2ffff82 models
    5604 
    5605 > show #!13 models
    5606 
    5607 > hide #!13 models
    5608 
    5609 > show #!13 models
    5610 
    5611 > hide #!13 models
    5612 
    5613 > show #!13 models
    5614 
    5615 > hide #!13 models
    5616 
    5617 > hide #!14 models
    5618 
    5619 > lighting soft
    5620 
    5621 > lighting full
    5622 
    5623 > show #!14 models
    5624 
    5625 > hide #!14 models
    5626 
    5627 > show #!15 models
    5628 
    5629 > hide #!15 models
    5630 
    5631 > show #!16 models
    5632 
    5633 > hide #!16 models
    5634 
    5635 > show #!17 models
    5636 
    5637 > hide #!17 models
    5638 
    5639 > show #!18 models
    5640 
    5641 > show #!14 models
    5642 
    5643 > hide #!18 models
    5644 
    5645 > hide #!12 models
    5646 
    5647 > show #!13 models
    5648 
    5649 > show #!18 models
    5650 
    5651 > hide #!14 models
    5652 
    5653 > hide #!18 models
    5654 
    5655 > show #!17 models
    5656 
    5657 > hide #!17 models
    5658 
    5659 > show #!16 models
    5660 
    5661 > hide #!16 models
    5662 
    5663 > show #!15 models
    5664 
    5665 > hide #!15 models
    5666 
    5667 > show #!14 models
    5668 
    5669 > hide #!14 models
    5670 
    5671 > show #!17 models
    5672 
    5673 > show #!18 models
    5674 
    5675 > hide #!17 models
    5676 
    5677 > show #!14 models
    5678 
    5679 > hide #!14 models
    5680 
    5681 > show #!14 models
    5682 
    5683 > hide #!14 models
    5684 
    5685 > show #!14 models
    5686 
    5687 > hide #!14 models
    5688 
    5689 > show #!14 models
    5690 
    5691 > hide #!14 models
    5692 
    5693 > show #!14 models
    5694 
    5695 > hide #!14 models
    5696 
    5697 > hide #!18 models
    5698 
    5699 > show #!12 models
    5700 
    5701 > hide #!12 models
    5702 
    5703 > show #!12 models
    5704 
    5705 > hide #!12 models
    5706 
    5707 > show #!12 models
    5708 
    5709 > hide #!12 models
    5710 
    5711 > hide #!13 models
    5712 
    5713 > show #!18 models
    5714 
    5715 > show #!14 models
    5716 
    5717 > hide #!14 models
    5718 
    5719 > show #!14 models
    5720 
    5721 > hide #!14 models
    5722 
    5723 > show #!14 models
    5724 
    5725 > hide #!14 models
    5726 
    5727 > show #!13 models
    5728 
    5729 > hide #!13 models
    5730 
    5731 > hide #!18 models
    5732 
    5733 > show #!5 models
    5734 
    5735 > show #!6 models
    5736 
    5737 > hide #!5 models
    5738 
    5739 > show #!5 models
    5740 
    5741 > hide #!6 models
    5742 
    5743 > show #!6 models
    5744 
    5745 > show #!4 models
    5746 
    5747 > hide #!4 models
    5748 
    5749 > hide #!5 models
    5750 
    5751 > show #!5 models
    5752 
    5753 > hide #!5 models
    5754 
    5755 > show #!5 models
    5756 
    5757 > hide #!5 models
    5758 
    5759 > show #!5 models
    5760 
    5761 > hide #!5 models
    5762 
    5763 > show #!5 models
    5764 
    5765 > hide #!5 models
    5766 
    5767 > hide #!6 models
    5768 
    5769 > show #!7 models
    5770 
    5771 > show #!8 models
    5772 
    5773 > show #!9 models
    5774 
    5775 > show #!10 models
    5776 
    5777 > hide #!10 models
    5778 
    5779 > hide #!9 models
    5780 
    5781 > hide #!8 models
    5782 
    5783 > hide #!7 models
