Changes between Initial Version and Version 1 of Ticket #16003


Ignore:
Timestamp:
Sep 24, 2024, 9:10:25 AM (15 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #16003

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

  • Ticket #16003 – Description

    initial v1  
    185185  "threads" : 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     187[deleted to fit within ticket limits]
    1736188],
    1737189  "sharedCache" : {
    … …  
    2015467 
    2016468
    2017 > open
    2018 > C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR52_6li3.pdb
    2019 
    2020 GPR52_6li3.pdb title: 
    2021 Cryo-em structure of GPR52-minigs-NB35 [more info...] 
    2022  
    2023 Chain information for GPR52_6li3.pdb #4 
    2024 --- 
    2025 Chain | Description | UniProt 
    2026 A | guanine nucleotide-binding protein G(S) subunit α isoforms short | GNAS2_HUMAN 
    2027 B | transducin β chain 1 | GBB1_HUMAN 
    2028 G | G γ-I | GBG2_HUMAN 
    2029 N | nanobody NB35 |   
    2030 R | G-protein coupled receptor 52 | GPR52_HUMAN 
    2031  
    2032 
    2033 > ui tool show "Fit to Segments"
    2034 
    2035 > ui tool show "Fit in Map"
    2036 
    2037 QWindowsWindow::setGeometry: Unable to set geometry 3200x1653+0+55 (frame:
    2038 3232x1741-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    2039 Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
    2040 16, 16 minimum size: 630x661 MINMAXINFO(maxSize=POINT(x=0, y=0),
    2041 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1607,
    2042 y=1741))) 
    2043 
    2044 > select add #1
    2045 
    2046 7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected 
    2047 
    2048 > select subtract #1
    2049 
    2050 Nothing selected 
    2051 
    2052 > select add #1
    2053 
    2054 7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected 
    2055 
    2056 > select subtract #1.1
    2057 
    2058 7903 atoms, 8059 bonds, 1005 residues, 1 model selected 
    2059 
    2060 > select add #1
    2061 
    2062 7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected 
    2063 
    2064 > ui tool show "Model Panel"
    2065 
    2066 > hide sel surfaces
    2067 
    2068 > show sel cartoons
    2069 
    2070 > hide sel atoms
    2071 
    2072 > select add #2
    2073 
    2074 16544 atoms, 16886 bonds, 8 pseudobonds, 2115 residues, 4 models selected 
    2075 
    2076 > select add #3
    2077 
    2078 24671 atoms, 25193 bonds, 12 pseudobonds, 3137 residues, 6 models selected 
    2079 
    2080 > select subtract #3.1
    2081 
    2082 24671 atoms, 25193 bonds, 8 pseudobonds, 3137 residues, 5 models selected 
    2083 
    2084 > select add #4
    2085 
    2086 32960 atoms, 33668 bonds, 10 pseudobonds, 4182 residues, 7 models selected 
    2087 
    2088 > select add #3.1
    2089 
    2090 32960 atoms, 33668 bonds, 14 pseudobonds, 4182 residues, 8 models selected 
    2091 
    2092 > select subtract #3
    2093 
    2094 24833 atoms, 25361 bonds, 10 pseudobonds, 3160 residues, 6 models selected 
    2095 
    2096 > select add #3
    2097 
    2098 32960 atoms, 33668 bonds, 14 pseudobonds, 4182 residues, 8 models selected 
    2099 
    2100 > show sel cartoons
    2101 
    2102 > hide sel atoms
    2103 
    2104 > view #3 clip false
    2105 
    2106 > show #!3 target m
    2107 
    2108 > select subtract #4
    2109 
    2110 24671 atoms, 25193 bonds, 12 pseudobonds, 3137 residues, 6 models selected 
    2111 
    2112 > select subtract #3
    2113 
    2114 16544 atoms, 16886 bonds, 8 pseudobonds, 2115 residues, 4 models selected 
    2115 
    2116 > select subtract #2
    2117 
    2118 7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected 
    2119 
    2120 > select subtract #1
    2121 
    2122 Nothing selected 
    2123 
    2124 > select add #1/G#3/G#4/G
    2125 
    2126 1308 atoms, 1326 bonds, 171 residues, 3 models selected 
    2127 
    2128 > select add #2/C
    2129 
    2130 2947 atoms, 2990 bonds, 3 pseudobonds, 377 residues, 5 models selected 
    2131 
    2132 > select add #1/A#3/C
    2133 
    2134 6710 atoms, 6821 bonds, 9 pseudobonds, 828 residues, 7 models selected 
    2135 
    2136 > select add #2/S
    2137 
    2138 8482 atoms, 8639 bonds, 10 pseudobonds, 1061 residues, 7 models selected 
    2139 
    2140 > select add #2/G
    2141 
    2142 8894 atoms, 9057 bonds, 10 pseudobonds, 1114 residues, 7 models selected 
    2143 
    2144 > select add #4/A
    2145 
    2146 10883 atoms, 11084 bonds, 11 pseudobonds, 1354 residues, 8 models selected 
    2147 
    2148 > select add #1/N
    2149 
    2150 11844 atoms, 12065 bonds, 11 pseudobonds, 1480 residues, 8 models selected 
    2151 
    2152 > select add #3/N#4/N
    2153 
    2154 13766 atoms, 14031 bonds, 11 pseudobonds, 1732 residues, 8 models selected 
    2155 
    2156 > select add #1/B#2/B#3/B#4/B
    2157 
    2158 24097 atoms, 24550 bonds, 11 pseudobonds, 3077 residues, 8 models selected 
    2159 
    2160 > delete atoms (#!1-4 & sel)
    2161 
    2162 > delete bonds (#!1-4 & sel)
    2163 
    2164 > ui tool show "Volume Viewer"
    2165 
    2166 QWindowsWindow::setGeometry: Unable to set geometry 3200x1730+0+55 (frame:
    2167 3232x1818-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    2168 Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
    2169 16, 16 minimum size: 426x692 MINMAXINFO(maxSize=POINT(x=0, y=0),
    2170 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
    2171 y=1818))) 
    2172 
    2173 QWindowsWindow::setGeometry: Unable to set geometry 3200x1835+0+55 (frame:
    2174 3232x1923-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    2175 Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
    2176 16, 16 minimum size: 426x734 MINMAXINFO(maxSize=POINT(x=0, y=0),
    2177 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
    2178 y=1923))) 
    2179 
    2180 > select add #1
    2181 
    2182 2035 atoms, 2084 bonds, 1 pseudobond, 260 residues, 2 models selected 
    2183 
    2184 > select add #3
    2185 
    2186 4272 atoms, 4392 bonds, 2 pseudobonds, 534 residues, 4 models selected 
    2187 
    2188 > select add #4
    2189 
    2190 6575 atoms, 6768 bonds, 3 pseudobonds, 818 residues, 6 models selected 
    2191 
    2192 > select subtract #4.1
    2193 
    2194 6575 atoms, 6768 bonds, 2 pseudobonds, 818 residues, 5 models selected 
    2195 
    2196 > select add #4.1
    2197 
    2198 6575 atoms, 6768 bonds, 3 pseudobonds, 818 residues, 6 models selected 
    2199 
    2200 > select add #2
    2201 
    2202 8863 atoms, 9118 bonds, 3 pseudobonds, 1105 residues, 7 models selected 
    2203 
    2204 > help help:user
    2205 
    2206 > ui tool show Matchmaker
    2207 
    2208 > matchmaker #!2-4 to #1
    2209 
    2210 Parameters 
    2211 --- 
    2212 Chain pairing | bb 
    2213 Alignment algorithm | Needleman-Wunsch 
    2214 Similarity matrix | BLOSUM-62 
    2215 SS fraction | 0.3 
    2216 Gap open (HH/SS/other) | 18/18/6 
    2217 Gap extend | 1 
    2218 SS matrix |  |  | H | S | O 
    2219 ---|---|---|--- 
    2220 H | 6 | -9 | -6 
    2221 S |  | 6 | -6 
    2222 O |  |  | 4 
    2223 Iteration cutoff | 2 
    2224  
    2225 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR17_7y89.pdb, chain A (#2),
    2226 sequence alignment score = 311.8 
    2227 RMSD between 118 pruned atom pairs is 1.154 angstroms; (across all 256 pairs:
    2228 5.669) 
    2229  
    2230 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR21_8hmv.pdb, chain A (#3),
    2231 sequence alignment score = 398.2 
    2232 RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 255 pairs:
    2233 4.042) 
    2234  
    2235 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
    2236 sequence alignment score = 369.8 
    2237 RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
    2238 5.085) 
    2239  
    2240 
    2241 > matchmaker #!2 to #1
    2242 
    2243 Parameters 
    2244 --- 
    2245 Chain pairing | bb 
    2246 Alignment algorithm | Needleman-Wunsch 
    2247 Similarity matrix | BLOSUM-62 
    2248 SS fraction | 0.3 
    2249 Gap open (HH/SS/other) | 18/18/6 
    2250 Gap extend | 1 
    2251 SS matrix |  |  | H | S | O 
    2252 ---|---|---|--- 
    2253 H | 6 | -9 | -6 
    2254 S |  | 6 | -6 
    2255 O |  |  | 4 
    2256 Iteration cutoff | 2 
    2257  
    2258 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR17_7y89.pdb, chain A (#2),
    2259 sequence alignment score = 311.8 
    2260 RMSD between 118 pruned atom pairs is 1.154 angstroms; (across all 256 pairs:
    2261 5.669) 
    2262  
    2263 
    2264 > matchmaker #!3 to #1
    2265 
    2266 Parameters 
    2267 --- 
    2268 Chain pairing | bb 
    2269 Alignment algorithm | Needleman-Wunsch 
    2270 Similarity matrix | BLOSUM-62 
    2271 SS fraction | 0.3 
    2272 Gap open (HH/SS/other) | 18/18/6 
    2273 Gap extend | 1 
    2274 SS matrix |  |  | H | S | O 
    2275 ---|---|---|--- 
    2276 H | 6 | -9 | -6 
    2277 S |  | 6 | -6 
    2278 O |  |  | 4 
    2279 Iteration cutoff | 2 
    2280  
    2281 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR21_8hmv.pdb, chain A (#3),
    2282 sequence alignment score = 398.2 
    2283 RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 255 pairs:
    2284 4.042) 
    2285  
    2286 
    2287 > matchmaker #!4 to #1
    2288 
    2289 Parameters 
    2290 --- 
    2291 Chain pairing | bb 
    2292 Alignment algorithm | Needleman-Wunsch 
    2293 Similarity matrix | BLOSUM-62 
    2294 SS fraction | 0.3 
    2295 Gap open (HH/SS/other) | 18/18/6 
    2296 Gap extend | 1 
    2297 SS matrix |  |  | H | S | O 
    2298 ---|---|---|--- 
    2299 H | 6 | -9 | -6 
    2300 S |  | 6 | -6 
    2301 O |  |  | 4 
    2302 Iteration cutoff | 2 
    2303  
    2304 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
    2305 sequence alignment score = 369.8 
    2306 RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
    2307 5.085) 
    2308  
    2309 
    2310 > matchmaker #!4 to #1
    2311 
    2312 Parameters 
    2313 --- 
    2314 Chain pairing | bb 
    2315 Alignment algorithm | Needleman-Wunsch 
    2316 Similarity matrix | BLOSUM-62 
    2317 SS fraction | 0.3 
    2318 Gap open (HH/SS/other) | 18/18/6 
    2319 Gap extend | 1 
    2320 SS matrix |  |  | H | S | O 
    2321 ---|---|---|--- 
    2322 H | 6 | -9 | -6 
    2323 S |  | 6 | -6 
    2324 O |  |  | 4 
    2325 Iteration cutoff | 2 
    2326  
    2327 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
    2328 sequence alignment score = 369.8 
    2329 RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
    2330 5.085) 
    2331  
    2332 
    2333 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    2334 
    2335 > view
    2336 
    2337 > set bgColor white
    2338 
    2339 > lighting soft
    2340 
    2341 > ui tool show "Side View"
    2342 
    2343 QWindowsWindow::setGeometry: Unable to set geometry 3200x1910+0+55 (frame:
    2344 3232x1998-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    2345 Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
    2346 16, 16 minimum size: 426x764 MINMAXINFO(maxSize=POINT(x=0, y=0),
    2347 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
    2348 y=1998))) 
    2349 
    2350 > ui tool show "Side View"
    2351 
    2352 [Repeated 1 time(s)]
    2353 
    2354 > lighting simple
    2355 
    2356 > lighting soft
    2357 
    2358 > lighting full
    2359 
    2360 > lighting soft
    2361 
    2362 > graphics silhouettes true
    2363 
    2364 > lighting flat
    2365 
    2366 [Repeated 1 time(s)]
    2367 
    2368 > lighting soft
    2369 
    2370 > view
    2371 
    2372 > view sel
    2373 
    2374 > ui tool show "Side View"
    2375 
    2376 > hide sel cartoons
    2377 
    2378 [Repeated 1 time(s)]
    2379 
    2380 > show sel cartoons
    2381 
    2382 > interfaces select & ~solvent
    2383 
    2384 Missing or invalid "atoms" argument: invalid atoms specifier 
    2385 
    2386 > interfaces select & ~solvent
    2387 
    2388 Missing or invalid "atoms" argument: invalid atoms specifier 
    2389 
    2390 > cartoon style protein modeHelix default arrows false xsection round width 1
    2391 > thickness 1
    2392 
    2393 > ui tool show "Basic Actions"
    2394 
    2395 QWindowsWindow::setGeometry: Unable to set geometry 3200x1750+0+55 (frame:
    2396 3232x1838-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    2397 Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
    2398 16, 16 minimum size: 426x700 MINMAXINFO(maxSize=POINT(x=0, y=0),
    2399 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
    2400 y=1838))) 
    2401 
    2402 > undo
    2403 
    2404 > ui tool show "Surface Color"
    2405 
    2406 QWindowsWindow::setGeometry: Unable to set geometry 3200x2108+0+55 (frame:
    2407 3232x2196-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    2408 Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
    2409 16, 16 minimum size: 426x843 MINMAXINFO(maxSize=POINT(x=0, y=0),
    2410 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
    2411 y=2196))) 
    2412 
    2413 > tile
    2414 
    2415 4 models tiled 
    2416 
    2417 > help help:user
    2418 
    2419 > tile columns 4
    2420 
    2421 4 models tiled 
    2422 
    2423 > help help:user
    2424 
    2425 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    2426 
    2427 > tile columns 4 spacingFactor 4
    2428 
    2429 4 models tiled 
    2430 
    2431 > tile columns 4 spacingFactor 1
    2432 
    2433 4 models tiled 
    2434 
    2435 > tile columns 4 spacingFactor 0.7
    2436 
    2437 4 models tiled 
    2438 
    2439 > color #1/R #dd53ff target c
    2440 
    2441 [Repeated 1 time(s)]
    2442 
    2443 > color #2/A #34ff3b target c
    2444 
    2445 [Repeated 1 time(s)]
    2446 
    2447 > color #3/A #0000ff target c
    2448 
    2449 [Repeated 1 time(s)]
    2450 
    2451 > color #3/A #5555ff target c
    2452 
    2453 [Repeated 1 time(s)]
    2454 
    2455 > color #4/R #ffaaff target c
    2456 
    2457 [Repeated 1 time(s)]
    2458 
    2459 > color #2/A #00ff7f target c
    2460 
    2461 [Repeated 1 time(s)]
    2462 
    2463 > color #1/R #aa557f target c
    2464 
    2465 [Repeated 1 time(s)]
    2466 
    2467 > color #1/R #aa5500 target c
    2468 
    2469 [Repeated 1 time(s)]
    2470 
    2471 > select subtract #1
    2472 
    2473 6828 atoms, 7034 bonds, 2 pseudobonds, 845 residues, 5 models selected 
    2474 
    2475 > select subtract #2
    2476 
    2477 4540 atoms, 4684 bonds, 2 pseudobonds, 558 residues, 4 models selected 
    2478 
    2479 > select subtract #2.1
    2480 
    2481 4540 atoms, 4684 bonds, 2 pseudobonds, 558 residues, 4 models selected 
    2482 
    2483 > select subtract #3
    2484 
    2485 2303 atoms, 2376 bonds, 1 pseudobond, 284 residues, 2 models selected 
    2486 
    2487 > select subtract #4
    2488 
    2489 Nothing selected 
    2490 
    2491 > lighting soft
    2492 
    2493 > lighting simple
    2494 
    2495 > color #1/R #bc5e00 target c
    2496 
    2497 [Repeated 1 time(s)]
    2498 
    2499 > color #1/R #c56300 target c
    2500 
    2501 [Repeated 1 time(s)]
    2502 
    2503 > color #3/A #5582ff target c
    2504 
    2505 [Repeated 1 time(s)]
    2506 
    2507 > save
    2508 > C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2_v1.cxs
    2509 
    2510 Traceback (most recent call last): 
    2511 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2512 packages\chimerax\core\session.py", line 285, in process 
    2513 data = sm.take_snapshot(obj, session, self.state_flags) 
    2514 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2515 packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot 
    2516 self.add_webview_state(data) 
    2517 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2518 packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state 
    2519 event_loop.exec_() 
    2520 AttributeError: 'QEventLoop' object has no attribute 'exec_' 
    2521  
    2522 The above exception was the direct cause of the following exception: 
    2523  
    2524 Traceback (most recent call last): 
    2525 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2526 packages\chimerax\core\session.py", line 262, in discovery 
    2527 self.processed[key] = self.process(obj, parents) 
    2528 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2529 packages\chimerax\core\session.py", line 290, in process 
    2530 raise RuntimeError(msg) from e 
    2531 RuntimeError: Error while saving session data for 'tools' ->
    2532  ->
    2533 
    2534 'Basic Actions' 
    2535  
    2536 During handling of the above exception, another exception occurred: 
    2537  
    2538 Traceback (most recent call last): 
    2539 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2540 packages\chimerax\core\session.py", line 896, in save 
    2541 session.save(output, version=version, include_maps=include_maps) 
    2542 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2543 packages\chimerax\core\session.py", line 625, in save 
    2544 mgr.discovery(self._state_containers) 
    2545 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2546 packages\chimerax\core\session.py", line 266, in discovery 
    2547 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    2548 ValueError: error processing: 'tools' ->  ->  'Basic Actions': Error while saving session data for
    2549 'tools' ->  ->
    2550 
    2551 'Basic Actions' 
    2552  
    2553 ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
    2554 saving session data for 'tools' -> -> 'Basic Actions' 
    2555  
    2556 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2557 packages\chimerax\core\session.py", line 266, in discovery 
    2558 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    2559  
    2560 See log for complete Python traceback. 
    2561  
    2562 Traceback (most recent call last): 
    2563 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2564 packages\chimerax\core\session.py", line 285, in process 
    2565 data = sm.take_snapshot(obj, session, self.state_flags) 
    2566 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2567 packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot 
    2568 self.add_webview_state(data) 
    2569 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2570 packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state 
    2571 event_loop.exec_() 
    2572 AttributeError: 'QEventLoop' object has no attribute 'exec_' 
    2573  
    2574 The above exception was the direct cause of the following exception: 
    2575  
    2576 Traceback (most recent call last): 
    2577 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2578 packages\chimerax\core\session.py", line 262, in discovery 
    2579 self.processed[key] = self.process(obj, parents) 
    2580 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2581 packages\chimerax\core\session.py", line 290, in process 
    2582 raise RuntimeError(msg) from e 
    2583 RuntimeError: Error while saving session data for 'tools' ->
    2584  ->
    2585 
    2586 'Basic Actions' 
    2587  
    2588 During handling of the above exception, another exception occurred: 
    2589  
    2590 Traceback (most recent call last): 
    2591 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2592 packages\chimerax\save_command\dialog.py", line 116, in   
    2593 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    2594 file", 
    2595 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2596 packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog 
    2597 _dlg.display(session, **kw) 
    2598 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2599 packages\chimerax\save_command\dialog.py", line 51, in display 
    2600 run(session, cmd) 
    2601 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2602 packages\chimerax\core\commands\run.py", line 38, in run 
    2603 results = command.run(text, log=log, return_json=return_json) 
    2604 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2605 packages\chimerax\core\commands\cli.py", line 2897, in run 
    2606 result = ci.function(session, **kw_args) 
    2607 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2608 packages\chimerax\save_command\cmd.py", line 75, in cmd_save 
    2609 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    2610 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2611 packages\chimerax\core\commands\cli.py", line 2897, in run 
    2612 result = ci.function(session, **kw_args) 
    2613 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2614 packages\chimerax\save_command\cmd.py", line 90, in provider_save 
    2615 saver_info.save(session, path, **provider_kw) 
    2616 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2617 packages\chimerax\core_formats\\__init__.py", line 84, in save 
    2618 return cxs_save(session, path, **kw) 
    2619 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2620 packages\chimerax\core\session.py", line 896, in save 
    2621 session.save(output, version=version, include_maps=include_maps) 
    2622 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2623 packages\chimerax\core\session.py", line 625, in save 
    2624 mgr.discovery(self._state_containers) 
    2625 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2626 packages\chimerax\core\session.py", line 266, in discovery 
    2627 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    2628 ValueError: error processing: 'tools' ->  ->  'Basic Actions': Error while saving session data for
    2629 'tools' ->  ->
    2630 
    2631 'Basic Actions' 
    2632  
    2633 ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
    2634 saving session data for 'tools' -> -> 'Basic Actions' 
    2635  
    2636 File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
    2637 packages\chimerax\core\session.py", line 266, in discovery 
    2638 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    2639  
    2640 See log for complete Python traceback. 
    2641  
    2642 
    2643 > save
    2644 > C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2.cxs
    2645 
    2646 ——— End of log from Thu Oct 26 00:31:26 2023 ———
    2647 
    2648 opened ChimeraX session 
    2649 
    2650 > select add #1
    2651 
    2652 2035 atoms, 2084 bonds, 1 pseudobond, 260 residues, 2 models selected 
    2653 
    2654 > ui tool show "Show Sequence Viewer"
    2655 
    2656 > sequence chain #1/R
    2657 
    2658 Alignment identifier is 1/R 
    2659 
    2660 > select #1/R:181
    2661 
    2662 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2663 
    2664 > select #1/R:181
    2665 
    2666 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2667 
    2668 > show sel atoms
    2669 
    2670 > select #1/R:188
    2671 
    2672 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2673 
    2674 > select #1/R:188
    2675 
    2676 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2677 
    2678 > show sel atoms
    2679 
    2680 > style sel stick
    2681 
    2682 Changed 6 atom styles 
    2683 
    2684 > select #1/R:181
    2685 
    2686 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2687 
    2688 > select #1/R:181
    2689 
    2690 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2691 
    2692 > style sel stick
    2693 
    2694 Changed 6 atom styles 
    2695 
    2696 > select #1/R:186
    2697 
    2698 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2699 
    2700 > select #1/R:186
    2701 
    2702 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2703 
    2704 > show sel atoms
    2705 
    2706 > style sel stick
    2707 
    2708 Changed 6 atom styles 
    2709 
    2710 > select #1/R:180
    2711 
    2712 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2713 
    2714 > show sel atoms
    2715 
    2716 > style sel stick
    2717 
    2718 Changed 8 atom styles 
    2719 
    2720 > select #1/R:193
    2721 
    2722 7 atoms, 7 bonds, 1 residue, 1 model selected 
    2723 
    2724 > select #1/R:193
    2725 
    2726 7 atoms, 7 bonds, 1 residue, 1 model selected 
    2727 
    2728 > show sel atoms
    2729 
    2730 > style sel stick
    2731 
    2732 Changed 7 atom styles 
    2733 
    2734 > select #1/R:192
    2735 
    2736 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2737 
    2738 > select #1/R:192
    2739 
    2740 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2741 
    2742 > show sel atoms
    2743 
    2744 > style sel stick
    2745 
    2746 Changed 11 atom styles 
    2747 
    2748 > select #1/R:191
    2749 
    2750 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2751 
    2752 > show sel atoms
    2753 
    2754 > style sel stick
    2755 
    2756 Changed 7 atom styles 
    2757 
    2758 > select
    2759 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    2760 
    2761 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    2762 
    2763 > select #1/R:113
    2764 
    2765 9 atoms, 8 bonds, 1 residue, 1 model selected 
    2766 
    2767 > select #1/R:113
    2768 
    2769 9 atoms, 8 bonds, 1 residue, 1 model selected 
    2770 
    2771 > show sel atoms
    2772 
    2773 > style sel stick
    2774 
    2775 Changed 9 atom styles 
    2776 
    2777 > select
    2778 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    2779 
    2780 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    2781 
    2782 > select #1/R:114
    2783 
    2784 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2785 
    2786 > select #1/R:114
    2787 
    2788 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2789 
    2790 > show sel atoms
    2791 
    2792 > style sel stick
    2793 
    2794 Changed 8 atom styles 
    2795 
    2796 > select
    2797 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    2798 
    2799 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    2800 
    2801 > select #1/R:117
    2802 
    2803 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2804 
    2805 > select #1/R:117
    2806 
    2807 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2808 
    2809 > show sel atoms
    2810 
    2811 > style sel stick
    2812 
    2813 Changed 8 atom styles 
    2814 
    2815 > select
    2816 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    2817 
    2818 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    2819 
    2820 > select #1/R:195
    2821 
    2822 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2823 
    2824 > select #1/R:195
    2825 
    2826 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2827 
    2828 > ui tool show "Show Sequence Viewer"
    2829 
    2830 > sequence chain #2/A
    2831 
    2832 Alignment identifier is 2/A 
    2833 
    2834 > select #2/A:204
    2835 
    2836 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2837 
    2838 > select #2/A:204
    2839 
    2840 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2841 
    2842 > select #2/A:201
    2843 
    2844 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2845 
    2846 > select #2/A:201
    2847 
    2848 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2849 
    2850 > select #2/A:208
    2851 
    2852 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2853 
    2854 > select #2/A:208
    2855 
    2856 7 atoms, 6 bonds, 1 residue, 1 model selected 
    2857 
    2858 > select
    2859 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    2860 
    2861 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    2862 
    2863 > select #2/A:209
    2864 
    2865 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2866 
    2867 > select #2/A:209
    2868 
    2869 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2870 
    2871 > show sel atoms
    2872 
    2873 > style sel stick
    2874 
    2875 Changed 6 atom styles 
    2876 
    2877 > select
    2878 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    2879 
    2880 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    2881 
    2882 > select #2/A:132
    2883 
    2884 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2885 
    2886 > select #2/A:132
    2887 
    2888 6 atoms, 5 bonds, 1 residue, 1 model selected 
    2889 
    2890 > show sel atoms
    2891 
    2892 > style sel stick
    2893 
    2894 Changed 6 atom styles 
    2895 
    2896 > select
    2897 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    2898 
    2899 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    2900 
    2901 > select #2/A:213
    2902 
    2903 12 atoms, 12 bonds, 1 residue, 1 model selected 
    2904 
    2905 > select #2/A:213
    2906 
    2907 12 atoms, 12 bonds, 1 residue, 1 model selected 
    2908 
    2909 > show sel atoms
    2910 
    2911 > style sel stick
    2912 
    2913 Changed 12 atom styles 
    2914 
    2915 > select #2/A:214
    2916 
    2917 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2918 
    2919 > select #2/A:214
    2920 
    2921 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2922 
    2923 > show sel atoms
    2924 
    2925 > style sel stick
    2926 
    2927 Changed 11 atom styles 
    2928 
    2929 > select #2/A:223-238
    2930 
    2931 121 atoms, 124 bonds, 16 residues, 1 model selected 
    2932 
    2933 > select #2/A:163-238
    2934 
    2935 594 atoms, 611 bonds, 76 residues, 1 model selected 
    2936 
    2937 > select
    2938 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    2939 
    2940 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    2941 
    2942 > select #2/A:308
    2943 
    2944 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2945 
    2946 > select #2/A:308
    2947 
    2948 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2949 
    2950 > show sel atoms
    2951 
    2952 > style sel stick
    2953 
    2954 Changed 11 atom styles 
    2955 
    2956 > select
    2957 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    2958 
    2959 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    2960 
    2961 > select #2/A:307
    2962 
    2963 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2964 
    2965 > select #2/A:307
    2966 
    2967 8 atoms, 7 bonds, 1 residue, 1 model selected 
    2968 
    2969 > show sel atoms
    2970 
    2971 > style sel stick
    2972 
    2973 Changed 8 atom styles 
    2974 
    2975 > select
    2976 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    2977 
    2978 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    2979 
    2980 > select #2/A:139
    2981 
    2982 11 atoms, 11 bonds, 1 residue, 1 model selected 
    2983 
    2984 > select #2/A:139
    2985 
    2986 11 atoms, 11 bonds, 1 residue, 1 model selected 
    2987 
    2988 > show sel atoms
    2989 
    2990 > style sel stick
    2991 
    2992 Changed 11 atom styles 
    2993 
    2994 > select
    2995 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    2996 
    2997 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    2998 
    2999 > select #2/A:140
    3000 
    3001 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3002 
    3003 > select #2/A:140
    3004 
    3005 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3006 
    3007 > show sel atoms
    3008 
    3009 > style sel stick
    3010 
    3011 Changed 12 atom styles 
    3012 
    3013 > select
    3014 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    3015 
    3016 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    3017 
    3018 > select #2/A:279
    3019 
    3020 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3021 
    3022 > select #2/A:279
    3023 
    3024 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3025 
    3026 > show sel atoms
    3027 
    3028 > style sel stick
    3029 
    3030 Changed 12 atom styles 
    3031 
    3032 > ui tool show "Show Sequence Viewer"
    3033 
    3034 > sequence chain #3/A
    3035 
    3036 Alignment identifier is 3/A 
    3037 
    3038 > select #3/A:170
    3039 
    3040 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3041 
    3042 > select #3/A:170
    3043 
    3044 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3045 
    3046 > show sel atoms
    3047 
    3048 > style sel stick
    3049 
    3050 Changed 9 atom styles 
    3051 
    3052 > select
    3053 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3054 
    3055 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3056 
    3057 > select #3/A:176
    3058 
    3059 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3060 
    3061 > select #3/A:176
    3062 
    3063 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3064 
    3065 > show sel atoms
    3066 
    3067 > style sel stick
    3068 
    3069 Changed 8 atom styles 
    3070 
    3071 > select
    3072 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3073 
    3074 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3075 
    3076 > select #3/A:174
    3077 
    3078 10 atoms, 10 bonds, 1 residue, 1 model selected 
    3079 
    3080 > select #3/A:174
    3081 
    3082 10 atoms, 10 bonds, 1 residue, 1 model selected 
    3083 
    3084 > show sel atoms
    3085 
    3086 > style sel stick
    3087 
    3088 Changed 10 atom styles 
    3089 
    3090 > select
    3091 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3092 
    3093 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3094 
    3095 > select #3/A:173-174
    3096 
    3097 22 atoms, 23 bonds, 2 residues, 1 model selected 
    3098 
    3099 > select #3/A:173
    3100 
    3101 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3102 
    3103 > show sel atoms
    3104 
    3105 > style sel stick
    3106 
    3107 Changed 12 atom styles 
    3108 
    3109 > select #3/A:168
    3110 
    3111 14 atoms, 15 bonds, 1 residue, 1 model selected 
    3112 
    3113 > select #3/A:168
    3114 
    3115 14 atoms, 15 bonds, 1 residue, 1 model selected 
    3116 
    3117 > select #3/A:168
    3118 
    3119 14 atoms, 15 bonds, 1 residue, 1 model selected 
    3120 
    3121 > select #3/A:168
    3122 
    3123 14 atoms, 15 bonds, 1 residue, 1 model selected 
    3124 
    3125 > show sel atoms
    3126 
    3127 > style sel stick
    3128 
    3129 Changed 14 atom styles 
    3130 
    3131 > hide sel atoms
    3132 
    3133 > select
    3134 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3135 
    3136 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3137 
    3138 > select #3/A:178
    3139 
    3140 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3141 
    3142 > select #3/A:178
    3143 
    3144 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3145 
    3146 > show sel atoms
    3147 
    3148 > style sel stick
    3149 
    3150 Changed 11 atom styles 
    3151 
    3152 > select
    3153 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3154 
    3155 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3156 
    3157 > select #3/A:177
    3158 
    3159 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3160 
    3161 > select #3/A:177
    3162 
    3163 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3164 
    3165 > show sel atoms
    3166 
    3167 > style sel stick
    3168 
    3169 Changed 7 atom styles 
    3170 
    3171 > select #3/A:179
    3172 
    3173 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3174 
    3175 > select #3/A:179
    3176 
    3177 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3178 
    3179 > select #3/A:180
    3180 
    3181 14 atoms, 15 bonds, 1 residue, 1 model selected 
    3182 
    3183 > select #3/A:180
    3184 
    3185 14 atoms, 15 bonds, 1 residue, 1 model selected 
    3186 
    3187 > select #3/A:181
    3188 
    3189 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3190 
    3191 > show sel atoms
    3192 
    3193 > style sel stick
    3194 
    3195 Changed 6 atom styles 
    3196 
    3197 > select
    3198 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3199 
    3200 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3201 
    3202 > select #3/A:122
    3203 
    3204 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3205 
    3206 > select #3/A:122
    3207 
    3208 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3209 
    3210 > select
    3211 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3212 
    3213 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3214 
    3215 > select #3/A:102
    3216 
    3217 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3218 
    3219 > select #3/A:102
    3220 
    3221 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3222 
    3223 > show sel atoms
    3224 
    3225 > style sel stick
    3226 
    3227 Changed 6 atom styles 
    3228 
    3229 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3230 
    3231 > lighting soft
    3232 
    3233 > save
    3234 > C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2.cxs
    3235 
    3236 > ui tool show "Show Sequence Viewer"
    3237 
    3238 > sequence chain #4/R
    3239 
    3240 Alignment identifier is 4/R 
    3241 
    3242 > select
    3243 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3244 
    3245 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3246 
    3247 > select #4/R:114
    3248 
    3249 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3250 
    3251 > select #4/R:114
    3252 
    3253 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3254 
    3255 > show sel atoms
    3256 
    3257 > style sel stick
    3258 
    3259 Changed 6 atom styles 
    3260 
    3261 > select
    3262 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3263 
    3264 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3265 
    3266 > select #4/R:193
    3267 
    3268 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3269 
    3270 > select #4/R:193
    3271 
    3272 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3273 
    3274 > show sel atoms
    3275 
    3276 > style sel stick
    3277 
    3278 Changed 6 atom styles 
    3279 
    3280 > select #4/R:69
    3281 
    3282 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3283 
    3284 > select #4/R:69-129
    3285 
    3286 476 atoms, 489 bonds, 61 residues, 1 model selected 
    3287 
    3288 > select #4/R:67-81
    3289 
    3290 126 atoms, 131 bonds, 15 residues, 1 model selected 
    3291 
    3292 > select #4/R:67-111
    3293 
    3294 350 atoms, 361 bonds, 45 residues, 1 model selected 
    3295 
    3296 > select
    3297 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3298 
    3299 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3300 
    3301 > select #4/R:40
    3302 
    3303 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3304 
    3305 > select #4/R:40
    3306 
    3307 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3308 
    3309 > select #4/R:182
    3310 
    3311 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3312 
    3313 > select #4/R:182
    3314 
    3315 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3316 
    3317 > show sel atoms
    3318 
    3319 > style sel stick
    3320 
    3321 Changed 9 atom styles 
    3322 
    3323 > select #4/R:185
    3324 
    3325 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3326 
    3327 > select #4/R:185
    3328 
    3329 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3330 
    3331 > show sel atoms
    3332 
    3333 > style sel stick
    3334 
    3335 Changed 12 atom styles 
    3336 
    3337 > select #4/R:186
    3338 
    3339 10 atoms, 10 bonds, 1 residue, 1 model selected 
    3340 
    3341 > select #4/R:186
    3342 
    3343 10 atoms, 10 bonds, 1 residue, 1 model selected 
    3344 
    3345 > show sel atoms
    3346 
    3347 > style sel stick
    3348 
    3349 Changed 10 atom styles 
    3350 
    3351 > select #4/R:188
    3352 
    3353 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3354 
    3355 > select #4/R:188
    3356 
    3357 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3358 
    3359 > show sel atoms
    3360 
    3361 > style sel stick
    3362 
    3363 Changed 8 atom styles 
    3364 
    3365 > select #4/R:189
    3366 
    3367 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3368 
    3369 > select #4/R:189
    3370 
    3371 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3372 
    3373 > show sel atoms
    3374 
    3375 > style sel stick
    3376 
    3377 Changed 8 atom styles 
    3378 
    3379 > select #4/R:190
    3380 
    3381 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3382 
    3383 > select #4/R:190
    3384 
    3385 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3386 
    3387 > show sel cartoons
    3388 
    3389 > style sel stick
    3390 
    3391 Changed 11 atom styles 
    3392 
    3393 > select
    3394 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3395 
    3396 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3397 
    3398 > select #4/R:281
    3399 
    3400 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3401 
    3402 > show sel atoms
    3403 
    3404 > style sel stick
    3405 
    3406 Changed 12 atom styles 
    3407 
    3408 > select
    3409 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3410 
    3411 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3412 
    3413 > select #4/R:284
    3414 
    3415 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3416 
    3417 > select #4/R:284
    3418 
    3419 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3420 
    3421 > show sel atoms
    3422 
    3423 > style sel stick
    3424 
    3425 Changed 12 atom styles 
    3426 
    3427 > select
    3428 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3429 
    3430 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3431 
    3432 > select #4/R:285
    3433 
    3434 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3435 
    3436 > select #4/R:285
    3437 
    3438 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3439 
    3440 > show sel atoms
    3441 
    3442 > style sel stick
    3443 
    3444 Changed 11 atom styles 
    3445 
    3446 > select
    3447 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3448 
    3449 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3450 
    3451 > select #4/R:300
    3452 
    3453 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3454 
    3455 > select #4/R:300
    3456 
    3457 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3458 
    3459 > select #4/R:300
    3460 
    3461 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3462 
    3463 > select #4/R:300
    3464 
    3465 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3466 
    3467 > show sel atoms
    3468 
    3469 > style sel stick
    3470 
    3471 Changed 11 atom styles 
    3472 
    3473 > hide sel atoms
    3474 
    3475 > show sel atoms
    3476 
    3477 > style sel ball
    3478 
    3479 Changed 11 atom styles 
    3480 
    3481 > hide sel atoms
    3482 
    3483 > ui tool show "Color Actions"
    3484 
    3485 > color sel byhetero
    3486 
    3487 > select
    3488 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3489 
    3490 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3491 
    3492 > color sel byhetero
    3493 
    3494 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3495 
    3496 > ui tool show "Show Sequence Viewer"
    3497 
    3498 > sequence chain #3/A
    3499 
    3500 Alignment identifier is 3/A 
    3501 
    3502 > select
    3503 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3504 
    3505 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3506 
    3507 > color sel byhetero
    3508 
    3509 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3510 
    3511 > ui tool show "Show Sequence Viewer"
    3512 
    3513 > sequence chain #2/A
    3514 
    3515 Alignment identifier is 2/A 
    3516 
    3517 > select
    3518 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    3519 
    3520 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    3521 
    3522 > color sel byhetero
    3523 
    3524 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3525 
    3526 > ui tool show "Show Sequence Viewer"
    3527 
    3528 > sequence chain #1/R
    3529 
    3530 Alignment identifier is 1/R 
    3531 
    3532 > select
    3533 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    3534 
    3535 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    3536 
    3537 > color sel byhetero
    3538 
    3539 delivering touch update to same window GraphicsWindow(0x2840860fb50) not
    3540 QWidgetWindow(0x28461326800, name="PopupClassWindow") 
    3541 
    3542 delivering touch update to same window QWidgetWindow(0x28461326800,
    3543 name="PopupClassWindow") not GraphicsWindow(0x2840860fb50) 
    3544 
    3545 delivering touch update to same window GraphicsWindow(0x2840860fb50) not
    3546 QWidgetWindow(0x28461326800, name="PopupClassWindow") 
    3547 
    3548 delivering touch update to same window QWidgetWindow(0x28461326800,
    3549 name="PopupClassWindow") not GraphicsWindow(0x2840860fb50) 
    3550 
    3551 delivering touch update to same window GraphicsWindow(0x2840860fb50) not
    3552 QWidgetWindow(0x28461326800, name="PopupClassWindow") 
    3553 
    3554 delivering touch update to same window QWidgetWindow(0x28461326800,
    3555 name="PopupClassWindow") not GraphicsWindow(0x2840860fb50) 
    3556 
    3557 delivering touch update to same window GraphicsWindow(0x2840860fb50) not
    3558 QWidgetWindow(0x28461326800, name="PopupClassWindow") 
    3559 
    3560 delivering touch update to same window QWidgetWindow(0x28461326800,
    3561 name="PopupClassWindow") not GraphicsWindow(0x2840860fb50) 
    3562 
    3563 delivering touch update to same window GraphicsWindow(0x2840860fb50) not
    3564 QWidgetWindow(0x28461326800, name="PopupClassWindow") 
    3565 
    3566 delivering touch update to same window QWidgetWindow(0x28461326800,
    3567 name="PopupClassWindow") not GraphicsWindow(0x2840860fb50) 
    3568 
    3569 delivering touch update to same window GraphicsWindow(0x2840860fb50) not
    3570 QWidgetWindow(0x28461326800, name="PopupClassWindow") 
    3571 
    3572 delivering touch update to same window QWidgetWindow(0x28461326800,
    3573 name="PopupClassWindow") not GraphicsWindow(0x2840860fb50) 
    3574 
    3575 delivering touch update to same window GraphicsWindow(0x2840860fb50) not
    3576 QWidgetWindow(0x28461326800, name="PopupClassWindow") 
    3577 
    3578 delivering touch update to same window QWidgetWindow(0x28461326800,
    3579 name="PopupClassWindow") not GraphicsWindow(0x2840860fb50) 
    3580 
    3581 > ui tool show "Side View"
    3582 
    3583 > tile columns 4 spacingFactor 0.7
    3584 
    3585 4 models tiled 
    3586 
    3587 > lighting soft
    3588 
    3589 > view
    3590 
    3591 > ui tool show "Side View"
    3592 
    3593 > tile columns 4 spacingFactor 0.7
    3594 
    3595 4 models tiled 
    3596 
    3597 > tile columns 4 spacingFactor 0.7
    3598 
    3599 4 models tiled 
    3600 
    3601 > lighting flat
    3602 
    3603 > lighting soft
    3604 
    3605 > lighting shadows true intensity 0.5
    3606 
    3607 > lighting simple
    3608 
    3609 > lighting full
    3610 
    3611 [Repeated 1 time(s)]
    3612 
    3613 > lighting soft
    3614 
    3615 > save
    3616 > C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2.cxs
    3617 
    3618 ——— End of log from Thu Oct 26 16:19:56 2023 ———
    3619 
    3620 opened ChimeraX session 
    3621 
    3622 > ui tool show "Show Sequence Viewer"
    3623 
    3624 > sequence chain #4/R
    3625 
    3626 Alignment identifier is 4/R 
    3627 
    3628 > select #4/R:155-156
    3629 
    3630 13 atoms, 13 bonds, 2 residues, 1 model selected 
    3631 
    3632 > select #4/R:149-156
    3633 
    3634 64 atoms, 65 bonds, 8 residues, 1 model selected 
    3635 
    3636 > select
    3637 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3638 
    3639 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3640 
    3641 > select #4/R:185-186
    3642 
    3643 22 atoms, 23 bonds, 2 residues, 1 model selected 
    3644 
    3645 > select #4/R:183-186
    3646 
    3647 33 atoms, 35 bonds, 4 residues, 1 model selected 
    3648 
    3649 > select #4/R:182
    3650 
    3651 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3652 
    3653 > select #4/R:178-182
    3654 
    3655 42 atoms, 44 bonds, 5 residues, 1 model selected 
    3656 
    3657 > select #4/R:181
    3658 
    3659 4 atoms, 3 bonds, 1 residue, 1 model selected 
    3660 
    3661 > select #4/R:181
    3662 
    3663 4 atoms, 3 bonds, 1 residue, 1 model selected 
    3664 
    3665 > select #4/R:182
    3666 
    3667 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3668 
    3669 > select #4/R:179
    3670 
    3671 4 atoms, 3 bonds, 1 residue, 1 model selected 
    3672 
    3673 > select #4/R:179
    3674 
    3675 4 atoms, 3 bonds, 1 residue, 1 model selected 
    3676 
    3677 > select #4/R:199
    3678 
    3679 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3680 
    3681 > select #4/R:199
    3682 
    3683 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3684 
    3685 > select #4/R:179-199
    3686 
    3687 171 atoms, 180 bonds, 21 residues, 1 model selected 
    3688 
    3689 > color sel light sea green
    3690 
    3691 > select #4/R:246
    3692 
    3693 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3694 
    3695 > select #4/R:246
    3696 
    3697 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3698 
    3699 > select
    3700 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3701 
    3702 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3703 
    3704 > color sel byhetero
    3705 
    3706 > select #4/R:71
    3707 
    3708 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3709 
    3710 > select #4/R:71
    3711 
    3712 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3713 
    3714 > select
    3715 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    3716 
    3717 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    3718 
    3719 > color sel byhetero
    3720 
    3721 > select #4/R:198
    3722 
    3723 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3724 
    3725 > select #4/R:198
    3726 
    3727 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3728 
    3729 > select #4/R:199
    3730 
    3731 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3732 
    3733 > select #4/R:179-199
    3734 
    3735 171 atoms, 180 bonds, 21 residues, 1 model selected 
    3736 
    3737 > color sel byhetero
    3738 
    3739 > select #4/R:150-151
    3740 
    3741 17 atoms, 16 bonds, 2 residues, 1 model selected 
    3742 
    3743 > select #4/R:150-151
    3744 
    3745 17 atoms, 16 bonds, 2 residues, 1 model selected 
    3746 
    3747 > view sel
    3748 
    3749 > view
    3750 
    3751 > ui tool show "Show Sequence Viewer"
    3752 
    3753 > sequence chain #1/R
    3754 
    3755 Alignment identifier is 1/R 
    3756 
    3757 > select #1/R:175-176
    3758 
    3759 14 atoms, 14 bonds, 2 residues, 1 model selected 
    3760 
    3761 > select #1/R:175-192
    3762 
    3763 140 atoms, 143 bonds, 18 residues, 1 model selected 
    3764 
    3765 > select #1/R:193
    3766 
    3767 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3768 
    3769 > select #1/R:175-193
    3770 
    3771 147 atoms, 151 bonds, 19 residues, 1 model selected 
    3772 
    3773 > color sel light sea green
    3774 
    3775 > select
    3776 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    3777 
    3778 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    3779 
    3780 > select #1/R:175-193
    3781 
    3782 147 atoms, 151 bonds, 19 residues, 1 model selected 
    3783 
    3784 > color sel byhetero
    3785 
    3786 > select
    3787 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    3788 
    3789 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    3790 
    3791 > select #1/R:150
    3792 
    3793 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3794 
    3795 > select #1/R:150
    3796 
    3797 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3798 
    3799 > select
    3800 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    3801 
    3802 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    3803 
    3804 > select #1/R:174
    3805 
    3806 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3807 
    3808 > select #1/R:174
    3809 
    3810 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3811 
    3812 > select
    3813 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    3814 
    3815 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    3816 
    3817 > select #1/R:194
    3818 
    3819 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3820 
    3821 > color sel light sea green
    3822 
    3823 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3824 
    3825 > ui tool show "Show Sequence Viewer"
    3826 
    3827 > sequence chain #2/A
    3828 
    3829 Alignment identifier is 2/A 
    3830 
    3831 > select #2/A:198
    3832 
    3833 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3834 
    3835 > select #2/A:198-218
    3836 
    3837 168 atoms, 170 bonds, 21 residues, 1 model selected 
    3838 
    3839 > color sel light sea green
    3840 
    3841 > color sel byhetero
    3842 
    3843 > select
    3844 > #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
    3845 
    3846 1950 atoms, 1992 bonds, 244 residues, 1 model selected 
    3847 
    3848 > select #2/A:252
    3849 
    3850 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3851 
    3852 > select #2/A:252
    3853 
    3854 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3855 
    3856 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3857 
    3858 > ui tool show "Show Sequence Viewer"
    3859 
    3860 > sequence chain #3/A
    3861 
    3862 Alignment identifier is 3/A 
    3863 
    3864 > select #3/A:166-167
    3865 
    3866 21 atoms, 22 bonds, 2 residues, 1 model selected 
    3867 
    3868 > select #3/A:166-187
    3869 
    3870 191 atoms, 203 bonds, 22 residues, 1 model selected 
    3871 
    3872 > color sel light sea green
    3873 
    3874 > color sel byhetero
    3875 
    3876 > select
    3877 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    3878 
    3879 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    3880 
    3881 > select #3/A:108
    3882 
    3883 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3884 
    3885 > select #3/A:108
    3886 
    3887 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3888 
    3889 > select #3/A:166-167
    3890 
    3891 21 atoms, 22 bonds, 2 residues, 1 model selected 
    3892 
    3893 > select #3/A:166-186
    3894 
    3895 184 atoms, 196 bonds, 21 residues, 1 model selected 
    3896 
    3897 > select #3/A:187
    3898 
    3899 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3900 
    3901 > select #3/A:166-187
    3902 
    3903 191 atoms, 203 bonds, 22 residues, 1 model selected 
    3904 
    3905 > color sel cyan
    3906 
    3907 > color sel byhetero
    3908 
    3909 > select #3/A:249
    3910 
    3911 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3912 
    3913 > select #3/A:249
    3914 
    3915 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3916 
    3917 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3918 
    3919 > ui tool show "Show Sequence Viewer"
    3920 
    3921 > sequence chain #2/A
    3922 
    3923 Alignment identifier is 2/A 
    3924 
    3925 > select #2/A:198
    3926 
    3927 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3928 
    3929 > select #2/A:198-215
    3930 
    3931 148 atoms, 150 bonds, 18 residues, 1 model selected 
    3932 
    3933 > select #2/A:218
    3934 
    3935 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3936 
    3937 > select #2/A:198-218
    3938 
    3939 168 atoms, 170 bonds, 21 residues, 1 model selected 
    3940 
    3941 > color sel cyan
    3942 
    3943 > color sel byhetero
    3944 
    3945 > select #2/A:252
    3946 
    3947 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3948 
    3949 > select #2/A:252
    3950 
    3951 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3952 
    3953 QMainWindowLayout::tabPosition called with out-of-bounds value '0' 
    3954 
    3955 > ui tool show "Show Sequence Viewer"
    3956 
    3957 > sequence chain #1/R
    3958 
    3959 Alignment identifier is 1/R 
    3960 
    3961 > select #1/R:175
    3962 
    3963 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3964 
    3965 > select #1/R:175-194
    3966 
    3967 155 atoms, 159 bonds, 20 residues, 1 model selected 
    3968 
    3969 > select #1/R:175-176
    3970 
    3971 14 atoms, 14 bonds, 2 residues, 1 model selected 
    3972 
    3973 > select #1/R:175-193
    3974 
    3975 147 atoms, 151 bonds, 19 residues, 1 model selected 
    3976 
    3977 > select #1/R:175
    3978 
    3979 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3980 
    3981 > select #1/R:175-194
    3982 
    3983 155 atoms, 159 bonds, 20 residues, 1 model selected 
    3984 
    3985 > color sel cyan
    3986 
    3987 > color sel byhetero
    3988 
    3989 > select
    3990 > #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
    3991 
    3992 1625 atoms, 1653 bonds, 210 residues, 1 model selected 
    3993 
    3994 > select #1/R:207
    3995 
    3996 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3997 
    3998 > select #1/R:207
    3999 
    4000 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4001 
    4002 > view
    4003 
    4004 > ui tool show "Show Sequence Viewer"
    4005 
    4006 > sequence chain #4/R
    4007 
    4008 Alignment identifier is 4/R 
    4009 
    4010 > select #4/R:179
    4011 
    4012 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4013 
    4014 > select #4/R:179-199
    4015 
    4016 171 atoms, 180 bonds, 21 residues, 1 model selected 
    4017 
    4018 > color sel cyan
    4019 
    4020 > color sel byhetero
    4021 
    4022 > select #4/R:245-246
    4023 
    4024 13 atoms, 13 bonds, 2 residues, 1 model selected 
    4025 
    4026 > select #4/R:245-246
    4027 
    4028 13 atoms, 13 bonds, 2 residues, 1 model selected 
    4029 
    4030 > save
    4031 > C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231026_Figure_2.cxs
    4032 
    4033 ——— End of log from Thu Oct 26 20:27:55 2023 ———
    4034 
    4035 opened ChimeraX session 
    4036 
    4037 > ui tool show "Show Sequence Viewer"
    4038 
    4039 > sequence chain #3/A
    4040 
    4041 Alignment identifier is 3/A 
    4042 
    4043 > select
    4044 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4045 
    4046 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4047 
    4048 > select #3/A:268
    4049 
    4050 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4051 
    4052 > select #3/A:268
    4053 
    4054 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4055 
    4056 > show sel atoms
    4057 
    4058 > style sel stick
    4059 
    4060 Changed 12 atom styles 
    4061 
    4062 > color sel cornflower blue
    4063 
    4064 > select
    4065 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4066 
    4067 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4068 
    4069 > select #3/A:268
    4070 
    4071 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4072 
    4073 > select #3/A:268
    4074 
    4075 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4076 
    4077 > select
    4078 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4079 
    4080 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4081 
    4082 > select #3/A:268
    4083 
    4084 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4085 
    4086 > select #3/A:268
    4087 
    4088 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4089 
    4090 > color sel #5582ffff
    4091 
    4092 > color sel byhetero
    4093 
    4094 > select
    4095 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4096 
    4097 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4098 
    4099 > select clear
    4100 
    4101 > select #3/A:271
    4102 
    4103 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4104 
    4105 > select #3/A:271
    4106 
    4107 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4108 
    4109 > style sel stick
    4110 
    4111 Changed 12 atom styles 
    4112 
    4113 > show sel atoms
    4114 
    4115 > select
    4116 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4117 
    4118 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4119 
    4120 > select #3/A:272
    4121 
    4122 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4123 
    4124 > select #3/A:272
    4125 
    4126 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4127 
    4128 > show sel atoms
    4129 
    4130 > style sel stick
    4131 
    4132 Changed 11 atom styles 
    4133 
    4134 > select
    4135 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4136 
    4137 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4138 
    4139 > select #3/A:275
    4140 
    4141 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4142 
    4143 > select #3/A:275
    4144 
    4145 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4146 
    4147 > show sel atoms
    4148 
    4149 > style sel stick
    4150 
    4151 Changed 9 atom styles 
    4152 
    4153 > select #3/A:276
    4154 
    4155 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4156 
    4157 > select #3/A:276
    4158 
    4159 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4160 
    4161 > show sel atoms
    4162 
    4163 > style sel stick
    4164 
    4165 Changed 6 atom styles 
    4166 
    4167 > select #3/A:110
    4168 
    4169 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4170 
    4171 > select #3/A:110
    4172 
    4173 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4174 
    4175 > show sel atoms
    4176 
    4177 > style sel stick
    4178 
    4179 Changed 6 atom styles 
    4180 
    4181 > select #3/A:113
    4182 
    4183 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4184 
    4185 > select #3/A:113
    4186 
    4187 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4188 
    4189 > show sel atoms
    4190 
    4191 > style sel stick
    4192 
    4193 Changed 9 atom styles 
    4194 
    4195 > select #3/A:65
    4196 
    4197 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4198 
    4199 > select #3/A:65-277
    4200 
    4201 1635 atoms, 1691 bonds, 1 pseudobond, 198 residues, 2 models selected 
    4202 
    4203 > select #3/A:224
    4204 
    4205 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4206 
    4207 > select #3/A:188-224
    4208 
    4209 310 atoms, 319 bonds, 37 residues, 1 model selected 
    4210 
    4211 > select #3/A:271
    4212 
    4213 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4214 
    4215 > select #3/A:271
    4216 
    4217 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4218 
    4219 > select #3/A:268
    4220 
    4221 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4222 
    4223 > select #3/A:268
    4224 
    4225 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4226 
    4227 > ui tool show "Color Actions"
    4228 
    4229 > select #3/A:271
    4230 
    4231 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4232 
    4233 > select #3/A:271
    4234 
    4235 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4236 
    4237 > select #3/A:268
    4238 
    4239 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4240 
    4241 > select #3/A:268
    4242 
    4243 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4244 
    4245 > color sel #aaaa7fff target a
    4246 
    4247 > style sel stick
    4248 
    4249 Changed 12 atom styles 
    4250 
    4251 > color sel byhetero
    4252 
    4253 > select clear
    4254 
    4255 > select #3/A:268
    4256 
    4257 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4258 
    4259 > select #3/A:268
    4260 
    4261 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4262 
    4263 > color sel byhetero
    4264 
    4265 > color sel #acac80ff
    4266 
    4267 > color sel #b8b889ff
    4268 
    4269 > color sel #b9b98aff
    4270 
    4271 > color sel #bdbd8dff
    4272 
    4273 > color sel #bfbf8eff
    4274 
    4275 > color sel #c2c291ff
    4276 
    4277 > color sel #c3c391ff
    4278 
    4279 > undo
    4280 
    4281 [Repeated 2 time(s)]
    4282 
    4283 > color sel #5582ffff
    4284 
    4285 > ui tool show "Color Actions"
    4286 
    4287 > color sel #aaaa7fff target a
    4288 
    4289 > color sel #acac80ff target a
    4290 
    4291 > color sel #adad81ff target a
    4292 
    4293 > color sel #c7c794ff target a
    4294 
    4295 > color sel #caca97ff target a
    4296 
    4297 > color sel #cbcb97ff target a
    4298 
    4299 > color sel #cfcf9aff target a
    4300 
    4301 > color sel #d0d09bff target a
    4302 
    4303 > color sel #d1d19cff target a
    4304 
    4305 > color sel #d5d59fff target a
    4306 
    4307 > color sel #d8d8a1ff target a
    4308 
    4309 > color sel #d9d9a2ff target a
    4310 
    4311 > color sel #dadaa2ff target a
    4312 
    4313 > color sel #dcdca4ff target a
    4314 
    4315 > color sel #dddda5ff target a
    4316 
    4317 > color sel #d6d69fff target a
    4318 
    4319 > color sel #c8c895ff target a
    4320 
    4321 > color sel #c7c794ff target a
    4322 
    4323 > color sel #c6c694ff target a
    4324 
    4325 > color sel #c3c391ff target a
    4326 
    4327 > select #3/A:271
    4328 
    4329 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4330 
    4331 > select #3/A:271
    4332 
    4333 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4334 
    4335 > select
    4336 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4337 
    4338 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4339 
    4340 > select #3/A:268
    4341 
    4342 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4343 
    4344 > select #3/A:268
    4345 
    4346 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4347 
    4348 > color sel byhetero target a
    4349 
    4350 [Repeated 1 time(s)]
    4351 
    4352 > color sel byhetero
    4353 
    4354 > select ~sel
    4355 
    4356 8851 atoms, 9104 bonds, 3 pseudobonds, 1104 residues, 7 models selected 
    4357 
    4358 > select clear
    4359 
    4360 > select #3/A:271
    4361 
    4362 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4363 
    4364 > select #3/A:271
    4365 
    4366 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4367 
    4368 > select #3/A:105
    4369 
    4370 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4371 
    4372 > select #3/A:105
    4373 
    4374 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4375 
    4376 > show sel atoms
    4377 
    4378 > style sel stick
    4379 
    4380 Changed 11 atom styles 
    4381 
    4382 > select
    4383 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4384 
    4385 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4386 
    4387 > select #3/A:110
    4388 
    4389 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4390 
    4391 > select #3/A:110
    4392 
    4393 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4394 
    4395 > select #4/R:117
    4396 
    4397 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4398 
    4399 > select #4/R:117
    4400 
    4401 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4402 
    4403 > show sel atoms
    4404 
    4405 > style sel stick
    4406 
    4407 Changed 11 atom styles 
    4408 
    4409 > select #4/R:122
    4410 
    4411 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4412 
    4413 > select #4/R:122
    4414 
    4415 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4416 
    4417 > show sel atoms
    4418 
    4419 > style sel stick
    4420 
    4421 Changed 6 atom styles 
    4422 
    4423 > select #4/R:125
    4424 
    4425 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4426 
    4427 > select #4/R:125
    4428 
    4429 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4430 
    4431 > show sel atoms
    4432 
    4433 > style sel stick
    4434 
    4435 Changed 9 atom styles 
    4436 
    4437 > select #4/R:304
    4438 
    4439 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4440 
    4441 > select #4/R:304
    4442 
    4443 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4444 
    4445 > show sel atoms
    4446 
    4447 > style sel stick
    4448 
    4449 Changed 14 atom styles 
    4450 
    4451 > select #4/R:303
    4452 
    4453 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4454 
    4455 > select #4/R:303
    4456 
    4457 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4458 
    4459 > show sel atoms
    4460 
    4461 > style sel stick
    4462 
    4463 Changed 7 atom styles 
    4464 
    4465 > select #4/R:307
    4466 
    4467 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4468 
    4469 > select #4/R:307
    4470 
    4471 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4472 
    4473 > show sel atoms
    4474 
    4475 > style sel stick
    4476 
    4477 Changed 8 atom styles 
    4478 
    4479 > select
    4480 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    4481 
    4482 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    4483 
    4484 > select #4/R:121
    4485 
    4486 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4487 
    4488 > select #4/R:121
    4489 
    4490 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4491 
    4492 > show sel atoms
    4493 
    4494 > style sel stick
    4495 
    4496 Changed 8 atom styles 
    4497 
    4498 > select #4/R:122
    4499 
    4500 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4501 
    4502 > select #4/R:122
    4503 
    4504 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4505 
    4506 > select #4/R:120
    4507 
    4508 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4509 
    4510 > select #4/R:120
    4511 
    4512 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4513 
    4514 > select #4/R:110
    4515 
    4516 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4517 
    4518 > select #4/R:110
    4519 
    4520 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4521 
    4522 > show sel atoms
    4523 
    4524 > style sel stick
    4525 
    4526 Changed 9 atom styles 
    4527 
    4528 > select #4/R:191
    4529 
    4530 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4531 
    4532 > select #4/R:191
    4533 
    4534 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4535 
    4536 > show sel atoms
    4537 
    4538 > style sel stick
    4539 
    4540 Changed 9 atom styles 
    4541 
    4542 > hide sel atoms
    4543 
    4544 > select #4/R:110
    4545 
    4546 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4547 
    4548 > select #4/R:110
    4549 
    4550 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4551 
    4552 > hide sel atoms
    4553 
    4554 > select #4/R:199-200
    4555 
    4556 13 atoms, 12 bonds, 2 residues, 1 model selected 
    4557 
    4558 > select #4/R:199
    4559 
    4560 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4561 
    4562 > show sel atoms
    4563 
    4564 > style sel stick
    4565 
    4566 Changed 7 atom styles 
    4567 
    4568 > select #4/R:288
    4569 
    4570 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4571 
    4572 > select #4/R:288
    4573 
    4574 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4575 
    4576 > show sel atoms
    4577 
    4578 > style sel stick
    4579 
    4580 Changed 9 atom styles 
    4581 
    4582 > select #4/R:111
    4583 
    4584 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4585 
    4586 > select #4/R:111
    4587 
    4588 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4589 
    4590 > show sel atoms
    4591 
    4592 > style sel stick
    4593 
    4594 Changed 6 atom styles 
    4595 
    4596 > select #4/R:192
    4597 
    4598 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4599 
    4600 > select #4/R:192
    4601 
    4602 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4603 
    4604 > show sel atoms
    4605 
    4606 > style sel stick
    4607 
    4608 Changed 14 atom styles 
    4609 
    4610 > select #4/R:177
    4611 
    4612 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4613 
    4614 > select #4/R:177
    4615 
    4616 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4617 
    4618 > select #4/R:176
    4619 
    4620 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4621 
    4622 > select #4/R:176
    4623 
    4624 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4625 
    4626 > show sel atoms
    4627 
    4628 > style sel stick
    4629 
    4630 Changed 6 atom styles 
    4631 
    4632 > select #4/R:177
    4633 
    4634 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4635 
    4636 > select #4/R:177
    4637 
    4638 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4639 
    4640 > show sel atoms
    4641 
    4642 > style sel stick
    4643 
    4644 Changed 11 atom styles 
    4645 
    4646 > hide sel atoms
    4647 
    4648 > select #4/R:173
    4649 
    4650 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4651 
    4652 > select #4/R:173
    4653 
    4654 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4655 
    4656 > show sel atoms
    4657 
    4658 > style sel stick
    4659 
    4660 Changed 11 atom styles 
    4661 
    4662 > select #4/R:183
    4663 
    4664 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4665 
    4666 > select #4/R:183
    4667 
    4668 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4669 
    4670 > show sel atoms
    4671 
    4672 > style sel stick
    4673 
    4674 Changed 7 atom styles 
    4675 
    4676 > select #4/R:190
    4677 
    4678 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4679 
    4680 > select #4/R:190
    4681 
    4682 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4683 
    4684 > show sel atoms
    4685 
    4686 > style sel stick
    4687 
    4688 Changed 11 atom styles 
    4689 
    4690 > select #4/R:300
    4691 
    4692 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4693 
    4694 > select #4/R:300
    4695 
    4696 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4697 
    4698 > show sel atoms
    4699 
    4700 > style sel stick
    4701 
    4702 Changed 11 atom styles 
    4703 
    4704 > select #3/A:287
    4705 
    4706 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4707 
    4708 > select #3/A:287
    4709 
    4710 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4711 
    4712 > show sel atoms
    4713 
    4714 > style sel stick
    4715 
    4716 Changed 11 atom styles 
    4717 
    4718 > select #3/A:291
    4719 
    4720 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4721 
    4722 > select #3/A:291
    4723 
    4724 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4725 
    4726 > show sel atoms
    4727 
    4728 > style sel stick
    4729 
    4730 Changed 14 atom styles 
    4731 
    4732 > select #3/A:290
    4733 
    4734 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4735 
    4736 > select #3/A:290
    4737 
    4738 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4739 
    4740 > show sel atoms
    4741 
    4742 > style sel stick
    4743 
    4744 Changed 7 atom styles 
    4745 
    4746 > select #3/A:187
    4747 
    4748 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4749 
    4750 > select #3/A:187
    4751 
    4752 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4753 
    4754 > show sel atoms
    4755 
    4756 > style sel stick
    4757 
    4758 Changed 7 atom styles 
    4759 
    4760 > select #4/R:289
    4761 
    4762 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4763 
    4764 > select #4/R:289
    4765 
    4766 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4767 
    4768 > show sel atoms
    4769 
    4770 > style sel stick
    4771 
    4772 Changed 6 atom styles 
    4773 
    4774 > select #3/A:109
    4775 
    4776 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4777 
    4778 > select #3/A:109
    4779 
    4780 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4781 
    4782 > show sel atoms
    4783 
    4784 > style sel stick
    4785 
    4786 Changed 7 atom styles 
    4787 
    4788 > select #3/A:180
    4789 
    4790 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4791 
    4792 > select #3/A:180
    4793 
    4794 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4795 
    4796 > show sel atoms
    4797 
    4798 > style sel stick
    4799 
    4800 Changed 14 atom styles 
    4801 
    4802 > select #3/A:99
    4803 
    4804 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4805 
    4806 > select #3/A:99
    4807 
    4808 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4809 
    4810 > show sel atoms
    4811 
    4812 > style sel stick
    4813 
    4814 Changed 6 atom styles 
    4815 
    4816 > select #3/A:178
    4817 
    4818 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4819 
    4820 > select #3/A:178
    4821 
    4822 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4823 
    4824 > select #3/A:105
    4825 
    4826 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4827 
    4828 > select #3/A:105
    4829 
    4830 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4831 
    4832 > select #4/R:179
    4833 
    4834 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4835 
    4836 > select #4/R:179
    4837 
    4838 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4839 
    4840 > select #4/R:175
    4841 
    4842 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4843 
    4844 > select #4/R:175
    4845 
    4846 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4847 
    4848 > select #4/R:179-180
    4849 
    4850 18 atoms, 19 bonds, 2 residues, 1 model selected 
    4851 
    4852 > select #4/R:179-181
    4853 
    4854 22 atoms, 23 bonds, 3 residues, 1 model selected 
    4855 
    4856 > select #4/R:190
    4857 
    4858 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4859 
    4860 > select #4/R:190
    4861 
    4862 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4863 
    4864 > select #4/R:309
    4865 
    4866 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4867 
    4868 > select #4/R:273-309
    4869 
    4870 315 atoms, 326 bonds, 37 residues, 1 model selected 
    4871 
    4872 > select
    4873 > #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
    4874 
    4875 1983 atoms, 2034 bonds, 244 residues, 1 model selected 
    4876 
    4877 > select #4/R:191
    4878 
    4879 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4880 
    4881 > select #4/R:191
    4882 
    4883 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4884 
    4885 > select #4/R:187
    4886 
    4887 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4888 
    4889 > select #4/R:187
    4890 
    4891 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4892 
    4893 > show sel atoms
    4894 
    4895 > style sel stick
    4896 
    4897 Changed 4 atom styles 
    4898 
    4899 > show sel atoms
    4900 
    4901 [Repeated 1 time(s)]
    4902 
    4903 > style sel stick
    4904 
    4905 Changed 4 atom styles 
    4906 
    4907 > color sel byhetero
    4908 
    4909 > select #4/R:188
    4910 
    4911 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4912 
    4913 > select #4/R:188-189
    4914 
    4915 16 atoms, 15 bonds, 2 residues, 1 model selected 
    4916 
    4917 > select #4/R:155-191
    4918 
    4919 309 atoms, 322 bonds, 37 residues, 1 model selected 
    4920 
    4921 > select #4/R:43-191
    4922 
    4923 1185 atoms, 1221 bonds, 149 residues, 1 model selected 
    4924 
    4925 > select #4/R:43
    4926 
    4927 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4928 
    4929 > select #4/R:43
    4930 
    4931 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4932 
    4933 > show sel atoms
    4934 
    4935 > style sel stick
    4936 
    4937 Changed 9 atom styles 
    4938 
    4939 > hide sel atoms
    4940 
    4941 > select #4/R:175
    4942 
    4943 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4944 
    4945 > select #4/R:175
    4946 
    4947 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4948 
    4949 > select #3/A:171
    4950 
    4951 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4952 
    4953 > select #3/A:171-172
    4954 
    4955 11 atoms, 11 bonds, 2 residues, 1 model selected 
    4956 
    4957 > show sel atoms
    4958 
    4959 > style sel stick
    4960 
    4961 Changed 11 atom styles 
    4962 
    4963 > select
    4964 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    4965 
    4966 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    4967 
    4968 > select #3/A:165
    4969 
    4970 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4971 
    4972 > select #3/A:165
    4973 
    4974 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4975 
    4976 > select #3/A:161
    4977 
    4978 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4979 
    4980 > select #3/A:161
    4981 
    4982 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4983 
    4984 > show sel atoms
    4985 
    4986 > style sel stick
    4987 
    4988 Changed 11 atom styles 
    4989 
    4990 > select #3/A:164
    4991 
    4992 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4993 
    4994 > select #3/A:164
    4995 
    4996 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4997 
    4998 > show sel atoms
    4999 
    5000 > style sel stick
    5001 
    5002 Changed 6 atom styles 
    5003 
    5004 > save
    5005 > C:/Users/fbumb/OneDrive/MIPS/papers/GPR_mini_review/Figures/20240206_Figure_2.cxs
    5006 
    5007 ——— End of log from Tue Feb 6 18:08:29 2024 ———
    5008 
    5009 opened ChimeraX session 
    5010 
    5011 > open 8KH4
    5012 
    5013 Summary of feedback from opening 8KH4 fetched from pdb 
    5014 --- 
    5015 note | Fetching compressed mmCIF 8kh4 from http://files.rcsb.org/download/8kh4.cif 
    5016  
    5017 8kh4 title: 
