Changes between Initial Version and Version 1 of Ticket #14599


Ignore:
Timestamp:
Feb 16, 2024, 9:35:53 AM (20 months ago)
Author:
pett
Comment:

Legend:

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  • Ticket #14599

    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → ISOLDE session save: ResidueStepper referenced closed AtomicStructure

  • Ticket #14599 – Description

    initial v1  
    19871987> #5,0.99994,-0.010644,-0.00020879,-9.6619,0.010644,0.99994,0.00022728,2.604,0.00020636,-0.00022949,1,-22.21
    19881988
    1989 > fitmap #5 inMap #2
    1990 
    1991 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    1992 postprocess_masked.mrc (#2) using 24834 atoms 
    1993 average map value = 0.002311, steps = 140 
    1994 shifted from previous position = 5.28 
    1995 rotated from previous position = 15.2 degrees 
    1996 atoms outside contour = 23075, contour level = 0.019827 
    1997  
    1998 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    1999 postprocess_masked.mrc (#2) coordinates: 
    2000 Matrix rotation and translation 
    2001 0.96227159 -0.26620691 -0.05627843 64.06555888 
    2002 0.26715068 0.96360461 0.00983169 -41.78527684 
    2003 0.05161289 -0.02449558 0.99836670 -27.45233423 
    2004 Axis -0.06295782 -0.19787775 0.97820280 
    2005 Axis point 201.33507376 206.77699646 0.00000000 
    2006 Rotation angle (degrees) 15.82030175 
    2007 Shift along axis -22.61900134 
    2008  
    2009 
    2010 > view matrix models
    2011 > #5,0.96227,-0.26621,-0.056278,64.795,0.26715,0.9636,0.0098317,-42.479,0.051613,-0.024496,0.99837,-28.115
    2012 
    2013 > fitmap #5 inMap #2
    2014 
    2015 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2016 postprocess_masked.mrc (#2) using 24834 atoms 
    2017 average map value = 0.002311, steps = 72 
    2018 shifted from previous position = 1.21 
    2019 rotated from previous position = 0.00778 degrees 
    2020 atoms outside contour = 23067, contour level = 0.019827 
    2021  
    2022 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2023 postprocess_masked.mrc (#2) coordinates: 
    2024 Matrix rotation and translation 
    2025 0.96227630 -0.26621683 -0.05615081 64.03132972 
    2026 0.26715515 0.96360384 0.00978643 -41.77085516 
    2027 0.05150183 -0.02441823 0.99837433 -27.45906013 
    2028 Axis -0.06273766 -0.19745476 0.97830241 
    2029 Axis point 201.23845109 206.67347327 0.00000000 
    2030 Rotation angle (degrees) 15.81908656 
    2031 Shift along axis -22.63258616 
    2032  
    2033 
    2034 > ui mousemode right "rotate selected models"
    2035 
    2036 > view matrix models
    2037 > #5,0.93557,-0.35111,-0.037823,83.492,0.35079,0.93633,-0.014992,-49.016,0.040678,0.00075813,0.99917,-30.487
    2038 
    2039 > view matrix models
    2040 > #5,0.89894,-0.43596,0.042909,92.983,0.43741,0.89863,-0.033745,-55.919,-0.023848,0.049104,0.99851,-26.667
    2041 
    2042 > fitmap #5 inMap #2
    2043 
    2044 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2045 postprocess_masked.mrc (#2) using 24834 atoms 
    2046 average map value = 0.002052, steps = 88 
    2047 shifted from previous position = 2 
    2048 rotated from previous position = 4.18 degrees 
    2049 atoms outside contour = 23183, contour level = 0.019827 
    2050  
    2051 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2052 postprocess_masked.mrc (#2) coordinates: 
    2053 Matrix rotation and translation 
    2054 0.92406760 -0.37866760 0.05205690 73.89695462 
    2055 0.38169123 0.92139174 -0.07313723 -40.57922884 
    2056 -0.02027010 0.08745341 0.99596236 -32.99758859 
    2057 Axis 0.20575592 0.09266859 0.97420585 
    2058 Axis point 138.09250324 178.70777332 0.00000000 
    2059 Rotation angle (degrees) 22.96977419 
    2060 Shift along axis -20.70212771 
    2061  
    2062 
    2063 > view matrix models
    2064 > #5,0.90369,-0.41191,0.11696,72.462,0.42201,0.90303,-0.08027,-43.934,-0.072554,0.1219,0.98989,-27.864
    2065 
    2066 > view matrix models
    2067 > #5,0.90022,-0.41912,0.1181,74.449,0.42492,0.9048,-0.027908,-55.02,-0.095159,0.075306,0.99261,-14.094
    2068 
    2069 > fitmap #5 inMap #2
    2070 
    2071 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2072 postprocess_masked.mrc (#2) using 24834 atoms 
    2073 average map value = 0.001909, steps = 404 
    2074 shifted from previous position = 3.17 
    2075 rotated from previous position = 6.17 degrees 
    2076 atoms outside contour = 23221, contour level = 0.019827 
    2077  
    2078 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2079 postprocess_masked.mrc (#2) coordinates: 
    2080 Matrix rotation and translation 
    2081 0.93656786 -0.32121576 0.14021796 44.62472122 
    2082 0.32805506 0.94424041 -0.02810572 -41.12297379 
    2083 -0.12337146 0.07232213 0.98972167 -4.88221826 
    2084 Axis 0.14186795 0.37235577 0.91718301 
    2085 Axis point 130.32589263 119.13280959 0.00000000 
    2086 Rotation angle (degrees) 20.72900456 
    2087 Shift along axis -13.45944659 
    2088  
    2089 
    2090 > ui mousemode right "translate selected models"
    2091 
    2092 > view matrix models
    2093 > #5,0.93657,-0.32122,0.14022,32.763,0.32806,0.94424,-0.028106,-29.6,-0.12337,0.072322,0.98972,-5.3666
    2094 
    2095 > view matrix models
    2096 > #5,0.93657,-0.32122,0.14022,28.22,0.32806,0.94424,-0.028106,-38.75,-0.12337,0.072322,0.98972,-7.9647
    2097 
    2098 > view matrix models
    2099 > #5,0.93657,-0.32122,0.14022,25.245,0.32806,0.94424,-0.028106,-41.161,-0.12337,0.072322,0.98972,-6.5536
    2100 
    2101 > fitmap #5 inMap #2
    2102 
    2103 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2104 postprocess_masked.mrc (#2) using 24834 atoms 
    2105 average map value = 0.001401, steps = 60 
    2106 shifted from previous position = 1.26 
    2107 rotated from previous position = 1.17 degrees 
    2108 atoms outside contour = 23384, contour level = 0.019827 
    2109  
    2110 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2111 postprocess_masked.mrc (#2) coordinates: 
    2112 Matrix rotation and translation 
    2113 0.93219333 -0.32865938 0.15165293 26.52063693 
    2114 0.33817841 0.94017952 -0.04120487 -39.39528113 
    2115 -0.12903861 0.08969665 0.98757458 -8.92742124 
    2116 Axis 0.17803624 0.38176233 0.90695128 
    2117 Axis point 107.80856997 68.42642644 0.00000000 
    2118 Rotation angle (degrees) 21.56928248 
    2119 Shift along axis -18.41473587 
    2120  
    2121 
    2122 > view matrix models
    2123 > #5,0.93219,-0.32866,0.15165,25.256,0.33818,0.94018,-0.041205,-35.516,-0.12904,0.089697,0.98757,-12.737
    2124 
    2125 > fitmap #5 inMap #2
    2126 
    2127 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2128 postprocess_masked.mrc (#2) using 24834 atoms 
    2129 average map value = 0.001878, steps = 140 
    2130 shifted from previous position = 6.24 
    2131 rotated from previous position = 6.15 degrees 
    2132 atoms outside contour = 23188, contour level = 0.019827 
    2133  
    2134 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2135 postprocess_masked.mrc (#2) coordinates: 
    2136 Matrix rotation and translation 
    2137 0.89615602 -0.42170549 0.13809005 57.15450912 
    2138 0.42449067 0.90537618 0.01008206 -59.37195822 
    2139 -0.12927510 0.04958284 0.99036836 -9.43010926 
    2140 Axis 0.04446741 0.30098223 0.95259243 
    2141 Axis point 145.42872810 102.28389026 0.00000000 
    2142 Rotation angle (degrees) 26.36924769 
    2143 Shift along axis -24.31144247 
    2144  
    2145 
    2146 > view matrix models
    2147 > #5,0.89616,-0.42171,0.13809,53.866,0.42449,0.90538,0.010082,-61.878,-0.12928,0.049583,0.99037,-4.2952
    2148 
    2149 > fitmap #5 inMap #2
    2150 
    2151 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2152 postprocess_masked.mrc (#2) using 24834 atoms 
    2153 average map value = 0.001688, steps = 100 
    2154 shifted from previous position = 2.56 
    2155 rotated from previous position = 1.51 degrees 
    2156 atoms outside contour = 23237, contour level = 0.019827 
    2157  
    2158 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2159 postprocess_masked.mrc (#2) coordinates: 
    2160 Matrix rotation and translation 
    2161 0.88597015 -0.43676391 0.15586592 58.11946311 
    2162 0.44136459 0.89731023 0.00562578 -62.21068705 
    2163 -0.14231722 0.06380943 0.98776220 -4.28648020 
    2164 Axis 0.06261709 0.32090390 0.94503957 
    2165 Axis point 148.74128880 97.15627990 0.00000000 
    2166 Rotation angle (degrees) 27.68426024 
    2167 Shift along axis -20.37527351 
    2168  
    2169 
    2170 > ui mousemode right "rotate selected models"
    2171 
    2172 > view matrix models
    2173 > #5,0.85599,-0.51139,0.075936,95.141,0.51232,0.85875,0.0080607,-69.732,-0.069332,0.032004,0.99708,-14.945
    2174 
    2175 > fitmap #5 inMap #2
    2176 
    2177 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2178 postprocess_masked.mrc (#2) using 24834 atoms 
    2179 average map value = 0.01333, steps = 116 
    2180 shifted from previous position = 7.91 
    2181 rotated from previous position = 4.99 degrees 
    2182 atoms outside contour = 20284, contour level = 0.019827 
    2183  
    2184 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2185 postprocess_masked.mrc (#2) coordinates: 
    2186 Matrix rotation and translation 
    2187 0.83683614 -0.54745338 -0.00027652 128.32384038 
    2188 0.54745337 0.83683618 -0.00009279 -69.29117619 
    2189 0.00028220 -0.00007373 0.99999996 -22.70827733 
    2190 Axis 0.00001741 -0.00051029 0.99999987 
    2191 Axis point 180.42570459 180.62776583 0.00000000 
    2192 Rotation angle (degrees) 33.19248364 
    2193 Shift along axis -22.67068115 
    2194  
    2195 
    2196 > fitmap #5 inMap #2
    2197 
    2198 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2199 postprocess_masked.mrc (#2) using 24834 atoms 
    2200 average map value = 0.01333, steps = 40 
    2201 shifted from previous position = 0.0155 
    2202 rotated from previous position = 0.0065 degrees 
    2203 atoms outside contour = 20283, contour level = 0.019827 
    2204  
    2205 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2206 postprocess_masked.mrc (#2) coordinates: 
    2207 Matrix rotation and translation 
    2208 0.83683861 -0.54744959 -0.00029675 128.32330644 
    2209 0.54744955 0.83683866 -0.00020432 -69.25506361 
    2210 0.00036019 0.00000853 0.99999994 -22.73829665 
    2211 Axis 0.00019441 -0.00060000 0.99999980 
    2212 Axis point 180.37124399 180.65241600 0.00000000 
    2213 Rotation angle (degrees) 33.19222565 
    2214 Shift along axis -22.67179200 
    2215  
    2216 
    2217 > combine #5 #6 name 6-Fla_2
    2218 
    2219 > select add #6
    2220 
    2221 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2222 
    2223 > select subtract #5
    2224 
    2225 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2226 
    2227 > view matrix models
    2228 > #6,-0.0033124,-0.99463,0.10341,376.75,0.99996,-0.0042073,-0.0084366,9.1925,0.0088264,0.10338,0.9946,-44.637
    2229 
    2230 > view matrix models
    2231 > #6,-0.022273,-0.99906,-0.037086,408.78,0.99533,-0.018675,-0.094678,29.78,0.093897,-0.039022,0.99482,-33.446
    2232 
    2233 > ui mousemode right "translate selected models"
    2234 
    2235 > view matrix models
    2236 > #6,-0.022273,-0.99906,-0.037086,373.69,0.99533,-0.018675,-0.094678,8.7357,0.093897,-0.039022,0.99482,-27.404
    2237 
    2238 > view matrix models
    2239 > #6,-0.022273,-0.99906,-0.037086,368.08,0.99533,-0.018675,-0.094678,16.252,0.093897,-0.039022,0.99482,-27.184
    2240 
    2241 > view matrix models
    2242 > #6,-0.022273,-0.99906,-0.037086,362.97,0.99533,-0.018675,-0.094678,2.1247,0.093897,-0.039022,0.99482,-29.071
    2243 
    2244 > select add #5
    2245 
    2246 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2247 
    2248 > select subtract #5
    2249 
    2250 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2251 
    2252 > ui mousemode right "rotate selected models"
    2253 
    2254 > view matrix models
    2255 > #6,-0.34295,-0.9393,-0.010251,413.08,0.92819,-0.33717,-0.15738,93.561,0.14437,-0.063487,0.98748,-33.277
    2256 
    2257 > mmaker #6 to #1
    2258 
    2259 Parameters 
    2260 --- 
    2261 Chain pairing | bb 
    2262 Alignment algorithm | Needleman-Wunsch 
    2263 Similarity matrix | BLOSUM-62 
    2264 SS fraction | 0.3 
    2265 Gap open (HH/SS/other) | 18/18/6 
    2266 Gap extend | 1 
    2267 SS matrix |  |  | H | S | O 
    2268 ---|---|---|--- 
    2269 H | 6 | -9 | -6 
    2270 S |  | 6 | -6 
    2271 O |  |  | 4 
    2272 Iteration cutoff | 2 
    2273  
    2274 Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_2, chain A (#6),
    2275 sequence alignment score = 2158.5 
    2276 RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
    2277 1.043) 
    2278  
    2279 
    2280 > select add #5
    2281 
    2282 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2283 
    2284 > select subtract #5
    2285 
    2286 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2287 
    2288 > select add #5
    2289 
    2290 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2291 
    2292 > view matrix models
    2293 > #5,0.93477,-0.35494,0.015253,70.104,0.35399,0.93419,0.044597,-62.86,-0.030078,-0.036288,0.99889,-10.023,#6,-0.87971,-0.47526,0.015731,419.23,0.47546,-0.87859,0.045013,242.64,-0.007572,0.047078,0.99886,-19.709
    2294 
    2295 > undo
    2296 
    2297 > select subtract #5
    2298 
    2299 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2300 
    2301 > view matrix models
    2302 > #6,-0.9036,-0.42669,0.037878,415.1,0.42761,-0.90373,0.020478,256.42,0.025493,0.034701,0.99907,-25.535
    2303 
    2304 > view matrix models
    2305 > #6,-0.8445,-0.49104,-0.21379,464.42,0.4721,-0.87103,0.13575,218.1,-0.25287,0.013705,0.9674,43.497
    2306 
    2307 > view matrix models
    2308 > #6,-0.81535,-0.57726,0.044421,426.07,0.57884,-0.81118,0.083177,193.53,-0.011982,0.093531,0.99554,-29.004
    2309 
    2310 > view matrix models
    2311 > #6,-0.9227,-0.38529,0.013304,415.39,0.38547,-0.92147,0.048129,263.59,-0.0062843,0.049537,0.99875,-21.818
    2312 
    2313 > view matrix models
    2314 > #6,-0.76232,-0.6043,0.23169,384.28,0.62063,-0.78409,-0.0030567,195.83,0.18351,0.14146,0.97279,-75.588
    2315 
    2316 > view matrix models
    2317 > #6,-0.75172,-0.65903,-0.024572,442.73,0.65527,-0.7506,0.084961,164.69,-0.074435,0.047766,0.99608,-6.5883
    2318 
    2319 > view matrix models
    2320 > #6,-0.73011,-0.67966,-0.070675,451.31,0.68297,-0.72918,-0.043123,179.2,-0.022226,-0.079753,0.99657,8.4246
    2321 
    2322 > ui mousemode right "translate selected models"
    2323 
    2324 > view matrix models
    2325 > #6,-0.73011,-0.67966,-0.070675,455.64,0.68297,-0.72918,-0.043123,194.39,-0.022226,-0.079753,0.99657,3.2864
    2326 
    2327 > select up
    2328 
    2329 101818 atoms, 102262 bonds, 10101 residues, 9 models selected 
    2330 
    2331 > select up
    2332 
    2333 101818 atoms, 102262 bonds, 10101 residues, 9 models selected 
    2334 
    2335 > select down
    2336 
    2337 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2338 
    2339 > mmaker #6 to #1
    2340 
    2341 Parameters 
    2342 --- 
    2343 Chain pairing | bb 
    2344 Alignment algorithm | Needleman-Wunsch 
    2345 Similarity matrix | BLOSUM-62 
    2346 SS fraction | 0.3 
    2347 Gap open (HH/SS/other) | 18/18/6 
    2348 Gap extend | 1 
    2349 SS matrix |  |  | H | S | O 
    2350 ---|---|---|--- 
    2351 H | 6 | -9 | -6 
    2352 S |  | 6 | -6 
    2353 O |  |  | 4 
    2354 Iteration cutoff | 2 
    2355  
    2356 Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_2, chain A (#6),
    2357 sequence alignment score = 2158.5 
    2358 RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
    2359 1.043) 
    2360  
    2361 
    2362 > select subtract #6
    2363 
    2364 Nothing selected 
    2365 
    2366 > select add #5
    2367 
    2368 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2369 
    2370 > select add #6
    2371 
    2372 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2373 
    2374 > fitmap #6 #2
    2375 
    2376 Missing required "in_map" argument 
    2377 
    2378 > fitmap #6 inMap #2
    2379 
    2380 Fit molecule 6-Fla_2 (#6) to map postprocess_masked.mrc (#2) using 24834 atoms 
    2381 average map value = 0.01338, steps = 28 
    2382 shifted from previous position = 0.0537 
    2383 rotated from previous position = 0.0411 degrees 
    2384 atoms outside contour = 20261, contour level = 0.019827 
    2385  
    2386 Position of 6-Fla_2 (#6) relative to postprocess_masked.mrc (#2) coordinates: 
    2387 Matrix rotation and translation 
    2388 -0.96147984 -0.27487507 0.00045540 403.48472611 
    2389 0.27487505 -0.96147995 -0.00011577 304.41101302 
    2390 0.00046968 0.00001386 0.99999989 -13.36530660 
    2391 Axis 0.00023581 -0.00002598 0.99999997 
    2392 Axis point 180.41440512 180.47703552 0.00000000 
    2393 Rotation angle (degrees) 164.04543077 
    2394 Shift along axis -13.27806788 
    2395  
    2396 
    2397 > select clear
    2398 
    2399 > fitmap #6 inMap #2
    2400 
    2401 Fit molecule 6-Fla_2 (#6) to map postprocess_masked.mrc (#2) using 24834 atoms 
    2402 average map value = 0.01338, steps = 36 
    2403 shifted from previous position = 0.0251 
    2404 rotated from previous position = 0.00535 degrees 
    2405 atoms outside contour = 20280, contour level = 0.019827 
    2406  
    2407 Position of 6-Fla_2 (#6) relative to postprocess_masked.mrc (#2) coordinates: 
    2408 Matrix rotation and translation 
    2409 -0.96148667 -0.27485133 0.00036776 403.47973857 
    2410 0.27485130 -0.96148674 -0.00013663 304.40474128 
    2411 0.00039115 -0.00003029 0.99999992 -13.33423168 
    2412 Axis 0.00019345 -0.00004255 0.99999998 
    2413 Axis point 180.41399663 180.47086028 0.00000000 
    2414 Rotation angle (degrees) 164.04684576 
    2415 Shift along axis -13.26912867 
    2416  
    2417 
    2418 > fitmap #5 inMap #2
    2419 
    2420 Fit molecule 6-Flagellin_Rebuild4_RelToModel.pdb (#5) to map
    2421 postprocess_masked.mrc (#2) using 24834 atoms 
    2422 average map value = 0.01333, steps = 28 
    2423 shifted from previous position = 0.018 
    2424 rotated from previous position = 0.00757 degrees 
    2425 atoms outside contour = 20281, contour level = 0.019827 
    2426  
    2427 Position of 6-Flagellin_Rebuild4_RelToModel.pdb (#5) relative to
    2428 postprocess_masked.mrc (#2) coordinates: 
    2429 Matrix rotation and translation 
    2430 0.83684417 -0.54744105 -0.00036124 128.33217468 
    2431 0.54744106 0.83684424 -0.00008955 -69.29329170 
    2432 0.00035132 -0.00012281 0.99999993 -22.71472391 
    2433 Axis -0.00003038 -0.00065081 0.99999979 
    2434 Axis point 180.44135023 180.64306030 0.00000000 
    2435 Rotation angle (degrees) 33.19164325 
    2436 Shift along axis -22.67352109 
    2437  
    2438 
    2439 > combine #6 #7 6-Fla_3
    2440 
    2441 Expected a keyword 
    2442 
    2443 > combine #6 #7 name 6-Fla_3
    2444 
    2445 > select add #7
    2446 
    2447 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2448 
    2449 > select subtract #7
    2450 
    2451 Nothing selected 
    2452 
    2453 > select add #6
    2454 
    2455 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2456 
    2457 > select subtract #6
    2458 
    2459 Nothing selected 
    2460 
    2461 > select add #7
    2462 
    2463 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2464 
    2465 > ui mousemode right "rotate selected models"
    2466 
    2467 > view matrix models
    2468 > #7,-0.99053,-0.0060293,0.13718,328.15,0.0041013,-0.99989,-0.014333,372.02,0.13725,-0.013635,0.99044,-37.525
    2469 
    2470 > view matrix models
    2471 > #7,-0.97138,0.14652,-0.18697,355.49,-0.15486,-0.98746,0.030725,394.25,-0.18012,0.058799,0.98189,16.135
    2472 
    2473 > view matrix models
    2474 > #7,-0.99651,0.022749,0.080302,334.51,-0.02303,-0.99973,-0.0025785,375.43,0.080222,-0.0044189,0.99677,-28.623
    2475 
    2476 > view matrix models
    2477 > #7,-0.85586,0.42143,0.29984,180.89,-0.40834,-0.90637,0.10838,416.04,0.31744,-0.029683,0.94781,-63.953
    2478 
    2479 > view matrix models
    2480 > #7,-0.70631,0.60075,0.37447,98.288,-0.63673,-0.7703,0.034806,450.49,0.30936,-0.21385,0.92659,-20.457
    2481 
    2482 > view matrix models
    2483 > #7,-0.65592,0.7548,0.0074148,127.02,-0.74849,-0.65165,0.12294,432.72,0.097629,0.075091,0.99239,-47.717
    2484 
    2485 > ui mousemode right "translate selected models"
    2486 
    2487 > view matrix models
    2488 > #7,-0.65592,0.7548,0.0074148,177.11,-0.74849,-0.65165,0.12294,425.83,0.097629,0.075091,0.99239,-46.232
    2489 
    2490 > ui mousemode right "rotate selected models"
    2491 
    2492 > view matrix models
    2493 > #7,-0.18744,0.96449,-0.18607,72.901,-0.93028,-0.11349,0.34886,310.34,0.31535,0.23849,0.91852,-111.26
    2494 
    2495 > view matrix models
    2496 > #7,0.33326,0.93334,0.13345,-92.072,-0.92753,0.29915,0.22407,249.4,0.16921,-0.19846,0.96539,-0.10432
    2497 
    2498 > view matrix models
    2499 > #7,0.46698,0.83035,0.30406,-132.09,-0.8842,0.43399,0.17276,222.58,0.011492,-0.34952,0.93686,69.54
    2500 
    2501 > view matrix models
    2502 > #7,0.61056,0.76184,0.21635,-131.37,-0.78416,0.54327,0.29992,154.59,0.11095,-0.35277,0.92911,50.757
    2503 
    2504 > view matrix models
    2505 > #7,0.49978,0.8021,0.3269,-137.63,-0.86609,0.46746,0.17711,211.08,-0.010752,-0.37164,0.92831,80.401
    2506 
    2507 > view matrix models
    2508 > #7,0.31329,0.93666,0.15658,-93.011,-0.93889,0.28074,0.19915,260.37,0.14257,-0.2094,0.96738,7.3615
    2509 
    2510 > view matrix models
    2511 > #7,0.26776,0.90309,0.33576,-111.15,-0.96301,0.26176,0.063941,295.44,-0.030143,-0.34046,0.93977,75.889
    2512 
    2513 > view matrix models
    2514 > #7,0.39729,0.91661,0.044669,-84.987,-0.86432,0.35738,0.35387,199.11,0.3084,-0.1792,0.93423,-27.338
    2515 
    2516 > view matrix models
    2517 > #7,0.42412,0.89838,-0.11415,-56.241,-0.89161,0.43631,0.12112,233.64,0.15861,0.050406,0.98605,-52.799
    2518 
    2519 > select add #6
    2520 
    2521 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2522 
    2523 > select subtract #6
    2524 
    2525 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2526 
    2527 > select add #6
    2528 
    2529 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2530 
    2531 > select subtract #6
    2532 
    2533 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2534 
    2535 > view matrix models
    2536 > #7,0.40471,0.91379,0.034637,-84.036,-0.90929,0.39813,0.12116,245.17,0.096924,-0.08053,0.99203,-14.162
    2537 
    2538 > select add #6
    2539 
    2540 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2541 
    2542 > select subtract #6
    2543 
    2544 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2545 
    2546 > select add #5
    2547 
    2548 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2549 
    2550 > select subtract #5
    2551 
    2552 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2553 
    2554 > select add #5
    2555 
    2556 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2557 
    2558 > select subtract #5
    2559 
    2560 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2561 
    2562 > mmaker #7 #1
    2563 
    2564 > matchmaker #7 #1
    2565 
    2566 Missing required "to" argument 
    2567 
    2568 > mmaker #7 to #1
    2569 
    2570 Parameters 
    2571 --- 
    2572 Chain pairing | bb 
    2573 Alignment algorithm | Needleman-Wunsch 
    2574 Similarity matrix | BLOSUM-62 
    2575 SS fraction | 0.3 
    2576 Gap open (HH/SS/other) | 18/18/6 
    2577 Gap extend | 1 
    2578 SS matrix |  |  | H | S | O 
    2579 ---|---|---|--- 
    2580 H | 6 | -9 | -6 
    2581 S |  | 6 | -6 
    2582 O |  |  | 4 
    2583 Iteration cutoff | 2 
    2584  
    2585 Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_3, chain A (#7),
    2586 sequence alignment score = 2158.5 
    2587 RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
    2588 1.043) 
    2589  
    2590 
    2591 > undo
    2592 
    2593 > select subtract #7
    2594 
    2595 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2596 
    2597 > select subtract #5
    2598 
    2599 Nothing selected 
    2600 
    2601 > select add #5
    2602 
    2603 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2604 
    2605 > select add #6
    2606 
    2607 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2608 
    2609 > select add #7
    2610 
    2611 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    2612 
    2613 > select subtract #7
    2614 
    2615 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2616 
    2617 > select subtract #6
    2618 
    2619 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2620 
    2621 > select subtract #5
    2622 
    2623 Nothing selected 
    2624 
    2625 > select add #7
    2626 
    2627 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2628 
    2629 > select subtract #7
    2630 
    2631 Nothing selected 
    2632 
    2633 > undo
    2634 
    2635 [Repeated 5 time(s)]
    2636 
    2637 > select subtract #6
    2638 
    2639 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2640 
    2641 > select subtract #5
    2642 
    2643 Nothing selected 
    2644 
    2645 > select add #5
    2646 
    2647 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2648 
    2649 > select add #6
    2650 