    5784 
    5785 > show #!5 models
    5786 
    5787 > show #!6 models
    5788 
    5789 > hide #!6 models
    5790 
    5791 > show #!6 models
    5792 
    5793 > hide #!6 models
    5794 
    5795 > show #!6 models
    5796 
    5797 > hide #!6 models
    5798 
    5799 > hide #!5 models
    5800 
    5801 > open /Users/roan.groh/Downloads/cryosparc_P346_J312_003_volume_map.mrc
    5802 
    5803 Opened cryosparc_P346_J312_003_volume_map.mrc as #19, grid size 384,384,384,
    5804 pixel 1.19, shown at level 0.252, step 2, values float32 
    5805 
    5806 > volume #19 step 1
    5807 
    5808 > hide #!19 models
    5809 
    5810 > open /Users/roan.groh/Downloads/cryosparc_P346_J311_map_sharp.mrc
    5811 
    5812 Opened cryosparc_P346_J311_map_sharp.mrc as #20, grid size 384,384,384, pixel
    5813 1.19, shown at level 0.113, step 2, values float32 
    5814 
    5815 > volume #20 step 1
    5816 
    5817 > hide #!20 models
    5818 
    5819 > open /Users/roan.groh/Downloads/cryosparc_P346_J313_003_volume_map.mrc
    5820 
    5821 Opened cryosparc_P346_J313_003_volume_map.mrc as #21, grid size 384,384,384,
    5822 pixel 1.19, shown at level 0.251, step 2, values float32 
    5823 
    5824 > volume #21 step 1
    5825 
    5826 > hide #!21 models
    5827 
    5828 > open /Users/roan.groh/Downloads/cryosparc_P346_J308_003_volume_map.mrc
    5829 
    5830 Opened cryosparc_P346_J308_003_volume_map.mrc as #22, grid size 384,384,384,
    5831 pixel 1.19, shown at level 0.233, step 2, values float32 
    5832 
    5833 > volume #22 step 1
    5834 
    5835 > show #!16 models
    5836 
    5837 > show #!15 models
    5838 
    5839 > hide #!16 models
    5840 
    5841 > show #!14 models
    5842 
    5843 > hide #!15 models
    5844 
    5845 > hide #!14 models
    5846 
    5847 > show #!16 models
    5848 
    5849 > hide #!16 models
    5850 
    5851 > open /Users/roan.groh/Downloads/cryosparc_P618_J136_003_volume_map.mrc
    5852 
    5853 Opened cryosparc_P618_J136_003_volume_map.mrc as #23, grid size 384,384,384,
    5854 pixel 1.19, shown at level 0.27, step 2, values float32 
    5855 
    5856 > open /Users/roan.groh/Downloads/cryosparc_P618_J135_003_volume_map.mrc
    5857 
    5858 Opened cryosparc_P618_J135_003_volume_map.mrc as #24, grid size 384,384,384,
    5859 pixel 1.19, shown at level 0.263, step 2, values float32 
    5860 
    5861 > hide #!22 models
    5862 
    5863 > volume #23 step 1
    5864 
    5865 > volume #24 step 1
    5866 
    5867 > view #23 clip false
    5868 
    5869 > hide #!24 models
    5870 
    5871 > show #!5 models
    5872 
    5873 > show #!6 models
    5874 
    5875 > hide #!23 models
    5876 
    5877 > hide #!5 models
    5878 
    5879 > show #!5 models
    5880 
    5881 > hide #!6 models
    5882 
    5883 > show #!6 models
    5884 
    5885 > hide #!5 models
    5886 
    5887 > show #!4 models
    5888 
    5889 > show #!5 models
    5890 
    5891 > hide #!4 models
    5892 
    5893 > hide #!5 models
    5894 
    5895 > hide #!6 models
    5896 
    5897 > open /Users/roan.groh/Downloads/cryosparc_P618_J86_map_sharp.mrc
    5898 
    5899 Opened cryosparc_P618_J86_map_sharp.mrc as #25, grid size 384,384,384, pixel
    5900 1.19, shown at level 0.0544, step 2, values float32 
    5901 
    5902 > volume #25 step 1
    5903 
    5904 > open /Users/roan.groh/Downloads/cryosparc_P618_J87_map_sharp.mrc