    5018 Cryo-EM structure of the GPR161-Gs complex [more info...] 
    5019  
    5020 Chain information for 8kh4 #5 
    5021 --- 
    5022 Chain | Description | UniProt 
    5023 A | G-protein coupled receptor 161 | GP161_HUMAN 2-348 
    5024 B | Guanine nucleotide-binding protein G(olf) subunit alpha,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAL_HUMAN 5-195, GNAS2_HUMAN 204-394 
    5025 C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    5026 D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    5027 E | Nanobody 35 |   
    5028  
    5029 Non-standard residues in 8kh4 #5 
    5030 --- 
    5031 CLR — cholesterol 
    5032  
    5033 
    5034 > select #5/A
    5035 
    5036 2076 atoms, 2142 bonds, 1 pseudobond, 267 residues, 2 models selected 
    5037 
    5038 > cartoon (#!5 & sel)
    5039 
    5040 > surface hidePatches (#!5 & sel)
    5041 
    5042 > select add #5
    5043 
    5044 7511 atoms, 7684 bonds, 2 pseudobonds, 1002 residues, 2 models selected 
    5045 
    5046 > select subtract #5
    5047 
    5048 Nothing selected 
    5049 
    5050 > select add #5
    5051 
    5052 7511 atoms, 7684 bonds, 2 pseudobonds, 1002 residues, 2 models selected 
    5053 
    5054 > cartoon (#!5 & sel)
    5055 
    5056 > hide (#!5 & sel) target a
    5057 
    5058 > surface hidePatches (#!5 & sel)
    5059 
    5060 > select #5/E
    5061 
    5062 936 atoms, 958 bonds, 127 residues, 1 model selected 
    5063 
    5064 > cartoon hide sel
    5065 
    5066 > select #5/D
    5067 
    5068 265 atoms, 267 bonds, 44 residues, 1 model selected 
    5069 
    5070 > select #5/C
    5071 
    5072 2425 atoms, 2471 bonds, 336 residues, 1 model selected 
    5073 
    5074 > cartoon hide sel
    5075 
    5076 > select #5/D
    5077 
    5078 265 atoms, 267 bonds, 44 residues, 1 model selected 
    5079 
    5080 > cartoon hide sel
    5081 
    5082 > select #5/B
    5083 
    5084 1809 atoms, 1846 bonds, 1 pseudobond, 228 residues, 2 models selected 
    5085 
    5086 > cartoon hide (#!5 & sel)
    5087 
    5088 > tile columns 2
    5089 
    5090 5 models tiled 
    5091 
    5092 > tile columns 1
    5093 
    5094 5 models tiled 
    5095 
    5096 > tile rows 1
    5097 
    5098 Expected a models specifier or a keyword 
    5099 
    5100 > tile rows 0
    5101 
    5102 Expected a models specifier or a keyword 
    5103 
    5104 > tile columns 0
    5105 
    5106 Traceback (most recent call last): 
    5107 File
    5108 "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5109 packages/chimerax/cmd_line/tool.py", line 319, in execute 
    5110 cmd.run(cmd_text) 
    5111 File
    5112 "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5113 packages/chimerax/core/commands/cli.py", line 2908, in run 
    5114 result = ci.function(session, **kw_args) 
    5115 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    5116 File
    5117 "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5118 packages/chimerax/std_commands/tile.py", line 32, in tile 
    5119 row, col = divmod(i, columns) 
    5120 ^^^^^^^^^^^^^^^^^^ 
    5121 ZeroDivisionError: integer division or modulo by zero 
    5122  
    5123 ZeroDivisionError: integer division or modulo by zero 
    5124  
    5125 File
    5126 "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5127 packages/chimerax/std_commands/tile.py", line 32, in tile 
    5128 row, col = divmod(i, columns) 
    5129 ^^^^^^^^^^^^^^^^^^ 
    5130  
    5131 See log for complete Python traceback. 
    5132  
    5133 
    5134 > tile columns 1
    5135 
    5136 5 models tiled 
    5137 
    5138 > tile columns 2
    5139 
    5140 5 models tiled 
    5141 
    5142 > tile columns 3
    5143 
    5144 5 models tiled 
    5145 
    5146 > tile columns 5
    5147 
    5148 5 models tiled 
    5149 
    5150 > ui tool show Matchmaker
    5151 
    5152 > matchmaker #!2 to #1
    5153 
    5154 Parameters 
    5155 --- 
    5156 Chain pairing | bb 
    5157 Alignment algorithm | Needleman-Wunsch 
    5158 Similarity matrix | BLOSUM-62 
    5159 SS fraction | 0.3 
    5160 Gap open (HH/SS/other) | 18/18/6 
    5161 Gap extend | 1 
    5162 SS matrix |  |  | H | S | O 
    5163 ---|---|---|--- 
    5164 H | 6 | -9 | -6 
    5165 S |  | 6 | -6 
    5166 O |  |  | 4 
    5167 Iteration cutoff | 2 
    5168  
    5169 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR17_7y89.pdb, chain A (#2),
    5170 sequence alignment score = 311.8 
    5171 RMSD between 118 pruned atom pairs is 1.154 angstroms; (across all 256 pairs:
    5172 5.669) 
    5173  
    5174 
    5175 > matchmaker #!3 to #1
    5176 
    5177 Parameters 
    5178 --- 
    5179 Chain pairing | bb 
    5180 Alignment algorithm | Needleman-Wunsch 
    5181 Similarity matrix | BLOSUM-62 
    5182 SS fraction | 0.3 
    5183 Gap open (HH/SS/other) | 18/18/6 
    5184 Gap extend | 1 
    5185 SS matrix |  |  | H | S | O 
    5186 ---|---|---|--- 
    5187 H | 6 | -9 | -6 
    5188 S |  | 6 | -6 
    5189 O |  |  | 4 
    5190 Iteration cutoff | 2 
    5191  
    5192 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR21_8hmv.pdb, chain A (#3),
    5193 sequence alignment score = 398.2 
    5194 RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 255 pairs:
    5195 4.042) 
    5196  
    5197 
    5198 > matchmaker #!4 to #1
    5199 
    5200 Parameters 
    5201 --- 
    5202 Chain pairing | bb 
    5203 Alignment algorithm | Needleman-Wunsch 
    5204 Similarity matrix | BLOSUM-62 
    5205 SS fraction | 0.3 
    5206 Gap open (HH/SS/other) | 18/18/6 
    5207 Gap extend | 1 
    5208 SS matrix |  |  | H | S | O 
    5209 ---|---|---|--- 
    5210 H | 6 | -9 | -6 
    5211 S |  | 6 | -6 
    5212 O |  |  | 4 
    5213 Iteration cutoff | 2 
    5214  
    5215 Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
    5216 sequence alignment score = 369.8 
    5217 RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
    5218 5.085) 
    5219  
    5220 
    5221 > matchmaker #!5 to #1
    5222 
    5223 Parameters 
    5224 --- 
    5225 Chain pairing | bb 
    5226 Alignment algorithm | Needleman-Wunsch 
    5227 Similarity matrix | BLOSUM-62 
    5228 SS fraction | 0.3 
    5229 Gap open (HH/SS/other) | 18/18/6 
    5230 Gap extend | 1 
    5231 SS matrix |  |  | H | S | O 
    5232 ---|---|---|--- 
    5233 H | 6 | -9 | -6 
    5234 S |  | 6 | -6 
    5235 O |  |  | 4 
    5236 Iteration cutoff | 2 
    5237  
    5238 Matchmaker GPR12_Gs.pdb, chain R (#1) with 8kh4, chain A (#5), sequence
    5239 alignment score = 317.9 
    5240 RMSD between 99 pruned atom pairs is 1.217 angstroms; (across all 248 pairs:
    5241 4.726) 
    5242  
    5243 
    5244 > matchmaker #!5 to #1
    5245 
    5246 Parameters 
    5247 --- 
    5248 Chain pairing | bb 
    5249 Alignment algorithm | Needleman-Wunsch 
    5250 Similarity matrix | BLOSUM-62 
    5251 SS fraction | 0.3 
    5252 Gap open (HH/SS/other) | 18/18/6 
    5253 Gap extend | 1 
    5254 SS matrix |  |  | H | S | O 
    5255 ---|---|---|--- 
    5256 H | 6 | -9 | -6 
    5257 S |  | 6 | -6 
    5258 O |  |  | 4 
    5259 Iteration cutoff | 2 
    5260  
    5261 Matchmaker GPR12_Gs.pdb, chain R (#1) with 8kh4, chain A (#5), sequence
    5262 alignment score = 317.9 
    5263 RMSD between 99 pruned atom pairs is 1.217 angstroms; (across all 248 pairs:
    5264 4.726) 
    5265  
    5266 
    5267 > tile columns 5
    5268 
    5269 5 models tiled 
    5270 
    5271 > color #5 #9437ffff
    5272 
    5273 > color #5 #941751ff
    5274 
    5275 > color #5 #945200ff
    5276 
    5277 > color #5 #ff9300ff
    5278 
    5279 > color #5 #e03d2cff
    5280 
    5281 > ui tool show "Show Sequence Viewer"
    5282 
    5283 > sequence chain #5/A
    5284 
    5285 Alignment identifier is 5/A 
    5286 
    5287 > select #5/A:121
    5288 
    5289 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5290 
    5291 > select #5/A:121-129
    5292 
    5293 76 atoms, 77 bonds, 9 residues, 1 model selected 
    5294 
    5295 > select #5/A:129
    5296 
    5297 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5298 
    5299 > select #5/A:121-129
    5300 
    5301 76 atoms, 77 bonds, 9 residues, 1 model selected 
    5302 
    5303 > ui mousemode right select
    5304 
    5305 > select clear
    5306 
    5307 > select #5/A:156
    5308 
    5309 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5310 
    5311 > select #5/A:154-156
    5312 
    5313 24 atoms, 24 bonds, 3 residues, 1 model selected 
    5314 
    5315 > select #5/A:27-91,96-131,134-165,185-219,267-297,302-338
    5316 
    5317 1805 atoms, 1852 bonds, 236 residues, 1 model selected 
    5318 
    5319 > select #5/A:169-172,177-180
    5320 
    5321 61 atoms, 60 bonds, 8 residues, 1 model selected 
    5322 
    5323 > select #5/A:166
    5324 
    5325 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5326 
    5327 > select #5/A:166-184
    5328 
    5329 157 atoms, 163 bonds, 19 residues, 1 model selected 
    5330 
    5331 > color sel cyan
    5332 
    5333 Drag select of 13 residues 
    5334 
    5335 > select clear
    5336 
    5337 [Repeated 1 time(s)]
    5338 
    5339 > ui mousemode right rotate
    5340 
    5341 > ui mousemode right "translate selected models"
    5342 
    5343 > ui mousemode right zoom
    5344 
    5345 > ui mousemode right translate
    5346 
    5347 > ui mousemode right rotate
    5348 
    5349 > tile spacingFactor 0.5 columns 5
    5350 
    5351 5 models tiled 
    5352 
    5353 > tile spacingFactor 0.4 columns 5
    5354 
    5355 5 models tiled 
    5356 
    5357 > tile spacingFactor 0.7 columns 5
    5358 
    5359 5 models tiled 
    5360 
    5361 > ui mousemode right translate
    5362 
    5363 > ui tool show "Show Sequence Viewer"
    5364 
    5365 > sequence chain #5/A
    5366 
    5367 Alignment identifier is 5/A 
    5368 
    5369 > select #5/A:169-172,177-180
    5370 
    5371 61 atoms, 60 bonds, 8 residues, 1 model selected 
    5372 
    5373 > select #5/A:27-91,96-131,134-165,185-219,267-297,302-338
    5374 
    5375 1805 atoms, 1852 bonds, 236 residues, 1 model selected 
    5376 
    5377 > select #5/A:169-172,177-180
    5378 
    5379 61 atoms, 60 bonds, 8 residues, 1 model selected 
    5380 
    5381 > select sequence 178
    5382 
    5383 Nothing selected 
    5384 
    5385 > select sequence C178
    5386 
    5387 Nothing selected 
    5388 
    5389 > select sequence C178
    5390 
    5391 Nothing selected 
    5392 
    5393 > select sequence C
    5394 
    5395 442 atoms, 375 bonds, 74 residues, 5 models selected 
    5396 
    5397 > help help:user/findseq.html
    5398 
    5399 > ui mousemode right select
    5400 
    5401 > select clear
    5402 
    5403 > select #5/A:169-172,177-180
    5404 
    5405 61 atoms, 60 bonds, 8 residues, 1 model selected 
    5406 
    5407 > select #5/A:174-175
    5408 
    5409 20 atoms, 20 bonds, 2 residues, 1 model selected 
    5410 
    5411 > select #5/A:174-178
    5412 
    5413 48 atoms, 50 bonds, 5 residues, 1 model selected 
    5414 
    5415 > select #5/A:181-182
    5416 
    5417 19 atoms, 20 bonds, 2 residues, 1 model selected 
    5418 
    5419 > select #5/A:174-182
    5420 
    5421 79 atoms, 83 bonds, 9 residues, 1 model selected 
    5422 
    5423 > select #5/A:178
    5424 
    5425 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5426 
    5427 > select #5/A:178
    5428 
    5429 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5430 
    5431 > show sel target ab
    5432 
    5433 > hide sel target a
    5434 
    5435 > show (sel-residues & sidechain) target ab
    5436 
    5437 > style sel stick
    5438 
    5439 Changed 6 atom styles 
    5440 
    5441 > color sel byelement
    5442 
    5443 > select clear
    5444 
    5445 [Repeated 1 time(s)]
    5446 
    5447 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/Fig2 with 161.aln"
    5448 
    5449 > color #5 #ff2600ff
    5450 
    5451 Drag select of 19 residues 
    5452 
    5453 > select clear
    5454 
    5455 [Repeated 1 time(s)]
    5456 
    5457 > ui mousemode right zoom
    5458 
    5459 > ui mousemode right rotate
    5460 
    5461 > ui mousemode right zoom
    5462 
    5463 > ui mousemode right rotate
    5464 
    5465 > ui mousemode right translate
    5466 
    5467 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5468 QFlags(NoModifier) 
    5469 
    5470 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5471 QFlags(ShiftModifier) 
    5472 
    5473 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5474 QFlags(ControlModifier) 
    5475 
    5476 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5477 QFlags(ShiftModifier|ControlModifier) 
    5478 
    5479 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5480 QFlags(AltModifier) 
    5481 
    5482 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5483 QFlags(ShiftModifier|AltModifier) 
    5484 
    5485 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5486 QFlags(ControlModifier|AltModifier) 
    5487 
    5488 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5489 QFlags(ShiftModifier|ControlModifier|AltModifier) 
    5490 
    5491 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5492 QFlags(MetaModifier) 
    5493 
    5494 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5495 QFlags(ShiftModifier|MetaModifier) 
    5496 
    5497 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5498 QFlags(ControlModifier|MetaModifier) 
    5499 
    5500 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5501 QFlags(ShiftModifier|ControlModifier|MetaModifier) 
    5502 
    5503 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5504 QFlags(AltModifier|MetaModifier) 
    5505 
    5506 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5507 QFlags(ShiftModifier|AltModifier|MetaModifier) 
    5508 
    5509 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5510 QFlags(ControlModifier|AltModifier|MetaModifier) 
    5511 
    5512 Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
    5513 QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) 
    5514 
    5515 > tile spacingFactor 0.8 columns 5
    5516 
    5517 5 models tiled 
    5518 
    5519 > ui mousemode right zoom
    5520 
    5521 > ui mousemode right translate
    5522 
    5523 > ui mousemode right "translate selected models"
    5524 
    5525 > ui mousemode right rotate
    5526 
    5527 > ui mousemode right translate
    5528 
    5529 [Repeated 1 time(s)]
    5530 
    5531 > ui mousemode right zoom
    5532 
    5533 > ui mousemode right translate
    5534 
    5535 > select #5/A:169-172,177-180
    5536 
    5537 61 atoms, 60 bonds, 8 residues, 1 model selected 
    5538 
    5539 > select #5/A:180
    5540 
    5541 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5542 
    5543 > select #5/A:172-180
    5544 
    5545 73 atoms, 75 bonds, 9 residues, 1 model selected 
    5546 
    5547 > select #5/A:166-167
    5548 
    5549 11 atoms, 10 bonds, 2 residues, 1 model selected 
    5550 
    5551 > select #5/A:166-184
    5552 
    5553 157 atoms, 163 bonds, 19 residues, 1 model selected 
    5554 
    5555 > color sel cyan
    5556 
    5557 > select #5/A:178
    5558 
    5559 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5560 
    5561 > select #5/A:178
    5562 
    5563 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5564 
    5565 > style sel stick
    5566 
    5567 Changed 6 atom styles 
    5568 
    5569 > show sel target ab
    5570 
    5571 > color sel byelement
    5572 
    5573 > ui mousemode right select
    5574 
    5575 > select clear
    5576 
    5577 > select #5/A:182-183
    5578 
    5579 24 atoms, 26 bonds, 2 residues, 1 model selected 
    5580 
    5581 > select #5/A:183
    5582 
    5583 10 atoms, 10 bonds, 1 residue, 1 model selected 
    5584 
    5585 > select #5/A:182-183
    5586 
    5587 24 atoms, 26 bonds, 2 residues, 1 model selected 
    5588 
    5589 > select #5/A:182-183
    5590 
    5591 24 atoms, 26 bonds, 2 residues, 1 model selected 
    5592 
    5593 > select #5/A:182
    5594 
    5595 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5596 
    5597 > show sel target ab
    5598 
    5599 > style sel stick
    5600 
    5601 Changed 14 atom styles 
    5602 
    5603 > color sel byelement
    5604 
    5605 > select clear
    5606 
    5607 [Repeated 1 time(s)]Drag select of 3 residues 
    5608 
    5609 > select clear
    5610 
    5611 [Repeated 1 time(s)]
    5612 
    5613 > select #5/A:182
    5614 
    5615 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5616 
    5617 > color sel light sea green
    5618 
    5619 > color sel cyan
    5620 
    5621 > color sel byhetero
    5622 
    5623 > select clear
    5624 
    5625 > select #5/A:178
    5626 
    5627 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5628 
    5629 > select #5/A:178
    5630 
    5631 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5632 
    5633 > select #5/A:182
    5634 
    5635 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5636 
    5637 > select #5/A:182
    5638 
    5639 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5640 
    5641 > select #5/A:178
    5642 
    5643 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5644 
    5645 > select #5/A:178
    5646 
    5647 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5648 
    5649 > color sel byhetero
    5650 
    5651 > select clear
    5652 
    5653 Drag select of 10 residues 
    5654 
    5655 > select clear
    5656 
    5657 [Repeated 1 time(s)]
    5658 
    5659 > ui mousemode right translate
    5660 
    5661 > ui mousemode right "translate selected models"
    5662 
    5663 > select #5/A:178
    5664 
    5665 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5666 
    5667 > color sel cyan
    5668 
    5669 > color sel byhetero
    5670 
    5671 > ui mousemode right select
    5672 
    5673 > select clear
    5674 
    5675 > select #5/A:189
    5676 
    5677 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5678 
    5679 > select #5/A:189
    5680 
    5681 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5682 
    5683 > show sel target ab
    5684 
    5685 > style sel stick
    5686 
    5687 Changed 7 atom styles 
    5688 
    5689 > select clear
    5690 
    5691 > select #5/A:189@CB
    5692 
    5693 1 atom, 1 residue, 1 model selected 
    5694 
    5695 > select clear
    5696 
    5697 > ui mousemode right "translate selected models"
    5698 
    5699 > ui mousemode right translate
    5700 
    5701 > color #5 #de723dff
    5702 
    5703 > color #5 #e07139ff
    5704 
    5705 > color #5 #e56c2fff
    5706 
    5707 > color #5 #ea692dff
    5708 
    5709 > select #5/A:166-167
    5710 
    5711 11 atoms, 10 bonds, 2 residues, 1 model selected 
    5712 
    5713 > select #5/A:166-184
    5714 
    5715 157 atoms, 163 bonds, 19 residues, 1 model selected 
    5716 
    5717 > color sel cyan
    5718 
    5719 > select #5/A:178
    5720 
    5721 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5722 
    5723 > show sel target ab
    5724 
    5725 > style sel stick
    5726 
    5727 Changed 6 atom styles 
    5728 
    5729 > color sel byhetero
    5730 
    5731 > select #5/A:189
    5732 
    5733 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5734 
    5735 > select #5/A:189
    5736 
    5737 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5738 
    5739 > show sel target ab
    5740 
    5741 > style sel stick
    5742 
    5743 Changed 7 atom styles 
    5744 
    5745 > color sel forest green
    5746 
    5747 > color sel lime
    5748 
    5749 > color sel medium blue
    5750 
    5751 > color sel byhetero
    5752 
    5753 > select #5/A:182-183
    5754 
    5755 24 atoms, 26 bonds, 2 residues, 1 model selected 
    5756 
    5757 > select #5/A:182-183
    5758 
    5759 24 atoms, 26 bonds, 2 residues, 1 model selected 
    5760 
    5761 > select #5/A:182
    5762 
    5763 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5764 
    5765 > select #5/A:182
    5766 
    5767 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5768 
    5769 > color sel byhetero
    5770 
    5771 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure2_DL/Aligned
    5772 > overall_17_21_52_161.cxs"
    5773 
    5774 > ui mousemode right select
    5775 
    5776 > select clear
    5777 
    5778 > select #5/A:179
    5779 
    5780 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5781 
    5782 > select #5/A:179
    5783 
    5784 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5785 
    5786 > select #5/A:177
    5787 
    5788 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5789 
    5790 > select #5/A:177
    5791 
    5792 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5793 
    5794 > select #5/A:179
    5795 
    5796 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5797 
    5798 > select #5/A:179
    5799 
    5800 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5801 
    5802 > select #5/A:177
    5803 
    5804 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5805 
    5806 > select #5/A:177
    5807 
    5808 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5809 
    5810 > select #5/A:177,179
    5811 
    5812 15 atoms, 13 bonds, 2 residues, 1 model selected 
    5813 
    5814 > show sel target ab
    5815 
    5816 > style sel stick
    5817 
    5818 Changed 15 atom styles 
    5819 
    5820 > color sel byhetero
    5821 
    5822 > select clear
    5823 
    5824 > select #5/A:179
    5825 
    5826 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5827 
    5828 > select #5/A:179
    5829 
    5830 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5831 
    5832 > select clear
    5833 
    5834 [Repeated 4 time(s)]
    5835 
    5836 > ui mousemode right translate
    5837 
    5838 > ui mousemode right zoom
    5839 
    5840 > ui mousemode right translate
    5841 
    5842 > ui mousemode right rotate
    5843 
    5844 [Repeated 1 time(s)]
    5845 
    5846 > ui mousemode right select
    5847 
    5848 > select clear
    5849 
    5850 Drag select of 24 residues 
    5851 
    5852 > select clear
    5853 
    5854 > ui tool show "Side View"
    5855 
    5856 > volume region all imageMode "full region"
    5857 
    5858 No volumes specified 
    5859 
    5860 > view orient
    5861 
    5862 > view
    5863 
    5864 > ui mousemode right translate
    5865 
    5866 > ui mousemode right rotate
    5867 
    5868 > ui mousemode right "translate selected models"
    5869 
    5870 > ui mousemode right translate
    5871 
    5872 > ui mousemode right rotate
    5873 
    5874 > ui mousemode right translate
    5875 
    5876 > ui mousemode right "move planes"
    5877 
    5878 > ui mousemode right "rotate slab"
    5879 
    5880 > ui mousemode right "move planes"
    5881 
    5882 > ui mousemode right rotate
    5883 
    5884 > ui mousemode right "move planes"
    5885 
    5886 > view orient
    5887 
    5888 [Repeated 2 time(s)]
    5889 
    5890 > tile spacingFactor 0.8 columns 5
    5891 
    5892 5 models tiled 
    5893 
    5894 > ui mousemode right translate
    5895 
    5896 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure2_DL/Aligned
    5897 > overall_17_21_52_161.cxs"
    5898 
    5899 ——— End of log from Wed Feb 14 23:29:37 2024 ———
    5900 
    5901 opened ChimeraX session 
    5902 
    5903 > close #1
    5904 
    5905 > close #2
    5906 
    5907 > close #5
    5908 
    5909 > save "/Users/dongju/Desktop/Research projects-
    5910 > Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52.cxs"
    5911 
    5912 > ui tool show "Show Sequence Viewer"
    5913 
    5914 > sequence chain #3/A
    5915 
    5916 Alignment identifier is 3/A 
    5917 
    5918 > sequence chain #4/R
    5919 
    5920 Alignment identifier is 4/R 
    5921 
    5922 > transparency #3 90 ribbons
    5923 
    5924 > lighting soft
    5925 
    5926 > graphics silhouettes false
    5927 
    5928 > lighting simple
    5929 
    5930 > transparency #3 0 ribbons
    5931 
    5932 > ui mousemode right select
    5933 
    5934 > select #3/A:180
    5935 
    5936 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5937 
    5938 > select #3/A:181-182
    5939 
    5940 11 atoms, 10 bonds, 2 residues, 1 model selected 
    5941 
    5942 > select #3/A:181-186
    5943 
    5944 50 atoms, 52 bonds, 6 residues, 1 model selected 
    5945 
    5946 > select #3/A:180
    5947 
    5948 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5949 
    5950 > select #3/A:180-270
    5951 
    5952 654 atoms, 676 bonds, 1 pseudobond, 76 residues, 2 models selected 
    5953 
    5954 > select clear
    5955 
    5956 > select
    5957 > #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
    5958 
    5959 1922 atoms, 1966 bonds, 236 residues, 1 model selected 
    5960 
    5961 > select clear
    5962 
    5963 > select #3/A:180
    5964 
    5965 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5966 
    5967 > select #3/A:180-278
    5968 
    5969 721 atoms, 745 bonds, 1 pseudobond, 84 residues, 2 models selected 
    5970 
    5971 > select clear
    5972 
    5973 [Repeated 1 time(s)]
    5974 
    5975 > select #3/A:164@CB
    5976 
    5977 1 atom, 1 residue, 1 model selected 
    5978 
    5979 > select #3/A:166
    5980 
    5981 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5982 
    5983 > select clear
    5984 
    5985 > select #3/A:166
    5986 
    5987 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5988 
    5989 > select add #3/A:164@CB
    5990 
    5991 12 atoms, 11 bonds, 2 residues, 1 model selected 
    5992 
    5993 > select add #3/A:167
    5994 
    5995 22 atoms, 21 bonds, 3 residues, 1 model selected 
    5996 
    5997 > select add #3/A:168
    5998 
    5999 36 atoms, 36 bonds, 4 residues, 1 model selected 
    6000 
    6001 > select add #3/A:169
    6002 
    6003 40 atoms, 39 bonds, 5 residues, 1 model selected 
    6004 
    6005 > select add #3/A:170
    6006 
    6007 49 atoms, 47 bonds, 6 residues, 1 model selected 
    6008 
    6009 > select add #3/A:171
    6010 
    6011 56 atoms, 54 bonds, 7 residues, 1 model selected 
    6012 
    6013 > select add #3/A:172
    6014 
    6015 60 atoms, 57 bonds, 8 residues, 1 model selected 
    6016 
    6017 > select add #3/A:173
    6018 
    6019 72 atoms, 69 bonds, 9 residues, 1 model selected 
    6020 
    6021 > select add #3/A:174
    6022 
    6023 82 atoms, 79 bonds, 10 residues, 1 model selected 
    6024 
    6025 > select add #3/A:175
    6026 
    6027 86 atoms, 82 bonds, 11 residues, 1 model selected 
    6028 
    6029 > select add #3/A:176
    6030 
    6031 94 atoms, 89 bonds, 12 residues, 1 model selected 
    6032 
    6033 > select add #3/A:177
    6034 
    6035 101 atoms, 95 bonds, 13 residues, 1 model selected 
    6036 
    6037 > select add #3/A:178
    6038 
    6039 112 atoms, 106 bonds, 14 residues, 1 model selected 
    6040 
    6041 > select add #3/A:179
    6042 
    6043 121 atoms, 114 bonds, 15 residues, 1 model selected 
    6044 
    6045 > select add #3/A:180
    6046 
    6047 135 atoms, 129 bonds, 16 residues, 1 model selected 
    6048 
    6049 > select add #3/A:181
    6050 
    6051 141 atoms, 134 bonds, 17 residues, 1 model selected 
    6052 
    6053 > select add #3/A:183
    6054 
    6055 150 atoms, 142 bonds, 18 residues, 1 model selected 
    6056 
    6057 > select add #3/A:184
    6058 
    6059 156 atoms, 147 bonds, 19 residues, 1 model selected 
    6060 
    6061 > select add #3/A:185
    6062 
    6063 170 atoms, 162 bonds, 20 residues, 1 model selected 
    6064 
    6065 > select add #3/A:186
    6066 
    6067 180 atoms, 172 bonds, 21 residues, 1 model selected 
    6068 
    6069 > select add #3/A:187
    6070 
    6071 187 atoms, 178 bonds, 22 residues, 1 model selected 
    6072 
    6073 > select add #3/A:99@CB
    6074 
    6075 188 atoms, 178 bonds, 23 residues, 1 model selected 
    6076 
    6077 > select add #3/A:102
    6078 
    6079 194 atoms, 184 bonds, 24 residues, 1 model selected 
    6080 
    6081 > select add #3/A:105@CB
    6082 
    6083 195 atoms, 184 bonds, 25 residues, 1 model selected 
    6084 
    6085 > select add #3/A:105@CZ
    6086 
    6087 196 atoms, 185 bonds, 25 residues, 1 model selected 
    6088 
    6089 > select add #3/A:161
    6090 
    6091 207 atoms, 196 bonds, 26 residues, 1 model selected 
    6092 
    6093 > select add #3/A:275
    6094 
    6095 216 atoms, 204 bonds, 27 residues, 1 model selected 
    6096 
    6097 > select add #3/A:287
    6098 
    6099 227 atoms, 215 bonds, 28 residues, 1 model selected 
    6100 
    6101 > select add #3/A:290
    6102 
    6103 234 atoms, 221 bonds, 29 residues, 1 model selected 
    6104 
    6105 > select add #3/A:268
    6106 
    6107 246 atoms, 233 bonds, 30 residues, 1 model selected 
    6108 
    6109 > select add #3/A:271
    6110 
    6111 258 atoms, 245 bonds, 31 residues, 1 model selected 
    6112 
    6113 > select add #3/A:291
    6114 
    6115 272 atoms, 260 bonds, 32 residues, 1 model selected 
    6116 
    6117 > select add #3/A:109
    6118 
    6119 279 atoms, 266 bonds, 33 residues, 1 model selected 
    6120 
    6121 > select add #3/A:113
    6122 
    6123 288 atoms, 274 bonds, 34 residues, 1 model selected 
    6124 Drag select of 19 atoms, 21 residues, 16 bonds 
    6125 Drag select of 2 residues 
    6126 
    6127 > select #3/A:173
    6128 
    6129 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6130 Drag select of 9 atoms, 10 residues, 8 bonds 
    6131 
    6132 > select #3/A:166
    6133 
    6134 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6135 
    6136 > select #3/A:167
    6137 
    6138 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6139 
    6140 > select add #3/A:166
    6141 
    6142 21 atoms, 21 bonds, 2 residues, 1 model selected 
    6143 
    6144 > select add #3/A:168
    6145 
    6146 35 atoms, 36 bonds, 3 residues, 1 model selected 
    6147 
    6148 > select add #3/A:169
    6149 
    6150 39 atoms, 39 bonds, 4 residues, 1 model selected 
    6151 
    6152 > select #3/A:170
    6153 
    6154 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6155 
    6156 > select #3/A:170-173
    6157 
    6158 32 atoms, 33 bonds, 4 residues, 1 model selected 
    6159 
    6160 > select #3/A:166
    6161 
    6162 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6163 
    6164 > select #3/A:166-179
    6165 
    6166 120 atoms, 127 bonds, 14 residues, 1 model selected 
    6167 
    6168 > select #3/A:180
    6169 
    6170 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6171 
    6172 > select #3/A:180-187
    6173 
    6174 71 atoms, 75 bonds, 8 residues, 1 model selected 
    6175 
    6176 > select #3/A:180-201
    6177 
    6178 190 atoms, 198 bonds, 22 residues, 1 model selected 
    6179 
    6180 > select #3/A:180-201
    6181 
    6182 190 atoms, 198 bonds, 22 residues, 1 model selected 
    6183 
    6184 > select #3/A:180-201
    6185 
    6186 190 atoms, 198 bonds, 22 residues, 1 model selected 
    6187 
    6188 > select #3/A:201
    6189 
    6190 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6191 
    6192 > select #3/A:188-201
    6193 
    6194 119 atoms, 122 bonds, 14 residues, 1 model selected 
    6195 
    6196 > select #3/A:165-166
    6197 
    6198 22 atoms, 23 bonds, 2 residues, 1 model selected 
    6199 
    6200 > select #3/A:166-187
    6201 
    6202 191 atoms, 203 bonds, 22 residues, 1 model selected 
    6203 
    6204 > name frozen ECL2 sel
    6205 
    6206 > select clear
    6207 
    6208 > select ECL2
    6209 
    6210 191 atoms, 203 bonds, 22 residues, 1 model selected 
    6211 
    6212 > name frozen GPR21_ECL2 sel
    6213 
    6214 > select clear
    6215 
    6216 Drag select of 2 atoms, 5 residues, 1 bonds 
    6217 
    6218 > select clear
    6219 
    6220 [Repeated 1 time(s)]
    6221 
    6222 > select #3/A:164
    6223 
    6224 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6225 
    6226 > select #3/A:161
    6227 
    6228 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6229 
    6230 > select add #3/A:164
    6231 
    6232 17 atoms, 16 bonds, 2 residues, 1 model selected 
    6233 
    6234 > select add #3/A:268
    6235 
    6236 29 atoms, 28 bonds, 3 residues, 1 model selected 
    6237 
    6238 > select add #3/A:272
    6239 
    6240 40 atoms, 39 bonds, 4 residues, 1 model selected 
    6241 
    6242 > select add #3/A:271
    6243 
    6244 52 atoms, 51 bonds, 5 residues, 1 model selected 
    6245 
    6246 > select add #3/A:275
    6247 
    6248 61 atoms, 59 bonds, 6 residues, 1 model selected 
    6249 
    6250 > select add #3/A:276
    6251 
    6252 67 atoms, 64 bonds, 7 residues, 1 model selected 
    6253 
    6254 > select add #3/A:110
    6255 
    6256 73 atoms, 69 bonds, 8 residues, 1 model selected 
    6257 Drag select of 1 atoms, 3 residues, 1 bonds 
    6258 Drag select of 3 residues 
    6259 
    6260 > select clear
    6261 
    6262 [Repeated 3 time(s)]
    6263 
    6264 > select #3/A:164
    6265 
    6266 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6267 
    6268 > select add #3/A:276
    6269 
    6270 12 atoms, 10 bonds, 2 residues, 1 model selected 
    6271 
    6272 > select add #3/A:275
    6273 
    6274 21 atoms, 18 bonds, 3 residues, 1 model selected 
    6275 
    6276 > select add #3/A:272
    6277 
    6278 32 atoms, 29 bonds, 4 residues, 1 model selected 
    6279 
    6280 > select add #3/A:271
    6281 
    6282 44 atoms, 41 bonds, 5 residues, 1 model selected 
    6283 
    6284 > select add #3/A:105
    6285 
    6286 55 atoms, 52 bonds, 6 residues, 1 model selected 
    6287 
    6288 > select add #3/A:99
    6289 
    6290 61 atoms, 57 bonds, 7 residues, 1 model selected 
    6291 
    6292 > select add #3/A:290
    6293 
    6294 68 atoms, 63 bonds, 8 residues, 1 model selected 
    6295 
    6296 > select add #3/A:110
    6297 
    6298 74 atoms, 68 bonds, 9 residues, 1 model selected 
    6299 
    6300 > select add #3/A:287
    6301 
    6302 85 atoms, 79 bonds, 10 residues, 1 model selected 
    6303 
    6304 > select add #3/A:161@CA
    6305 
    6306 86 atoms, 79 bonds, 11 residues, 1 model selected 
    6307 
    6308 > select subtract #3/A:161
    6309 
    6310 85 atoms, 79 bonds, 10 residues, 1 model selected 
    6311 
    6312 > select add #3/A:161
    6313 
    6314 96 atoms, 90 bonds, 11 residues, 1 model selected 
    6315 
    6316 > select add #3/A:109
    6317 
    6318 103 atoms, 96 bonds, 12 residues, 1 model selected 
    6319 
    6320 > select add #3/A:291
    6321 
    6322 117 atoms, 111 bonds, 13 residues, 1 model selected 
    6323 
    6324 > select add #3/A:268
    6325 
    6326 129 atoms, 123 bonds, 14 residues, 1 model selected 
    6327 
    6328 > select add #3/A:113
    6329 
    6330 138 atoms, 131 bonds, 15 residues, 1 model selected 
    6331 
    6332 > select add #3/A:102
    6333 
    6334 144 atoms, 136 bonds, 16 residues, 1 model selected 
    6335 
    6336 > name frozen "GPR21_binding sites" sel
    6337 
    6338 Not registering illegal selector name "GPR21_binding sites" 
    6339 
    6340 > name frozen "GPR21_binding sites" sel
    6341 
    6342 Not registering illegal selector name "GPR21_binding sites" 
    6343 
    6344 > name frozen GPR21_BS sel
    6345 
    6346 [Repeated 1 time(s)]
    6347 
    6348 > select GPR21_ECL2
    6349 
    6350 191 atoms, 203 bonds, 22 residues, 1 model selected 
    6351 
    6352 > transparency #3 90 ribbons
    6353 
    6354 > select ECL2
    6355 
    6356 191 atoms, 203 bonds, 22 residues, 1 model selected 
    6357 
    6358 > transparency #3:select 0 ribbons
    6359 
    6360 > transparency #3:select/ 0 ribbons
    6361 
    6362 Missing or invalid "percent" argument: Expected a number 
    6363 
    6364 > transparency #3:select 0 ribbons
    6365 
    6366 [Repeated 1 time(s)]
    6367 
    6368 > select GPR21_BS
    6369 
    6370 144 atoms, 140 bonds, 16 residues, 1 model selected 
    6371 
    6372 > transparency #3:select 0 ribbons
    6373 
    6374 > transparency #3:select/R 0 ribbons
    6375 
    6376 > transparency #3:select/ 0 ribbons
    6377 
    6378 Missing or invalid "percent" argument: Expected a number 
    6379 
    6380 > transparency #3:select 0 ribbons
    6381 
    6382 > transparency #3:select 70 ribbons
    6383 
    6384 > transparency #3:select 0 ribbons
    6385 
    6386 > transparency #3 0 ribbons
    6387 
    6388 > transparency #3/select 90 ribbons
    6389 
    6390 > transparency #3:select 90 ribbons
    6391 
    6392 [Repeated 1 time(s)]
    6393 
    6394 > select #3/A:37
    6395 
    6396 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6397 
    6398 > transparency #3:select 90 ribbons
    6399 
    6400 > select GPR21_BS
    6401 
    6402 144 atoms, 140 bonds, 16 residues, 1 model selected 
    6403 
    6404 > transparency select 90 ribbons
    6405 
    6406 Missing or invalid "percent" argument: Expected a number 
    6407 
    6408 > transparency #3:GPR21_BS GPR21_ECL2 90 ribbons
    6409 
    6410 Missing or invalid "percent" argument: Expected a number 
    6411 
    6412 > transparency #3:GPR21_BS/GPR21_ECL2 90 ribbons
    6413 
    6414 > transparency #3:select/GPR21_BS/GPR21_ECL2 90 ribbons
    6415 
    6416 > transparency select/ 90 ribbons
    6417 
    6418 Missing or invalid "percent" argument: Expected a number 
    6419 
    6420 > transparency select/ 90 ribbon
    6421 
    6422 Missing or invalid "percent" argument: Expected a number 
    6423 
    6424 > transparency #select/ 90 ribbon
    6425 
    6426 Missing or invalid "percent" argument: Expected a number 
    6427 
    6428 > transparency #select 90 ribbon
    6429 
    6430 Missing or invalid "percent" argument: Expected a number 
    6431 
    6432 > transparency #3:select 90 ribbons
    6433 
    6434 > transparency #3:select/ 90 ribbon
    6435 
    6436 Missing or invalid "percent" argument: Expected a number 
    6437 
    6438 > transparency #3:select> 90 ribbon
    6439 
    6440 Missing or invalid "percent" argument: Expected a number 
    6441 
    6442 > transparency #3:select transparency #3: transparency #3:>select 90 ribbon
    6443 
    6444 Missing or invalid "percent" argument: Expected a number 
    6445 
    6446 > transparency  90 ribbon
    6447 
    6448 Missing or invalid "percent" argument: Expected a number 
    6449 
    6450 > transparency  transparency select> 90 ribbon
    6451 
    6452 Missing or invalid "percent" argument: Expected a number 
    6453 
    6454 > transparency ~select 90 ribbon
    6455 
    6456 Missing or invalid "percent" argument: Expected a number 
    6457 
    6458 > transparency #3:~select 90 ribbon
    6459 
    6460 Missing or invalid "percent" argument: Expected a number 
    6461 
    6462 > transparency #3:~select/ 90 ribbon
    6463 
    6464 Missing or invalid "percent" argument: Expected a number 
    6465 
    6466 > transparency #3~select 90 ribbon
    6467 
    6468 Missing or invalid "percent" argument: Expected a number 
    6469 
    6470 > transparency ~select 90 ribbon
    6471 
    6472 Missing or invalid "percent" argument: Expected a number 
    6473 
    6474 > transparency ~select/ 90 ribbon
    6475 
    6476 Missing or invalid "percent" argument: Expected a number 
    6477 
    6478 > transparency ~select 90 ribbon
    6479 
    6480 Missing or invalid "percent" argument: Expected a number 
    6481 
    6482 > transparency #3~select 90 ribbon
    6483 
    6484 Missing or invalid "percent" argument: Expected a number 
    6485 
    6486 > transparency ~select 90 ribbon
    6487 
    6488 Missing or invalid "percent" argument: Expected a number 
    6489 
    6490 > transparency [~select] 90 ribbon
    6491 
    6492 Missing or invalid "percent" argument: Expected a number 
    6493 
    6494 > transparency #3:~select 90 ribbon
    6495 
    6496 Missing or invalid "percent" argument: Expected a number 
    6497 
    6498 > transparency #3:~select/ 90 ribbon
    6499 
    6500 Missing or invalid "percent" argument: Expected a number 
    6501 
    6502 > transparency ~sele 90 ribbon
    6503 
    6504 Missing or invalid "percent" argument: Expected a number 
    6505 
    6506 > transparency ~select 90 all
    6507 
    6508 Missing or invalid "percent" argument: Expected a number 
    6509 
    6510 > transparency #3:~select 90 all
    6511 
    6512 Missing or invalid "percent" argument: Expected a number 
    6513 
    6514 > transparency ~$select 90 ribbons
    6515 
    6516 Missing or invalid "percent" argument: Expected a number 
    6517 
    6518 > transparency $select 90 ribbons
    6519 
    6520 Missing or invalid "percent" argument: Expected a number 
    6521 
    6522 > transparency ~select$ 90 ribbons
    6523 
    6524 Missing or invalid "percent" argument: Expected a number 
    6525 
    6526 > select clear
    6527 
    6528 > select #3/A:216
    6529 
    6530 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6531 
    6532 > select add #3/A:220
    6533 
    6534 20 atoms, 18 bonds, 2 residues, 1 model selected 
    6535 
    6536 > color sel red
    6537 
    6538 > select clear
    6539 
    6540 > select GPR21_ECL2
    6541 
    6542 191 atoms, 203 bonds, 22 residues, 1 model selected 
    6543 
    6544 > transparency sel 90 All
    6545 
    6546 > transparency sel 0 All
    6547 
    6548 > select #3/A:216
    6549 
    6550 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6551 
    6552 > select add #3/A:220
    6553 
    6554 20 atoms, 18 bonds, 2 residues, 1 model selected 
    6555 
    6556 > color sel cornflower blue
    6557 
    6558 > select clear
    6559 
    6560 > select #3/A:216
    6561 
    6562 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6563 
    6564 > select add #3/A:220
    6565 
    6566 20 atoms, 18 bonds, 2 residues, 1 model selected 
    6567 
    6568 > color sel #5780ffff
    6569 
    6570 > select clear
    6571 
    6572 > transparency #3 90 ribbons
    6573 
    6574 > select GPR21_BS
    6575 
    6576 144 atoms, 140 bonds, 16 residues, 1 model selected 
    6577 
    6578 > transparency sel 0 ribbons
    6579 
    6580 > select GPR21_ECL2
    6581 
    6582 191 atoms, 203 bonds, 22 residues, 1 model selected 
    6583 
    6584 > transparency sel 0 ribbons
    6585 
    6586 > select clear
    6587 
    6588 [Repeated 2 time(s)]Drag select of 4 atoms, 8 residues, 3 bonds 
    6589 
    6590 > select #4/R:179
    6591 
    6592 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6593 
    6594 > select #4/R:179-180
    6595 
    6596 18 atoms, 19 bonds, 2 residues, 1 model selected 
    6597 
    6598 > select #4/R:179-209
    6599 
    6600 248 atoms, 260 bonds, 31 residues, 1 model selected 
    6601 
    6602 > select #4/R:179-209
    6603 
    6604 248 atoms, 260 bonds, 31 residues, 1 model selected 
    6605 
    6606 > select #4/R:179-209
    6607 
    6608 248 atoms, 260 bonds, 31 residues, 1 model selected 
    6609 
    6610 > name frozen GPR52_ECL2 sel
    6611 
    6612 > select clear
    6613 
    6614 > select #4/R:117
    6615 
    6616 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6617 
    6618 > select add #4/R:176
    6619 
    6620 17 atoms, 16 bonds, 2 residues, 1 model selected 
    6621 
    6622 > select add #4/R:173
    6623 
    6624 28 atoms, 27 bonds, 3 residues, 1 model selected 
    6625 
    6626 > select add #4/R:122
    6627 
    6628 34 atoms, 32 bonds, 4 residues, 1 model selected 
    6629 
    6630 > select add #4/R:125
    6631 
    6632 43 atoms, 40 bonds, 5 residues, 1 model selected 
    6633 
    6634 > select add #4/R:121
    6635 
    6636 51 atoms, 47 bonds, 6 residues, 1 model selected 
    6637 
    6638 > select add #4/R:284
    6639 
    6640 63 atoms, 59 bonds, 7 residues, 1 model selected 
    6641 
    6642 > select add #4/R:281
    6643 
    6644 75 atoms, 71 bonds, 8 residues, 1 model selected 
    6645 
    6646 > select add #4/R:305
    6647 
    6648 83 atoms, 79 bonds, 9 residues, 1 model selected 
    6649 
    6650 > select subtract #4/R:305
    6651 
    6652 75 atoms, 72 bonds, 8 residues, 1 model selected 
    6653 
    6654 > select add #4/R:304
    6655 
    6656 89 atoms, 87 bonds, 9 residues, 1 model selected 
    6657 
    6658 > select add #4/R:300
    6659 
    6660 100 atoms, 98 bonds, 10 residues, 1 model selected 
    6661 
    6662 > select add #4/R:288
    6663 
    6664 109 atoms, 106 bonds, 11 residues, 1 model selected 
    6665 
    6666 > select add #4/R:307
    6667 
    6668 117 atoms, 113 bonds, 12 residues, 1 model selected 
    6669 
    6670 > select add #4/R:285
    6671 
    6672 128 atoms, 123 bonds, 13 residues, 1 model selected 
    6673 Drag select of 7 atoms, 5 residues, 6 bonds 
    6674 
    6675 > select add #4/R:111@CA
    6676 
    6677 44 atoms, 6 bonds, 7 residues, 1 model selected 
    6678 
    6679 > select add #4/R:176
    6680 
    6681 50 atoms, 11 bonds, 8 residues, 1 model selected 
    6682 
    6683 > select add #4/R:173
    6684 
    6685 61 atoms, 22 bonds, 9 residues, 1 model selected 