    2651 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2652 
    2653 > select subtract #6
    2654 
    2655 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2656 
    2657 > select add #7
    2658 
    2659 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2660 
    2661 > select subtract #7
    2662 
    2663 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2664 
    2665 > select add #6
    2666 
    2667 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2668 
    2669 > select subtract #5
    2670 
    2671 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2672 
    2673 > select subtract #6
    2674 
    2675 Nothing selected 
    2676 
    2677 > select add #6
    2678 
    2679 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2680 
    2681 > select add #5
    2682 
    2683 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2684 
    2685 > select subtract #6
    2686 
    2687 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2688 
    2689 > select subtract #5
    2690 
    2691 Nothing selected 
    2692 
    2693 > select add #7
    2694 
    2695 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2696 
    2697 > view matrix models
    2698 > #7,-0.96136,-0.27523,-0.0063932,404.81,0.27522,-0.96138,0.0019673,303.89,-0.0066878,0.00013167,0.99998,-11.857
    2699 
    2700 > view matrix models
    2701 > #7,-0.3805,0.92477,-0.0048112,36.57,-0.92454,-0.38028,0.024655,433.22,0.020971,0.01383,0.99968,-20.429
    2702 
    2703 > ui mousemode right "translate selected models"
    2704 
    2705 > view matrix models
    2706 > #7,-0.3805,0.92477,-0.0048112,90.625,-0.92454,-0.38028,0.024655,414.72,0.020971,0.01383,0.99968,-19.177
    2707 
    2708 > ui mousemode right "rotate selected models"
    2709 
    2710 > view matrix models
    2711 > #7,-0.18901,0.98195,-0.0071606,39.049,-0.98165,-0.18875,0.027125,387.06,0.025284,0.012156,0.99961,-19.728
    2712 
    2713 > select add #6
    2714 
    2715 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2716 
    2717 > select add #5
    2718 
    2719 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    2720 
    2721 > select add #4
    2722 
    2723 74502 atoms, 74718 bonds, 4914 residues, 6 models selected 
    2724 
    2725 > select subtract #4
    2726 
    2727 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    2728 
    2729 > select subtract #5
    2730 
    2731 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2732 
    2733 > select subtract #6
    2734 
    2735 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2736 
    2737 > select subtract #7
    2738 
    2739 Nothing selected 
    2740 
    2741 > select add #7
    2742 
    2743 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2744 
    2745 > view matrix models
    2746 > #7,-0.18666,0.98228,-0.016851,40.358,-0.98227,-0.1863,0.020866,387.9,0.017357,0.020448,0.99964,-19.762
    2747 
    2748 > fitmap #7 inMap #2
    2749 
    2750 Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms 
    2751 average map value = 0.002948, steps = 80 
    2752 shifted from previous position = 1.64 
    2753 rotated from previous position = 1.99 degrees 
    2754 atoms outside contour = 22938, contour level = 0.019827 
    2755  
    2756 Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates: 
    2757 Matrix rotation and translation 
    2758 -0.17039812 0.98536777 0.00385086 32.94944410 
    2759 -0.98537471 -0.17039244 -0.00175857 388.91585111 
    2760 -0.00107668 -0.00409420 0.99999104 -9.62680299 
    2761 Axis -0.00118515 0.00250034 -0.99999617 
    2762 Axis point 180.18663414 180.57028280 0.00000000 
    2763 Rotation angle (degrees) 99.81106279 
    2764 Shift along axis 10.56013679 
    2765  
    2766 
    2767 > mmaker #7 #1
    2768 
    2769 > matchmaker #7 #1
    2770 
    2771 Missing required "to" argument 
    2772 
    2773 > mmaker #7 to #1
    2774 
    2775 Parameters 
    2776 --- 
    2777 Chain pairing | bb 
    2778 Alignment algorithm | Needleman-Wunsch 
    2779 Similarity matrix | BLOSUM-62 
    2780 SS fraction | 0.3 
    2781 Gap open (HH/SS/other) | 18/18/6 
    2782 Gap extend | 1 
    2783 SS matrix |  |  | H | S | O 
    2784 ---|---|---|--- 
    2785 H | 6 | -9 | -6 
    2786 S |  | 6 | -6 
    2787 O |  |  | 4 
    2788 Iteration cutoff | 2 
    2789  
    2790 Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_3, chain A (#7),
    2791 sequence alignment score = 2158.5 
    2792 RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
    2793 1.043) 
    2794  
    2795 
    2796 > undo
    2797 
    2798 > ui mousemode right "translate selected models"
    2799 
    2800 > view matrix models
    2801 > #7,-0.18901,0.98195,-0.0071606,42.068,-0.98165,-0.18875,0.027125,385.13,0.025284,0.012156,0.99961,-36.918
    2802 
    2803 > view matrix models
    2804 > #7,-0.18901,0.98195,-0.0071606,40.657,-0.98165,-0.18875,0.027125,387.3,0.025284,0.012156,0.99961,-40.674
    2805 
    2806 > fitmap #7 inMap #2
    2807 
    2808 Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms 
    2809 average map value = 0.01322, steps = 84 
    2810 shifted from previous position = 1.01 
    2811 rotated from previous position = 3.61 degrees 
    2812 atoms outside contour = 20292, contour level = 0.019827 
    2813  
    2814 Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates: 
    2815 Matrix rotation and translation 
    2816 -0.13312076 0.99109981 0.00014608 25.62829726 
    2817 -0.99109973 -0.13312081 0.00041842 383.23840063 
    2818 0.00043415 -0.00008908 0.99999990 -32.12944258 
    2819 Axis -0.00025603 -0.00014533 -0.99999996 
    2820 Axis point 180.42269068 180.40987157 0.00000000 
    2821 Rotation angle (degrees) 97.64997121 
    2822 Shift along axis 32.06718481 
    2823  
    2824 
    2825 > select clear
    2826 
    2827 > fitmap #7 inMap #2
    2828 
    2829 Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms 
    2830 average map value = 0.01322, steps = 28 
    2831 shifted from previous position = 0.00789 
    2832 rotated from previous position = 0.0046 degrees 
    2833 atoms outside contour = 20288, contour level = 0.019827 
    2834  
    2835 Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates: 
    2836 Matrix rotation and translation 
    2837 -0.13311082 0.99110115 0.00006736 25.63719568 
    2838 -0.99110107 -0.13311084 0.00040580 383.24602689 
    2839 0.00041115 -0.00001275 0.99999991 -32.14108844 
    2840 Axis -0.00021115 -0.00017344 -0.99999996 
    2841 Axis point 180.43184899 180.41076127 0.00000000 
    2842 Rotation angle (degrees) 97.64939516 
    2843 Shift along axis 32.06920413 
    2844  
    2845 
    2846 > mmaker #7 to #1
    2847 
    2848 Parameters 
    2849 --- 
    2850 Chain pairing | bb 
    2851 Alignment algorithm | Needleman-Wunsch 
    2852 Similarity matrix | BLOSUM-62 
    2853 SS fraction | 0.3 
    2854 Gap open (HH/SS/other) | 18/18/6 
    2855 Gap extend | 1 
    2856 SS matrix |  |  | H | S | O 
    2857 ---|---|---|--- 
    2858 H | 6 | -9 | -6 
    2859 S |  | 6 | -6 
    2860 O |  |  | 4 
    2861 Iteration cutoff | 2 
    2862  
    2863 Matchmaker Rhom_2Ring_Trimmed.pdb, chain A (#1) with 6-Fla_3, chain A (#7),
    2864 sequence alignment score = 2158.5 
    2865 RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 273 pairs:
    2866 1.043) 
    2867  
    2868 
    2869 > select add #7
    2870 
    2871 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2872 
    2873 > select add #6
    2874 
    2875 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    2876 
    2877 > select subtract #6
    2878 
    2879 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2880 
    2881 > select subtract #7
    2882 
    2883 Nothing selected 
    2884 
    2885 > undo
    2886 
    2887 [Repeated 3 time(s)]
    2888 
    2889 > select add #7
    2890 
    2891 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2892 
    2893 > undo
    2894 
    2895 [Repeated 3 time(s)]
    2896 
    2897 > select subtract #7
    2898 
    2899 Nothing selected 
    2900 
    2901 > select add #7
    2902 
    2903 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2904 
    2905 > select subtract #7
    2906 
    2907 Nothing selected 
    2908 
    2909 > select add #7
    2910 
    2911 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2912 
    2913 > select subtract #7
    2914 
    2915 Nothing selected 
    2916 
    2917 > select add #6
    2918 
    2919 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2920 
    2921 > select subtract #6
    2922 
    2923 Nothing selected 
    2924 
    2925 > select add #5
    2926 
    2927 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2928 
    2929 > select subtract #5
    2930 
    2931 Nothing selected 
    2932 
    2933 > select add #7
    2934 
    2935 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2936 
    2937 > select up
    2938 
    2939 126652 atoms, 127168 bonds, 11739 residues, 10 models selected 
    2940 
    2941 > select up
    2942 
    2943 126652 atoms, 127168 bonds, 11739 residues, 10 models selected 
    2944 
    2945 > select down
    2946 
    2947 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2948 
    2949 > fitmap #7 inMap #2
    2950 
    2951 Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms 
    2952 average map value = 0.004753, steps = 76 
    2953 shifted from previous position = 4.26 
    2954 rotated from previous position = 2.55 degrees 
    2955 atoms outside contour = 22292, contour level = 0.019827 
    2956  
    2957 Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates: 
    2958 Matrix rotation and translation 
    2959 -0.15645985 0.98768383 0.00098440 30.11038902 
    2960 -0.98768324 -0.15645813 -0.00163356 387.51635627 
    2961 -0.00145942 -0.00122786 0.99999818 -26.10685507 
    2962 Axis 0.00020538 0.00123715 -0.99999921 
    2963 Axis point 180.51939745 180.88633563 0.00000000 
    2964 Rotation angle (degrees) 99.00147566 
    2965 Shift along axis 26.59243395 
    2966  
    2967 
    2968 > select clear
    2969 
    2970 > select add #7
    2971 
    2972 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    2973 
    2974 > view matrix models
    2975 > #7,-0.15646,0.98768,0.0009844,30.102,-0.98768,-0.15646,-0.0016336,386.29,-0.0014594,-0.0012279,1,-28.373
    2976 
    2977 > view matrix models
    2978 > #7,-0.15646,0.98768,0.0009844,31.432,-0.98768,-0.15646,-0.0016336,385.41,-0.0014594,-0.0012279,1,-31.436
    2979 
    2980 > fitmap #7 inMap #2
    2981 
    2982 Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms 
    2983 average map value = 0.01322, steps = 60 
    2984 shifted from previous position = 2.23 
    2985 rotated from previous position = 1.36 degrees 
    2986 atoms outside contour = 20305, contour level = 0.019827 
    2987  
    2988 Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates: 
    2989 Matrix rotation and translation 
    2990 -0.13310064 0.99110252 0.00004395 25.64193442 
    2991 -0.99110246 -0.13310065 0.00035545 383.24194175 
    2992 0.00035813 0.00000375 0.99999993 -32.13108482 
    2993 Axis -0.00017743 -0.00015850 -0.99999997 
    2994 Axis point 180.43341724 180.40676231 0.00000000 
    2995 Rotation angle (degrees) 97.64880580 
    2996 Shift along axis 32.06579051 
    2997  
    2998 
    2999 > fitmap #7 inMap #2
    3000 
    3001 Fit molecule 6-Fla_3 (#7) to map postprocess_masked.mrc (#2) using 24834 atoms 
    3002 average map value = 0.01322, steps = 24 
    3003 shifted from previous position = 0.0081 
    3004 rotated from previous position = 0.00345 degrees 
    3005 atoms outside contour = 20302, contour level = 0.019827 
    3006  
    3007 Position of 6-Fla_3 (#7) relative to postprocess_masked.mrc (#2) coordinates: 
    3008 Matrix rotation and translation 
    3009 -0.13311188 0.99110101 0.00008566 25.64479424 
    3010 -0.99110093 -0.13311190 0.00039740 383.23592512 
    3011 0.00040526 -0.00003200 0.99999991 -32.13263726 
    3012 Axis -0.00021663 -0.00016124 -0.99999996 
    3013 Axis point 180.43096548 180.40212616 0.00000000 
    3014 Rotation angle (degrees) 97.64945630 
    3015 Shift along axis 32.06528877 
    3016  
    3017 
    3018 > select add #6
    3019 
    3020 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3021 
    3022 > select subtract #6
    3023 
    3024 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3025 
    3026 > select add #6
    3027 
    3028 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3029 
    3030 > select add #5
    3031 
    3032 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    3033 
    3034 > select subtract #5
    3035 
    3036 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3037 
    3038 > select add #5
    3039 
    3040 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    3041 
    3042 > combine #7/A #8 name 6_Fla_Monomer1
    3043 
    3044 > select subtract #5
    3045 
    3046 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3047 
    3048 > select add #5
    3049 
    3050 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    3051 
    3052 > select add #8
    3053 
    3054 99336 atoms, 99624 bonds, 6552 residues, 4 models selected 
    3055 
    3056 > select subtract #8
    3057 
    3058 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    3059 
    3060 > select subtract #7
    3061 
    3062 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3063 
    3064 > select subtract #5
    3065 
    3066 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3067 
    3068 > select add #7
    3069 
    3070 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3071 
    3072 > select subtract #6
    3073 
    3074 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3075 
    3076 > select add #8
    3077 
    3078 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3079 
    3080 > select subtract #7
    3081 
    3082 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3083 
    3084 > select subtract #8
    3085 
    3086 Nothing selected 
    3087 
    3088 > select add #8
    3089 
    3090 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3091 
    3092 > select subtract #8
    3093 
    3094 Nothing selected 
    3095 
    3096 > select add #8
    3097 
    3098 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3099 
    3100 > select add #7
    3101 
    3102 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3103 
    3104 > select subtract #8
    3105 
    3106 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3107 
    3108 > select add #8
    3109 
    3110 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3111 
    3112 > select subtract #7
    3113 
    3114 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3115 
    3116 > select add #7
    3117 
    3118 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3119 
    3120 > select subtract #7
    3121 
    3122 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3123 
    3124 > select subtract #8
    3125 
    3126 Nothing selected 
    3127 
    3128 > select add #8
    3129 
    3130 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3131 
    3132 > delete #8/B-F
    3133 
    3134 > select add #7
    3135 
    3136 28973 atoms, 29057 bonds, 1911 residues, 2 models selected 
    3137 
    3138 > select subtract #7
    3139 
    3140 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3141 
    3142 > view matrix models
    3143 > #8,-0.13311,0.9911,8.5659e-05,44.795,-0.9911,-0.13311,0.0003974,427.64,0.00040526,-3.1999e-05,1,-33.511
    3144 
    3145 > view matrix models
    3146 > #8,-0.13311,0.9911,8.5659e-05,41.571,-0.9911,-0.13311,0.0003974,423.63,0.00040526,-3.1999e-05,1,-33.376
    3147 
    3148 > ui mousemode right "rotate selected models"
    3149 
    3150 > view matrix models
    3151 > #8,0.67167,0.73957,0.043424,-84.466,-0.73824,0.67307,-0.044412,216.17,-0.062073,-0.0022272,0.99807,-19.472
    3152 
    3153 > view matrix models
    3154 > #8,0.67292,0.7391,0.03027,-81.935,-0.73832,0.6736,-0.033979,213.94,-0.045504,0.00051658,0.99896,-23.677
    3155 
    3156 > ui mousemode right "translate selected models"
    3157 
    3158 > view matrix models
    3159 > #8,0.67292,0.7391,0.03027,-82.426,-0.73832,0.6736,-0.033979,210.59,-0.045504,0.00051658,0.99896,-23.56
    3160 
    3161 > select add #7
    3162 
    3163 28973 atoms, 29057 bonds, 1911 residues, 2 models selected 
    3164 
    3165 > select subtract #7
    3166 
    3167 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3168 
    3169 > select add #6
    3170 
    3171 28973 atoms, 29057 bonds, 1911 residues, 2 models selected 
    3172 
    3173 > select subtract #6
    3174 
    3175 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3176 
    3177 > select up
    3178 
    3179 130791 atoms, 131319 bonds, 12012 residues, 11 models selected 
    3180 
    3181 > select down
    3182 
    3183 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3184 
    3185 > fitmap #8 inMap #2
    3186 
    3187 Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
    3188 atoms 
    3189 average map value = 0.005275, steps = 252 
    3190 shifted from previous position = 4.08 
    3191 rotated from previous position = 19.9 degrees 
    3192 atoms outside contour = 3692, contour level = 0.019827 
    3193  
    3194 Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
    3195 coordinates: 
    3196 Matrix rotation and translation 
    3197 0.88039194 0.47320616 -0.03140001 -56.14567410 
    3198 -0.47304862 0.88094421 0.01273975 102.14463011 
    3199 0.03369018 0.00363775 0.99942570 -40.30507882 
    3200 Axis -0.00959585 -0.06862185 -0.99759659 
    3201 Axis point 179.70163110 163.38691856 0.00000000 
    3202 Rotation angle (degrees) 28.31165131 
    3203 Shift along axis 33.73762183 
    3204  
    3205 
    3206 > view matrix models
    3207 > #8,0.88039,0.47321,-0.0314,-56.666,-0.47305,0.88094,0.01274,101.26,0.03369,0.0036378,0.99943,-35.255
    3208 
    3209 > fitmap #8 inMap #2
    3210 
    3211 Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
    3212 atoms 
    3213 average map value = 0.01362, steps = 72 
    3214 shifted from previous position = 0.757 
    3215 rotated from previous position = 4.49 degrees 
    3216 atoms outside contour = 3391, contour level = 0.019827 
    3217  
    3218 Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
    3219 coordinates: 
    3220 Matrix rotation and translation 
    3221 0.84534656 0.53421830 -0.00000202 -68.46907860 
    3222 -0.53421830 0.84534656 -0.00002583 124.36855897 
    3223 -0.00001209 0.00002292 1.00000000 -27.37540725 
    3224 Axis 0.00004563 0.00000942 -1.00000000 
    3225 Axis point 180.56711272 180.44243762 0.00000000 
    3226 Rotation angle (degrees) 32.29091433 
    3227 Shift along axis 27.37345516 
    3228  
    3229 
    3230 > fitmap #8 inMap #2
    3231 
    3232 Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
    3233 atoms 
    3234 average map value = 0.01361, steps = 40 
    3235 shifted from previous position = 0.00296 
    3236 rotated from previous position = 0.0911 degrees 
    3237 atoms outside contour = 3392, contour level = 0.019827 
    3238  
    3239 Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
    3240 coordinates: 
    3241 Matrix rotation and translation 
    3242 0.84453848 0.53549483 0.00017731 -68.59387229 
    3243 -0.53549471 0.84453844 -0.00049030 124.89151405 
    3244 -0.00041230 0.00031913 0.99999986 -27.35105929 
    3245 Axis 0.00075578 0.00055052 -0.99999956 
    3246 Axis point 180.76429705 180.61135552 0.00000000 
    3247 Rotation angle (degrees) 32.37748776 
    3248 Shift along axis 27.36796099 
    3249  
    3250 
    3251 > fitmap #8 inMap #2
    3252 
    3253 Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
    3254 atoms 
    3255 average map value = 0.01361, steps = 40 
    3256 shifted from previous position = 0.000859 
    3257 rotated from previous position = 0.00142 degrees 
    3258 atoms outside contour = 3392, contour level = 0.019827 
    3259  
    3260 Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
    3261 coordinates: 
    3262 Matrix rotation and translation 
    3263 0.84454327 0.53548729 0.00015643 -68.58842105 
    3264 -0.53548718 0.84454322 -0.00048031 124.88709384 
    3265 -0.00038931 0.00032188 0.99999987 -27.35631170 
    3266 Axis 0.00074903 0.00050957 -0.99999959 
    3267 Axis point 180.76501432 180.60196756 0.00000000 
    3268 Rotation angle (degrees) 32.37697559 
    3269 Shift along axis 27.36856450 
    3270  
    3271 
    3272 > fitmap #8 inMap #2
    3273 
    3274 Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
    3275 atoms 
    3276 average map value = 0.01361, steps = 40 
    3277 shifted from previous position = 0.000154 
    3278 rotated from previous position = 0.000457 degrees 
    3279 atoms outside contour = 3392, contour level = 0.019827 
    3280  
    3281 Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
    3282 coordinates: 
    3283 Matrix rotation and translation 
    3284 0.84454160 0.53548991 0.00016297 -68.58994058 
    3285 -0.53548979 0.84454156 -0.00048364 124.88878117 
    3286 -0.00039663 0.00032119 0.99999987 -27.35464582 
    3287 Axis 0.00075149 0.00052251 -0.99999958 
    3288 Axis point 180.76527318 180.60468360 0.00000000 
    3289 Rotation angle (degrees) 32.37715340 
    3290 Shift along axis 27.36834565 
    3291  
    3292 
    3293 > fitmap #8 inMap #2
    3294 
    3295 Fit molecule 6_Fla_Monomer1 (#8) to map postprocess_masked.mrc (#2) using 4139
    3296 atoms 
    3297 average map value = 0.01361, steps = 40 
    3298 shifted from previous position = 0.000216 
    3299 rotated from previous position = 0.00017 degrees 
    3300 atoms outside contour = 3392, contour level = 0.019827 
    3301  
    3302 Position of 6_Fla_Monomer1 (#8) relative to postprocess_masked.mrc (#2)
    3303 coordinates: 
    3304 Matrix rotation and translation 
    3305 0.84454029 0.53549199 0.00016433 -68.59055554 
    3306 -0.53549187 0.84454024 -0.00048461 124.88961280 
    3307 -0.00039829 0.00032128 0.99999987 -27.35433597 
    3308 Axis 0.00075248 0.00052534 -0.99999958 
    3309 Axis point 180.76526451 180.60562425 0.00000000 
    3310 Rotation angle (degrees) 32.37729427 
    3311 Shift along axis 27.36832082 
    3312  
    3313 
    3314 > select add #7
    3315 
    3316 28973 atoms, 29057 bonds, 1911 residues, 2 models selected 
    3317 
    3318 > select subtract #7
    3319 
    3320 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3321 
    3322 > select add #6
    3323 
    3324 28973 atoms, 29057 bonds, 1911 residues, 2 models selected 
    3325 
    3326 > select add #7
    3327 
    3328 53807 atoms, 53963 bonds, 3549 residues, 3 models selected 
    3329 
    3330 > select add #5
    3331 
    3332 78641 atoms, 78869 bonds, 5187 residues, 4 models selected 
    3333 
    3334 > select add #4
    3335 
    3336 78641 atoms, 78869 bonds, 5187 residues, 8 models selected 
    3337 
    3338 > select subtract #4
    3339 
    3340 78641 atoms, 78869 bonds, 5187 residues, 4 models selected 
    3341 
    3342 > combine #8 #9 name 6_Fla_Monomer2
    3343 
    3344 > select subtract #8
    3345 
    3346 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    3347 
    3348 > select subtract #7
    3349 
    3350 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3351 
    3352 > select subtract #5
    3353 
    3354 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3355 
    3356 > select subtract #6
    3357 
    3358 Nothing selected 
    3359 
    3360 > select add #9
    3361 
    3362 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3363 
    3364 > select add #8
    3365 
    3366 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3367 
    3368 > select subtract #8
    3369 
    3370 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3371 
    3372 > view matrix models
    3373 > #9,0.84454,0.53549,0.00016433,-147.63,-0.53549,0.84454,-0.00048461,150.22,-0.00039829,0.00032128,1,-30.937
    3374 
    3375 > ui mousemode right "rotate selected models"
    3376 
    3377 > view matrix models
    3378 > #9,0.071953,-0.99709,0.025378,320.07,0.9899,0.074504,0.12061,-37.067,-0.12215,0.016444,0.99238,-7.1972
    3379 
    3380 > ui mousemode right "translate selected models"
    3381 
    3382 > view matrix models
    3383 > #9,0.071953,-0.99709,0.025378,336.17,0.9899,0.074504,0.12061,-39.657,-0.12215,0.016444,0.99238,-6.6416
    3384 
    3385 > select up
    3386 
    3387 134930 atoms, 135470 bonds, 12285 residues, 12 models selected 
    3388 
    3389 > select down
    3390 
    3391 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3392 
    3393 > fitmap #9 inMap #2
    3394 
    3395 Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
    3396 atoms 
    3397 average map value = 0.003164, steps = 80 
    3398 shifted from previous position = 2.13 
    3399 rotated from previous position = 2.79 degrees 
    3400 atoms outside contour = 3796, contour level = 0.019827 
    3401  
    3402 Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
    3403 coordinates: 
    3404 Matrix rotation and translation 
    3405 0.06608397 -0.99773206 0.01279239 340.82449864 
    3406 0.99499722 0.06685465 0.07423609 -31.20329529 
    3407 -0.07492295 0.00782258 0.99715864 -17.44096315 
    3408 Axis -0.03327723 0.04395076 0.99847932 
    3409 Axis point 186.09105146 166.40592038 0.00000000 
    3410 Rotation angle (degrees) 86.27035458 
    3411 Shift along axis -30.12754573 
    3412  
    3413 
    3414 > select add #8
    3415 
    3416 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3417 
    3418 > select add #7