    5905 
    5906 Opened cryosparc_P618_J87_map_sharp.mrc as #26, grid size 384,384,384, pixel
    5907 1.19, shown at level 0.0564, step 2, values float32 
    5908 
    5909 > volume #26 step 1
    5910 
    5911 > open /Users/roan.groh/Downloads/cryosparc_P618_J88_map_sharp.mrc
    5912 
    5913 Opened cryosparc_P618_J88_map_sharp.mrc as #27, grid size 384,384,384, pixel
    5914 1.19, shown at level 0.0349, step 2, values float32 
    5915 
    5916 > volume #27 step 1
    5917 
    5918 > fitmap #25 inMap #4
    5919 
    5920 Fit map cryosparc_P618_J86_map_sharp.mrc in map
    5921 cryosparc_P618_J51_003_volume_map.mrc gaussian using 564176 points 
    5922 correlation = 0.875, correlation about mean = 0.7311, overlap = 5.529e+04 
    5923 steps = 28, shift = 0.0652, angle = 0.00553 degrees 
    5924  
    5925 Position of cryosparc_P618_J86_map_sharp.mrc (#25) relative to
    5926 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    5927 Matrix rotation and translation 
    5928 1.00000000 0.00004080 -0.00000838 -0.05713261 
    5929 -0.00004080 1.00000000 -0.00008708 0.04208369 
    5930 0.00000837 0.00008708 1.00000000 -0.06105469 
    5931 Axis 0.90212433 -0.08676510 -0.42266240 
    5932 Axis point 0.00000000 843.75775233 453.93670404 
    5933 Rotation angle (degrees) 0.00553082 
    5934 Shift along axis -0.02938660 
    5935  
    5936 
    5937 > fitmap #26 inMap #4
    5938 
    5939 Fit map cryosparc_P618_J87_map_sharp.mrc in map
    5940 cryosparc_P618_J51_003_volume_map.mrc gaussian using 566545 points 
    5941 correlation = 0.8241, correlation about mean = 0.4999, overlap = 4.618e+04 
    5942 steps = 96, shift = 1.37, angle = 1.63 degrees 
    5943  
    5944 Position of cryosparc_P618_J87_map_sharp.mrc (#26) relative to
    5945 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    5946 Matrix rotation and translation 
    5947 0.99999279 0.00313949 -0.00213450 -0.02596276 
    5948 -0.00319827 0.99959954 -0.02811645 6.89238144 
    5949 0.00204537 0.02812307 0.99960238 -7.78464333 
    5950 Axis 0.99101095 -0.07365466 -0.11167943 
    5951 Axis point 0.00000000 278.89421676 242.04490105 
    5952 Rotation angle (degrees) 1.62597582 
    5953 Shift along axis 0.33599915 
    5954  
    5955 
    5956 > fitmap #27 inMap #4
    5957 
    5958 Fit map cryosparc_P618_J88_map_sharp.mrc in map
    5959 cryosparc_P618_J51_003_volume_map.mrc gaussian using 565831 points 
    5960 correlation = 0.813, correlation about mean = 0.5465, overlap = 4.037e+04 
    5961 steps = 84, shift = 1.23, angle = 1.68 degrees 
    5962  
    5963 Position of cryosparc_P618_J88_map_sharp.mrc (#27) relative to
    5964 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    5965 Matrix rotation and translation 
    5966 0.99998949 0.00396510 -0.00230253 -0.21513651 
    5967 -0.00403028 0.99957038 -0.02903138 7.26879188 
    5968 0.00218642 0.02904036 0.99957585 -8.07792156 
    5969 Axis 0.98776267 -0.07635415 -0.13599616 
    5970 Axis point 0.00000000 280.22063752 247.10089355 
    5971 Rotation angle (degrees) 1.68448598 
    5972 Shift along axis 0.33106002 
    5973  
    5974 
    5975 > hide #!25 models
    5976 
    5977 > hide #!26 models
    5978 
    5979 > hide #!27 models
    5980 
    5981 > show #!1 models
    5982 
    5983 > open "/Users/roan.groh/Downloads/cryosparc_P618_J93_005_volume_map (1).mrc"