    6686 
    6687 > select add #4/R:125
    6688 
    6689 70 atoms, 30 bonds, 10 residues, 1 model selected 
    6690 
    6691 > select add #4/R:122
    6692 
    6693 76 atoms, 35 bonds, 11 residues, 1 model selected 
    6694 
    6695 > select add #4/R:282
    6696 
    6697 84 atoms, 42 bonds, 12 residues, 1 model selected 
    6698 
    6699 > select subtract #4/R:282
    6700 
    6701 76 atoms, 35 bonds, 11 residues, 1 model selected 
    6702 
    6703 > select add #4/R:281
    6704 
    6705 88 atoms, 47 bonds, 12 residues, 1 model selected 
    6706 
    6707 > select add #4/R:285
    6708 
    6709 99 atoms, 58 bonds, 13 residues, 1 model selected 
    6710 
    6711 > select add #4/R:307@CA
    6712 
    6713 100 atoms, 58 bonds, 14 residues, 1 model selected 
    6714 
    6715 > select subtract #4/R:307@CA
    6716 
    6717 99 atoms, 58 bonds, 13 residues, 1 model selected 
    6718 
    6719 > select add #4/R:307
    6720 
    6721 107 atoms, 65 bonds, 14 residues, 1 model selected 
    6722 
    6723 > select add #4/R:121
    6724 
    6725 115 atoms, 72 bonds, 15 residues, 1 model selected 
    6726 
    6727 > select add #4/R:304
    6728 
    6729 129 atoms, 87 bonds, 16 residues, 1 model selected 
    6730 
    6731 > select add #4/R:300
    6732 
    6733 140 atoms, 98 bonds, 17 residues, 1 model selected 
    6734 
    6735 > select add #4/R:289
    6736 
    6737 146 atoms, 103 bonds, 18 residues, 1 model selected 
    6738 
    6739 > select add #4/R:303
    6740 
    6741 153 atoms, 109 bonds, 19 residues, 1 model selected 
    6742 
    6743 > select add #4/R:284
    6744 
    6745 165 atoms, 121 bonds, 20 residues, 1 model selected 
    6746 
    6747 > name frozen GPR52_BS sel
    6748 
    6749 > transparency #4 90 ribbons
    6750 
    6751 > select GPR52_BS
    6752 
    6753 165 atoms, 161 bonds, 20 residues, 1 model selected 
    6754 
    6755 > transparency sel 0 ribbons
    6756 
    6757 > select GPR52_ECL2
    6758 
    6759 248 atoms, 263 bonds, 31 residues, 1 model selected 
    6760 
    6761 > transparency sel 0 ribbons
    6762 
    6763 > select clear
    6764 
    6765 Drag select of 5 atoms, 26 residues, 4 bonds 
    6766 
    6767 > tile Spaingfactor 2 columns 2
    6768 
    6769 Expected a models specifier or a keyword 
    6770 
    6771 > tile Spaingfactor 80 columns 2
    6772 
    6773 Expected a models specifier or a keyword 
    6774 
    6775 > tile Spaingfactor 0.8 columns 2
    6776 
    6777 Expected a models specifier or a keyword 
    6778 
    6779 > tile spacingFactor 2 columns 2
    6780 
    6781 2 models tiled 
    6782 
    6783 > tile spacingFactor 9 columns 2
    6784 
    6785 2 models tiled 
    6786 
    6787 > tile spacingFactor 0.5 columns 2
    6788 
    6789 2 models tiled 
    6790 
    6791 > tile spacingFactor 0.8 columns 2
    6792 
    6793 2 models tiled 
    6794 
    6795 > select clear
    6796 
    6797 [Repeated 1 time(s)]
    6798 
    6799 > tile spacingFactor 0.7 columns 2
    6800 
    6801 2 models tiled 
    6802 
    6803 > ui tool show Matchmaker
    6804 
    6805 > matchmaker #!4 to #3
    6806 
    6807 Parameters 
    6808 --- 
    6809 Chain pairing | bb 
    6810 Alignment algorithm | Needleman-Wunsch 
    6811 Similarity matrix | BLOSUM-62 
    6812 SS fraction | 0.3 
    6813 Gap open (HH/SS/other) | 18/18/6 
    6814 Gap extend | 1 
    6815 SS matrix |  |  | H | S | O 
    6816 ---|---|---|--- 
    6817 H | 6 | -9 | -6 
    6818 S |  | 6 | -6 
    6819 O |  |  | 4 
    6820 Iteration cutoff | 2 
    6821  
    6822 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    6823 sequence alignment score = 1120.2 
    6824 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    6825 2.619) 
    6826  
    6827 
    6828 > matchmaker #!4 to #3
    6829 
    6830 Parameters 
    6831 --- 
    6832 Chain pairing | bb 
    6833 Alignment algorithm | Needleman-Wunsch 
    6834 Similarity matrix | BLOSUM-62 
    6835 SS fraction | 0.3 
    6836 Gap open (HH/SS/other) | 18/18/6 
    6837 Gap extend | 1 
    6838 SS matrix |  |  | H | S | O 
    6839 ---|---|---|--- 
    6840 H | 6 | -9 | -6 
    6841 S |  | 6 | -6 
    6842 O |  |  | 4 
    6843 Iteration cutoff | 2 
    6844  
    6845 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    6846 sequence alignment score = 1120.2 
    6847 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    6848 2.619) 
    6849  
    6850 Drag select of 7 atoms, 15 residues, 7 bonds 
    6851 
    6852 > select clear
    6853 
    6854 > tile spacingFactor 0.7 columns 2
    6855 
    6856 2 models tiled 
    6857 
    6858 > tile spacingFactor 0.6 columns 2
    6859 
    6860 2 models tiled 
    6861 
    6862 > ui mousemode right zoom
    6863 
    6864 > lighting soft
    6865 
    6866 > lighting simple
    6867 
    6868 > graphics silhouettes true
    6869 
    6870 > graphics silhouettes false
    6871 
    6872 > lighting flat
    6873 
    6874 [Repeated 1 time(s)]
    6875 
    6876 > lighting shadows true intensity 0.5
    6877 
    6878 > lighting flat
    6879 
    6880 [Repeated 1 time(s)]
    6881 
    6882 > lighting shadows true intensity 0.5
    6883 
    6884 > lighting soft
    6885 
    6886 > lighting full
    6887 
    6888 > graphics silhouettes false
    6889 
    6890 > lighting soft
    6891 
    6892 > lighting simple
    6893 
    6894 > lighting full
    6895 
    6896 > lighting soft
    6897 
    6898 > lighting simple
    6899 
    6900 [Repeated 1 time(s)]
    6901 
    6902 > lighting soft
    6903 
    6904 > preset "overall look" interactive
    6905 
    6906 Using preset: Overall Look / Interactive 
    6907 Preset expands to these ChimeraX commands:
    6908 
    6909    
    6910    
    6911     ~set bg
    6912     graphics silhouettes f
    6913     lighting depthCue t
    6914 
    6915  
    6916 
    6917 > preset "overall look" "publication 1 (silhouettes)"
    6918 
    6919 Using preset: Overall Look / Publication 1 (Silhouettes) 
    6920 Preset expands to these ChimeraX commands:
    6921 
    6922    
    6923    
    6924     set bg white
    6925     graphics silhouettes t
    6926     lighting depthCue f
    6927 
    6928  
    6929 
    6930 > preset "overall look" "publication 2 (depth-cued)"
    6931 
    6932 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    6933 Preset expands to these ChimeraX commands:
    6934 
    6935    
    6936    
    6937     set bg white
    6938     graphics silhouettes f
    6939     lighting depthCue t
    6940 
    6941  
    6942 
    6943 > select GPR21_BS
    6944 
    6945 144 atoms, 140 bonds, 16 residues, 1 model selected 
    6946 
    6947 > transparency sel 90 ribbons
    6948 
    6949 > select GPR52_BS
    6950 
    6951 165 atoms, 161 bonds, 20 residues, 1 model selected 
    6952 
    6953 > transparency sel 90 ribbons
    6954 
    6955 > ui mousemode right select
    6956 
    6957 > select clear
    6958 
    6959 > select GPR52_ECL2
    6960 
    6961 248 atoms, 263 bonds, 31 residues, 1 model selected 
    6962 Drag select of 43 atoms, 30 residues, 37 bonds 
    6963 
    6964 > select clear
    6965 
    6966 > select GPR52_ECL2
    6967 
    6968 248 atoms, 263 bonds, 31 residues, 1 model selected 
    6969 
    6970 > select #4/R:114
    6971 
    6972 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6973 
    6974 > select GPR52_ECL2
    6975 
    6976 248 atoms, 263 bonds, 31 residues, 1 model selected 
    6977 
    6978 > select add #4/R:114
    6979 
    6980 254 atoms, 266 bonds, 32 residues, 1 model selected 
    6981 
    6982 > select subtract #4/R:114
    6983 
    6984 248 atoms, 260 bonds, 31 residues, 1 model selected 
    6985 
    6986 > select subtract #4/R:200
    6987 
    6988 242 atoms, 253 bonds, 30 residues, 1 model selected 
    6989 
    6990 > select subtract #4/R:201
    6991 
    6992 237 atoms, 248 bonds, 29 residues, 1 model selected 
    6993 
    6994 > select subtract #4/R:202
    6995 
    6996 225 atoms, 235 bonds, 28 residues, 1 model selected 
    6997 
    6998 > select subtract #4/R:203
    6999 
    7000 214 atoms, 223 bonds, 27 residues, 1 model selected 
    7001 
    7002 > select subtract #4/R:204
    7003 
    7004 207 atoms, 216 bonds, 26 residues, 1 model selected 
    7005 
    7006 > select subtract #4/R:205
    7007 
    7008 203 atoms, 212 bonds, 25 residues, 1 model selected 
    7009 
    7010 > select subtract #4/R:206
    7011 
    7012 192 atoms, 200 bonds, 24 residues, 1 model selected 
    7013 
    7014 > select subtract #4/R:208
    7015 
    7016 185 atoms, 192 bonds, 23 residues, 1 model selected 
    7017 
    7018 > select subtract #4/R:207
    7019 
    7020 177 atoms, 185 bonds, 22 residues, 1 model selected 
    7021 
    7022 > select subtract #4/R:209
    7023 
    7024 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7025 
    7026 > name frozen GPR52_ECL2 sel
    7027 
    7028 > select GPR52_ECL2
    7029 
    7030 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7031 
    7032 > select clear
    7033 
    7034 > select add #4/R:114
    7035 
    7036 6 atoms, 5 bonds, 1 residue, 1 model selected 
    7037 
    7038 > select add #4/R:200
    7039 
    7040 12 atoms, 10 bonds, 2 residues, 1 model selected 
    7041 
    7042 > select add #4/R:201
    7043 
    7044 17 atoms, 14 bonds, 3 residues, 1 model selected 
    7045 
    7046 > select add #4/R:202
    7047 
    7048 29 atoms, 26 bonds, 4 residues, 1 model selected 
    7049 
    7050 > select add #4/R:203
    7051 
    7052 40 atoms, 37 bonds, 5 residues, 1 model selected 
    7053 
    7054 > select add #4/R:204
    7055 
    7056 47 atoms, 43 bonds, 6 residues, 1 model selected 
    7057 
    7058 > select add #4/R:205
    7059 
    7060 51 atoms, 46 bonds, 7 residues, 1 model selected 
    7061 
    7062 > select add #4/R:206
    7063 
    7064 62 atoms, 57 bonds, 8 residues, 1 model selected 
    7065 
    7066 > select add #4/R:207
    7067 
    7068 70 atoms, 64 bonds, 9 residues, 1 model selected 
    7069 
    7070 > select add #4/R:208
    7071 
    7072 77 atoms, 70 bonds, 10 residues, 1 model selected 
    7073 
    7074 > select add #4/R:209
    7075 
    7076 83 atoms, 75 bonds, 11 residues, 1 model selected 
    7077 
    7078 > transparency sel 90 ribbons
    7079 
    7080 > select clear
    7081 
    7082 Drag select of 15 residues 
    7083 
    7084 > select clear
    7085 
    7086 > select add #3
    7087 
    7088 2237 atoms, 2308 bonds, 1 pseudobond, 274 residues, 2 models selected 
    7089 
    7090 > select add #4
    7091 
    7092 4540 atoms, 4684 bonds, 2 pseudobonds, 558 residues, 4 models selected 
    7093 
    7094 > cartoon style (#!3-4 & sel & coil) xsection oval
    7095 
    7096 > cartoon style (#!3-4 & sel) xsection barbell modeHelix default
    7097 
    7098 > cartoon style (#!3-4 & sel) modeHelix tube sides 20
    7099 
    7100 > cartoon style (#!3-4 & sel) xsection rectangle modeHelix default
    7101 
    7102 > cartoon style (#!3-4 & sel) xsection oval modeHelix default
    7103 
    7104 > select clear
    7105 
    7106 > select GPR21_BS
    7107 
    7108 144 atoms, 140 bonds, 16 residues, 1 model selected 
    7109 
    7110 > transparency sel 90 All
    7111 
    7112 > select GPR52_BS
    7113 
    7114 165 atoms, 161 bonds, 20 residues, 1 model selected 
    7115 
    7116 > transparency sel 90 All
    7117 
    7118 > select clear
    7119 
    7120 [Repeated 1 time(s)]
    7121 
    7122 > tile spacingFactor 0.7 columns 2
    7123 
    7124 2 models tiled 
    7125 
    7126 > tile spacingFactor 0.5 columns 2
    7127 
    7128 2 models tiled 
    7129 
    7130 > select clear
    7131 
    7132 > ui tool show Matchmaker
    7133 
    7134 > matchmaker #!4 to #3
    7135 
    7136 Parameters 
    7137 --- 
    7138 Chain pairing | bb 
    7139 Alignment algorithm | Needleman-Wunsch 
    7140 Similarity matrix | BLOSUM-62 
    7141 SS fraction | 0.3 
    7142 Gap open (HH/SS/other) | 18/18/6 
    7143 Gap extend | 1 
    7144 SS matrix |  |  | H | S | O 
    7145 ---|---|---|--- 
    7146 H | 6 | -9 | -6 
    7147 S |  | 6 | -6 
    7148 O |  |  | 4 
    7149 Iteration cutoff | 2 
    7150  
    7151 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    7152 sequence alignment score = 1120.2 
    7153 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    7154 2.619) 
    7155  
    7156 
    7157 > matchmaker #!4 to #3
    7158 
    7159 Parameters 
    7160 --- 
    7161 Chain pairing | bb 
    7162 Alignment algorithm | Needleman-Wunsch 
    7163 Similarity matrix | BLOSUM-62 
    7164 SS fraction | 0.3 
    7165 Gap open (HH/SS/other) | 18/18/6 
    7166 Gap extend | 1 
    7167 SS matrix |  |  | H | S | O 
    7168 ---|---|---|--- 
    7169 H | 6 | -9 | -6 
    7170 S |  | 6 | -6 
    7171 O |  |  | 4 
    7172 Iteration cutoff | 2 
    7173  
    7174 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    7175 sequence alignment score = 1120.2 
    7176 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    7177 2.619) 
    7178  
    7179 
    7180 > select #3/A:205
    7181 
    7182 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7183 
    7184 > select clear
    7185 
    7186 > ui mousemode right translate
    7187 
    7188 > tile spacingFactor 0.5 columns 2
    7189 
    7190 2 models tiled 
    7191 
    7192 > save "/Users/dongju/Desktop/Research projects-
    7193 > Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52.cxs"
    7194 
    7195 ——— End of log from Tue Feb 27 18:06:41 2024 ———
    7196 
    7197 opened ChimeraX session 
    7198 
    7199 > ui tool show Matchmaker
    7200 
    7201 > matchmaker #!4 to #3
    7202 
    7203 Parameters 
    7204 --- 
    7205 Chain pairing | bb 
    7206 Alignment algorithm | Needleman-Wunsch 
    7207 Similarity matrix | BLOSUM-62 
    7208 SS fraction | 0.3 
    7209 Gap open (HH/SS/other) | 18/18/6 
    7210 Gap extend | 1 
    7211 SS matrix |  |  | H | S | O 
    7212 ---|---|---|--- 
    7213 H | 6 | -9 | -6 
    7214 S |  | 6 | -6 
    7215 O |  |  | 4 
    7216 Iteration cutoff | 2 
    7217  
    7218 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    7219 sequence alignment score = 1120.2 
    7220 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    7221 2.619) 
    7222  
    7223 
    7224 > matchmaker #!4 to #3
    7225 
    7226 Parameters 
    7227 --- 
    7228 Chain pairing | bb 
    7229 Alignment algorithm | Needleman-Wunsch 
    7230 Similarity matrix | BLOSUM-62 
    7231 SS fraction | 0.3 
    7232 Gap open (HH/SS/other) | 18/18/6 
    7233 Gap extend | 1 
    7234 SS matrix |  |  | H | S | O 
    7235 ---|---|---|--- 
    7236 H | 6 | -9 | -6 
    7237 S |  | 6 | -6 
    7238 O |  |  | 4 
    7239 Iteration cutoff | 2 
    7240  
    7241 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    7242 sequence alignment score = 1120.2 
    7243 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    7244 2.619) 
    7245  
    7246 
    7247 > ui tool show "Render by Attribute"
    7248 
    7249 > ui tool show Matchmaker
    7250 
    7251 > matchmaker #!4 to #3
    7252 
    7253 Parameters 
    7254 --- 
    7255 Chain pairing | bb 
    7256 Alignment algorithm | Needleman-Wunsch 
    7257 Similarity matrix | BLOSUM-62 
    7258 SS fraction | 0.3 
    7259 Gap open (HH/SS/other) | 18/18/6 
    7260 Gap extend | 1 
    7261 SS matrix |  |  | H | S | O 
    7262 ---|---|---|--- 
    7263 H | 6 | -9 | -6 
    7264 S |  | 6 | -6 
    7265 O |  |  | 4 
    7266 Iteration cutoff | 2 
    7267  
    7268 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    7269 sequence alignment score = 1120.2 
    7270 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    7271 2.619) 
    7272  
    7273 
    7274 > tile spacingFactor 2 columns 2
    7275 
    7276 2 models tiled 
    7277 
    7278 > tile spacingFactor 1 columns 2
    7279 
    7280 2 models tiled 
    7281 
    7282 > select GPR52_ECL2
    7283 
    7284 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7285 
    7286 > color sel purple
    7287 
    7288 > transparency sel 0 All
    7289 
    7290 > color sel byhetero
    7291 
    7292 > ui mousemode right select
    7293 
    7294 > select add #4/R:112
    7295 
    7296 179 atoms, 187 bonds, 22 residues, 1 model selected 
    7297 
    7298 > select subtract #4/R:112
    7299 
    7300 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7301 
    7302 > select add #4/R:112
    7303 
    7304 179 atoms, 187 bonds, 22 residues, 1 model selected 
    7305 
    7306 > select subtract #4/R:112
    7307 
    7308 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7309 
    7310 > select add #4/R:114@SG
    7311 
    7312 172 atoms, 180 bonds, 22 residues, 1 model selected 
    7313 
    7314 > select subtract #4/R:114@SG
    7315 
    7316 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7317 
    7318 > select add #4/R:113
    7319 
    7320 178 atoms, 186 bonds, 22 residues, 1 model selected 
    7321 
    7322 > select subtract #4/R:113
    7323 
    7324 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7325 
    7326 > select add #4/R:114@CB
    7327 
    7328 172 atoms, 180 bonds, 22 residues, 1 model selected 
    7329 
    7330 > select subtract #4/R:193@SG
    7331 
    7332 171 atoms, 180 bonds, 22 residues, 1 model selected 
    7333 
    7334 > select add #4/R:193@SG
    7335 
    7336 172 atoms, 180 bonds, 22 residues, 1 model selected 
    7337 Drag select of 1 bonds 
    7338 
    7339 > select GPR52_ECL2
    7340 
    7341 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7342 
    7343 > ui mousemode right translate
    7344 
    7345 > ui mousemode right rotate
    7346 
    7347 [Repeated 2 time(s)]
    7348 
    7349 > ui mousemode right select
    7350 
    7351 > select clear
    7352 
    7353 > select #4/R:114@CB
    7354 
    7355 1 atom, 1 residue, 1 model selected 
    7356 
    7357 > select clear
    7358 
    7359 > ui mousemode right translate
    7360 
    7361 > ui mousemode right select
    7362 
    7363 > select #4/R:111@CB
    7364 
    7365 1 atom, 1 residue, 1 model selected 
    7366 
    7367 > hide sel atoms
    7368 
    7369 > select #4/R:111@OG
    7370 
    7371 1 atom, 1 residue, 1 model selected 
    7372 
    7373 > select #4/R:111@OG
    7374 
    7375 1 atom, 1 residue, 1 model selected 
    7376 Drag select of 1 residues 
    7377 
    7378 > select #4/R:111@OG
    7379 
    7380 1 atom, 1 residue, 1 model selected 
    7381 
    7382 > hide sel atoms
    7383 
    7384 > select clear
    7385 
    7386 > ui mousemode right rotate
    7387 
    7388 > ui mousemode right translate
    7389 
    7390 > ui mousemode right rotate
    7391 
    7392 > select GPR21_ECL2
    7393 
    7394 191 atoms, 203 bonds, 22 residues, 1 model selected 
    7395 
    7396 > color sel medium blue
    7397 
    7398 > color sel byhetero
    7399 
    7400 > ui mousemode right select
    7401 
    7402 > select clear
    7403 
    7404 > ui tool show Matchmaker
    7405 
    7406 > matchmaker #!4 to #3
    7407 
    7408 Parameters 
    7409 --- 
    7410 Chain pairing | bb 
    7411 Alignment algorithm | Needleman-Wunsch 
    7412 Similarity matrix | BLOSUM-62 
    7413 SS fraction | 0.3 
    7414 Gap open (HH/SS/other) | 18/18/6 
    7415 Gap extend | 1 
    7416 SS matrix |  |  | H | S | O 
    7417 ---|---|---|--- 
    7418 H | 6 | -9 | -6 
    7419 S |  | 6 | -6 
    7420 O |  |  | 4 
    7421 Iteration cutoff | 2 
    7422  
    7423 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    7424 sequence alignment score = 1120.2 
    7425 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    7426 2.619) 
    7427  
    7428 
    7429 > matchmaker #!4 to #3
    7430 
    7431 Parameters 
    7432 --- 
    7433 Chain pairing | bb 
    7434 Alignment algorithm | Needleman-Wunsch 
    7435 Similarity matrix | BLOSUM-62 
    7436 SS fraction | 0.3 
    7437 Gap open (HH/SS/other) | 18/18/6 
    7438 Gap extend | 1 
    7439 SS matrix |  |  | H | S | O 
    7440 ---|---|---|--- 
    7441 H | 6 | -9 | -6 
    7442 S |  | 6 | -6 
    7443 O |  |  | 4 
    7444 Iteration cutoff | 2 
    7445  
    7446 Matchmaker GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
    7447 sequence alignment score = 1120.2 
    7448 RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
    7449 2.619) 
    7450  
    7451 Drag select of 8 residues 
    7452 
    7453 > select clear
    7454 
    7455 > ui mousemode right translate
    7456 
    7457 > select GPR52_ECL2
    7458 
    7459 171 atoms, 180 bonds, 21 residues, 1 model selected 
    7460 
    7461 > color sel hot pink
    7462 
    7463 > color sel #db8de4ff
    7464 
    7465 > color sel #dc8de4ff
    7466 
    7467 [Repeated 1 time(s)]
    7468 
    7469 > color sel #dd90e5ff
    7470 
    7471 > color sel #dd94e5ff
    7472 
    7473 > color sel #de9ae6ff
    7474 
    7475 > color sel #df9ee6ff
    7476 
    7477 > color sel #e0a1e7ff
    7478 
    7479 > color sel #e1a4e7ff
    7480 
    7481 > color sel #e1a5e8ff
    7482 
    7483 > color sel #e1a6e8ff
    7484 
    7485 > color sel #e1a5e8ff
    7486 
    7487 > color sel #e1a6e7ff
    7488 
    7489 > color sel #e0a6e8ff
    7490 
    7491 > color sel #dfa7e8ff
    7492 
    7493 > color sel #dfa6e8ff
    7494 
    7495 > color sel #dea6e8ff
    7496 
    7497 > color sel #dea4e6ff
    7498 
    7499 > color sel #dc9fe6ff
    7500 
    7501 > color sel #d88de4ff
    7502 
    7503 > color sel #d789e3ff
    7504 
    7505 > color sel #d686e3ff
    7506 
    7507 > color sel #d684e2ff
    7508 
    7509 > color sel #d484e2ff
    7510 
    7511 > color sel #d484e3ff
    7512 
    7513 [Repeated 3 time(s)]
    7514 
    7515 > color sel #d283e3ff
    7516 
    7517 [Repeated 2 time(s)]
    7518 
    7519 > color sel #d384e2ff
    7520 
    7521 [Repeated 1 time(s)]
    7522 
    7523 > color sel #d388e3ff
    7524 
    7525 > color sel #d48ae3ff
    7526 
    7527 > color sel #d58de3ff
    7528 
    7529 [Repeated 2 time(s)]
    7530 
    7531 > color sel #d68ee3ff
    7532 
    7533 > color sel #d791e4ff
    7534 
    7535 > color sel #d896e5ff
    7536 
    7537 > color sel #da98e4ff
    7538 
    7539 > color sel #da98e5ff
    7540 
    7541 > color sel #da99e5ff
    7542 
    7543 > color sel #da9ae5ff
    7544 
    7545 > color sel #db9de6ff
    7546 
    7547 > color sel #dc9fe6ff
    7548 
    7549 > color sel #dda2e6ff
    7550 
    7551 [Repeated 1 time(s)]
    7552 
    7553 > color sel #dea5e7ff
    7554 
    7555 > color sel #dfa9e7ff
    7556 
    7557 > color sel #e0ace8ff
    7558 
    7559 > color sel #e0ade9ff
    7560 
    7561 > color sel #e1aee8ff
    7562 
    7563 > color sel #e0ade9ff
    7564 
    7565 > color sel #e1ade9ff
    7566 
    7567 > color sel #e0abe8ff
    7568 
    7569 > color sel #e1aae8ff
    7570 
    7571 > color sel #e1a9e8ff
    7572 
    7573 [Repeated 3 time(s)]
    7574 
    7575 > color sel #e1a7e8ff
    7576 
    7577 > color sel #e1a8e7ff
    7578 
    7579 > color sel #e0a7e7ff
    7580 
    7581 > color sel #e0a8e7ff
    7582 
    7583 > color sel #dfa7e7ff
    7584 
    7585 [Repeated 3 time(s)]
    7586 
    7587 > color sel #dea6e7ff
    7588 
    7589 > color sel #dea6e8ff
    7590 
    7591 [Repeated 2 time(s)]
    7592 
    7593 > color sel #dda6e8ff
    7594 
    7595 [Repeated 1 time(s)]
    7596 
    7597 > color sel #dca7e8ff
    7598 
    7599 [Repeated 4 time(s)]
    7600 
    7601 > color sel #dca7e7ff
    7602 
    7603 > color sel #dba6e8ff
    7604 
    7605 > color sel #dba6e7ff
    7606 
    7607 > color sel #daa6e8ff
    7608 
    7609 > color sel #daa6e7ff
    7610 
    7611 [Repeated 3 time(s)]
    7612 
    7613 > color sel #daa6e8ff
    7614 
    7615 [Repeated 1 time(s)]
    7616 
    7617 > color sel #d9a7e8ff
    7618 
    7619 > color sel #d8a7e8ff
    7620 
    7621 > color sel #d8a7e7ff
    7622 
    7623 > color sel #d6a7e7ff
    7624 
    7625 [Repeated 1 time(s)]
    7626 
    7627 > color sel #d4a6e7ff
    7628 
    7629 > color sel #d4a7e7ff
    7630 
    7631 > color sel #d4a6e7ff
    7632 
    7633 [Repeated 1 time(s)]
    7634 
    7635 > color sel #d4a7e7ff
    7636 
    7637 > color sel #d3a7e7ff
    7638 
    7639 [Repeated 1 time(s)]
    7640 
    7641 > color sel #d4a9e7ff
    7642 
    7643 > color sel #d6ade8ff
    7644 
    7645 > color sel #d7b2eaff
    7646 
    7647 > color sel #d9b7eaff
    7648 
    7649 > color sel #dbbcebff
    7650 
    7651 > color sel #ddbfecff
    7652 
    7653 > color sel #dec1ecff
    7654 
    7655 [Repeated 1 time(s)]
    7656 
    7657 > color sel #dec2edff
    7658 
    7659 > color sel #dfc3edff
    7660 
    7661 [Repeated 1 time(s)]
    7662 
    7663 > color sel #dec1ecff
    7664 
    7665 > color sel #dbbbebff
    7666 
    7667 > color sel #dab9ebff
    7668 
    7669 > color sel #d8b3eaff
    7670 
    7671 > color sel #d4aae7ff
    7672 
    7673 > color sel #ce99e5ff
    7674 
    7675 > color sel #cc94e4ff
    7676 
    7677 > color sel #cb8fe4ff
    7678 
    7679 > color sel #ca8de3ff
    7680 
    7681 [Repeated 1 time(s)]
    7682 
    7683 > color sel #ca8be3ff
    7684 
    7685 > color sel #c886e3ff
    7686 
    7687 > color sel #c783e2ff
    7688 
    7689 > color sel #c781e2ff
    7690 
    7691 > color sel #c680e1ff
    7692 
    7693 > color sel #c77fe1ff
    7694 
    7695 > color sel #c880e1ff
    7696 
    7697 > color sel #c982e2ff
    7698 
    7699 > color sel #ca85e3ff
    7700 
    7701 > color sel #cb89e3ff
    7702 
    7703 > color sel #cc8be3ff
    7704 
    7705 > color sel #cc8ce3ff
    7706 
    7707 > color sel #cd8ce3ff
    7708 
    7709 [Repeated 2 time(s)]
    7710 
    7711 > color sel #cc8be3ff
    7712 
    7713 > color sel #cc8ae3ff
    7714 
    7715 > color sel #cc89e2ff
    7716 
    7717 > color sel #cb89e2ff
    7718 
    7719 > color sel #cb89e3ff
    7720 
    7721 [Repeated 1 time(s)]
    7722 
    7723 > color sel #c989e3ff
    7724 
    7725 > color sel #c989e2ff
    7726 
    7727 [Repeated 1 time(s)]
    7728 
    7729 > color sel #c889e2ff
    7730 
    7731 > color sel #c88ae2ff
    7732 
    7733 > color sel #c88ae3ff
    7734 
    7735 [Repeated 1 time(s)]
    7736 
    7737 > color sel #c88ae2ff
    7738 
    7739 > color sel #c68ae2ff
    7740 
    7741 > color sel #c689e2ff
    7742 
    7743 > color sel #c489e3ff
    7744 
    7745 > color sel #c387e3ff
    7746 
    7747 > color sel #c085e2ff
    7748 
    7749 > color sel #bf84e2ff
    7750 
    7751 > color sel #bf83e2ff
    7752 
    7753 > color sel #bd82e2ff
    7754 
    7755 > color sel #bc7fe1ff
    7756 
    7757 > color sel #bb7ce1ff
    7758 
    7759 > color sel #ba79e1ff
    7760 
    7761 > color sel #b874e1ff
    7762 
    7763 [Repeated 1 time(s)]
    7764 
    7765 > color sel #b670e1ff
    7766 
    7767 > color sel #b468e0ff
    7768 
    7769 > color sel #b060e1ff
    7770 
    7771 > color sel #ae59e1ff
    7772 
    7773 > color sel #ac56e1ff
    7774 
    7775 > color sel #ab55e1ff
    7776 
    7777 [Repeated 1 time(s)]
    7778 
    7779 > color sel #ac55e1ff
    7780 
    7781 [Repeated 1 time(s)]
    7782 
    7783 > color sel #ad56e1ff
    7784 
    7785 > color sel #ae56e1ff
    7786 
    7787 [Repeated 1 time(s)]
    7788 
    7789 > color sel #af57e1ff
    7790 
    7791 > color sel #b157e1ff
    7792 
    7793 [Repeated 1 time(s)]
    7794 
    7795 > color sel #b359e1ff
    7796 
    7797 > color sel #b35ae1ff
    7798 
    7799 > color sel #b35be1ff
    7800 
    7801 > color sel #b35be0ff
    7802 
    7803 [Repeated 1 time(s)]
    7804 
    7805 > color sel #b35ce0ff
    7806 
    7807 > color sel #b45ce0ff
    7808 
    7809 > color sel #b35ce0ff
    7810 
    7811 [Repeated 1 time(s)]
    7812 
    7813 > color sel #b45ce0ff
    7814 
    7815 > color sel #b55de0ff
    7816 
    7817 > color sel #b660e1ff
    7818 
    7819 > color sel #b766e0ff
    7820 
    7821 > color sel #ba6ce0ff
    7822 
    7823 > color sel #bb70e1ff
    7824 
    7825 > color sel #bb72e1ff
    7826 
    7827 [Repeated 1 time(s)]
    7828 
    7829 > color sel #bc72e1ff
    7830 
    7831 > color sel #bc73e1ff
    7832 
    7833 > color sel #bb73e1ff
    7834 
    7835 > color sel #bc74e0ff
    7836 
    7837 > color sel #ba75e1ff
    7838 
    7839 > color sel #ba75e0ff
    7840 
    7841 > color sel #b976e0ff
    7842 
    7843 > color sel #ba78e1ff
    7844 
    7845 > color sel #ba79e1ff
    7846 
    7847 > color sel #b979e1ff
    7848 
    7849 > color sel #ba7ae1ff
    7850 
    7851 > color sel #b97ae1ff
    7852 
    7853 > color sel #b87ae1ff
    7854 
    7855 > color sel #b77ae1ff
    7856 
    7857 > color sel #b87be1ff
    7858 
    7859 > color sel #bb82e2ff
    7860 
    7861 > color sel #be88e3ff
    7862 
    7863 > color sel #c18fe4ff
    7864 
    7865 > color sel #c699e5ff
    7866 
    7867 > color sel #c79ae4ff
    7868 
    7869 [Repeated 1 time(s)]
    7870 
    7871 > color sel #c899e5ff
    7872 
    7873 [Repeated 1 time(s)]
    7874 
    7875 > color sel #c998e5ff
    7876 
    7877 > color sel #ca99e4ff
    7878 
    7879 > color sel #cb98e4ff
    7880 
    7881 [Repeated 2 time(s)]
    7882 
    7883 > color sel #cb99e4ff
    7884 
    7885 [Repeated 1 time(s)]
    7886 
    7887 > color sel #cb98e5ff
    7888 
    7889 [Repeated 1 time(s)]
    7890 
    7891 > color sel #cb97e5ff
    7892 
    7893 > color sel #cc96e4ff
    7894 
    7895 > color sel #cc95e4ff
    7896 
    7897 [Repeated 1 time(s)]
    7898 
    7899 > color sel #cc94e4ff
    7900 
    7901 > color sel #cc93e4ff
    7902 
    7903 > color sel #cc94e4ff
    7904 
    7905 > color sel #cc93e4ff
    7906 
    7907 > color sel #cd94e4ff
    7908 
    7909 [Repeated 1 time(s)]
    7910 
    7911 > color sel #cc93e4ff
    7912 
    7913 [Repeated 1 time(s)]
    7914 
    7915 > color sel #cc92e4ff
    7916 
    7917 > color sel #cc91e3ff
    7918 
    7919 > color sel #cd91e4ff
    7920 
    7921 > color sel #cd90e4ff
    7922 
    7923 > color sel #cd8fe4ff
    7924 
    7925 > color sel #cd8ee3ff
    7926 
    7927 [Repeated 1 time(s)]
    7928 
    7929 > color sel #cc8be3ff
    7930 
    7931 > color sel #c885e3ff
    7932 
    7933 > color sel #c680e1ff
    7934 
    7935 > color sel #c47ae1ff
    7936 
    7937 > color sel #c377e1ff
    7938 
    7939 > color sel #c376e1ff
    7940 
    7941 [Repeated 2 time(s)]
    7942 
    7943 > color sel #c577e1ff
    7944 
    7945 > color sel #c678e1ff
    7946 
    7947 [Repeated 1 time(s)]
    7948 
    7949 > color sel #c778e2ff
    7950 
    7951 > color sel #c678e1ff
    7952 
    7953 > color sel #c478e1ff
    7954 
    7955 > color sel #c379e1ff
    7956 
    7957 > color sel #c278e1ff
    7958 
    7959 > color sel #c178e1ff
    7960 
    7961 > color sel #be79e1ff
    7962 
    7963 > color sel #be79e2ff
    7964 
    7965 [Repeated 2 time(s)]
    7966 
    7967 > color sel #be7ae1ff
    7968 
    7969 > color sel #bc7be1ff
    7970 
    7971 > color sel #bc7ce1ff
    7972 
    7973 > color sel #bc7ee1ff
    7974 
    7975 [Repeated 3 time(s)]
    7976 
    7977 > color sel #bc7fe1ff
    7978 
    7979 > color sel #bc80e2ff
    7980 
    7981 > color sel #ba80e2ff
    7982 
    7983 [Repeated 2 time(s)]
    7984 
    7985 > color sel #bc80e2ff
    7986 
    7987 > color sel #bd80e2ff
    7988 
    7989 [Repeated 1 time(s)]
    7990 
    7991 > color sel #be81e3ff
    7992 
    7993 > color sel #be81e2ff
    7994 
    7995 > color sel #bf82e3ff
    7996 
    7997 [Repeated 3 time(s)]
    7998 
    7999 > color sel #c182e2ff
    8000 
    8001 [Repeated 2 time(s)]
    8002 
    8003 > color sel #c283e2ff
    8004 
    8005 > color sel #c284e2ff
    8006 
    8007 > color sel #c385e2ff
    8008 
    8009 [Repeated 2 time(s)]
    8010 
    8011 > color sel #c386e2ff
    8012 
    8013 > color sel #c488e3ff
    8014 
    8015 > color sel #c58be2ff
    8016 
    8017 > color sel #c78ee4ff
    8018 
    8019 > color sel #c892e4ff
    8020 
    8021 > color sel #c893e4ff
    8022 
    8023 [Repeated 1 time(s)]
    8024 
    8025 > color sel #c993e4ff
    8026 
    8027 [Repeated 1 time(s)]
    8028 
    8029 > color sel #c994e4ff
    8030 
    8031 > color sel #c996e4ff
    8032 
    8033 > color sel #ca97e5ff
    8034 
    8035 > color sel #cb98e4ff
    8036 
    8037 > color sel #cc9ce5ff
    8038 
    8039 > color sel #cd9ee6ff
    8040 
    8041 [Repeated 1 time(s)]
    8042 
    8043 > color sel #ce9fe6ff
    8044 
    8045 > color sel byhetero
    8046 
    8047 > ui mousemode right select
    8048 
    8049 > select clear
    8050 
    8051 > select GPR21_ECL2
    8052 
    8053 191 atoms, 203 bonds, 22 residues, 1 model selected 
    8054 
    8055 > color sel #8393e2ff
    8056 
    8057 > color sel #8b99e3ff
    8058 
    8059 > color sel #929fe4ff
    8060 
    8061 > color sel #99a2e4ff
    8062 
    8063 > color sel #9ca5e5ff
    8064 
    8065 > color sel #9da6e5ff
    8066 
    8067 [Repeated 3 time(s)]
    8068 
    8069 > color sel #9ca8e5ff
    8070 
    8071 [Repeated 5 time(s)]
    8072 
    8073 > color sel #9aa6e5ff
    8074 
    8075 > color sel #97a5e4ff
    8076 
    8077 > color sel #93a2e4ff
    8078 
    8079 > color sel #8e9ee3ff
    8080 
    8081 > color sel #8598e2ff
    8082 
    8083 > color sel #8395e3ff
    8084 
    8085 > color sel #8294e2ff
    8086 
    8087 [Repeated 1 time(s)]
    8088 
    8089 > color sel #8194e2ff
    8090 
    8091 > color sel #8093e2ff
    8092 
    8093 > color sel #7e91e1ff
    8094 
    8095 > color sel #798ee1ff
    8096 
    8097 > color sel #758be1ff
    8098 
    8099 > color sel #6d84e1ff
    8100 
    8101 > color sel #6b83e1ff
    8102 
    8103 > color sel #6983e1ff
    8104 
    8105 > color sel #6982e0ff
    8106 
    8107 > color sel #6882e0ff
    8108 
    8109 [Repeated 1 time(s)]
    8110 
    8111 > color sel #607be0ff
    8112 
    8113 > color sel #5975e0ff
    8114 
    8115 > color sel #5473e1ff
    8116 
    8117 > color sel #5172e1ff
    8118 
    8119 > color sel #4f70e1ff
    8120 
    8121 > color sel #4e70e2ff
    8122 
    8123 [Repeated 1 time(s)]
    8124 
    8125 > color sel #4e6fe2ff
    8126 
    8127 > color sel #4c6ee1ff
    8128 
    8129 > color sel #486be1ff
    8130 
    8131 > color sel #4266e2ff
    8132 
    8133 > color sel #3d62e3ff
    8134 
    8135 > color sel #385fe4ff
    8136 
    8137 > color sel #355de4ff
    8138 
    8139 > color sel #345ce5ff
    8140 
    8141 > color sel #325ce5ff
    8142 
    8143 > color sel #2f59e6ff
    8144 
    8145 > color sel #2e59e6ff
    8146 
    8147 > color sel #2e58e6ff
    8148 
    8149 > color sel #2d58e6ff
    8150 
    8151 > color sel #2d59e6ff
    8152 
    8153 [Repeated 1 time(s)]
    8154 
    8155 > color sel #2e5ae7ff
    8156 
    8157 > color sel #2e5be7ff
    8158 
    8159 > color sel #3061e7ff
    8160 
    8161 > color sel #3161e7ff
    8162 
    8163 > color sel #3163e7ff
    8164 
    8165 > color sel #3164e7ff
    8166 
    8167 > color sel #3266e7ff
    8168 
    8169 > color sel #346ae7ff
    8170 
    8171 > color sel #356fe7ff
    8172 
    8173 > color sel #3670e7ff
    8174 
    8175 > color sel #3773e8ff
    8176 
    8177 > color sel #3874e8ff
    8178 
    8179 > color sel #3774e8ff
    8180 
    8181 > color sel #3874e8ff
    8182 
    8183 [Repeated 1 time(s)]
    8184 
    8185 > color sel #3875e8ff
    8186 
    8187 > color sel #3976e8ff
    8188 
    8189 > color sel #3a7ae8ff
    8190 
    8191 > color sel #3b7be8ff
    8192 
    8193 > color sel #3c7ee8ff
    8194 
    8195 [Repeated 1 time(s)]
    8196 
    8197 > color sel #3d80e8ff
    8198 
    8199 > color sel #3e82e8ff
    8200 
    8201 > color sel #3f84e8ff
    8202 
    8203 [Repeated 1 time(s)]
    8204 
    8205 > color sel #3f85e8ff
    8206 
    8207 [Repeated 1 time(s)]
    8208 
    8209 > color sel #3f84e9ff
    8210 
    8211 > color sel #3d83e9ff
    8212 
    8213 > color sel #3a81ebff
    8214 
    8215 [Repeated 1 time(s)]
    8216 
    8217 > color sel #397feaff
    8218 
    8219 > color sel #3a81eaff
    8220 
    8221 > color sel #3981ecff
    8222 
    8223 > color sel #377eecff
    8224 
    8225 > color sel #367deeff
    8226 
    8227 [Repeated 1 time(s)]
    8228 
    8229 > color sel #347aeeff
    8230 
    8231 > color sel #357ceeff
    8232 
    8233 > color sel #337aefff
    8234 
    8235 > color sel #357defff
    8236 
    8237 > color sel #357ef0ff
    8238 
    8239 > color sel #347cf0ff
    8240 
    8241 > color sel #357df0ff
    8242 
    8243 > color sel #347df0ff
    8244 
    8245 > color sel #347cf0ff
    8246 
    8247 > color sel #347df0ff
    8248 
    8249 [Repeated 1 time(s)]
    8250 
    8251 > color sel #347df1ff
    8252 
    8253 [Repeated 1 time(s)]
    8254 
    8255 > color sel #347df2ff
    8256 
    8257 > color sel #357ef1ff
    8258 
    8259 > color sel #347ef1ff
    8260 
    8261 [Repeated 1 time(s)]
    8262 
    8263 > color sel #347ef2ff
    8264 
    8265 > color sel #3681f2ff
    8266 
    8267 [Repeated 1 time(s)]
    8268 
    8269 > color sel #3682f3ff
    8270 
    8271 > color sel #3581f3ff
    8272 
    8273 > color sel #3580f3ff
    8274 
    8275 [Repeated 1 time(s)]
    8276 
    8277 > color sel #3581f4ff
    8278 
    8279 > color sel #3581f3ff
    8280 
    8281 [Repeated 1 time(s)]
    8282 
    8283 > color sel #3580f5ff
    8284 
    8285 [Repeated 3 time(s)]
    8286 
    8287 > color sel #3581f4ff
    8288 
    8289 > color sel #3581f6ff
    8290 
    8291 > color sel #3581f5ff
    8292 
    8293 [Repeated 1 time(s)]
    8294 
    8295 > color sel #3581f6ff
    8296 
    8297 > color sel #3481f7ff
    8298 
    8299 > color sel #3480f7ff
    8300 
    8301 > color sel #327cf6ff
    8302 
    8303 > color sel #327df6ff
    8304 
    8305 > color sel #327cf6ff
    8306 
    8307 > color sel #2f76f5ff
    8308 
    8309 > color sel #2e75f5ff
    8310 
    8311 > color sel #2d74f5ff
    8312 
    8313 [Repeated 1 time(s)]
    8314 
    8315 > color sel #2e74f4ff
    8316 
    8317 > color sel #2e75f4ff
    8318 
    8319 [Repeated 1 time(s)]
    8320 
    8321 > color sel #2e75f3ff
    8322 
    8323 > color sel #2f76f3ff
    8324 
    8325 [Repeated 1 time(s)]
    8326 
    8327 > color sel #3076f2ff
    8328 
    8329 > color sel #3077f1ff
    8330 
    8331 > color sel #3077f0ff
    8332 
    8333 > color sel #3076efff
    8334 
    8335 > color sel #3075eaff
    8336 
    8337 > color sel #3073e0ff
    8338 
    8339 > color sel #3070d8ff
    8340 
    8341 > color sel #306ecfff
    8342 
    8343 > color sel #306bc9ff
    8344 
    8345 > color sel #2f69c6ff
    8346 
    8347 [Repeated 1 time(s)]
    8348 
    8349 > color sel byhetero
    8350 
    8351 > select clear
    8352 
    8353 > save "/Users/dongju/Desktop/Research projects-
    8354 > Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52_focus1.png" width 2000 height 1502
    8355 > supersample 3
    8356 
    8357 > save "/Users/dongju/Desktop/Research projects-
    8358 > Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52_superimposed.cxs"
    8359 
    8360 > close session
    8361 
    8362 > open 8HS3
    8363 
    8364 8hs3 title: 
    8365 Gi bound orphan GPR20 in ligand-free state [more info...] 
    8366  
    8367 Chain information for 8hs3 #1 
    8368 --- 
    8369 Chain | Description | UniProt 
    8370 A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 
    8371 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340 
    8372 C | Ggama |   
    8373 R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -106--1, GPR20_HUMAN 1-358 
    8374 S | scFv16 |   
    8375  
    8376 
    8377 > open 8HS2
    8378 
    8379 Summary of feedback from opening 8HS2 fetched from pdb 
    8380 --- 
    8381 note | Fetching compressed mmCIF 8hs2 from http://files.rcsb.org/download/8hs2.cif 
    8382  
    8383 8hs2 title: 
    8384 Orphan GPR20 in complex with Fab046 [more info...] 
    8385  
    8386 Chain information for 8hs2 #2 
    8387 --- 
    8388 Chain | Description | UniProt 
    8389 B | heavy chain of Fab046 |   
    8390 C | Light chain of Fab046 |   
    8391 R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -98--1, GPR20_HUMAN 1-316 
    8392  
    8393 
    8394 > open 8HSC
    8395 
    8396 Summary of feedback from opening 8HSC fetched from pdb 
    8397 --- 
    8398 note | Fetching compressed mmCIF 8hsc from http://files.rcsb.org/download/8hsc.cif 
    8399  
    8400 8hsc title: 
    8401 Gi bound Orphan GPR20 complex with Fab046 in ligand-free state [more info...] 
    8402  
    8403 Chain information for 8hsc #3 
    8404 --- 
    8405 Chain | Description | UniProt 
    8406 A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 
    8407 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340 
    8408 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    8409 E | light chain of Fab046 |   
    8410 F | heavy chain of Fab046 |   
    8411 R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -98--1, GPR20_HUMAN 1-358 
    8412 S | scFv16 |   
    8413  
    8414 
    8415 > hide atoms
    8416 
    8417 > show cartoons
    8418 
    8419 > hide atoms
    8420 
    8421 > show cartoons
    8422 
    8423 > hide atoms
    8424 
    8425 > show cartoons
    8426 
    8427 > rename #1 GPR20_Gi
    8428 
    8429 > rename #2 GPR20_Gi_Fab046
    8430 
    8431 > rename #3 GPR20_Gi_Fab046_ligand
    8432 
    8433 > ui tool show Matchmaker
    8434 
    8435 > matchmaker #!2-3 to #1
    8436 
    8437 Parameters 
    8438 --- 
    8439 Chain pairing | bb 
    8440 Alignment algorithm | Needleman-Wunsch 
    8441 Similarity matrix | BLOSUM-62 
    8442 SS fraction | 0.3 
    8443 Gap open (HH/SS/other) | 18/18/6 
    8444 Gap extend | 1 
    8445 SS matrix |  |  | H | S | O 
    8446 ---|---|---|--- 
    8447 H | 6 | -9 | -6 
    8448 S |  | 6 | -6 
    8449 O |  |  | 4 
    8450 Iteration cutoff | 2 
    8451  
    8452 Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046, chain R (#2), sequence
    8453 alignment score = 1937.2 
    8454 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    8455 2.786) 
    8456  
    8457 Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046_ligand, chain R (#3),
    8458 sequence alignment score = 2126.4 
    8459 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    8460 1.114) 
    8461  
    8462 
    8463 > matchmaker #!2-3 to #1
    8464 
    8465 Parameters 
    8466 --- 
    8467 Chain pairing | bb 
    8468 Alignment algorithm | Needleman-Wunsch 
    8469 Similarity matrix | BLOSUM-62 
    8470 SS fraction | 0.3 
    8471 Gap open (HH/SS/other) | 18/18/6 
    8472 Gap extend | 1 
    8473 SS matrix |  |  | H | S | O 
    8474 ---|---|---|--- 
    8475 H | 6 | -9 | -6 
    8476 S |  | 6 | -6 
    8477 O |  |  | 4 
    8478 Iteration cutoff | 2 
    8479  
    8480 Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046, chain R (#2), sequence
    8481 alignment score = 1937.2 
    8482 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    8483 2.786) 
    8484  
    8485 Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046_ligand, chain R (#3),
    8486 sequence alignment score = 2126.4 
    8487 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    8488 1.114) 
    8489  
    8490 
    8491 > select clear
    8492 
    8493 [Repeated 2 time(s)]
    8494 
    8495 > ui mousemode right translate
    8496 
    8497 > select #2/B#3/F
    8498 
    8499 2542 atoms, 2605 bonds, 1 pseudobond, 340 residues, 3 models selected 
    8500 
    8501 > hide sel cartoons
    8502 
    8503 > select #2/B#3/F
    8504 
    8505 2542 atoms, 2605 bonds, 1 pseudobond, 340 residues, 3 models selected 
    8506 
    8507 > hide sel cartoons
    8508 
    8509 > select #3/E
    8510 
    8511 747 atoms, 764 bonds, 105 residues, 1 model selected 
    8512 
    8513 > hide sel cartoons
    8514 
    8515 > select #2/C
    8516 
    8517 1623 atoms, 1658 bonds, 211 residues, 1 model selected 
    8518 
    8519 > hide sel cartoons
    8520 
    8521 > select #1/C
    8522 
    8523 438 atoms, 444 bonds, 57 residues, 1 model selected 
    8524 
    8525 > hide sel cartoons
    8526 
    8527 > select #3/C
    8528 
    8529 438 atoms, 444 bonds, 57 residues, 1 model selected 
    8530 
    8531 > hide sel cartoons
    8532 
    8533 > select #1/B#3/B
    8534 
    8535 5180 atoms, 5274 bonds, 676 residues, 2 models selected 
    8536 
    8537 > hide sel cartoons
    8538 
    8539 > select #1/A#3/A
    8540 
    8541 3421 atoms, 3479 bonds, 4 pseudobonds, 436 residues, 4 models selected 
    8542 
    8543 > hide sel cartoons
    8544 
    8545 > select #1/S#3/S
    8546 
    8547 3520 atoms, 3612 bonds, 2 pseudobonds, 464 residues, 4 models selected 
    8548 
    8549 > hide sel cartoons
    8550 
    8551 > color #1 #de9a85ff
    8552 
    8553 > color #2 #6debf4ff
    8554 
    8555 > color #2 #5daee5ff
    8556 
    8557 > color #3 #9ce5a7ff
    8558 
    8559 > color #3 #afe9ccff
    8560 
    8561 > color #3 #a4e7b8ff
    8562 
    8563 > rename #2 8HS2_GPR20_Fab046_inactive
    8564 
    8565 > rename #1 8HS3_GPR20_Gi
    8566 
    8567 > rename #3 8HSC_GPR20_Gi_Fab046
    8568 
    8569 > open /Users/dongju/Downloads/8hsc.cif
    8570 
    8571 8hsc.cif title: 