    3419 
    3420 33112 atoms, 33208 bonds, 2184 residues, 3 models selected 
    3421 
    3422 > select add #6
    3423 
    3424 57946 atoms, 58114 bonds, 3822 residues, 4 models selected 
    3425 
    3426 > select add #5
    3427 
    3428 82780 atoms, 83020 bonds, 5460 residues, 5 models selected 
    3429 
    3430 > select subtract #5
    3431 
    3432 57946 atoms, 58114 bonds, 3822 residues, 4 models selected 
    3433 
    3434 > select subtract #6
    3435 
    3436 33112 atoms, 33208 bonds, 2184 residues, 3 models selected 
    3437 
    3438 > select subtract #7
    3439 
    3440 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3441 
    3442 > select subtract #8
    3443 
    3444 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3445 
    3446 > view matrix models
    3447 > #9,0.066084,-0.99773,0.012792,341.43,0.995,0.066855,0.074236,-33.495,-0.074923,0.0078226,0.99716,-4.1931
    3448 
    3449 > fitmap #9 inMap #2
    3450 
    3451 Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
    3452 atoms 
    3453 average map value = 0.01364, steps = 100 
    3454 shifted from previous position = 3.33 
    3455 rotated from previous position = 12.9 degrees 
    3456 atoms outside contour = 3342, contour level = 0.019827 
    3457  
    3458 Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
    3459 coordinates: 
    3460 Matrix rotation and translation 
    3461 -0.14498463 -0.98943378 0.00051181 384.96719737 
    3462 0.98943293 -0.14498374 0.00147862 27.68621852 
    3463 -0.00138880 0.00072078 0.99999878 -17.81806743 
    3464 Axis -0.00038297 0.00096045 0.99999947 
    3465 Axis point 180.51027029 180.18269389 0.00000000 
    3466 Rotation angle (degrees) 98.33639859 
    3467 Shift along axis -17.93889795 
    3468  
    3469 
    3470 > fitmap #9 inMap #2
    3471 
    3472 Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
    3473 atoms 
    3474 average map value = 0.01364, steps = 40 
    3475 shifted from previous position = 0.00127 
    3476 rotated from previous position = 0.109 degrees 
    3477 atoms outside contour = 3345, contour level = 0.019827 
    3478  
    3479 Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
    3480 coordinates: 
    3481 Matrix rotation and translation 
    3482 -0.14676224 -0.98917172 0.00039066 385.31476749 
    3483 0.98917148 -0.14676187 0.00085590 28.22606872 
    3484 -0.00078929 0.00051204 0.99999956 -17.90327289 
    3485 Axis -0.00017381 0.00059643 0.99999981 
    3486 Axis point 180.47761578 180.29906026 0.00000000 
    3487 Rotation angle (degrees) 98.43934213 
    3488 Shift along axis -17.95340589 
    3489  
    3490 
    3491 > fitmap #9 inMap #2
    3492 
    3493 Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
    3494 atoms 
    3495 average map value = 0.01365, steps = 28 
    3496 shifted from previous position = 0.0164 
    3497 rotated from previous position = 0.0109 degrees 
    3498 atoms outside contour = 3351, contour level = 0.019827 
    3499  
    3500 Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
    3501 coordinates: 
    3502 Matrix rotation and translation 
    3503 -0.14675343 -0.98917308 0.00022654 385.35781735 
    3504 0.98917269 -0.14675316 0.00095140 28.19548176 
    3505 -0.00090785 0.00036371 0.99999952 -17.85199234 
    3506 Axis -0.00029706 0.00057341 0.99999979 
    3507 Axis point 180.51130704 180.30264652 0.00000000 
    3508 Rotation angle (degrees) 98.43883572 
    3509 Shift along axis -17.95029652 
    3510  
    3511 
    3512 > fitmap #9 inMap #2
    3513 
    3514 Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
    3515 atoms 
    3516 average map value = 0.01365, steps = 28 
    3517 shifted from previous position = 0.0115 
    3518 rotated from previous position = 0.0103 degrees 
    3519 atoms outside contour = 3346, contour level = 0.019827 
    3520  
    3521 Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
    3522 coordinates: 
    3523 Matrix rotation and translation 
    3524 -0.14681231 -0.98916430 0.00035831 385.33422856 
    3525 0.98916406 -0.14681197 0.00084478 28.23755612 
    3526 -0.00078302 0.00047845 0.99999958 -17.89901299 
    3527 Axis -0.00018517 0.00057692 0.99999982 
    3528 Axis point 180.48306518 180.30442734 0.00000000 
    3529 Rotation angle (degrees) 98.44224246 
    3530 Shift along axis -17.95407060 
    3531  
    3532 
    3533 > fitmap #9 inMap #2
    3534 
    3535 Fit molecule 6_Fla_Monomer2 (#9) to map postprocess_masked.mrc (#2) using 4139
    3536 atoms 
    3537 average map value = 0.01365, steps = 36 
    3538 shifted from previous position = 0.00316 
    3539 rotated from previous position = 0.00893 degrees 
    3540 atoms outside contour = 3347, contour level = 0.019827 
    3541  
    3542 Position of 6_Fla_Monomer2 (#9) relative to postprocess_masked.mrc (#2)
    3543 coordinates: 
    3544 Matrix rotation and translation 
    3545 -0.14676431 -0.98917146 0.00026204 385.34321950 
    3546 0.98917107 -0.14676400 0.00095726 28.20713253 
    3547 -0.00090844 0.00039970 0.99999951 -17.85590075 
    3548 Axis -0.00028184 0.00059165 0.99999979 
    3549 Axis point 180.49911304 180.30061414 0.00000000 
    3550 Rotation angle (degrees) 98.43946491 
    3551 Shift along axis -17.94781150 
    3552  
    3553 
    3554 > select add #8
    3555 
    3556 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3557 
    3558 > select add #7
    3559 
    3560 33112 atoms, 33208 bonds, 2184 residues, 3 models selected 
    3561 
    3562 > select add #6
    3563 
    3564 57946 atoms, 58114 bonds, 3822 residues, 4 models selected 
    3565 
    3566 > select add #5
    3567 
    3568 82780 atoms, 83020 bonds, 5460 residues, 5 models selected 
    3569 
    3570 > hide #!4 models
    3571 
    3572 > show #!3 models
    3573 
    3574 > hide #!3 models
    3575 
    3576 > show #!4 models
    3577 
    3578 > select subtract #5
    3579 
    3580 57946 atoms, 58114 bonds, 3822 residues, 4 models selected 
    3581 
    3582 > select add #5
    3583 
    3584 82780 atoms, 83020 bonds, 5460 residues, 5 models selected 
    3585 
    3586 > select subtract #8
    3587 
    3588 78641 atoms, 78869 bonds, 5187 residues, 4 models selected 
    3589 
    3590 > select add #8
    3591 
    3592 82780 atoms, 83020 bonds, 5460 residues, 5 models selected 
    3593 
    3594 > select subtract #7
    3595 
    3596 57946 atoms, 58114 bonds, 3822 residues, 4 models selected 
    3597 
    3598 > select subtract #6
    3599 
    3600 33112 atoms, 33208 bonds, 2184 residues, 3 models selected 
    3601 
    3602 > select subtract #5
    3603 
    3604 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3605 
    3606 > select subtract #8
    3607 
    3608 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3609 
    3610 > select add #8
    3611 
    3612 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3613 
    3614 > combine #9 #10 name 6_Fla_Monomer3
    3615 
    3616 > combine #9 #11 name 6_Fla_Monomer4
    3617 
    3618 > select subtract #8
    3619 
    3620 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3621 
    3622 > select subtract #9
    3623 
    3624 Nothing selected 
    3625 
    3626 > select add #4
    3627 
    3628 4 models selected 
    3629 
    3630 > select subtract #4
    3631 
    3632 Nothing selected 
    3633 
    3634 > select add #5
    3635 
    3636 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3637 
    3638 > select add #7
    3639 
    3640 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3641 
    3642 > select add #6
    3643 
    3644 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    3645 
    3646 > select add #8
    3647 
    3648 78641 atoms, 78869 bonds, 5187 residues, 4 models selected 
    3649 
    3650 > select add #10
    3651 
    3652 82780 atoms, 83020 bonds, 5460 residues, 5 models selected 
    3653 
    3654 > select add #9
    3655 
    3656 86919 atoms, 87171 bonds, 5733 residues, 6 models selected 
    3657 
    3658 > select subtract #10
    3659 
    3660 82780 atoms, 83020 bonds, 5460 residues, 5 models selected 
    3661 
    3662 > select subtract #9
    3663 
    3664 78641 atoms, 78869 bonds, 5187 residues, 4 models selected 
    3665 
    3666 > select subtract #8
    3667 
    3668 74502 atoms, 74718 bonds, 4914 residues, 3 models selected 
    3669 
    3670 > select subtract #7
    3671 
    3672 49668 atoms, 49812 bonds, 3276 residues, 2 models selected 
    3673 
    3674 > select subtract #6
    3675 
    3676 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3677 
    3678 > select subtract #5
    3679 
    3680 Nothing selected 
    3681 
    3682 > select add #10
    3683 
    3684 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3685 
    3686 > view matrix models
    3687 > #10,-0.14676,-0.98917,0.00026204,377.36,0.98917,-0.14676,0.00095726,41.468,-0.00090844,0.0003997,1,-25.047
    3688 
    3689 > view matrix models
    3690 > #10,-0.14676,-0.98917,0.00026204,391.76,0.98917,-0.14676,0.00095726,25.981,-0.00090844,0.0003997,1,-63.238
    3691 
    3692 > view matrix models
    3693 > #10,-0.14676,-0.98917,0.00026204,384.23,0.98917,-0.14676,0.00095726,30.554,-0.00090844,0.0003997,1,-70.058
    3694 
    3695 > view matrix models
    3696 > #10,-0.14676,-0.98917,0.00026204,382.35,0.98917,-0.14676,0.00095726,31.703,-0.00090844,0.0003997,1,-69.935
    3697 
    3698 > ui mousemode right "rotate selected models"
    3699 
    3700 > view matrix models
    3701 > #10,-0.16966,-0.98153,-0.088369,403.74,0.98269,-0.17526,0.060025,26.747,-0.074404,-0.076656,0.99428,-37.743
    3702 
    3703 > view matrix models
    3704 > #10,-0.17265,-0.97427,-0.14486,414.46,0.97684,-0.18823,0.10174,22.061,-0.12639,-0.12394,0.98421,-15.207
    3705 
    3706 > ui mousemode right "translate selected models"
    3707 
    3708 > view matrix models
    3709 > #10,-0.17265,-0.97427,-0.14486,408.91,0.97684,-0.18823,0.10174,22.165,-0.12639,-0.12394,0.98421,-14.388
    3710 
    3711 > select add #9
    3712 
    3713 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3714 
    3715 > select subtract #9
    3716 
    3717 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3718 
    3719 > view matrix models
    3720 > #10,-0.17265,-0.97427,-0.14486,408.04,0.97684,-0.18823,0.10174,22.453,-0.12639,-0.12394,0.98421,-12.738
    3721 
    3722 > fitmap #10 inMap #2
    3723 
    3724 Fit molecule 6_Fla_Monomer3 (#10) to map postprocess_masked.mrc (#2) using
    3725 4139 atoms 
    3726 average map value = 0.003256, steps = 324 
    3727 shifted from previous position = 2.15 
    3728 rotated from previous position = 8.13 degrees 
    3729 atoms outside contour = 3868, contour level = 0.019827 
    3730  
    3731 Position of 6_Fla_Monomer3 (#10) relative to postprocess_masked.mrc (#2)
    3732 coordinates: 
    3733 Matrix rotation and translation 
    3734 -0.30727066 -0.94030200 -0.14634510 430.33688794 
    3735 0.94669191 -0.31767640 0.05344291 66.76667909 
    3736 -0.09674286 -0.12212228 0.98778893 -20.36766932 
    3737 Axis -0.09260781 -0.02616438 0.99535884 
    3738 Axis point 190.69511849 186.44740585 0.00000000 
    3739 Rotation angle (degrees) 108.57701430 
    3740 Shift along axis -61.87260426 
    3741  
    3742 
    3743 > ui mousemode right "rotate selected models"
    3744 
    3745 > view matrix models
    3746 > #10,-0.38441,-0.91262,-0.13909,439.36,0.92314,-0.37906,-0.064162,108.25,0.0058315,-0.15307,0.9882,-35.611
    3747 
    3748 > ui mousemode right "translate selected models"
    3749 
    3750 > view matrix models
    3751 > #10,-0.38441,-0.91262,-0.13909,440.02,0.92314,-0.37906,-0.064162,101.51,0.0058315,-0.15307,0.9882,-35.909
    3752 
    3753 > view matrix models
    3754 > #10,-0.38441,-0.91262,-0.13909,440.38,0.92314,-0.37906,-0.064162,102.09,0.0058315,-0.15307,0.9882,-36.575
    3755 
    3756 > fitmap #10 inMap #2
    3757 
    3758 Fit molecule 6_Fla_Monomer3 (#10) to map postprocess_masked.mrc (#2) using
    3759 4139 atoms 
    3760 average map value = 0.01282, steps = 188 
    3761 shifted from previous position = 6.87 
    3762 rotated from previous position = 16.4 degrees 
    3763 atoms outside contour = 3431, contour level = 0.019827 
    3764  
    3765 Position of 6_Fla_Monomer3 (#10) relative to postprocess_masked.mrc (#2)
    3766 coordinates: 
    3767 Matrix rotation and translation 
    3768 -0.15210785 -0.98836389 0.00013844 386.19706766 
    3769 0.98836390 -0.15210783 0.00011519 29.47743686 
    3770 -0.00009279 0.00015435 0.99999998 -69.64503544 
    3771 Axis 0.00001981 0.00011698 0.99999999 
    3772 Axis point 180.45175955 180.39768622 0.00000000 
    3773 Rotation angle (degrees) 98.74909916 
    3774 Shift along axis -69.63393480 
    3775  
    3776 
    3777 > select clear
    3778 
    3779 > fitmap #10 inMap #2
    3780 
    3781 Fit molecule 6_Fla_Monomer3 (#10) to map postprocess_masked.mrc (#2) using
    3782 4139 atoms 
    3783 average map value = 0.01282, steps = 28 
    3784 shifted from previous position = 0.0101 
    3785 rotated from previous position = 0.121 degrees 
    3786 atoms outside contour = 3429, contour level = 0.019827 
    3787  
    3788 Position of 6_Fla_Monomer3 (#10) relative to postprocess_masked.mrc (#2)
    3789 coordinates: 
    3790 Matrix rotation and translation 
    3791 -0.15009935 -0.98867089 0.00022026 385.82172304 
    3792 0.98867071 -0.15009917 0.00068194 28.90158341 
    3793 -0.00064115 0.00032012 0.99999974 -69.56249875 
    3794 Axis -0.00018298 0.00043564 0.99999989 
    3795 Axis point 180.46898771 180.29429093 0.00000000 
    3796 Rotation angle (degrees) 98.63268654 
    3797 Shift along axis -69.62049814 
    3798  
    3799 
    3800 > select add #9
    3801 
    3802 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3803 
    3804 > select add #10
    3805 
    3806 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3807 
    3808 > select add #4
    3809 
    3810 8278 atoms, 8302 bonds, 546 residues, 6 models selected 
    3811 
    3812 > select subtract #4
    3813 
    3814 8278 atoms, 8302 bonds, 546 residues, 2 models selected 
    3815 
    3816 > select add #5
    3817 
    3818 33112 atoms, 33208 bonds, 2184 residues, 3 models selected 
    3819 
    3820 > select add #6
    3821 
    3822 57946 atoms, 58114 bonds, 3822 residues, 4 models selected 
    3823 
    3824 > select add #7
    3825 
    3826 82780 atoms, 83020 bonds, 5460 residues, 5 models selected 
    3827 
    3828 > select add #8
    3829 
    3830 86919 atoms, 87171 bonds, 5733 residues, 6 models selected 
    3831 
    3832 > select add #11
    3833 
    3834 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    3835 
    3836 > view matrix models
    3837 > #11,-0.14676,-0.98917,0.00026204,456.86,0.98917,-0.14676,0.00095726,-0.099371,-0.00090844,0.0003997,1,-25.193
    3838 
    3839 > ui mousemode right "rotate selected models"
    3840 
    3841 > view matrix models
    3842 > #11,0.71651,0.6735,0.18169,-98.564,-0.69095,0.72103,0.052022,164.41,-0.095966,-0.16281,0.98198,31.528
    3843 
    3844 > ui mousemode right "translate selected models"
    3845 
    3846 > view matrix models
    3847 > #11,0.71651,0.6735,0.18169,-100.07,-0.69095,0.72103,0.052022,170.7,-0.095966,-0.16281,0.98198,31.71
    3848 
    3849 > view matrix models
    3850 > #11,0.71651,0.6735,0.18169,-107.74,-0.69095,0.72103,0.052022,173.76,-0.095966,-0.16281,0.98198,-20.719
    3851 
    3852 > view matrix models
    3853 > #11,0.71651,0.6735,0.18169,-100.24,-0.69095,0.72103,0.052022,177.8,-0.095966,-0.16281,0.98198,-22.944
    3854 
    3855 > ui mousemode right "rotate selected models"
    3856 
    3857 > view matrix models
    3858 > #11,0.94859,0.30979,0.064806,-50.932,-0.3152,0.94324,0.10467,43.316,-0.028702,-0.11972,0.99239,-47.895
    3859 
    3860 > view matrix models
    3861 > #11,0.94451,0.3281,-0.015844,-37.277,-0.32821,0.94459,-0.004972,68.222,0.013335,0.0098964,0.99986,-84.544
    3862 
    3863 > ui mousemode right "translate selected models"
    3864 
    3865 > view matrix models
    3866 > #11,0.94451,0.3281,-0.015844,-40.657,-0.32821,0.94459,-0.004972,60.612,0.013335,0.0098964,0.99986,-81.548
    3867 
    3868 > ui mousemode right "rotate selected models"
    3869 
    3870 > view matrix models
    3871 > #11,0.95708,0.28603,0.046744,-47.559,-0.28881,0.9547,0.071633,34.63,-0.024137,-0.082059,0.99634,-54.31
    3872 
    3873 > ui mousemode right "translate selected models"
    3874 
    3875 > view matrix models
    3876 > #11,0.95708,0.28603,0.046744,-45.233,-0.28881,0.9547,0.071633,37.519,-0.024137,-0.082059,0.99634,-55.228
    3877 
    3878 > fitmap #11 inMap #2
    3879 
    3880 Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
    3881 4139 atoms 
    3882 average map value = 0.003344, steps = 84 
    3883 shifted from previous position = 0.623 
    3884 rotated from previous position = 1.4 degrees 
    3885 atoms outside contour = 3835, contour level = 0.019827 
    3886  
    3887 Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
    3888 coordinates: 
    3889 Matrix rotation and translation 
    3890 0.96307272 0.26729387 0.03232519 -39.23847922 
    3891 -0.26896467 0.96056575 0.07050845 32.41090759 
    3892 -0.01220400 -0.07659910 0.99698728 -58.95744077 
    3893 Axis -0.26370445 0.07982286 -0.96129510 
    3894 Axis point 86.63481695 90.09261132 0.00000000 
    3895 Rotation angle (degrees) 16.19605786 
    3896 Shift along axis 69.60999184 
    3897  
    3898 
    3899 > view matrix models
    3900 > #11,0.96307,0.26729,0.032325,-41.575,-0.26896,0.96057,0.070508,33.398,-0.012204,-0.076599,0.99699,-60.307
    3901 
    3902 > fitmap #11 inMap #2
    3903 
    3904 Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
    3905 4139 atoms 
    3906 average map value = 0.003226, steps = 88 
    3907 shifted from previous position = 2.42 
    3908 rotated from previous position = 1.57 degrees 
    3909 atoms outside contour = 3856, contour level = 0.019827 
    3910  
    3911 Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
    3912 coordinates: 
    3913 Matrix rotation and translation 
    3914 0.96039732 0.27799392 0.01887770 -38.57917168 
    3915 -0.27853682 0.95606531 0.09141314 32.15060089 
    3916 0.00736398 -0.09305107 0.99563411 -59.44005072 
    3917 Axis -0.31456096 0.01963398 -0.94903420 
    3918 Axis point 98.78772311 74.57330397 0.00000000 
    3919 Rotation angle (degrees) 17.05017251 
    3920 Shift along axis 69.17738637 
    3921  
    3922 
    3923 > ui mousemode right "rotate selected models"
    3924 
    3925 > view matrix models
    3926 > #11,0.90415,0.42479,-0.045421,-43.471,-0.42017,0.90343,0.085232,73.721,0.077241,-0.057977,0.99533,-81.111
    3927 
    3928 > ui mousemode right "translate selected models"
    3929 
    3930 > view matrix models
    3931 > #11,0.90415,0.42479,-0.045421,-48.569,-0.42017,0.90343,0.085232,76.107,0.077241,-0.057977,0.99533,-83.543
    3932 
    3933 > fitmap #11 inMap #2
    3934 
    3935 Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
    3936 4139 atoms 
    3937 average map value = 0.01254, steps = 116 
    3938 shifted from previous position = 4.46 
    3939 rotated from previous position = 9.04 degrees 
    3940 atoms outside contour = 3470, contour level = 0.019827 
    3941  
    3942 Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
    3943 coordinates: 
    3944 Matrix rotation and translation 
    3945 0.84647631 0.53242613 0.00052982 -68.47324164 
    3946 -0.53242584 0.84647644 -0.00059386 124.07981372 
    3947 -0.00076467 0.00022059 0.99999968 -78.91212291 
    3948 Axis 0.00076485 0.00121566 -0.99999897 
    3949 Axis point 180.72371449 180.83080451 0.00000000 
    3950 Rotation angle (degrees) 32.16955305 
    3951 Shift along axis 79.01050812 
    3952  
    3953 
    3954 > select clear
    3955 
    3956 > fitmap #11 inMap #2
    3957 
    3958 Fit molecule 6_Fla_Monomer4 (#11) to map postprocess_masked.mrc (#2) using
    3959 4139 atoms 
    3960 average map value = 0.01254, steps = 28 
    3961 shifted from previous position = 0.0215 
    3962 rotated from previous position = 0.101 degrees 
    3963 atoms outside contour = 3469, contour level = 0.019827 
    3964  
    3965 Position of 6_Fla_Monomer4 (#11) relative to postprocess_masked.mrc (#2)
    3966 coordinates: 
    3967 Matrix rotation and translation 
    3968 0.84558674 0.53383723 0.00093164 -68.64814399 
    3969 -0.53383639 0.84558718 -0.00101661 124.62125189 
    3970 -0.00133049 0.00036229 0.99999905 -78.81907728 
    3971 Axis 0.00129149 0.00211874 -0.99999692 
    3972 Axis point 180.75669809 181.06903942 0.00000000 
    3973 Rotation angle (degrees) 32.26517239 
    3974 Shift along axis 78.99421609 
    3975  
    3976 
    3977 > select add #5
    3978 
    3979 24834 atoms, 24906 bonds, 1638 residues, 1 model selected 
    3980 
    3981 > select subtract #5
    3982 
    3983 Nothing selected 
    3984 
    3985 > combine #5-11 name 22-Flagellin_double-ring
    3986 
    3987 Remapping chain ID 'A' in 6-Fla_2 #6 to 'G' 
    3988 Remapping chain ID 'B' in 6-Fla_2 #6 to 'H' 
    3989 Remapping chain ID 'C' in 6-Fla_2 #6 to 'I' 
    3990 Remapping chain ID 'D' in 6-Fla_2 #6 to 'J' 
    3991 Remapping chain ID 'E' in 6-Fla_2 #6 to 'K' 
    3992 Remapping chain ID 'F' in 6-Fla_2 #6 to 'L' 
    3993 Remapping chain ID 'A' in 6-Fla_3 #7 to 'M' 
    3994 Remapping chain ID 'B' in 6-Fla_3 #7 to 'N' 
    3995 Remapping chain ID 'C' in 6-Fla_3 #7 to 'O' 
    3996 Remapping chain ID 'D' in 6-Fla_3 #7 to 'P' 
    3997 Remapping chain ID 'E' in 6-Fla_3 #7 to 'Q' 
    3998 Remapping chain ID 'F' in 6-Fla_3 #7 to 'R' 
    3999 Remapping chain ID 'A' in 6_Fla_Monomer1 #8 to 'S' 
    4000 Remapping chain ID 'A' in 6_Fla_Monomer2 #9 to 'T' 
    4001 Remapping chain ID 'A' in 6_Fla_Monomer3 #10 to 'U' 
    4002 Remapping chain ID 'A' in 6_Fla_Monomer4 #11 to 'V' 
    4003 
    4004 > select add #11
    4005 
    4006 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    4007 
    4008 > select subtract #11
    4009 
    4010 Nothing selected 
    4011 
    4012 > select add #12
    4013 
    4014 91058 atoms, 91322 bonds, 6006 residues, 1 model selected 
    4015 
    4016 > hide #!11 models
    4017 
    4018 > hide #!10 models
    4019 
    4020 > hide #!9 models
    4021 
    4022 > hide #!8 models
    4023 
    4024 > hide #!7 models
    4025 
    4026 > hide #!6 models
    4027 
    4028 > hide #!5 models
    4029 
    4030 > hide #!4 models
    4031 
    4032 > show #!4 models
    4033 
    4034 > select clear
    4035 
    4036 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    4037 > determination/Reference_models/22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb"
    4038 > models #12 relModel #4
    4039 
    4040 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    4041 > determination/Reference_models/Rhom_2Ring_Rebuild4_Building.cxs"
    4042 
    4043 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    4044 > determination/Reference_models/PP234_Masked10A_2Ring.mrc" models #4
    4045 
    4046 > close session
    4047 
    4048 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    4049 > determination/Reference_models/22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb"
    4050 
    4051 Chain information for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb #1 
    4052 --- 
    4053 Chain | Description 
    4054 A B C D E F G H I J K L M N O P Q R S T U V | No description available 
    4055  
    4056 
    4057 > hide atoms
    4058 
    4059 > show cartoons
    4060 
    4061 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    4062 > determination/Reference_models/PP234_Masked10A_2Ring.mrc"
    4063 
    4064 Opened PP234_Masked10A_2Ring.mrc as #2, grid size 138,139,259, pixel
    4065 0.94,0.94,0.94, shown at level 0.0371, step 1, values float32 
    4066 
    4067 > volume #2 level 0.0118
    4068 
    4069 > isolde start
    4070 
    4071 > clipper associate #2 #1
    4072 
    4073 The toModel argument must be provided! 
    4074 
    4075 > clipper associate #2 toModel #1
    4076 
    4077 Opened PP234_Masked10A_2Ring.mrc as #1.1.1.1, grid size 138,139,259, pixel
    4078 0.94,0.94,0.94, shown at level 0.0212, step 1, values float32 
    4079 Chain information for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    4080 --- 
    4081 Chain | Description 
    4082 1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M
    4083 1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V | No description
    4084 available 
    4085  
    4086 
    4087 > volume #1.1.1.1 style surface
    4088 
    4089 > volume #1.1.1.1
    4090 
    4091 > volume #1.1.1.1 level 0.01248
    4092 
    4093 > volume #1.1.1.1 level 0.005977
    4094 
    4095 > volume #1.1.1.1 level 0.009264
    4096 
    4097 > volume #1.1.1.1 color #00ffff3f
    4098 
    4099 > volume #1.1.1.1 color #00ffff40
    4100 
    4101 > volume gaussian #1 bfactor 150
    4102 
    4103 Opened PP234_Masked10A_2Ring.mrc gaussian as #2, grid size 138,139,259, pixel
    4104 0.94,0.94,0.94, shown at step 1, values float32 
    4105 
    4106 > clipper associate #2 #1
    4107 
    4108 The toModel argument must be provided! 
    4109 
    4110 > clipper associate #2 toModel #1
    4111 
    4112 Opened PP234_Masked10A_2Ring.mrc gaussian as #1.1.1.2, grid size 138,139,259,
    4113 pixel 0.94,0.94,0.94, shown at step 1, values float32 
    4114 
    4115 > volume #1.1.1.2 level -5.071e-35
    4116 
    4117 > volume #1.1.1.2 level -5.656e-36
    4118 
    4119 > volume #1.1.1.2 region 0,0,0,137,138,258 step 1
    4120 
    4121 [Repeated 1 time(s)]