    5984 
    5985 Opened cryosparc_P618_J93_005_volume_map (1).mrc as #28, grid size
    5986 384,384,384, pixel 1.19, shown at level 0.127, step 2, values float32 
    5987 
    5988 > open "/Users/roan.groh/Downloads/cryosparc_P618_J92_003_volume_map (1).mrc"
    5989 
    5990 Opened cryosparc_P618_J92_003_volume_map (1).mrc as #29, grid size
    5991 384,384,384, pixel 1.19, shown at level 0.266, step 2, values float32 
    5992 
    5993 > open "/Users/roan.groh/Downloads/cryosparc_P618_J91_004_volume_map (1).mrc"
    5994 
    5995 Opened cryosparc_P618_J91_004_volume_map (1).mrc as #30, grid size
    5996 384,384,384, pixel 1.19, shown at level 0.268, step 2, values float32 
    5997 
    5998 > open "/Users/roan.groh/Downloads/cryosparc_P618_J90_004_volume_map (1).mrc"
    5999 
    6000 Opened cryosparc_P618_J90_004_volume_map (1).mrc as #31, grid size
    6001 384,384,384, pixel 1.19, shown at level 0.264, step 2, values float32 
    6002 
    6003 > fitmap #28 inMap #4
    6004 
    6005 Fit map cryosparc_P618_J93_005_volume_map (1).mrc in map
    6006 cryosparc_P618_J51_003_volume_map.mrc gaussian using 70701 points 
    6007 correlation = 0.8837, correlation about mean = 0.3608, overlap = 2460 
    6008 steps = 64, shift = 1.48, angle = 0.515 degrees 
    6009  
    6010 Position of cryosparc_P618_J93_005_volume_map (1).mrc (#28) relative to
    6011 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    6012 Matrix rotation and translation 
    6013 0.99999174 0.00406012 -0.00019806 0.23269156 
    6014 -0.00405840 0.99995966 0.00801275 -2.19061133 
    6015 0.00023059 -0.00801188 0.99996788 1.17880203 
    6016 Axis -0.89179607 -0.02385513 -0.45180825 
    6017 Axis point 0.00000000 107.23586350 275.97823423 
    6018 Rotation angle (degrees) 0.51477940 
    6019 Shift along axis -0.68784860 
    6020  
    6021 
    6022 > fitmap #29 inMap #4
    6023 
    6024 Fit map cryosparc_P618_J92_003_volume_map (1).mrc in map
    6025 cryosparc_P618_J51_003_volume_map.mrc gaussian using 70730 points 
    6026 correlation = 0.9304, correlation about mean = 0.6545, overlap = 9559 
    6027 steps = 76, shift = 1.3, angle = 2.09 degrees 
    6028  
    6029 Position of cryosparc_P618_J92_003_volume_map (1).mrc (#29) relative to
    6030 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    6031 Matrix rotation and translation 
    6032 0.99966377 0.02535608 0.00542395 -6.59261686 
    6033 -0.02520929 0.99935420 -0.02560621 11.27488385 
    6034 -0.00606972 0.02546086 0.99965739 -5.23047046 
    6035 Axis 0.70167155 0.15792516 -0.69477815 
    6036 Axis point 0.00000000 189.70342087 430.66938909 
    6037 Rotation angle (degrees) 2.08542989 
    6038 Shift along axis 0.78875268 
    6039  
    6040 
    6041 > fitmap #30 inMap #4
    6042 
    6043 Fit map cryosparc_P618_J91_004_volume_map (1).mrc in map
    6044 cryosparc_P618_J51_003_volume_map.mrc gaussian using 70772 points 
    6045 correlation = 0.9375, correlation about mean = 0.6623, overlap = 9371 
    6046 steps = 68, shift = 1.24, angle = 1.87 degrees 
    6047  
    6048 Position of cryosparc_P618_J91_004_volume_map (1).mrc (#30) relative to
    6049 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    6050 Matrix rotation and translation 
    6051 0.99993362 -0.00974242 -0.00615192 3.90075157 
    6052 0.00955015 0.99948773 -0.03054611 4.49253885 
    6053 0.00644636 0.03048534 0.99951443 -9.23580452 