    8572 Gi bound Orphan GPR20 complex with Fab046 in ligand-free state [more info...] 
    8573  
    8574 Chain information for 8hsc.cif #4 
    8575 --- 
    8576 Chain | Description | UniProt 
    8577 A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 
    8578 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340 
    8579 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    8580 E | light chain of Fab046 |   
    8581 F | heavy chain of Fab046 |   
    8582 R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -98--1, GPR20_HUMAN 1-358 
    8583 S | scFv16 |   
    8584  
    8585 
    8586 > close #4
    8587 
    8588 > ui tool show "Show Sequence Viewer"
    8589 
    8590 > sequence chain #1/R #3/R
    8591 
    8592 Alignment identifier is 1 
    8593 
    8594 > sequence chain #2/R
    8595 
    8596 Alignment identifier is 2/R 
    8597 
    8598 > ui mousemode right select
    8599 
    8600 > select #2/R:31
    8601 
    8602 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8603 
    8604 > select #2/R:31-32
    8605 
    8606 16 atoms, 15 bonds, 2 residues, 1 model selected 
    8607 
    8608 > select #2/R:31-51
    8609 
    8610 172 atoms, 178 bonds, 21 residues, 1 model selected 
    8611 
    8612 > select #2/R:51
    8613 
    8614 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8615 
    8616 > select #2/R:50-51
    8617 
    8618 11 atoms, 11 bonds, 2 residues, 1 model selected 
    8619 
    8620 > select #2/R:48
    8621 
    8622 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8623 
    8624 > select #2/R:33-48
    8625 
    8626 134 atoms, 138 bonds, 16 residues, 1 model selected 
    8627 
    8628 > open /Users/dongju/Downloads/emd_34993_8HSC.map
    8629 
    8630 Opened emd_34993_8HSC.map as #4, grid size 288,288,288, pixel 0.832, shown at
    8631 level 0.0663, step 2, values float32 
    8632 
    8633 > open /Users/dongju/Downloads/emd_34984_8HS3.map
    8634 
    8635 Opened emd_34984_8HS3.map as #5, grid size 256,256,256, pixel 0.832, shown at
    8636 level 0.0743, step 1, values float32 
    8637 
    8638 > open /Users/dongju/Downloads/emd_34983_8HS2.map
    8639 
    8640 Opened emd_34983_8HS2.map as #6, grid size 288,288,288, pixel 0.832, shown at
    8641 level 0.0516, step 2, values float32 
    8642 
    8643 > volume #4 step 1
    8644 
    8645 > volume #4 level 0.1209
    8646 
    8647 > volume #4 level 0.1482
    8648 
    8649 > volume #5 level 0.2588
    8650 
    8651 > ui tool show Matchmaker
    8652 
    8653 > ui tool show "Volume Viewer"
    8654 
    8655 > volume #6 level 0.07988
    8656 
    8657 > volume #6 step 1
    8658 
    8659 > hide #!1 models
    8660 
    8661 > hide #!2 models
    8662 
    8663 > hide #!5 models
    8664 
    8665 > hide #!6 models
    8666 
    8667 > ui tool show Matchmaker
    8668 
    8669 > ui mousemode right "translate selected models"
    8670 
    8671 > view matrix models
    8672 > #2,-0.66094,-0.49694,0.56232,175.69,-0.53308,0.83831,0.11426,53.27,-0.52819,-0.22424,-0.81898,328.71
    8673 
    8674 > view matrix models
    8675 > #2,-0.66094,-0.49694,0.56232,187.93,-0.53308,0.83831,0.11426,49.694,-0.52819,-0.22424,-0.81898,321.04
    8676 
    8677 > ui mousemode right select
    8678 
    8679 > select #3/R:72
    8680 
    8681 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8682 
    8683 > ui mousemode right "translate selected models"
    8684 
    8685 > view matrix models
    8686 > #3,0.93357,0.34606,0.093248,-43.297,0.33762,-0.93645,0.095263,167.2,0.12029,-0.057452,-0.99108,194.25
    8687 
    8688 > view matrix models
    8689 > #3,-0.51119,0.84884,0.13475,77.887,0.81415,0.42801,0.39238,-82.802,0.27539,0.31028,-0.90988,123.36
    8690 
    8691 > view matrix models
    8692 > #3,-0.88503,0.45316,0.10663,174.49,0.42766,0.70091,0.57081,-83.556,0.18393,0.55079,-0.81413,97.227
    8693 
    8694 > view matrix models
    8695 > #3,-0.88503,0.45316,0.10663,170.85,0.42766,0.70091,0.57081,-81.442,0.18393,0.55079,-0.81413,95.902
    8696 
    8697 > view matrix models
    8698 > #3,-0.80184,0.58234,0.13393,142.41,0.55335,0.63904,0.53426,-86.516,0.22553,0.5025,-0.83464,98.322
    8699 
    8700 > view matrix models
    8701 > #3,-0.67352,0.69432,0.25358,100.83,0.69464,0.47726,0.53824,-86.06,0.25269,0.53866,-0.80374,87.501
    8702 
    8703 > view matrix models
    8704 > #3,-0.67352,0.69432,0.25358,99.559,0.69464,0.47726,0.53824,-84.317,0.25269,0.53866,-0.80374,86.836
    8705 
    8706 > view matrix models
    8707 > #3,-0.67352,0.69432,0.25358,103.6,0.69464,0.47726,0.53824,-78.659,0.25269,0.53866,-0.80374,87.642
    8708 
    8709 > view matrix models
    8710 > #3,-0.67352,0.69432,0.25358,101.9,0.69464,0.47726,0.53824,-81.537,0.25269,0.53866,-0.80374,87.881
    8711 
    8712 > view matrix models
    8713 > #3,-0.77048,0.63329,-0.072754,154.6,0.61462,0.7683,0.17876,-68.663,0.16911,0.093017,-0.9812,168.54
    8714 
    8715 > view matrix models
    8716 > #3,-0.82945,0.55796,-0.026453,166.17,0.54449,0.81819,0.18466,-66.146,0.12467,0.13876,-0.98245,169
    8717 
    8718 > view matrix models
    8719 > #3,-0.7649,0.62275,-0.16465,163.96,0.57843,0.77652,0.24987,-72.652,0.28346,0.095892,-0.95418,150.42
    8720 
    8721 > view matrix models
    8722 > #3,-0.57526,0.80453,-0.14766,116.89,0.78725,0.59357,0.16707,-69.492,0.22206,-0.020139,-0.97482,173.87
    8723 
    8724 > view matrix models
    8725 > #3,-0.52785,0.84917,-0.016692,92.307,0.79491,0.50085,0.34243,-77.518,0.29914,0.16748,-0.93939,138.57
    8726 
    8727 > view matrix models
    8728 > #3,-0.52785,0.84917,-0.016692,93.135,0.79491,0.50085,0.34243,-77.648,0.29914,0.16748,-0.93939,138.03
    8729 
    8730 > view matrix models
    8731 > #3,0.093474,0.99512,-0.031604,-1.4959,0.97954,-0.086236,0.18183,-16.375,0.17821,-0.047953,-0.98282,182.96
    8732 
    8733 > view matrix models
    8734 > #3,0.093474,0.99512,-0.031604,2.2278,0.97954,-0.086236,0.18183,-13.581,0.17821,-0.047953,-0.98282,182.85
    8735 
    8736 > view matrix models
    8737 > #3,0.093474,0.99512,-0.031604,-1.127,0.97954,-0.086236,0.18183,-11.923,0.17821,-0.047953,-0.98282,186.13
    8738 
    8739 > view matrix models
    8740 > #3,0.093474,0.99512,-0.031604,0.47057,0.97954,-0.086236,0.18183,-11.34,0.17821,-0.047953,-0.98282,185.1
    8741 
    8742 > view matrix models
    8743 > #3,-0.66744,0.74453,-0.014128,124.82,0.71103,0.64281,0.28501,-72.629,0.22128,0.18018,-0.95842,150.54
    8744 
    8745 > view matrix models
    8746 > #3,-0.80751,0.58888,-0.033914,162.82,0.5487,0.77103,0.32318,-70.785,0.21646,0.24236,-0.94573,142.61
    8747 
    8748 > view matrix models
    8749 > #3,-0.80751,0.58888,-0.033914,162.81,0.5487,0.77103,0.32318,-74.395,0.21646,0.24236,-0.94573,141.53
    8750 
    8751 > view matrix models
    8752 > #3,-0.80751,0.58888,-0.033914,162.85,0.5487,0.77103,0.32318,-75.3,0.21646,0.24236,-0.94573,142.26
    8753 
    8754 > view matrix models
    8755 > #3,-0.80751,0.58888,-0.033914,162.54,0.5487,0.77103,0.32318,-76.609,0.21646,0.24236,-0.94573,142.33
    8756 
    8757 > view matrix models
    8758 > #3,-0.80751,0.58888,-0.033914,162.1,0.5487,0.77103,0.32318,-74.881,0.21646,0.24236,-0.94573,139.97
    8759 
    8760 > view matrix models
    8761 > #3,-0.80751,0.58888,-0.033914,162.34,0.5487,0.77103,0.32318,-75.253,0.21646,0.24236,-0.94573,140.88
    8762 
    8763 > view matrix models
    8764 > #3,0.83163,0.46396,-0.30519,-4.2444,0.41363,-0.88419,-0.21704,189.9,-0.37054,0.054263,-0.92723,235.69
    8765 
    8766 > view matrix models
    8767 > #3,0.83163,0.46396,-0.30519,-3.0296,0.41363,-0.88419,-0.21704,193.24,-0.37054,0.054263,-0.92723,236.66
    8768 
    8769 > view matrix models
    8770 > #3,0.86824,0.41245,-0.27576,-4.6855,0.41429,-0.90851,-0.054441,179.43,-0.27299,-0.066978,-0.95968,241.67
    8771 
    8772 > view matrix models
    8773 > #3,0.89953,0.21953,-0.3777,24.199,0.22188,-0.97434,-0.037874,209.92,-0.37633,-0.049738,-0.92515,249.31
    8774 
    8775 > view matrix models
    8776 > #3,0.89953,0.21953,-0.3777,23.944,0.22188,-0.97434,-0.037874,209.58,-0.37633,-0.049738,-0.92515,248.86
    8777 
    8778 > fitmap #3 inMap #4
    8779 
    8780 Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
    8781 10180 atoms 
    8782 average map value = 0.0274, steps = 2000 
    8783 shifted from previous position = 3.33 
    8784 rotated from previous position = 5.74 degrees 
    8785 atoms outside contour = 9387, contour level = 0.14824 
    8786  
    8787 Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
    8788 coordinates: 
    8789 Matrix rotation and translation 
    8790 0.91461808 0.14723549 -0.37655739 30.60679389 
    8791 0.12928020 -0.98894154 -0.07267228 223.46689144 
    8792 -0.38309319 0.01778597 -0.92353845 242.16145145 
    8793 Axis 0.97841004 0.07069214 -0.19420714 
    8794 Axis point 0.00000000 107.76880125 126.76037093 
    8795 Rotation angle (degrees) 177.35043408 
    8796 Shift along axis -1.28613697 
    8797  
    8798 
    8799 > volume #4 level 0.1452
    8800 
    8801 > view matrix models
    8802 > #3,0.91462,0.14724,-0.37656,32.421,0.12928,-0.98894,-0.072672,223.3,-0.38309,0.017786,-0.92354,241.83
    8803 
    8804 > view matrix models
    8805 > #3,0.91462,0.14724,-0.37656,32.18,0.12928,-0.98894,-0.072672,226.13,-0.38309,0.017786,-0.92354,243.77
    8806 
    8807 > view matrix models
    8808 > #3,0.91462,0.14724,-0.37656,32.165,0.12928,-0.98894,-0.072672,226.84,-0.38309,0.017786,-0.92354,244.46
    8809 
    8810 > view matrix models
    8811 > #3,0.90511,0.026312,-0.42436,52.339,-0.0035374,-0.99758,-0.0694,244.43,-0.42516,0.064316,-0.90283,242.29
    8812 
    8813 > view matrix models
    8814 > #3,0.90252,0.18234,-0.39015,30.999,0.15711,-0.98291,-0.095931,224.96,-0.40097,0.025284,-0.91574,245.07
    8815 
    8816 > view matrix models
    8817 > #3,0.88972,0.12733,-0.4384,43.954,0.20136,-0.97131,0.12653,195.32,-0.40971,-0.20085,-0.88983,269.9
    8818 
    8819 > view matrix models
    8820 > #3,0.88972,0.12733,-0.4384,40.716,0.20136,-0.97131,0.12653,194.54,-0.40971,-0.20085,-0.88983,269.4
    8821 
    8822 > view matrix models
    8823 > #3,0.88972,0.12733,-0.4384,46.55,0.20136,-0.97131,0.12653,190.73,-0.40971,-0.20085,-0.88983,266.09
    8824 
    8825 > view matrix models
    8826 > #3,0.32337,-0.74179,-0.58752,235.18,-0.78565,-0.55653,0.27023,253.47,-0.52743,0.3742,-0.76276,201.11
    8827 
    8828 > view matrix models
    8829 > #3,0.010257,-0.81438,-0.58024,282.74,-0.92007,-0.23495,0.31349,228.73,-0.39163,0.53064,-0.7517,164.66
    8830 
    8831 > view matrix models
    8832 > #3,-0.39048,-0.77953,-0.48976,320.5,-0.88506,0.17147,0.43274,164.75,-0.25335,0.60244,-0.75689,139.21
    8833 
    8834 > view matrix models
    8835 > #3,-0.39048,-0.77953,-0.48976,316.86,-0.88506,0.17147,0.43274,167.11,-0.25335,0.60244,-0.75689,139.26
    8836 
    8837 > view matrix models
    8838 > #3,-0.39048,-0.77953,-0.48976,318.95,-0.88506,0.17147,0.43274,165.76,-0.25335,0.60244,-0.75689,140.57
    8839 
    8840 > view matrix models
    8841 > #3,-0.39048,-0.77953,-0.48976,323.43,-0.88506,0.17147,0.43274,129.86,-0.25335,0.60244,-0.75689,136.61
    8842 
    8843 > view matrix models
    8844 > #3,-0.39048,-0.77953,-0.48976,323.18,-0.88506,0.17147,0.43274,132.09,-0.25335,0.60244,-0.75689,136.97
    8845 
    8846 > view matrix models
    8847 > #3,-0.39048,-0.77953,-0.48976,323.92,-0.88506,0.17147,0.43274,125.72,-0.25335,0.60244,-0.75689,136.07
    8848 
    8849 > view matrix models
    8850 > #3,-0.18508,-0.80947,-0.55722,308.12,-0.93879,-0.02201,0.34378,164.18,-0.29055,0.58674,-0.75585,142.53
    8851 
    8852 > view matrix models
    8853 > #3,0.77449,-0.24089,-0.58493,122.45,-0.37681,-0.91839,-0.12071,244.39,-0.50811,0.31389,-0.80205,206.75
    8854 
    8855 > view matrix models
    8856 > #3,0.77934,-0.3091,-0.54505,125.72,-0.43088,-0.89592,-0.10802,247.36,-0.45493,0.31904,-0.83142,202.37
    8857 
    8858 > view matrix models
    8859 > #3,0.77934,-0.3091,-0.54505,125.74,-0.43088,-0.89592,-0.10802,246.8,-0.45493,0.31904,-0.83142,202.13
    8860 
    8861 > volume #4 level 0.1179
    8862 
    8863 > volume #4 step 2
    8864 
    8865 > volume #4 level 0.112
    8866 
    8867 > view matrix models
    8868 > #3,0.77934,-0.3091,-0.54505,125.33,-0.43088,-0.89592,-0.10802,246.76,-0.45493,0.31904,-0.83142,200.81
    8869 
    8870 > view matrix models
    8871 > #3,0.082947,-0.78047,-0.61966,276.57,-0.94992,-0.24991,0.18761,207.46,-0.30128,0.57307,-0.76212,144.58
    8872 
    8873 > view matrix models
    8874 > #3,-0.4667,-0.70065,-0.53971,329.13,-0.8764,0.28438,0.38866,115.34,-0.11883,0.65439,-0.74676,110.3
    8875 
    8876 > view matrix models
    8877 > #3,0.58693,-0.61049,-0.5318,183.62,-0.70194,-0.71102,0.041526,244.5,-0.40348,0.34892,-0.84585,192.25
    8878 
    8879 > view matrix models
    8880 > #3,-0.22678,-0.77554,-0.58916,312.34,-0.94693,0.034069,0.31964,160.53,-0.22783,0.63037,-0.74211,126.5
    8881 
    8882 > view matrix models
    8883 > #3,-0.22678,-0.77554,-0.58916,312.47,-0.94693,0.034069,0.31964,159.06,-0.22783,0.63037,-0.74211,125.76
    8884 
    8885 > view matrix models
    8886 > #3,-0.22678,-0.77554,-0.58916,306.62,-0.94693,0.034069,0.31964,194.89,-0.22783,0.63037,-0.74211,134.82
    8887 
    8888 > view matrix models
    8889 > #3,-0.20904,-0.79913,-0.56364,304.52,-0.94623,0.019792,0.32288,196.14,-0.24687,0.60083,-0.7603,142.55
    8890 
    8891 > view matrix models
    8892 > #3,-0.40537,-0.74265,-0.53305,319.82,-0.89876,0.21723,0.38083,161.18,-0.16703,0.63347,-0.75553,128.08
    8893 
    8894 > view matrix models
    8895 > #3,-0.21668,-0.8158,-0.53621,304.64,-0.94315,0.033144,0.3307,193.39,-0.25201,0.57738,-0.77661,147.59
    8896 
    8897 > view matrix models
    8898 > #3,-0.04307,-0.80758,-0.58819,286.86,-0.95413,-0.14134,0.26393,221.93,-0.29628,0.57257,-0.76445,152.55
    8899 
    8900 > view matrix models
    8901 > #3,-0.13131,-0.78665,-0.60327,297.2,-0.84368,-0.23086,0.48467,195.82,-0.52054,0.57261,-0.63337,167.77
    8902 
    8903 > view matrix models
    8904 > #3,-0.13131,-0.78665,-0.60327,296.82,-0.84368,-0.23086,0.48467,199.02,-0.52054,0.57261,-0.63337,169.11
    8905 
    8906 > view matrix models
    8907 > #3,-0.27126,-0.77367,-0.57259,310.01,-0.83724,-0.10381,0.53689,178.07,-0.47482,0.62503,-0.61959,155.77
    8908 
    8909 > view matrix models
    8910 > #3,-0.27126,-0.77367,-0.57259,310.24,-0.83724,-0.10381,0.53689,176.06,-0.47482,0.62503,-0.61959,154.92
    8911 
    8912 > view matrix models
    8913 > #3,-0.14382,-0.80407,-0.57688,297.99,-0.83585,-0.21337,0.50578,191.82,-0.52978,0.55493,-0.6414,172.31
    8914 
    8915 > view matrix models
    8916 > #3,-0.29277,-0.76871,-0.56866,312,-0.84265,-0.073663,0.5334,173.59,-0.45192,0.63534,-0.62619,151.47
    8917 
    8918 > view matrix models
    8919 > #3,-0.23586,-0.78322,-0.57527,307.12,-0.84616,-0.1256,0.51792,181.67,-0.47789,0.60893,-0.63311,158.56
    8920 
    8921 > view matrix models
    8922 > #3,-0.21033,-0.76212,-0.61232,305.18,-0.8526,-0.16347,0.49633,189.1,-0.47837,0.62645,-0.6154,154.78
    8923 
    8924 > view matrix models
    8925 > #3,-0.26491,-0.74784,-0.60873,310.1,-0.75848,-0.22821,0.61044,173.04,-0.59543,0.62342,-0.50676,158.98
    8926 
    8927 > view matrix models
    8928 > #3,-0.29475,-0.74763,-0.59512,312.49,-0.75583,-0.19865,0.6239,167.89,-0.58467,0.63371,-0.50653,156.38
    8929 
    8930 > view matrix models
    8931 > #3,-0.45299,-0.7036,-0.5475,322.66,-0.73873,-0.047553,0.67232,143.16,-0.49908,0.70901,-0.49823,135.86
    8932 
    8933 > view matrix models
    8934 > #3,-0.41221,-0.79577,-0.44366,317.64,-0.72441,-0.0090641,0.68931,135.12,-0.55255,0.60553,-0.57273,162.32
    8935 
    8936 > view matrix models
    8937 > #3,-0.45091,-0.78185,-0.43056,319.61,-0.73886,0.056334,0.6715,131.16,-0.50076,0.62091,-0.60308,157.02
    8938 
    8939 > view matrix models
    8940 > #3,-0.43427,-0.81195,-0.39007,316.88,-0.76085,0.098815,0.64136,132.07,-0.48221,0.57531,-0.66068,165.84
    8941 
    8942 > view matrix models
    8943 > #3,-0.45261,-0.83042,-0.32488,314.73,-0.70845,0.11363,0.69655,118.05,-0.54152,0.54542,-0.63974,174.74
    8944 
    8945 > view matrix models
    8946 > #3,-0.32649,-0.87591,-0.35521,307.06,-0.77098,0.029381,0.63619,141.98,-0.54681,0.48157,-0.6849,187.46
    8947 
    8948 > volume #4 level 0.1297
    8949 
    8950 > view matrix models
    8951 > #3,-0.61561,-0.73719,-0.27852,319.9,-0.66216,0.29225,0.69002,92,-0.42728,0.60921,-0.66805,155.64
    8952 
    8953 > view matrix models
    8954 > #3,-0.61561,-0.73719,-0.27852,320.13,-0.66216,0.29225,0.69002,91.878,-0.42728,0.60921,-0.66805,155.52
    8955 
    8956 > view matrix models
    8957 > #3,-0.61561,-0.73719,-0.27852,320.08,-0.66216,0.29225,0.69002,91.943,-0.42728,0.60921,-0.66805,155.44
    8958 
    8959 > view matrix models
    8960 > #3,-0.6096,-0.72746,-0.31495,321.89,-0.69807,0.30439,0.64811,99.371,-0.3756,0.61494,-0.69337,150.77
    8961 
    8962 > fitmap #3 inMap #4
    8963 
    8964 Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
    8965 10180 atoms 
    8966 average map value = 0.0221, steps = 104 
    8967 shifted from previous position = 2.25 
    8968 rotated from previous position = 3.51 degrees 
    8969 atoms outside contour = 9538, contour level = 0.12972 
    8970  
    8971 Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
    8972 coordinates: 
    8973 Matrix rotation and translation 
    8974 -0.62301685 -0.69907813 -0.35091276 323.82273294 
    8975 -0.68755815 0.27551529 0.67182967 98.03304027 
    8976 -0.37297960 0.65983413 -0.65230754 141.85275258 
    8977 Axis -0.43411156 0.79858647 0.41690143 
    8978 Axis point 189.17599306 0.00000000 43.94258769 
    8979 Rotation angle (degrees) 179.20836547 
    8980 Shift along axis -3.14871614 
    8981  
    8982 
    8983 > view matrix models
    8984 > #3,-0.50698,-0.76943,-0.38852,321.07,-0.75712,0.18207,0.62739,122.31,-0.41199,0.61223,-0.67486,154.67
    8985 
    8986 > view matrix models
    8987 > #3,-0.44059,-0.77377,-0.45516,319.91,-0.77446,0.071218,0.6286,137.32,-0.45398,0.62945,-0.63063,153.5
    8988 
    8989 > view matrix models
    8990 > #3,-0.43453,-0.81371,-0.38608,316.74,-0.72342,0.059974,0.6878,126.04,-0.53652,0.57816,-0.61472,168.45
    8991 
    8992 > fitmap #3 inMap #4
    8993 
    8994 Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
    8995 10180 atoms 
    8996 average map value = 0.023, steps = 96 
    8997 shifted from previous position = 2.09 
    8998 rotated from previous position = 1.11 degrees 
    8999 atoms outside contour = 9505, contour level = 0.12972 
    9000  
    9001 Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
    9002 coordinates: 
    9003 Matrix rotation and translation 
    9004 -0.44845125 -0.81009030 -0.37768396 315.90059723 
    9005 -0.71094998 0.06720042 0.70002444 120.88839438 
    9006 -0.54170249 0.58244124 -0.60606979 166.07985794 
    9007 Axis -0.52294492 0.72946357 0.44092121 
    9008 Axis point 207.76601541 0.00000000 34.37096576 
    9009 Rotation angle (degrees) 173.54492804 
    9010 Shift along axis -3.78680211 
    9011  
    9012 
    9013 > view matrix models
    9014 > #3,-0.44845,-0.81009,-0.37768,317.11,-0.71095,0.0672,0.70002,122.03,-0.5417,0.58244,-0.60607,166.15
    9015 
    9016 > view matrix models
    9017 > #3,-0.67213,-0.70147,-0.23705,318.61,-0.62506,0.36592,0.68949,77.347,-0.39691,0.61159,-0.68441,152.29
    9018 
    9019 > fitmap #3 inMap #4
    9020 
    9021 Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
    9022 10180 atoms 
    9023 average map value = 0.02221, steps = 116 
    9024 shifted from previous position = 4.71 
    9025 rotated from previous position = 3.45 degrees 
    9026 atoms outside contour = 9519, contour level = 0.12972 
    9027  
    9028 Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
    9029 coordinates: 
    9030 Matrix rotation and translation 
    9031 -0.68110775 -0.69314286 -0.23589237 317.39915571 
    9032 -0.59453884 0.33553836 0.73071032 75.24072237 
    9033 -0.42733570 0.63793964 -0.64063813 150.39958608 
    9034 Axis -0.39564854 0.81646779 0.42052656 
    9035 Axis point 182.36124367 0.00000000 44.40256038 
    9036 Rotation angle (degrees) 173.26723037 
    9037 Shift along axis -0.89986505 
    9038  
    9039 
    9040 > ui mousemode right select
    9041 
    9042 > select #4
    9043 
    9044 2 models selected 
    9045 
    9046 > transparency sel 50
    9047 
    9048 > volume sel style surface
    9049 
    9050 > volume sel style mesh
    9051 
    9052 > volume sel style surface
    9053 
    9054 > volume sel style image
    9055 
    9056 > volume sel style surface
    9057 
    9058 > ui mousemode right "translate selected models"
    9059 
    9060 > view matrix models #4,1,0,0,2.0559,0,1,0,1.5028,0,0,1,1.3583
    9061 
    9062 > view matrix models #4,1,0,0,1.2063,0,1,0,1.1243,0,0,1,1.5043
    9063 
    9064 > view matrix models
    9065 > #4,0.99528,0.092143,0.030326,-13.044,-0.09264,0.99558,0.015378,10.758,-0.028775,-0.018115,0.99942,7.1682
    9066 
    9067 > view matrix models
    9068 > #4,0.9954,-0.095297,-0.00972,14.534,0.095052,0.9952,-0.023185,-6.7552,0.011883,0.022155,0.99968,-2.5645
    9069 
    9070 > view matrix models
    9071 > #4,0.99962,-0.026307,0.0080892,3.5248,0.026384,0.99961,-0.0096414,-0.80377,-0.0078324,0.0098512,0.99992,1.2291
    9072 
    9073 > view matrix models
    9074 > #4,0.99943,-0.014015,-0.030553,6.5485,0.013272,0.99961,-0.024392,2.4556,0.030883,0.023973,0.99924,-4.9672
    9075 
    9076 > view matrix models
    9077 > #4,0.99801,0.061414,-0.014131,-4.4232,-0.06141,0.99811,0.00069911,8.4896,0.014147,0.00017007,0.9999,-0.16726
    9078 
    9079 > view matrix models
    9080 > #4,0.99089,-0.057526,-0.12175,23.505,0.052269,0.99758,-0.045941,0.63473,0.1241,0.039159,0.9915,-16.875
    9081 
    9082 > ui mousemode right select
    9083 
    9084 > select #3/R:165
    9085 
    9086 5 atoms, 4 bonds, 1 residue, 1 model selected 
    9087 
    9088 > ui mousemode right "translate selected models"
    9089 
    9090 > ui mousemode right "rotate selected models"
    9091 
    9092 > view matrix models
    9093 > #3,-0.68111,-0.69314,-0.23589,318.13,-0.59454,0.33554,0.73071,75.013,-0.42734,0.63794,-0.64064,150.08
    9094 
    9095 > view matrix models
    9096 > #3,-0.30352,-0.91347,-0.27102,299.3,-0.71182,0.028301,0.70179,128.71,-0.6334,0.40592,-0.65881,205.22
    9097 
    9098 > ui mousemode right "translate selected models"
    9099 
    9100 > view matrix models
    9101 > #3,-0.39102,-0.87862,-0.27411,306.7,-0.71384,0.10152,0.69291,121.34,-0.58097,0.46661,-0.66689,192.29
    9102 
    9103 > view matrix models
    9104 > #3,-0.39102,-0.87862,-0.27411,308.87,-0.71384,0.10152,0.69291,120.65,-0.58097,0.46661,-0.66689,191.34
    9105 
    9106 > view matrix models
    9107 > #3,-0.39102,-0.87862,-0.27411,308.84,-0.71384,0.10152,0.69291,120.75,-0.58097,0.46661,-0.66689,191.24
    9108 
    9109 > view matrix models
    9110 > #3,-0.087412,-0.95333,-0.28899,280.39,-0.7309,-0.13574,0.66885,153.03,-0.67686,0.26969,-0.68493,228.24
    9111 
    9112 > view matrix models
    9113 > #3,-0.11851,-0.95337,-0.27755,283.19,-0.74734,-0.098397,0.65711,151.97,-0.65378,0.2853,-0.70084,225.1
    9114 
    9115 > view matrix models
    9116 > #3,0.036028,-0.94281,-0.33138,267.76,-0.67988,-0.26616,0.68332,160.26,-0.73244,0.20068,-0.65058,239.87
    9117 
    9118 > view matrix models
    9119 > #3,-0.1925,-0.92137,-0.33766,295.01,-0.80409,-0.049135,0.59248,160.04,-0.56248,0.38556,-0.7314,204.9
    9120 
    9121 > view matrix models
    9122 > #3,0.4473,-0.83501,-0.32044,201.69,-0.80506,-0.53198,0.26244,250.05,-0.38961,0.14058,-0.91019,229.64
    9123 
    9124 > view matrix models
    9125 > #3,0.4473,-0.83501,-0.32044,195.3,-0.80506,-0.53198,0.26244,240.47,-0.38961,0.14058,-0.91019,233.16
    9126 
    9127 > view matrix models
    9128 > #3,0.4473,-0.83501,-0.32044,188.25,-0.80506,-0.53198,0.26244,230.93,-0.38961,0.14058,-0.91019,235.44
    9129 
    9130 > view matrix models
    9131 > #3,0.4473,-0.83501,-0.32044,230.96,-0.80506,-0.53198,0.26244,289.01,-0.38961,0.14058,-0.91019,240.37
    9132 
    9133 > view matrix models
    9134 > #3,0.4473,-0.83501,-0.32044,223.38,-0.80506,-0.53198,0.26244,247.86,-0.38961,0.14058,-0.91019,226.42
    9135 
    9136 > view matrix models
    9137 > #3,0.4473,-0.83501,-0.32044,223.64,-0.80506,-0.53198,0.26244,249.3,-0.38961,0.14058,-0.91019,226.89
    9138 
    9139 > view matrix models
    9140 > #3,-0.24783,-0.89783,-0.36398,323.94,-0.86959,0.040535,0.4921,167.4,-0.42707,0.43847,-0.79079,184.78
    9141 
    9142 > view matrix models
    9143 > #3,-0.24783,-0.89783,-0.36398,324.62,-0.86959,0.040535,0.4921,170.77,-0.42707,0.43847,-0.79079,187
    9144 
    9145 > view matrix models
    9146 > #3,-0.40052,-0.83909,-0.36812,337.64,-0.82293,0.15273,0.54723,146.13,-0.40295,0.52211,-0.75169,170.2
    9147 
    9148 > view matrix models
    9149 > #3,-0.66378,-0.71028,-0.23431,342.53,-0.67755,0.43838,0.59055,89.907,-0.31674,0.55075,-0.77224,157.97
    9150 
    9151 > view matrix models
    9152 > #3,-0.66378,-0.71028,-0.23431,325.95,-0.67755,0.43838,0.59055,82.907,-0.31674,0.55075,-0.77224,156.03
    9153 
    9154 > view matrix models
    9155 > #3,-0.69074,-0.68633,-0.22769,325.92,-0.66086,0.47135,0.58403,77.601,-0.29352,0.55388,-0.77914,153.41
    9156 
    9157 > view matrix models
    9158 > #3,-0.69074,-0.68633,-0.22769,320.83,-0.66086,0.47135,0.58403,79.577,-0.29352,0.55388,-0.77914,157.1
    9159 
    9160 > view matrix models
    9161 > #3,-0.69074,-0.68633,-0.22769,320.18,-0.66086,0.47135,0.58403,79.727,-0.29352,0.55388,-0.77914,158.04
    9162 
    9163 > view matrix models
    9164 > #3,-0.5367,-0.81372,-0.22319,314.96,-0.66133,0.2414,0.71019,93.745,-0.52401,0.52876,-0.6677,178.97
    9165 
    9166 > fitmap #3 inMap #4
    9167 
    9168 Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
    9169 10180 atoms 
    9170 average map value = 0.02623, steps = 168 
    9171 shifted from previous position = 7.8 
    9172 rotated from previous position = 5.59 degrees 
    9173 atoms outside contour = 9480, contour level = 0.12972 
    9174  
    9175 Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
    9176 coordinates: 
    9177 Matrix rotation and translation 
    9178 -0.59306195 -0.73885769 -0.31994817 318.13604787 
    9179 -0.65777968 0.21544711 0.72173985 93.72466182 
    9180 -0.46433113 0.63849185 -0.61377906 156.06749494 
    9181 Axis -0.44916764 0.77902358 0.43745935 
    9182 Axis point 190.76006571 0.00000000 42.25841955 
    9183 Rotation angle (degrees) 174.68281772 
    9184 Shift along axis -1.60951241 
    9185  
    9186 
    9187 > view matrix models
    9188 > #3,-0.53041,-0.80704,-0.25953,314.83,-0.63319,0.17359,0.75428,94.005,-0.56368,0.56441,-0.60308,178.09
    9189 
    9190 > view matrix models
    9191 > #3,-0.53041,-0.80704,-0.25953,317.35,-0.63319,0.17359,0.75428,94.585,-0.56368,0.56441,-0.60308,178.61
    9192 
    9193 > view matrix models
    9194 > #3,-0.53041,-0.80704,-0.25953,316.87,-0.63319,0.17359,0.75428,94.921,-0.56368,0.56441,-0.60308,178.46
    9195 
    9196 > view matrix models
    9197 > #3,-0.7039,-0.70885,-0.045309,305.71,-0.45936,0.40564,0.79022,42.071,-0.54177,0.57705,-0.61114,175.02
    9198 
    9199 > view matrix models
    9200 > #3,-0.71122,-0.66849,-0.21747,319.47,-0.54681,0.33167,0.76877,64.017,-0.44178,0.66567,-0.60142,150.96
    9201 
    9202 > view matrix models
    9203 > #3,-0.71122,-0.66849,-0.21747,318.59,-0.54681,0.33167,0.76877,64.359,-0.44178,0.66567,-0.60142,147.55
    9204 
    9205 > view matrix models
    9206 > #3,-0.64685,-0.68909,-0.32671,323.92,-0.65073,0.27534,0.70763,90.387,-0.39767,0.67033,-0.62651,143.94
    9207 
    9208 > view matrix models
    9209 > #3,-0.64685,-0.68909,-0.32671,322.75,-0.65073,0.27534,0.70763,92.037,-0.39767,0.67033,-0.62651,143.52
    9210 
    9211 > view matrix models
    9212 > #3,-0.64685,-0.68909,-0.32671,323.43,-0.65073,0.27534,0.70763,93.307,-0.39767,0.67033,-0.62651,144.23
    9213 
    9214 > view matrix models
    9215 > #3,-0.64685,-0.68909,-0.32671,322.99,-0.65073,0.27534,0.70763,92.41,-0.39767,0.67033,-0.62651,143.82
    9216 
    9217 > view matrix models
    9218 > #3,-0.8561,-0.51391,-0.054693,301.52,-0.40635,0.60395,0.68566,25.217,-0.31934,0.60922,-0.72586,151.08
    9219 
    9220 > view matrix models
    9221 > #3,-0.89985,0.2759,0.33787,175.05,0.41006,0.79917,0.43951,-76.458,-0.14876,0.53404,-0.83227,148.95
    9222 
    9223 > view matrix models
    9224 > #3,-0.89985,0.2759,0.33787,173.89,0.41006,0.79917,0.43951,-75.983,-0.14876,0.53404,-0.83227,149.22
    9225 
    9226 > fitmap #3 inMap #4
    9227 
    9228 Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
    9229 10180 atoms 
    9230 average map value = 0.02646, steps = 268 
    9231 shifted from previous position = 2.93 
    9232 rotated from previous position = 9.59 degrees 
    9233 atoms outside contour = 9392, contour level = 0.12972 
    9234  
    9235 Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
    9236 coordinates: 
    9237 Matrix rotation and translation 
    9238 -0.84257923 0.50989234 0.17340714 152.86231643 
    9239 0.53790691 0.78072321 0.31800536 -75.48199611 
    9240 0.02676552 0.36122161 -0.93209578 157.19052038 
    9241 Axis 0.27805618 0.94350176 0.18024756 
    9242 Axis point 90.79673476 0.00000000 82.65077544 
    9243 Rotation angle (degrees) 175.54297318 
    9244 Shift along axis -0.37987697 
    9245  
    9246 
    9247 > hide #!4 models
    9248 
    9249 > hide #!3 models
    9250 
    9251 > show #!1 models
    9252 
    9253 > show #!5 models
    9254 
    9255 > volume #5 step 2
    9256 
    9257 > volume #5 level 0.1551
    9258 
    9259 > view matrix models
    9260 > #3,-0.86911,0.41636,0.26702,157.96,0.49133,0.78889,0.36912,-75.685,-0.056959,0.452,-0.8902,147.3
    9261 
    9262 > view matrix models
    9263 > #3,-0.86911,0.41636,0.26702,156.59,0.49133,0.78889,0.36912,-76.483,-0.056959,0.452,-0.8902,140.11
    9264 
    9265 > fitmap #1 inMap #5
    9266 
    9267 Fit molecule 8HS3_GPR20_Gi (#1) to map emd_34984_8HS3.map (#5) using 8258
    9268 atoms 
    9269 average map value = 0.269, steps = 44 
    9270 shifted from previous position = 0.00996 
    9271 rotated from previous position = 0.0165 degrees 
    9272 atoms outside contour = 3526, contour level = 0.15506 
    9273  
    9274 Position of 8HS3_GPR20_Gi (#1) relative to emd_34984_8HS3.map (#5)
    9275 coordinates: 
    9276 Matrix rotation and translation 
    9277 0.99999996 -0.00026805 -0.00008915 0.03509652 
    9278 0.00026805 0.99999996 -0.00005430 -0.03064672 
    9279 0.00008916 0.00005428 0.99999999 -0.00869959 
    9280 Axis 0.18873347 -0.30992483 0.93184027 
    9281 Axis point 105.08226922 125.27152504 0.00000000 
    9282 Rotation angle (degrees) 0.01648161 
    9283 Shift along axis 0.00801544 
    9284  
    9285 
    9286 > view matrix models
    9287 > #3,-0.86911,0.41636,0.26702,154.9,0.49133,0.78889,0.36912,-77.884,-0.056959,0.452,-0.8902,134.62
    9288 
    9289 > ui mousemode right translate
    9290 
    9291 > volume #!5 style mesh
    9292 
    9293 > volume #5 color #0029f4
    9294 
    9295 > volume #5 color #0119f0
    9296 
    9297 > volume #5 level 0.1066
    9298 
    9299 > transparency #5.1 50
    9300 
    9301 > volume #!5 style surface
    9302 
    9303 > volume #5 style mesh
    9304 
    9305 > volume #5 level 0.09625
    9306 
    9307 > volume #5 step 4
    9308 
    9309 > volume #5 step 1
    9310 
    9311 > volume #5 level 0.1123
    9312 
    9313 > volume #!5 style surface
    9314 
    9315 > ui mousemode right select
    9316 
    9317 > select #5
    9318 
    9319 2 models selected 
    9320 
    9321 > select clear
    9322 
    9323 > select #1/R:48
    9324 
    9325 4 atoms, 3 bonds, 1 residue, 1 model selected 
    9326 
    9327 > select clear
    9328 
    9329 > select #5
    9330 
    9331 2 models selected 
    9332 
    9333 > select clear
    9334 
    9335 > vop gaussian #5 sdev 2.5
    9336 
    9337 Opened emd_34984_8HS3.map gaussian as #7, grid size 256,256,256, pixel 0.832,
    9338 shown at step 1, values float32 
    9339 
    9340 > volume #5 level 0.1324
    9341 
    9342 > volume #!5,7 style surface
    9343 
    9344 > volume #!5,7 style mesh
    9345 
    9346 > surface dust #5 size 8.32
    9347 
    9348 > surface dust #7 size 8.32
    9349 
    9350 > transparency #5 80 All
    9351 
    9352 > close #7
    9353 
    9354 > transparency #5 50 All
    9355 
    9356 > transparency #5 00 All
    9357 
    9358 > transparency #5 0 All
    9359 
    9360 > ui mousemode right translate
    9361 
    9362 > ui mousemode right select
    9363 
    9364 > select #1/R:32
    9365 
    9366 2 atoms, 1 bond, 1 residue, 1 model selected 
    9367 
    9368 > select #1/R:32 #3/R:32
    9369 
    9370 9 atoms, 7 bonds, 2 residues, 2 models selected 
    9371 
    9372 > select #1/R:32-47 #3/R:32-47
    9373 
    9374 203 atoms, 207 bonds, 32 residues, 2 models selected 
    9375 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    9376 [165-180] RMSD: 48.751 
    9377  
    9378 
    9379 > color (#!1 & sel) red
    9380 
    9381 > select clear
    9382 
    9383 > select #1/R:48 #3/R:48
    9384 
    9385 11 atoms, 9 bonds, 2 residues, 2 models selected 
    9386 
    9387 > select #1/R:48-50 #3/R:48-50
    9388 
    9389 35 atoms, 35 bonds, 6 residues, 2 models selected 
    9390 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    9391 [181-183] RMSD: 52.299 
    9392  
    9393 
    9394 > color (#!1 & sel) red
    9395 
    9396 > select clear
    9397 
    9398 > show #!2 models
    9399 
    9400 > hide #!1 models
    9401 
    9402 > hide #!5 models
    9403 
    9404 > show #!6 models
    9405 
    9406 > select #2/C
    9407 
    9408 1623 atoms, 1658 bonds, 211 residues, 1 model selected 
    9409 
    9410 > show sel cartoons
    9411 
    9412 > select #2/B
    9413 
    9414 1617 atoms, 1658 bonds, 1 pseudobond, 218 residues, 2 models selected 
    9415 
    9416 > show sel cartoons
    9417 
    9418 > select add #2
    9419 
    9420 5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected 
    9421 
    9422 > select subtract #2
    9423 
    9424 Nothing selected 
    9425 
    9426 > select add #2
    9427 
    9428 5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected 
    9429 
    9430 > select clear
    9431 
    9432 > select add #2
    9433 
    9434 5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected 
    9435 
    9436 > ui mousemode right "translate selected models"
    9437 
    9438 > view matrix models
    9439 > #2,-0.66094,-0.49694,0.56232,186.68,-0.53308,0.83831,0.11426,60.01,-0.52819,-0.22424,-0.81898,281.82
    9440 
    9441 > view matrix models
    9442 > #2,-0.66094,-0.49694,0.56232,188.67,-0.53308,0.83831,0.11426,63.838,-0.52819,-0.22424,-0.81898,283.67
    9443 
    9444 > view matrix models
    9445 > #2,-0.66094,-0.49694,0.56232,187.08,-0.53308,0.83831,0.11426,60.411,-0.52819,-0.22424,-0.81898,281.41
    9446 
    9447 > view matrix models
    9448 > #2,0.58142,0.79399,0.17756,-75.97,0.80952,-0.54272,-0.22392,103,-0.081428,0.27393,-0.9583,182.82
    9449 
    9450 > view matrix models
    9451 > #2,0.99888,0.017769,0.043786,-18.095,0.011651,-0.99061,0.13621,214.8,0.045795,-0.13555,-0.98971,220.37
    9452 
    9453 > view matrix models
    9454 > #2,0.99888,0.017769,0.043786,-11.26,0.011651,-0.99061,0.13621,224.28,0.045795,-0.13555,-0.98971,218.73
    9455 
    9456 > view matrix models
    9457 > #2,0.93929,-0.1923,0.28416,-2.7799,-0.21633,-0.97475,0.055431,257.09,0.26633,-0.11354,-0.95717,187.01
    9458 
    9459 > view matrix models
    9460 > #2,0.9123,-0.21473,0.3487,-3.31,-0.24816,-0.96723,0.053642,260.1,0.32576,-0.13547,-0.9357,180.56
    9461 
    9462 > view matrix models
    9463 > #2,0.9123,-0.21473,0.3487,0.33037,-0.24816,-0.96723,0.053642,261.34,0.32576,-0.13547,-0.9357,171.44
    9464 
    9465 > view matrix models
    9466 > #2,0.96001,-0.08967,0.2652,-12.058,-0.11979,-0.98778,0.099654,244.21,0.25303,-0.12744,-0.95903,181.31
    9467 
    9468 > view matrix models
    9469 > #2,0.67114,0.53376,-0.51446,23.927,0.68612,-0.71002,0.15843,110.46,-0.28071,-0.45932,-0.84275,272.34
    9470 
    9471 > view matrix models
    9472 > #2,0.33857,0.69362,-0.63582,55.666,0.8656,-0.49454,-0.078568,86.942,-0.36893,-0.52376,-0.76783,283.02
    9473 
    9474 > view matrix models
    9475 > #2,0.92958,-0.13757,0.34198,-10.327,-0.13747,-0.9902,-0.024653,258.89,0.34202,-0.024093,-0.93939,156.48
    9476 
    9477 > view matrix models
    9478 > #2,0.90289,-0.2973,0.31049,15.171,-0.23737,-0.94699,-0.21649,284.4,0.35839,0.12177,-0.9256,135.62
    9479 
    9480 > view matrix models
    9481 > #2,0.88079,-0.47224,0.034439,66.199,-0.47216,-0.88144,-0.011027,283.66,0.035564,-0.0065484,-0.99935,196.23
    9482 
    9483 > view matrix models
    9484 > #2,0.88079,-0.47224,0.034439,65.702,-0.47216,-0.88144,-0.011027,282.33,0.035564,-0.0065484,-0.99935,194.5
    9485 
    9486 > view matrix models
    9487 > #2,-0.232,-0.93471,0.26924,228.58,-0.86137,0.068819,-0.5033,262.2,0.45191,-0.34868,-0.82109,169.27
    9488 
    9489 > volume #6 level 0.1472
    9490 
    9491 > view matrix models
    9492 > #2,-0.232,-0.93471,0.26924,230.61,-0.86137,0.068819,-0.5033,264.67,0.45191,-0.34868,-0.82109,170.66
    9493 
    9494 > view matrix models
    9495 > #2,-0.61583,0.78224,-0.094081,104.69,-0.73807,-0.531,0.41628,231.38,0.27567,0.3258,0.90436,-60.945
    9496 
    9497 > view matrix models
    9498 > #2,-0.28546,0.89244,-0.34937,77.985,-0.9426,-0.19553,0.2707,229.35,0.17327,0.40659,0.89703,-57.953
    9499 
    9500 > view matrix models
    9501 > #2,0.81389,0.5784,-0.055017,-42.181,-0.53846,0.71531,-0.44542,143.18,-0.21828,0.39214,0.89363,-9.9877
    9502 
    9503 > view matrix models
    9504 > #2,0.88366,0.448,-0.13582,-26.635,-0.45407,0.74967,-0.48147,132.72,-0.11388,0.48713,0.86587,-30.918
    9505 
    9506 > view matrix models
    9507 > #2,0.70269,0.59329,-0.39273,2.5241,-0.71069,0.55904,-0.42707,180.38,-0.033821,0.57921,0.81448,-46.305
    9508 
    9509 > view matrix models
    9510 > #2,0.037685,0.96779,-0.24893,21.08,-0.98724,-0.0025044,-0.15919,253.92,-0.15469,0.25175,0.95535,-6.6367
    9511 
    9512 > view matrix models
    9513 > #2,0.90926,-0.40815,0.081629,51.992,0.41603,0.89724,-0.14793,-20.088,-0.012863,0.16847,0.98562,-16.222
    9514 
    9515 > view matrix models
    9516 > #2,0.96404,-0.26272,-0.04011,40.111,0.25384,0.95494,-0.15382,-7.4497,0.078716,0.13811,0.98728,-23.461
    9517 
    9518 > view matrix models
    9519 > #2,0.98153,-0.17266,-0.082332,31.391,0.1637,0.98086,-0.10541,-4.8074,0.098956,0.089983,0.99102,-20.403
    9520 
    9521 > view matrix models
    9522 > #2,0.99543,-0.092709,-0.022941,14.242,0.094586,0.99023,0.10251,-18.439,0.013213,-0.10421,0.99447,12.706
    9523 
    9524 > view matrix models
    9525 > #2,0.96165,-0.26987,-0.048961,42.129,0.26131,0.95571,-0.13538,-10.247,0.083326,0.11739,0.98958,-21.732
    9526 
    9527 > view matrix models
    9528 > #2,0.94523,-0.32565,0.022176,43.726,0.32352,0.92572,-0.19591,-7.9242,0.04327,0.19236,0.98037,-25.159
    9529 
    9530 > view matrix models
    9531 > #2,0.9504,-0.30707,0.049457,38.177,0.31086,0.93262,-0.18324,-8.5281,0.010143,0.18953,0.98182,-21.079
    9532 
    9533 > view matrix models
    9534 > #2,0.95795,-0.28453,0.037064,35.805,0.28619,0.93816,-0.19483,-5.1547,0.020663,0.19725,0.98014,-23.076
    9535 
    9536 > view matrix models
    9537 > #2,0.95795,-0.28453,0.037064,32.871,0.28619,0.93816,-0.19483,-6.5318,0.020663,0.19725,0.98014,-23.265
    9538 
    9539 > view matrix models
    9540 > #2,0.95795,-0.28453,0.037064,32.497,0.28619,0.93816,-0.19483,-5.0674,0.020663,0.19725,0.98014,-24.068
    9541 
    9542 > view matrix models
    9543 > #2,0.95754,-0.2075,-0.20015,46.769,0.16855,0.96616,-0.19526,5.3874,0.23389,0.15324,0.96011,-41.77
    9544 
    9545 > view matrix models
    9546 > #2,0.95754,-0.2075,-0.20015,46.378,0.16855,0.96616,-0.19526,6.915,0.23389,0.15324,0.96011,-42.527
    9547 
    9548 > view matrix models
    9549 > #2,0.95754,-0.2075,-0.20015,50.043,0.16855,0.96616,-0.19526,3.4407,0.23389,0.15324,0.96011,-41.412
    9550 
    9551 > view matrix models
    9552 > #2,0.98738,-0.15064,-0.048823,24.698,0.14773,0.98729,-0.058587,-10.209,0.057028,0.050636,0.99709,-11.983
    9553 
    9554 > view matrix models
    9555 > #2,0.96931,-0.24388,0.030943,30.148,0.24571,0.96513,-0.090284,-15.881,-0.0078458,0.095117,0.99544,-9.5766
    9556 
    9557 > view matrix models
    9558 > #2,0.9797,-0.1996,0.018946,24.783,0.20029,0.97012,-0.13694,-6.5359,0.0089525,0.13795,0.9904,-16.209
    9559 
    9560 > fitmap #2 inMap #6
    9561 
    9562 Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
    9563 using 5456 atoms 
    9564 average map value = 0.1675, steps = 132 
    9565 shifted from previous position = 1.28 
    9566 rotated from previous position = 14.1 degrees 
    9567 atoms outside contour = 2742, contour level = 0.14718 
    9568  
    9569 Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
    9570 (#6) coordinates: 
    9571 Matrix rotation and translation 
    9572 0.99999996 0.00029288 0.00005649 -0.04427819 
    9573 -0.00029287 0.99999995 -0.00015927 0.04795484 
    9574 -0.00005654 0.00015925 0.99999999 -0.02100094 
    9575 Axis 0.47100843 0.16715054 -0.86614765 
    9576 Axis point 160.65915521 159.81308670 0.00000000 
    9577 Rotation angle (degrees) 0.01937345 
    9578 Shift along axis 0.00535019 
    9579  
    9580 
    9581 > transparency #6.1 50
    9582 
    9583 > volume #!6 style mesh
    9584 
    9585 > volume #6 color #c64ee2
    9586 
    9587 > view matrix models
    9588 > #2,1,0.00029288,5.6495e-05,-0.02648,-0.00029287,1,-0.00015927,0.051205,-5.6542e-05,0.00015925,1,-0.016536
    9589 
    9590 > view matrix models
    9591 > #2,1,0.00029288,5.6495e-05,-0.032278,-0.00029287,1,-0.00015927,0.036181,-5.6542e-05,0.00015925,1,0.01956
    9592 
    9593 > ui mousemode right select
    9594 
    9595 > select clear
    9596 
    9597 [Repeated 1 time(s)]
    9598 
    9599 > ui mousemode right translate
    9600 
    9601 > hide #!2 models
    9602 
    9603 > show #!1 models
    9604 
    9605 > hide #!6 models
    9606 
    9607 > show #!5 models
    9608 
    9609 > hide #!5 models
    9610 
    9611 > show #!4 models
    9612 
    9613 > hide #!1 models
    9614 
    9615 > show #!2 models
    9616 
    9617 > hide #!2 models
    9618 
    9619 > show #!3 models
    9620 
    9621 > select #1/C
    9622 
    9623 438 atoms, 444 bonds, 57 residues, 1 model selected 
    9624 
    9625 > show #!3 cartoons
    9626 
    9627 > select #1/C
    9628 
    9629 438 atoms, 444 bonds, 57 residues, 1 model selected 
    9630 
    9631 > hide #!3 cartoons
    9632 
    9633 > select #3/C
    9634 
    9635 438 atoms, 444 bonds, 57 residues, 1 model selected 
    9636 
    9637 > show sel cartoons
    9638 
    9639 > select #3/B
    9640 
    9641 2590 atoms, 2637 bonds, 338 residues, 1 model selected 
    9642 
    9643 > show sel cartoons
    9644 
    9645 > select #3/A
    9646 
    9647 1712 atoms, 1741 bonds, 2 pseudobonds, 218 residues, 2 models selected 
    9648 
    9649 > show sel cartoons
    9650 
    9651 > select #3/R
    9652 
    9653 2008 atoms, 2057 bonds, 1 pseudobond, 273 residues, 2 models selected 
    9654 
    9655 > show sel cartoons
    9656 
    9657 > select #3/S
    9658 
    9659 1760 atoms, 1806 bonds, 1 pseudobond, 232 residues, 2 models selected 
    9660 
    9661 > show sel cartoons
    9662 
    9663 > ui mousemode right "translate selected models"
    9664 
    9665 > view matrix models
    9666 > #3,-0.86911,0.41636,0.26702,155.98,0.49133,0.78889,0.36912,-80.605,-0.056959,0.452,-0.8902,152.29
    9667 
    9668 > view matrix models
    9669 > #3,-0.66756,0.22149,0.71085,99.352,0.38154,0.92161,0.071149,-45.825,-0.63937,0.31871,-0.69974,212.86
    9670 
    9671 > view matrix models
    9672 > #3,0.54806,0.83275,0.078515,-38.227,-0.8235,0.52075,0.22511,125.94,0.14657,-0.18803,0.97116,-31.727
    9673 
    9674 > view matrix models
    9675 > #3,0.64327,0.71665,0.26948,-58.656,-0.75863,0.64412,0.097917,121.17,-0.1034,-0.26742,0.95802,7.736
    9676 
    9677 > view matrix models
    9678 > #3,0.64327,0.71665,0.26948,-54.188,-0.75863,0.64412,0.097917,120.75,-0.1034,-0.26742,0.95802,37.301
    9679 
    9680 > view matrix models
    9681 > #3,0.89172,-0.010251,0.45248,-16.627,-0.13029,0.95161,0.27833,-14.608,-0.43344,-0.30715,0.84723,95.327
    9682 
    9683 > view matrix models
    9684 > #3,0.82502,0.49556,0.27159,-48.362,-0.5611,0.77551,0.28941,56.534,-0.067198,-0.39116,0.91787,53.591
    9685 
    9686 > view matrix models
    9687 > #3,0.96478,0.11914,0.23454,-13.248,-0.21008,0.88555,0.41433,-14.52,-0.15833,-0.44901,0.87939,76.455
    9688 
    9689 > view matrix models
    9690 > #3,0.81556,0.10096,0.5698,-36.594,-0.22318,0.96336,0.14875,11.541,-0.53391,-0.24848,0.80821,104.88
    9691 
    9692 > view matrix models
    9693 > #3,0.60976,0.79249,0.012723,-26.618,-0.73923,0.56284,0.3698,93.574,0.2859,-0.23489,0.92903,-8.8083
    9694 
    9695 > view matrix models
    9696 > #3,0.84238,-0.53604,0.055253,105.66,0.52292,0.8379,0.15647,-61.633,-0.13017,-0.10291,0.98614,16.383
    9697 
    9698 > view matrix models
    9699 > #3,0.84238,-0.53604,0.055253,93.688,0.52292,0.8379,0.15647,-73.491,-0.13017,-0.10291,0.98614,34.825
    9700 
    9701 > view matrix models
    9702 > #3,0.91319,-0.38121,-0.14409,91.777,0.38033,0.9242,-0.034755,-42.825,0.14641,-0.023062,0.98895,-8.0004
    9703 
    9704 > view matrix models
    9705 > #3,0.91319,-0.38121,-0.14409,81.07,0.38033,0.9242,-0.034755,-27.667,0.14641,-0.023062,0.98895,-12.814
    9706 
    9707 > view matrix models
    9708 > #3,0.98085,-0.12237,-0.15153,41.896,0.12265,0.99242,-0.0074978,-9.3413,0.1513,-0.011231,0.98842,-14.791
    9709 
    9710 > view matrix models
    9711 > #3,0.98005,-0.13189,-0.14868,42.807,0.13018,0.99126,-0.021211,-8.3175,0.15018,0.0014318,0.98866,-16.263
    9712 
    9713 > view matrix models
    9714 > #3,0.98005,-0.13189,-0.14868,36.695,0.13018,0.99126,-0.021211,-11.96,0.15018,0.0014318,0.98866,-17.284
    9715 
    9716 > view matrix models
    9717 > #3,0.97548,-0.19276,-0.10619,39.328,0.19111,0.98123,-0.025622,-17.313,0.10914,0.0046991,0.99402,-13.551
    9718 
    9719 > view matrix models
    9720 > #3,0.97548,-0.19276,-0.10619,38.988,0.19111,0.98123,-0.025622,-15.234,0.10914,0.0046991,0.99402,-13.389
    9721 
    9722 > fitmap #3 inMap #4
    9723 
    9724 Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
    9725 10180 atoms 
    9726 average map value = 0.2065, steps = 128 
    9727 shifted from previous position = 2.41 
    9728 rotated from previous position = 8.13 degrees 
    9729 atoms outside contour = 4469, contour level = 0.12972 
    9730  
    9731 Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
    9732 coordinates: 
    9733 Matrix rotation and translation 
    9734 0.99999999 0.00003315 -0.00001114 0.00119912 
    9735 -0.00003315 0.99999999 0.00008964 -0.01294704 
    9736 0.00001114 -0.00008964 0.99999999 0.01100475 
    9737 Axis -0.93162165 -0.11577308 -0.34449629 
    9738 Axis point 0.00000000 109.66127837 148.84780670 
    9739 Rotation angle (degrees) 0.00551275 
    9740 Shift along axis -0.00340930 
    9741  
    9742 
    9743 > ui mousemode right select
    9744 
    9745 > ui mousemode right translate
    9746 
    9747 > ui mousemode right select
    9748 
    9749 > select clear
    9750 
    9751 > show #!1 models
    9752 
    9753 > show #!2 models
    9754 
    9755 > show #!5 models
    9756 
    9757 > show #!6 models
    9758 
    9759 > ui tool show Matchmaker
    9760 
    9761 > matchmaker #!2-3 to #1
    9762 
    9763 Parameters 
    9764 --- 
    9765 Chain pairing | bb 
    9766 Alignment algorithm | Needleman-Wunsch 
    9767 Similarity matrix | BLOSUM-62 
    9768 SS fraction | 0.3 
    9769 Gap open (HH/SS/other) | 18/18/6 
    9770 Gap extend | 1 
    9771 SS matrix |  |  | H | S | O 
    9772 ---|---|---|--- 
    9773 H | 6 | -9 | -6 
    9774 S |  | 6 | -6 
    9775 O |  |  | 4 
    9776 Iteration cutoff | 2 
    9777  
    9778 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
    9779 R (#2), sequence alignment score = 1937.2 
    9780 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    9781 2.786) 
    9782  
    9783 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
    9784 (#3), sequence alignment score = 2126.4 
    9785 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    9786 1.114) 
    9787  
    9788 
    9789 > matchmaker #!2-3 to #1
    9790 
    9791 Parameters 
    9792 --- 
    9793 Chain pairing | bb 
    9794 Alignment algorithm | Needleman-Wunsch 
    9795 Similarity matrix | BLOSUM-62 
    9796 SS fraction | 0.3 
    9797 Gap open (HH/SS/other) | 18/18/6 
    9798 Gap extend | 1 
    9799 SS matrix |  |  | H | S | O 
    9800 ---|---|---|--- 
    9801 H | 6 | -9 | -6 
    9802 S |  | 6 | -6 
    9803 O |  |  | 4 
    9804 Iteration cutoff | 2 
    9805  
    9806 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
    9807 R (#2), sequence alignment score = 1937.2 
    9808 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    9809 2.786) 
    9810  
    9811 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
    9812 (#3), sequence alignment score = 2126.4 
    9813 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    9814 1.114) 
    9815  
    9816 
    9817 > select clear
    9818 
    9819 [Repeated 2 time(s)]
    9820 
    9821 > ui mousemode right translate
    9822 
    9823 > hide #!2 models
    9824 
    9825 > hide #!3 models
    9826 
    9827 > hide #!4 models
    9828 
    9829 > hide #!6 models
    9830 
    9831 > ui mousemode right select
    9832 
    9833 > select #1/R:32
    9834 
    9835 2 atoms, 1 bond, 1 residue, 1 model selected 
    9836 
    9837 > select #1/R:32-33 #3/R:32-33
    9838 
    9839 19 atoms, 18 bonds, 4 residues, 2 models selected 
    9840 
    9841 > select #1/R:32-54 #3/R:32-54
    9842 
    9843 286 atoms, 294 bonds, 46 residues, 2 models selected 
    9844 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    9845 [165-187] RMSD: 1.016 
    9846  
    9847 
    9848 > select #1/R:32-56 #3/R:32-56
    9849 
    9850 308 atoms, 316 bonds, 50 residues, 2 models selected 
    9851 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    9852 [165-187] + 1 other block RMSD: 1.000 
    9853  
    9854 
    9855 > color (#!1 & sel) #de9a85ff
    9856 
    9857 > select clear
    9858 
    9859 [Repeated 3 time(s)]
    9860 
    9861 > ui mousemode right translate
    9862 
    9863 > show #!2 models
    9864 
    9865 > show #!6 models
    9866 
    9867 > hide #!5 models
    9868 
    9869 > hide #!1 models
    9870 
    9871 > select add #6
    9872 
    9873 2 models selected 
    9874 
    9875 > ui mousemode right "translate selected models"
    9876 
    9877 > view matrix models #6,1,0,0,-7.5788,0,1,0,-21.126,0,0,1,10.346
    9878 