    4122 
    4123 > volume #1.1.1.1 level 0.01795
    4124 
    4125 > volume #1.1.1.1 level 0.02103
    4126 
    4127 > volume #1.1.1.1 level 0.02162
    4128 
    4129 > volume #1.1.1.2 level 0.002942
    4130 
    4131 > volume #1.1.1.1 level 0.01044
    4132 
    4133 > volume #1.1.1.2 level 0.004965
    4134 
    4135 > view #1/A:1
    4136 
    4137 > view #1/A:1-5
    4138 
    4139 > hide atoms
    4140 
    4141 > view #1/B:1-5
    4142 
    4143 No displayed objects specified. 
    4144 
    4145 > view #1/C:1-5
    4146 
    4147 No displayed objects specified. 
    4148 
    4149 > view #1/D:1-5
    4150 
    4151 No displayed objects specified. 
    4152 
    4153 > view #1/E:1-5
    4154 
    4155 No displayed objects specified. 
    4156 
    4157 > view #1/F:1-5
    4158 
    4159 No displayed objects specified. 
    4160 
    4161 > view #1/G:1-5
    4162 
    4163 No displayed objects specified. 
    4164 
    4165 > select /B
    4166 
    4167 4139 atoms, 4151 bonds, 273 residues, 1 model selected 
    4168 
    4169 > view #1/G:1-5
    4170 
    4171 No displayed objects specified. 
    4172 
    4173 > view #1
    4174 
    4175 > view #1:F
    4176 
    4177 No objects specified. 
    4178 
    4179 > view #1:A
    4180 
    4181 No objects specified. 
    4182 
    4183 > view #1:C
    4184 
    4185 No objects specified. 
    4186 
    4187 > view #1:B
    4188 
    4189 No objects specified. 
    4190 
    4191 > view #1/A:1
    4192 
    4193 No displayed objects specified. 
    4194 
    4195 > view #1/A
    4196 
    4197 No displayed objects specified. 
    4198 
    4199 > select add #1.2
    4200 
    4201 91058 atoms, 91322 bonds, 6006 residues, 1 model selected 
    4202 
    4203 > select subtract #1.2
    4204 
    4205 Nothing selected 
    4206 
    4207 > view #1/A
    4208 
    4209 No displayed objects specified. 
    4210 
    4211 > view #1
    4212 
    4213 > view all
    4214 
    4215 > show all
    4216 
    4217 > hide cartoons
    4218 
    4219 > show cartoons
    4220 
    4221 > hide atoms
    4222 
    4223 > select #1/A:1-5
    4224 
    4225 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4226 
    4227 > view #1/A:1-5
    4228 
    4229 No displayed objects specified. 
    4230 
    4231 > select #1/A:1-5
    4232 
    4233 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4234 
    4235 > select #1/A:1-5
    4236 
    4237 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4238 
    4239 > view sel
    4240 
    4241 No displayed objects specified. 
    4242 
    4243 > select #1/A:1-5
    4244 
    4245 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4246 
    4247 > view sel
    4248 
    4249 No displayed objects specified. 
    4250 
    4251 > select #1/A:1-5
    4252 
    4253 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4254 
    4255 > view sel
    4256 
    4257 No displayed objects specified. 
    4258 
    4259 > select #1/A:1-5
    4260 
    4261 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4262 
    4263 > view sel
    4264 
    4265 No displayed objects specified. 
    4266 
    4267 > show sel cartoons
    4268 
    4269 > show sel atoms
    4270 
    4271 > select #1/A:1-5
    4272 
    4273 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4274 
    4275 > view sel
    4276 
    4277 > select #1/B:1-5
    4278 
    4279 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4280 
    4281 > view sel
    4282 
    4283 No displayed objects specified. 
    4284 
    4285 > select #1/B:1-5
    4286 
    4287 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4288 
    4289 > show all
    4290 
    4291 > select up
    4292 
    4293 111 atoms, 111 bonds, 6 residues, 1 model selected 
    4294 
    4295 > select up
    4296 
    4297 2162 atoms, 2166 bonds, 143 residues, 1 model selected 
    4298 
    4299 > select #1/B:1-5
    4300 
    4301 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4302 
    4303 > select #1/B:1-5
    4304 
    4305 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4306 
    4307 > view sel
    4308 
    4309 > hide all
    4310 
    4311 > select #1/B:1-5
    4312 
    4313 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4314 
    4315 > show sel
    4316 
    4317 > view sel
    4318 
    4319 > select #1/B:1-5
    4320 
    4321 97 atoms, 97 bonds, 5 residues, 1 model selected 
    4322 
    4323 > show sel
    4324 
    4325 > view sel
    4326 
    4327 > hide sel
    4328 
    4329 > volume #1.1.1.2 level 0.004271
    4330 
    4331 > volume #1.1.1.1 level 0.02312
    4332 
    4333 > select #1/B:1-10
    4334 
    4335 159 atoms, 159 bonds, 10 residues, 1 model selected 
    4336 
    4337 > show sel
    4338 
    4339 > view sel
    4340 
    4341 > hide sel
    4342 
    4343 > select #1/B:1-8
    4344 
    4345 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4346 
    4347 > show sel
    4348 
    4349 > view sel
    4350 
    4351 > hide sel
    4352 
    4353 > select #1/C:1-8
    4354 
    4355 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4356 
    4357 > show sel
    4358 
    4359 > view sel
    4360 
    4361 > hide sel
    4362 
    4363 > select #1/D:1-8
    4364 
    4365 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4366 
    4367 > show sel
    4368 
    4369 > view sel
    4370 
    4371 > hide sel
    4372 
    4373 > select #1/E:1-8
    4374 
    4375 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4376 
    4377 > show sel
    4378 
    4379 > view sel
    4380 
    4381 > hide sel
    4382 
    4383 > select #1/F:1-8
    4384 
    4385 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4386 
    4387 > show sel
    4388 
    4389 > view sel
    4390 
    4391 > hide sel
    4392 
    4393 > select #1/G:1-8
    4394 
    4395 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4396 
    4397 > show sel
    4398 
    4399 > view sel
    4400 
    4401 > hide sel
    4402 
    4403 > select #1/H:1-8
    4404 
    4405 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4406 
    4407 > show sel
    4408 
    4409 > view sel
    4410 
    4411 > hide sel
    4412 
    4413 > select #1/I:1-8
    4414 
    4415 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4416 
    4417 > show sel
    4418 
    4419 > view sel
    4420 
    4421 > hide sel
    4422 
    4423 > select #1/J:1-8
    4424 
    4425 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4426 
    4427 > show sel
    4428 
    4429 > view sel
    4430 
    4431 > hide sel
    4432 
    4433 > select #1/K:1-8
    4434 
    4435 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4436 
    4437 > show sel
    4438 
    4439 > view sel
    4440 
    4441 > hide sel
    4442 
    4443 > select #1/L:1-8
    4444 
    4445 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4446 
    4447 > show sel
    4448 
    4449 > view sel
    4450 
    4451 > hide sel
    4452 
    4453 > select #1/M:1-8
    4454 
    4455 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4456 
    4457 > show sel
    4458 
    4459 > view sel
    4460 
    4461 > hide sel
    4462 
    4463 > select #1/N:1-8
    4464 
    4465 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4466 
    4467 > show sel
    4468 
    4469 > view sel
    4470 
    4471 > hide sel
    4472 
    4473 > select #1/O:1-8
    4474 
    4475 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4476 
    4477 > show sel
    4478 
    4479 > view sel
    4480 
    4481 > hide sel
    4482 
    4483 > select #1/P:1-8
    4484 
    4485 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4486 
    4487 > show sel
    4488 
    4489 > view sel
    4490 
    4491 > hide sel
    4492 
    4493 > select #1/Q:1-8
    4494 
    4495 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4496 
    4497 > show sel
    4498 
    4499 > view sel
    4500 
    4501 > hide sel
    4502 
    4503 > select #1/R:1-8
    4504 
    4505 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4506 
    4507 > show sel
    4508 
    4509 > view sel
    4510 
    4511 > hide sel
    4512 
    4513 > select #1/S:1-8
    4514 
    4515 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4516 
    4517 > show sel
    4518 
    4519 > view sel
    4520 
    4521 > hide sel
    4522 
    4523 > select #1/T:1-8
    4524 
    4525 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4526 
    4527 > show sel
    4528 
    4529 > view sel
    4530 
    4531 > hide sel
    4532 
    4533 > select #1/U:1-8
    4534 
    4535 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4536 
    4537 > show sel
    4538 
    4539 > view sel
    4540 
    4541 > hide sel
    4542 
    4543 > select #1/V:1-8
    4544 
    4545 138 atoms, 138 bonds, 8 residues, 1 model selected 
    4546 
    4547 > show sel
    4548 
    4549 > view sel
    4550 
    4551 > hide sel
    4552 
    4553 > select #1/W:1-8
    4554 
    4555 Nothing selected 
    4556 
    4557 > show sel
    4558 
    4559 > view sel
    4560 
    4561 No objects specified. 
    4562 
    4563 > select #1/A:500
    4564 
    4565 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4566 
    4567 > show sel
    4568 
    4569 > view sel
    4570 
    4571 > hide sel
    4572 
    4573 > select #1/A:500-505
    4574 
    4575 107 atoms, 106 bonds, 6 residues, 1 model selected 
    4576 
    4577 > show sel
    4578 
    4579 > view sel
    4580 
    4581 > hide sel
    4582 
    4583 > select #1/A:500-506
    4584 
    4585 125 atoms, 124 bonds, 7 residues, 1 model selected 
    4586 
    4587 > show sel
    4588 
    4589 > view sel
    4590 
    4591 > hide sel
    4592 
    4593 > select #1/A:500-507
    4594 
    4595 125 atoms, 124 bonds, 7 residues, 1 model selected 
    4596 
    4597 > show sel
    4598 
    4599 > view sel
    4600 
    4601 > hide sel
    4602 
    4603 > select #1/A:507
    4604 
    4605 Nothing selected 
    4606 
    4607 > show sel
    4608 
    4609 > view sel
    4610 
    4611 No objects specified. 
    4612 
    4613 > select #1/A:502-506
    4614 
    4615 92 atoms, 91 bonds, 5 residues, 1 model selected 
    4616 
    4617 > show sel
    4618 
    4619 > view sel
    4620 
    4621 > hide sel
    4622 
    4623 > select #1/A:501-506
    4624 
    4625 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4626 
    4627 > show sel
    4628 
    4629 > view sel
    4630 
    4631 > hide sel
    4632 
    4633 > select #1/B:501-506
    4634 
    4635 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4636 
    4637 > show sel
    4638 
    4639 > view sel
    4640 
    4641 > hide sel
    4642 
    4643 > select #1/C:501-506
    4644 
    4645 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4646 
    4647 > show sel
    4648 
    4649 > view sel
    4650 
    4651 > hide sel
    4652 
    4653 > select #1/D:501-506
    4654 
    4655 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4656 
    4657 > show sel
    4658 
    4659 > view sel
    4660 
    4661 > hide sel
    4662 
    4663 > volume #1.1.1.1 level 0.02568
    4664 
    4665 > select #1/E:501-506
    4666 
    4667 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4668 
    4669 > show sel
    4670 
    4671 > view sel
    4672 
    4673 > hide sel
    4674 
    4675 > select #1/F:501-506
    4676 
    4677 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4678 
    4679 > show sel
    4680 
    4681 > view sel
    4682 
    4683 > hide sel
    4684 
    4685 > select #1/G:501-506
    4686 
    4687 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4688 
    4689 > show sel
    4690 
    4691 > view sel
    4692 
    4693 > hide sel
    4694 
    4695 > select #1/H:501-506
    4696 
    4697 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4698 
    4699 > show sel
    4700 
    4701 > view sel
    4702 
    4703 > hide sel
    4704 
    4705 > select #1/I:501-506
    4706 
    4707 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4708 
    4709 > show sel
    4710 
    4711 > view sel
    4712 
    4713 > hide sel
    4714 
    4715 > select #1/J:501-506
    4716 
    4717 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4718 
    4719 > show sel
    4720 
    4721 > view sel
    4722 
    4723 > hide sel
    4724 
    4725 > select #1/K:501-506
    4726 
    4727 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4728 
    4729 > show sel
    4730 
    4731 > view sel
    4732 
    4733 > hide sel
    4734 
    4735 > select #1/L:501-506
    4736 
    4737 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4738 
    4739 > show sel
    4740 
    4741 > view sel
    4742 
    4743 > hide sel
    4744 
    4745 > select #1/M:501-506
    4746 
    4747 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4748 
    4749 > show sel
    4750 
    4751 > view sel
    4752 
    4753 > hide sel
    4754 
    4755 > view matrix models #1.2,1,0,0,0.86557,0,1,0,-0.55253,0,0,1,6.461
    4756 
    4757 > undo
    4758 
    4759 > ui mousemode right translate
    4760 
    4761 > select up
    4762 
    4763 578 atoms, 580 bonds, 37 residues, 1 model selected 
    4764 
    4765 > select #1/N:501-506
    4766 
    4767 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4768 
    4769 > show sel
    4770 
    4771 > view sel
    4772 
    4773 > hide sel
    4774 
    4775 > select #1/O:501-506
    4776 
    4777 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4778 
    4779 > show sel
    4780 
    4781 > view sel
    4782 
    4783 > hide sel
    4784 
    4785 > select #1/P:501-506
    4786 
    4787 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4788 
    4789 > show sel
    4790 
    4791 > view sel
    4792 
    4793 > hide sel
    4794 
    4795 > select #1/Q:501-506
    4796 
    4797 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4798 
    4799 > show sel
    4800 
    4801 > view sel
    4802 
    4803 > hide sel
    4804 
    4805 > select #1/R:501-506
    4806 
    4807 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4808 
    4809 > show sel
    4810 
    4811 > view sel
    4812 
    4813 > hide sel
    4814 
    4815 > select #1/S:501-506
    4816 
    4817 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4818 
    4819 > show sel
    4820 
    4821 > view sel
    4822 
    4823 > hide sel
    4824 
    4825 > select #1/S:501-506
    4826 
    4827 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4828 
    4829 > show sel
    4830 
    4831 > view sel
    4832 
    4833 > hide sel
    4834 
    4835 > select #1/T:501-506
    4836 
    4837 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4838 
    4839 > show sel
    4840 
    4841 > view sel
    4842 
    4843 > hide sel
    4844 
    4845 > select #1/U:501-506
    4846 
    4847 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4848 
    4849 > show sel
    4850 
    4851 > view sel
    4852 
    4853 > hide sel
    4854 
    4855 > select #1/V:501-506
    4856 
    4857 108 atoms, 107 bonds, 6 residues, 1 model selected 
    4858 
    4859 > show sel
    4860 
    4861 > view sel
    4862 
    4863 > hide sel
    4864 
    4865 > select #1/W:501-506
    4866 
    4867 Nothing selected 
    4868 
    4869 > show sel
    4870 
    4871 > view sel
    4872 
    4873 No objects specified. 
    4874 
    4875 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    4876 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_PreSim.cxs"
    4877 
    4878 > view all
    4879 
    4880 > show all
    4881 
    4882 > view all
    4883 
    4884 > select all
    4885 
    4886 91058 atoms, 91322 bonds, 6006 residues, 9 models selected 
    4887 
    4888 > ui tool show "Ramachandran Plot"
    4889 
    4890 [Repeated 1 time(s)]
    4891 
    4892 > isolde start
    4893 
    4894 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4895 chains... 
    4896 
    4897 > isolde set simFidelityMode Highest/Slowest
    4898 
    4899 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    4900 nonbonded_cutoff_distance = 1.700000 
    4901 use_gbsa = True 
    4902 gbsa_cutoff = 2.000000 
    4903 
    4904 > isolde set simFidelityMode Highest/Slowest
    4905 
    4906 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    4907 nonbonded_cutoff_distance = 1.700000 
    4908 use_gbsa = True 
    4909 gbsa_cutoff = 2.000000 
    4910 
    4911 > sell all
    4912 
    4913 Unknown command: sell all 
    4914 
    4915 > select all
    4916 
    4917 91058 atoms, 91322 bonds, 6006 residues, 19 models selected 
    4918 
    4919 > isolde sim start /A-V
    4920 
    4921 ISOLDE: started sim 
    4922 
    4923 > isolde sim stop discardTo start
    4924 
    4925 Sim termination reason: None 
    4926 reverting to start 
    4927 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4928 chains... 
    4929 ISOLDE: stopped sim 
    4930 
    4931 > isolde set simFidelityMode Medium/Medium
    4932 
    4933 ISOLDE: setting sim fidelity mode to Medium/Medium 
    4934 nonbonded_cutoff_distance = 0.900000 
    4935 use_gbsa = True 
    4936 gbsa_cutoff = 1.100000 
    4937 
    4938 > isolde set simFidelityMode Medium/Medium
    4939 
    4940 ISOLDE: setting sim fidelity mode to Medium/Medium 
    4941 nonbonded_cutoff_distance = 0.900000 
    4942 use_gbsa = True 
    4943 gbsa_cutoff = 1.100000 
    4944 
    4945 > select all
    4946 
    4947 91058 atoms, 91322 bonds, 6006 residues, 24 models selected 
    4948 
    4949 > isolde sim start /A-V
    4950 
    4951 ISOLDE: started sim 
    4952 
    4953 > isolde sim stop
    4954 
    4955 Sim termination reason: None 
    4956 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4957 chains... 
    4958 ISOLDE: Corrected atom nomenclature of 70 residues in model #1.2 to IUPAC-IUB
    4959 standards. 
    4960 ISOLDE: stopped sim 
    4961 
    4962 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    4963 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_All-
    4964 > Sim.cxs"
    4965 
    4966 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    4967 
    4968 > isolde set simFidelityMode Highest/Slowest
    4969 
    4970 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    4971 nonbonded_cutoff_distance = 1.700000 
    4972 use_gbsa = True 
    4973 gbsa_cutoff = 2.000000 
    4974 
    4975 > isolde set simFidelityMode Highest/Slowest
    4976 
    4977 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    4978 nonbonded_cutoff_distance = 1.700000 
    4979 use_gbsa = True 
    4980 gbsa_cutoff = 2.000000 
    4981 
    4982 > isolde sim start /F:107
    4983 
    4984 ISOLDE: started sim 
    4985 
    4986 > isolde pepflip /F:107
    4987 
    4988 > select clear
    4989 
    4990 > isolde pepflip /F:108
    4991 
    4992 > ui mousemode right translate
    4993 
    4994 > isolde sim stop
    4995 
    4996 Sim termination reason: None 
    4997 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4998 chains... 
    4999 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5000 standards. 
    5001 ISOLDE: stopped sim 
    5002 
    5003 > isolde sim start /E:107
    5004 
    5005 ISOLDE: started sim 
    5006 
    5007 > isolde sim stop
    5008 
    5009 Sim termination reason: None 
    5010 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5011 chains... 
    5012 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5013 standards. 
    5014 ISOLDE: stopped sim 
    5015 
    5016 > isolde sim start /K:107
    5017 
    5018 ISOLDE: started sim 
    5019 
    5020 > isolde sim stop
    5021 
    5022 Sim termination reason: None 
    5023 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5024 chains... 
    5025 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5026 standards. 
    5027 ISOLDE: stopped sim 
    5028 
    5029 > isolde sim start /L:107
    5030 
    5031 ISOLDE: started sim 
    5032 
    5033 > isolde sim stop
    5034 
    5035 Sim termination reason: None 
    5036 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5037 chains... 
    5038 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5039 standards. 
    5040 ISOLDE: stopped sim 
    5041 
    5042 > isolde sim start /Q:107
    5043 
    5044 ISOLDE: started sim 
    5045 
    5046 > isolde sim stop
    5047 
    5048 Sim termination reason: None 
    5049 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5050 chains... 
    5051 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5052 standards. 
    5053 ISOLDE: stopped sim 
    5054 
    5055 > isolde sim start /R:107
    5056 
    5057 ISOLDE: started sim 
    5058 
    5059 > isolde sim stop
    5060 
    5061 Sim termination reason: None 
    5062 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5063 chains... 
    5064 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5065 standards. 
    5066 ISOLDE: stopped sim 
    5067 
    5068 > isolde sim start /K:4
    5069 
    5070 ISOLDE: started sim 
    5071 
    5072 > isolde pepflip /K:4
    5073 
    5074 > isolde pepflip /K:5
    5075 
    5076 > isolde pepflip /K:6
    5077 
    5078 > isolde sim stop
    5079 
    5080 Sim termination reason: None 
    5081 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5082 chains... 
    5083 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5084 standards. 
    5085 ISOLDE: stopped sim 
    5086 
    5087 > isolde sim start /M:501
    5088 
    5089 ISOLDE: started sim 
    5090 
    5091 > isolde sim stop discardTo start
    5092 
    5093 Sim termination reason: None 
    5094 reverting to start 
    5095 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5096 chains... 
    5097 ISOLDE: stopped sim 
    5098 
    5099 > isolde sim start /A:133
    5100 
    5101 ISOLDE: started sim 
    5102 
    5103 > isolde pepflip /A:133
    5104 
    5105 > isolde pepflip /A:134
    5106 
    5107 > isolde sim stop
    5108 
    5109 Sim termination reason: None 
    5110 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5111 chains... 
    5112 ISOLDE: stopped sim 
    5113 
    5114 > isolde sim start /B:133
    5115 
    5116 ISOLDE: started sim 
    5117 
    5118 > isolde sim stop
    5119 
    5120 Sim termination reason: None 
    5121 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5122 chains... 
    5123 ISOLDE: stopped sim 
    5124 
    5125 > isolde sim start /K:383
    5126 
    5127 ISOLDE: started sim 
    5128 
    5129 > isolde pepflip #!1.2/K:383
    5130 
    5131 > isolde sim stop
    5132 
    5133 Sim termination reason: None 
    5134 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5135 chains... 
    5136 ISOLDE: stopped sim 
    5137 
    5138 > isolde sim start /D:383
    5139 
    5140 ISOLDE: started sim 
    5141 
    5142 > isolde sim stop
    5143 
    5144 Sim termination reason: None 
    5145 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5146 chains... 
    5147 ISOLDE: stopped sim 
    5148 
    5149 > isolde sim start /F:383
    5150 
    5151 ISOLDE: started sim 
    5152 
    5153 > isolde sim stop
    5154 
    5155 Sim termination reason: None 
    5156 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5157 chains... 
    5158 ISOLDE: stopped sim 
    5159 
    5160 > isolde sim start /L:383
    5161 
    5162 ISOLDE: started sim 
    5163 
    5164 > isolde sim stop
    5165 
    5166 Sim termination reason: None 
    5167 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5168 chains... 
    5169 ISOLDE: stopped sim 
    5170 
    5171 > isolde sim start /N:410
    5172 
    5173 ISOLDE: started sim 
    5174 
    5175 > isolde sim stop
    5176 
    5177 Sim termination reason: None 
    5178 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5179 chains... 
    5180 ISOLDE: stopped sim 
    5181 
    5182 > isolde sim start /J:383
    5183 
    5184 ISOLDE: started sim 
    5185 
    5186 > isolde sim stop
    5187 
    5188 Sim termination reason: None 
    5189 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5190 chains... 
    5191 ISOLDE: stopped sim 
    5192 
    5193 > isolde sim start /G:383
    5194 
    5195 ISOLDE: started sim 
    5196 
    5197 > isolde sim stop
    5198 
    5199 Sim termination reason: None 
    5200 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5201 chains... 
    5202 ISOLDE: stopped sim 
    5203 
    5204 > isolde sim start /B:383
    5205 
    5206 ISOLDE: started sim 
    5207 
    5208 > isolde sim stop
    5209 
    5210 Sim termination reason: None 
    5211 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5212 chains... 
    5213 ISOLDE: stopped sim 
    5214 
    5215 > isolde sim start /F:383
    5216 
    5217 ISOLDE: started sim 
    5218 
    5219 > isolde sim stop
    5220 
    5221 Sim termination reason: None 
    5222 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5223 chains... 
    5224 ISOLDE: stopped sim 
    5225 
    5226 > isolde sim start /H:383
    5227 
    5228 ISOLDE: started sim 
    5229 
    5230 > isolde sim stop
    5231 
    5232 Sim termination reason: None 
    5233 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5234 chains... 
    5235 ISOLDE: stopped sim 
    5236 
    5237 > isolde sim start /I:383
    5238 
    5239 ISOLDE: started sim 
    5240 
    5241 > isolde sim stop
    5242 
    5243 Sim termination reason: None 
    5244 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5245 chains... 
    5246 ISOLDE: stopped sim 
    5247 
    5248 > isolde sim start /M:383
    5249 
    5250 ISOLDE: started sim 
    5251 
    5252 > isolde sim stop
    5253 
    5254 Sim termination reason: None 
    5255 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5256 chains... 
    5257 ISOLDE: stopped sim 
    5258 
    5259 > isolde sim start /T:383
    5260 
    5261 ISOLDE: started sim 
    5262 
    5263 > isolde sim stop
    5264 
    5265 Sim termination reason: None 
    5266 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5267 chains... 
    5268 ISOLDE: stopped sim 
    5269 
    5270 > isolde sim start /O:383
    5271 
    5272 ISOLDE: started sim 
    5273 
    5274 > isolde sim stop
    5275 
    5276 Sim termination reason: None 
    5277 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5278 chains... 
    5279 ISOLDE: stopped sim 
    5280 
    5281 > isolde sim start /R:383
    5282 
    5283 ISOLDE: started sim 
    5284 
    5285 > isolde sim stop
    5286 
    5287 Sim termination reason: None 
    5288 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5289 chains... 
    5290 ISOLDE: stopped sim 
    5291 
    5292 > isolde sim start /F:383
    5293 
    5294 ISOLDE: started sim 
    5295 
    5296 > isolde sim stop
    5297 
    5298 Sim termination reason: None 
    5299 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5300 chains... 
    5301 ISOLDE: stopped sim 
    5302 
    5303 > isolde sim start /O:133
    5304 
    5305 ISOLDE: started sim 
    5306 
    5307 > isolde pepflip /O:133
    5308 
    5309 [Repeated 1 time(s)]
    5310 
    5311 > isolde sim stop
    5312 
    5313 Sim termination reason: None 
    5314 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5315 chains... 
    5316 ISOLDE: stopped sim 
    5317 
    5318 > isolde sim start /N:133
    5319 
    5320 ISOLDE: started sim 
    5321 
    5322 > isolde sim stop
    5323 
    5324 Sim termination reason: None 
    5325 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5326 chains... 
    5327 ISOLDE: stopped sim 
    5328 
    5329 > isolde sim start /D:133
    5330 
    5331 ISOLDE: started sim 
    5332 
    5333 > isolde sim stop
    5334 
    5335 Sim termination reason: None 
    5336 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5337 chains... 
    5338 ISOLDE: stopped sim 
    5339 
    5340 > isolde sim start /C:133
    5341 
    5342 ISOLDE: started sim 
    5343 
    5344 > isolde sim stop
    5345 
    5346 Sim termination reason: None 
    5347 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5348 chains... 
    5349 ISOLDE: stopped sim 
    5350 
    5351 > isolde sim start /R:133
    5352 
    5353 ISOLDE: started sim 
    5354 
    5355 > isolde sim stop
    5356 
    5357 Sim termination reason: None 
    5358 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5359 chains... 
    5360 ISOLDE: stopped sim 
    5361 
    5362 > isolde sim start /G:133
    5363 
    5364 ISOLDE: started sim 
    5365 
    5366 > isolde sim stop
    5367 
    5368 Sim termination reason: None 
    5369 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5370 chains... 
    5371 ISOLDE: stopped sim 
    5372 
    5373 > isolde sim start /P:133
    5374 
    5375 ISOLDE: started sim 
    5376 
    5377 > isolde sim stop
    5378 
    5379 Sim termination reason: None 
    5380 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5381 chains... 
    5382 ISOLDE: stopped sim 
    5383 
    5384 > isolde sim start /Q:133
    5385 
    5386 ISOLDE: started sim 
    5387 
    5388 > isolde sim stop
    5389 
    5390 Sim termination reason: None 
    5391 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5392 chains... 
    5393 ISOLDE: stopped sim 
    5394 
    5395 > isolde sim start /A:133
    5396 
    5397 ISOLDE: started sim 
    5398 
    5399 > select clear
    5400 
    5401 > isolde sim stop
    5402 
    5403 Sim termination reason: None 
    5404 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5405 chains... 