    6054 Axis 0.93554619 -0.19311803 0.29573428 
    6055 Axis point -0.00000000 305.71386687 142.26571544 
    6056 Rotation angle (degrees) 1.86921016 
    6057 Shift along axis 0.05039906 
    6058  
    6059 
    6060 > fitmap #31 inMap #4
    6061 
    6062 Fit map cryosparc_P618_J90_004_volume_map (1).mrc in map
    6063 cryosparc_P618_J51_003_volume_map.mrc gaussian using 70735 points 
    6064 correlation = 0.9699, correlation about mean = 0.7573, overlap = 9299 
    6065 steps = 48, shift = 0.163, angle = 0.323 degrees 
    6066  
    6067 Position of cryosparc_P618_J90_004_volume_map (1).mrc (#31) relative to
    6068 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    6069 Matrix rotation and translation 
    6070 0.99999286 -0.00325504 -0.00192154 1.20897040 
    6071 0.00326303 0.99998599 0.00416766 -1.82640551 
    6072 0.00190795 -0.00417391 0.99998947 0.61690219 
    6073 Axis -0.74097712 -0.34017119 0.57899609 
    6074 Axis point 0.00000000 135.24420588 431.94048330 
    6075 Rotation angle (degrees) 0.32250610 
    6076 Shift along axis 0.08265508 
    6077  
    6078 
    6079 > hide #!29 models
    6080 
    6081 > hide #!30 models
    6082 
    6083 > hide #!31 models
    6084 
    6085 > hide #!1 models
    6086 
    6087 > close #28
    6088 
    6089 > show #!29 models
    6090 
    6091 > volume #29 step 1
    6092 
    6093 > volume #30 step 1
    6094 
    6095 > volume #31 step 1
    6096 
    6097 > show #!30 models
    6098 
    6099 > show #!31 models
    6100 
    6101 > hide #!29 models
    6102 
    6103 > hide #!30 models
    6104 
    6105 > show #!30 models
    6106 
    6107 > show #!29 models
    6108 
    6109 > hide #!30 models
    6110 
    6111 > hide #!31 models
    6112 
    6113 > hide #!29 models
    6114 
    6115 > show #!1 models
    6116 
    6117 > show #!2 models
    6118 
    6119 > show #!3 models
    6120 
    6121 > hide #!2 models
    6122 
    6123 > hide #!1 models
    6124 
    6125 > close #29-31
    6126 
    6127 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    6128 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
    6129 > Refine_tRNA/cryosparc_P618_J54_003_volume_map.mrc
    6130 
    6131 Opened cryosparc_P618_J54_003_volume_map.mrc as #28, grid size 384,384,384,
    6132 pixel 1.19, shown at level 0.29, step 2, values float32 
    6133 
    6134 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    6135 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
    6136 > Refine_tRNA/cryosparc_P618_J56_003_volume_map.mrc
    6137 
    6138 Opened cryosparc_P618_J56_003_volume_map.mrc as #29, grid size 384,384,384,
    6139 pixel 1.19, shown at level 0.263, step 2, values float32 
    6140 
    6141 > open /Users/roan.groh/Library/CloudStorage/OneDrive-
    6142 > VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P618_2025_PTG-23/Germinated_Processing/J54-J56_NU-
    6143 > Refine_tRNA/cryosparc_P618_J55_003_volume_map.mrc
    6144 
    6145 Opened cryosparc_P618_J55_003_volume_map.mrc as #30, grid size 384,384,384,
    6146 pixel 1.19, shown at level 0.305, step 2, values float32 
    6147 
    6148 > hide #!3 models
    6149 
    6150 > fitmap #28 inMap #4
    6151 
    6152 Fit map cryosparc_P618_J54_003_volume_map.mrc in map
    6153 cryosparc_P618_J51_003_volume_map.mrc gaussian using 70762 points 