    9879 > view matrix models #6,1,0,0,-6.7037,0,1,0,-18.716,0,0,1,9.1326
    9880 
    9881 > view matrix models #6,1,0,0,-4.7324,0,1,0,-13.395,0,0,1,6.3349
    9882 
    9883 > view matrix models
    9884 > #6,-0.46718,0.86174,0.19788,46.733,0.83372,0.35484,0.42308,-79.394,0.29437,0.36263,-0.88422,122.6
    9885 
    9886 > view matrix models
    9887 > #6,-0.46718,0.86174,0.19788,33.776,0.83372,0.35484,0.42308,-88.419,0.29437,0.36263,-0.88422,157.01
    9888 
    9889 > view matrix models
    9890 > #6,-0.92366,0.26069,0.28089,150.28,0.35867,0.84619,0.3941,-87.267,-0.13495,0.46476,-0.87509,194.82
    9891 
    9892 > view matrix models
    9893 > #6,-0.91473,0.33219,0.23003,146.01,0.40057,0.82022,0.40839,-90.628,-0.053009,0.46571,-0.88335,185.86
    9894 
    9895 > view matrix models
    9896 > #6,-0.093186,0.99094,-0.096728,4.5688,0.68576,0.13431,0.71532,-74.932,0.72184,0.00032588,-0.69207,129.45
    9897 
    9898 > view matrix models
    9899 > #6,-0.093186,0.99094,-0.096728,2.9774,0.68576,0.13431,0.71532,-69.177,0.72184,0.00032588,-0.69207,135.21
    9900 
    9901 > view matrix models
    9902 > #6,-0.57974,0.80882,0.098567,61.982,0.69174,0.42463,0.58412,-90.682,0.43059,0.40682,-0.80566,133.35
    9903 
    9904 > view matrix models
    9905 > #6,-0.53845,0.81858,0.19998,45.503,0.71628,0.31962,0.62031,-84.905,0.44385,0.47725,-0.75844,118.59
    9906 
    9907 > view matrix models
    9908 > #6,-0.53845,0.81858,0.19998,45.239,0.71628,0.31962,0.62031,-93.444,0.44385,0.47725,-0.75844,116.99
    9909 
    9910 > view matrix models
    9911 > #6,-0.53845,0.81858,0.19998,41.776,0.71628,0.31962,0.62031,-94.277,0.44385,0.47725,-0.75844,113.51
    9912 
    9913 > view matrix models
    9914 > #6,-0.63642,0.77126,0.011,78.417,0.51175,0.41152,0.75417,-94.706,0.57713,0.4856,-0.65659,86.262
    9915 
    9916 > view matrix models
    9917 > #6,-0.63642,0.77126,0.011,83.544,0.51175,0.41152,0.75417,-92.652,0.57713,0.4856,-0.65659,90.441
    9918 
    9919 > view matrix models
    9920 > #6,-0.61271,0.79005,-0.020348,81.744,0.49944,0.40703,0.76478,-91.758,0.61249,0.45842,-0.64397,88.168
    9921 
    9922 > view matrix models
    9923 > #6,-0.61271,0.79005,-0.020348,81.505,0.49944,0.40703,0.76478,-97.794,0.61249,0.45842,-0.64397,82.105
    9924 
    9925 > view matrix models
    9926 > #6,-0.61271,0.79005,-0.020348,81.581,0.49944,0.40703,0.76478,-96.533,0.61249,0.45842,-0.64397,83.763
    9927 
    9928 > view matrix models
    9929 > #6,-0.61271,0.79005,-0.020348,81.439,0.49944,0.40703,0.76478,-97.445,0.61249,0.45842,-0.64397,82.956
    9930 
    9931 > view matrix models
    9932 > #6,-0.76991,-0.21513,0.6008,154.88,-0.068878,0.96398,0.25691,-43.708,-0.63442,0.15642,-0.75699,277.86
    9933 
    9934 > view matrix models
    9935 > #6,-0.90769,-0.086655,0.4106,175.58,0.095072,0.91054,0.40233,-71.769,-0.40874,0.40423,-0.81825,228.17
    9936 
    9937 > view matrix models
    9938 > #6,-0.90769,-0.086655,0.4106,179.77,0.095072,0.91054,0.40233,-68.884,-0.40874,0.40423,-0.81825,233.72
    9939 
    9940 > view matrix models
    9941 > #6,-0.862,0.26626,0.43135,130.53,0.42367,0.84564,0.32466,-92.112,-0.27832,0.46261,-0.84174,213.8
    9942 
    9943 > view matrix models
    9944 > #6,-0.862,0.26626,0.43135,129.93,0.42367,0.84564,0.32466,-93.494,-0.27832,0.46261,-0.84174,216.86
    9945 
    9946 > view matrix models
    9947 > #6,-0.862,0.26626,0.43135,125.46,0.42367,0.84564,0.32466,-95.767,-0.27832,0.46261,-0.84174,212.15
    9948 
    9949 > view matrix models
    9950 > #6,-0.9278,0.28405,0.24186,150.65,0.33474,0.92007,0.2035,-81.565,-0.16473,0.26977,-0.94873,232.5
    9951 
    9952 > view matrix models
    9953 > #6,-0.9278,0.28405,0.24186,157.88,0.33474,0.92007,0.2035,-78.095,-0.16473,0.26977,-0.94873,240.3
    9954 
    9955 > ui mousemode right translate
    9956 
    9957 > ui mousemode right "rotate selected models"
    9958 
    9959 > ui mousemode right "translate selected models"
    9960 
    9961 > view matrix models
    9962 > #6,-0.9278,0.28405,0.24186,150.7,0.33474,0.92007,0.2035,-71.058,-0.16473,0.26977,-0.94873,238.81
    9963 
    9964 > view matrix models
    9965 > #6,-0.81634,0.56079,0.13821,115.48,0.57751,0.78886,0.21018,-84.976,0.0088387,0.2514,-0.96784,222.41
    9966 
    9967 > view matrix models
    9968 > #6,-0.81634,0.56079,0.13821,118.12,0.57751,0.78886,0.21018,-88.409,0.0088387,0.2514,-0.96784,222.87
    9969 
    9970 > view matrix models
    9971 > #6,-0.72877,0.68433,0.024424,104.87,0.66878,0.70364,0.24005,-92.216,0.14709,0.19127,-0.97045,213.88
    9972 
    9973 > view matrix models
    9974 > #6,-0.90019,-0.046344,0.43302,169.43,0.063082,0.96996,0.23495,-51.468,-0.4309,0.23882,-0.87023,266.36
    9975 
    9976 > view matrix models
    9977 > #6,-0.60307,-0.60859,0.51568,192.19,-0.56167,0.78301,0.26724,41.245,-0.56642,-0.12848,-0.81404,320.02
    9978 
    9979 > view matrix models
    9980 > #6,-0.60307,-0.60859,0.51568,192.34,-0.56167,0.78301,0.26724,41.792,-0.56642,-0.12848,-0.81404,319.91
    9981 
    9982 > view matrix models
    9983 > #6,-0.60307,-0.60859,0.51568,187.97,-0.56167,0.78301,0.26724,41.027,-0.56642,-0.12848,-0.81404,318.56
    9984 
    9985 > view matrix models
    9986 > #6,-0.58764,-0.56507,0.57911,174.47,-0.52116,0.81183,0.2633,33.233,-0.61892,-0.14708,-0.77156,322.6
    9987 
    9988 > view matrix models
    9989 > #6,-0.585,-0.56083,0.58587,172.96,-0.51905,0.81395,0.2609,32.978,-0.62319,-0.15147,-0.76726,323.18
    9990 
    9991 > view matrix models
    9992 > #6,-0.585,-0.56083,0.58587,173.17,-0.51905,0.81395,0.2609,34.93,-0.62319,-0.15147,-0.76726,323.99
    9993 
    9994 > view matrix models
    9995 > #6,-0.62592,-0.52364,0.57795,174.44,-0.48265,0.84219,0.24033,29.403,-0.61259,-0.12852,-0.77988,321.33
    9996 
    9997 > view matrix models
    9998 > #6,-0.69111,-0.45479,0.56172,175.69,-0.42947,0.88352,0.18694,23.722,-0.58131,-0.11205,-0.80593,318.36
    9999 
    10000 > view matrix models
    10001 > #6,-0.65976,-0.48623,0.57297,174.54,-0.42481,0.87026,0.24935,18.312,-0.61988,-0.078893,-0.78072,316.41
    10002 
    10003 > view matrix models
    10004 > #6,-0.77557,-0.36253,0.51678,179.41,-0.37089,0.92414,0.091687,21.793,-0.51081,-0.12056,-0.8512,315.68
    10005 
    10006 > fitmap #2 inMap #6
    10007 
    10008 Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
    10009 using 5456 atoms 
    10010 average map value = 0.1675, steps = 100 
    10011 shifted from previous position = 5.08 
    10012 rotated from previous position = 11.4 degrees 
    10013 atoms outside contour = 2741, contour level = 0.14718 
    10014  
    10015 Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
    10016 (#6) coordinates: 
    10017 Matrix rotation and translation 
    10018 0.99999997 0.00023517 -0.00007495 -0.02467320 
    10019 -0.00023517 0.99999997 0.00004464 0.02238681 
    10020 0.00007496 -0.00004462 1.00000000 -0.01444419 
    10021 Axis -0.17792930 -0.29884110 -0.93756875 
    10022 Axis point 109.46996506 96.42443602 0.00000000 
    10023 Rotation angle (degrees) 0.01437141 
    10024 Shift along axis 0.01124241 
    10025  
    10026 
    10027 > ui tool show "Fit in Map"
    10028 
    10029 > fitmap #2 inMap #6
    10030 
    10031 Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
    10032 using 5456 atoms 
    10033 average map value = 0.1675, steps = 44 
    10034 shifted from previous position = 0.0144 
    10035 rotated from previous position = 0.0126 degrees 
    10036 atoms outside contour = 2742, contour level = 0.14718 
    10037  
    10038 Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
    10039 (#6) coordinates: 
    10040 Matrix rotation and translation 
    10041 0.99999998 0.00016427 0.00012151 -0.03276013 
    10042 -0.00016428 0.99999998 0.00011396 0.00467381 
    10043 -0.00012149 -0.00011398 0.99999999 0.03076738 
    10044 Axis -0.48712062 0.51931506 -0.70215766 
    10045 Axis point 38.59729398 208.97661225 0.00000000 
    10046 Rotation angle (degrees) 0.01340494 
    10047 Shift along axis -0.00321824 
    10048  
    10049 
    10050 > ui mousemode right select
    10051 
    10052 > select clear
    10053 
    10054 > show #!1 models
    10055 
    10056 > show #!5 models
    10057 
    10058 > ui tool show Matchmaker
    10059 
    10060 > matchmaker #!2-3 to #1
    10061 
    10062 Parameters 
    10063 --- 
    10064 Chain pairing | bb 
    10065 Alignment algorithm | Needleman-Wunsch 
    10066 Similarity matrix | BLOSUM-62 
    10067 SS fraction | 0.3 
    10068 Gap open (HH/SS/other) | 18/18/6 
    10069 Gap extend | 1 
    10070 SS matrix |  |  | H | S | O 
    10071 ---|---|---|--- 
    10072 H | 6 | -9 | -6 
    10073 S |  | 6 | -6 
    10074 O |  |  | 4 
    10075 Iteration cutoff | 2 
    10076  
    10077 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
    10078 R (#2), sequence alignment score = 1937.2 
    10079 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    10080 2.786) 
    10081  
    10082 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
    10083 (#3), sequence alignment score = 2126.4 
    10084 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    10085 1.114) 
    10086  
    10087 
    10088 > matchmaker #!2-3 to #1
    10089 
    10090 Parameters 
    10091 --- 
    10092 Chain pairing | bb 
    10093 Alignment algorithm | Needleman-Wunsch 
    10094 Similarity matrix | BLOSUM-62 
    10095 SS fraction | 0.3 
    10096 Gap open (HH/SS/other) | 18/18/6 
    10097 Gap extend | 1 
    10098 SS matrix |  |  | H | S | O 
    10099 ---|---|---|--- 
    10100 H | 6 | -9 | -6 
    10101 S |  | 6 | -6 
    10102 O |  |  | 4 
    10103 Iteration cutoff | 2 
    10104  
    10105 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
    10106 R (#2), sequence alignment score = 1937.2 
    10107 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    10108 2.786) 
    10109  
    10110 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
    10111 (#3), sequence alignment score = 2126.4 
    10112 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    10113 1.114) 
    10114  
    10115 
    10116 > hide #!5 models
    10117 
    10118 > show #!5 models
    10119 
    10120 > hide #!5 models
    10121 
    10122 > hide #!1 models
    10123 
    10124 > undo
    10125 
    10126 [Repeated 3 time(s)]
    10127 
    10128 > select clear
    10129 
    10130 > hide #!1 models
    10131 
    10132 > hide #!5 models
    10133 
    10134 > fitmap #2 inMap #6
    10135 
    10136 Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
    10137 using 5456 atoms 
    10138 average map value = 0.1675, steps = 100 
    10139 shifted from previous position = 5.08 
    10140 rotated from previous position = 11.4 degrees 
    10141 atoms outside contour = 2741, contour level = 0.14718 
    10142  
    10143 Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
    10144 (#6) coordinates: 
    10145 Matrix rotation and translation 
    10146 0.99999997 0.00023517 -0.00007495 -0.02467320 
    10147 -0.00023517 0.99999997 0.00004464 0.02238681 
    10148 0.00007496 -0.00004462 1.00000000 -0.01444419 
    10149 Axis -0.17792930 -0.29884110 -0.93756875 
    10150 Axis point 109.46996368 96.42443805 0.00000000 
    10151 Rotation angle (degrees) 0.01437141 
    10152 Shift along axis 0.01124241 
    10153  
    10154 Drag select of 7 residues, 6 emd_34983_8HS2.map 
    10155 
    10156 > select clear
    10157 
    10158 > ui mousemode right translate
    10159 
    10160 > volume #5 level 0.1484
    10161 
    10162 > volume #6 level 0.1934
    10163 
    10164 > volume #6 level 0.1195
    10165 
    10166 > hide #!6 models
    10167 
    10168 > show #!1 models
    10169 
    10170 > show #!3 models
    10171 
    10172 > ui tool show Matchmaker
    10173 
    10174 > matchmaker #!2-3 to #1
    10175 
    10176 Parameters 
    10177 --- 
    10178 Chain pairing | bb 
    10179 Alignment algorithm | Needleman-Wunsch 
    10180 Similarity matrix | BLOSUM-62 
    10181 SS fraction | 0.3 
    10182 Gap open (HH/SS/other) | 18/18/6 
    10183 Gap extend | 1 
    10184 SS matrix |  |  | H | S | O 
    10185 ---|---|---|--- 
    10186 H | 6 | -9 | -6 
    10187 S |  | 6 | -6 
    10188 O |  |  | 4 
    10189 Iteration cutoff | 2 
    10190  
    10191 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
    10192 R (#2), sequence alignment score = 1937.2 
    10193 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    10194 2.786) 
    10195  
    10196 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
    10197 (#3), sequence alignment score = 2126.4 
    10198 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    10199 1.114) 
    10200  
    10201 
    10202 > matchmaker #!2-3 to #1
    10203 
    10204 Parameters 
    10205 --- 
    10206 Chain pairing | bb 
    10207 Alignment algorithm | Needleman-Wunsch 
    10208 Similarity matrix | BLOSUM-62 
    10209 SS fraction | 0.3 
    10210 Gap open (HH/SS/other) | 18/18/6 
    10211 Gap extend | 1 
    10212 SS matrix |  |  | H | S | O 
    10213 ---|---|---|--- 
    10214 H | 6 | -9 | -6 
    10215 S |  | 6 | -6 
    10216 O |  |  | 4 
    10217 Iteration cutoff | 2 
    10218  
    10219 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
    10220 R (#2), sequence alignment score = 1937.2 
    10221 RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
    10222 2.786) 
    10223  
    10224 Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
    10225 (#3), sequence alignment score = 2126.4 
    10226 RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
    10227 1.114) 
    10228  
    10229 
    10230 > select #1/R:32-56 #3/R:32-56
    10231 
    10232 308 atoms, 316 bonds, 50 residues, 2 models selected 
    10233 
    10234 > select #1/R:38 #3/R:38
    10235 
    10236 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10237 
    10238 > select #1/R:38 #3/R:38
    10239 
    10240 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10241 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10242 [171] RMSD: 0.428 
    10243  
    10244 
    10245 > ui mousemode right select
    10246 
    10247 > select add #2/R:38
    10248 
    10249 33 atoms, 33 bonds, 3 residues, 3 models selected 
    10250 
    10251 > select subtract #1/R:38
    10252 
    10253 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10254 
    10255 > select add #1/R:38
    10256 
    10257 33 atoms, 33 bonds, 3 residues, 3 models selected 
    10258 
    10259 > select subtract #3/R:38
    10260 
    10261 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10262 
    10263 > style sel stick
    10264 
    10265 Changed 22 atom styles 
    10266 
    10267 > show sel atoms
    10268 
    10269 > select add #3/R:38
    10270 
    10271 33 atoms, 33 bonds, 3 residues, 3 models selected 
    10272 
    10273 > show sel atoms
    10274 
    10275 > style sel stick
    10276 
    10277 Changed 33 atom styles 
    10278 
    10279 > name frozen F84 sel
    10280 
    10281 > color sel byhetero
    10282 
    10283 [Repeated 1 time(s)]
    10284 
    10285 > select clear
    10286 
    10287 [Repeated 1 time(s)]
    10288 
    10289 > ui mousemode right translate
    10290 
    10291 > select #1/R:130-131 #3/R:130-131
    10292 
    10293 46 atoms, 48 bonds, 4 residues, 2 models selected 
    10294 
    10295 > select #1/R:130 #3/R:130
    10296 
    10297 24 atoms, 24 bonds, 2 residues, 2 models selected 
    10298 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10299 [263] RMSD: 0.875 
    10300  
    10301 
    10302 > ui mousemode right select
    10303 
    10304 > select add #2/R:131
    10305 
    10306 35 atoms, 35 bonds, 3 residues, 3 models selected 
    10307 
    10308 > select subtract #1/R:130
    10309 
    10310 23 atoms, 23 bonds, 2 residues, 2 models selected 
    10311 
    10312 > select add #1/R:130
    10313 
    10314 35 atoms, 35 bonds, 3 residues, 3 models selected 
    10315 
    10316 > select subtract #3/R:130
    10317 
    10318 23 atoms, 23 bonds, 2 residues, 2 models selected 
    10319 
    10320 > show sel atoms
    10321 
    10322 > style sel stick
    10323 
    10324 Changed 23 atom styles 
    10325 
    10326 > select add #3/R:131
    10327 
    10328 34 atoms, 34 bonds, 3 residues, 3 models selected 
    10329 
    10330 > select subtract #3/R:131
    10331 
    10332 23 atoms, 23 bonds, 2 residues, 2 models selected 
    10333 
    10334 > select add #3/R:130
    10335 
    10336 35 atoms, 35 bonds, 3 residues, 3 models selected 
    10337 
    10338 > show sel atoms
    10339 
    10340 > style sel stick
    10341 
    10342 Changed 35 atom styles 
    10343 
    10344 > name frozen Y130 sel
    10345 
    10346 > color sel byhetero
    10347 
    10348 > select subtract #2/R:131
    10349 
    10350 24 atoms, 24 bonds, 2 residues, 2 models selected 
    10351 
    10352 > select add #2/R:131
    10353 
    10354 35 atoms, 35 bonds, 3 residues, 3 models selected 
    10355 
    10356 > select subtract #2/R:131
    10357 
    10358 24 atoms, 24 bonds, 2 residues, 2 models selected 
    10359 
    10360 > select add #2/R:130
    10361 
    10362 36 atoms, 36 bonds, 3 residues, 3 models selected 
    10363 
    10364 > show sel atoms
    10365 
    10366 > name frozen Y130 sel
    10367 
    10368 > color sel byhetero
    10369 
    10370 > select clear
    10371 
    10372 > select #2/R:131
    10373 
    10374 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10375 
    10376 > hide sel atoms
    10377 
    10378 > select clear
    10379 
    10380 > select Y130
    10381 
    10382 36 atoms, 36 bonds, 3 residues, 3 models selected 
    10383 
    10384 > select clear
    10385 
    10386 > select #1/R:134 #3/R:134
    10387 
    10388 16 atoms, 14 bonds, 2 residues, 2 models selected 
    10389 
    10390 > select #1/R:134 #3/R:134
    10391 
    10392 16 atoms, 14 bonds, 2 residues, 2 models selected 
    10393 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10394 [267] RMSD: 1.838 
    10395  
    10396 
    10397 > select add #2/R:134
    10398 
    10399 24 atoms, 21 bonds, 3 residues, 3 models selected 
    10400 
    10401 > show sel atoms
    10402 
    10403 > style sel stick
    10404 
    10405 Changed 24 atom styles 
    10406 
    10407 > name frozen M134 sel
    10408 
    10409 > color sel byhetero
    10410 
    10411 > select clear
    10412 
    10413 [Repeated 1 time(s)]
    10414 
    10415 > select #1/R:257-258 #3/R:257-258
    10416 
    10417 42 atoms, 44 bonds, 4 residues, 2 models selected 
    10418 
    10419 > select #1/R:257-258 #3/R:257-258
    10420 
    10421 42 atoms, 44 bonds, 4 residues, 2 models selected 
    10422 
    10423 > select #1/R:257-258 #3/R:257-258
    10424 
    10425 42 atoms, 44 bonds, 4 residues, 2 models selected 
    10426 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10427 [390-391] RMSD: 0.722 
    10428  
    10429 
    10430 > select #1/R:257-258 #3/R:257-258
    10431 
    10432 42 atoms, 44 bonds, 4 residues, 2 models selected 
    10433 
    10434 > select #1/R:257-258 #3/R:257-258
    10435 
    10436 42 atoms, 44 bonds, 4 residues, 2 models selected 
    10437 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10438 [390-391] RMSD: 0.722 
    10439  
    10440 
    10441 > select #1/R:257 #3/R:257
    10442 
    10443 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10444 
    10445 > select #1/R:257 #3/R:257
    10446 
    10447 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10448 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10449 [390] RMSD: 0.473 
    10450  
    10451 
    10452 > select subtract #1/R:257
    10453 
    10454 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10455 
    10456 > select add #1/R:257
    10457 
    10458 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10459 
    10460 > select add #2/R:258
    10461 
    10462 32 atoms, 32 bonds, 3 residues, 3 models selected 
    10463 
    10464 > select subtract #2/R:258
    10465 
    10466 22 atoms, 22 bonds, 2 residues, 2 models selected 
    10467 
    10468 > select add #2/R:257
    10469 
    10470 33 atoms, 33 bonds, 3 residues, 3 models selected 
    10471 
    10472 > show sel atoms
    10473 
    10474 > style sel stick
    10475 
    10476 Changed 33 atom styles 
    10477 
    10478 > color sel byhetero
    10479 
    10480 > name frozen F257 sel
    10481 
    10482 > select clear
    10483 
    10484 > select #2/B
    10485 
    10486 1617 atoms, 1658 bonds, 1 pseudobond, 218 residues, 2 models selected 
    10487 
    10488 > hide sel cartoons
    10489 
    10490 > select #2/C
    10491 
    10492 1623 atoms, 1658 bonds, 211 residues, 1 model selected 
    10493 
    10494 > hide sel cartoons
    10495 
    10496 > select #3/C
    10497 
    10498 438 atoms, 444 bonds, 57 residues, 1 model selected 
    10499 
    10500 > hide sel cartoons
    10501 
    10502 > select #3/B
    10503 
    10504 2590 atoms, 2637 bonds, 338 residues, 1 model selected 
    10505 
    10506 > hide sel cartoons
    10507 
    10508 > select #3/A
    10509 
    10510 1712 atoms, 1741 bonds, 2 pseudobonds, 218 residues, 2 models selected 
    10511 
    10512 > hide sel cartoons
    10513 
    10514 > select #3/S
    10515 
    10516 1760 atoms, 1806 bonds, 1 pseudobond, 232 residues, 2 models selected 
    10517 
    10518 > hide sel cartoons
    10519 
    10520 > select #2/R:31
    10521 
    10522 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10523 
    10524 > select #1/R:32
    10525 
    10526 2 atoms, 1 bond, 1 residue, 1 model selected 
    10527 
    10528 > select #1/R:32-33 #3/R:32-33
    10529 
    10530 19 atoms, 18 bonds, 4 residues, 2 models selected 
    10531 
    10532 > select #1/R:32-52 #3/R:32-52
    10533 
    10534 256 atoms, 262 bonds, 42 residues, 2 models selected 
    10535 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10536 [165-185] RMSD: 1.047 
    10537  
    10538 
    10539 > select #1/R:32 #3/R:32
    10540 
    10541 9 atoms, 7 bonds, 2 residues, 2 models selected 
    10542 
    10543 > select #1/R:32-49 #3/R:32-49
    10544 
    10545 228 atoms, 233 bonds, 36 residues, 2 models selected 
    10546 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10547 [165-182] RMSD: 1.077 
    10548  
    10549 
    10550 > select subtract #1/R:38@CG
    10551 
    10552 227 atoms, 230 bonds, 36 residues, 2 models selected 
    10553 
    10554 > select subtract #3/R:38
    10555 
    10556 216 atoms, 217 bonds, 35 residues, 2 models selected 
    10557 
    10558 > select subtract #1/R:38@CZ
    10559 
    10560 215 atoms, 215 bonds, 35 residues, 2 models selected 
    10561 
    10562 > select subtract #1/R:38@CE1
    10563 
    10564 214 atoms, 214 bonds, 35 residues, 2 models selected 
    10565 
    10566 > select subtract #1/R:38@CD1
    10567 
    10568 213 atoms, 214 bonds, 35 residues, 2 models selected 
    10569 
    10570 > ui mousemode right zoom
    10571 
    10572 > ui mousemode right translate
    10573 
    10574 > ui mousemode right select
    10575 
    10576 > select subtract #1/R:38@CD2
    10577 
    10578 212 atoms, 212 bonds, 35 residues, 2 models selected 
    10579 
    10580 > select subtract #1/R:38@CE2
    10581 
    10582 211 atoms, 212 bonds, 35 residues, 2 models selected 
    10583 
    10584 > select subtract #1/R:38@CB
    10585 
    10586 210 atoms, 212 bonds, 35 residues, 2 models selected 
    10587 
    10588 > select clear
    10589 
    10590 > select sequence VPLFHLFARLDEELHGFT
    10591 
    10592 Nothing selected 
    10593 
    10594 > select sequence VPLFHLFARLDEELHGFT
    10595 
    10596 Nothing selected 
    10597 
    10598 > select sequence VPLFHLFARLDEELHGFT
    10599 
    10600 Nothing selected 
    10601 
    10602 > select sequence VPLFHLFARLDEELHGFT
    10603 
    10604 Nothing selected 
    10605 
    10606 > select sequence VPLFHLFARLDEELHGFT
    10607 
    10608 Nothing selected 
    10609 
    10610 > select #1/R:32 #3/R:32
    10611 
    10612 9 atoms, 7 bonds, 2 residues, 2 models selected 
    10613 
    10614 > select #1/R:32-49 #3/R:32-49
    10615 
    10616 228 atoms, 233 bonds, 36 residues, 2 models selected 
    10617 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10618 [165-182] RMSD: 1.077 
    10619  
    10620 
    10621 > select clear
    10622 
    10623 > select #1/R:32 #3/R:32
    10624 
    10625 9 atoms, 7 bonds, 2 residues, 2 models selected 
    10626 
    10627 > select #1/R:32-49 #3/R:32-49
    10628 
    10629 228 atoms, 233 bonds, 36 residues, 2 models selected 
    10630 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10631 [165-182] RMSD: 1.077 
    10632  
    10633 
    10634 > select clear
    10635 
    10636 > ui tool show "Show Sequence Viewer"
    10637 
    10638 > sequence chain #1/R #3/R
    10639 
    10640 Alignment identifier is 1 
    10641 
    10642 > select #1/R:32 #3/R:32
    10643 
    10644 9 atoms, 7 bonds, 2 residues, 2 models selected 
    10645 
    10646 > select #1/R:32-49 #3/R:32-49
    10647 
    10648 228 atoms, 233 bonds, 36 residues, 2 models selected 
    10649 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10650 [165-182] RMSD: 1.077 
    10651  
    10652 
    10653 > select clear
    10654 
    10655 > transparency #1 #2 #3 70 ribbons
    10656 
    10657 > select #1/R:32 #3/R:32
    10658 
    10659 9 atoms, 7 bonds, 2 residues, 2 models selected 
    10660 
    10661 > select #1/R:32-49 #3/R:32-49
    10662 
    10663 228 atoms, 233 bonds, 36 residues, 2 models selected 
    10664 Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
    10665 [165-182] RMSD: 1.077 
    10666  
    10667 
    10668 > transparency sel 0 ribbons
    10669 
    10670 > ui tool show "Show Sequence Viewer"
    10671 
    10672 > sequence chain #2/R
    10673 
    10674 Alignment identifier is 2/R 
    10675 
    10676 > select #2/R:32
    10677 
    10678 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10679 
    10680 > select #2/R:32-49
    10681 
    10682 152 atoms, 157 bonds, 18 residues, 1 model selected 
    10683 
    10684 > transparency sel 0 ribbons
    10685 
    10686 > select clear
    10687 
    10688 > select F257
    10689 
    10690 33 atoms, 33 bonds, 3 residues, 3 models selected 
    10691 
    10692 > transparency sel 0 ribbons
    10693 
    10694 > select F84
    10695 
    10696 33 atoms, 33 bonds, 3 residues, 3 models selected 
    10697 
    10698 > transparency sel 0 ribbons
    10699 
    10700 > select M134
    10701 
    10702 24 atoms, 21 bonds, 3 residues, 3 models selected 
    10703 
    10704 > transparency sel 0 ribbons
    10705 
    10706 > select Y130
    10707 
    10708 36 atoms, 36 bonds, 3 residues, 3 models selected 
    10709 
    10710 > transparency sel 0 ribbons
    10711 
    10712 > ui mousemode right translate
    10713 
    10714 > ui mousemode right select
    10715 
    10716 > select clear
    10717 
    10718 > ui mousemode right translate
    10719 
    10720 > save "/Users/dongju/Desktop/Research projects-
    10721 > Monash/NRE/Figure2_DL/Fig3A_overlay with N-cap.cxs"
    10722 
    10723 > save "/Users/dongju/Desktop/Research projects-
    10724 > Monash/NRE/Figure2_DL/Fig3A_overlay with N-cap.png" width 3000 height 2253
    10725 > supersample 3
    10726 
    10727 > ui mousemode right select
    10728 
    10729 > select #2/R:278
    10730 
    10731 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10732 
    10733 > select add #2/R:277
    10734 
    10735 14 atoms, 12 bonds, 2 residues, 1 model selected 
    10736 
    10737 > select add #1/R:278
    10738 
    10739 19 atoms, 16 bonds, 3 residues, 2 models selected 
    10740 
    10741 > select add #1/R:280
    10742 
    10743 29 atoms, 26 bonds, 4 residues, 2 models selected 
    10744 
    10745 > select add #1/R:279
    10746 
    10747 41 atoms, 38 bonds, 5 residues, 2 models selected 
    10748 
    10749 > select add #1/R:282
    10750 
    10751 46 atoms, 42 bonds, 6 residues, 2 models selected 
    10752 
    10753 > select add #2/R:282
    10754 
    10755 51 atoms, 46 bonds, 7 residues, 2 models selected 
    10756 
    10757 > select add #1/R:281
    10758 
    10759 56 atoms, 50 bonds, 8 residues, 2 models selected 
    10760 
    10761 > select add #2/R:281
    10762 
    10763 63 atoms, 56 bonds, 9 residues, 2 models selected 
    10764 
    10765 > select add #1/R:257
    10766 
    10767 74 atoms, 67 bonds, 10 residues, 2 models selected 
    10768 
    10769 > select add #1/R:255
    10770 
    10771 81 atoms, 73 bonds, 11 residues, 2 models selected 
    10772 
    10773 > select add #1/R:256
    10774 
    10775 88 atoms, 80 bonds, 12 residues, 2 models selected 
    10776 
    10777 > select add #2/R:256
    10778 
    10779 95 atoms, 87 bonds, 13 residues, 2 models selected 
    10780 
    10781 > transparency sel 80 ribbons
    10782 
    10783 > select #2/R:257
    10784 
    10785 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10786 
    10787 > transparency sel 80 ribbons
    10788 
    10789 > select #1/R:256
    10790 
    10791 7 atoms, 7 bonds, 1 residue, 1 model selected 
    10792 
    10793 > transparency sel 80 ribbons
    10794 
    10795 > select #2/R:256
    10796 
    10797 7 atoms, 7 bonds, 1 residue, 1 model selected 
    10798 
    10799 > transparency sel 80 ribbons
    10800 
    10801 > select #2/R:278
    10802 
    10803 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10804 
    10805 > transparency sel 80 ribbons
    10806 
    10807 > select #1/R:278
    10808 
    10809 5 atoms, 4 bonds, 1 residue, 1 model selected 
    10810 
    10811 > transparency sel 80 ribbons
    10812 
    10813 > select #1/R:279
    10814 
    10815 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10816 
    10817 > transparency sel 80 ribbons
    10818 
    10819 > select #2/R:280
    10820 
    10821 10 atoms, 10 bonds, 1 residue, 1 model selected 
    10822 
    10823 > transparency sel 80 ribbons
    10824 
    10825 > select #2/R:281
    10826 
    10827 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10828 
    10829 > transparency sel 80 ribbons
    10830 
    10831 > select #1/R:281
    10832 
    10833 5 atoms, 4 bonds, 1 residue, 1 model selected 
    10834 
    10835 > transparency sel 80 ribbons
    10836 
    10837 > select #2/R:282
    10838 
    10839 5 atoms, 4 bonds, 1 residue, 1 model selected 
    10840 
    10841 > transparency sel 80 ribbons
    10842 
    10843 > select #2/R:281
    10844 
    10845 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10846 
    10847 > transparency sel 80 ribbons
    10848 
    10849 > select #3/R:283
    10850 
    10851 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10852 
    10853 > transparency sel 80 ribbons
    10854 
    10855 > select #1/R:284
    10856 
    10857 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10858 
    10859 > transparency sel 80 ribbons
    10860 
    10861 > select #1/R:283
    10862 
    10863 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10864 
    10865 > transparency sel 80 ribbons
    10866 
    10867 > select #2/R:256
    10868 
    10869 7 atoms, 7 bonds, 1 residue, 1 model selected 
    10870 
    10871 > transparency sel 80 ribbons
    10872 
    10873 > select #1/R:256
    10874 
    10875 7 atoms, 7 bonds, 1 residue, 1 model selected 
    10876 
    10877 > transparency sel 80 ribbons
    10878 
    10879 > select #1/R:255
    10880 
    10881 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10882 
    10883 > transparency sel 80 ribbons
    10884 
    10885 > select #2/R:255
    10886 
    10887 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10888 
    10889 > transparency sel 80 ribbons
    10890 
    10891 > select #1/R:257
    10892 
    10893 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10894 
    10895 > select #2/R:257
    10896 
    10897 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10898 
    10899 > transparency sel 80 ribbons
    10900 
    10901 > select #2/R:284
    10902 
    10903 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10904 
    10905 > transparency sel 80 ribbons
    10906 
    10907 > select #2/R:285
    10908 
    10909 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10910 
    10911 > transparency sel 80 ribbons
    10912 
    10913 > select #1/R:285
    10914 
    10915 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10916 
    10917 > transparency sel 80 ribbons
    10918 
    10919 > select #3/R:284
    10920 
    10921 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10922 
    10923 > transparency sel 80 ribbons
    10924 
    10925 > select #3/R:285
    10926 
    10927 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10928 
    10929 > transparency sel 80 ribbons
    10930 
    10931 > save "/Users/dongju/Desktop/Research projects-
    10932 > Monash/NRE/Figure2_DL/Fig3A_overlay focus on sites.png" width 2000 height
    10933 > 1502 supersample 3 transparentBackground true
    10934 
    10935 > hide #!1 models
    10936 
    10937 > hide #!3 models
    10938 
    10939 > show #!6 models
    10940 
    10941 > fitmap #2 inMap #6
    10942 
    10943 Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
    10944 using 5456 atoms 
    10945 average map value = 0.1675, steps = 100 
    10946 shifted from previous position = 5.08 
    10947 rotated from previous position = 11.4 degrees 
    10948 atoms outside contour = 2107, contour level = 0.11947 
    10949  
    10950 Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
    10951 (#6) coordinates: 
    10952 Matrix rotation and translation 
    10953 0.99999997 0.00023103 -0.00007011 -0.02470953 
    10954 -0.00023103 0.99999997 0.00004231 0.02222854 
    10955 0.00007012 -0.00004230 1.00000000 -0.01412533 
    10956 Axis -0.17258750 -0.28605508 -0.94254233 
    10957 Axis point 110.09560083 98.58536558 0.00000000 
    10958 Rotation angle (degrees) 0.01404400 
    10959 Shift along axis 0.01121969 
    10960  
    10961 
    10962 > volume #!6 showOutlineBox true
    10963 
    10964 > transparency #6.1 50
    10965 
    10966 > volume #!6 style surface
    10967 
    10968 > transparency #6.1 0
    10969 
    10970 > transparency #6.1 50
    10971 
    10972 > ui tool show "Volume Viewer"
    10973 
    10974 > volume #6 level 0.09308
    10975 
    10976 Drag select of 4 residues, 6 emd_34983_8HS2.map 
    10977 
    10978 > select clear
    10979 
    10980 > ui mousemode right translate
    10981 
    10982 > transparency #2 0 ribbons
    10983 
    10984 > ui mousemode right select
    10985 
    10986 > select #6
    10987 
    10988 2 models selected 
    10989 
    10990 > select #6
    10991 
    10992 2 models selected 
    10993 
    10994 > select #6
    10995 
    10996 2 models selected 
    10997 
    10998 > select #6
    10999 
    11000 2 models selected 
    11001 
    11002 > select #6
    11003 
    11004 2 models selected 
    11005 
    11006 > select #6
    11007 
    11008 2 models selected 
    11009 
    11010 > ui mousemode right "map eraser"
    11011 
    11012 > ui mousemode right translate
    11013 
    11014 > ui mousemode right zone
    11015 
    11016 > ui mousemode right select
    11017 
    11018 > select clear
    11019 
    11020 > ui mousemode right zone
    11021 
    11022 > surface dust #6 size 8.32
    11023 
    11024 > color zone #6 near #2 distance 4.99
    11025 
    11026 > transparency #6.1 0
    11027 
    11028 > transparency #6.1 50
    11029 
    11030 > color zone #6 near #2 distance 4.99
    11031 
    11032 > volume #!6 style mesh
    11033 
    11034 > volume #!6 style surface
    11035 
    11036 > transparency #6.1 0
    11037 
    11038 > transparency #6.1 50
    11039 
    11040 > ui tool show "Show Volume Menu"
    11041 
    11042 > ui tool show "Map Eraser"
    11043 
    11044 > volume erase #6 center 124.57,110.05,133.7 radius 6.5895
    11045 
    11046 Opened emd_34983_8HS2.map copy as #8, grid size 288,288,288, pixel 0.832,
    11047 shown at step 1, values float32 
    11048 
    11049 > volume erase #8 center 120.56,104.96,144.21 radius 6.5894
    11050 
    11051 > volume erase #8 center 117.1,104.97,149.62 radius 6.5894
    11052 
    11053 > volume erase #8 center 120.05,95.441,152.15 radius 6.5894
    11054 
    11055 > volume erase #8 center 109.24,96.945,141.85 radius 8.3866 outside true
    11056 
    11057 > volume erase #8 center 118.04,103.24,141.03 radius 8.3866
    11058 
    11059 > volume erase #8 center 111.63,95.96,140.03 radius 7.3083 outside true
    11060 
    11061 > ui mousemode right translate
    11062 
    11063 > ui mousemode right "map eraser"
    11064 
    11065 > volume erase #8 center 115.66,94.691,144.82 radius 3.2348
    11066 
    11067 > volume erase #8 center 113.16,95.458,147.38 radius 3.2348
    11068 
    11069 > volume erase #8 center 112.7,100.2,146.3 radius 3.2348
    11070 
    11071 > volume erase #8 center 110.12,98.585,145.4 radius 3.2348
    11072 
    11073 > volume erase #8 center 105.8,98.357,144.04 radius 3.2348
    11074 
    11075 > volume erase #8 center 105.85,99.35,141.39 radius 3.2348
    11076 
    11077 > volume erase #8 center 114.67,98.698,141.82 radius 3.2348
    11078 
    11079 > volume erase #8 center 113.72,98.218,138.99 radius 3.2348
    11080 
    11081 > volume erase #8 center 116.45,94.204,139.61 radius 3.2348
    11082 
    11083 > ui mousemode right translate
    11084 
    11085 > ui mousemode right "map eraser"
    11086 
    11087 > volume erase #8 center 108.61,87.652,142 radius 3.2348
    11088 
    11089 > volume erase #8 center 102.85,92.868,142.98 radius 3.2348
    11090 
    11091 > volume erase #8 center 103.11,93.869,142.87 radius 3.2348
    11092 
    11093 > volume erase #8 center 102.9,94.021,139.02 radius 3.2348
    11094 
    11095 > ui mousemode right translate
    11096 
    11097 > ui mousemode right "map eraser"
    11098 
    11099 > volume erase #8 center 103.68,93.71,140.23 radius 3.2348
    11100 
    11101 > undo
    11102 
    11103 [Repeated 2 time(s)]
    11104 
    11105 > volume erase #8 center 106.2,89.507,139.97 radius 3.2348
    11106 
    11107 > volume erase #8 center 109.44,100.3,138.17 radius 3.2348
    11108 
    11109 > volume erase #8 center 107.5,101.57,137.78 radius 3.2348
    11110 
    11111 > ui mousemode right translate
    11112 
    11113 > ui mousemode right "map eraser"
    11114 
    11115 > volume erase #8 center 108.5,101.66,141.97 radius 3.2348
    11116 
    11117 > ui mousemode right select
    11118 
    11119 > ui mousemode right rotate
    11120 
    11121 > ui mousemode right translate
    11122 
    11123 > select add #8
    11124 
    11125 4 models selected 
    11126 
    11127 > volume sel & #!8 style mesh
    11128 
    11129 > volume sel & #!8 style surface
    11130 
    11131 > volume sel & #!8 style image
    11132 
    11133 > volume sel & #!8 style mesh
    11134 
    11135 > volume #8 color #c64ee2
    11136 
    11137 > volume #8 color #c64ee200
    11138 
    11139 > volume #8 color #d736f5
    11140 
    11141 > volume #8 step 2
    11142 
    11143 > volume #8 step 1
    11144 
    11145 > ui mousemode right select
    11146 
    11147 > select clear
    11148 
    11149 > transparency #2 70 ribbons
    11150 
    11151 > volume #8 level 0.06783
    11152 
    11153 > ui mousemode right "map eraser"
    11154 
    11155 > volume erase #8 center 112.61,89.834,142.12 radius 1.8827
    11156 
    11157 > ui mousemode right select
    11158 
    11159 > ui mousemode right translate
    11160 
    11161 > ui mousemode right "map eraser"
    11162 
    11163 > preset "overall look" "publication 2 (depth-cued)"
    11164 
    11165 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    11166 Preset expands to these ChimeraX commands:
    11167 
    11168    
    11169    
    11170     set bg white
    11171     graphics silhouettes f
    11172     lighting depthCue t
    11173 
    11174  
    11175 
    11176 > select add #2
    11177 
    11178 5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected 
    11179 
    11180 > preset "overall look" "publication 1 (silhouettes)"
    11181 
    11182 Using preset: Overall Look / Publication 1 (Silhouettes) 
    11183 Preset expands to these ChimeraX commands:
    11184 
    11185    
    11186    
    11187     set bg white
    11188     graphics silhouettes t
    11189     lighting depthCue f
    11190 
    11191  
    11192 
    11193 > ui mousemode right select
    11194 
    11195 > select clear
    11196 
    11197 [Repeated 1 time(s)]
    11198 
    11199 > ui mousemode right translate
    11200 
    11201 > save "/Users/dongju/Desktop/Research projects-
    11202 > Monash/NRE/Figure2_DL/Fig3B_inactive GPR20 with the map.cxs"
    11203 
    11204 ——— End of log from Wed Feb 28 18:29:12 2024 ———
    11205 
    11206 opened ChimeraX session 
    11207 
    11208 > volume #!8 showOutlineBox false
    11209 
    11210 > hide #!8 models
    11211 
    11212 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
    11213 > draft/Figure 7C-GPR20 inactive-no G protein.cxs"
    11214 
    11215 > select add #2
    11216 
    11217 5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected 
    11218 
    11219 > show sel cartoons
    11220 
    11221 > ui mousemode right select
    11222 
    11223 > select clear
    11224 
    11225 > select #2/C
    11226 
    11227 1623 atoms, 1658 bonds, 211 residues, 1 model selected 
    11228 
    11229 > color sel #d3b5eaff
    11230 
    11231 > color sel #d4b6eaff
    11232 
    11233 > color sel #d7b9eaff
    11234 
    11235 > color sel #d8baebff
    11236 
    11237 > color sel #dbbdebff
    11238 
    11239 > color sel #dcbdebff
    11240 
    11241 > color sel #ddc0ecff
    11242 
    11243 [Repeated 1 time(s)]
    11244 
    11245 > color sel #dcc1ecff
    11246 
    11247 > color sel #dcc1edff
    11248 
    11249 > color sel #dcc3edff
    11250 
    11251 > color sel #ddc3edff
    11252 
    11253 [Repeated 1 time(s)]
    11254 
    11255 > color sel #dcc3edff
    11256 
    11257 [Repeated 1 time(s)]
    11258 
    11259 > color sel #dcc4edff
    11260 
    11261 > color sel #ddc6edff
    11262 
    11263 > color sel #dcc8eeff
    11264 
    11265 [Repeated 1 time(s)]
    11266 
    11267 > color sel #dbc8eeff
    11268 
    11269 [Repeated 2 time(s)]
    11270 
    11271 > color sel #dac8eeff
    11272 
    11273 [Repeated 2 time(s)]
    11274 
    11275 > color sel #d9c8eeff
    11276 
    11277 > color sel #d9caefff
    11278 
    11279 [Repeated 1 time(s)]
    11280 
    11281 > color sel #d8caefff
    11282 
    11283 > color sel #d7caefff
    11284 
    11285 > color sel #d7cbefff
    11286 
    11287 > color sel #d7caefff
    11288 
    11289 > color sel #d5caefff
    11290 
    11291 [Repeated 1 time(s)]
    11292 
    11293 > color sel #d4c9eeff
    11294 
    11295 > color sel #d3c8edff
    11296 
    11297 > color sel #d2c8edff
    11298 
    11299 > color sel #d1c7edff
    11300 
    11301 > color sel #d0c6edff
    11302 
    11303 [Repeated 1 time(s)]
    11304 
    11305 > color sel #cfc4ecff
    11306 
    11307 > color sel #c9beebff
    11308 
    11309 > color sel #c7baebff
    11310 
    11311 > color sel #c3b5e9ff
    11312 
    11313 > color sel #c1b2e9ff
    11314 
    11315 > color sel #c0b1e9ff
    11316 
    11317 > color sel #bfafe8ff
    11318 
    11319 > color sel #b5a2e6ff
    11320 
    11321 > color sel #b09ce5ff
    11322 
    11323 > color sel #ae9be5ff
    11324 
    11325 > color sel #ab98e4ff
    11326 
    11327 > color sel #a696e4ff
    11328 
    11329 > color sel #a496e4ff
    11330 
    11331 > color sel #a093e4ff
    11332 
    11333 > color sel #9e93e4ff
    11334 
    11335 > color sel #9d93e4ff
    11336 
    11337 > color sel #9e93e3ff
    11338 
    11339 [Repeated 2 time(s)]
    11340 
    11341 > color sel #9d93e3ff
    11342 
    11343 [Repeated 1 time(s)]
    11344 
    11345 > color sel #9e94e4ff
    11346 
    11347 > color sel #aaa1e5ff
    11348 
    11349 > color sel #bab3e9ff
    11350 
    11351 > color sel #c3bdebff
    11352 
    11353 > color sel #c4beebff
    11354 
    11355 > color sel #c4beecff
    11356 
    11357 > color sel #c4bfecff
    11358 
    11359 > color sel #c6c1ecff
    11360 
    11361 > color sel #cbc7edff
    11362 
    11363 > color sel #d1ccefff
    11364 
    11365 > color sel #d1cdefff
    11366 
    11367 [Repeated 1 time(s)]
    11368 
    11369 > color sel #d2cef0ff
    11370 
    11371 > color sel #d3d0f0ff
    11372 
    11373 > color sel #d6d4f0ff
    11374 
    11375 > color sel #dedcf2ff
    11376 
    11377 > color sel #e4e2f5ff
    11378 
    11379 > color sel #e5e4f6ff
    11380 
    11381 > color sel #ecebf7ff
    11382 
    11383 [Repeated 3 time(s)]
    11384 
    11385 > color sel #ebe8f6ff
    11386 
    11387 > color sel #e6e3f5ff
    11388 
    11389 > color sel #ded6f1ff
    11390 
    11391 > color sel #d8cdefff
    11392 
    11393 > color sel #c5afe8ff
    11394 
    11395 > color sel #bca2e6ff
    11396 
    11397 > color sel #b292e4ff
    11398 
    11399 > color sel #af8de3ff
    11400 
    11401 > color sel #af8ce3ff
    11402 
    11403 > color sel #af8de3ff
    11404 
    11405 > color sel #b18de3ff
    11406 
    11407 > color sel #b58ee3ff
    11408 
    11409 > color sel #bf8de3ff
    11410 
    11411 > color sel #c68ee4ff
    11412 
    11413 > color sel #d391e4ff
    11414 
    11415 > color sel #d993e4ff
    11416 
    11417 > color sel #dc94e5ff
    11418 
    11419 > color sel #dd95e4ff
    11420 
    11421 > color sel #dd95e3ff
    11422 
    11423 > color sel #dd94e3ff
    11424 
    11425 > color sel #dd95e1ff
    11426 
    11427 > color sel #de98dfff
    11428 
    11429 > color sel #df9de0ff
    11430 
    11431 > color sel #e1a7e2ff
    11432 
    11433 > color sel #e5b6e5ff
    11434 
    11435 > color sel #e8bee7ff
    11436 
    11437 > color sel #e9c3e7ff
    11438 
    11439 > color sel #e9c4e8ff
    11440 
    11441 > color sel #eac5e9ff
    11442 
    11443 > color sel #eed4ecff
    11444 
    11445 > color sel #efd8edff
    11446 
    11447 > color sel #f0d9eeff
    11448 
    11449 > color sel #f0daeeff
    11450 
    11451 > color sel #f0daedff
    11452 
    11453 [Repeated 2 time(s)]
    11454 
    11455 > color sel #efd8ecff
    11456 
    11457 > color sel #eac6e4ff
    11458 
    11459 > color sel #e8c1e3ff
    11460 
    11461 > color sel #e8c0e3ff
    11462 
    11463 [Repeated 1 time(s)]
    11464 
    11465 > color sel #e7bde2ff
    11466 
    11467 > color sel #e6b9e0ff
    11468 
    11469 > color sel #e5b7e0ff
    11470 
    11471 > color sel #e5b2deff
    11472 
    11473 > color sel #e3aedcff
    11474 
    11475 > color sel #e3addcff
    11476 
    11477 [Repeated 5 time(s)]
    11478 
    11479 > color sel #e3addaff
    11480 
    11481 [Repeated 2 time(s)]
    11482 
    11483 > color sel #e3add9ff
    11484 
    11485 [Repeated 1 time(s)]
    11486 
    11487 > color sel #e3aedaff
    11488 
    11489 > color sel #e4b0daff
    11490 
    11491 > color sel #e5b3dbff
    11492 
    11493 > color sel #e5b3dcff
    11494 
    11495 > color sel #e5b4dbff
    11496 
    11497 > color sel #e6b8ddff
    11498 
    11499 > color sel #e8c1dfff
    11500 
    11501 > color sel #e8c2e0ff
    11502 
    11503 [Repeated 1 time(s)]
    11504 
    11505 > color sel #e9c2e0ff
    11506 
    11507 > color sel #e8c2e0ff
    11508 
    11509 > color sel #e8c2dfff
    11510 
    11511 > color sel #e9c3e0ff
    11512 
    11513 [Repeated 2 time(s)]
    11514 
    11515 > select #2/B
    11516 
    11517 1617 atoms, 1658 bonds, 1 pseudobond, 218 residues, 2 models selected 
    11518 
    11519 > color (#!2 & sel) #3e6122ff
    11520 
    11521 > color (#!2 & sel) #3e6323ff
    11522 
    11523 > color (#!2 & sel) #406924ff
    11524 
    11525 > color (#!2 & sel) #406c25ff
    11526 
    11527 > color (#!2 & sel) #416f26ff
    11528 
    11529 > color (#!2 & sel) #437126ff
    11530 
    11531 > color (#!2 & sel) #447327ff
    11532 
    11533 > color (#!2 & sel) #467a2aff
    11534 
    11535 > color (#!2 & sel) #477c2aff
    11536 
    11537 [Repeated 2 time(s)]
    11538 
    11539 > color (#!2 & sel) #487b2aff
    11540 
    11541 > color (#!2 & sel) #497b2aff
    11542 
    11543 > color (#!2 & sel) #4b7829ff
    11544 
    11545 > color (#!2 & sel) #4b7528ff
    11546 
    11547 > color (#!2 & sel) #4c7428ff
    11548 
    11549 > color (#!2 & sel) #4c7327ff
    11550 
    11551 > color (#!2 & sel) #4c7227ff
    11552 
    11553 [Repeated 1 time(s)]
    11554 
    11555 > color (#!2 & sel) #4d6f27ff
    11556 
    11557 > color (#!2 & sel) #4f6d26ff
    11558 
    11559 > color (#!2 & sel) #516d26ff
    11560 
    11561 > color (#!2 & sel) #536d26ff
    11562 
    11563 > color (#!2 & sel) #556e27ff
    11564 
    11565 > color (#!2 & sel) #566d26ff
    11566 
    11567 > color (#!2 & sel) #5a6d27ff
    11568 
    11569 > color (#!2 & sel) #5b6c27ff
    11570 
    11571 > color (#!2 & sel) #5e6d27ff
    11572 
    11573 [Repeated 1 time(s)]
    11574 
    11575 > color (#!2 & sel) #5f6d27ff
    11576 
    11577 > color (#!2 & sel) #616f27ff
    11578 
    11579 > color (#!2 & sel) #626f28ff
    11580 
    11581 > color (#!2 & sel) #68762aff
    11582 
    11583 > color (#!2 & sel) #74832eff
    11584 
    11585 > color (#!2 & sel) #7d8b31ff
    11586 
    11587 > color (#!2 & sel) #808f32ff
    11588 
    11589 > color (#!2 & sel) #899835ff
    11590 
    11591 > color (#!2 & sel) #8e9e36ff
    11592 
    11593 > color (#!2 & sel) #93a438ff
    11594 
    11595 > color (#!2 & sel) #97a93aff
    11596 
    11597 > color (#!2 & sel) #99ac3aff
    11598 
    11599 > color (#!2 & sel) #9ab13cff
    11600 
    11601 > color (#!2 & sel) #9db63dff
    11602 
    11603 > color (#!2 & sel) #a0ba3eff
    11604 
    11605 > color (#!2 & sel) #a1bc3fff
    11606 
    11607 > color (#!2 & sel) #a7c542ff
    11608 
    11609 > color (#!2 & sel) #a7c842ff
    11610 
    11611 > color (#!2 & sel) #a8ca43ff
    11612 
    11613 > color (#!2 & sel) #a8cb43ff
    11614 
    11615 [Repeated 1 time(s)]
    11616 
    11617 > color (#!2 & sel) #a6ca43ff
    11618 
    11619 > color (#!2 & sel) #a5c942ff
    11620 
    11621 > color (#!2 & sel) #a1c842ff
    11622 
    11623 > color (#!2 & sel) #9ec541ff
    11624 
    11625 > color (#!2 & sel) #96be3fff
    11626 
    11627 > color (#!2 & sel) #92b83dff
    11628 
    11629 > color (#!2 & sel) #8baf3bff
    11630 
    11631 > color (#!2 & sel) #86ab39ff
    11632 
    11633 > color (#!2 & sel) #83a738ff
    11634 
    11635 > color (#!2 & sel) #79a036ff
    11636 
    11637 > color (#!2 & sel) #729934ff
    11638 
    11639 > color (#!2 & sel) #709733ff
    11640 
    11641 > color (#!2 & sel) #6e9633ff
    11642 
    11643 > color (#!2 & sel) #6d9532ff
    11644 
    11645 > color (#!2 & sel) #6b9332ff
    11646 
    11647 > color (#!2 & sel) #699231ff
    11648 
    11649 > color (#!2 & sel) #659131ff
    11650 
    11651 > color (#!2 & sel) #618d30ff
    11652 
    11653 > color (#!2 & sel) #5f8c30ff
    11654 
    11655 [Repeated 1 time(s)]
    11656 
    11657 > color (#!2 & sel) #5f8d30ff
    11658 
    11659 > color (#!2 & sel) #5e8d30ff