    5406 ISOLDE: stopped sim 
    5407 
    5408 > isolde sim start /B:133
    5409 
    5410 ISOLDE: started sim 
    5411 
    5412 > isolde sim stop
    5413 
    5414 Sim termination reason: None 
    5415 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5416 chains... 
    5417 ISOLDE: stopped sim 
    5418 
    5419 > isolde sim start /J:133
    5420 
    5421 ISOLDE: started sim 
    5422 
    5423 > isolde sim stop
    5424 
    5425 Sim termination reason: None 
    5426 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5427 chains... 
    5428 ISOLDE: stopped sim 
    5429 
    5430 > isolde sim start /E:133
    5431 
    5432 ISOLDE: started sim 
    5433 
    5434 > isolde sim stop
    5435 
    5436 Sim termination reason: None 
    5437 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5438 chains... 
    5439 ISOLDE: stopped sim 
    5440 
    5441 > isolde sim start /F:133
    5442 
    5443 ISOLDE: started sim 
    5444 
    5445 > isolde sim stop
    5446 
    5447 Sim termination reason: None 
    5448 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5449 chains... 
    5450 ISOLDE: stopped sim 
    5451 
    5452 > isolde sim start /T:438
    5453 
    5454 ISOLDE: started sim 
    5455 
    5456 > isolde sim stop
    5457 
    5458 Sim termination reason: None 
    5459 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5460 chains... 
    5461 ISOLDE: stopped sim 
    5462 
    5463 > isolde sim start /Q:438
    5464 
    5465 ISOLDE: started sim 
    5466 
    5467 > isolde sim stop
    5468 
    5469 Sim termination reason: None 
    5470 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5471 chains... 
    5472 ISOLDE: stopped sim 
    5473 
    5474 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    5475 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
    5476 
    5477 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    5478 
    5479 > addh
    5480 
    5481 Summary of feedback from adding hydrogens to
    5482 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb #1.2 
    5483 --- 
    5484 notes | Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain
    5485 A determined from SEQRES records 
    5486 Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain B
    5487 determined from SEQRES records 
    5488 Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain C
    5489 determined from SEQRES records 
    5490 Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain D
    5491 determined from SEQRES records 
    5492 Termini for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb (#1.2) chain E
    5493 determined from SEQRES records 
    5494 17 messages similar to the above omitted 
    5495 Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
    5496 1, /D MET 1, /E MET 1, /F MET 1, /G MET 1, /H MET 1, /I MET 1, /J MET 1, /K
    5497 MET 1, /L MET 1, /M MET 1, /N MET 1, /O MET 1, /P MET 1, /Q MET 1, /R MET 1,
    5498 /S MET 1, /T MET 1, /U MET 1, /V MET 1 
    5499 Chain-initial residues that are not actual N termini: /A GLY 377, /B GLY 377,
    5500 /C GLY 377, /D GLY 377, /E GLY 377, /F GLY 377, /G GLY 377, /H GLY 377, /I GLY
    5501 377, /J GLY 377, /K GLY 377, /L GLY 377, /M GLY 377, /N GLY 377, /O GLY 377,
    5502 /P GLY 377, /Q GLY 377, /R GLY 377, /S GLY 377, /T GLY 377, /U GLY 377, /V GLY
    5503 377 
    5504 Chain-final residues that are actual C termini: /A GLN 506, /B GLN 506, /C GLN
    5505 506, /D GLN 506, /E GLN 506, /F GLN 506, /G GLN 506, /H GLN 506, /I GLN 506,
    5506 /J GLN 506, /K GLN 506, /L GLN 506, /M GLN 506, /N GLN 506, /O GLN 506, /P GLN
    5507 506, /Q GLN 506, /R GLN 506, /S GLN 506, /T GLN 506, /U GLN 506, /V GLN 506 
    5508 Chain-final residues that are not actual C termini: /A THR 143, /B THR 143, /C
    5509 THR 143, /D THR 143, /E THR 143, /F THR 143, /G THR 143, /H THR 143, /I THR
    5510 143, /J THR 143, /K THR 143, /L THR 143, /M THR 143, /N THR 143, /O THR 143,
    5511 /P THR 143, /Q THR 143, /R THR 143, /S THR 143, /T THR 143, /U THR 143, /V THR
    5512 143 
    5513 6583 hydrogen bonds 
    5514 /A THR 143 is not terminus, removing H atom from 'C' 
    5515 /B THR 143 is not terminus, removing H atom from 'C' 
    5516 /C THR 143 is not terminus, removing H atom from 'C' 
    5517 /D THR 143 is not terminus, removing H atom from 'C' 
    5518 /E THR 143 is not terminus, removing H atom from 'C' 
    5519 17 messages similar to the above omitted 
    5520 13 hydrogens added 
    5521  
    5522 
    5523 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    5524 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
    5525 
    5526 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    5527 
    5528 ——— End of log from Thu Jan 25 14:40:09 2024 ———
    5529 
    5530 opened ChimeraX session 
    5531 
    5532 > view all
    5533 
    5534 > isolde start
    5535 
    5536 > set selectionWidth 4
    5537 
    5538 Forcefield cache not found or out of date. Regenerating from ffXML files. This
    5539 is normal if running ISOLDE for the first time, or after upgrading OpenMM. 
    5540 
    5541 Done loading forcefield 
    5542 
    5543 > isolde set simFidelityMode Medium/Medium
    5544 
    5545 ISOLDE: setting sim fidelity mode to Medium/Medium 
    5546 nonbonded_cutoff_distance = 0.900000 
    5547 use_gbsa = True 
    5548 gbsa_cutoff = 1.100000 
    5549 
    5550 > ui tool show "Ramachandran Plot"
    5551 
    5552 > isolde set simFidelityMode Highest/Slowest
    5553 
    5554 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    5555 nonbonded_cutoff_distance = 1.700000 
    5556 use_gbsa = True 
    5557 gbsa_cutoff = 2.000000 
    5558 
    5559 > isolde set simFidelityMode Highest/Slowest
    5560 
    5561 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    5562 nonbonded_cutoff_distance = 1.700000 
    5563 use_gbsa = True 
    5564 gbsa_cutoff = 2.000000 
    5565 
    5566 > select clear
    5567 
    5568 > isolde sim start /V:497
    5569 
    5570 ISOLDE: started sim 
    5571 
    5572 > isolde pepflip /V:497
    5573 
    5574 > isolde sim stop discardTo start
    5575 
    5576 Sim termination reason: None 
    5577 reverting to start 
    5578 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5579 chains... 
    5580 ISOLDE: stopped sim 
    5581 
    5582 > isolde sim start /V:497
    5583 
    5584 ISOLDE: started sim 
    5585 
    5586 > isolde sim stop
    5587 
    5588 Sim termination reason: None 
    5589 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5590 chains... 
    5591 ISOLDE: stopped sim 
    5592 
    5593 > isolde sim start /D:498
    5594 
    5595 ISOLDE: started sim 
    5596 
    5597 > isolde sim stop
    5598 
    5599 Sim termination reason: None 
    5600 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5601 chains... 
    5602 ISOLDE: stopped sim 
    5603 
    5604 > isolde sim start /H:499
    5605 
    5606 ISOLDE: started sim 
    5607 
    5608 > isolde pepflip /H:499
    5609 
    5610 > isolde cisflip /H:499
    5611 
    5612 > isolde cisflip /H:500
    5613 
    5614 > isolde pepflip /H:500
    5615 
    5616 > isolde sim stop discardTo start
    5617 
    5618 Sim termination reason: None 
    5619 reverting to start 
    5620 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5621 chains... 
    5622 ISOLDE: stopped sim 
    5623 
    5624 > isolde sim start /G:441
    5625 
    5626 ISOLDE: started sim 
    5627 
    5628 > isolde sim stop
    5629 
    5630 Sim termination reason: None 
    5631 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5632 chains... 
    5633 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5634 standards. 
    5635 ISOLDE: stopped sim 
    5636 
    5637 > isolde sim start /M:106
    5638 
    5639 ISOLDE: started sim 
    5640 
    5641 > select clear
    5642 
    5643 > ui tool show "Show Volume Menu"
    5644 
    5645 > ui tool show "Volume Viewer"
    5646 
    5647 > volume #1.1.1.2 level 0.002141
    5648 
    5649 > isolde sim stop
    5650 
    5651 Sim termination reason: None 
    5652 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5653 chains... 
    5654 ISOLDE: stopped sim 
    5655 
    5656 > isolde sim start /O:50
    5657 
    5658 ISOLDE: started sim 
    5659 
    5660 > volume #1.1.1.2 level 0.007621
    5661 
    5662 > isolde sim stop
    5663 
    5664 Sim termination reason: None 
    5665 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5666 chains... 
    5667 ISOLDE: stopped sim 
    5668 
    5669 > isolde sim start #!1.2/H:50
    5670 
    5671 ISOLDE: started sim 
    5672 
    5673 > isolde sim stop
    5674 
    5675 Sim termination reason: None 
    5676 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5677 chains... 
    5678 ISOLDE: stopped sim 
    5679 
    5680 > isolde sim start /U:50
    5681 
    5682 ISOLDE: started sim 
    5683 
    5684 > select clear
    5685 
    5686 [Repeated 1 time(s)]
    5687 
    5688 > isolde sim stop
    5689 
    5690 Sim termination reason: None 
    5691 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5692 chains... 
    5693 ISOLDE: stopped sim 
    5694 
    5695 > isolde sim start /G:429
    5696 
    5697 ISOLDE: started sim 
    5698 
    5699 > volume #1.1.1.2 level 0.003035
    5700 
    5701 > isolde sim stop
    5702 
    5703 Sim termination reason: None 
    5704 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5705 chains... 
    5706 ISOLDE: stopped sim 
    5707 
    5708 > isolde sim start /J:40
    5709 
    5710 ISOLDE: started sim 
    5711 
    5712 > isolde sim stop
    5713 
    5714 Sim termination reason: None 
    5715 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5716 chains... 
    5717 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5718 standards. 
    5719 ISOLDE: stopped sim 
    5720 
    5721 > isolde sim start /C:40
    5722 
    5723 ISOLDE: started sim 
    5724 
    5725 > isolde sim stop
    5726 
    5727 Sim termination reason: None 
    5728 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5729 chains... 
    5730 ISOLDE: stopped sim 
    5731 
    5732 > isolde sim start /C:17
    5733 
    5734 ISOLDE: started sim 
    5735 
    5736 > isolde sim stop
    5737 
    5738 Sim termination reason: None 
    5739 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5740 chains... 
    5741 ISOLDE: stopped sim 
    5742 
    5743 > isolde sim start /R:479
    5744 
    5745 ISOLDE: started sim 
    5746 
    5747 > isolde sim stop
    5748 
    5749 Sim termination reason: None 
    5750 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5751 chains... 
    5752 ISOLDE: stopped sim 
    5753 
    5754 > isolde sim start /C:142
    5755 
    5756 ISOLDE: started sim 
    5757 
    5758 > isolde sim stop
    5759 
    5760 Sim termination reason: None 
    5761 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5762 chains... 
    5763 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5764 standards. 
    5765 ISOLDE: stopped sim 
    5766 
    5767 > isolde sim start /C:50
    5768 
    5769 ISOLDE: started sim 
    5770 
    5771 > isolde sim stop
    5772 
    5773 Sim termination reason: None 
    5774 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5775 chains... 
    5776 ISOLDE: stopped sim 
    5777 
    5778 > isolde sim start /B:429
    5779 
    5780 ISOLDE: started sim 
    5781 
    5782 > isolde sim stop
    5783 
    5784 Sim termination reason: None 
    5785 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5786 chains... 
    5787 ISOLDE: stopped sim 
    5788 
    5789 > isolde sim start /R:445
    5790 
    5791 ISOLDE: started sim 
    5792 
    5793 > isolde sim stop
    5794 
    5795 Sim termination reason: None 
    5796 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5797 chains... 
    5798 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5799 standards. 
    5800 ISOLDE: stopped sim 
    5801 
    5802 > isolde sim start /R:142
    5803 
    5804 ISOLDE: started sim 
    5805 
    5806 > isolde sim stop
    5807 
    5808 Sim termination reason: None 
    5809 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5810 chains... 
    5811 ISOLDE: stopped sim 
    5812 
    5813 > isolde sim start /B:458
    5814 
    5815 ISOLDE: started sim 
    5816 
    5817 > isolde sim stop
    5818 
    5819 Sim termination reason: None 
    5820 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5821 chains... 
    5822 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5823 standards. 
    5824 ISOLDE: stopped sim 
    5825 
    5826 > isolde sim start /P:106
    5827 
    5828 ISOLDE: started sim 
    5829 
    5830 > isolde pepflip /P:106
    5831 
    5832 > isolde sim stop
    5833 
    5834 Sim termination reason: None 
    5835 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5836 chains... 
    5837 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5838 standards. 
    5839 ISOLDE: stopped sim 
    5840 
    5841 > isolde sim start /F:142
    5842 
    5843 ISOLDE: started sim 
    5844 
    5845 > isolde sim stop
    5846 
    5847 Sim termination reason: None 
    5848 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5849 chains... 
    5850 ISOLDE: stopped sim 
    5851 
    5852 > isolde sim start /I:17
    5853 
    5854 ISOLDE: started sim 
    5855 
    5856 > volume #1.1.1.2 level 0.003035
    5857 
    5858 > isolde sim stop
    5859 
    5860 Sim termination reason: None 
    5861 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5862 chains... 
    5863 ISOLDE: stopped sim 
    5864 
    5865 > isolde sim start /C:445
    5866 
    5867 ISOLDE: started sim 
    5868 
    5869 > isolde sim stop
    5870 
    5871 Sim termination reason: None 
    5872 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5873 chains... 
    5874 ISOLDE: stopped sim 
    5875 
    5876 > isolde sim start /T:445
    5877 
    5878 ISOLDE: started sim 
    5879 
    5880 > select clear
    5881 
    5882 > isolde sim stop
    5883 
    5884 Sim termination reason: None 
    5885 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5886 chains... 
    5887 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5888 standards. 
    5889 ISOLDE: stopped sim 
    5890 
    5891 > isolde sim start /D:84
    5892 
    5893 ISOLDE: started sim 
    5894 
    5895 > isolde sim stop
    5896 
    5897 Sim termination reason: None 
    5898 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5899 chains... 
    5900 ISOLDE: stopped sim 
    5901 
    5902 > isolde sim start /N:50
    5903 
    5904 ISOLDE: started sim 
    5905 
    5906 > isolde sim stop
    5907 
    5908 Sim termination reason: None 
    5909 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5910 chains... 
    5911 ISOLDE: stopped sim 
    5912 
    5913 > isolde sim start /G:407
    5914 
    5915 ISOLDE: started sim 
    5916 
    5917 > isolde sim stop
    5918 
    5919 Sim termination reason: None 
    5920 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5921 chains... 
    5922 ISOLDE: stopped sim 
    5923 
    5924 > isolde sim start /G:407
    5925 
    5926 ISOLDE: started sim 
    5927 
    5928 > isolde sim stop
    5929 
    5930 Sim termination reason: None 
    5931 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5932 chains... 
    5933 ISOLDE: stopped sim 
    5934 
    5935 > isolde sim start /C:388
    5936 
    5937 ISOLDE: started sim 
    5938 
    5939 > isolde sim stop
    5940 
    5941 Sim termination reason: None 
    5942 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5943 chains... 
    5944 ISOLDE: stopped sim 
    5945 
    5946 > isolde sim start /M:17
    5947 
    5948 ISOLDE: started sim 
    5949 
    5950 > isolde sim stop
    5951 
    5952 Sim termination reason: None 
    5953 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5954 chains... 
    5955 ISOLDE: stopped sim 
    5956 
    5957 > isolde sim start /J:394
    5958 
    5959 ISOLDE: started sim 
    5960 
    5961 > isolde sim stop
    5962 
    5963 Sim termination reason: None 
    5964 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5965 chains... 
    5966 ISOLDE: stopped sim 
    5967 
    5968 > isolde sim start /N:3
    5969 
    5970 ISOLDE: started sim 
    5971 
    5972 > isolde sim stop
    5973 
    5974 Sim termination reason: None 
    5975 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5976 chains... 
    5977 ISOLDE: stopped sim 
    5978 
    5979 > isolde sim start /I:50
    5980 
    5981 ISOLDE: started sim 
    5982 
    5983 > select clear
    5984 
    5985 > isolde sim stop
    5986 
    5987 Sim termination reason: None 
    5988 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5989 chains... 
    5990 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5991 standards. 
    5992 ISOLDE: stopped sim 
    5993 
    5994 > isolde sim start /J:429
    5995 
    5996 ISOLDE: started sim 
    5997 
    5998 > select clear
    5999 
    6000 > isolde sim stop
    6001 
    6002 Sim termination reason: None 
    6003 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6004 chains... 
    6005 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6006 standards. 
    6007 ISOLDE: stopped sim 
    6008 
    6009 > isolde sim start /P:445
    6010 
    6011 ISOLDE: started sim 
    6012 
    6013 > isolde sim stop
    6014 
    6015 Sim termination reason: None 
    6016 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6017 chains... 
    6018 ISOLDE: stopped sim 
    6019 
    6020 > isolde sim start /H:429
    6021 
    6022 ISOLDE: started sim 
    6023 
    6024 > isolde sim stop
    6025 
    6026 Sim termination reason: None 
    6027 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6028 chains... 
    6029 ISOLDE: stopped sim 
    6030 
    6031 > isolde sim start /B:50
    6032 
    6033 ISOLDE: started sim 
    6034 
    6035 > isolde sim stop
    6036 
    6037 Sim termination reason: None 
    6038 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6039 chains... 
    6040 ISOLDE: stopped sim 
    6041 
    6042 > select clear
    6043 
    6044 > isolde sim start /Q:445
    6045 
    6046 ISOLDE: started sim 
    6047 
    6048 > volume #1.1.1.2 level 0.00159
    6049 
    6050 > isolde sim stop
    6051 
    6052 Sim termination reason: None 
    6053 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6054 chains... 
    6055 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6056 standards. 
    6057 ISOLDE: stopped sim 
    6058 
    6059 > isolde sim start /D:50
    6060 
    6061 ISOLDE: started sim 
    6062 
    6063 > isolde sim stop
    6064 
    6065 Sim termination reason: None 
    6066 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6067 chains... 
    6068 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6069 standards. 
    6070 ISOLDE: stopped sim 
    6071 
    6072 > isolde sim start /V:50
    6073 
    6074 ISOLDE: started sim 
    6075 
    6076 > isolde sim stop
    6077 
    6078 Sim termination reason: None 
    6079 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6080 chains... 
    6081 ISOLDE: stopped sim 
    6082 
    6083 > isolde sim start /P:50
    6084 
    6085 ISOLDE: started sim 
    6086 
    6087 > isolde sim stop
    6088 
    6089 Sim termination reason: None 
    6090 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6091 chains... 
    6092 ISOLDE: stopped sim 
    6093 
    6094 > isolde sim start /D:17
    6095 
    6096 ISOLDE: started sim 
    6097 
    6098 > isolde sim stop
    6099 
    6100 Sim termination reason: None 
    6101 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6102 chains... 
    6103 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6104 standards. 
    6105 ISOLDE: stopped sim 
    6106 
    6107 > isolde sim start /U:3
    6108 
    6109 ISOLDE: started sim 
    6110 
    6111 > select clear
    6112 
    6113 > isolde sim stop
    6114 
    6115 Sim termination reason: None 
    6116 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6117 chains... 
    6118 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6119 standards. 
    6120 ISOLDE: stopped sim 
    6121 
    6122 > isolde sim start /D:106
    6123 
    6124 ISOLDE: started sim 
    6125 
    6126 > select clear
    6127 
    6128 > isolde sim stop
    6129 
    6130 Sim termination reason: None 
    6131 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6132 chains... 
    6133 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6134 standards. 
    6135 ISOLDE: stopped sim 
    6136 
    6137 > isolde sim start /I:40
    6138 
    6139 ISOLDE: started sim 
    6140 
    6141 > isolde sim stop
    6142 
    6143 Sim termination reason: None 
    6144 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6145 chains... 
    6146 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6147 standards. 
    6148 ISOLDE: stopped sim 
    6149 
    6150 > isolde sim start /I:3
    6151 
    6152 ISOLDE: started sim 
    6153 
    6154 > isolde sim stop
    6155 
    6156 Sim termination reason: None 
    6157 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6158 chains... 
    6159 ISOLDE: stopped sim 
    6160 
    6161 > isolde sim start /I:3
    6162 
    6163 ISOLDE: started sim 
    6164 
    6165 > isolde sim stop
    6166 
    6167 Sim termination reason: None 
    6168 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6169 chains... 
    6170 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6171 standards. 
    6172 ISOLDE: stopped sim 
    6173 
    6174 > isolde sim start /I:2
    6175 
    6176 ISOLDE: started sim 
    6177 
    6178 > isolde sim stop
    6179 
    6180 Sim termination reason: None 
    6181 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6182 chains... 
    6183 ISOLDE: stopped sim 
    6184 
    6185 > isolde sim start /O:394
    6186 
    6187 ISOLDE: started sim 
    6188 
    6189 > isolde sim stop
    6190 
    6191 Sim termination reason: None 
    6192 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6193 chains... 
    6194 ISOLDE: stopped sim 
    6195 
    6196 > isolde sim start /N:504
    6197 
    6198 ISOLDE: started sim 
    6199 
    6200 > isolde sim stop
    6201 
    6202 Sim termination reason: None 
    6203 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6204 chains... 
    6205 ISOLDE: stopped sim 
    6206 
    6207 > isolde sim start /P:3
    6208 
    6209 ISOLDE: started sim 
    6210 
    6211 > isolde sim stop
    6212 
    6213 Sim termination reason: None 
    6214 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6215 chains... 
    6216 ISOLDE: stopped sim 
    6217 
    6218 > isolde sim start /B:445
    6219 
    6220 ISOLDE: started sim 
    6221 
    6222 > isolde sim stop
    6223 
    6224 Sim termination reason: None 
    6225 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6226 chains... 
    6227 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6228 standards. 
    6229 ISOLDE: stopped sim 
    6230 
    6231 > isolde sim start /V:1
    6232 
    6233 ISOLDE: started sim 
    6234 
    6235 > isolde sim stop
    6236 
    6237 Sim termination reason: None 
    6238 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6239 chains... 
    6240 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6241 standards. 
    6242 ISOLDE: stopped sim 
    6243 
    6244 > isolde sim start /V:3
    6245 
    6246 ISOLDE: started sim 
    6247 
    6248 > isolde sim stop
    6249 
    6250 Sim termination reason: None 
    6251 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6252 chains... 
    6253 ISOLDE: stopped sim 
    6254 
    6255 > isolde sim start /D:3
    6256 
    6257 ISOLDE: started sim 
    6258 
    6259 > isolde sim stop
    6260 
    6261 Sim termination reason: None 
    6262 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6263 chains... 
    6264 ISOLDE: stopped sim 
    6265 
    6266 > isolde sim start /D:501
    6267 
    6268 ISOLDE: started sim 
    6269 
    6270 > isolde pepflip /D:501
    6271 
    6272 > isolde sim stop discardTo start
    6273 
    6274 Sim termination reason: None 
    6275 reverting to start 
    6276 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6277 chains... 
    6278 ISOLDE: stopped sim 
    6279 
    6280 > isolde sim start /U:502
    6281 
    6282 ISOLDE: started sim 
    6283 
    6284 > isolde sim stop
    6285 
    6286 Sim termination reason: None 
    6287 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6288 chains... 
    6289 ISOLDE: stopped sim 
    6290 
    6291 > isolde sim start /J:50
    6292 
    6293 ISOLDE: started sim 
    6294 
    6295 > isolde sim stop
    6296 
    6297 Sim termination reason: None 
    6298 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6299 chains... 
    6300 ISOLDE: stopped sim 
    6301 
    6302 > isolde sim start /P:84
    6303 
    6304 ISOLDE: started sim 
    6305 
    6306 > isolde sim stop
    6307 
    6308 Sim termination reason: None 
    6309 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6310 chains... 
    6311 ISOLDE: stopped sim 
    6312 
    6313 > isolde sim start /A:100
    6314 
    6315 ISOLDE: started sim 
    6316 
    6317 > isolde sim stop
    6318 
    6319 Sim termination reason: None 
    6320 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6321 chains... 
    6322 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6323 standards. 
    6324 ISOLDE: stopped sim 
    6325 
    6326 > isolde sim start /O:3
    6327 
    6328 ISOLDE: started sim 
    6329 
    6330 > isolde sim stop
    6331 
    6332 Sim termination reason: None 
    6333 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6334 chains... 
    6335 ISOLDE: stopped sim 
    6336 
    6337 > isolde sim start /F:429
    6338 
    6339 ISOLDE: started sim 
    6340 
    6341 > isolde sim stop
    6342 
    6343 Sim termination reason: None 
    6344 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6345 chains... 
    6346 ISOLDE: stopped sim 
    6347 
    6348 > isolde sim start /D:500
    6349 
    6350 ISOLDE: started sim 
    6351 
    6352 > isolde sim stop discardTo start
    6353 
    6354 Sim termination reason: None 
    6355 reverting to start 
    6356 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6357 chains... 
    6358 ISOLDE: stopped sim 
    6359 
    6360 > isolde sim start /V:3
    6361 
    6362 ISOLDE: started sim 
    6363 
    6364 > isolde sim stop
    6365 
    6366 Sim termination reason: None 
    6367 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6368 chains... 
    6369 ISOLDE: stopped sim 
    6370 
    6371 > isolde sim start /S:100
    6372 
    6373 ISOLDE: started sim 
    6374 
    6375 > isolde sim stop
    6376 
    6377 Sim termination reason: None 
    6378 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6379 chains... 
    6380 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6381 standards. 
    6382 ISOLDE: stopped sim 
    6383 
    6384 > isolde sim start /N:141
    6385 
    6386 ISOLDE: started sim 
    6387 
    6388 > isolde sim stop
    6389 
    6390 Sim termination reason: None 
    6391 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6392 chains... 
    6393 ISOLDE: stopped sim 
    6394 
    6395 > isolde sim start /E:84
    6396 
    6397 ISOLDE: started sim 
    6398 
    6399 > isolde sim stop
    6400 
    6401 Sim termination reason: None 
    6402 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6403 chains... 
    6404 ISOLDE: stopped sim 
    6405 
    6406 > isolde sim start /E:119
    6407 
    6408 ISOLDE: started sim 
    6409 
    6410 > volume #1.1.1.2 level 0.0003392
    6411 
    6412 > isolde sim stop
    6413 
    6414 Sim termination reason: None 
    6415 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6416 chains... 
    6417 ISOLDE: stopped sim 
    6418 
    6419 > isolde sim start /E:84
    6420 
    6421 ISOLDE: started sim 
    6422 
    6423 > select clear
    6424 
    6425 > isolde pepflip /E:84
    6426 
    6427 > isolde sim stop
    6428 
    6429 Sim termination reason: None 
    6430 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6431 chains... 