    6154 correlation = 0.9114, correlation about mean = 0.5594, overlap = 1.001e+04 
    6155 steps = 92, shift = 1.44, angle = 1.66 degrees 
    6156  
    6157 Position of cryosparc_P618_J54_003_volume_map.mrc (#28) relative to
    6158 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    6159 Matrix rotation and translation 
    6160 0.99998746 0.00440507 -0.00238390 -0.28288346 
    6161 -0.00447125 0.99958350 -0.02851031 7.27268808 
    6162 0.00225732 0.02852061 0.99959066 -7.93511999 
    6163 Axis 0.98492449 -0.08015398 -0.15329411 
    6164 Axis point 0.00000000 279.93358189 251.99789756 
    6165 Rotation angle (degrees) 1.65905498 
    6166 Shift along axis 0.35485344 
    6167  
    6168 
    6169 > fitmap #29 inMap #4
    6170 
    6171 Fit map cryosparc_P618_J56_003_volume_map.mrc in map
    6172 cryosparc_P618_J51_003_volume_map.mrc gaussian using 70763 points 
    6173 correlation = 0.942, correlation about mean = 0.6785, overlap = 1.077e+04 
    6174 steps = 44, shift = 0.0325, angle = 0.0594 degrees 
    6175  
    6176 Position of cryosparc_P618_J56_003_volume_map.mrc (#29) relative to
    6177 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    6178 Matrix rotation and translation 
    6179 0.99999967 0.00077557 0.00024116 -0.20967061 
    6180 -0.00077573 0.99999949 0.00064404 0.04735992 
    6181 -0.00024066 -0.00064423 0.99999976 0.18164953 
    6182 Axis -0.62138303 0.23239670 -0.74824789 
    6183 Axis point 59.26828730 266.06367560 0.00000000 
    6184 Rotation angle (degrees) 0.05939398 
    6185 Shift along axis 0.00537317 
    6186  
    6187 
    6188 > fitmap #30 inMap #4
    6189 
    6190 Fit map cryosparc_P618_J55_003_volume_map.mrc in map
    6191 cryosparc_P618_J51_003_volume_map.mrc gaussian using 70747 points 
    6192 correlation = 0.9444, correlation about mean = 0.65, overlap = 1.294e+04 
    6193 steps = 44, shift = 0.0701, angle = 0.0804 degrees 
    6194  
    6195 Position of cryosparc_P618_J55_003_volume_map.mrc (#30) relative to
    6196 cryosparc_P618_J51_003_volume_map.mrc gaussian (#4) coordinates: 
    6197 Matrix rotation and translation 
    6198 0.99999930 0.00094630 0.00071295 -0.37140461 
    6199 -0.00094683 0.99999927 0.00075004 0.03755462 
    6200 -0.00071224 -0.00075071 0.99999946 0.26497712 
    6201 Axis -0.53504974 0.50811003 -0.67494146 
    6202 Axis point 18.47156924 370.46749346 0.00000000 
    6203 Rotation angle (degrees) 0.08035409 
    6204 Shift along axis 0.03895778 
    6205  
    6206 
    6207 > volume #28 step 1
    6208 
    6209 > volume #29 step 1
    6210 
    6211 > volume #30 step 1
    6212 
    6213 > hide #!30 models
    6214 
    6215 > show #!30 models
    6216 
    6217 > hide #!30 models
    6218 
    6219 > show #!30 models
    6220 
    6221 > hide #!29 models
    6222 
    6223 > hide #!30 models
    6224 
    6225 > show #!29 models
    6226 
    6227 > hide #!29 models
    6228 
    6229 > show #!29 models
    6230 
    6231 > hide #!29 models
    6232 
    6233 > show #!29 models
    6234 
    6235 > show #!30 models
    6236 
    6237 > hide #!30 models
    6238 
    6239 > show #!30 models
    6240 
    6241 > hide #!30 models
    6242 
    6243 > show #!30 models
    6244 
    6245 > hide #!29 models
    6246 
    6247 > show #!29 models
    6248 
    6249 > vop gaussian #28,29,30 sdev 1
    6250 
    6251 Opened cryosparc_P618_J54_003_volume_map.mrc gaussian as #31, grid size