    11660 
    11661 > color (#!2 & sel) #5d8f30ff
    11662 
    11663 > color (#!2 & sel) #5c9231ff
    11664 
    11665 > color (#!2 & sel) #5c9331ff
    11666 
    11667 > color (#!2 & sel) #5d9732ff
    11668 
    11669 > color (#!2 & sel) #5c9732ff
    11670 
    11671 > color (#!2 & sel) #5d9833ff
    11672 
    11673 > color (#!2 & sel) #5d9c34ff
    11674 
    11675 > color (#!2 & sel) #5fa035ff
    11676 
    11677 > color (#!2 & sel) #61a336ff
    11678 
    11679 > color (#!2 & sel) #62a737ff
    11680 
    11681 > color (#!2 & sel) #62a837ff
    11682 
    11683 > color (#!2 & sel) #62a937ff
    11684 
    11685 > color (#!2 & sel) #62aa38ff
    11686 
    11687 > color (#!2 & sel) #63ac38ff
    11688 
    11689 > color (#!2 & sel) #63af39ff
    11690 
    11691 > color (#!2 & sel) #66b53aff
    11692 
    11693 > color (#!2 & sel) #68bb3cff
    11694 
    11695 > color (#!2 & sel) #6ac03eff
    11696 
    11697 > color (#!2 & sel) #6bc13eff
    11698 
    11699 > color (#!2 & sel) #6cc23eff
    11700 
    11701 > color (#!2 & sel) #6ac43eff
    11702 
    11703 > color (#!2 & sel) #6cc840ff
    11704 
    11705 > color (#!2 & sel) #6ecc41ff
    11706 
    11707 > color (#!2 & sel) #6fd042ff
    11708 
    11709 > color (#!2 & sel) #70d242ff
    11710 
    11711 [Repeated 1 time(s)]
    11712 
    11713 > color (#!2 & sel) #6fd242ff
    11714 
    11715 [Repeated 1 time(s)]
    11716 
    11717 > color (#!2 & sel) #6cd041ff
    11718 
    11719 > color (#!2 & sel) #67c840ff
    11720 
    11721 > color (#!2 & sel) #64c33eff
    11722 
    11723 > color (#!2 & sel) #5eb73bff
    11724 
    11725 > color (#!2 & sel) #5db53aff
    11726 
    11727 [Repeated 2 time(s)]
    11728 
    11729 > color (#!2 & sel) #5ab139ff
    11730 
    11731 > color (#!2 & sel) #58af39ff
    11732 
    11733 > color (#!2 & sel) #55ab37ff
    11734 
    11735 > color (#!2 & sel) #50a536ff
    11736 
    11737 > color (#!2 & sel) #4da235ff
    11738 
    11739 > color (#!2 & sel) #489832ff
    11740 
    11741 > color (#!2 & sel) #459030ff
    11742 
    11743 > color (#!2 & sel) #42892eff
    11744 
    11745 > color (#!2 & sel) #3d7e2bff
    11746 
    11747 > color (#!2 & sel) #3c7c2aff
    11748 
    11749 > color (#!2 & sel) #3a7929ff
    11750 
    11751 > color (#!2 & sel) #397628ff
    11752 
    11753 > color (#!2 & sel) #387528ff
    11754 
    11755 > color (#!2 & sel) #397528ff
    11756 
    11757 > color (#!2 & sel) #377227ff
    11758 
    11759 > color (#!2 & sel) #377127ff
    11760 
    11761 [Repeated 1 time(s)]
    11762 
    11763 > color (#!2 & sel) #367026ff
    11764 
    11765 > color (#!2 & sel) #356c25ff
    11766 
    11767 > color (#!2 & sel) #377127ff
    11768 
    11769 > color (#!2 & sel) #3c7c2bff
    11770 
    11771 > color (#!2 & sel) #3e822eff
    11772 
    11773 > color (#!2 & sel) #3f822eff
    11774 
    11775 > color (#!2 & sel) #3f842eff
    11776 
    11777 > color (#!2 & sel) #438c30ff
    11778 
    11779 > color (#!2 & sel) #469333ff
    11780 
    11781 [Repeated 2 time(s)]
    11782 
    11783 > color (#!2 & sel) #479534ff
    11784 
    11785 > color (#!2 & sel) #4a9b35ff
    11786 
    11787 > color (#!2 & sel) #4c9f37ff
    11788 
    11789 > color (#!2 & sel) #4ea338ff
    11790 
    11791 > color (#!2 & sel) #50a839ff
    11792 
    11793 > color (#!2 & sel) #52ad3bff
    11794 
    11795 > color (#!2 & sel) #57b83eff
    11796 
    11797 > color (#!2 & sel) #57b93eff
    11798 
    11799 > color (#!2 & sel) #58b93eff
    11800 
    11801 > color (#!2 & sel) #5bc140ff
    11802 
    11803 > color (#!2 & sel) #60cb43ff
    11804 
    11805 > color (#!2 & sel) #61ce44ff
    11806 
    11807 > color (#!2 & sel) #62d044ff
    11808 
    11809 > color (#!2 & sel) #63d345ff
    11810 
    11811 > color (#!2 & sel) #64d446ff
    11812 
    11813 > color (#!2 & sel) #64d546ff
    11814 
    11815 [Repeated 1 time(s)]
    11816 
    11817 > color (#!2 & sel) #65d646ff
    11818 
    11819 > color (#!2 & sel) #65d746ff
    11820 
    11821 > color (#!2 & sel) #66d847ff
    11822 
    11823 > color (#!2 & sel) #66d945ff
    11824 
    11825 > color (#!2 & sel) #67db45ff
    11826 
    11827 > color (#!2 & sel) #69df46ff
    11828 
    11829 > color (#!2 & sel) #69e046ff
    11830 
    11831 > color (#!2 & sel) #6ae146ff
    11832 
    11833 > color (#!2 & sel) #6ae346ff
    11834 
    11835 > color (#!2 & sel) #6ce447ff
    11836 
    11837 [Repeated 3 time(s)]
    11838 
    11839 > color (#!2 & sel) #6de447ff
    11840 
    11841 > color (#!2 & sel) #6ee547ff
    11842 
    11843 > color (#!2 & sel) #6ee447ff
    11844 
    11845 > color (#!2 & sel) #6fe347ff
    11846 
    11847 > color (#!2 & sel) #71e246ff
    11848 
    11849 > color (#!2 & sel) #71e146ff
    11850 
    11851 > color (#!2 & sel) #73e146ff
    11852 
    11853 [Repeated 1 time(s)]
    11854 
    11855 > color (#!2 & sel) #73e046ff
    11856 
    11857 [Repeated 1 time(s)]
    11858 
    11859 > color (#!2 & sel) #73df45ff
    11860 
    11861 > color (#!2 & sel) #74de45ff
    11862 
    11863 > color (#!2 & sel) #75df46ff
    11864 
    11865 > color (#!2 & sel) #74dd45ff
    11866 
    11867 > color (#!2 & sel) #74db45ff
    11868 
    11869 > color (#!2 & sel) #74da44ff
    11870 
    11871 > color (#!2 & sel) #74d844ff
    11872 
    11873 > color (#!2 & sel) #74d543ff
    11874 
    11875 > color (#!2 & sel) #73d342ff
    11876 
    11877 > color (#!2 & sel) #73d242ff
    11878 
    11879 > color (#!2 & sel) #72d042ff
    11880 
    11881 > color (#!2 & sel) #6ecd41ff
    11882 
    11883 > color (#!2 & sel) #6dcb40ff
    11884 
    11885 > color (#!2 & sel) #69c83fff
    11886 
    11887 > color (#!2 & sel) #68c63fff
    11888 
    11889 > color (#!2 & sel) #67c53eff
    11890 
    11891 > color (#!2 & sel) #66c33eff
    11892 
    11893 > color (#!2 & sel) #64c33eff
    11894 
    11895 > color (#!2 & sel) #61c03dff
    11896 
    11897 > color (#!2 & sel) #5fbf3dff
    11898 
    11899 > color (#!2 & sel) #5fbe3dff
    11900 
    11901 > color (#!2 & sel) #5dbd3cff
    11902 
    11903 > color (#!2 & sel) #5cbd3cff
    11904 
    11905 [Repeated 1 time(s)]
    11906 
    11907 > color (#!2 & sel) #5cbc3cff
    11908 
    11909 [Repeated 3 time(s)]
    11910 
    11911 > color (#!2 & sel) #5bbb3cff
    11912 
    11913 [Repeated 1 time(s)]
    11914 
    11915 > color (#!2 & sel) #5abb3cff
    11916 
    11917 [Repeated 2 time(s)]
    11918 
    11919 > color (#!2 & sel) #59bb3cff
    11920 
    11921 [Repeated 8 time(s)]
    11922 
    11923 > color (#!2 & sel) #58bb3cff
    11924 
    11925 > color (#!2 & sel) #59bb3cff
    11926 
    11927 > color (#!2 & sel) #58bb3cff
    11928 
    11929 > color (#!2 & sel) #59bb3dff
    11930 
    11931 [Repeated 1 time(s)]
    11932 
    11933 > color (#!2 & sel) #59bc3eff
    11934 
    11935 [Repeated 6 time(s)]
    11936 
    11937 > color (#!2 & sel) #59bd3fff
    11938 
    11939 [Repeated 2 time(s)]
    11940 
    11941 > color (#!2 & sel) #59bd40ff
    11942 
    11943 [Repeated 1 time(s)]
    11944 
    11945 > color (#!2 & sel) #5abe40ff
    11946 
    11947 [Repeated 1 time(s)]
    11948 
    11949 > color (#!2 & sel) #5bc041ff
    11950 
    11951 > color (#!2 & sel) #5cc342ff
    11952 
    11953 [Repeated 1 time(s)]
    11954 
    11955 > color (#!2 & sel) #5dc444ff
    11956 
    11957 > color (#!2 & sel) #5ec745ff
    11958 
    11959 > color (#!2 & sel) #5fc945ff
    11960 
    11961 > color (#!2 & sel) #5fca46ff
    11962 
    11963 > color (#!2 & sel) #60cb46ff
    11964 
    11965 > color (#!2 & sel) #5dc645ff
    11966 
    11967 > color (#!2 & sel) #5bbf42ff
    11968 
    11969 > color (#!2 & sel) #59bc42ff
    11970 
    11971 [Repeated 3 time(s)]
    11972 
    11973 > color (#!2 & sel) #58bb41ff
    11974 
    11975 > color (#!2 & sel) #56b540ff
    11976 
    11977 > color (#!2 & sel) #55b440ff
    11978 
    11979 > color (#!2 & sel) #55b33fff
    11980 
    11981 [Repeated 2 time(s)]
    11982 
    11983 > color (#!2 & sel) #53af3eff
    11984 
    11985 > color (#!2 & sel) #52ae3eff
    11986 
    11987 > color (#!2 & sel) #53ae40ff
    11988 
    11989 > color (#!2 & sel) #52ae40ff
    11990 
    11991 > color (#!2 & sel) #53ae41ff
    11992 
    11993 > color (#!2 & sel) #54b143ff
    11994 
    11995 > color (#!2 & sel) #54b245ff
    11996 
    11997 [Repeated 1 time(s)]
    11998 
    11999 > color (#!2 & sel) #55b345ff
    12000 
    12001 > color (#!2 & sel) #56b646ff
    12002 
    12003 > color (#!2 & sel) #58b949ff
    12004 
    12005 > color (#!2 & sel) #59bc4bff
    12006 
    12007 > color (#!2 & sel) #59bd4cff
    12008 
    12009 > color (#!2 & sel) #5abf4cff
    12010 
    12011 > color (#!2 & sel) #5bc14dff
    12012 
    12013 > color (#!2 & sel) #5dc44fff
    12014 
    12015 > color (#!2 & sel) #5ec852ff
    12016 
    12017 > color (#!2 & sel) #5fc953ff
    12018 
    12019 [Repeated 2 time(s)]
    12020 
    12021 > color (#!2 & sel) #5fca53ff
    12022 
    12023 [Repeated 2 time(s)]
    12024 
    12025 > color (#!2 & sel) #5fc953ff
    12026 
    12027 > color (#!2 & sel) #5bc151ff
    12028 
    12029 > color (#!2 & sel) #5abf50ff
    12030 
    12031 > color (#!2 & sel) #59bd4fff
    12032 
    12033 [Repeated 1 time(s)]
    12034 
    12035 > color (#!2 & sel) #58bb4fff
    12036 
    12037 > color (#!2 & sel) #57b74bff
    12038 
    12039 > color (#!2 & sel) #54b246ff
    12040 
    12041 > color (#!2 & sel) #54b245ff
    12042 
    12043 > color (#!2 & sel) #53b041ff
    12044 
    12045 > color (#!2 & sel) #53af41ff
    12046 
    12047 [Repeated 2 time(s)]
    12048 
    12049 > color (#!2 & sel) #53af40ff
    12050 
    12051 > color (#!2 & sel) #51ab3aff
    12052 
    12053 > color (#!2 & sel) #4fa636ff
    12054 
    12055 > color (#!2 & sel) #4e9f34ff
    12056 
    12057 > color (#!2 & sel) #4b9932ff
    12058 
    12059 > color (#!2 & sel) #3f7929ff
    12060 
    12061 [Repeated 1 time(s)]
    12062 
    12063 > color (#!2 & sel) #3e7829ff
    12064 
    12065 > color (#!2 & sel) #3d7628ff
    12066 
    12067 > color (#!2 & sel) #396e25ff
    12068 
    12069 > color (#!2 & sel) #315e21ff
    12070 
    12071 > color (#!2 & sel) #2f5a1fff
    12072 
    12073 > color (#!2 & sel) #2b531dff
    12074 
    12075 > color (#!2 & sel) #294d1bff
    12076 
    12077 > color (#!2 & sel) #27491aff
    12078 
    12079 > color (#!2 & sel) #28481aff
    12080 
    12081 > color (#!2 & sel) #284719ff
    12082 
    12083 > color (#!2 & sel) #294619ff
    12084 
    12085 > color (#!2 & sel) #2a4619ff
    12086 
    12087 [Repeated 1 time(s)]
    12088 
    12089 > color (#!2 & sel) #2b4519ff
    12090 
    12091 > color (#!2 & sel) #2c4519ff
    12092 
    12093 > color (#!2 & sel) #2e471aff
    12094 
    12095 > color (#!2 & sel) #30491aff
    12096 
    12097 > color (#!2 & sel) #334b1bff
    12098 
    12099 > color (#!2 & sel) #37511dff
    12100 
    12101 > color (#!2 & sel) #3c561fff
    12102 
    12103 > color (#!2 & sel) #3e5920ff
    12104 
    12105 > color (#!2 & sel) #445f22ff
    12106 
    12107 > color (#!2 & sel) #466122ff
    12108 
    12109 > color (#!2 & sel) #476223ff
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    12111 > color (#!2 & sel) #4b6825ff
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    12113 > color (#!2 & sel) #517027ff
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    12115 > color (#!2 & sel) #547629ff
    12116 
    12117 > color (#!2 & sel) #557a2aff
    12118 
    12119 > color (#!2 & sel) #577c2bff
    12120 
    12121 > color (#!2 & sel) #577e2bff
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    12123 > color (#!2 & sel) #5a812cff
    12124 
    12125 > color (#!2 & sel) #5c852dff
    12126 
    12127 > color (#!2 & sel) #5e882eff
    12128 
    12129 > color (#!2 & sel) #5f8b2fff
    12130 
    12131 > color (#!2 & sel) #639231ff
    12132 
    12133 [Repeated 1 time(s)]
    12134 
    12135 > color (#!2 & sel) #639331ff
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    12137 [Repeated 1 time(s)]
    12138 
    12139 > color (#!2 & sel) #659733ff
    12140 
    12141 > color (#!2 & sel) #669933ff
    12142 
    12143 > color (#!2 & sel) #679b34ff
    12144 
    12145 [Repeated 2 time(s)]
    12146 
    12147 > color (#!2 & sel) #679933ff
    12148 
    12149 > color (#!2 & sel) #6b9933ff
    12150 
    12151 > color (#!2 & sel) #6b9a33ff
    12152 
    12153 > color (#!2 & sel) #6c9933ff
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    12155 > color (#!2 & sel) #6f9934ff
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    12157 > color (#!2 & sel) #709934ff
    12158 
    12159 > color (#!2 & sel) #729934ff
    12160 
    12161 > color (#!2 & sel) #739934ff
    12162 
    12163 > color (#!2 & sel) #739834ff
    12164 
    12165 > color (#!2 & sel) #729834ff
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    12167 > color (#!2 & sel) #749834ff
    12168 
    12169 > color (#!2 & sel) #759834ff
    12170 
    12171 > color (#!2 & sel) #779834ff
    12172 
    12173 > color (#!2 & sel) #789834ff
    12174 
    12175 [Repeated 1 time(s)]
    12176 
    12177 > color (#!2 & sel) #7a9834ff
    12178 
    12179 [Repeated 1 time(s)]
    12180 
    12181 > color (#!2 & sel) #7b9734ff
    12182 
    12183 [Repeated 2 time(s)]
    12184 
    12185 > color (#!2 & sel) #7c9734ff
    12186 
    12187 > color (#!2 & sel) #7c9834ff
    12188 
    12189 [Repeated 1 time(s)]
    12190 
    12191 > color (#!2 & sel) #7f9834ff
    12192 
    12193 [Repeated 1 time(s)]
    12194 
    12195 > color (#!2 & sel) #809734ff
    12196 
    12197 > color (#!2 & sel) #829534ff
    12198 
    12199 > color (#!2 & sel) #839634ff
    12200 
    12201 > color (#!2 & sel) #829533ff
    12202 
    12203 [Repeated 1 time(s)]
    12204 
    12205 > color (#!2 & sel) #829534ff
    12206 
    12207 > color (#!2 & sel) #839534ff
    12208 
    12209 > color (#!2 & sel) #829533ff
    12210 
    12211 > color (#!2 & sel) #839534ff
    12212 
    12213 [Repeated 4 time(s)]
    12214 
    12215 > color (#!2 & sel) #839634ff
    12216 
    12217 [Repeated 1 time(s)]
    12218 
    12219 > color (#!2 & sel) #839734ff
    12220 
    12221 > color (#!2 & sel) #819533ff
    12222 
    12223 > color (#!2 & sel) #798b30ff
    12224 
    12225 > color (#!2 & sel) #778930ff
    12226 
    12227 > color (#!2 & sel) #74882fff
    12228 
    12229 > color (#!2 & sel) #71862fff
    12230 
    12231 > color (#!2 & sel) #6e852eff
    12232 
    12233 > color (#!2 & sel) #6d852eff
    12234 
    12235 > color (#!2 & sel) #69842eff
    12236 
    12237 > color (#!2 & sel) #68842eff
    12238 
    12239 > color (#!2 & sel) #68832dff
    12240 
    12241 > color (#!2 & sel) #66832dff
    12242 
    12243 [Repeated 1 time(s)]
    12244 
    12245 > color (#!2 & sel) #65832dff
    12246 
    12247 > color (#!2 & sel) #63832dff
    12248 
    12249 > color (#!2 & sel) #60822cff
    12250 
    12251 [Repeated 2 time(s)]
    12252 
    12253 > color (#!2 & sel) #5e822cff
    12254 
    12255 > color (#!2 & sel) #5c822cff
    12256 
    12257 [Repeated 2 time(s)]
    12258 
    12259 > color (#!2 & sel) #5b822cff
    12260 
    12261 > color (#!2 & sel) #5a822cff
    12262 
    12263 > color (#!2 & sel) #5a832dff
    12264 
    12265 > color (#!2 & sel) #5c882eff
    12266 
    12267 > color (#!2 & sel) #5b8b2fff
    12268 
    12269 > color (#!2 & sel) #5c8d30ff
    12270 
    12271 > color (#!2 & sel) #5e9131ff
    12272 
    12273 > color (#!2 & sel) #609532ff
    12274 
    12275 [Repeated 2 time(s)]
    12276 
    12277 > select clear
    12278 
    12279 [Repeated 1 time(s)]
    12280 
    12281 > ui mousemode right translate
    12282 
    12283 > transparency all 0 ribbons
    12284 
    12285 > lighting soft
    12286 
    12287 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
    12288 > draft/Figure 7C-GPR20 inactive-no G protein.cxs"
    12289 
    12290 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
    12291 > draft/Figure 7C-GPR20 inactive structure with tags.png" width 1751 height
    12292 > 1200 supersample 3
    12293 
    12294 > close session
    12295 
    12296 > open 8tb7
    12297 
    12298 8tb7 title: 
    12299 Cryo-EM Structure of GPR61- [more info...] 
    12300  
    12301 Chain information for 8tb7 #1 
    12302 --- 
    12303 Chain | Description | UniProt 
    12304 H | Fab24 BAK5 heavy chain |   
    12305 L | Fab24 BAK5 light chain |   
    12306 N | Fab hinge-binding nanobody |   
    12307 R | G-protein coupled receptor 61,Soluble cytochrome b562 | GPR61_HUMAN 11-242 365-532, C562_ECOLX 248-352 
    12308  
    12309 Non-standard residues in 8tb7 #1 
    12310 --- 
    12311 ZOB —
    12312 6-{[(3,5-difluoropyridin-4-yl)methyl]amino}-N-(4-ethoxy-6-methylpyrimidin-2-yl)-2-methoxy-N-(2-methoxyethyl)pyridine-3-sulfonamide 
    12313  
    12314 
    12315 > rename #1 GPR61_BRIL_8tb7
    12316 
    12317 > hide atoms
    12318 
    12319 > select /R
    12320 
    12321 5276 atoms, 5329 bonds, 4 pseudobonds, 330 residues, 2 models selected 
    12322 
    12323 > color (#!1 & sel) byhetero
    12324 
    12325 > color (#!1 & sel) #131db3ff
    12326 
    12327 > color (#!1 & sel) #101dbfff
    12328 
    12329 > color (#!1 & sel) #0b1ccfff
    12330 
    12331 > color (#!1 & sel) #061cd8ff
    12332 
    12333 > color (#!1 & sel) #001aeeff
    12334 
    12335 > color (#!1 & sel) #001bf1ff
    12336 
    12337 > color (#!1 & sel) #001bf3ff
    12338 
    12339 > color (#!1 & sel) #001bf5ff
    12340 
    12341 > color (#!1 & sel) #001df1ff
    12342 
    12343 > color (#!1 & sel) #001ef0ff
    12344 
    12345 [Repeated 1 time(s)]
    12346 
    12347 > color (#!1 & sel) #001feeff
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    12349 > color (#!1 & sel) #0923eaff
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    12351 > color (#!1 & sel) #0b26ebff
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    12353 > color (#!1 & sel) #2150ebff
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    12355 > color (#!1 & sel) #4ca7edff
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    12357 > color (#!1 & sel) #61d3f1ff
    12358 
    12359 > color (#!1 & sel) #70f1eeff
    12360 
    12361 > color (#!1 & sel) #71f1e5ff
    12362 
    12363 [Repeated 1 time(s)]
    12364 
    12365 > color (#!1 & sel) #70efe6ff
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    12369 > color (#!1 & sel) #6cdceaff
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    12371 > color (#!1 & sel) #5bade5ff
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    12373 > color (#!1 & sel) #5391e3ff
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    12375 > color (#!1 & sel) #528ee3ff
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    12377 > color (#!1 & sel) #5391e3ff
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    12379 > color (#!1 & sel) #65b3e4ff
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    12381 > color (#!1 & sel) #72cae5ff
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    12383 > color (#!1 & sel) #76cce4ff
    12384 
    12385 > color (#!1 & sel) #84d1e5ff
    12386 
    12387 > color (#!1 & sel) #8ad4e5ff
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    12389 [Repeated 1 time(s)]
    12390 
    12391 > color (#!1 & sel) #8ad5e5ff
    12392 
    12393 > color (#!1 & sel) #8cd8e5ff
    12394 
    12395 > color (#!1 & sel) #8edae5ff
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    12397 > color (#!1 & sel) #8cd3e4ff
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    12399 > color (#!1 & sel) #8194e2ff
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    12401 > color (#!1 & sel) #7d7fe1ff
    12402 
    12403 > color (#!1 & sel) #817fe1ff
    12404 
    12405 > color (#!1 & sel) #857fe2ff
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    12407 > color (#!1 & sel) #8d7ae1ff
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    12409 > color (#!1 & sel) #ab77e0ff
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    12411 > color (#!1 & sel) #c26ae1ff
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    12413 > color (#!1 & sel) #c368e0ff
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    12415 [Repeated 1 time(s)]
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    12423 > color (#!1 & sel) #d27ee2ff
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    12425 > color (#!1 & sel) #d486e3ff
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    12427 > color (#!1 & sel) #d488e3ff
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    12429 > color (#!1 & sel) #d58ae3ff
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    12431 > color (#!1 & sel) #d893e4ff
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    12433 > color (#!1 & sel) #d995e5ff
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    12435 [Repeated 1 time(s)]
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    12439 > color (#!1 & sel) #e1a1e7ff
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    12441 [Repeated 1 time(s)]
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    12445 > color (#!1 & sel) #e0a2e5ff
    12446 
    12447 > color (#!1 & sel) #df9ee2ff
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    12449 > color (#!1 & sel) #d978d8ff
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    12451 > color (#!1 & sel) #da47d4ff
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    12453 > color (#!1 & sel) #e439d5ff
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    12455 > color (#!1 & sel) #e738d7ff
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    12457 > color (#!1 & sel) #e937c8ff
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    12459 > color (#!1 & sel) #dd36bcff
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    12461 > color (#!1 & sel) #d935b7ff
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    12463 > color (#!1 & sel) #d734b5ff
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    12465 > color (#!1 & sel) #cb33b4ff
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    12467 > color (#!1 & sel) #b830b3ff
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    12469 > color (#!1 & sel) #af30b6ff
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    12471 > color (#!1 & sel) #ae2fb6ff
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    12473 [Repeated 1 time(s)]
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    12477 > color (#!1 & sel) #a42db3ff
    12478 
    12479 > color (#!1 & sel) #a42eb3ff
    12480 
    12481 [Repeated 1 time(s)]
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    12483 > color (#!1 & sel) #b531ceff
    12484 
    12485 > color (#!1 & sel) #bd32dbff
    12486 
    12487 [Repeated 1 time(s)]
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    12491 > color (#!1 & sel) #c533deff
    12492 
    12493 > color (#!1 & sel) #c934dfff
    12494 
    12495 > color (#!1 & sel) #d136ddff
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    12497 > color (#!1 & sel) #ce35d0ff
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    12499 > color (#!1 & sel) #c933c2ff
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    12501 > color (#!1 & sel) #c633baff
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    12505 > color (#!1 & sel) #b12f9bff
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    12511 > color (#!1 & sel) #a52c90ff
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    12514 
    12515 > color (#!1 & sel) #902886ff
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    12519 > color (#!1 & sel) #7c2473ff
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    12521 > color (#!1 & sel) #7b2472ff
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    12523 > color (#!1 & sel) #7c2470ff
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    12525 > color (#!1 & sel) #7f2468ff
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    12527 > color (#!1 & sel) #812465ff
    12528 
    12529 > color (#!1 & sel) #822464ff
    12530 
    12531 > color (#!1 & sel) #8e287eff
    12532 
    12533 > color (#!1 & sel) #922983ff
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    12535 [Repeated 1 time(s)]
    12536 
    12537 > color (#!1 & sel) #9c2ba1ff
    12538 
    12539 > color (#!1 & sel) #a02ca9ff
    12540 
    12541 > color (#!1 & sel) #a32dadff
    12542 
    12543 > color (#!1 & sel) #aa2fb5ff
    12544 
    12545 [Repeated 1 time(s)]
    12546 
    12547 > color (#!1 & sel) #b230bbff
    12548 
    12549 > color (#!1 & sel) #b630b0ff
    12550 
    12551 > color (#!1 & sel) #b630acff
    12552 
    12553 > color (#!1 & sel) #b630aaff
    12554 
    12555 > color (#!1 & sel) #b630a9ff
    12556 
    12557 > color (#!1 & sel) #b730a3ff
    12558 
    12559 > color (#!1 & sel) #b730a0ff
    12560 
    12561 > color (#!1 & sel) #b9309cff
    12562 
    12563 > color (#!1 & sel) #ba2f98ff
    12564 
    12565 > color (#!1 & sel) #bb3097ff
    12566 
    12567 > color (#!1 & sel) #bb308fff
    12568 
    12569 > color (#!1 & sel) #be3086ff
    12570 
    12571 > color (#!1 & sel) #bf3086ff
    12572 
    12573 > color (#!1 & sel) #bf3084ff
    12574 
    12575 > color (#!1 & sel) #be3086ff
    12576 
    12577 > color (#!1 & sel) #b02e83ff
    12578 
    12579 > color (#!1 & sel) #aa2c83ff
    12580 
    12581 > color (#!1 & sel) #a02b80ff
    12582 
    12583 > color (#!1 & sel) #9c2a7fff
    12584 
    12585 > color (#!1 & sel) #9b2a7eff
    12586 
    12587 > color (#!1 & sel) #932979ff
    12588 
    12589 > color (#!1 & sel) #8a2774ff
    12590 
    12591 > color (#!1 & sel) #892673ff
    12592 
    12593 > color (#!1 & sel) #882672ff
    12594 
    12595 > color (#!1 & sel) #832572ff
    12596 
    12597 > color (#!1 & sel) #832571ff
    12598 
    12599 > color (#!1 & sel) #8a2774ff
    12600 
    12601 > color (#!1 & sel) #92287aff
    12602 
    12603 > color (#!1 & sel) #95297bff
    12604 
    12605 > color (#!1 & sel) #98297dff
    12606 
    12607 > color (#!1 & sel) #9c2a80ff
    12608 
    12609 > color (#!1 & sel) #9e2a81ff
    12610 
    12611 > color (#!1 & sel) #9f2b82ff
    12612 
    12613 > color (#!1 & sel) #ae2e8fff
    12614 
    12615 > color (#!1 & sel) #b62f94ff
    12616 
    12617 [Repeated 2 time(s)]
    12618 
    12619 > color (#!1 & sel) #ae2e95ff
    12620 
    12621 > color (#!1 & sel) #a32c93ff
    12622 
    12623 > color (#!1 & sel) #a12c91ff
    12624 
    12625 > color (#!1 & sel) #9f2b90ff
    12626 
    12627 > color (#!1 & sel) #9e2b93ff
    12628 
    12629 > color (#!1 & sel) #9e2b94ff
    12630 
    12631 > color (#!1 & sel) #962a95ff
    12632 
    12633 > color (#!1 & sel) #962a96ff
    12634 
    12635 > color (#!1 & sel) #972b96ff
    12636 
    12637 > color (#!1 & sel) #9b2b9bff
    12638 
    12639 > color (#!1 & sel) #9e2c9eff
    12640 
    12641 > color (#!1 & sel) #a22da7ff
    12642 
    12643 > color (#!1 & sel) #a42eadff
    12644 
    12645 > color (#!1 & sel) #a62eb0ff
    12646 
    12647 > color (#!1 & sel) #a72eb2ff
    12648 
    12649 > color (#!1 & sel) #a82eb3ff
    12650 
    12651 > color (#!1 & sel) #ac2fb7ff
    12652 
    12653 > color (#!1 & sel) #b030bbff
    12654 
    12655 > color (#!1 & sel) #b030bcff
    12656 
    12657 > color (#!1 & sel) #b330bfff
    12658 
    12659 > color (#!1 & sel) #ba32c5ff
    12660 
    12661 > color (#!1 & sel) #be32c9ff
    12662 
    12663 > color (#!1 & sel) #c133ccff
    12664 
    12665 > color (#!1 & sel) #c233cdff
    12666 
    12667 > color (#!1 & sel) #c233ceff
    12668 
    12669 > color (#!1 & sel) #bc32d2ff
    12670 
    12671 > color (#!1 & sel) #b731d4ff
    12672 
    12673 > color (#!1 & sel) #b631d4ff
    12674 
    12675 > color (#!1 & sel) #b12fd4ff
    12676 
    12677 > color (#!1 & sel) #b02fd5ff
    12678 
    12679 > color (#!1 & sel) #ac2fd6ff
    12680 
    12681 > color (#!1 & sel) #ac2ed7ff
    12682 
    12683 > color (#!1 & sel) #ac2fd9ff
    12684 
    12685 > color (#!1 & sel) #ad2fd9ff
    12686 
    12687 > color (#!1 & sel) #ae2fdbff
    12688 
    12689 > color (#!1 & sel) #b22fdfff
    12690 
    12691 > color (#!1 & sel) #b330e1ff
    12692 
    12693 > color (#!1 & sel) #b630e3ff
    12694 
    12695 > color (#!1 & sel) #c232eaff
    12696 
    12697 > color (#!1 & sel) #c733ebff
    12698 
    12699 > color (#!1 & sel) #ca34ecff
    12700 
    12701 > color (#!1 & sel) #cf35edff
    12702 
    12703 > color (#!1 & sel) #d035edff
    12704 
    12705 > color (#!1 & sel) #d336eeff
    12706 
    12707 > color (#!1 & sel) #db37f0ff
    12708 
    12709 > color (#!1 & sel) #e038f1ff
    12710 
    12711 > color (#!1 & sel) #e639f2ff
    12712 
    12713 > color (#!1 & sel) #e739efff
    12714 
    12715 > color (#!1 & sel) #e839ebff
    12716 
    12717 > color (#!1 & sel) #e839e9ff
    12718 
    12719 [Repeated 1 time(s)]
    12720 
    12721 > color (#!1 & sel) #e938e2ff
    12722 
    12723 > color (#!1 & sel) #e837cdff
    12724 
    12725 > color (#!1 & sel) #c63191ff
    12726 
    12727 > color (#!1 & sel) #b82e86ff
    12728 
    12729 > color (#!1 & sel) #b72f8fff
    12730 
    12731 > color (#!1 & sel) #b42f96ff
    12732 
    12733 > color (#!1 & sel) #ae2e96ff
    12734 
    12735 > color (#!1 & sel) #a52d94ff
    12736 
    12737 > color (#!1 & sel) #a12c97ff
    12738 
    12739 > color (#!1 & sel) #a02c96ff
    12740 
    12741 > color (#!1 & sel) #9f2c95ff
    12742 
    12743 > color (#!1 & sel) #9e2b96ff
    12744 
    12745 > color (#!1 & sel) #9e2b99ff
    12746 
    12747 > color (#!1 & sel) #9d2b98ff
    12748 
    12749 > color (#!1 & sel) #9c2b98ff
    12750 
    12751 [Repeated 1 time(s)]
    12752 
    12753 > color (#!1 & sel) #9c2b94ff
    12754 
    12755 > color (#!1 & sel) #9d2b87ff
    12756 
    12757 > color (#!1 & sel) #9e2a81ff
    12758 
    12759 > color (#!1 & sel) #9e2a80ff
    12760 
    12761 > color (#!1 & sel) #a02b7cff
    12762 
    12763 > color (#!1 & sel) #a12b7cff
    12764 
    12765 > color (#!1 & sel) #a22b79ff
    12766 
    12767 > color (#!1 & sel) #a32b72ff
    12768 
    12769 > color (#!1 & sel) #a22b6eff
    12770 
    12771 > color (#!1 & sel) #a22a69ff
    12772 
    12773 > color (#!1 & sel) #a12a62ff
    12774 
    12775 > color (#!1 & sel) #a02a5cff
    12776 
    12777 > color (#!1 & sel) #9f2a5cff
    12778 
    12779 > color (#!1 & sel) #9f2a5bff
    12780 
    12781 > color (#!1 & sel) #93286bff
    12782 
    12783 > color (#!1 & sel) #902772ff
    12784 
    12785 > color (#!1 & sel) #902873ff
    12786 
    12787 > color (#!1 & sel) #8f2874ff
    12788 
    12789 > color (#!1 & sel) #8c2774ff
    12790 
    12791 [Repeated 3 time(s)]
    12792 
    12793 > color (#!1 & sel) #8d2771ff
    12794 
    12795 [Repeated 1 time(s)]
    12796 
    12797 > color (#!1 & sel) #8e276eff
    12798 
    12799 > color (#!1 & sel) #8f2769ff
    12800 
    12801 > color (#!1 & sel) #8f286aff
    12802 
    12803 > color (#!1 & sel) #96296fff
    12804 
    12805 > color (#!1 & sel) #9d2a76ff
    12806 
    12807 > color (#!1 & sel) #9e2a77ff
    12808 
    12809 > color (#!1 & sel) #9e2a76ff
    12810 
    12811 > color (#!1 & sel) #9e2a74ff
    12812 
    12813 [Repeated 1 time(s)]
    12814 
    12815 > color (#!1 & sel) #9e2a75ff
    12816 
    12817 > color (#!1 & sel) #a22b79ff
    12818 
    12819 > select /L
    12820 
    12821 3197 atoms, 3234 bonds, 212 residues, 1 model selected 
    12822 
    12823 > color sel #d3f0edff
    12824 
    12825 [Repeated 1 time(s)]
    12826 
    12827 > color sel #d5f1edff
    12828 
    12829 > color sel #d7f2ecff
    12830 
    12831 > color sel #d9f2ebff
    12832 
    12833 > color sel #daf2ebff
    12834 
    12835 > color sel #daf3ebff
    12836 
    12837 > color sel #dbf3ecff
    12838 
    12839 > color sel #dcf3eeff
    12840 
    12841 > color sel #dff3eeff
    12842 
    12843 > color sel #e1f5f0ff
    12844 
    12845 > color sel #e4f6f2ff
    12846 
    12847 > color sel #e5f6f2ff
    12848 
    12849 [Repeated 2 time(s)]
    12850 
    12851 > color sel #e5f5f2ff
    12852 
    12853 > color sel #e6f6f3ff
    12854 
    12855 > color sel #e7f7f4ff
    12856 
    12857 > color sel #e8f7f4ff
    12858 
    12859 [Repeated 2 time(s)]
    12860 
    12861 > color sel #e7f6f3ff
    12862 
    12863 > color sel #e6f6f2ff
    12864 
    12865 > color sel #e5f6f2ff
    12866 
    12867 > color sel #e4f6f2ff
    12868 
    12869 > color sel #e3f5f1ff
    12870 
    12871 > color sel #e2f5f0ff
    12872 
    12873 > color sel #e0f4efff
    12874 
    12875 > color sel #dff3eeff
    12876 
    12877 > color sel #dbf3ecff
    12878 
    12879 > color sel #daf3ebff
    12880 
    12881 > color sel #d9f2ebff
    12882 
    12883 > color sel #d8f2eaff
    12884 
    12885 > color sel #d7f2e8ff
    12886 
    12887 > color sel #d6f2e8ff
    12888 
    12889 [Repeated 1 time(s)]
    12890 
    12891 > color sel #d5f2e8ff
    12892 
    12893 > color sel #d2f0e7ff
    12894 
    12895 > color sel #d1f0e5ff
    12896 
    12897 > color sel #ccefe3ff
    12898 
    12899 > color sel #cbeee2ff
    12900 
    12901 > color sel #caeee2ff
    12902 
    12903 [Repeated 2 time(s)]
    12904 
    12905 > color sel #c9eee3ff
    12906 
    12907 > color sel #c9eee2ff
    12908 
    12909 > color sel #c7eee0ff
    12910 
    12911 > color sel #c5eddfff
    12912 
    12913 > color sel #c4eddfff
    12914 
    12915 > color sel #c3eddfff
    12916 
    12917 > color sel #c3eddeff
    12918 
    12919 > color sel #c2eddcff
    12920 
    12921 > color sel #c1ecd9ff
    12922 
    12923 > color sel #beecd7ff
    12924 
    12925 > color sel #bcecd6ff
    12926 
    12927 > color sel #b8ebd3ff
    12928 
    12929 > color sel #b8ebd2ff
    12930 
    12931 > color sel #b6ead2ff
    12932 
    12933 > color sel #b5e9d2ff
    12934 
    12935 > color sel #b1e9d0ff
    12936 
    12937 > color sel #afe8cfff
    12938 
    12939 > color sel #aee8ceff
    12940 
    12941 > color sel #ace8ceff
    12942 
    12943 > color sel #abe8cfff
    12944 
    12945 > color sel #aae8d0ff
    12946 
    12947 > color sel #a9e7d1ff
    12948 
    12949 [Repeated 1 time(s)]
    12950 
    12951 > color sel #a8e7d1ff
    12952 
    12953 > color sel #a7e7d0ff
    12954 
    12955 > color sel #a5e7cfff
    12956 
    12957 > color sel #a3e7ceff
    12958 
    12959 > color sel #9fe6ccff
    12960 
    12961 > color sel #99e5c9ff
    12962 
    12963 > color sel #98e5c8ff
    12964 
    12965 [Repeated 2 time(s)]
    12966 
    12967 > color sel #99e5cbff
    12968 
    12969 > color sel #9ae5ceff
    12970 
    12971 > color sel #9be5d3ff
    12972 
    12973 > color sel #9ce6d9ff
    12974 
    12975 > color sel #9ce6daff
    12976 
    12977 > color sel #9ce6dbff
    12978 
    12979 [Repeated 1 time(s)]
    12980 
    12981 > color sel #9ce6dcff
    12982 
    12983 [Repeated 1 time(s)]
    12984 
    12985 > color sel #9ce6ddff
    12986 
    12987 > color sel #9ce6deff
    12988 
    12989 > color sel #9de6dfff
    12990 
    12991 > color sel #9de6e1ff
    12992 
    12993 > color sel #9ee6e2ff
    12994 
    12995 > color sel #9fe6e4ff
    12996 
    12997 > color sel #9fe6e5ff
    12998 
    12999 > color sel #9fe6e6ff
    13000 
    13001 > color sel #9fe6e7ff
    13002 
    13003 [Repeated 1 time(s)]
    13004 
    13005 > color sel #a0e6e8ff
    13006 
    13007 > color sel #a0e2e8ff
    13008 
    13009 > color sel #a1e2e8ff
    13010 
    13011 > color sel #a1e0e8ff
    13012 
    13013 > color sel #a1dbe7ff
    13014 
    13015 > color sel #a1d8e7ff
    13016 
    13017 > color sel #a1d7e7ff
    13018 
    13019 > color sel #a1d5e7ff
    13020 
    13021 > color sel #a1d2e7ff
    13022 
    13023 > color sel #a1d1e7ff
    13024 
    13025 [Repeated 1 time(s)]
    13026 
    13027 > color sel #a1d0e7ff
    13028 
    13029 > color sel #a1cce6ff
    13030 
    13031 [Repeated 1 time(s)]
    13032 
    13033 > color sel #a1cbe6ff
    13034 
    13035 > color sel #a2cbe6ff
    13036 
    13037 > color sel #a3cae7ff
    13038 
    13039 > color sel #a3c8e7ff
    13040 
    13041 > color sel #a5c7e8ff
    13042 
    13043 > color sel #a9c6e8ff
    13044 
    13045 > color sel #aac7e9ff
    13046 
    13047 > color sel #acc7e8ff
    13048 
    13049 > color sel #adc7e9ff
    13050 
    13051 [Repeated 1 time(s)]
    13052 
    13053 > color sel #afc8e9ff
    13054 
    13055 > color sel #afc7e9ff
    13056 
    13057 > color sel #b0c7e9ff
    13058 
    13059 > color sel #b2c6e9ff
    13060 
    13061 > color sel #b4c7eaff
    13062 
    13063 > color sel #b6c8eaff
    13064 
    13065 > color sel #b7c8eaff
    13066 
    13067 > color sel #b8c8eaff
    13068 
    13069 > color sel #b9c9eaff
    13070 
    13071 [Repeated 1 time(s)]
    13072 
    13073 > color sel #bacaebff
    13074 
    13075 [Repeated 1 time(s)]
    13076 
    13077 > color sel #bacaecff
    13078 
    13079 > color sel #bbc9ebff
    13080 
    13081 > color sel #bccaebff
    13082 
    13083 > color sel #becaebff
    13084 
    13085 > color sel #bfcbebff
    13086 
    13087 > color sel #c1cbecff
    13088 
    13089 [Repeated 2 time(s)]
    13090 
    13091 > color sel #c2ccecff
    13092 
    13093 > color sel #c1ccecff
    13094 
    13095 [Repeated 1 time(s)]
    13096 
    13097 > color sel #b8c0eaff
    13098 
    13099 > color sel #b7beeaff
    13100 
    13101 > color sel #b5bee9ff
    13102 
    13103 > color sel #b3bceaff
    13104 
    13105 > color sel #b1bae9ff
    13106 
    13107 > color sel #afb8e8ff
    13108 
    13109 > color sel #adb8e8ff
    13110 
    13111 [Repeated 1 time(s)]
    13112 
    13113 > color sel #acb7e8ff
    13114 
    13115 > color sel #abb6e8ff
    13116 
    13117 > color sel #abb5e8ff
    13118 
    13119 > color sel #a9b4e8ff
    13120 
    13121 > color sel #a7b2e7ff
    13122 
    13123 [Repeated 2 time(s)]
    13124 
    13125 > color sel #a6b1e7ff
    13126 
    13127 > color sel #a5b0e7ff
    13128 
    13129 > color sel #a4b0e7ff
    13130 
    13131 > select /H
    13132 
    13133 3275 atoms, 3324 bonds, 1 pseudobond, 222 residues, 2 models selected 
    13134 
    13135 > color (#!1 & sel) #efddccff
    13136 
    13137 [Repeated 1 time(s)]
    13138 
    13139 > color (#!1 & sel) #eedcccff
    13140 
    13141 > color (#!1 & sel) #eedbcaff
    13142 
    13143 > color (#!1 & sel) #eedbc9ff
    13144 
    13145 > color (#!1 & sel) #ecd6c3ff
    13146 
    13147 > color (#!1 & sel) #ebd3bfff
    13148 
    13149 > color (#!1 & sel) #ebd3beff
    13150 
    13151 > color (#!1 & sel) #ecdac3ff
    13152 
    13153 > color (#!1 & sel) #eeddc6ff
    13154 
    13155 > color (#!1 & sel) #eedec8ff
    13156 
    13157 > color (#!1 & sel) #eedfc8ff
    13158 
    13159 > color (#!1 & sel) #efe0caff
    13160 
    13161 > color (#!1 & sel) #efe1cdff
    13162 
    13163 > color (#!1 & sel) #f0e3ceff
    13164 
    13165 > color (#!1 & sel) #efe3cdff
    13166 
    13167 > color (#!1 & sel) #eeddc8ff
    13168 
    13169 > color (#!1 & sel) #ead0baff
    13170 
    13171 > color (#!1 & sel) #e8c9b2ff
    13172 
    13173 > color (#!1 & sel) #e6c3abff
    13174 
    13175 > color (#!1 & sel) #e3b89fff
    13176 
    13177 > color (#!1 & sel) #e1ae94ff
    13178 
    13179 > color (#!1 & sel) #dfa58aff
    13180 
    13181 > color (#!1 & sel) #de9f84ff
    13182 
    13183 > color (#!1 & sel) #de9d82ff
    13184 
    13185 > color (#!1 & sel) #de9e82ff
    13186 
    13187 [Repeated 2 time(s)]
    13188 
    13189 > color (#!1 & sel) #de9c82ff
    13190 
    13191 [Repeated 1 time(s)]
    13192 
    13193 > color (#!1 & sel) #de9d83ff
    13194 
    13195 > color (#!1 & sel) #de9c83ff
    13196 
    13197 [Repeated 2 time(s)]
    13198 
    13199 > color (#!1 & sel) #de9d85ff
    13200 
    13201 > color (#!1 & sel) #de9e8aff
    13202 
    13203 > color (#!1 & sel) #dfa390ff
    13204 
    13205 > color (#!1 & sel) #e0a895ff
    13206 
    13207 > color (#!1 & sel) #e1aa99ff
    13208 
    13209 > color (#!1 & sel) #e2ad9cff
    13210 
    13211 > color (#!1 & sel) #e2ad9dff
    13212 
    13213 > color (#!1 & sel) #e2ae9dff
    13214 
    13215 [Repeated 1 time(s)]
    13216 
    13217 > color (#!1 & sel) #e2af9dff
    13218 
    13219 > color (#!1 & sel) #e2ae9cff
    13220 
    13221 > color (#!1 & sel) #e0aa93ff
    13222 
    13223 > color (#!1 & sel) #dea184ff
    13224 
    13225 > color (#!1 & sel) #dea082ff
    13226 
    13227 [Repeated 1 time(s)]
    13228 
    13229 > color (#!1 & sel) #dea081ff
    13230 
    13231 > color (#!1 & sel) #de9f81ff
    13232 
    13233 > color (#!1 & sel) #dd9c7dff
    13234 
    13235 > color (#!1 & sel) #dd9b7bff
    13236 
    13237 [Repeated 2 time(s)]
    13238 
    13239 > color (#!1 & sel) #dc9878ff
    13240 
    13241 > color (#!1 & sel) #dc9473ff
    13242 
    13243 > color (#!1 & sel) #dc936eff
    13244 
    13245 > color (#!1 & sel) #dc946eff
    13246 
    13247 > color (#!1 & sel) #dc946dff
    13248 
    13249 [Repeated 1 time(s)]
    13250 
    13251 > color (#!1 & sel) #dc956dff
    13252 
    13253 [Repeated 1 time(s)]
    13254 
    13255 > color (#!1 & sel) #dc966eff
    13256 
    13257 > color (#!1 & sel) #dd996eff
    13258 
    13259 > color (#!1 & sel) #dd9c6eff
    13260 
    13261 > color (#!1 & sel) #dd9f6fff
    13262 
    13263 > color (#!1 & sel) #dea16fff
    13264 
    13265 > color (#!1 & sel) #dea26fff
    13266 
    13267 > color (#!1 & sel) #dea570ff
    13268 
    13269 > color (#!1 & sel) #dfa972ff
    13270 
    13271 > color (#!1 & sel) #dfad77ff
    13272 
    13273 > color (#!1 & sel) #e0b37cff
    13274 
    13275 > color (#!1 & sel) #e1b47eff
    13276 
    13277 > color (#!1 & sel) #e0b47eff
    13278 
    13279 [Repeated 1 time(s)]
    13280 
    13281 > color (#!1 & sel) #e1b782ff
    13282 
    13283 > color (#!1 & sel) #e2bc87ff
    13284 
    13285 > color (#!1 & sel) #e2bd8aff
    13286 
    13287 > color (#!1 & sel) #e3bf8dff
    13288 
    13289 > color (#!1 & sel) #e3c08fff
    13290 
    13291 > color (#!1 & sel) #e4c293ff
    13292 
    13293 [Repeated 2 time(s)]
    13294 
    13295 > color (#!1 & sel) #e2bc87ff
    13296 
    13297 > color (#!1 & sel) #e0b67dff
    13298 
    13299 > color (#!1 & sel) #e0b073ff
    13300 
    13301 > color (#!1 & sel) #dfac6cff
    13302 
    13303 > color (#!1 & sel) #dfa564ff
    13304 
    13305 > color (#!1 & sel) #de9a5dff
    13306 
    13307 > color (#!1 & sel) #dd9058ff
    13308 
    13309 > color (#!1 & sel) #dd8952ff
    13310 
    13311 > color (#!1 & sel) #dc804eff
    13312 
    13313 > color (#!1 & sel) #dc7b4aff
    13314 
    13315 > color (#!1 & sel) #dc7847ff
    13316 
    13317 > color (#!1 & sel) #dc7746ff
    13318 
    13319 > color (#!1 & sel) #dc7345ff
    13320 
    13321 > color (#!1 & sel) #dc7244ff
    13322 
    13323 > color (#!1 & sel) #dc7142ff
    13324 
    13325 > color (#!1 & sel) #dd7041ff
    13326 
    13327 > color (#!1 & sel) #dd6e3fff
    13328 
    13329 > color (#!1 & sel) #dd6f3fff
    13330 
    13331 > color (#!1 & sel) #dd6e3fff
    13332 
    13333 > color (#!1 & sel) #dd7040ff
    13334 
    13335 > color (#!1 & sel) #dd7442ff
    13336 
    13337 > color (#!1 & sel) #dd7742ff
    13338 
    13339 > color (#!1 & sel) #dd7843ff
    13340 
    13341 [Repeated 2 time(s)]
    13342 
    13343 > color (#!1 & sel) #dd7943ff
    13344 
    13345 > color (#!1 & sel) #dd7944ff
    13346 
    13347 > color (#!1 & sel) #dd7e45ff
    13348 
    13349 > color (#!1 & sel) #de8347ff
    13350 
    13351 > color (#!1 & sel) #de8648ff
    13352 
    13353 > color (#!1 & sel) #df8a48ff
    13354 
    13355 [Repeated 1 time(s)]
    13356 
    13357 > color (#!1 & sel) #df8c48ff
    13358 
    13359 > color (#!1 & sel) #df954bff
    13360 
    13361 > color (#!1 & sel) #e09d4dff
    13362 
    13363 > color (#!1 & sel) #e0a14eff
    13364 
    13365 > color (#!1 & sel) #e1a44fff
    13366 
    13367 [Repeated 2 time(s)]
    13368 
    13369 > color (#!1 & sel) #e1a650ff
    13370 
    13371 [Repeated 1 time(s)]
    13372 
    13373 > color (#!1 & sel) #e09d4dff
    13374 
    13375 > color (#!1 & sel) #df8e48ff
    13376 
    13377 > color (#!1 & sel) #de7a40ff
    13378 
    13379 > color (#!1 & sel) #de6f3cff
    13380 
    13381 > color (#!1 & sel) #de6c3cff
    13382 
    13383 > color (#!1 & sel) #dd673aff
    13384 
    13385 > color (#!1 & sel) #de6038ff
    13386 
    13387 > color (#!1 & sel) #dd5b38ff
    13388 
    13389 > color (#!1 & sel) #dd5937ff
    13390 
    13391 [Repeated 1 time(s)]
    13392 
    13393 > color (#!1 & sel) #dd5a38ff
    13394 
    13395 > color (#!1 & sel) #dc603dff
    13396 
    13397 > color (#!1 & sel) #db6745ff
    13398 
    13399 > color (#!1 & sel) #db6846ff
    13400 
    13401 [Repeated 1 time(s)]
    13402 
    13403 > color (#!1 & sel) #db6747ff
    13404 
    13405 > color (#!1 & sel) #d95f49ff
    13406 
    13407 > color (#!1 & sel) #d95e4bff
    13408 
    13409 > color (#!1 & sel) #d95c4cff
    13410 
    13411 > color (#!1 & sel) #d95b4cff
    13412 
    13413 [Repeated 1 time(s)]
    13414 
    13415 > color (#!1 & sel) #d95a4eff
    13416 
    13417 > color (#!1 & sel) #d95b4eff
    13418 
    13419 [Repeated 1 time(s)]
    13420 
    13421 > color (#!1 & sel) #d86157ff
    13422 
    13423 > color (#!1 & sel) #d9655bff
    13424 
    13425 > color (#!1 & sel) #d9665bff
    13426 
    13427 > color (#!1 & sel) #d9675dff
    13428 
    13429 > color (#!1 & sel) #d9685dff
    13430 
    13431 > color (#!1 & sel) #d8685eff
    13432 
    13433 > color (#!1 & sel) #d86b62ff
    13434 
    13435 > color (#!1 & sel) #d96d64ff
    13436 
    13437 > color (#!1 & sel) #d97369ff
    13438 
    13439 > color (#!1 & sel) #d97870ff
    13440 
    13441 > color (#!1 & sel) #da7e76ff
    13442 
    13443 [Repeated 1 time(s)]
    13444 
    13445 > color (#!1 & sel) #da8077ff
    13446 
    13447 > color (#!1 & sel) #db8179ff
    13448 
    13449 > color (#!1 & sel) #db857dff
    13450 
    13451 > color (#!1 & sel) #dc8980ff
    13452 
    13453 > color (#!1 & sel) #dc8a81ff
    13454 
    13455 [Repeated 4 time(s)]
    13456 
    13457 > select /N
    13458 
    13459 1746 atoms, 1764 bonds, 1 pseudobond, 117 residues, 2 models selected 
    13460 
    13461 > color (#!1 & sel) #66af39ff
    13462 
    13463 > color (#!1 & sel) #60a235ff
    13464 
    13465 > color (#!1 & sel) #5a9732ff
    13466 
    13467 > color (#!1 & sel) #548a2eff
    13468 
    13469 > color (#!1 & sel) #50832cff
    13470 
    13471 > color (#!1 & sel) #4d7f2bff
    13472 
    13473 > color (#!1 & sel) #4c7e2bff
    13474 
    13475 > color (#!1 & sel) #4b7d2aff
    13476 
    13477 > color (#!1 & sel) #4b7c2aff
    13478 
    13479 > color (#!1 & sel) #4b7b2aff
    13480 
    13481 [Repeated 1 time(s)]
    13482 
    13483 > color (#!1 & sel) #4f7d2bff
    13484 
    13485 > color (#!1 & sel) #517f2bff
    13486 
    13487 > color (#!1 & sel) #51802bff
    13488 
    13489 > color (#!1 & sel) #52822cff
    13490 
    13491 > color (#!1 & sel) #5f9632ff
    13492 
    13493 > color (#!1 & sel) #65a035ff
    13494 
    13495 > color (#!1 & sel) #67a236ff
    13496 
    13497 > color (#!1 & sel) #68a336ff
    13498 
    13499 > color (#!1 & sel) #69a737ff
    13500 
    13501 > color (#!1 & sel) #69a937ff
    13502 
    13503 > color (#!1 & sel) #6aae39ff
    13504 
    13505 > color (#!1 & sel) #6bb23aff
    13506 
    13507 > color (#!1 & sel) #6bb83bff
    13508 
    13509 > color (#!1 & sel) #6cbc3dff
    13510 
    13511 > color (#!1 & sel) #6dbd3dff
    13512 
    13513 [Repeated 1 time(s)]
    13514 
    13515 > color (#!1 & sel) #6bbc3dff
    13516 
    13517 > color (#!1 & sel) #64b83bff
    13518 
    13519 > color (#!1 & sel) #61b63bff
    13520 
    13521 > color (#!1 & sel) #5db53aff
    13522 
    13523 [Repeated 1 time(s)]
    13524 
    13525 > color (#!1 & sel) #5cb73bff
    13526 
    13527 > color (#!1 & sel) #5fbd3cff
    13528 
    13529 > color (#!1 & sel) #63c73fff
    13530 
    13531 > color (#!1 & sel) #64ca40ff
    13532 
    13533 > color (#!1 & sel) #64ce41ff
    13534 
    13535 > color (#!1 & sel) #64d242ff
    13536 
    13537 > color (#!1 & sel) #64d443ff
    13538 
    13539 [Repeated 1 time(s)]
    13540 
    13541 > color (#!1 & sel) #64d544ff
    13542 
    13543 > color (#!1 & sel) #64d545ff
    13544 
    13545 > color (#!1 & sel) #63d346ff
    13546 
    13547 > color (#!1 & sel) #61ce46ff
    13548 
    13549 > color (#!1 & sel) #5abf42ff
    13550 
    13551 > color (#!1 & sel) #59bc42ff
    13552 
    13553 > color (#!1 & sel) #57b841ff
    13554 
    13555 > color (#!1 & sel) #55b440ff
    13556 
    13557 > color (#!1 & sel) #52ad3eff
    13558 
    13559 > color (#!1 & sel) #4a9c38ff
    13560 
    13561 > color (#!1 & sel) #459135ff
    13562 
    13563 > color (#!1 & sel) #428a33ff
    13564 
    13565 [Repeated 1 time(s)]
    13566 
    13567 > color (#!1 & sel) #428933ff
    13568 
    13569 > color (#!1 & sel) #418837ff
    13570 
    13571 [Repeated 2 time(s)]
    13572 
    13573 > color (#!1 & sel) #418938ff
    13574 
    13575 > color (#!1 & sel) #489740ff
    13576 
    13577 > color (#!1 & sel) #4fa74cff
    13578 
    13579 > color (#!1 & sel) #50a84fff
    13580 
    13581 > color (#!1 & sel) #50a950ff
    13582 
    13583 > color (#!1 & sel) #4fa74eff
    13584 
    13585 > color (#!1 & sel) #499a49ff
    13586 
    13587 > color (#!1 & sel) #449046ff
    13588 
    13589 > color (#!1 & sel) #448f46ff
    13590 
    13591 > color (#!1 & sel) #479444ff
    13592 
    13593 > color (#!1 & sel) #489842ff
    13594 
    13595 > color (#!1 & sel) #489742ff
    13596 
    13597 > color (#!1 & sel) #469441ff
    13598 
    13599 > color (#!1 & sel) #469341ff
    13600 
    13601 > color (#!1 & sel) #469241ff
    13602 
    13603 > color (#!1 & sel) #459140ff
    13604 
    13605 > color (#!1 & sel) #45903fff
    13606 
    13607 > color (#!1 & sel) #448e3fff
    13608 
    13609 > color (#!1 & sel) #428b3eff
    13610 
    13611 [Repeated 1 time(s)]
    13612 
    13613 > color (#!1 & sel) #428a3eff
    13614 
    13615 > color (#!1 & sel) #428a3dff
    13616 
    13617 > color (#!1 & sel) #41873cff
    13618 
    13619 [Repeated 2 time(s)]
    13620 
    13621 > ui mousemode right select
    13622 
    13623 > select clear
    13624 
    13625 > ui mousemode right translate
    13626 
    13627 > ui tool show "Show Sequence Viewer"
    13628 
    13629 > sequence chain /R
    13630 
    13631 Alignment identifier is 1/R 
    13632 
    13633 > lighting soft
    13634 
    13635 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
    13636 > draft/Figure 7D-GPR61-BRIL fused structure.cxs"
    13637 
    13638 ——— End of log from Mon Apr 1 18:14:01 2024 ———
    13639 
    13640 opened ChimeraX session 
    13641 
    13642 Could not find virtual screen for QCocoaScreen(0x600001b2b9c0, "DELL P2422H",
    13643 QRect(-1920,0 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833 
    13644 
    13645 > open 8TB0
    13646 
    13647 8tb0 title: 
    13648 Cryo-EM Structure of GPR61-G protein complex stabilized by scFv16 [more
    13649 info...] 