    6432 ISOLDE: stopped sim 
    6433 
    6434 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    6435 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
    6436 
    6437 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    6438 
    6439 ——— End of log from Wed Jan 31 17:03:39 2024 ———
    6440 
    6441 opened ChimeraX session 
    6442 
    6443 > isolde start
    6444 
    6445 > set selectionWidth 4
    6446 
    6447 Done loading forcefield 
    6448 
    6449 > isolde set simFidelityMode Medium/Medium
    6450 
    6451 ISOLDE: setting sim fidelity mode to Medium/Medium 
    6452 nonbonded_cutoff_distance = 0.900000 
    6453 use_gbsa = True 
    6454 gbsa_cutoff = 1.100000 
    6455 
    6456 QDockWidget failed to find relevant screen info. screenFrom:
    6457 QScreen(0x600001d095a0, name="DELL U2415") screenTo: QScreen(0x0) wdgScreen:
    6458 QScreen(0x600001d095a0, name="DELL U2415") orgWdgScreen
    6459 QScreen(0x600001d09670, name="Built-in Retina Display") 
    6460 
    6461 [Repeated 39 time(s)]
    6462 
    6463 > isolde set simFidelityMode Highest/Slowest
    6464 
    6465 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    6466 nonbonded_cutoff_distance = 1.700000 
    6467 use_gbsa = True 
    6468 gbsa_cutoff = 2.000000 
    6469 
    6470 > isolde set simFidelityMode Highest/Slowest
    6471 
    6472 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    6473 nonbonded_cutoff_distance = 1.700000 
    6474 use_gbsa = True 
    6475 gbsa_cutoff = 2.000000 
    6476 
    6477 > isolde sim start /V:3
    6478 
    6479 ISOLDE: started sim 
    6480 
    6481 > isolde sim stop
    6482 
    6483 Sim termination reason: None 
    6484 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6485 chains... 
    6486 ISOLDE: stopped sim 
    6487 
    6488 > isolde sim start /E:84
    6489 
    6490 ISOLDE: started sim 
    6491 
    6492 > isolde sim stop
    6493 
    6494 Sim termination reason: None 
    6495 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6496 chains... 
    6497 ISOLDE: stopped sim 
    6498 
    6499 > isolde sim start /A:142
    6500 
    6501 ISOLDE: started sim 
    6502 
    6503 > isolde pepflip /A:142
    6504 
    6505 > isolde sim stop
    6506 
    6507 Sim termination reason: None 
    6508 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6509 chains... 
    6510 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6511 standards. 
    6512 ISOLDE: stopped sim 
    6513 
    6514 > isolde sim start /D:2
    6515 
    6516 ISOLDE: started sim 
    6517 
    6518 > select clear
    6519 
    6520 > isolde sim stop
    6521 
    6522 Sim termination reason: None 
    6523 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6524 chains... 
    6525 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6526 standards. 
    6527 ISOLDE: stopped sim 
    6528 
    6529 > isolde sim start /V:3
    6530 
    6531 ISOLDE: started sim 
    6532 
    6533 > isolde sim stop
    6534 
    6535 Sim termination reason: None 
    6536 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6537 chains... 
    6538 ISOLDE: stopped sim 
    6539 
    6540 > isolde sim start /O:143
    6541 
    6542 ISOLDE: started sim 
    6543 
    6544 > isolde sim stop
    6545 
    6546 Sim termination reason: None 
    6547 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6548 chains... 
    6549 ISOLDE: stopped sim 
    6550 
    6551 > isolde sim start /T:84
    6552 
    6553 ISOLDE: started sim 
    6554 
    6555 > isolde sim stop
    6556 
    6557 Sim termination reason: None 
    6558 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6559 chains... 
    6560 ISOLDE: stopped sim 
    6561 
    6562 > isolde sim start /V:432
    6563 
    6564 ISOLDE: started sim 
    6565 
    6566 > isolde sim stop
    6567 
    6568 Sim termination reason: None 
    6569 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6570 chains... 
    6571 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6572 standards. 
    6573 ISOLDE: stopped sim 
    6574 
    6575 > isolde sim start /D:388
    6576 
    6577 ISOLDE: started sim 
    6578 
    6579 > isolde pepflip /D:389
    6580 
    6581 > isolde sim stop
    6582 
    6583 Sim termination reason: None 
    6584 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6585 chains... 
    6586 ISOLDE: stopped sim 
    6587 
    6588 > isolde sim start /F:1
    6589 
    6590 ISOLDE: started sim 
    6591 
    6592 > isolde sim stop discardTo start
    6593 
    6594 Sim termination reason: None 
    6595 reverting to start 
    6596 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6597 chains... 
    6598 ISOLDE: stopped sim 
    6599 
    6600 > isolde sim start /F:1
    6601 
    6602 ISOLDE: started sim 
    6603 
    6604 > isolde sim stop
    6605 
    6606 Sim termination reason: None 
    6607 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6608 chains... 
    6609 ISOLDE: stopped sim 
    6610 
    6611 > isolde sim start /K:100
    6612 
    6613 ISOLDE: started sim 
    6614 
    6615 > isolde pepflip /K:100
    6616 
    6617 > select clear
    6618 
    6619 [Repeated 1 time(s)]
    6620 
    6621 > isolde sim stop
    6622 
    6623 Sim termination reason: None 
    6624 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6625 chains... 
    6626 ISOLDE: stopped sim 
    6627 
    6628 > select clear
    6629 
    6630 > isolde sim start /M:1
    6631 
    6632 ISOLDE: started sim 
    6633 
    6634 > isolde sim stop
    6635 
    6636 Sim termination reason: None 
    6637 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6638 chains... 
    6639 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6640 standards. 
    6641 ISOLDE: stopped sim 
    6642 
    6643 > isolde sim start /R:20
    6644 
    6645 ISOLDE: started sim 
    6646 
    6647 > select clear
    6648 
    6649 > isolde sim stop
    6650 
    6651 Sim termination reason: None 
    6652 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6653 chains... 
    6654 ISOLDE: stopped sim 
    6655 
    6656 > isolde sim start /T:84
    6657 
    6658 ISOLDE: started sim 
    6659 
    6660 > select clear
    6661 
    6662 > isolde sim stop
    6663 
    6664 Sim termination reason: None 
    6665 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6666 chains... 
    6667 ISOLDE: stopped sim 
    6668 
    6669 > isolde sim start /M:3
    6670 
    6671 ISOLDE: started sim 
    6672 
    6673 > isolde sim stop
    6674 
    6675 Sim termination reason: None 
    6676 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6677 chains... 
    6678 ISOLDE: stopped sim 
    6679 
    6680 > isolde sim start /K:1
    6681 
    6682 ISOLDE: started sim 
    6683 
    6684 > isolde pepflip /K:2
    6685 
    6686 > isolde sim stop
    6687 
    6688 Sim termination reason: None 
    6689 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6690 chains... 
    6691 ISOLDE: stopped sim 
    6692 
    6693 > isolde sim start /M:142
    6694 
    6695 ISOLDE: started sim 
    6696 
    6697 > ui tool show "Volume Viewer"
    6698 
    6699 > volume #1.1.1.1 level 0.005023
    6700 
    6701 > volume #1.1.1.2 level 0.0007055
    6702 
    6703 > volume #1.1.1.1 level 0.01489
    6704 
    6705 > isolde sim stop
    6706 
    6707 Sim termination reason: None 
    6708 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6709 chains... 
    6710 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6711 standards. 
    6712 ISOLDE: stopped sim 
    6713 
    6714 > isolde sim start /V:445
    6715 
    6716 ISOLDE: started sim 
    6717 
    6718 > isolde sim stop
    6719 
    6720 Sim termination reason: None 
    6721 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6722 chains... 
    6723 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6724 standards. 
    6725 ISOLDE: stopped sim 
    6726 
    6727 > isolde sim start /B:40
    6728 
    6729 ISOLDE: started sim 
    6730 
    6731 > volume #1.1.1.1 level 0.00336
    6732 
    6733 > volume #1.1.1.1 level 0.01945
    6734 
    6735 > select clear
    6736 
    6737 [Repeated 2 time(s)]
    6738 
    6739 > volume #1.1.1.1 level 0.01248
    6740 
    6741 > select clear
    6742 
    6743 > isolde sim stop
    6744 
    6745 Sim termination reason: None 
    6746 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6747 chains... 
    6748 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6749 standards. 
    6750 ISOLDE: stopped sim 
    6751 
    6752 > isolde sim start /A:445
    6753 
    6754 ISOLDE: started sim 
    6755 
    6756 > isolde sim stop
    6757 
    6758 Sim termination reason: None 
    6759 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6760 chains... 
    6761 ISOLDE: stopped sim 
    6762 
    6763 > isolde sim start /D:472
    6764 
    6765 ISOLDE: started sim 
    6766 
    6767 > volume #1.1.1.1 level 0.0001158
    6768 
    6769 > volume #1.1.1.1 level 0.008715
    6770 
    6771 > volume #1.1.1.2 level -0.001536
    6772 
    6773 > isolde sim stop
    6774 
    6775 Sim termination reason: None 
    6776 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6777 chains... 
    6778 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6779 standards. 
    6780 ISOLDE: stopped sim 
    6781 
    6782 > isolde sim start /I:441
    6783 
    6784 ISOLDE: started sim 
    6785 
    6786 > isolde sim stop
    6787 
    6788 Sim termination reason: None 
    6789 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6790 chains... 
    6791 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6792 standards. 
    6793 ISOLDE: stopped sim 
    6794 
    6795 > isolde sim start /A:100
    6796 
    6797 ISOLDE: started sim 
    6798 
    6799 > isolde sim stop
    6800 
    6801 Sim termination reason: None 
    6802 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6803 chains... 
    6804 ISOLDE: stopped sim 
    6805 
    6806 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    6807 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
    6808 
    6809 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    6810 
    6811 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    6812 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
    6813 
    6814 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    6815 
    6816 ——— End of log from Tue Feb 6 15:50:30 2024 ———
    6817 
    6818 opened ChimeraX session 
    6819 
    6820 > isolde start
    6821 
    6822 > set selectionWidth 4
    6823 
    6824 Done loading forcefield 
    6825 
    6826 > isolde set simFidelityMode Medium/Medium
    6827 
    6828 ISOLDE: setting sim fidelity mode to Medium/Medium 
    6829 nonbonded_cutoff_distance = 0.900000 
    6830 use_gbsa = True 
    6831 gbsa_cutoff = 1.100000 
    6832 
    6833 > isolde set simFidelityMode Highest/Slowest
    6834 
    6835 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    6836 nonbonded_cutoff_distance = 1.700000 
    6837 use_gbsa = True 
    6838 gbsa_cutoff = 2.000000 
    6839 
    6840 > isolde set simFidelityMode Highest/Slowest
    6841 
    6842 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    6843 nonbonded_cutoff_distance = 1.700000 
    6844 use_gbsa = True 
    6845 gbsa_cutoff = 2.000000 
    6846 
    6847 > select clear
    6848 
    6849 > isolde sim start /S:441
    6850 
    6851 ISOLDE: started sim 
    6852 
    6853 > isolde sim stop
    6854 
    6855 Sim termination reason: None 
    6856 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6857 chains... 
    6858 ISOLDE: stopped sim 
    6859 
    6860 > isolde sim start /V:40
    6861 
    6862 ISOLDE: started sim 
    6863 
    6864 > isolde sim stop
    6865 
    6866 Sim termination reason: None 
    6867 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6868 chains... 
    6869 ISOLDE: stopped sim 
    6870 
    6871 > isolde sim start /F:3
    6872 
    6873 ISOLDE: started sim 
    6874 
    6875 > isolde sim stop
    6876 
    6877 Sim termination reason: None 
    6878 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6879 chains... 
    6880 ISOLDE: stopped sim 
    6881 
    6882 > ui tool show "Show Volume Menu"
    6883 
    6884 > ui tool show "Volume Viewer"
    6885 
    6886 > volume #1.1.1.1 level 0.007575
    6887 
    6888 > volume #1.1.1.1 level 0.001855
    6889 
    6890 > volume #1.1.1.1 level 0.008033
    6891 
    6892 > isolde sim start /C:40
    6893 
    6894 ISOLDE: started sim 
    6895 
    6896 > isolde sim stop
    6897 
    6898 Sim termination reason: None 
    6899 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6900 chains... 
    6901 ISOLDE: stopped sim 
    6902 
    6903 > isolde sim start /C:50
    6904 
    6905 ISOLDE: started sim 
    6906 
    6907 > isolde sim stop
    6908 
    6909 Sim termination reason: None 
    6910 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6911 chains... 
    6912 ISOLDE: stopped sim 
    6913 
    6914 > isolde sim start /K:100
    6915 
    6916 ISOLDE: started sim 
    6917 
    6918 > isolde pepflip /K:100
    6919 
    6920 > isolde sim stop
    6921 
    6922 Sim termination reason: None 
    6923 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6924 chains... 
    6925 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6926 standards. 
    6927 ISOLDE: stopped sim 
    6928 
    6929 > isolde sim start /A:100
    6930 
    6931 ISOLDE: started sim 
    6932 
    6933 > isolde pepflip /A:101
    6934 
    6935 > isolde sim stop
    6936 
    6937 Sim termination reason: None 
    6938 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6939 chains... 
    6940 ISOLDE: stopped sim 
    6941 
    6942 > ui tool show "Ramachandran Plot"
    6943 
    6944 > isolde sim start /D:498
    6945 
    6946 ISOLDE: started sim 
    6947 
    6948 > isolde pepflip /D:498
    6949 
    6950 > volume #1.1.1.1 level 0.01525
    6951 
    6952 > isolde pepflip /D:501
    6953 
    6954 > isolde sim stop discardTo start
    6955 
    6956 Sim termination reason: None 
    6957 reverting to start 
    6958 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6959 chains... 
    6960 ISOLDE: stopped sim 
    6961 
    6962 > view all
    6963 
    6964 > select #1/A
    6965 
    6966 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    6967 
    6968 > view #1/A
    6969 
    6970 > isolde sim start /A
    6971 
    6972 ISOLDE: started sim 
    6973 
    6974 > isolde shorthand
    6975    
    6976    
    6977     Initialising ISOLDE-specific command aliases:
    6978     Alias       Equivalent full command
    6979     -------------------------------------------------
    6980     st  isolde step {arguments}
    6981     aw  isolde add water {arguments}
    6982     awsf        isolde add water {arguments} sim false
    6983     al  isolde add ligand {arguments}
    6984     aa  isolde add aa $1 sel {arguments}
    6985     ht  isolde mod his sel {arguments}
    6986     so  setattr sel atoms occupancy {arguments}
    6987     ab  isolde adjust bfactors {arguments}
    6988     ss  isolde sim start sel
    6989     rt  isolde release torsions sel {arguments}
    6990     rd  isolde release distances sel {arguments}
    6991     ra  rd; rt
    6992     pf  isolde pepflip sel
    6993     cf  isolde cisflip sel
    6994     cbb color bfactor {arguments}
    6995     cbo color byattr occupancy {arguments}
    6996     cbc color {arguments} bychain; color {arguments} byhet
    6997     cs  clipper set contourSensitivity {arguments}
    6998    
    6999 
    7000  
    7001 
    7002 > select #1/A:1
    7003 
    7004 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7005 
    7006 > view #1/A:1
    7007 
    7008 > isolde sim stop discardTo start
    7009 
    7010 Sim termination reason: None 
    7011 reverting to start 
    7012 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7013 chains... 
    7014 ISOLDE: stopped sim 
    7015 
    7016 > select #1/A:1-200
    7017 
    7018 2162 atoms, 2166 bonds, 143 residues, 1 model selected 
    7019 
    7020 > isolde sim start /A:1-143
    7021 
    7022 ISOLDE: started sim 
    7023 
    7024 > select #1/A:1
    7025 
    7026 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7027 
    7028 > select #1/A:1
    7029 
    7030 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7031 
    7032 > volume #1.1.1.1 level 0.006304
    7033 
    7034 > isolde pepflip /A:2
    7035 
    7036 > select #1/A:1
    7037 
    7038 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7039 
    7040 > volume #1.1.1.1 level 0.01796
    7041 
    7042 > st
    7043 
    7044 > isolde pepflip /A:3
    7045 
    7046 > isolde sim stop discardTo start
    7047 
    7048 Sim termination reason: None 
    7049 reverting to start 
    7050 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7051 chains... 
    7052 ISOLDE: stopped sim 
    7053 
    7054 > select #1/A:1-200
    7055 
    7056 2162 atoms, 2166 bonds, 143 residues, 1 model selected 
    7057 
    7058 > isolde sim start /A:1-143
    7059 
    7060 ISOLDE: started sim 
    7061 
    7062 > select #1/A:1
    7063 
    7064 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7065 
    7066 > st
    7067 
    7068 > st -1
    7069 
    7070 Unrecognised residue argument! If specified, must be either a residue,
    7071 "first", "last", "next" or "prev" 
    7072 
    7073 > st prev
    7074 
    7075 [Repeated 1 time(s)]
    7076 
    7077 > volume #1.1.1.1 level 0.006033
    7078 
    7079 > st
    7080 
    7081 [Repeated 10 time(s)]
    7082 
    7083 > volume #1.1.1.1 level 0.012
    7084 
    7085 > st
    7086 
    7087 [Repeated 11 time(s)]
    7088 
    7089 > select clear
    7090 
    7091 [Repeated 1 time(s)]
    7092 
    7093 > st
    7094 
    7095 [Repeated 24 time(s)]
    7096 
    7097 > st prev
    7098 
    7099 [Repeated 16 time(s)]
    7100 
    7101 > st
    7102 
    7103 [Repeated 18 time(s)]
    7104 
    7105 > st prev
    7106 
    7107 > st
    7108 
    7109 [Repeated 33 time(s)]
    7110 
    7111 > st prev
    7112 
    7113 > st
    7114 
    7115 [Repeated 6 time(s)]
    7116 
    7117 > volume #1.1.1.2 level -0.0006175
    7118 
    7119 > st
    7120 
    7121 [Repeated 13 time(s)]
    7122 
    7123 > isolde sim stop
    7124 
    7125 Sim termination reason: None 
    7126 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7127 chains... 
    7128 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7129 standards. 
    7130 ISOLDE: stopped sim 
    7131 
    7132 > select #1/A:100-300
    7133 
    7134 676 atoms, 676 bonds, 44 residues, 1 model selected 
    7135 
    7136 > select #1/A:100-200
    7137 
    7138 676 atoms, 676 bonds, 44 residues, 1 model selected 
    7139 
    7140 > isolde sim start /A:100-143
    7141 
    7142 ISOLDE: started sim 
    7143 
    7144 > st
    7145 
    7146 [Repeated 40 time(s)]
    7147 
    7148 > isolde sim stop
    7149 
    7150 Sim termination reason: None 
    7151 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7152 chains... 
    7153 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    7154 standards. 
    7155 ISOLDE: stopped sim 
    7156 
    7157 > select #1/A:300-400
    7158 
    7159 362 atoms, 363 bonds, 24 residues, 1 model selected 
    7160 
    7161 > isolde sim start /A:377-400
    7162 
    7163 ISOLDE: started sim 
    7164 
    7165 > st prev
    7166 
    7167 > st
    7168 
    7169 [Repeated 28 time(s)]
    7170 
    7171 > isolde sim stop
    7172 
    7173 Sim termination reason: None 
    7174 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7175 chains... 
    7176 ISOLDE: stopped sim 
    7177 
    7178 > select #1/A:350-500
    7179 
    7180 1870 atoms, 1878 bonds, 124 residues, 1 model selected 
    7181 
    7182 > isolde sim start /A:377-500
    7183 
    7184 ISOLDE: started sim 
    7185 
    7186 > st
    7187 
    7188 [Repeated 91 time(s)]
    7189 
    7190 > isolde pepflip /A:499
    7191 
    7192 > select clear
    7193 
    7194 > st
    7195 
    7196 [Repeated 7 time(s)]
    7197 
    7198 > isolde sim stop
    7199 
    7200 Sim termination reason: None 
    7201 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7202 chains... 
    7203 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7204 standards. 