    6252 384,384,384, pixel 1.19, shown at step 1, values float32 
    6253 Opened cryosparc_P618_J56_003_volume_map.mrc gaussian as #32, grid size
    6254 384,384,384, pixel 1.19, shown at step 1, values float32 
    6255 Opened cryosparc_P618_J55_003_volume_map.mrc gaussian as #33, grid size
    6256 384,384,384, pixel 1.19, shown at step 1, values float32 
    6257 
    6258 > volume #31 level 0.1366
    6259 
    6260 > volume #32 level 0.1006
    6261 
    6262 > volume #32 level 0.08143
    6263 
    6264 > volume #33 level 0.08398
    6265 
    6266 > volume #33 level 0.05618
    6267 
    6268 > close #28-33
    6269 
    6270 > open /Users/roan.groh/Downloads/cryosparc_P618_J137_003_volume_map.mrc
    6271 
    6272 Opened cryosparc_P618_J137_003_volume_map.mrc as #28, grid size 384,384,384,
    6273 pixel 1.19, shown at level 0.254, step 2, values float32 
    6274 
    6275 > volume #28 step 1
    6276 
    6277 > show #!1 models
    6278 
    6279 > hide #!28 models
    6280 
    6281 > show #!28 models
    6282 
    6283 > hide #!1 models
    6284 
    6285 > hide #!28 models
    6286 
    6287 > open /Users/roan.groh/Downloads/cryosparc_P346_J314_map_sharp.mrc
    6288 
    6289 Opened cryosparc_P346_J314_map_sharp.mrc as #29, grid size 384,384,384, pixel
    6290 1.19, shown at level 0.112, step 2, values float32 
    6291 
    6292 > volume #29 step 1
    6293 
    6294 > show #!19 models
    6295 
    6296 > hide #!19 models
    6297 
    6298 > show #!19 models
    6299 
    6300 > color #19 #ff9300ff models
    6301 
    6302 > volume #29 level 0.1738
    6303 
    6304 > hide #!19 models
    6305 
    6306 > hide #!29 models
    6307 
    6308 > open /Users/roan.groh/Downloads/cryosparc_P618_J142_003_volume_map.mrc
    6309 
    6310 Opened cryosparc_P618_J142_003_volume_map.mrc as #30, grid size 384,384,384,
    6311 pixel 1.19, shown at level 0.282, step 2, values float32 
    6312 
    6313 > open /Users/roan.groh/Downloads/cryosparc_P618_J141_003_volume_map.mrc
    6314 
    6315 Opened cryosparc_P618_J141_003_volume_map.mrc as #31, grid size 384,384,384,
    6316 pixel 1.19, shown at level 0.271, step 2, values float32 
    6317 
    6318 > open /Users/roan.groh/Downloads/cryosparc_P618_J139_003_volume_map.mrc
    6319 
    6320 Opened cryosparc_P618_J139_003_volume_map.mrc as #32, grid size 384,384,384,
    6321 pixel 1.19, shown at level 0.272, step 2, values float32 
    6322 
    6323 > volume #30 step 1
    6324 
    6325 > volume #31 step 1
    6326 
    6327 > volume #32 step 1
    6328 
    6329 > hide #!31 models
    6330 
    6331 > hide #!32 models
    6332 
    6333 > hide #!30 models
    6334 
    6335 > show #!31 models
    6336 
    6337 > hide #!31 models
    6338 
    6339 > show #!32 models
    6340 
    6341 > hide #!32 models
    6342 
    6343 > show #!31 models
    6344 
    6345 > show #!30 models
    6346 
    6347 > hide #!30 models
    6348 
    6349 > hide #!31 models
    6350 
    6351 > open /Users/roan.groh/Downloads/cryosparc_P618_J133_map_sharp.mrc
    6352 
    6353 Opened cryosparc_P618_J133_map_sharp.mrc as #33, grid size 384,384,384, pixel
    6354 1.19, shown at level 0.0979, step 2, values float32 
    6355 
    6356 > volume #33 step 1
     252[deleted to fit within ticket limits]
     253
    6357254
    6358255> open /Users/roan.groh/Downloads/cryosparc_P346_J317_map_sharp.mrc