    13650  
    13651 Chain information for 8tb0 #2 
    13652 --- 
    13653 Chain | Description | UniProt 
    13654 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340 
    13655 F | Single-chain Fv16 |   
    13656 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    13657 R | GPR61 fused to dominant negative G alpha S/I N18 chimera | GPR61_HUMAN 2-1446, GNAS2_HUMAN 1481-1849 
    13658  
    13659 
    13660 > ui tool show Matchmaker
    13661 
    13662 > matchmaker #!1 to #2/R pairing bs
    13663 
    13664 Parameters 
    13665 --- 
    13666 Chain pairing | bs 
    13667 Alignment algorithm | Needleman-Wunsch 
    13668 Similarity matrix | BLOSUM-62 
    13669 SS fraction | 0.3 
    13670 Gap open (HH/SS/other) | 18/18/6 
    13671 Gap extend | 1 
    13672 SS matrix |  |  | H | S | O 
    13673 ---|---|---|--- 
    13674 H | 6 | -9 | -6 
    13675 S |  | 6 | -6 
    13676 O |  |  | 4 
    13677 Iteration cutoff | 2 
    13678  
    13679 Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
    13680 alignment score = 1623.9 
    13681 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    13682 1.770) 
    13683  
    13684 
    13685 > matchmaker #!1 to #2/R pairing bs
    13686 
    13687 Parameters 
    13688 --- 
    13689 Chain pairing | bs 
    13690 Alignment algorithm | Needleman-Wunsch 
    13691 Similarity matrix | BLOSUM-62 
    13692 SS fraction | 0.3 
    13693 Gap open (HH/SS/other) | 18/18/6 
    13694 Gap extend | 1 
    13695 SS matrix |  |  | H | S | O 
    13696 ---|---|---|--- 
    13697 H | 6 | -9 | -6 
    13698 S |  | 6 | -6 
    13699 O |  |  | 4 
    13700 Iteration cutoff | 2 
    13701  
    13702 Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
    13703 alignment score = 1623.9 
    13704 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    13705 1.770) 
    13706  
    13707 
    13708 > select #2/G
    13709 
    13710 385 atoms, 391 bonds, 50 residues, 1 model selected 
    13711 
    13712 > color sel #e9e19aff
    13713 
    13714 > color sel #e9e19eff
    13715 
    13716 > color sel #eae2a1ff
    13717 
    13718 > color sel #eae2a3ff
    13719 
    13720 > color sel #ede7b6ff
    13721 
    13722 > color sel #ede9b9ff
    13723 
    13724 > color sel #eeeabdff
    13725 
    13726 > color sel #f1edc9ff
    13727 
    13728 [Repeated 4 time(s)]
    13729 
    13730 > color sel #f1ecc8ff
    13731 
    13732 > color sel #f0ebc8ff
    13733 
    13734 > color sel #f0e8c8ff
    13735 
    13736 > color sel #f0e7ccff
    13737 
    13738 > color sel #f0e6cdff
    13739 
    13740 > color sel #f0e6ccff
    13741 
    13742 > color sel #f0e5cdff
    13743 
    13744 > color sel #f0e5ccff
    13745 
    13746 > color sel #f0e5cdff
    13747 
    13748 [Repeated 3 time(s)]
    13749 
    13750 > color sel #f0e8cdff
    13751 
    13752 [Repeated 1 time(s)]
    13753 
    13754 > select #2/B
    13755 
    13756 2539 atoms, 2587 bonds, 333 residues, 1 model selected 
    13757 
    13758 > color sel #c5caecff
    13759 
    13760 [Repeated 2 time(s)]
    13761 
    13762 > color sel #c8cbeeff
    13763 
    13764 > color sel #c9cdeeff
    13765 
    13766 > color sel #cacdeeff
    13767 
    13768 > color sel #caceeeff
    13769 
    13770 [Repeated 1 time(s)]
    13771 
    13772 > color sel #cbcfefff
    13773 
    13774 > color sel #cccfeeff
    13775 
    13776 > color sel #cdcfeeff
    13777 
    13778 > color sel #b8b9ebff
    13779 
    13780 > color sel #b7b8ebff
    13781 
    13782 > color sel #b7b7eaff
    13783 
    13784 > color sel #b6b7eaff
    13785 
    13786 > color sel #b6b6eaff
    13787 
    13788 > color sel #b5b5eaff
    13789 
    13790 > color sel #b6b6eaff
    13791 
    13792 > color sel #b7b6eaff
    13793 
    13794 > color sel #b8b6e9ff
    13795 
    13796 > color sel #bbb6e9ff
    13797 
    13798 > color sel #bcb6e9ff
    13799 
    13800 > color sel #bdb7eaff
    13801 
    13802 > color sel #c5beecff
    13803 
    13804 [Repeated 2 time(s)]
    13805 
    13806 > color sel #c4beebff
    13807 
    13808 > color sel #c5beecff
    13809 
    13810 > color sel #c6bfecff
    13811 
    13812 > color sel #c7bfecff
    13813 
    13814 > color sel #cac2ebff
    13815 
    13816 > color sel #d0caeeff
    13817 
    13818 > color sel #d1caefff
    13819 
    13820 > color sel #d5cdeeff
    13821 
    13822 > color sel #dfd7f1ff
    13823 
    13824 > color sel #e1d8f1ff
    13825 
    13826 > color sel #e2d8f1ff
    13827 
    13828 > color sel #e1d6f1ff
    13829 
    13830 > color sel #dfd3f1ff
    13831 
    13832 > color sel #dbcbeeff
    13833 
    13834 > color sel #d0bcebff
    13835 
    13836 > color sel #cebaebff
    13837 
    13838 > color sel #cdb7eaff
    13839 
    13840 > color sel #c9b3e9ff
    13841 
    13842 > color sel #c9b2e9ff
    13843 
    13844 > color sel #c7afe8ff
    13845 
    13846 > color sel #c5ade8ff
    13847 
    13848 > color sel #c4ace8ff
    13849 
    13850 > color sel #c5ace8ff
    13851 
    13852 > color sel #bda1e6ff
    13853 
    13854 > color sel #bc9ee6ff
    13855 
    13856 [Repeated 1 time(s)]
    13857 
    13858 > color sel #bb9de5ff
    13859 
    13860 > color sel #b99ce5ff
    13861 
    13862 > color sel #b899e4ff
    13863 
    13864 > color sel #b798e5ff
    13865 
    13866 [Repeated 2 time(s)]
    13867 
    13868 > color sel #c299e4ff
    13869 
    13870 > color sel #c29ae4ff
    13871 
    13872 [Repeated 1 time(s)]
    13873 
    13874 > color sel #c299e4ff
    13875 
    13876 > color sel #c29ae4ff
    13877 
    13878 > color sel #c39ae4ff
    13879 
    13880 > color sel #c49ce6ff
    13881 
    13882 > color sel #c49de5ff
    13883 
    13884 > color sel #c49ee5ff
    13885 
    13886 > color sel #c59fe6ff
    13887 
    13888 > color sel #c6a0e6ff
    13889 
    13890 > color sel #ceade8ff
    13891 
    13892 > color sel #d2b6eaff
    13893 
    13894 > color sel #d8beebff
    13895 
    13896 > color sel #dcc4edff
    13897 
    13898 > color sel #ddc6edff
    13899 
    13900 > color sel #ddc7edff
    13901 
    13902 > color sel #e7cdefff
    13903 
    13904 > color sel #e8cdefff
    13905 
    13906 > color sel #e9ceefff
    13907 
    13908 > color sel #ebcbedff
    13909 
    13910 > color sel #ecccecff
    13911 
    13912 > color sel #ecccebff
    13913 
    13914 > color sel #eccce7ff
    13915 
    13916 > color sel #eccde7ff
    13917 
    13918 [Repeated 2 time(s)]
    13919 
    13920 > color sel #eccee6ff
    13921 
    13922 [Repeated 1 time(s)]
    13923 
    13924 > color sel #edcfe6ff
    13925 
    13926 > color sel #edd1e8ff
    13927 
    13928 > color sel #eed3e8ff
    13929 
    13930 > color sel #efd6e8ff
    13931 
    13932 > color sel #efd7e9ff
    13933 
    13934 > color sel #f0d9e9ff
    13935 
    13936 > color sel #f1dbeaff
    13937 
    13938 > color sel #f1dcebff
    13939 
    13940 > color sel #f2deecff
    13941 
    13942 > color sel #f2dfecff
    13943 
    13944 > color sel #f3dfecff
    13945 
    13946 > color sel #f3e2eeff
    13947 
    13948 > color sel #f5e6f0ff
    13949 
    13950 > color sel #f8f0f6ff
    13951 
    13952 > color sel #fbf7faff
    13953 
    13954 > color sel #fcf8fbff
    13955 
    13956 > color sel #fcf8faff
    13957 
    13958 [Repeated 1 time(s)]
    13959 
    13960 > color sel #fbf7faff
    13961 
    13962 [Repeated 1 time(s)]
    13963 
    13964 > color sel #f8eff7ff
    13965 
    13966 > color sel #f7ecf6ff
    13967 
    13968 > color sel #f5e9f5ff
    13969 
    13970 > color sel #f5e8f5ff
    13971 
    13972 > color sel #f5e5f4ff
    13973 
    13974 > color sel #f3e3f4ff
    13975 
    13976 > color sel #f0daf1ff
    13977 
    13978 > color sel #efd6f1ff
    13979 
    13980 > color sel #edd2efff
    13981 
    13982 > color sel #eccdefff
    13983 
    13984 > color sel #e6bdebff
    13985 
    13986 [Repeated 1 time(s)]
    13987 
    13988 > color sel #e6bcebff
    13989 
    13990 > color sel #e5bbebff
    13991 
    13992 > color sel #e3b7eaff
    13993 
    13994 [Repeated 1 time(s)]
    13995 
    13996 > color sel #e2b6e9ff
    13997 
    13998 [Repeated 1 time(s)]
    13999 
    14000 > color sel #e3b7eaff
    14001 
    14002 [Repeated 1 time(s)]
    14003 
    14004 > color sel #e3bdebff
    14005 
    14006 > color sel #e3c1ecff
    14007 
    14008 [Repeated 3 time(s)]
    14009 
    14010 > color sel #e4c1ecff
    14011 
    14012 > color sel #e4c2ecff
    14013 
    14014 [Repeated 2 time(s)]
    14015 
    14016 > color sel #e3c3edff
    14017 
    14018 > color sel #e4c3edff
    14019 
    14020 [Repeated 1 time(s)]
    14021 
    14022 > color sel #e4c5edff
    14023 
    14024 > color sel #e3c7eeff
    14025 
    14026 > color sel #e4caefff
    14027 
    14028 > color sel #e5cdefff
    14029 
    14030 > color sel #e6cfefff
    14031 
    14032 > color sel #e5cfefff
    14033 
    14034 [Repeated 3 time(s)]
    14035 
    14036 > color sel #e5d0efff
    14037 
    14038 [Repeated 3 time(s)]
    14039 
    14040 > color sel #e4d2f1ff
    14041 
    14042 > color sel #e4d3f1ff
    14043 
    14044 [Repeated 1 time(s)]
    14045 
    14046 > color sel #e4d4f1ff
    14047 
    14048 [Repeated 1 time(s)]
    14049 
    14050 > select #2/F
    14051 
    14052 1780 atoms, 1826 bonds, 1 pseudobond, 233 residues, 2 models selected 
    14053 
    14054 > color (#!2 & sel) #d6edbeff
    14055 
    14056 > color (#!2 & sel) #d8edbfff
    14057 
    14058 > color (#!2 & sel) #dceec4ff
    14059 
    14060 > color (#!2 & sel) #dfeec6ff
    14061 
    14062 > color (#!2 & sel) #e4f0ceff
    14063 
    14064 > color (#!2 & sel) #e5f1d0ff
    14065 
    14066 > color (#!2 & sel) #e7f3d7ff
    14067 
    14068 > color (#!2 & sel) #e9f3dcff
    14069 
    14070 > color (#!2 & sel) #e8f3dbff
    14071 
    14072 > color (#!2 & sel) #e8f3d9ff
    14073 
    14074 > color (#!2 & sel) #e8f3d7ff
    14075 
    14076 > color (#!2 & sel) #e8f3d6ff
    14077 
    14078 [Repeated 1 time(s)]
    14079 
    14080 > color (#!2 & sel) #e8f2d3ff
    14081 
    14082 > color (#!2 & sel) #e6f1ceff
    14083 
    14084 > color (#!2 & sel) #e5f1cdff
    14085 
    14086 > color (#!2 & sel) #e7efc5ff
    14087 
    14088 > color (#!2 & sel) #e9efc3ff
    14089 
    14090 > color (#!2 & sel) #e5efc4ff
    14091 
    14092 > color (#!2 & sel) #e1efc4ff
    14093 
    14094 > color (#!2 & sel) #deeec5ff
    14095 
    14096 > color (#!2 & sel) #dbefc7ff
    14097 
    14098 > color (#!2 & sel) #dbefc8ff
    14099 
    14100 > color (#!2 & sel) #daefc8ff
    14101 
    14102 > color (#!2 & sel) #daf0c9ff
    14103 
    14104 > color (#!2 & sel) #daf0caff
    14105 
    14106 > color (#!2 & sel) #dbf0ccff
    14107 
    14108 > color (#!2 & sel) #dbf0cdff
    14109 
    14110 > color (#!2 & sel) #daf0cdff
    14111 
    14112 [Repeated 1 time(s)]
    14113 
    14114 > color (#!2 & sel) #d9f0cdff
    14115 
    14116 > color (#!2 & sel) #d8f0cdff
    14117 
    14118 [Repeated 3 time(s)]
    14119 
    14120 > color (#!2 & sel) #d7f0cdff
    14121 
    14122 > color (#!2 & sel) #d6f0cdff
    14123 
    14124 > color (#!2 & sel) #d6f0ccff
    14125 
    14126 > color (#!2 & sel) #cdeec6ff
    14127 
    14128 > color (#!2 & sel) #cbeec4ff
    14129 
    14130 > color (#!2 & sel) #caeec3ff
    14131 
    14132 > color (#!2 & sel) #c4edbeff
    14133 
    14134 [Repeated 1 time(s)]
    14135 
    14136 > color (#!2 & sel) #c4edbdff
    14137 
    14138 > color (#!2 & sel) #c3ecbcff
    14139 
    14140 > color (#!2 & sel) #c2ecbaff
    14141 
    14142 > color (#!2 & sel) #c2ecbbff
    14143 
    14144 > color (#!2 & sel) #c2edbcff
    14145 
    14146 [Repeated 1 time(s)]
    14147 
    14148 > color (#!2 & sel) #c3edbdff
    14149 
    14150 > color (#!2 & sel) #c8eec4ff
    14151 
    14152 > color (#!2 & sel) #c9eec5ff
    14153 
    14154 > color (#!2 & sel) #c9eec6ff
    14155 
    14156 > color (#!2 & sel) #cbeec9ff
    14157 
    14158 > color (#!2 & sel) #cdefccff
    14159 
    14160 > color (#!2 & sel) #ceefccff
    14161 
    14162 [Repeated 1 time(s)]
    14163 
    14164 > color (#!2 & sel) #cbeecaff
    14165 
    14166 > color (#!2 & sel) #c8eec8ff
    14167 
    14168 > color (#!2 & sel) #c6edc4ff
    14169 
    14170 > color (#!2 & sel) #c3edc3ff
    14171 
    14172 > color (#!2 & sel) #c2edc2ff
    14173 
    14174 [Repeated 1 time(s)]
    14175 
    14176 > color (#!2 & sel) #b6eab6ff
    14177 
    14178 > color (#!2 & sel) #ace8acff
    14179 
    14180 > color (#!2 & sel) #ace8abff
    14181 
    14182 > color (#!2 & sel) #abe8aaff
    14183 
    14184 > color (#!2 & sel) #a9e7a7ff
    14185 
    14186 [Repeated 2 time(s)]
    14187 
    14188 > select #2/G
    14189 
    14190 385 atoms, 391 bonds, 50 residues, 1 model selected 
    14191 
    14192 > hide sel cartoons
    14193 
    14194 > select #2/B
    14195 
    14196 2539 atoms, 2587 bonds, 333 residues, 1 model selected 
    14197 
    14198 > hide sel cartoons
    14199 
    14200 > select #2/F
    14201 
    14202 1780 atoms, 1826 bonds, 1 pseudobond, 233 residues, 2 models selected 
    14203 
    14204 > hide sel cartoons
    14205 
    14206 > select #2/R
    14207 
    14208 3756 atoms, 3841 bonds, 7 pseudobonds, 474 residues, 2 models selected 
    14209 
    14210 > ui mousemode right select
    14211 
    14212 > select clear
    14213 
    14214 [Repeated 1 time(s)]
    14215 
    14216 > ui mousemode right translate
    14217 
    14218 > open 3SN6
    14219 
    14220 Summary of feedback from opening 3SN6 fetched from pdb 
    14221 --- 
    14222 note | Fetching compressed mmCIF 3sn6 from http://files.rcsb.org/download/3sn6.cif 
    14223  
    14224 3sn6 title: 
    14225 Crystal structure of the beta2 adrenergic receptor-Gs protein complex [more
    14226 info...] 
    14227  
    14228 Chain information for 3sn6 #3 
    14229 --- 
    14230 Chain | Description | UniProt 
    14231 A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_BOVIN 1-394 
    14232 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340 
    14233 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN 1-68 
    14234 N | Camelid antibody VHH fragment |   
    14235 R | Endolysin,Beta-2 adrenergic receptor | ENLYS_BPT4 1002-1161, ADRB2_HUMAN 29-365 
    14236  
    14237 Non-standard residues in 3sn6 #3 
    14238 --- 
    14239 P0G —
    14240 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one 
    14241  
    14242 
    14243 > select add #3
    14244 
    14245 10274 atoms, 10478 bonds, 6 pseudobonds, 1319 residues, 2 models selected 
    14246 
    14247 > hide sel cartoons
    14248 
    14249 > show sel cartoons
    14250 
    14251 > hide sel atoms
    14252 
    14253 > ui tool show Matchmaker
    14254 
    14255 > matchmaker #!1,3 to #2/R pairing bs
    14256 
    14257 Parameters 
    14258 --- 
    14259 Chain pairing | bs 
    14260 Alignment algorithm | Needleman-Wunsch 
    14261 Similarity matrix | BLOSUM-62 
    14262 SS fraction | 0.3 
    14263 Gap open (HH/SS/other) | 18/18/6 
    14264 Gap extend | 1 
    14265 SS matrix |  |  | H | S | O 
    14266 ---|---|---|--- 
    14267 H | 6 | -9 | -6 
    14268 S |  | 6 | -6 
    14269 O |  |  | 4 
    14270 Iteration cutoff | 2 
    14271  
    14272 Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
    14273 alignment score = 1623.9 
    14274 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    14275 1.770) 
    14276  
    14277 Matchmaker 8tb0, chain R (#2) with 3sn6, chain A (#3), sequence alignment
    14278 score = 1487.5 
    14279 RMSD between 167 pruned atom pairs is 1.125 angstroms; (across all 219 pairs:
    14280 1.940) 
    14281  
    14282 
    14283 > matchmaker #!1,3 to #2/R pairing bs
    14284 
    14285 Parameters 
    14286 --- 
    14287 Chain pairing | bs 
    14288 Alignment algorithm | Needleman-Wunsch 
    14289 Similarity matrix | BLOSUM-62 
    14290 SS fraction | 0.3 
    14291 Gap open (HH/SS/other) | 18/18/6 
    14292 Gap extend | 1 
    14293 SS matrix |  |  | H | S | O 
    14294 ---|---|---|--- 
    14295 H | 6 | -9 | -6 
    14296 S |  | 6 | -6 
    14297 O |  |  | 4 
    14298 Iteration cutoff | 2 
    14299  
    14300 Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
    14301 alignment score = 1623.9 
    14302 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    14303 1.770) 
    14304  
    14305 Matchmaker 8tb0, chain R (#2) with 3sn6, chain A (#3), sequence alignment
    14306 score = 1487.5 
    14307 RMSD between 167 pruned atom pairs is 1.125 angstroms; (across all 219 pairs:
    14308 1.940) 
    14309  
    14310 
    14311 > select #3/N
    14312 
    14313 970 atoms, 992 bonds, 128 residues, 1 model selected 
    14314 
    14315 > delete atoms sel
    14316 
    14317 > delete bonds sel
    14318 
    14319 > select #1/N
    14320 
    14321 1746 atoms, 1764 bonds, 1 pseudobond, 117 residues, 2 models selected 
    14322 
    14323 > delete atoms (#!1 & sel)
    14324 
    14325 > delete bonds (#!1 & sel)
    14326 
    14327 > select #1/H
    14328 
    14329 3275 atoms, 3324 bonds, 1 pseudobond, 222 residues, 2 models selected 
    14330 
    14331 > delete atoms (#!1 & sel)
    14332 
    14333 > delete bonds (#!1 & sel)
    14334 
    14335 > select #2/G#3/G
    14336 
    14337 823 atoms, 835 bonds, 108 residues, 2 models selected 
    14338 
    14339 > delete atoms sel
    14340 
    14341 > delete bonds sel
    14342 
    14343 > select #2/B#3/B
    14344 
    14345 5131 atoms, 5226 bonds, 673 residues, 2 models selected 
    14346 
    14347 > delete atoms sel
    14348 
    14349 > delete bonds sel
    14350 
    14351 > select #3/A
    14352 
    14353 2814 atoms, 2870 bonds, 3 pseudobonds, 349 residues, 2 models selected 
    14354 
    14355 > delete atoms (#!3 & sel)
    14356 
    14357 > delete bonds (#!3 & sel)
    14358 
    14359 > select #2/F
    14360 
    14361 1780 atoms, 1826 bonds, 1 pseudobond, 233 residues, 2 models selected 
    14362 
    14363 > delete atoms (#!2 & sel)
    14364 
    14365 > delete bonds (#!2 & sel)
    14366 
    14367 > select #1/L
    14368 
    14369 3197 atoms, 3234 bonds, 212 residues, 1 model selected 
    14370 
    14371 > delete atoms sel
    14372 
    14373 > delete bonds sel
    14374 
    14375 > ui tool show Matchmaker
    14376 
    14377 > matchmaker #!2-3 to #1/R pairing bs
    14378 
    14379 Parameters 
    14380 --- 
    14381 Chain pairing | bs 
    14382 Alignment algorithm | Needleman-Wunsch 
    14383 Similarity matrix | BLOSUM-62 
    14384 SS fraction | 0.3 
    14385 Gap open (HH/SS/other) | 18/18/6 
    14386 Gap extend | 1 
    14387 SS matrix |  |  | H | S | O 
    14388 ---|---|---|--- 
    14389 H | 6 | -9 | -6 
    14390 S |  | 6 | -6 
    14391 O |  |  | 4 
    14392 Iteration cutoff | 2 
    14393  
    14394 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
    14395 alignment score = 1623.9 
    14396 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    14397 1.770) 
    14398  
    14399 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
    14400 alignment score = 339.4 
    14401 RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
    14402 5.318) 
    14403  
    14404 
    14405 > matchmaker #!2-3 to #1/R pairing bs
    14406 
    14407 Parameters 
    14408 --- 
    14409 Chain pairing | bs 
    14410 Alignment algorithm | Needleman-Wunsch 
    14411 Similarity matrix | BLOSUM-62 
    14412 SS fraction | 0.3 
    14413 Gap open (HH/SS/other) | 18/18/6 
    14414 Gap extend | 1 
    14415 SS matrix |  |  | H | S | O 
    14416 ---|---|---|--- 
    14417 H | 6 | -9 | -6 
    14418 S |  | 6 | -6 
    14419 O |  |  | 4 
    14420 Iteration cutoff | 2 
    14421  
    14422 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
    14423 alignment score = 1623.9 
    14424 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    14425 1.770) 
    14426  
    14427 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
    14428 alignment score = 339.4 
    14429 RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
    14430 5.318) 
    14431  
    14432 
    14433 > select #3/R
    14434 
    14435 3460 atoms, 3533 bonds, 3 pseudobonds, 444 residues, 2 models selected 
    14436 
    14437 > color (#!3 & sel) #e8652cff
    14438 
    14439 > color (#!3 & sel) #eb652cff
    14440 
    14441 > color (#!3 & sel) #ed652cff
    14442 
    14443 > color (#!3 & sel) #ec642bff
    14444 
    14445 > color (#!3 & sel) #ec622bff
    14446 
    14447 > color (#!3 & sel) #ea5a2aff
    14448 
    14449 > color (#!3 & sel) #e95629ff
    14450 
    14451 > color (#!3 & sel) #e94e28ff
    14452 
    14453 > color (#!3 & sel) #e84326ff
    14454 
    14455 > color (#!3 & sel) #e73e25ff
    14456 
    14457 [Repeated 2 time(s)]
    14458 
    14459 > color (#!3 & sel) #e63d25ff
    14460 
    14461 > color (#!3 & sel) #e63c25ff
    14462 
    14463 [Repeated 2 time(s)]
    14464 
    14465 > color (#!3 & sel) #e73a25ff
    14466 
    14467 > color (#!3 & sel) #e93925ff
    14468 
    14469 > color (#!3 & sel) #e93924ff
    14470 
    14471 > color (#!3 & sel) #eb3c25ff
    14472 
    14473 > color (#!3 & sel) #eb3d25ff
    14474 
    14475 > color (#!3 & sel) #eb3f25ff
    14476 
    14477 > color (#!3 & sel) #eb4025ff
    14478 
    14479 > color (#!3 & sel) #eb4125ff
    14480 
    14481 > color (#!3 & sel) #eb4927ff
    14482 
    14483 > color (#!3 & sel) #ec5f2aff
    14484 
    14485 > color (#!3 & sel) #ed6e2dff
    14486 
    14487 > color (#!3 & sel) #f08a34ff
    14488 
    14489 > color (#!3 & sel) #f19b38ff
    14490 
    14491 > color (#!3 & sel) #efb23fff
    14492 
    14493 > color (#!3 & sel) #ebad3fff
    14494 
    14495 > color (#!3 & sel) #e4953dff
    14496 
    14497 > color (#!3 & sel) #e08440ff
    14498 
    14499 > color (#!3 & sel) #de7e40ff
    14500 
    14501 [Repeated 1 time(s)]
    14502 
    14503 > color (#!3 & sel) #de7e41ff
    14504 
    14505 > color (#!3 & sel) #de7741ff
    14506 
    14507 > color (#!3 & sel) #dd7643ff
    14508 
    14509 > color (#!3 & sel) #dd7445ff
    14510 
    14511 > color (#!3 & sel) #dc7445ff
    14512 
    14513 > color (#!3 & sel) #dc7547ff
    14514 
    14515 > color (#!3 & sel) #db7c56ff
    14516 
    14517 > color (#!3 & sel) #db815fff
    14518 
    14519 > color (#!3 & sel) #dc9578ff
    14520 
    14521 > color (#!3 & sel) #dd997fff
    14522 
    14523 > color (#!3 & sel) #dd9a7eff
    14524 
    14525 > color (#!3 & sel) #dc9373ff
    14526 
    14527 > color (#!3 & sel) #dc7c48ff
    14528 
    14529 > color (#!3 & sel) #e47d36ff
    14530 
    14531 > color (#!3 & sel) #e78736ff
    14532 
    14533 > color (#!3 & sel) #fcec4fff
    14534 
    14535 > color (#!3 & sel) #fdf451ff
    14536 
    14537 > color (#!3 & sel) #fdfb54ff
    14538 
    14539 > color (#!3 & sel) #eefb53ff
    14540 
    14541 > color (#!3 & sel) #e4f652ff
    14542 
    14543 [Repeated 1 time(s)]
    14544 
    14545 > color (#!3 & sel) #e5f552ff
    14546 
    14547 > color (#!3 & sel) #e3f052ff
    14548 
    14549 > color (#!3 & sel) #e0ed56ff
    14550 
    14551 > color (#!3 & sel) #d6ea5bff
    14552 
    14553 > color (#!3 & sel) #d4ea5aff
    14554 
    14555 > color (#!3 & sel) #d1e959ff
    14556 
    14557 > color (#!3 & sel) #c8eb54ff
    14558 
    14559 > color (#!3 & sel) #b9ed50ff
    14560 
    14561 > color (#!3 & sel) #91f34dff
    14562 
    14563 > color (#!3 & sel) #75f74cff
    14564 
    14565 > color (#!3 & sel) #74f756ff
    14566 
    14567 > color (#!3 & sel) #73f560ff
    14568 
    14569 > color (#!3 & sel) #72f465ff
    14570 
    14571 > color (#!3 & sel) #72f269ff
    14572 
    14573 > color (#!3 & sel) #71f06cff
    14574 
    14575 > color (#!3 & sel) #71f06dff
    14576 
    14577 > color (#!3 & sel) #71ee6fff
    14578 
    14579 [Repeated 1 time(s)]
    14580 
    14581 > color (#!3 & sel) #71ee7dff
    14582 
    14583 > color (#!3 & sel) #71ee95ff
    14584 
    14585 > color (#!3 & sel) #72f28aff
    14586 
    14587 > color (#!3 & sel) #75f963ff
    14588 
    14589 > color (#!3 & sel) #6de84cff
    14590 
    14591 > color (#!3 & sel) #68de48ff
    14592 
    14593 > color (#!3 & sel) #66d946ff
    14594 
    14595 > color (#!3 & sel) #61cd41ff
    14596 
    14597 > color (#!3 & sel) #5abf3dff
    14598 
    14599 > color (#!3 & sel) #5abf3cff
    14600 
    14601 > color (#!3 & sel) #5abe3eff
    14602 
    14603 > color (#!3 & sel) #5abe46ff
    14604 
    14605 > color (#!3 & sel) #5dc664ff
    14606 
    14607 > color (#!3 & sel) #62d195ff
    14608 
    14609 > color (#!3 & sel) #67dec8ff
    14610 
    14611 > color (#!3 & sel) #5ccaefff
    14612 
    14613 > color (#!3 & sel) #4baaeeff
    14614 
    14615 > color (#!3 & sel) #347eeeff
    14616 
    14617 > color (#!3 & sel) #001df3ff
    14618 
    14619 > color (#!3 & sel) #0018f4ff
    14620 
    14621 [Repeated 5 time(s)]
    14622 
    14623 > color (#!3 & sel) #0019f5ff
    14624 
    14625 > color (#!3 & sel) #0019f3ff
    14626 
    14627 > color (#!3 & sel) #001af3ff
    14628 
    14629 > color (#!3 & sel) #001af1ff
    14630 
    14631 > color (#!3 & sel) #001af2ff
    14632 
    14633 > color (#!3 & sel) #011bf0ff
    14634 
    14635 > color (#!3 & sel) #0e1deeff
    14636 
    14637 > color (#!3 & sel) #1a20eaff
    14638 
    14639 > color (#!3 & sel) #2427e8ff
    14640 
    14641 > color (#!3 & sel) #2929e6ff
    14642 
    14643 > color (#!3 & sel) #2522eaff
    14644 
    14645 > color (#!3 & sel) #261bf1ff
    14646 
    14647 > color (#!3 & sel) #351bf4ff
    14648 
    14649 > color (#!3 & sel) #3e1cf3ff
    14650 
    14651 > color (#!3 & sel) #461cf3ff
    14652 
    14653 > color (#!3 & sel) #8226e8ff
    14654 
    14655 > color (#!3 & sel) #9d2be8ff
    14656 
    14657 > color (#!3 & sel) #a82de8ff
    14658 
    14659 > color (#!3 & sel) #bf31f1ff
    14660 
    14661 > color (#!3 & sel) #c131f5ff
    14662 
    14663 > color (#!3 & sel) #c131f6ff
    14664 
    14665 > color (#!3 & sel) #c231f6ff
    14666 
    14667 > color (#!3 & sel) #c532f6ff
    14668 
    14669 > color (#!3 & sel) #c732f5ff
    14670 
    14671 > color (#!3 & sel) #c234edff
    14672 
    14673 > color (#!3 & sel) #c335eeff
    14674 
    14675 > color (#!3 & sel) #c437ebff
    14676 
    14677 > color (#!3 & sel) #c73ee6ff
    14678 
    14679 [Repeated 1 time(s)]
    14680 
    14681 > color (#!3 & sel) #c33ee7ff
    14682 
    14683 > color (#!3 & sel) #bb39e8ff
    14684 
    14685 > color (#!3 & sel) #a22febff
    14686 
    14687 > color (#!3 & sel) #8226f2ff
    14688 
    14689 > color (#!3 & sel) #541ff1ff
    14690 
    14691 > color (#!3 & sel) #4b1fe2ff
    14692 
    14693 > color (#!3 & sel) #121db9ff
    14694 
    14695 > color (#!3 & sel) #4b9d5bff
    14696 
    14697 > color (#!3 & sel) #4c9f3fff
    14698 
    14699 > color (#!3 & sel) #4c9f36ff
    14700 
    14701 > color (#!3 & sel) #56a235ff
    14702 
    14703 > color (#!3 & sel) #63a235ff
    14704 
    14705 > color (#!3 & sel) #a1a339ff
    14706 
    14707 > color (#!3 & sel) #ad5728ff
    14708 
    14709 > color (#!3 & sel) #b73e25ff
    14710 
    14711 > color (#!3 & sel) #c43324ff
    14712 
    14713 > color (#!3 & sel) #ffffffff
    14714 
    14715 > color (#!3 & sel) #ea332440
    14716 
    14717 > color (#!3 & sel) #ea3424ff
    14718 
    14719 > color (#!3 & sel) #eb3824ff
    14720 
    14721 > color (#!3 & sel) #eb4826ff
    14722 
    14723 > color (#!3 & sel) #ec5028ff
    14724 
    14725 > color (#!3 & sel) #ec5228ff
    14726 
    14727 [Repeated 1 time(s)]
    14728 
    14729 > color (#!3 & sel) #ec5128ff
    14730 
    14731 [Repeated 2 time(s)]
    14732 
    14733 > color (#!3 & sel) #ec5028ff
    14734 
    14735 [Repeated 1 time(s)]
    14736 
    14737 > color (#!3 & sel) #ec4f28ff
    14738 
    14739 > color (#!3 & sel) #e94b27ff
    14740 
    14741 > color (#!3 & sel) #e74b28ff
    14742 
    14743 [Repeated 1 time(s)]
    14744 
    14745 > color (#!3 & sel) #e54b29ff
    14746 
    14747 > color (#!3 & sel) #e34c2aff
    14748 
    14749 > color (#!3 & sel) #e04b2dff
    14750 
    14751 > color (#!3 & sel) #df4d30ff
    14752 
    14753 > color (#!3 & sel) #de4a31ff
    14754 
    14755 > color (#!3 & sel) #de4b33ff
    14756 
    14757 > color (#!3 & sel) #db483aff
    14758 
    14759 > color (#!3 & sel) #da483cff
    14760 
    14761 > color (#!3 & sel) #da4a40ff
    14762 
    14763 > color (#!3 & sel) #d94c44ff
    14764 
    14765 > color (#!3 & sel) #d9534ded
    14766 
    14767 > color (#!3 & sel) #d8554f36
    14768 
    14769 > color (#!3 & sel) #ffffffff
    14770 
    14771 > color (#!3 & sel) #d86d696d
    14772 
    14773 > color (#!3 & sel) #d97673fe
    14774 
    14775 > color (#!3 & sel) #da7b79c2
    14776 
    14777 > color (#!3 & sel) #da7c799a
    14778 
    14779 > color (#!3 & sel) #da7c79a4
    14780 
    14781 > color (#!3 & sel) #da7b79ff
    14782 
    14783 > color (#!3 & sel) #d97771ff
    14784 
    14785 > color (#!3 & sel) #d96f67ff
    14786 
    14787 > color (#!3 & sel) #d86a61ff
    14788 
    14789 > color (#!3 & sel) #da5241ff
    14790 
    14791 > color (#!3 & sel) #db4c39ff
    14792 
    14793 > color (#!3 & sel) #dc4a38ff
    14794 
    14795 > color (#!3 & sel) #dc4a37ff
    14796 
    14797 > color (#!3 & sel) #dc4937ff
    14798 
    14799 > color (#!3 & sel) #dd4734ff
    14800 
    14801 > color (#!3 & sel) #dd4531ff
    14802 
    14803 [Repeated 1 time(s)]
    14804 
    14805 > color (#!3 & sel) #de4330ff
    14806 
    14807 > color (#!3 & sel) #df422fff
    14808 
    14809 > color (#!3 & sel) #df422eff
    14810 
    14811 [Repeated 2 time(s)]
    14812 
    14813 > color (#!3 & sel) #df422fff
    14814 
    14815 > color (#!3 & sel) #de4430ff
    14816 
    14817 > color (#!3 & sel) #dd4632ff
    14818 
    14819 > color (#!3 & sel) #dd4835ff
    14820 
    14821 > color (#!3 & sel) #dc4a37ff
    14822 
    14823 > color (#!3 & sel) #db4c3aff
    14824 
    14825 > color (#!3 & sel) #db4d3bff
    14826 
    14827 > color (#!3 & sel) #db4e3bff
    14828 
    14829 > color (#!3 & sel) #da5644ff
    14830 
    14831 > color (#!3 & sel) #da5a47ff
    14832 
    14833 > color (#!3 & sel) #d95f4aff
    14834 
    14835 > color (#!3 & sel) #da644eff
    14836 
    14837 > color (#!3 & sel) #d9664fff
    14838 
    14839 > color (#!3 & sel) #da6950ff
    14840 
    14841 > color (#!3 & sel) #da6a4fff
    14842 
    14843 > color (#!3 & sel) #db784dff
    14844 
    14845 > color (#!3 & sel) #dc7a4aff
    14846 
    14847 > color (#!3 & sel) #dc7c4aff
    14848 
    14849 > color (#!3 & sel) #de884aff
    14850 
    14851 > color (#!3 & sel) #df954bff
    14852 
    14853 > color (#!3 & sel) #e0994bff
    14854 
    14855 [Repeated 1 time(s)]
    14856 
    14857 > color (#!3 & sel) #e09e4cff
    14858 
    14859 > color (#!3 & sel) #e1a04cff
    14860 
    14861 [Repeated 2 time(s)]
    14862 
    14863 > color (#!3 & sel) #e19f4cff
    14864 
    14865 > color (#!3 & sel) #e19c4bff
    14866 
    14867 > color (#!3 & sel) #e19343ff
    14868 
    14869 > color (#!3 & sel) #e18e40ff
    14870 
    14871 > color (#!3 & sel) #e28b3dff
    14872 
    14873 > color (#!3 & sel) #e3863aff
    14874 
    14875 > color (#!3 & sel) #e38539ff
    14876 
    14877 > color (#!3 & sel) #e48538ff
    14878 
    14879 > color (#!3 & sel) #e48537ff
    14880 
    14881 > color (#!3 & sel) #e58337ff
    14882 
    14883 > color (#!3 & sel) #e58336ff
    14884 
    14885 > color (#!3 & sel) #e58236ff
    14886 
    14887 > color (#!3 & sel) #e78134ff
    14888 
    14889 [Repeated 1 time(s)]
    14890 
    14891 > color (#!3 & sel) #e88134ff
    14892 
    14893 > color (#!3 & sel) #ec7f32ff
    14894 
    14895 [Repeated 3 time(s)]
    14896 
    14897 > color (#!3 & sel) #ed7f31ff
    14898 
    14899 [Repeated 1 time(s)]
    14900 
    14901 > color (#!3 & sel) #ed7e31ff
    14902 
    14903 > color (#!3 & sel) #ef7f31ff
    14904 
    14905 > color (#!3 & sel) #ef8432ff
    14906 
    14907 > color (#!3 & sel) #ee8432ff
    14908 
    14909 [Repeated 3 time(s)]
    14910 
    14911 > color (#!3 & sel) #ed8532ff
    14912 
    14913 > color (#!3 & sel) #ed8432ff
    14914 
    14915 [Repeated 1 time(s)]
    14916 
    14917 > color (#!3 & sel) #ed8533ff
    14918 
    14919 > color (#!3 & sel) #ee8a34ff
    14920 
    14921 > color (#!3 & sel) #ee8b34ff
    14922 
    14923 [Repeated 1 time(s)]
    14924 
    14925 > color (#!3 & sel) #ef8e35ff
    14926 
    14927 > color (#!3 & sel) #ef9135ff
    14928 
    14929 > color (#!3 & sel) #f09637ff
    14930 
    14931 > color (#!3 & sel) #f09a38ff
    14932 
    14933 > color (#!3 & sel) #f2a13aff
    14934 
    14935 > color (#!3 & sel) #f3a93cff
    14936 
    14937 [Repeated 1 time(s)]
    14938 
    14939 > color (#!3 & sel) #f3af3eff
    14940 
    14941 > color (#!3 & sel) #f6c644ff
    14942 
    14943 > color (#!3 & sel) #f7c945ff
    14944 
    14945 > color (#!3 & sel) #fbe94eff
    14946 
    14947 > color (#!3 & sel) #faec4fff
    14948 
    14949 > color (#!3 & sel) #f8ec4fff
    14950 
    14951 > color (#!3 & sel) #f8eb4fff
    14952 
    14953 > color (#!3 & sel) #f8ea4fff
    14954 
    14955 > color (#!3 & sel) #f8e94fff
    14956 
    14957 [Repeated 1 time(s)]
    14958 
    14959 > color (#!3 & sel) #f8e44dff
    14960 
    14961 > color (#!3 & sel) #f6d248ff
    14962 
    14963 > color (#!3 & sel) #f5d047ff
    14964 
    14965 [Repeated 1 time(s)]
    14966 
    14967 > color (#!3 & sel) #f6d047ff
    14968 
    14969 > color (#!3 & sel) #f5ca45ff
    14970 
    14971 > color (#!3 & sel) #f4bd41ff
    14972 
    14973 > color (#!3 & sel) #f4b840ff
    14974 
    14975 [Repeated 3 time(s)]
    14976 
    14977 > color (#!3 & sel) #f4b53fff
    14978 
    14979 > color (#!3 & sel) #f4b23eff
    14980 
    14981 [Repeated 2 time(s)]
    14982 
    14983 > color (#!3 & sel) #f3af3eff
    14984 
    14985 > color (#!3 & sel) #f3ae3dff
    14986 
    14987 [Repeated 1 time(s)]
    14988 
    14989 > color (#!3 & sel) #f2ae3dff
    14990 
    14991 > color (#!3 & sel) #f2a93cff
    14992 
    14993 > color (#!3 & sel) #efa83cff
    14994 
    14995 > color (#!3 & sel) #eea73cff
    14996 
    14997 > color (#!3 & sel) #eda83cff
    14998 
    14999 > color (#!3 & sel) #eda73cff
    15000 
    15001 > color (#!3 & sel) #eda63bff
    15002 
    15003 > color (#!3 & sel) #eca63bff
    15004 
    15005 > color (#!3 & sel) #eca53bff
    15006 
    15007 [Repeated 1 time(s)]
    15008 
    15009 > color (#!3 & sel) #eba63bff
    15010 
    15011 [Repeated 1 time(s)]
    15012 
    15013 > color (#!3 & sel) #eba93cff
    15014 
    15015 [Repeated 1 time(s)]
    15016 
    15017 > color (#!3 & sel) #eaac3dff
    15018 
    15019 > color (#!3 & sel) #e7ab3cff
    15020 
    15021 > color (#!3 & sel) #e7ab3dff
    15022 
    15023 > color (#!3 & sel) #e5aa3cff
    15024 
    15025 > color (#!3 & sel) #e1a73cff
    15026 
    15027 > color (#!3 & sel) #d1a13aff
    15028 
    15029 > color (#!3 & sel) #c89c38ff
    15030 
    15031 > color (#!3 & sel) #c49b38ff
    15032 
    15033 > color (#!3 & sel) #c19938ff
    15034 
    15035 > color (#!3 & sel) #af8c34ff
    15036 
    15037 > color (#!3 & sel) #ac8a33ff
    15038 
    15039 > color (#!3 & sel) #aa8933ff
    15040 
    15041 > color (#!3 & sel) #a98832ff
    15042 
    15043 > color (#!3 & sel) #a78632ff
    15044 
    15045 [Repeated 1 time(s)]
    15046 
    15047 > color (#!3 & sel) #a68131ff
    15048 
    15049 > color (#!3 & sel) #a6782fff
    15050 
    15051 > color (#!3 & sel) #a66c2cff
    15052 
    15053 > color (#!3 & sel) #ab5a29ff
    15054 
    15055 [Repeated 2 time(s)]
    15056 
    15057 > color (#!3 & sel) #ac5929ff
    15058 
    15059 > color (#!3 & sel) #af5a29ff
    15060 
    15061 > color (#!3 & sel) #ba602bff
    15062 
    15063 > color (#!3 & sel) #cd682cff
    15064 
    15065 > color (#!3 & sel) #cf672cff
    15066 
    15067 > color (#!3 & sel) #d4692dff
    15068 
    15069 > color (#!3 & sel) #e06a2dff
    15070 
    15071 > color (#!3 & sel) #e26b2dff
    15072 
    15073 > color (#!3 & sel) #e5692dff
    15074 
    15075 > color (#!3 & sel) #e7682cff
    15076 
    15077 [Repeated 1 time(s)]
    15078 
    15079 > color (#!3 & sel) #e8662cff
    15080 
    15081 > color (#!3 & sel) #e8642cff
    15082 
    15083 > color (#!3 & sel) #e9642cff
    15084 
    15085 > color (#!3 & sel) #ea642cff
    15086 
    15087 > color (#!3 & sel) #ea632bff
    15088 
    15089 [Repeated 1 time(s)]
    15090 
    15091 > color (#!3 & sel) #eb642bff
    15092 
    15093 > color (#!3 & sel) #eb622bff
    15094 
    15095 > color (#!3 & sel) #ec612bff
    15096 
    15097 > color (#!3 & sel) #eb5e2aff
    15098 
    15099 > color (#!3 & sel) #ec5a29ff
    15100 
    15101 [Repeated 1 time(s)]
    15102 
    15103 > color (#!3 & sel) #ec5829ff
    15104 
    15105 > color (#!3 & sel) #ec5529ff
    15106 
    15107 > color (#!3 & sel) #ec5528ff
    15108 
    15109 > color (#!3 & sel) #eb5228ff
    15110 
    15111 > color (#!3 & sel) #eb5128ff
    15112 
    15113 > color (#!3 & sel) #eb5228ff
    15114 
    15115 > color (#!3 & sel) #ea5128ff
    15116 
    15117 > color (#!3 & sel) #ea5229ff
    15118 
    15119 > color (#!3 & sel) #ea5329ff
    15120 
    15121 > color (#!3 & sel) #e7542aff
    15122 
    15123 > color (#!3 & sel) #e5572bff
    15124 
    15125 > color (#!3 & sel) #e4592cff
    15126 
    15127 > color (#!3 & sel) #e25a2fff
    15128 
    15129 > color (#!3 & sel) #e05c31ff
    15130 
    15131 > color (#!3 & sel) #df5e34ff
    15132 
    15133 > color (#!3 & sel) #dd5f3aff
    15134 
    15135 > color (#!3 & sel) #dc603cff
    15136 
    15137 > color (#!3 & sel) #db6442ff
    15138 
    15139 > color (#!3 & sel) #db6444ff
    15140 
    15141 > color (#!3 & sel) #da6448ff
    15142 
    15143 > color (#!3 & sel) #da664bff
    15144 
    15145 > color (#!3 & sel) #da684eff
    15146 
    15147 > color (#!3 & sel) #d96a51ff
    15148 
    15149 > color (#!3 & sel) #d96c53ff
    15150 
    15151 > color (#!3 & sel) #d9715eff
    15152 
    15153 > color (#!3 & sel) #d97260ff
    15154 
    15155 > color (#!3 & sel) #d97362ff
    15156 
    15157 > color (#!3 & sel) #d97264ff
    15158 
    15159 [Repeated 1 time(s)]
    15160 
    15161 > color (#!3 & sel) #d97164ff
    15162 
    15163 > color (#!3 & sel) #d97266ff
    15164 
    15165 > color (#!3 & sel) #d97066ff
    15166 
    15167 > color (#!3 & sel) #d97266ff
    15168 
    15169 > color (#!3 & sel) #d97267ff
    15170 
    15171 > color (#!3 & sel) #d97367ff
    15172 
    15173 > ui mousemode right select
    15174 
    15175 > select clear
    15176 
    15177 [Repeated 2 time(s)]
    15178 
    15179 > open 2RH1
    15180 
    15181 2rh1 title: 
    15182 High resolution crystal structure of human B2-adrenergic G protein-coupled
    15183 receptor. [more info...] 