    7205 ISOLDE: stopped sim 
    7206 
    7207 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    7208 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
    7209 
    7210 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    7211 
    7212 ——— End of log from Thu Feb 8 16:08:43 2024 ———
    7213 
    7214 opened ChimeraX session 
    7215 
    7216 > view all
    7217 
    7218 > combine #1/A #2
    7219 
    7220 > hide #2 models
    7221 
    7222 > show #2 models
    7223 
    7224 > ui mousemode right "translate selected models"
    7225 
    7226 > select add #2
    7227 
    7228 91090 atoms, 91353 bonds, 6007 residues, 2 models selected 
    7229 
    7230 > select subtract #2
    7231 
    7232 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7233 
    7234 > select add #1.2
    7235 
    7236 91071 atoms, 91335 bonds, 6006 residues, 25 models selected 
    7237 
    7238 > select add #1.2
    7239 
    7240 91071 atoms, 91335 bonds, 6006 residues, 25 models selected 
    7241 
    7242 > select add #1
    7243 
    7244 91071 atoms, 91335 bonds, 6006 residues, 35 models selected 
    7245 
    7246 > select add #1
    7247 
    7248 91071 atoms, 91335 bonds, 6006 residues, 35 models selected 
    7249 
    7250 > select add #1
    7251 
    7252 91071 atoms, 91335 bonds, 6006 residues, 35 models selected 
    7253 
    7254 > hide #!1 models
    7255 
    7256 > show #!1 models
    7257 
    7258 > select clear
    7259 
    7260 > select add #2
    7261 
    7262 91071 atoms, 91335 bonds, 6006 residues, 1 model selected 
    7263 
    7264 > view matrix models #2,1,0,0,42.021,0,1,0,149.92,0,0,1,36.759
    7265 
    7266 > view matrix models #2,1,0,0,53.235,0,1,0,239.35,0,0,1,110.74
    7267 
    7268 > hide sel atoms
    7269 
    7270 > delete #2/B-L
    7271 
    7272 > delete #2/L-Q
    7273 
    7274 > delete #2/R-U
    7275 
    7276 > delete #2/V
    7277 
    7278 > select #2/A
    7279 
    7280 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    7281 
    7282 > view matrix models #2,1,0,0,-4.4005,0,1,0,91.276,0,0,1,62.808
    7283 
    7284 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    7285 > determination/Reference_models/22-ring_Sims/Rhom_Monomer-v5.pdb" models #2
    7286 
    7287 > close #2
    7288 
    7289 > select clear
    7290 
    7291 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    7292 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild4_Current.cxs"
    7293 
    7294 Taking snapshot of stepper: 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb 
    7295 
    7296 ——— End of log from Mon Feb 12 16:01:42 2024 ———
    7297 
    7298 opened ChimeraX session 
    7299 
    7300 > close session
    7301 
    7302 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    7303 > determination/Reference_models/22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb"
    7304 > format pdb
    7305 
    7306 Chain information for 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb #1 
    7307 --- 
    7308 Chain | Description 
    7309 A B C D E F G H I J K L M N O P Q R S T U V | No description available 
    7310  
    7311 
    7312 > hide atoms
    7313 
    7314 > show cartoons
    7315 
    7316 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    7317 > determination/Reference_models/22-ring_Sims/Rhom_Monomer-v5.pdb" format pdb
    7318 
    7319 Chain information for Rhom_Monomer-v5.pdb #2 
    7320 --- 
    7321 Chain | Description 
    7322 A | No description available 
    7323  
    7324 
    7325 > combine #2 #3 name Rhom_Monomer-V5_B
    7326 
    7327 > combine #2 #4 name Rhom_Monomer-V5_C
    7328 
    7329 > combine #2 #5 name Rhom_Monomer-V5_C
    7330 
    7331 > combine #2 #6 name Rhom_Monomer-V5_D
    7332 
    7333 > combine #2 #7 name Rhom_Monomer-V5_E
    7334 
    7335 > combine #2 #8 name Rhom_Monomer-V5_F
    7336 
    7337 > combine #2 #9 name Rhom_Monomer-V5_G
    7338 
    7339 > combine #2 #10 name Rhom_Monomer-V5_H
    7340 
    7341 > combine #2 #11 name Rhom_Monomer-V5_I
    7342 
    7343 > combine #2 #12 name Rhom_Monomer-V5_J
    7344 
    7345 > combine #2 #13 name Rhom_Monomer-V5_K
    7346 
    7347 > combine #2 #14 name Rhom_Monomer-V5_L
    7348 
    7349 > combine #2 #15 name Rhom_Monomer-V5_M
    7350 
    7351 > combine #2 #16 name Rhom_Monomer-V5_N
    7352 
    7353 > combine #2 #17 name Rhom_Monomer-V5_O
    7354 
    7355 > combine #2 #18 name Rhom_Monomer-V5_P
    7356 
    7357 > combine #2 #19 name Rhom_Monomer-V5_Q
    7358 
    7359 > combine #2 #20 name Rhom_Monomer-V5_R
    7360 
    7361 > combine #2 #21 name Rhom_Monomer-V5_S
    7362 
    7363 > combine #2 #22 name Rhom_Monomer-V5_T
    7364 
    7365 > mmaker #2 #1/A
    7366 
    7367 > matchmaker #2 #1/A
    7368 
    7369 Missing required "to" argument 
    7370 
    7371 > mmaker #2 to #1/A
    7372 
    7373 Parameters 
    7374 --- 
    7375 Chain pairing | bb 
    7376 Alignment algorithm | Needleman-Wunsch 
    7377 Similarity matrix | BLOSUM-62 
    7378 SS fraction | 0.3 
    7379 Gap open (HH/SS/other) | 18/18/6 
    7380 Gap extend | 1 
    7381 SS matrix |  |  | H | S | O 
    7382 ---|---|---|--- 
    7383 H | 6 | -9 | -6 
    7384 S |  | 6 | -6 
    7385 O |  |  | 4 
    7386 Iteration cutoff | 2 
    7387  
    7388 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain A (#1) with
    7389 Rhom_Monomer-v5.pdb, chain A (#2), sequence alignment score = 2177.7 
    7390 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7391 0.277) 
    7392  
    7393 
    7394 > mmaker #3 to #1/B
    7395 
    7396 Parameters 
    7397 --- 
    7398 Chain pairing | bb 
    7399 Alignment algorithm | Needleman-Wunsch 
    7400 Similarity matrix | BLOSUM-62 
    7401 SS fraction | 0.3 
    7402 Gap open (HH/SS/other) | 18/18/6 
    7403 Gap extend | 1 
    7404 SS matrix |  |  | H | S | O 
    7405 ---|---|---|--- 
    7406 H | 6 | -9 | -6 
    7407 S |  | 6 | -6 
    7408 O |  |  | 4 
    7409 Iteration cutoff | 2 
    7410  
    7411 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain B (#1) with
    7412 Rhom_Monomer-V5_B, chain A (#3), sequence alignment score = 2177.7 
    7413 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7414 0.277) 
    7415  
    7416 
    7417 > mmaker #4 to #1/C
    7418 
    7419 Parameters 
    7420 --- 
    7421 Chain pairing | bb 
    7422 Alignment algorithm | Needleman-Wunsch 
    7423 Similarity matrix | BLOSUM-62 
    7424 SS fraction | 0.3 
    7425 Gap open (HH/SS/other) | 18/18/6 
    7426 Gap extend | 1 
    7427 SS matrix |  |  | H | S | O 
    7428 ---|---|---|--- 
    7429 H | 6 | -9 | -6 
    7430 S |  | 6 | -6 
    7431 O |  |  | 4 
    7432 Iteration cutoff | 2 
    7433  
    7434 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain C (#1) with
    7435 Rhom_Monomer-V5_C, chain A (#4), sequence alignment score = 2177.7 
    7436 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7437 0.277) 
    7438  
    7439 
    7440 > mmaker #5 to #1/D
    7441 
    7442 Parameters 
    7443 --- 
    7444 Chain pairing | bb 
    7445 Alignment algorithm | Needleman-Wunsch 
    7446 Similarity matrix | BLOSUM-62 
    7447 SS fraction | 0.3 
    7448 Gap open (HH/SS/other) | 18/18/6 
    7449 Gap extend | 1 
    7450 SS matrix |  |  | H | S | O 
    7451 ---|---|---|--- 
    7452 H | 6 | -9 | -6 
    7453 S |  | 6 | -6 
    7454 O |  |  | 4 
    7455 Iteration cutoff | 2 
    7456  
    7457 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain D (#1) with
    7458 Rhom_Monomer-V5_C, chain A (#5), sequence alignment score = 2177.7 
    7459 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7460 0.277) 
    7461  
    7462 
    7463 > mmaker #6 to #1/E
    7464 
    7465 Parameters 
    7466 --- 
    7467 Chain pairing | bb 
    7468 Alignment algorithm | Needleman-Wunsch 
    7469 Similarity matrix | BLOSUM-62 
    7470 SS fraction | 0.3 
    7471 Gap open (HH/SS/other) | 18/18/6 
    7472 Gap extend | 1 
    7473 SS matrix |  |  | H | S | O 
    7474 ---|---|---|--- 
    7475 H | 6 | -9 | -6 
    7476 S |  | 6 | -6 
    7477 O |  |  | 4 
    7478 Iteration cutoff | 2 
    7479  
    7480 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain E (#1) with
    7481 Rhom_Monomer-V5_D, chain A (#6), sequence alignment score = 2177.7 
    7482 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7483 0.277) 
    7484  
    7485 
    7486 > mmaker #7 to #1/F
    7487 
    7488 Parameters 
    7489 --- 
    7490 Chain pairing | bb 
    7491 Alignment algorithm | Needleman-Wunsch 
    7492 Similarity matrix | BLOSUM-62 
    7493 SS fraction | 0.3 
    7494 Gap open (HH/SS/other) | 18/18/6 
    7495 Gap extend | 1 
    7496 SS matrix |  |  | H | S | O 
    7497 ---|---|---|--- 
    7498 H | 6 | -9 | -6 
    7499 S |  | 6 | -6 
    7500 O |  |  | 4 
    7501 Iteration cutoff | 2 
    7502  
    7503 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain F (#1) with
    7504 Rhom_Monomer-V5_E, chain A (#7), sequence alignment score = 2177.7 
    7505 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7506 0.277) 
    7507  
    7508 
    7509 > mmaker #8 to #1/G
    7510 
    7511 Parameters 
    7512 --- 
    7513 Chain pairing | bb 
    7514 Alignment algorithm | Needleman-Wunsch 
    7515 Similarity matrix | BLOSUM-62 
    7516 SS fraction | 0.3 
    7517 Gap open (HH/SS/other) | 18/18/6 
    7518 Gap extend | 1 
    7519 SS matrix |  |  | H | S | O 
    7520 ---|---|---|--- 
    7521 H | 6 | -9 | -6 
    7522 S |  | 6 | -6 
    7523 O |  |  | 4 
    7524 Iteration cutoff | 2 
    7525  
    7526 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain G (#1) with
    7527 Rhom_Monomer-V5_F, chain A (#8), sequence alignment score = 2177.7 
    7528 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7529 0.277) 
    7530  
    7531 
    7532 > mmaker #9 to #1/H
    7533 
    7534 Parameters 
    7535 --- 
    7536 Chain pairing | bb 
    7537 Alignment algorithm | Needleman-Wunsch 
    7538 Similarity matrix | BLOSUM-62 
    7539 SS fraction | 0.3 
    7540 Gap open (HH/SS/other) | 18/18/6 
    7541 Gap extend | 1 
    7542 SS matrix |  |  | H | S | O 
    7543 ---|---|---|--- 
    7544 H | 6 | -9 | -6 
    7545 S |  | 6 | -6 
    7546 O |  |  | 4 
    7547 Iteration cutoff | 2 
    7548  
    7549 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain H (#1) with
    7550 Rhom_Monomer-V5_G, chain A (#9), sequence alignment score = 2177.7 
    7551 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7552 0.277) 
    7553  
    7554 
    7555 > mmaker #10 to #1/I
    7556 
    7557 Parameters 
    7558 --- 
    7559 Chain pairing | bb 
    7560 Alignment algorithm | Needleman-Wunsch 
    7561 Similarity matrix | BLOSUM-62 
    7562 SS fraction | 0.3 
    7563 Gap open (HH/SS/other) | 18/18/6 
    7564 Gap extend | 1 
    7565 SS matrix |  |  | H | S | O 
    7566 ---|---|---|--- 
    7567 H | 6 | -9 | -6 
    7568 S |  | 6 | -6 
    7569 O |  |  | 4 
    7570 Iteration cutoff | 2 
    7571  
    7572 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain I (#1) with
    7573 Rhom_Monomer-V5_H, chain A (#10), sequence alignment score = 2177.7 
    7574 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7575 0.277) 
    7576  
    7577 
    7578 > mmaker #11 to #1/J
    7579 
    7580 Parameters 
    7581 --- 
    7582 Chain pairing | bb 
    7583 Alignment algorithm | Needleman-Wunsch 
    7584 Similarity matrix | BLOSUM-62 
    7585 SS fraction | 0.3 
    7586 Gap open (HH/SS/other) | 18/18/6 
    7587 Gap extend | 1 
    7588 SS matrix |  |  | H | S | O 
    7589 ---|---|---|--- 
    7590 H | 6 | -9 | -6 
    7591 S |  | 6 | -6 
    7592 O |  |  | 4 
    7593 Iteration cutoff | 2 
    7594  
    7595 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain J (#1) with
    7596 Rhom_Monomer-V5_I, chain A (#11), sequence alignment score = 2177.7 
    7597 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7598 0.277) 
    7599  
    7600 
    7601 > mmaker #12 to #1/K
    7602 
    7603 Parameters 
    7604 --- 
    7605 Chain pairing | bb 
    7606 Alignment algorithm | Needleman-Wunsch 
    7607 Similarity matrix | BLOSUM-62 
    7608 SS fraction | 0.3 
    7609 Gap open (HH/SS/other) | 18/18/6 
    7610 Gap extend | 1 
    7611 SS matrix |  |  | H | S | O 
    7612 ---|---|---|--- 
    7613 H | 6 | -9 | -6 
    7614 S |  | 6 | -6 
    7615 O |  |  | 4 
    7616 Iteration cutoff | 2 
    7617  
    7618 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain K (#1) with
    7619 Rhom_Monomer-V5_J, chain A (#12), sequence alignment score = 2177.7 
    7620 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7621 0.277) 
    7622  
    7623 
    7624 > mmaker #13 to #1/L
    7625 
    7626 Parameters 
    7627 --- 
    7628 Chain pairing | bb 
    7629 Alignment algorithm | Needleman-Wunsch 
    7630 Similarity matrix | BLOSUM-62 
    7631 SS fraction | 0.3 
    7632 Gap open (HH/SS/other) | 18/18/6 
    7633 Gap extend | 1 
    7634 SS matrix |  |  | H | S | O 
    7635 ---|---|---|--- 
    7636 H | 6 | -9 | -6 
    7637 S |  | 6 | -6 
    7638 O |  |  | 4 
    7639 Iteration cutoff | 2 
    7640  
    7641 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain L (#1) with
    7642 Rhom_Monomer-V5_K, chain A (#13), sequence alignment score = 2177.7 
    7643 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7644 0.277) 
    7645  
    7646 
    7647 > mmaker #14 to #1/M
    7648 
    7649 Parameters 
    7650 --- 
    7651 Chain pairing | bb 
    7652 Alignment algorithm | Needleman-Wunsch 
    7653 Similarity matrix | BLOSUM-62 
    7654 SS fraction | 0.3 
    7655 Gap open (HH/SS/other) | 18/18/6 
    7656 Gap extend | 1 
    7657 SS matrix |  |  | H | S | O 
    7658 ---|---|---|--- 
    7659 H | 6 | -9 | -6 
    7660 S |  | 6 | -6 
    7661 O |  |  | 4 
    7662 Iteration cutoff | 2 
    7663  
    7664 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain M (#1) with
    7665 Rhom_Monomer-V5_L, chain A (#14), sequence alignment score = 2177.7 
    7666 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7667 0.277) 
    7668  
    7669 
    7670 > mmaker #15 to #1/N
    7671 
    7672 Parameters 
    7673 --- 
    7674 Chain pairing | bb 
    7675 Alignment algorithm | Needleman-Wunsch 
    7676 Similarity matrix | BLOSUM-62 
    7677 SS fraction | 0.3 
    7678 Gap open (HH/SS/other) | 18/18/6 
    7679 Gap extend | 1 
    7680 SS matrix |  |  | H | S | O 
    7681 ---|---|---|--- 
    7682 H | 6 | -9 | -6 
    7683 S |  | 6 | -6 
    7684 O |  |  | 4 
    7685 Iteration cutoff | 2 
    7686  
    7687 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain N (#1) with
    7688 Rhom_Monomer-V5_M, chain A (#15), sequence alignment score = 2177.7 
    7689 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7690 0.277) 
    7691  
    7692 
    7693 > mmaker #16 to #1/O
    7694 
    7695 Parameters 
    7696 --- 
    7697 Chain pairing | bb 
    7698 Alignment algorithm | Needleman-Wunsch 
    7699 Similarity matrix | BLOSUM-62 
    7700 SS fraction | 0.3 
    7701 Gap open (HH/SS/other) | 18/18/6 
    7702 Gap extend | 1 
    7703 SS matrix |  |  | H | S | O 
    7704 ---|---|---|--- 
    7705 H | 6 | -9 | -6 
    7706 S |  | 6 | -6 
    7707 O |  |  | 4 
    7708 Iteration cutoff | 2 
    7709  
    7710 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain O (#1) with
    7711 Rhom_Monomer-V5_N, chain A (#16), sequence alignment score = 2177.7 
    7712 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7713 0.277) 
    7714  
    7715 
    7716 > mmaker #17 to #1/P
    7717 
    7718 Parameters 
    7719 --- 
    7720 Chain pairing | bb 
    7721 Alignment algorithm | Needleman-Wunsch 
    7722 Similarity matrix | BLOSUM-62 
    7723 SS fraction | 0.3 
    7724 Gap open (HH/SS/other) | 18/18/6 
    7725 Gap extend | 1 
    7726 SS matrix |  |  | H | S | O 
    7727 ---|---|---|--- 
    7728 H | 6 | -9 | -6 
    7729 S |  | 6 | -6 
    7730 O |  |  | 4 
    7731 Iteration cutoff | 2 
    7732  
    7733 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain P (#1) with
    7734 Rhom_Monomer-V5_O, chain A (#17), sequence alignment score = 2177.7 
    7735 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7736 0.277) 
    7737  
    7738 
    7739 > mmaker #18 to #1/Q
    7740 
    7741 Parameters 
    7742 --- 
    7743 Chain pairing | bb 
    7744 Alignment algorithm | Needleman-Wunsch 
    7745 Similarity matrix | BLOSUM-62 
    7746 SS fraction | 0.3 
    7747 Gap open (HH/SS/other) | 18/18/6 
    7748 Gap extend | 1 
    7749 SS matrix |  |  | H | S | O 
    7750 ---|---|---|--- 
    7751 H | 6 | -9 | -6 
    7752 S |  | 6 | -6 
    7753 O |  |  | 4 
    7754 Iteration cutoff | 2 
    7755  
    7756 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain Q (#1) with
    7757 Rhom_Monomer-V5_P, chain A (#18), sequence alignment score = 2177.7 
    7758 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7759 0.277) 
    7760  
    7761 
    7762 > mmaker #19 to #1/R
    7763 
    7764 Parameters 
    7765 --- 
    7766 Chain pairing | bb 
    7767 Alignment algorithm | Needleman-Wunsch 
    7768 Similarity matrix | BLOSUM-62 
    7769 SS fraction | 0.3 
    7770 Gap open (HH/SS/other) | 18/18/6 
    7771 Gap extend | 1 
    7772 SS matrix |  |  | H | S | O 
    7773 ---|---|---|--- 
    7774 H | 6 | -9 | -6 
    7775 S |  | 6 | -6 
    7776 O |  |  | 4 
    7777 Iteration cutoff | 2 
    7778  
    7779 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain R (#1) with
    7780 Rhom_Monomer-V5_Q, chain A (#19), sequence alignment score = 2177.7 
    7781 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7782 0.277) 
    7783  
    7784 
    7785 > mmaker #20 to #1/S
    7786 
    7787 Parameters 
    7788 --- 
    7789 Chain pairing | bb 
    7790 Alignment algorithm | Needleman-Wunsch 
    7791 Similarity matrix | BLOSUM-62 
    7792 SS fraction | 0.3 
    7793 Gap open (HH/SS/other) | 18/18/6 
    7794 Gap extend | 1 
    7795 SS matrix |  |  | H | S | O 
    7796 ---|---|---|--- 
    7797 H | 6 | -9 | -6 
    7798 S |  | 6 | -6 
    7799 O |  |  | 4 
    7800 Iteration cutoff | 2 
    7801  
    7802 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain S (#1) with
    7803 Rhom_Monomer-V5_R, chain A (#20), sequence alignment score = 2177.7 
    7804 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7805 0.277) 
    7806  
    7807 
    7808 > mmaker #21 to #1/T
    7809 
    7810 Parameters 
    7811 --- 
    7812 Chain pairing | bb 
    7813 Alignment algorithm | Needleman-Wunsch 
    7814 Similarity matrix | BLOSUM-62 
    7815 SS fraction | 0.3 
    7816 Gap open (HH/SS/other) | 18/18/6 
    7817 Gap extend | 1 
    7818 SS matrix |  |  | H | S | O 
    7819 ---|---|---|--- 
    7820 H | 6 | -9 | -6 
    7821 S |  | 6 | -6 
    7822 O |  |  | 4 
    7823 Iteration cutoff | 2 
    7824  
    7825 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain T (#1) with
    7826 Rhom_Monomer-V5_S, chain A (#21), sequence alignment score = 2177.7 
    7827 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7828 0.277) 
    7829  
    7830 
    7831 > mmaker #22 to #1U
    7832 
    7833 > matchmaker #22 to #1U
    7834 
    7835 Invalid "to" argument: only initial part "#1" of atom specifier valid 
    7836 
    7837 > mmaker #22 to #1/U
    7838 
    7839 Parameters 
    7840 --- 
    7841 Chain pairing | bb 
    7842 Alignment algorithm | Needleman-Wunsch 
    7843 Similarity matrix | BLOSUM-62 
    7844 SS fraction | 0.3 
    7845 Gap open (HH/SS/other) | 18/18/6 
    7846 Gap extend | 1 
    7847 SS matrix |  |  | H | S | O 
    7848 ---|---|---|--- 
    7849 H | 6 | -9 | -6 
    7850 S |  | 6 | -6 
    7851 O |  |  | 4 
    7852 Iteration cutoff | 2 
    7853  
    7854 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain U (#1) with
    7855 Rhom_Monomer-V5_T, chain A (#22), sequence alignment score = 2177.7 
    7856 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7857 0.277) 
    7858  
    7859 
    7860 > hide #1 models
    7861 
    7862 > show #1 models
    7863 
    7864 > hide #1 models
    7865 
    7866 > show #1 models
    7867 
    7868 > hide #1 models
    7869 
    7870 > show #1 models
    7871 
    7872 > combine #2 #23 name Rhom_Monomer-V5_U
    7873 
    7874 > combine #2 #24 name Rhom_Monomer-V5_V
    7875 
    7876 > mmaker #23 to #1/V
    7877 
    7878 Parameters 
    7879 --- 
    7880 Chain pairing | bb 
    7881 Alignment algorithm | Needleman-Wunsch 
    7882 Similarity matrix | BLOSUM-62 
    7883 SS fraction | 0.3 
    7884 Gap open (HH/SS/other) | 18/18/6 
    7885 Gap extend | 1 
    7886 SS matrix |  |  | H | S | O 
    7887 ---|---|---|--- 
    7888 H | 6 | -9 | -6 
    7889 S |  | 6 | -6 
    7890 O |  |  | 4 
    7891 Iteration cutoff | 2 
    7892  
    7893 Matchmaker 22-Flagellin_Rebuild4_DoubleRing_RelTo234.pdb, chain V (#1) with
    7894 Rhom_Monomer-V5_U, chain A (#23), sequence alignment score = 2177.7 
    7895 RMSD between 273 pruned atom pairs is 0.277 angstroms; (across all 273 pairs:
    7896 0.277) 
    7897  
    7898 
    7899 > mmaker #24 to #1/W
    7900 
    7901 No 'to' model specified 
    7902 
    7903 > ui mousemode right "translate selected models"
    7904 
    7905 > select add #24
    7906 
    7907 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    7908 
    7909 > view matrix models
    7910 > #24,1,-0.001903,-0.0019137,-43.385,0.0019027,1,-0.00018112,-57.254,0.001914,0.00017748,1,0.29519
    7911 
    7912 > hide #1 models
    7913 
    7914 > show #1 models
    7915 
    7916 > hide #1 models
    7917 
    7918 > show #1 models
    7919 
    7920 > hide #1 models
    7921 
    7922 > show #1 models
    7923 
    7924 > hide #1 models
    7925 
    7926 > show #1 models
    7927 
    7928 > hide #1 models
    7929 
    7930 > show #1 models
    7931 
    7932 > hide #1 models
    7933 
    7934 > show #1 models
    7935 
    7936 > hide #1 models
    7937 
    7938 > show #1 models
    7939 
    7940 > hide #1 models
    7941 
    7942 > show #1 models
    7943 
    7944 > hide #1 models
    7945 
    7946 > show #1 models
    7947 
    7948 > hide #1 models
    7949 
    7950 > show #1 models
    7951 
    7952 > hide #1 models
    7953 
    7954 > color #3 #38ef78ff
    7955 
    7956 > color #3 #34ee63ff
    7957 
    7958 > color #3 #2dd157ff
    7959 
    7960 > color #4 #a7ef36ff
    7961 
    7962 > color #5 #ef4123ff
    7963 
    7964 > color #6 #ef4ce8ff
    7965 
    7966 > color #7 #8e3eefff
    7967 
    7968 > color #8 #0c23efff
    7969 
    7970 > color #9 #c6ebefff
    7971 
    7972 > color #10 #10ef0cff
    7973 
    7974 > color #10 #11ff0dff
    7975 
    7976 > color #11 #ef9b00ff
    7977 
    7978 > color #12 #ef0679ff
    7979 
    7980 > color #13 #efb8b7ff
    7981 
    7982 > color #14 #efeeaeff
    7983 
    7984 > color #15 #a5b0efff
    7985 
    7986 > color #16 #ef64c7ff
    7987 
    7988 > color #17 #efa767ff
    7989 
    7990 > color #18 #83b0efff
    7991 
    7992 > color #19 #6c9cadff
    7993 
    7994 > color #19 #ad2b3dff
    7995 
    7996 > color #19 #943fadff
    7997 
    7998 > color #20 #6d9dafff
    7999 
    8000 > color #20 #2f69afff
    8001 
    8002 > color #21 #70a1b2ff
    8003 
    8004 > color #21 #58b244ff
    8005 
    8006 > color #21 #51b244ff
    8007 
    8008 > color #22 #af9c2eff
    8009 
    8010 > color #23 #93c06cff
    8011 
    8012 > select clear
    8013 
    8014 [Repeated 2 time(s)]Drag select of 227 residues 
    8015 
    8016 > select add #24
    8017 
    8018 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8019 
    8020 > select subtract #24
    8021 
    8022 Nothing selected 
    8023 
    8024 > select add #24
    8025 
    8026 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8027 
    8028 > view matrix models
    8029 > #24,1,-0.001903,-0.0019137,-38.583,0.0019027,1,-0.00018112,80.577,0.001914,0.00017748,1,-2.4242
    8030 
    8031 > combine #2-23 name 22-Flagellin_Rebuild5
    8032 
    8033 Remapping chain ID 'A' in Rhom_Monomer-V5_B #3 to 'B' 
    8034 Remapping chain ID 'A' in Rhom_Monomer-V5_C #4 to 'C' 
    8035 Remapping chain ID 'A' in Rhom_Monomer-V5_C #5 to 'D' 
    8036 Remapping chain ID 'A' in Rhom_Monomer-V5_D #6 to 'E' 
    8037 Remapping chain ID 'A' in Rhom_Monomer-V5_E #7 to 'F' 
    8038 Remapping chain ID 'A' in Rhom_Monomer-V5_F #8 to 'G' 
    8039 Remapping chain ID 'A' in Rhom_Monomer-V5_G #9 to 'H' 
    8040 Remapping chain ID 'A' in Rhom_Monomer-V5_H #10 to 'I' 
    8041 Remapping chain ID 'A' in Rhom_Monomer-V5_I #11 to 'J' 
    8042 Remapping chain ID 'A' in Rhom_Monomer-V5_J #12 to 'K' 
    8043 Remapping chain ID 'A' in Rhom_Monomer-V5_K #13 to 'L' 
    8044 Remapping chain ID 'A' in Rhom_Monomer-V5_L #14 to 'M' 
    8045 Remapping chain ID 'A' in Rhom_Monomer-V5_M #15 to 'N' 
    8046 Remapping chain ID 'A' in Rhom_Monomer-V5_N #16 to 'O' 
    8047 Remapping chain ID 'A' in Rhom_Monomer-V5_O #17 to 'P' 
    8048 Remapping chain ID 'A' in Rhom_Monomer-V5_P #18 to 'Q' 
    8049 Remapping chain ID 'A' in Rhom_Monomer-V5_Q #19 to 'R' 
    8050 Remapping chain ID 'A' in Rhom_Monomer-V5_R #20 to 'S' 
    8051 Remapping chain ID 'A' in Rhom_Monomer-V5_S #21 to 'T' 
    8052 Remapping chain ID 'A' in Rhom_Monomer-V5_T #22 to 'U' 
    8053 Remapping chain ID 'A' in Rhom_Monomer-V5_U #23 to 'V' 
    8054 
    8055 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8056 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5.cxs"
    8057 
    8058 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8059 > determination/Reference_models/22-ring_Sims/Rhom_22-Ring_v5.pdb" models #25
    8060 
    8061 > close session
    8062 
    8063 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8064 > determination/Reference_models/22-ring_Sims/Rhom_22-Ring_v5.pdb"
    8065 
    8066 Chain information for Rhom_22-Ring_v5.pdb #1 
    8067 --- 
    8068 Chain | Description 
    8069 A B C D E F G H I J K L M N O P Q R S T U V | No description available 
    8070  
    8071 
    8072 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8073 > determination/Reference_models/job234/postprocess_masked.mrc"
    8074 
    8075 Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
    8076 at level 0.0177, step 2, values float32 
    8077 
    8078 > fitmap #1 inMap #2
    8079 
    8080 Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc (#2) using
    8081 91080 atoms 
    8082 average map value = 0.01352, steps = 44 
    8083 shifted from previous position = 0.0209 
    8084 rotated from previous position = 0.031 degrees 
    8085 atoms outside contour = 70404, contour level = 0.017739 
    8086  
    8087 Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc (#2)
    8088 coordinates: 
    8089 Matrix rotation and translation 
    8090 0.99999986 0.00053437 0.00002071 -0.09756272 
    8091 -0.00053437 0.99999985 -0.00008341 0.12510606 
    8092 -0.00002076 0.00008340 1.00000000 0.00294575 
    8093 Axis 0.15410529 0.03830679 -0.98731158 
    8094 Axis point 235.01181344 178.84439944 0.00000000 
    8095 Rotation angle (degrees) 0.03101077 
    8096 Shift along axis -0.01315089 
    8097  
    8098 
    8099 > volume #2 color #b2b2b27e
    8100 
    8101 > volume #2 color #b2b2b280
    8102 
    8103 > hide atoms
    8104 
    8105 > show cartoons
    8106 
    8107 > volume #2 color #b2b2b24e
    8108 
    8109 > volume #2 color #b2b2b24d
    8110 
    8111 > volume #2 color #b2b2b2a6
    8112 
    8113 > fitmap #1 inMap #2
    8114 
    8115 Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc (#2) using
    8116 91080 atoms 
    8117 average map value = 0.01352, steps = 40 
    8118 shifted from previous position = 0.0181 
    8119 rotated from previous position = 0.00761 degrees 
    8120 atoms outside contour = 70402, contour level = 0.017739 
    8121  
    8122 Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc (#2)
    8123 coordinates: 
    8124 Matrix rotation and translation 
    8125 0.99999984 0.00055578 0.00007217 -0.10933460 
    8126 -0.00055578 0.99999984 0.00003718 0.09136404 
    8127 -0.00007215 -0.00003722 1.00000000 0.03367751 
    8128 Axis -0.06623089 0.12847923 -0.98949813 
    8129 Axis point 167.64958758 198.48073340 0.00000000 
    8130 Rotation angle (degrees) 0.03218170 
    8131 Shift along axis -0.01434412 
    8132  
    8133 
    8134 > select #1/A
    8135 
    8136 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8137 
    8138 > select #1/B
    8139 
    8140 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8141 
    8142 > select #1/A
    8143 
    8144 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8145 
    8146 > isolde start
    8147 
    8148 > set selectionWidth 4
    8149 
    8150 Done loading forcefield 
    8151 
    8152 > isolde set simFidelityMode Medium/Medium
    8153 
    8154 ISOLDE: setting sim fidelity mode to Medium/Medium 
    8155 nonbonded_cutoff_distance = 0.900000 
    8156 use_gbsa = True 
    8157 gbsa_cutoff = 1.100000 
    8158 
    8159 QDockWidget failed to find relevant screen info. screenFrom:
    8160 QScreen(0x600003dac380, name="DELL U2415") screenTo: QScreen(0x0) wdgScreen:
    8161 QScreen(0x600003dac380, name="DELL U2415") orgWdgScreen
    8162 QScreen(0x600003da75a0, name="Built-in Retina Display") 
    8163 
    8164 [Repeated 11 time(s)]
    8165 
    8166 > clipper associate #1 #2
    8167 
    8168 The toModel argument must be provided! 
    8169 
    8170 > clipper associate #2 toModel #1
    8171 
    8172 Opened postprocess_masked.mrc as #1.1.1.1, grid size 384,384,384, pixel 0.94,
    8173 shown at level 0.0216, step 1, values float32 
    8174 Chain information for Rhom_22-Ring_v5.pdb 
    8175 --- 
    8176 Chain | Description 
    8177 1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M
    8178 1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V | No description
    8179 available 
    8180  
    8181 
    8182 > undo
    8183 
    8184 > close session
    8185 
    8186 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8187 > determination/Reference_models/22-ring_Sims/Rhom_22-Ring_v5.pdb" format pdb
    8188 
    8189 Chain information for Rhom_22-Ring_v5.pdb #1 
    8190 --- 
    8191 Chain | Description 
    8192 A B C D E F G H I J K L M N O P Q R S T U V | No description available 
    8193  
    8194 
    8195 > open "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8196 > determination/Reference_models/job234/postprocess_masked.mrc"
    8197 
    8198 Opened postprocess_masked.mrc as #2, grid size 384,384,384, pixel 0.94, shown
    8199 at level 0.0177, step 2, values float32 
    8200 
    8201 > fitmap #1 inMap #2
    8202 
    8203 Fit molecule Rhom_22-Ring_v5.pdb (#1) to map postprocess_masked.mrc (#2) using
    8204 91080 atoms 
    8205 average map value = 0.01352, steps = 44 
    8206 shifted from previous position = 0.0209 
    8207 rotated from previous position = 0.031 degrees 
    8208 atoms outside contour = 70404, contour level = 0.017739 
    8209  
    8210 Position of Rhom_22-Ring_v5.pdb (#1) relative to postprocess_masked.mrc (#2)
    8211 coordinates: 
    8212 Matrix rotation and translation 
    8213 0.99999986 0.00053437 0.00002071 -0.09756272 
    8214 -0.00053437 0.99999985 -0.00008341 0.12510606 
    8215 -0.00002076 0.00008340 1.00000000 0.00294575 
    8216 Axis 0.15410529 0.03830679 -0.98731158 
    8217 Axis point 235.01181344 178.84439944 0.00000000 
    8218 Rotation angle (degrees) 0.03101077 
    8219 Shift along axis -0.01315089 
    8220  
    8221 
    8222 > hide atoms
    8223 
    8224 > show cartoons
    8225 
    8226 > lighting simple
    8227 
    8228 > volume #2 color #b2b2b27e
    8229 
    8230 > volume #2 color #b2b2b27d
    8231 
    8232 > molmap #1
    8233 
    8234 Missing or invalid "resolution" argument: Expected a number 
    8235 
    8236 > molmap #1 resolution 3
    8237 
    8238 Missing or invalid "resolution" argument: Expected a number 
    8239 
    8240 > molmap #1 3
    8241 
    8242 Opened Rhom_22-Ring_v5.pdb map 3 as #3, grid size 141,142,259, pixel 1, shown
    8243 at level 0.119, step 1, values float32 
    8244 
    8245 > molmap #1 2
    8246 
    8247 Opened Rhom_22-Ring_v5.pdb map 2 as #3, grid size 203,203,379, pixel 0.667,
    8248 shown at level 0.15, step 1, values float32 
    8249 
    8250 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8251 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_PreSim.cxs"
    8252 
    8253 > volume mask #3 #2
    8254 
    8255 Missing required "surfaces" argument 
    8256 
    8257 > volume mask #2 surfaces #3
    8258 
    8259 Opened postprocess_masked.mrc masked as #4, grid size 136,136,260, pixel 0.94,
    8260 shown at step 1, values float32 
    8261 
    8262 > hide #!3 models
    8263 
    8264 > show #!3 models
    8265 
    8266 > hide #!3 models
    8267 
    8268 > isolde start
    8269 
    8270 > clipper associate #1 #4
    8271 
    8272 The toModel argument must be provided! 
    8273 
    8274 > clipper associate #4 toModel #1
    8275 
    8276 Opened postprocess_masked.mrc masked as #1.1.1.1, grid size 136,136,260, pixel
    8277 0.94, shown at level 0.0187, step 1, values float32 
    8278 Chain information for Rhom_22-Ring_v5.pdb 
    8279 --- 
    8280 Chain | Description 
    8281 1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M
    8282 1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V | No description
    8283 available 
    8284  
    8285 
    8286 > select all
    8287 
    8288 91080 atoms, 91344 bonds, 6006 residues, 11 models selected 
    8289 
    8290 > select all
    8291 
    8292 91080 atoms, 91344 bonds, 6006 residues, 11 models selected 
    8293 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8294 chains... 
    8295 
    8296 > isolde sim start /A-V
    8297 
    8298 ISOLDE: started sim 
    8299 
    8300 > ui tool show "Ramachandran Plot"
    8301 
    8302 > isolde sim stop
    8303 
    8304 Sim termination reason: None 
    8305 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8306 chains... 
    8307 ISOLDE: Corrected atom nomenclature of 76 residues in model #1.2 to IUPAC-IUB
    8308 standards. 
    8309 ISOLDE: stopped sim 
    8310 
    8311 > view #1/A:1
    8312 
    8313 > volume gaussian #1 bfactor 150
    8314 
    8315 Opened postprocess_masked.mrc masked gaussian as #4, grid size 136,136,260,
    8316 pixel 0.94, shown at step 1, values float32 
    8317 
    8318 > clipper associate #4 toModel #1
    8319 
    8320 Opened postprocess_masked.mrc masked gaussian as #1.1.1.2, grid size
    8321 136,136,260, pixel 0.94, shown at step 1, values float32 
    8322 
    8323 > volume #1.1.1.1 style surface
    8324 
    8325 > volume #1.1.1.1 color #00ffff34
    8326 
    8327 > volume #1.1.1.1 color #00ffff33
    8328 
    8329 > volume #1.1.1.2 region 0,0,0,135,135,259 step 1
    8330 
    8331 [Repeated 1 time(s)]
    8332 
    8333 > volume #1.1.1.1 level 0.02312
    8334 
    8335 > volume #1.1.1.2 level 0.004236
    8336 
    8337 > view #1/A:1
    8338 
    8339 > isolde shorthand
    8340    
    8341    
    8342     Initialising ISOLDE-specific command aliases:
    8343     Alias       Equivalent full command
    8344     -------------------------------------------------
    8345     st  isolde step {arguments}
    8346     aw  isolde add water {arguments}
    8347     awsf        isolde add water {arguments} sim false
    8348     al  isolde add ligand {arguments}
    8349     aa  isolde add aa $1 sel {arguments}
    8350     ht  isolde mod his sel {arguments}
    8351     so  setattr sel atoms occupancy {arguments}
    8352     ab  isolde adjust bfactors {arguments}
    8353     ss  isolde sim start sel
    8354     rt  isolde release torsions sel {arguments}
    8355     rd  isolde release distances sel {arguments}
    8356     ra  rd; rt
    8357     pf  isolde pepflip sel
    8358     cf  isolde cisflip sel
    8359     cbb color bfactor {arguments}
    8360     cbo color byattr occupancy {arguments}
    8361     cbc color {arguments} bychain; color {arguments} byhet
    8362     cs  clipper set contourSensitivity {arguments}
    8363    
    8364 
    8365  
    8366 
    8367 > st
    8368 
    8369 [Repeated 1 time(s)]
    8370 
    8371 > isolde set simFidelityMode Highest/Slowest
    8372 
    8373 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    8374 nonbonded_cutoff_distance = 1.700000 
    8375 use_gbsa = True 
    8376 gbsa_cutoff = 2.000000 
    8377 
    8378 > isolde set simFidelityMode Highest/Slowest
    8379 
    8380 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    8381 nonbonded_cutoff_distance = 1.700000 
    8382 use_gbsa = True 
    8383 gbsa_cutoff = 2.000000 
    8384 
    8385 > isolde sim start /A:2
    8386 
    8387 ISOLDE: started sim 
    8388 
    8389 > isolde pepflip /A:2
    8390 
    8391 > isolde sim stop
    8392 
    8393 Sim termination reason: None 
    8394 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8395 chains... 
    8396 ISOLDE: stopped sim 
    8397 
    8398 > st
    8399 
    8400 > isolde sim start /A:3
    8401 
    8402 ISOLDE: started sim 
    8403 
    8404 > isolde sim stop
    8405 
    8406 Sim termination reason: None 
    8407 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8408 chains... 
    8409 ISOLDE: stopped sim 
    8410 
    8411 > st
    8412 
    8413 [Repeated 9 time(s)]
    8414 
    8415 > isolde sim start /A:13
    8416 
    8417 ISOLDE: started sim 
    8418 
    8419 > isolde sim stop
    8420 
    8421 Sim termination reason: None 
    8422 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8423 chains... 
    8424 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8425 standards. 
    8426 ISOLDE: stopped sim 
    8427 
    8428 > st
    8429 
    8430 [Repeated 3 time(s)]
    8431 
    8432 > volume #1.1.1.2 level 0.003616
    8433 
    8434 > st
    8435 
    8436 [Repeated 9 time(s)]
    8437 
    8438 > volume #1.1.1.2 level 0.002229
    8439 
    8440 > st
    8441 
    8442 [Repeated 7 time(s)]
    8443 
    8444 > volume #1.1.1.1 level 0.001899
    8445 
    8446 > volume #1.1.1.1 level 0.02252
    8447 
    8448 > isolde sim start /A:35
    8449 
    8450 ISOLDE: started sim 
    8451 
    8452 > volume #1.1.1.2 level 0.001528
    8453 
    8454 > isolde sim stop
    8455 
    8456 Sim termination reason: None 
    8457 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8458 chains... 
    8459 ISOLDE: stopped sim 
    8460 
    8461 > st
    8462 
    8463 [Repeated 41 time(s)]
    8464 
    8465 > isolde sim start /A:77
    8466 
    8467 ISOLDE: started sim 
    8468 
    8469 > isolde sim stop discardTo start
    8470 
    8471 Sim termination reason: None 
    8472 reverting to start 
    8473 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8474 chains... 
    8475 ISOLDE: stopped sim 
    8476 
    8477 > st
    8478 
    8479 [Repeated 4 time(s)]
    8480 
    8481 > volume #1.1.1.2 level 9.276e-05
    8482 
    8483 > volume #1.1.1.2 level 0.002873
    8484 
    8485 > volume #1.1.1.1 level 0.001436
    8486 
    8487 > volume #1.1.1.2 level 0.0007206
    8488 
    8489 > volume #1.1.1.1 level 0.01483
    8490 
    8491 > volume #1.1.1.1 level 0.02559
    8492 
    8493 > st
    8494 
    8495 [Repeated 1 time(s)]
    8496 
    8497 > isolde sim start /A:84
    8498 
    8499 ISOLDE: started sim 
    8500 
    8501 > volume #1.1.1.2 level 0.003232
    8502 
    8503 > isolde sim stop
    8504 
    8505 Sim termination reason: None 
    8506 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8507 chains... 
    8508 ISOLDE: stopped sim 
    8509 
    8510 > st
    8511 
    8512 > volume #1.1.1.1 level 0.02405
    8513 
    8514 > volume #1.1.1.1 level 0.02691
    8515 
    8516 > volume #1.1.1.2 level 0.0004515
    8517 
    8518 > isolde sim start /A:85
    8519 
    8520 ISOLDE: started sim 
    8521 
    8522 > volume #1.1.1.2 level 0.001262
    8523 
    8524 > volume #1.1.1.1 level 0.005169
    8525 
    8526 > volume #1.1.1.1 level 0.02296
    8527 
    8528 > isolde sim stop
    8529 
    8530 Sim termination reason: None 
    8531 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8532 chains... 
    8533 ISOLDE: stopped sim 
    8534 
    8535 > st
    8536 
    8537 [Repeated 5 time(s)]
    8538 
    8539 > volume #1.1.1.1 level 0.001779
    8540 
    8541 > isolde sim start /A:91
    8542 
    8543 ISOLDE: started sim 
    8544 
    8545 > volume #1.1.1.1 level 2.26e-05
    8546 
    8547 > volume #1.1.1.1 level 0.0143
    8548 
    8549 > volume #1.1.1.2 level 0.002428
    8550 
    8551 > volume #1.1.1.1 level 0.02001
    8552 
    8553 > isolde sim stop
    8554 
    8555 Sim termination reason: None 
    8556 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8557 chains... 
    8558 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8559 standards. 
    8560 ISOLDE: stopped sim 
    8561 
    8562 > st
    8563 
    8564 [Repeated 3 time(s)]
    8565 
    8566 > st prev
    8567 
    8568 > st
    8569 
    8570 [Repeated 10 time(s)]
    8571 
    8572 > isolde sim start /A:105
    8573 
    8574 ISOLDE: started sim 
    8575 
    8576 > isolde sim stop
    8577 
    8578 Sim termination reason: None 
    8579 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8580 chains... 
    8581 ISOLDE: stopped sim 
    8582 
    8583 > st
    8584 
    8585 > volume #1.1.1.1 level 0.0182
    8586 
    8587 > volume #1.1.1.2 level 0.0004029
    8588 
    8589 > isolde sim start /A:106
    8590 
    8591 ISOLDE: started sim 
    8592 
    8593 > isolde sim stop
    8594 
    8595 Sim termination reason: None 
    8596 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8597 chains... 
    8598 ISOLDE: stopped sim 
    8599 
    8600 > st
    8601 
    8602 [Repeated 1 time(s)]
    8603 
    8604 > volume #1.1.1.2 level 0.001857
    8605 
    8606 > volume #1.1.1.1 level 0.0297
    8607 
    8608 > st
    8609 
    8610 [Repeated 31 time(s)]
    8611 
    8612 > volume #1.1.1.2 level 0.00294
    8613 
    8614 > st
    8615 
    8616 [Repeated 7 time(s)]
    8617 
    8618 > isolde sim start /A:381
    8619 
    8620 ISOLDE: started sim 
    8621 
    8622 > isolde sim stop
    8623 
    8624 Sim termination reason: None 
    8625 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8626 chains... 
    8627 ISOLDE: stopped sim 
    8628 
    8629 > st
    8630 
    8631 [Repeated 9 time(s)]
    8632 
    8633 > isolde sim start /A:391
    8634 
    8635 ISOLDE: started sim 
    8636 
    8637 > isolde sim stop
    8638 
    8639 Sim termination reason: None 
    8640 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8641 chains... 
    8642 ISOLDE: stopped sim 
    8643 
    8644 > st
    8645 
    8646 [Repeated 4 time(s)]
    8647 
    8648 > st prev
    8649 
    8650 [Repeated 85 time(s)]
    8651 
    8652 > st
    8653 
    8654 [Repeated 35 time(s)]
    8655 
    8656 > select clear
    8657 
    8658 > isolde sim start /A:391
    8659 
    8660 ISOLDE: started sim 
    8661 
    8662 > isolde sim stop
    8663 
    8664 Sim termination reason: None 
    8665 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8666 chains... 
    8667 ISOLDE: stopped sim 
    8668 
    8669 > st
    8670 
    8671 [Repeated 35 time(s)]
    8672 
    8673 > ui tool show "Show Sequence Viewer"
    8674 
    8675 > sequence chain /A
    8676 
    8677 Alignment identifier is 1.2/A 
    8678 
    8679 > select /A:7-32,43-98,105-128,415-466,470-505
    8680 
    8681 2941 atoms, 2944 bonds, 194 residues, 1 model selected 
    8682 
    8683 > select clear
    8684 
    8685 > st
    8686 
    8687 [Repeated 3 time(s)]
    8688 
    8689 > st prev
    8690 
    8691 [Repeated 16 time(s)]
    8692 
    8693 > st
    8694 
    8695 [Repeated 18 time(s)]
    8696 
    8697 > isolde sim start /A:433
    8698 
    8699 ISOLDE: started sim 
    8700 
    8701 > isolde sim stop
    8702 
    8703 Sim termination reason: None 
    8704 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8705 chains... 
    8706 ISOLDE: stopped sim 
    8707 
    8708 > st
    8709 
    8710 [Repeated 2 time(s)]
    8711 
    8712 > isolde sim start /A:436
    8713 
    8714 ISOLDE: started sim 
    8715 
    8716 > isolde sim stop
    8717 
    8718 Sim termination reason: None 
    8719 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8720 chains... 
    8721 ISOLDE: stopped sim 
    8722 
    8723 > st
    8724 
    8725 [Repeated 4 time(s)]
    8726 
    8727 > st prev
    8728 
    8729 > st
    8730 
    8731 [Repeated 5 time(s)]
    8732 
    8733 > st prev
    8734 
    8735 [Repeated 5 time(s)]
    8736 
    8737 > st
    8738 
    8739 [Repeated 7 time(s)]
    8740 
    8741 > isolde sim start /A:448
    8742 
    8743 ISOLDE: started sim 
    8744 
    8745 > isolde sim stop discardTo start
    8746 
    8747 Sim termination reason: None 
    8748 reverting to start 
    8749 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8750 chains... 
    8751 ISOLDE: stopped sim 
    8752 
    8753 > st
    8754 
    8755 > isolde sim start /A:449
    8756 
    8757 ISOLDE: started sim 
    8758 
    8759 > isolde sim stop
    8760 
    8761 Sim termination reason: None 
    8762 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8763 chains... 
    8764 ISOLDE: stopped sim 
    8765 
    8766 > st
    8767 
    8768 [Repeated 1 time(s)]
    8769 
    8770 > st prev
    8771 
    8772 > st
    8773 
    8774 [Repeated 2 time(s)]
    8775 
    8776 > isolde sim start /A:453
    8777 
    8778 ISOLDE: started sim 
    8779 
    8780 > volume #1.1.1.2 level 0.001327
    8781 
    8782 > isolde sim stop
    8783 
    8784 Sim termination reason: None 
    8785 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8786 chains... 
    8787 ISOLDE: stopped sim 
    8788 
    8789 > st
    8790 
    8791 [Repeated 2 time(s)]
    8792 
    8793 > isolde sim start /A:456
    8794 
    8795 ISOLDE: started sim 
    8796 
    8797 > volume #1.1.1.1 level 0.000749
    8798 
    8799 > volume #1.1.1.1 level 0.02158
    8800 
    8801 > isolde sim stop
    8802 
    8803 Sim termination reason: None 
    8804 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8805 chains... 
    8806 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8807 standards. 
    8808 ISOLDE: stopped sim 
    8809 
    8810 > st
    8811 
    8812 [Repeated 6 time(s)]
    8813 
    8814 > isolde sim start /A:463
    8815 
    8816 ISOLDE: started sim 
    8817 
    8818 > isolde sim stop
    8819 
    8820 Sim termination reason: None 
    8821 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8822 chains... 
    8823 ISOLDE: stopped sim 
    8824 
    8825 > st
    8826 
    8827 [Repeated 3 time(s)]
    8828 
    8829 > volume #1.1.1.2 level 0.006082
    8830 
    8831 > st
    8832 
    8833 [Repeated 4 time(s)]
    8834 
    8835 > volume #1.1.1.2 level 0.003741
    8836 
    8837 > isolde sim start /A:472
    8838 
    8839 ISOLDE: started sim 
    8840 
    8841 > isolde sim stop
    8842 
    8843 Sim termination reason: None 
    8844 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8845 chains... 
    8846 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8847 standards. 
    8848 ISOLDE: stopped sim 
    8849 
    8850 > st
    8851 
    8852 [Repeated 5 time(s)]
    8853 
    8854 > isolde sim start /A:478
    8855 
    8856 ISOLDE: started sim 
    8857 
    8858 > isolde sim stop
    8859 
    8860 Sim termination reason: None 
    8861 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8862 chains... 
    8863 ISOLDE: stopped sim 
    8864 
    8865 > st
    8866 
    8867 > isolde sim start /A:479
    8868 
    8869 ISOLDE: started sim 
    8870 
    8871 > isolde sim stop
    8872 
    8873 Sim termination reason: None 
    8874 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8875 chains... 
    8876 ISOLDE: stopped sim 
    8877 
    8878 > st
    8879 
    8880 [Repeated 4 time(s)]
    8881 
    8882 > volume #1.1.1.2 level 0.002231
    8883 
    8884 > isolde sim start /A:484
    8885 
    8886 ISOLDE: started sim 
    8887 
    8888 > isolde sim stop
    8889 
    8890 Sim termination reason: None 
    8891 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8892 chains... 
    8893 ISOLDE: stopped sim 
    8894 
    8895 > st
    8896 
    8897 [Repeated 3 time(s)]
    8898 
    8899 > volume #1.1.1.2 level 0.003208
    8900 
    8901 > st
    8902 
    8903 [Repeated 7 time(s)]
    8904 
    8905 > isolde sim start /A:496
    8906 
    8907 ISOLDE: started sim 
    8908 
    8909 > isolde sim stop discardTo start
    8910 
    8911 Sim termination reason: None 
    8912 reverting to start 
    8913 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8914 chains... 
    8915 ISOLDE: stopped sim 
    8916 
    8917 > st
    8918 
    8919 > st prev
    8920 
    8921 > isolde sim start /A:496
    8922 
    8923 ISOLDE: started sim 
    8924 
    8925 > isolde sim stop
    8926 
    8927 Sim termination reason: None 
    8928 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8929 chains... 
    8930 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8931 standards. 
    8932 ISOLDE: stopped sim 
    8933 
    8934 > st prev
    8935 
    8936 > st
    8937 
    8938 [Repeated 11 time(s)]
    8939 
    8940 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8941 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_Current.cxs"
    8942 
    8943 Taking snapshot of stepper: Rhom_22-Ring_v5.pdb 
    8944 
    8945 > save "/Users/mbell/Desktop/Projects/3. Flagellin Structure
    8946 > determination/Reference_models/22-ring_Sims/Rhom_22-ring_Rebuild5_Current.cxs"
    8947 
    8948 Taking snapshot of stepper: Rhom_22-Ring_v5.pdb 
    8949 
    8950 ——— End of log from Tue Feb 13 14:02:34 2024 ———
    8951 
    8952 opened ChimeraX session 
    8953 
    8954 > select #1/M
    8955 
    8956 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8957 
    8958 > select #1/A]
    8959 
    8960 Nothing selected 
    8961 
    8962 > select #1/A
    8963 
    8964 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8965 
    8966 > select ~sel & ##selected
    8967 
    8968 86940 atoms, 87192 bonds, 5733 residues, 1 model selected 
    8969 
    8970 > select ~sel & ##selected
    8971 
    8972 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8973 
    8974 > select #1/B
    8975 
    8976 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8977 
    8978 > select ~sel & ##selected
    8979 
    8980 86940 atoms, 87192 bonds, 5733 residues, 1 model selected 
    8981 
    8982 > select down
    8983 
    8984 86940 atoms, 87192 bonds, 5733 residues, 2 models selected 
    8985 
    8986 > select up
    8987 
    8988 91080 atoms, 91344 bonds, 6006 residues, 2 models selected 
    8989 
    8990 > select down
    8991 
    8992 86940 atoms, 87192 bonds, 5733 residues, 2 models selected 
    8993 
    8994 > select #1/C
    8995 
    8996 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    8997 
    8998 > select #1/D
    8999 
    9000 4140 atoms, 4152 bonds, 273 residues, 1 model selected 
    9001 
    9002 > select #1/D:1
    9003 
    9004 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9005 
    9006 > select #1/D:90
    9007 
    9008 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9009 
    9010 > view #1/D:90
    9011 
    9012 > st
    9013 
    9014 > view #1/D:90
    9015 
    9016 [Repeated 1 time(s)]
    9017 
    9018 > select #1/D:90
    9019 
    9020 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9021 
    9022 > select /D:90
    9023 
    9024 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9025 
    9026 > isolde start
    9027 
    9028 > set selectionWidth 4
    9029 
    9030 Done loading forcefield 
    9031 
    9032 > isolde set simFidelityMode Medium/Medium
    9033 
    9034 ISOLDE: setting sim fidelity mode to Medium/Medium 
    9035 nonbonded_cutoff_distance = 0.900000 
    9036 use_gbsa = True 
    9037 gbsa_cutoff = 1.100000 
    9038 
    9039 > isolde stepto /D:90
    9040 
    9041 > st
    9042 
    9043 > volume #1.1.1.2 level -0.0001976
    9044 
    9045 > volume #1.1.1.2 level 0.0005322
    9046 
    9047 > view #1/A:91
    9048 
    9049 > view #1/B:91
    9050 
    9051 > volume #1.1.1.2 level 0.005833
    9052 
    9053 > volume #1.1.1.2 level 0.001767
    9054 
    9055 > view #1/C:91
    9056 
    9057 > view #1/D:91
    9058 
    9059 > view #1/E:91
    9060 
    9061 > volume #1.1.1.1 level 0.0006354
    9062 
    9063 > isolde set simFidelityMode Highest/Slowest
    9064 
    9065 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    9066 nonbonded_cutoff_distance = 1.700000 
    9067 use_gbsa = True 
    9068 gbsa_cutoff = 2.000000 
    9069 
    9070 > isolde set simFidelityMode Highest/Slowest
    9071 
    9072 ISOLDE: setting sim fidelity mode to Highest/Slowest 
    9073 nonbonded_cutoff_distance = 1.700000 
    9074 use_gbsa = True 
    9075 gbsa_cutoff = 2.000000 
    9076 
    9077 > isolde sim start /E:91
    9078 
    9079 ISOLDE: started sim 
    9080 
    9081 > volume #1.1.1.1 level 0.0002176
    9082 
    9083 > isolde sim stop
    9084 
    9085 Sim termination reason: None 
    9086 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9087 chains... 
    9088 ISOLDE: stopped sim 
    9089 
    9090 > view #1/F:91
    9091 
    9092 > volume #1.1.1.1 level 0.01124
    9093 
    9094 > volume #1.1.1.2 level 0.00583
    9095 
    9096 > volume #1.1.1.1 level 0.00634
    9097 
    9098 > view #1/G:91
    9099 
    9100 > view #1/H:91
    9101 
    9102 > volume #1.1.1.1 level 0.01485
    9103 
    9104 > volume #1.1.1.2 level 0.001053
    9105 
    9106 > view #1/I:91
    9107 
    9108 > view #1/J:91
    9109 
    9110 > view #1/K:91
    9111 
    9112 > view #1/L:91
    9113 
    9114 > volume #1.1.1.2 level 0.003594
    9115 
    9116 > volume #1.1.1.1 level 0.008011
    9117 
    9118 > volume #1.1.1.1 level 0.01094
    9119 
    9120 > view #1/M:91
    9121 
    9122 > view #1/N:91
    9123 
    9124 > view #1/O:91
    9125 
    9126 > view #1/P:91
    9127 
    9128 > view #1/Q:91
    9129 
    9130 > view #1/R:91
    9131 
    9132 > view #1/S:91
    9133 
    9134 > volume #1.1.1.2 level 0.002077
    9135 
    9136 > view #1/T:91
    9137 
    9138 > view #1/U:91
    9139 
    9140 > view #1/V:91
    9141 
    9142 > volume #1.1.1.2 level 0.001709
    9143 
    9144 > view #1/W:91
    9145 
    9146 No objects specified. 
    9147 
    9148 > view #1/J:91
    9149 
    9150 > view #1/C:91
    9151 
    9152 > view #1/B:91
    9153 
    9154 > view #1/D:91
    9155 
    9156 > view #1/E:91
    9157 
    9158 > view #1/F:91
    9159 
    9160 > volume #1.1.1.2 level 0.002124
    9161 
    9162 > volume #1.1.1.1 level 0.0005339
    9163 
    9164 > view #1/G:91
    9165 
    9166 > isolde sim start /G:91
    9167 
    9168 ISOLDE: started sim 
    9169 
    9170 > volume #1.1.1.2 level 0.004674
    9171 
    9172 > volume #1.1.1.1 level -0.0006614
    9173 
    9174 > volume #1.1.1.1 level 0.0005339
    9175 
    9176 > volume #1.1.1.1 level 0.03424
    9177 
    9178 > volume #1.1.1.2 level 0.003229
    9179 
    9180 > volume #1.1.1.1 level 0.000773
    9181 
    9182 > isolde sim stop
    9183 
    9184 Sim termination reason: None 
    9185 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9186 chains... 
    9187 ISOLDE: stopped sim 
    9188 
    9189 > view #1/G:1
    9190 
    9191 > volume #1.1.1.2 level 0.003522
    9192 
    9193 > volume #1.1.1.1 level 0.02145
    9194 
    9195 > isolde stepto /G:1
    9196 
    9197 > st
    9198 
    9199 [Repeated 83 time(s)]
    9200 
    9201 > volume #1.1.1.1 level 0.02026
    9202 
    9203 > volume #1.1.1.2 level 0.0007171
    9204 
    9205 > st
    9206 
    9207 [Repeated 1 time(s)]
    9208 
    9209 > volume #1.1.1.2 level 0.002077
    9210 
    9211 > volume #1.1.1.1 level 0.0302
     1989[deleted to fit within ticket limits]
    92121990
    92131991> st