    15184  
    15185 Chain information for 2rh1 #4 
    15186 --- 
    15187 Chain | Description | UniProt 
    15188 A | beta-2-adrenergic receptor/T4-lysozyme chimera | ADRB2_HUMAN 1-230 263-365, LYS_BPT4 1002-1161 
    15189  
    15190 Non-standard residues in 2rh1 #4 
    15191 --- 
    15192 12P — dodecaethylene glycol (polyethylene glycol PEG400) 
    15193 ACM — acetamide 
    15194 BU1 — 1,4-butanediol 
    15195 CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
    15196 ((S)-Carazolol) 
    15197 CLR — cholesterol 
    15198 GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose) 
    15199 PLM — palmitic acid 
    15200 SO4 — sulfate ion 
    15201  
    15202 
    15203 > select add #4
    15204 
    15205 3804 atoms, 3842 bonds, 507 residues, 1 model selected 
    15206 
    15207 > show sel cartoons
    15208 
    15209 > hide sel atoms
    15210 
    15211 > ui tool show Matchmaker
    15212 
    15213 > matchmaker #4#!1,3 to #2/R pairing bs
    15214 
    15215 Parameters 
    15216 --- 
    15217 Chain pairing | bs 
    15218 Alignment algorithm | Needleman-Wunsch 
    15219 Similarity matrix | BLOSUM-62 
    15220 SS fraction | 0.3 
    15221 Gap open (HH/SS/other) | 18/18/6 
    15222 Gap extend | 1 
    15223 SS matrix |  |  | H | S | O 
    15224 ---|---|---|--- 
    15225 H | 6 | -9 | -6 
    15226 S |  | 6 | -6 
    15227 O |  |  | 4 
    15228 Iteration cutoff | 2 
    15229  
    15230 Matchmaker 8tb0, chain R (#2) with 2rh1, chain A (#4), sequence alignment
    15231 score = 320.5 
    15232 RMSD between 104 pruned atom pairs is 1.311 angstroms; (across all 244 pairs:
    15233 3.824) 
    15234  
    15235 Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
    15236 alignment score = 1623.9 
    15237 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    15238 1.770) 
    15239  
    15240 Matchmaker 8tb0, chain R (#2) with 3sn6, chain R (#3), sequence alignment
    15241 score = 428 
    15242 RMSD between 144 pruned atom pairs is 1.295 angstroms; (across all 245 pairs:
    15243 2.972) 
    15244  
    15245 
    15246 > matchmaker #4#!1,3 to #2/R pairing bs
    15247 
    15248 Parameters 
    15249 --- 
    15250 Chain pairing | bs 
    15251 Alignment algorithm | Needleman-Wunsch 
    15252 Similarity matrix | BLOSUM-62 
    15253 SS fraction | 0.3 
    15254 Gap open (HH/SS/other) | 18/18/6 
    15255 Gap extend | 1 
    15256 SS matrix |  |  | H | S | O 
    15257 ---|---|---|--- 
    15258 H | 6 | -9 | -6 
    15259 S |  | 6 | -6 
    15260 O |  |  | 4 
    15261 Iteration cutoff | 2 
    15262  
    15263 Matchmaker 8tb0, chain R (#2) with 2rh1, chain A (#4), sequence alignment
    15264 score = 320.5 
    15265 RMSD between 104 pruned atom pairs is 1.311 angstroms; (across all 244 pairs:
    15266 3.824) 
    15267  
    15268 Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
    15269 alignment score = 1623.9 
    15270 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    15271 1.770) 
    15272  
    15273 Matchmaker 8tb0, chain R (#2) with 3sn6, chain R (#3), sequence alignment
    15274 score = 428 
    15275 RMSD between 144 pruned atom pairs is 1.295 angstroms; (across all 245 pairs:
    15276 2.972) 
    15277  
    15278 
    15279 > select clear
    15280 
    15281 > open 2RH1
    15282 
    15283 2rh1 title: 
    15284 High resolution crystal structure of human B2-adrenergic G protein-coupled
    15285 receptor. [more info...] 
    15286  
    15287 Chain information for 2rh1 #5 
    15288 --- 
    15289 Chain | Description | UniProt 
    15290 A | beta-2-adrenergic receptor/T4-lysozyme chimera | ADRB2_HUMAN 1-230 263-365, LYS_BPT4 1002-1161 
    15291  
    15292 Non-standard residues in 2rh1 #5 
    15293 --- 
    15294 12P — dodecaethylene glycol (polyethylene glycol PEG400) 
    15295 ACM — acetamide 
    15296 BU1 — 1,4-butanediol 
    15297 CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
    15298 ((S)-Carazolol) 
    15299 CLR — cholesterol 
    15300 GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose) 
    15301 PLM — palmitic acid 
    15302 SO4 — sulfate ion 
    15303  
    15304 
    15305 > close #5
    15306 
    15307 > open 2RH1
    15308 
    15309 2rh1 title: 
    15310 High resolution crystal structure of human B2-adrenergic G protein-coupled
    15311 receptor. [more info...] 
    15312  
    15313 Chain information for 2rh1 #5 
    15314 --- 
    15315 Chain | Description | UniProt 
    15316 A | beta-2-adrenergic receptor/T4-lysozyme chimera | ADRB2_HUMAN 1-230 263-365, LYS_BPT4 1002-1161 
    15317  
    15318 Non-standard residues in 2rh1 #5 
    15319 --- 
    15320 12P — dodecaethylene glycol (polyethylene glycol PEG400) 
    15321 ACM — acetamide 
    15322 BU1 — 1,4-butanediol 
    15323 CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
    15324 ((S)-Carazolol) 
    15325 CLR — cholesterol 
    15326 GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose) 
    15327 PLM — palmitic acid 
    15328 SO4 — sulfate ion 
    15329  
    15330 
    15331 > close #5
    15332 
    15333 Drag select of 21 residues 
    15334 
    15335 > select clear
    15336 
    15337 [Repeated 1 time(s)]
    15338 
    15339 > ui mousemode right translate
    15340 
    15341 > preset cartoons/nucleotides licorice/ovals
    15342 
    15343 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    15344 Changed 3433 atom styles 
    15345 Preset expands to these ChimeraX commands:
    15346 
    15347    
    15348    
    15349     show nucleic
    15350     hide protein|solvent|H
    15351     surf hide
    15352     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    15353     cartoon
    15354     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    15355     cartoon style ~(nucleic|strand) x round
    15356     cartoon style (nucleic|strand) x rect
    15357     cartoon style protein modeh default arrows f x round width 1 thick 1
    15358     cartoon style nucleic x round width 1.6 thick 1.6
    15359     nucleotides tube/slab shape ellipsoid
    15360 
    15361  
    15362 
    15363 > preset cartoons/nucleotides cylinders/stubs
    15364 
    15365 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    15366 Changed 0 atom styles 
    15367 Preset expands to these ChimeraX commands:
    15368 
    15369    
    15370    
    15371     show nucleic
    15372     hide protein|solvent|H
    15373     surf hide
    15374     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    15375     cartoon
    15376     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    15377     cartoon style ~(nucleic|strand) x round
    15378     cartoon style (nucleic|strand) x rect
    15379     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    15380     cartoon style nucleic x round width 1.6 thick 1.6
    15381     nucleotides stubs
    15382 
    15383  
    15384 
    15385 > preset cartoons/nucleotides ribbons/slabs
    15386 
    15387 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    15388 Changed 0 atom styles 
    15389 Preset expands to these ChimeraX commands:
    15390 
    15391    
    15392    
    15393     show nucleic
    15394     hide protein|solvent|H
    15395     surf hide
    15396     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    15397     cartoon
    15398     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    15399     cartoon style ~(nucleic|strand) x round
    15400     cartoon style (nucleic|strand) x rect
    15401     nucleotides tube/slab shape box
    15402 
    15403  
    15404 
    15405 > ui mousemode right select
    15406 
    15407 > select #4/A:1161
    15408 
    15409 12 atoms, 12 bonds, 1 residue, 1 model selected 
    15410 
    15411 > select clear
    15412 
    15413 Drag select of 34 residues 
    15414 
    15415 > delete atoms sel
    15416 
    15417 > delete bonds sel
    15418 
    15419 > undo
    15420 
    15421 Undo failed, probably because structures have been modified. 
    15422 Drag select of 21 residues 
    15423 
    15424 > delete atoms sel
    15425 
    15426 > delete bonds sel
    15427 
    15428 Drag select of 5 residues 
    15429 Drag select of 39 residues 
    15430 
    15431 > delete atoms sel
    15432 
    15433 > delete bonds sel
    15434 
    15435 Drag select of 63 residues, 4 pseudobonds 
    15436 
    15437 > delete atoms (#!2,4 & sel)
    15438 
    15439 > delete bonds (#!2,4 & sel)
    15440 
    15441 > hide #!1 models
    15442 
    15443 Drag select of 162 residues, 10 pseudobonds 
    15444 
    15445 > delete atoms (#!2,4 & sel)
    15446 
    15447 > delete bonds (#!2,4 & sel)
    15448 
    15449 Drag select of 3 residues 
    15450 
    15451 > delete atoms sel
    15452 
    15453 > delete bonds sel
    15454 
    15455 Drag select of 1 pseudobonds 
    15456 No visible atoms or bonds selected 
    15457 Drag select of 21 residues, 1 pseudobonds 
    15458 
    15459 > delete atoms (#!2,4 & sel)
    15460 
    15461 > delete bonds (#!2,4 & sel)
    15462 
    15463 > select clear
    15464 
    15465 > select #4/A:1102
    15466 
    15467 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15468 
    15469 > select add #4/A:1101
    15470 
    15471 16 atoms, 14 bonds, 2 residues, 1 model selected 
    15472 
    15473 > select add #4/A:1146
    15474 
    15475 21 atoms, 18 bonds, 1 pseudobond, 3 residues, 2 models selected 
    15476 
    15477 > select add #4/A:1149
    15478 
    15479 28 atoms, 24 bonds, 1 pseudobond, 4 residues, 2 models selected 
    15480 
    15481 > select add #4/A:1147
    15482 
    15483 37 atoms, 32 bonds, 2 pseudobonds, 5 residues, 3 models selected 
    15484 
    15485 > select add #4/A:1145
    15486 
    15487 48 atoms, 42 bonds, 2 pseudobonds, 6 residues, 3 models selected 
    15488 
    15489 > select add #4/A:1144
    15490 
    15491 56 atoms, 49 bonds, 2 pseudobonds, 7 residues, 3 models selected 
    15492 
    15493 > delete atoms (#!4 & sel)
    15494 
    15495 > delete bonds (#!4 & sel)
    15496 
    15497 > select clear
    15498 
    15499 [Repeated 1 time(s)]Drag select of 3 residues, 1 pseudobonds 
    15500 
    15501 > delete atoms (#!4 & sel)
    15502 
    15503 > delete bonds (#!4 & sel)
    15504 
    15505 > select clear
    15506 
    15507 [Repeated 1 time(s)]Drag select of 2 pseudobonds 
    15508 
    15509 > hide #!2-4 cartoons
    15510 
    15511 > undo
    15512 
    15513 Drag select of 11 residues 
    15514 
    15515 > select clear
    15516 
    15517 > select #4/A:1010
    15518 
    15519 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15520 
    15521 > select add #4/A:1009
    15522 
    15523 16 atoms, 14 bonds, 2 residues, 1 model selected 
    15524 
    15525 > delete atoms sel
    15526 
    15527 > delete bonds sel
    15528 
    15529 > select clear
    15530 
    15531 > select #2/R:1809
    15532 
    15533 5 atoms, 4 bonds, 1 residue, 1 model selected 
    15534 
    15535 > select add #2/R:1810
    15536 
    15537 9 atoms, 7 bonds, 2 residues, 1 model selected 
    15538 
    15539 > delete atoms sel
    15540 
    15541 > delete bonds sel
    15542 
    15543 > ui mousemode right translate
    15544 
    15545 > ui mousemode right select
    15546 
    15547 Drag select of 158 residues, 1 pseudobonds 
    15548 
    15549 > delete atoms (#!3 & sel)
    15550 
    15551 > delete bonds (#!3 & sel)
    15552 
    15553 Drag select of 1 pseudobonds 
    15554 No visible atoms or bonds selected 
    15555 
    15556 > hide #!2-4 cartoons
    15557 
    15558 > show #!2-4 cartoons
    15559 
    15560 > select clear
    15561 
    15562 [Repeated 1 time(s)]Drag select of 6 residues 
    15563 
    15564 > select clear
    15565 
    15566 > ui mousemode right translate
    15567 
    15568 > lighting soft
    15569 
    15570 > lighting simple
    15571 
    15572 [Repeated 1 time(s)]
    15573 
    15574 > lighting soft
    15575 
    15576 > save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
    15577 > draft/Figure 7D-GPR61-BRIL fused structure v2.cxs"
    15578 
    15579 ——— End of log from Thu Apr 4 16:40:01 2024 ———
    15580 
    15581 opened ChimeraX session 
    15582 
    15583 > show #!1 models
    15584 
    15585 > hide #!1 models
    15586 
    15587 > show #!1 models
    15588 
    15589 > hide #!4 models
    15590 
    15591 > hide #!3 models
    15592 
    15593 > ui tool show "Side View"
    15594 
    15595 > select ligand
    15596 
    15597 302 atoms, 307 bonds, 19 residues, 3 models selected 
    15598 
    15599 > select #1 ligand
    15600 
    15601 Expected a keyword 
    15602 
    15603 > select #1:ligand
    15604 
    15605 Nothing selected 
    15606 
    15607 > select #2:ligand
    15608 
    15609 Nothing selected 
    15610 
    15611 > select #3:ligand
    15612 
    15613 Nothing selected 
    15614 
    15615 > select #4:ligand
    15616 
    15617 Nothing selected 
    15618 
    15619 > select liand
    15620 
    15621 Expected an objects specifier or a keyword 
    15622 
    15623 > select ligand
    15624 
    15625 302 atoms, 307 bonds, 19 residues, 3 models selected 
    15626 
    15627 > show sel & #!1 atoms
    15628 
    15629 > color (#!1 & sel) dark gray
    15630 
    15631 > color (#!1 & sel) dim gray
    15632 
    15633 > color (#!1 & sel) byhetero
    15634 
    15635 > select clear
    15636 
    15637 > show #!3 models
    15638 
    15639 > show #!4 models
    15640 
    15641 > hide #!2 models
    15642 
    15643 > hide #!3 models
    15644 
    15645 > hide #!4 models
    15646 
    15647 > show #!2 models
    15648 
    15649 > show #!4 models
    15650 
    15651 > hide #!4 models
    15652 
    15653 > show #!3 models
    15654 
    15655 > show #!4 models
    15656 
    15657 > hide #!3 models
    15658 
    15659 > hide #!4 models
    15660 
    15661 > ui tool show "Show Sequence Viewer"
    15662 
    15663 > sequence chain #1/R
    15664 
    15665 Alignment identifier is 1/R 
    15666 
    15667 > select #1/R:286
    15668 
    15669 12 atoms, 11 bonds, 1 residue, 1 model selected 
    15670 
    15671 > select
    15672 > #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
    15673 
    15674 4407 atoms, 4449 bonds, 275 residues, 1 model selected 
    15675 
    15676 > select clear
    15677 
    15678 > select #1/R:354
    15679 
    15680 15 atoms, 14 bonds, 1 residue, 1 model selected 
    15681 
    15682 > select #1/R:354
    15683 
    15684 15 atoms, 14 bonds, 1 residue, 1 model selected 
    15685 
    15686 > select #1/R:225-354
    15687 
    15688 2086 atoms, 2101 bonds, 130 residues, 1 model selected 
    15689 
    15690 > select clear
    15691 
    15692 > hide #!1 models
    15693 
    15694 > show #!1 models
    15695 
    15696 > select ligand
    15697 
    15698 302 atoms, 307 bonds, 19 residues, 3 models selected 
    15699 
    15700 > color (#!1 & sel) yellow
    15701 
    15702 > color (#!1 & sel) #eae15aff
    15703 
    15704 > color (#!1 & sel) #e9db5cff
    15705 
    15706 > color (#!1 & sel) #e7d960ff
    15707 
    15708 > color (#!1 & sel) #e6d865ff
    15709 
    15710 > color (#!1 & sel) #e7d868ff
    15711 
    15712 > color (#!1 & sel) #e7d86bff
    15713 
    15714 > color (#!1 & sel) #e6d672ff
    15715 
    15716 > color (#!1 & sel) #e5d47eff
    15717 
    15718 > color (#!1 & sel) #e5d580ff
    15719 
    15720 > color (#!1 & sel) #e6d788ff
    15721 
    15722 > color (#!1 & sel) #e8dc92ff
    15723 
    15724 > color (#!1 & sel) #e8dc94ff
    15725 
    15726 > color (#!1 & sel) #e8dc96ff
    15727 
    15728 > color (#!1 & sel) #e8dd99ff
    15729 
    15730 > color (#!1 & sel) #e9dc9dff
    15731 
    15732 > color (#!1 & sel) #e9dc9eff
    15733 
    15734 > color (#!1 & sel) #e9dfa3ff
    15735 
    15736 > color (#!1 & sel) #eae0a3ff
    15737 
    15738 > color (#!1 & sel) #eae0a4ff
    15739 
    15740 > color (#!1 & sel) #eae1a3ff
    15741 
    15742 > color (#!1 & sel) #e9e0a2ff
    15743 
    15744 > color (#!1 & sel) #eae1a2ff
    15745 
    15746 > color (#!1 & sel) #e9e0a2ff
    15747 
    15748 > color (#!1 & sel) #e9dfa2ff
    15749 
    15750 > color (#!1 & sel) #e9dca3ff
    15751 
    15752 > color (#!1 & sel) #e9daa5ff
    15753 
    15754 > color (#!1 & sel) #e9d9a5ff
    15755 
    15756 > color (#!1 & sel) #e8d6a2ff
    15757 
    15758 > color (#!1 & sel) #e6d399ff
    15759 
    15760 > color (#!1 & sel) #e5cc87ff
    15761 
    15762 > color (#!1 & sel) #e4cb81ff
    15763 
    15764 > color (#!1 & sel) #e3c97eff
    15765 
    15766 > color (#!1 & sel) #e3c87bff
    15767 
    15768 > color (#!1 & sel) #e3c875ff
    15769 
    15770 > color (#!1 & sel) #e3c873ff
    15771 
    15772 > color (#!1 & sel) #e3c76aff
    15773 
    15774 [Repeated 1 time(s)]
    15775 
    15776 > color (#!1 & sel) #e4c669ff
    15777 
    15778 > color (#!1 & sel) #e4c769ff
    15779 
    15780 > color (#!1 & sel) #e4c868ff
    15781 
    15782 > color (#!1 & sel) #e4ca68ff
    15783 
    15784 > color (#!1 & sel) #e4c968ff
    15785 
    15786 > color (#!1 & sel) #e4ca66ff
    15787 
    15788 > color (#!1 & sel) #e4ca64ff
    15789 
    15790 > color (#!1 & sel) #e4c962ff
    15791 
    15792 > color (#!1 & sel) #e4ca63ff
    15793 
    15794 > color (#!1 & sel) #e5cc63ff
    15795 
    15796 > color (#!1 & sel) #e5cd63ff
    15797 
    15798 > color (#!1 & sel) #e5ce63ff
    15799 
    15800 > color (#!1 & sel) #e5d066ff
    15801 
    15802 > color (#!1 & sel) #e6d46aff
    15803 
    15804 [Repeated 1 time(s)]
    15805 
    15806 > color (#!1 & sel) #e6d46bff
    15807 
    15808 > color (#!1 & sel) #e5d66eff
    15809 
    15810 > color (#!1 & sel) #e5d66fff
    15811 
    15812 > color (#!1 & sel) #e5d670ff
    15813 
    15814 > color (#!1 & sel) #e6d571ff
    15815 
    15816 > color (#!1 & sel) #e6d673ff
    15817 
    15818 > color (#!1 & sel) #e6d877ff
    15819 
    15820 > color (#!1 & sel) #e6d879ff
    15821 
    15822 > color (#!1 & sel) #e6dc7dff
    15823 
    15824 > color (#!1 & sel) #e7db7fff
    15825 
    15826 > color (#!1 & sel) #e6dc80ff
    15827 
    15828 [Repeated 1 time(s)]
    15829 
    15830 > color (#!1 & sel) #e6dd80ff
    15831 
    15832 [Repeated 1 time(s)]
    15833 
    15834 > color (#!1 & sel) #e7dd80ff
    15835 
    15836 > color (#!1 & sel) #e7dd7fff
    15837 
    15838 > color (#!1 & sel) #e7dd7eff
    15839 
    15840 > color (#!1 & sel) #e6dd7dff
    15841 
    15842 > color (#!1 & sel) #e6dc7cff
    15843 
    15844 > color (#!1 & sel) #e6da76ff
    15845 
    15846 > color (#!1 & sel) #e6d973ff
    15847 
    15848 > color (#!1 & sel) #e6d972ff
    15849 
    15850 > color (#!1 & sel) #e6d772ff
    15851 
    15852 > color (#!1 & sel) #e6d771ff
    15853 
    15854 > color (#!1 & sel) #e5d770ff
    15855 
    15856 > color (#!1 & sel) #e5d76fff
    15857 
    15858 > color (#!1 & sel) #e5d76eff
    15859 
    15860 > color (#!1 & sel) #e6d56cff
    15861 
    15862 > color (#!1 & sel) #e6d46bff
    15863 
    15864 > color (#!1 & sel) #e6d56bff
    15865 
    15866 > color (#!1 & sel) #e6d56aff
    15867 
    15868 [Repeated 2 time(s)]
    15869 
    15870 > color (#!1 & sel) #e6d469ff
    15871 
    15872 > color (#!1 & sel) #e6d467ff
    15873 
    15874 > color (#!1 & sel) #e6d466ff
    15875 
    15876 > color (#!1 & sel) #e6d366ff
    15877 
    15878 > color (#!1 & sel) #e6d365ff
    15879 
    15880 > color (#!1 & sel) #e6d364ff
    15881 
    15882 > color (#!1 & sel) #e6d463ff
    15883 
    15884 > color (#!1 & sel) #e7d460ff
    15885 
    15886 [Repeated 2 time(s)]
    15887 
    15888 > color (#!1 & sel) #e7d45fff
    15889 
    15890 [Repeated 2 time(s)]
    15891 
    15892 > color (#!1 & sel) byhetero
    15893 
    15894 > select clear
    15895 
    15896 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    15897 > chimera files and png files/Figure 7/Figure7C.cxs"
    15898 
    15899 > open 8KGK
    15900 
    15901 8kgk title: 
    15902 Cryo-EM structure of the GPR61-Gs complex [more info...] 
    15903  
    15904 Chain information for 8kgk #5 
    15905 --- 
    15906 Chain | Description | UniProt 
    15907 A | G-protein coupled receptor 61 | GPR61_HUMAN 1-365 
    15908 B | Guanine nucleotide-binding protein G(olf) subunit alpha,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAL_HUMAN 5-195, GNAS2_HUMAN 204-384 
    15909 C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    15910 D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    15911 E | Nanobody 35 |   
    15912  
    15913 
    15914 > ui tool show Matchmaker
    15915 
    15916 > matchmaker #!2-5 to #1
    15917 
    15918 Parameters 
    15919 --- 
    15920 Chain pairing | bb 
    15921 Alignment algorithm | Needleman-Wunsch 
    15922 Similarity matrix | BLOSUM-62 
    15923 SS fraction | 0.3 
    15924 Gap open (HH/SS/other) | 18/18/6 
    15925 Gap extend | 1 
    15926 SS matrix |  |  | H | S | O 
    15927 ---|---|---|--- 
    15928 H | 6 | -9 | -6 
    15929 S |  | 6 | -6 
    15930 O |  |  | 4 
    15931 Iteration cutoff | 2 
    15932  
    15933 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
    15934 alignment score = 1623.9 
    15935 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    15936 1.770) 
    15937  
    15938 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
    15939 alignment score = 339.4 
    15940 RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
    15941 5.318) 
    15942  
    15943 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 2rh1, chain A (#4), sequence
    15944 alignment score = 372.2 
    15945 RMSD between 106 pruned atom pairs is 1.222 angstroms; (across all 221 pairs:
    15946 4.766) 
    15947  
    15948 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8kgk, chain A (#5), sequence
    15949 alignment score = 1320.5 
    15950 RMSD between 188 pruned atom pairs is 0.925 angstroms; (across all 219 pairs:
    15951 1.672) 
    15952  
    15953 
    15954 > matchmaker #!2-5 to #1
    15955 
    15956 Parameters 
    15957 --- 
    15958 Chain pairing | bb 
    15959 Alignment algorithm | Needleman-Wunsch 
    15960 Similarity matrix | BLOSUM-62 
    15961 SS fraction | 0.3 
    15962 Gap open (HH/SS/other) | 18/18/6 
    15963 Gap extend | 1 
    15964 SS matrix |  |  | H | S | O 
    15965 ---|---|---|--- 
    15966 H | 6 | -9 | -6 
    15967 S |  | 6 | -6 
    15968 O |  |  | 4 
    15969 Iteration cutoff | 2 
    15970  
    15971 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
    15972 alignment score = 1623.9 
    15973 RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
    15974 1.770) 
    15975  
    15976 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
    15977 alignment score = 339.4 
    15978 RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
    15979 5.318) 
    15980  
    15981 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 2rh1, chain A (#4), sequence
    15982 alignment score = 372.2 
    15983 RMSD between 106 pruned atom pairs is 1.222 angstroms; (across all 221 pairs:
    15984 4.766) 
    15985  
    15986 Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8kgk, chain A (#5), sequence
    15987 alignment score = 1320.5 
    15988 RMSD between 188 pruned atom pairs is 0.925 angstroms; (across all 219 pairs:
    15989 1.672) 
    15990  
    15991 
    15992 > show #!1-2,5 atoms
    15993 
    15994 > undo
    15995 
    15996 > show #!1-2,5 cartoons
    15997 
    15998 > select add #5
    15999 
    16000 7470 atoms, 7626 bonds, 4 pseudobonds, 1006 residues, 2 models selected 
    16001 
    16002 > hide sel atoms
    16003 
    16004 > show sel atoms
    16005 
    16006 > style sel stick
    16007 
    16008 Changed 7470 atom styles 
    16009 
    16010 > hide sel atoms
    16011 
    16012 > select clear
    16013 
    16014 > select #5/D
    16015 
    16016 353 atoms, 359 bonds, 56 residues, 1 model selected 
    16017 
    16018 > hide sel cartoons
    16019 
    16020 > select #5/E
    16021 
    16022 928 atoms, 949 bonds, 126 residues, 1 model selected 
    16023 
    16024 > hide sel cartoons
    16025 
    16026 > select #5/D
    16027 
    16028 353 atoms, 359 bonds, 56 residues, 1 model selected 
    16029 
    16030 > delete atoms sel
    16031 
    16032 > delete bonds sel
    16033 
    16034 > select #5/C
    16035 
    16036 2497 atoms, 2544 bonds, 339 residues, 1 model selected 
    16037 
    16038 > delete atoms sel
    16039 
    16040 > delete bonds sel
    16041 
    16042 > select #5/E
    16043 
    16044 928 atoms, 949 bonds, 126 residues, 1 model selected 
    16045 
    16046 > delete atoms sel
    16047 
    16048 > delete bonds sel
    16049 
    16050 > select #5/B
    16051 
    16052 1804 atoms, 1841 bonds, 1 pseudobond, 229 residues, 2 models selected 
    16053 
    16054 > delete atoms (#!5 & sel)
    16055 
    16056 > delete bonds (#!5 & sel)
    16057 
    16058 > select clear
    16059 
    16060 > color #5 #e4c398ff
    16061 
    16062 > color #5 #eae7a0ff
    16063 
    16064 > color #5 #e2b09cff
    16065 
    16066 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    16067 > chimera files and png files/Figure 7/Figure7D.cxs"
    16068 
    16069 ——— End of log from Thu May 30 20:40:46 2024 ———
    16070 
    16071 opened ChimeraX session 
    16072 
    16073 > transparency 80 ribbons
    16074 
    16075 > select
    16076 > #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
    16077 
    16078 4407 atoms, 4449 bonds, 275 residues, 1 model selected 
    16079 
    16080 > select #1/R:137
    16081 
    16082 19 atoms, 18 bonds, 1 residue, 1 model selected 
    16083 
    16084 > select #1/R:137
    16085 
    16086 19 atoms, 18 bonds, 1 residue, 1 model selected 
    16087 
    16088 > select #1/R:346
    16089 
    16090 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16091 
    16092 > select #1/R:346
    16093 
    16094 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16095 
    16096 > select #1/R:149
    16097 
    16098 24 atoms, 23 bonds, 1 residue, 1 model selected 
    16099 
    16100 > select #1/R:149
    16101 
    16102 24 atoms, 23 bonds, 1 residue, 1 model selected 
    16103 
    16104 > show sel atoms
    16105 
    16106 > style sel stick
    16107 
    16108 Changed 24 atom styles 
    16109 
    16110 > select #1/R:426
    16111 
    16112 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16113 
    16114 > select #1/R:426
    16115 
    16116 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16117 
    16118 > show sel atoms
    16119 
    16120 > style sel stick
    16121 
    16122 Changed 14 atom styles 
    16123 
    16124 > select #1/R:146
    16125 
    16126 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16127 
    16128 > select #1/R:146
    16129 
    16130 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16131 
    16132 > show sel atoms
    16133 
    16134 > style sel stick
    16135 
    16136 Changed 14 atom styles 
    16137 Drag select of 2 residues 
    16138 
    16139 > select clear
    16140 
    16141 > color #1-2,5 byhetero
    16142 
    16143 > select clear
    16144 
    16145 > select #1/R:146
    16146 
    16147 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16148 
    16149 > select add #1/R:426
    16150 
    16151 28 atoms, 26 bonds, 2 residues, 1 model selected 
    16152 
    16153 > select add #1/R:149
    16154 
    16155 52 atoms, 49 bonds, 3 residues, 1 model selected 
    16156 
    16157 > ribbon sel suppressBackboneDisplay true
    16158 
    16159 > ribbon sel suppressBackboneDisplay false
    16160 
    16161 > true
    16162 
    16163 Unknown command: true 
    16164 
    16165 > select H
    16166 
    16167 2677 atoms, 329 residues, 1 model selected 
    16168 
    16169 > hide sel atoms
    16170 
    16171 > select clear
    16172 
    16173 > select #1/R:149@NH2
    16174 
    16175 1 atom, 1 residue, 1 model selected 
    16176 
    16177 > ui tool show H-Bonds
    16178 
    16179 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    16180 > false intraRes false select true reveal true log true
    16181    
    16182    
    16183     Finding intramodel H-bonds
    16184     Constraints relaxed by 0.4 angstroms and 20 degrees
    16185     Models used:
    16186         1 GPR61_BRIL_8tb7
    16187    
    16188     0 H-bonds
    16189     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16190    
    16191 
    16192  
    16193 0 hydrogen bonds found 
    16194 
    16195 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    16196 > false intraRes false select true reveal true log true
    16197 
    16198 Atom specifier selects no atoms 
    16199 
    16200 > select #1/R:426
    16201 
    16202 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16203 
    16204 > ui tool show H-Bonds
    16205 
    16206 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    16207 > false intraRes false select true reveal true log true
    16208    
    16209    
    16210     Finding intramodel H-bonds
    16211     Constraints relaxed by 0.4 angstroms and 20 degrees
    16212     Models used:
    16213         1 GPR61_BRIL_8tb7
    16214    
    16215     2 H-bonds
    16216     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16217     GPR61_BRIL_8tb7 #1/R ASN 426 ND2  GPR61_BRIL_8tb7 #1/R ZOB 601 O16  GPR61_BRIL_8tb7 #1/R ASN 426 HD21  3.516  2.918
    16218     GPR61_BRIL_8tb7 #1/R ASN 426 ND2  GPR61_BRIL_8tb7 #1/R ZOB 601 O17  GPR61_BRIL_8tb7 #1/R ASN 426 HD21  2.909  2.040
    16219    
    16220 
    16221  
    16222 2 hydrogen bonds found 
    16223 
    16224 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    16225 > false intraRes false select true reveal true log true
    16226    
    16227    
    16228     Finding intramodel H-bonds
    16229     Constraints relaxed by 0.4 angstroms and 20 degrees
    16230     Models used:
    16231         1 GPR61_BRIL_8tb7
    16232    
    16233     3 H-bonds
    16234     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16235     GPR61_BRIL_8tb7 #1/R ASN 426 ND2  GPR61_BRIL_8tb7 #1/R ZOB 601 O16  GPR61_BRIL_8tb7 #1/R ASN 426 HD21  3.516  2.918
    16236     GPR61_BRIL_8tb7 #1/R ASN 426 ND2  GPR61_BRIL_8tb7 #1/R ZOB 601 O17  GPR61_BRIL_8tb7 #1/R ASN 426 HD21  2.909  2.040
    16237     GPR61_BRIL_8tb7 #1/R HOH 701 O    GPR61_BRIL_8tb7 #1/R ZOB 601 O17  no hydrogen                        2.261  N/A
    16238    
    16239 
    16240  
    16241 3 hydrogen bonds found 
    16242 
    16243 > select clear
    16244 
    16245 > ui tool show "Side View"
    16246 
    16247 > transparency 100 ribbons
    16248 
    16249 > transparency 80 ribbons
    16250 
    16251 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    16252 > chimera files and png files/Figure 7/Figure7C_antagonist binding.png" width
    16253 > 2000 height 1521 supersample 3 transparentBackground true
    16254 
    16255 > hide #!1 models
    16256 
    16257 > show #!1 models
    16258 
    16259 > select
    16260 > #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
    16261 
    16262 4407 atoms, 4449 bonds, 275 residues, 1 model selected 
    16263 
    16264 > select clear
    16265 
    16266 > ui tool show "Show Sequence Viewer"
    16267 
    16268 > sequence chain #2/R
    16269 
    16270 Alignment identifier is 2/R 
    16271 
    16272 > select #1/R:146
    16273 
    16274 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16275 
    16276 > select #1/R:146
    16277 
    16278 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16279 
    16280 > select #2/R:137
    16281 
    16282 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16283 
    16284 > select #2/R:137
    16285 
    16286 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16287 
    16288 > select
    16289 > #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
    16290 
    16291 4407 atoms, 4449 bonds, 275 residues, 1 model selected 
    16292 
    16293 > select #1/R:149
    16294 
    16295 24 atoms, 23 bonds, 1 residue, 1 model selected 
    16296 
    16297 > select #1/R:149
    16298 
    16299 24 atoms, 23 bonds, 1 residue, 1 model selected 
    16300 
    16301 > select #1/R:426
    16302 
    16303 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16304 
    16305 > select #1/R:426
    16306 
    16307 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16308 
    16309 > select
    16310 > #2/R:46-68,70-101,114-145,148-180,202-237,284-313,321-342,345-353,1728-1846
    16311 
    16312 1788 atoms, 1826 bonds, 1 pseudobond, 226 residues, 2 models selected 
    16313 
    16314 > close session
    16315 
    16316 > open 7xz5
    16317 
    16318 7xz5 title: 
    16319 GPR119-Gs-LPC complex [more info...] 
    16320  
    16321 Chain information for 7xz5 #1 
    16322 --- 
    16323 Chain | Description | UniProt 
    16324 A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |   
    16325 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    16326 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    16327 N | Nanobody35 |   
    16328 R | Soluble cytochrome b562,Glucose-dependent insulinotropic receptor | C562_ECOLX -121--17, GP119_HUMAN 1-335 
    16329  
    16330 Non-standard residues in 7xz5 #1 
    16331 --- 
    16332 LSC —
    16333 (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium
    16334 4-oxide 
    16335  
    16336 
    16337 > style stick
    16338 
    16339 Changed 16508 atom styles 
    16340 
    16341 > hide atoms
    16342 
    16343 > show cartoons
    16344 
    16345 > select /A/B/G/N
    16346 
    16347 11812 atoms, 11923 bonds, 2 pseudobonds, 760 residues, 2 models selected 
    16348 
    16349 > delete atoms (#!1 & sel)
    16350 
    16351 > delete bonds (#!1 & sel)
    16352 
    16353 > color #1 #e43426ff
    16354 
    16355 > color #1 #db4739ff
    16356 
    16357 > color #1 #e83624ff
    16358 
    16359 > color #1 #db3624ff
    16360 
    16361 > color #1 #c73725ff
    16362 
    16363 > color #1 #e53424ff
    16364 
    16365 > color #1 #bb3124ff
    16366 
    16367 > color #1 #b23023ff
    16368 
    16369 > color #1 #c23324ff
    16370 
    16371 > color #1 #b23023ff
    16372 
    16373 > color #1 #b23323ff
    16374 
    16375 > color #1 #a82c23ff
    16376 
    16377 > color #1 #b93123ff
    16378 
    16379 > color #1 #c91a07ff
    16380 
    16381 > color #1 #b11707ff
    16382 
    16383 > color #1 #bb1807ff
    16384 
    16385 > color #1 #af1707ff
    16386 
    16387 > color #1 #ac1606ff
    16388 
    16389 > color #1 #a91606ff
    16390 
    16391 > color #1 #be1807ff
    16392 
    16393 > color #1 #be1000ff
    16394 
    16395 > color #1 #be0e00ff
    16396 
    16397 > color #1 #ab0d00ff
    16398 
    16399 > color #1 #a90d00ff
    16400 
    16401 > open /Users/dongju/Downloads/emd_33525_7xz5.map
    16402 
    16403 Opened emd_33525_7xz5.map as #2, grid size 200,200,200, pixel 1.07, shown at
    16404 level 0.0158, step 1, values float32 
    16405 
    16406 > volume #2 level 0.02079
    16407 
    16408 > fitmap #1 inMap #2
    16409 
    16410 Fit molecule 7xz5 (#1) to map emd_33525_7xz5.map (#2) using 4696 atoms 
    16411 average map value = 0.02279, steps = 40 
    16412 shifted from previous position = 0.0482 
    16413 rotated from previous position = 0.208 degrees 
    16414 atoms outside contour = 2544, contour level = 0.020794 
    16415  
    16416 Position of 7xz5 (#1) relative to emd_33525_7xz5.map (#2) coordinates: 
    16417 Matrix rotation and translation 
    16418 0.99999353 0.00337605 -0.00124113 -0.23274448 
    16419 -0.00337657 0.99999421 -0.00041941 0.38358314 
    16420 0.00123971 0.00042360 0.99999914 -0.16257974 
    16421 Axis 0.11638676 -0.34250927 -0.93227760 
    16422 Axis point 112.78332959 68.91815420 0.00000000 
    16423 Rotation angle (degrees) 0.20750123 
    16424 Shift along axis -0.00689971 
    16425  
    16426 
    16427 > color #2 #829abfff models
    16428 
    16429 > color #2 #95bfe5ff models
    16430 
    16431 > volume style image
    16432 
    16433 [Repeated 1 time(s)]
    16434 
    16435 > volume style surface
    16436 
    16437 > transparency 50
    16438 
    16439 > surface dust #2 size 10.7
    16440 
    16441 > select ligand
    16442 
    16443 87 atoms, 86 bonds, 1 residue, 1 model selected 
    16444 
    16445 > show sel atoms
    16446 
    16447 > style sel stick
    16448 
    16449 Changed 87 atom styles 
    16450 
    16451 > color sel #8db9e4ff
    16452 
    16453 > color sel #8ab5e4ff
    16454 
    16455 > color sel #88b4e3ff
    16456 
    16457 > color sel #84b1e3ff
    16458 
    16459 > color sel #7dade2ff
    16460 
    16461 > color sel #7cace2ff
    16462 
    16463 > color sel #7aabe2ff
    16464 
    16465 > color sel #78a9e2ff
    16466 
    16467 > color sel #78aae2ff
    16468 
    16469 [Repeated 1 time(s)]
    16470 
    16471 > color sel #78a9e2ff
    16472 
    16473 [Repeated 1 time(s)]
    16474 
    16475 > color sel #78a6e2ff
    16476 
    16477 > color sel #77a6e2ff
    16478 
    16479 [Repeated 1 time(s)]
    16480 
    16481 > color sel #77a4e2ff
    16482 
    16483 > color sel #77a3e2ff
    16484 
    16485 > color sel #76a0e2ff
    16486 
    16487 > color sel #779fe2ff
    16488 
    16489 > color sel #769be1ff
    16490 
    16491 > color sel #7699e1ff
    16492 
    16493 > color sel #7798e1ff
    16494 
    16495 > color sel #7695e1ff
    16496 
    16497 > color sel #7997e2ff
    16498 
    16499 > color sel #7996e1ff
    16500 
    16501 [Repeated 1 time(s)]
    16502 
    16503 > color sel #7993e1ff
    16504 
    16505 [Repeated 1 time(s)]
    16506 
    16507 > color sel #7891e1ff
    16508 
    16509 > color sel #7791e1ff
    16510 
    16511 > color sel #748de1ff
    16512 
    16513 > color sel #6d88e1ff
    16514 
    16515 > color sel #6a86e1ff
    16516 
    16517 > color sel #6884e1ff
    16518 
    16519 > color sel #6783e0ff
    16520 
    16521 > color sel #6782e0ff
    16522 
    16523 > color sel #6682e0ff
    16524 
    16525 > color sel #6581e0ff
    16526 
    16527 > color sel #6481e0ff
    16528 
    16529 [Repeated 1 time(s)]
    16530 
    16531 > color sel #617fe0ff
    16532 
    16533 > color sel #5e7de0ff
    16534 
    16535 > color sel #5a7ae0ff
    16536 
    16537 > color sel #5777e1ff
    16538 
    16539 > color sel #5475e1ff
    16540 
    16541 > color sel #4e71e2ff
    16542 
    16543 > color sel #4b6fe2ff
    16544 
    16545 > color sel #4a6de1ff
    16546 
    16547 > color sel #486ce2ff
    16548 
    16549 > color sel #476be1ff
    16550 
    16551 > color sel #456ae2ff
    16552 
    16553 > color sel #4368e2ff
    16554 
    16555 > color sel #4066e3ff
    16556 
    16557 > color sel #3f65e3ff
    16558 
    16559 > color sel #3e64e3ff
    16560 
    16561 > color sel #3d63e3ff
    16562 
    16563 > color sel #3b62e3ff
    16564 
    16565 > color sel #3a62e3ff
    16566 
    16567 [Repeated 1 time(s)]
    16568 
    16569 > color sel #3961e4ff
    16570 
    16571 > color sel #3860e4ff
    16572 
    16573 > color sel #375fe4ff
    16574 
    16575 > color sel #355ce4ff
    16576 
    16577 > color sel #345be5ff
    16578 
    16579 > color sel #335be5ff
    16580 
    16581 > color sel #325ae5ff
    16582 
    16583 > color sel #315ae5ff
    16584 
    16585 > color sel #3159e5ff
    16586 
    16587 > color sel #305ae5ff
    16588 
    16589 > color sel #2f5ae6ff
    16590 
    16591 > color sel #2e59e6ff
    16592 
    16593 > color sel #2d5ae7ff
    16594 
    16595 [Repeated 1 time(s)]
    16596 
    16597 > color sel #2c59e7ff
    16598 
    16599 > color sel #2b58e7ff
    16600 
    16601 > color sel #2b58e8ff
    16602 
    16603 > color sel #2957e7ff
    16604 
    16605 > color sel #2857e8ff
    16606 
    16607 > color sel #2856e8ff
    16608 
    16609 > color sel #2756e9ff
    16610 
    16611 > color sel #2655e8ff
    16612 
    16613 > color sel #2654e9ff
    16614 
    16615 > color sel #2554e9ff
    16616 
    16617 [Repeated 1 time(s)]
    16618 
    16619 > color sel #2554eaff
    16620 
    16621 > color sel #2554e9ff
    16622 
    16623 > color sel #2759eaff
    16624 
    16625 > color sel #285beaff
    16626 
    16627 > color sel #2c63eaff
    16628 
    16629 > color sel #2c64eaff
    16630 
    16631 > color sel #2d66eaff
    16632 
    16633 [Repeated 1 time(s)]
    16634 
    16635 > color sel #2f69ebff
    16636 
    16637 [Repeated 1 time(s)]
    16638 
    16639 > color sel #2f6aebff
    16640 
    16641 > color sel #3372ebff
    16642 
    16643 > color sel #3373ebff
    16644 
    16645 > color sel #3474ebff
    16646 
    16647 > color sel #3576ebff
    16648 
    16649 > color sel #387cebff
    16650 
    16651 > color sel byhetero
    16652 
    16653 > select ~sel & ##selected
    16654 
    16655 4609 atoms, 4664 bonds, 1 pseudobond, 292 residues, 2 models selected 
    16656 
    16657 > hide sel cartoons
    16658 
    16659 > show sel cartoons
    16660 
    16661 > select clear
    16662 
    16663 > select ligand
    16664 
    16665 87 atoms, 86 bonds, 1 residue, 1 model selected 
    16666 
    16667 > select H
    16668 
    16669 2402 atoms, 293 residues, 1 model selected 
    16670 
    16671 > hide sel atoms
    16672 
    16673 > select clear
    16674 
    16675 > hide cartoons
    16676 
    16677 > ui mousemode right "map eraser"
    16678 
    16679 > volume erase #2 center 98.213,117.33,82.726 radius 15.569 outside true
    16680 
    16681 Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
    16682 at step 1, values float32 
    16683 
    16684 > volume erase #4 center 99.634,96.291,77.937 radius 15.529
    16685 
    16686 > volume erase #4 center 81.449,107.72,86.478 radius 15.529
    16687 
    16688 > volume erase #4 center 86.376,106.33,90.936 radius 15.529
    16689 
    16690 > volume erase #4 center 110.95,133.83,84.039 radius 15.529
    16691 
    16692 > volume erase #4 center 101.08,108.57,100.43 radius 15.529
    16693 
    16694 > volume erase #4 center 111.29,112.72,96.933 radius 15.529
    16695 
    16696 > volume erase #4 center 116.67,108.27,82.34 radius 15.529
    16697 
    16698 > volume erase #4 center 115.72,109.16,85.984 radius 15.529
    16699 
    16700 > undo
    16701 
    16702 [Repeated 9 time(s)]
    16703 
    16704 > hide #!1 models
    16705 
    16706 > show #!1 models
    16707 
    16708 > hide sel cartoons
    16709 
    16710 > hide #!4 models
    16711 
    16712 > show #!4 models
    16713 
    16714 > close #4
    16715 
    16716 > show #!2 models
    16717 
    16718 > volume erase #2 center 98.575,122.65,81.082 radius 14.458 outside true
    16719 
    16720 Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
    16721 at step 1, values float32 
    16722 
    16723 > close #4
    16724 
    16725 > show #!2 models
    16726 
    16727 > volume erase #2 center 99.341,121.03,81.417 radius 17.993 outside true
    16728 
    16729 Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
    16730 at step 1, values float32 
    16731 
    16732 > volume erase #4 center 110.79,124.48,90.565 radius 8.1396
    16733 
    16734 > volume erase #4 center 110.84,122.75,82.866 radius 8.1396
    16735 
    16736 > volume erase #4 center 109.8,120.88,75.103 radius 8.1396
    16737 
    16738 > volume erase #4 center 110.45,116.63,74.645 radius 8.1396
    16739 
    16740 > volume erase #4 center 98.611,132.52,71.034 radius 8.1396
    16741 
    16742 > volume erase #4 center 101.33,130.98,76.631 radius 8.1396
    16743 
    16744 > volume erase #4 center 101.74,127.44,71.519 radius 8.1396
    16745 
    16746 > volume erase #4 center 87.562,133.37,74.695 radius 8.1396
    16747 
    16748 > hide #!1 models
    16749 
    16750 > show #!1 models
    16751 
    16752 > show sel cartoons
    16753 
    16754 > ui tool show "Show Sequence Viewer"
    16755 
    16756 > sequence chain /R
    16757 
    16758 Alignment identifier is 1/R 
    16759 
    16760 > select /R:157
    16761 
    16762 20 atoms, 20 bonds, 1 residue, 1 model selected 
    16763 
    16764 > select /R:157
    16765 
    16766 20 atoms, 20 bonds, 1 residue, 1 model selected 
    16767 
    16768 > show sel atoms
    16769 
    16770 > style sel stick
    16771 
    16772 Changed 20 atom styles 
    16773 
    16774 > select /R:265
    16775 
    16776 24 atoms, 25 bonds, 1 residue, 1 model selected 
    16777 
    16778 > show sel atoms
    16779 
    16780 > select /R:241
    16781 
    16782 20 atoms, 20 bonds, 1 residue, 1 model selected 
    16783 
    16784 > select /R:241
    16785 
    16786 20 atoms, 20 bonds, 1 residue, 1 model selected 
    16787 
    16788 > show sel atoms
    16789 
    16790 > select /R:82
    16791 
    16792 17 atoms, 16 bonds, 1 residue, 1 model selected 
    16793 
    16794 > select /R:82
    16795 
    16796 17 atoms, 16 bonds, 1 residue, 1 model selected 
    16797 
    16798 > show sel atoms
    16799 
    16800 > select /R:85
    16801 
    16802 16 atoms, 15 bonds, 1 residue, 1 model selected 
    16803 
    16804 > select /R:85
    16805 
    16806 16 atoms, 15 bonds, 1 residue, 1 model selected 
    16807 
    16808 > show sel atoms
    16809 
    16810 > select /R:82,85
    16811 
    16812 33 atoms, 31 bonds, 2 residues, 1 model selected 
    16813 
    16814 > select /R:82,85,157
    16815 
    16816 53 atoms, 51 bonds, 3 residues, 1 model selected 
    16817 
    16818 > select /R:82,85,157,241
    16819 
    16820 73 atoms, 71 bonds, 4 residues, 1 model selected 
    16821 
    16822 > select /R:82,85,157,241,265
    16823 
    16824 97 atoms, 96 bonds, 5 residues, 1 model selected 
    16825 
    16826 > show sel atoms
    16827 
    16828 > name frozen stacking_pocket sel
    16829 
    16830 > ui mousemode right select
    16831 
    16832 > select clear
    16833 
    16834 > select /R:241
    16835 
    16836 20 atoms, 20 bonds, 1 residue, 1 model selected 
    16837 
    16838 > select /R:241
    16839 
    16840 20 atoms, 20 bonds, 1 residue, 1 model selected 
    16841 
    16842 > select /R:93,241
    16843 
    16844 36 atoms, 35 bonds, 2 residues, 1 model selected 
    16845 
    16846 > select /R:82,93,241
    16847 
    16848 53 atoms, 51 bonds, 3 residues, 1 model selected 
    16849 
    16850 > select /R:82,93,157,241
    16851 
    16852 73 atoms, 71 bonds, 4 residues, 1 model selected 
    16853 
    16854 > select /R:82,93,157-158,241
    16855 
    16856 93 atoms, 92 bonds, 5 residues, 1 model selected 
    16857 
    16858 > select /R:82,93,157-158,161,241
    16859 
    16860 113 atoms, 112 bonds, 6 residues, 1 model selected 
    16861 
    16862 > select /R:82,93,157-158,161,165,241
    16863 
    16864 133 atoms, 132 bonds, 7 residues, 1 model selected 
    16865 
    16866 > select /R:82,93,157-158,161,165,169,241
    16867 
    16868 152 atoms, 150 bonds, 8 residues, 1 model selected 
    16869 
    16870 > select /R:82,93,157-158,161,165,169,174,241
    16871 
    16872 172 atoms, 170 bonds, 9 residues, 1 model selected 
    16873 
    16874 > select /R:82,93,157-158,161,165,169,174,238,241
    16875 
    16876 196 atoms, 195 bonds, 10 residues, 1 model selected 
    16877 
    16878 > show sel atoms
    16879 
    16880 > name frozen hydrophobic_cavity sel
    16881 
    16882 > select clear
    16883 
    16884 > select /R:156
    16885 
    16886 11 atoms, 10 bonds, 1 residue, 1 model selected 
    16887 
    16888 > select /R:156
    16889 
    16890 11 atoms, 10 bonds, 1 residue, 1 model selected 
    16891 
    16892 > select /R:65,156
    16893 
    16894 28 atoms, 26 bonds, 2 residues, 1 model selected 
    16895 
    16896 > select /R:65,156,262
    16897 
    16898 52 atoms, 49 bonds, 3 residues, 1 model selected 
    16899 
    16900 > select /R:65,156,261-262
    16901 
    16902 67 atoms, 64 bonds, 4 residues, 1 model selected 
    16903 
    16904 > show sel atoms
    16905 
    16906 > name frozen head_H_bond sel
    16907 
    16908 > movie record
    16909 
    16910 > turn y 2 180
    16911 
    16912 > wait 180
    16913 
    16914 > movie encode /Users/dongju/Desktop/movie1.mp4
    16915 
    16916 Movie saved to /Users/dongju/Desktop/movie1.mp4 
    16917  
    16918 
    16919 > show sel atoms
    16920 
    16921 > select clear
    16922 
    16923 > select /R:261
    16924 
    16925 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16926 
    16927 > select /R:261-262
    16928 
    16929 39 atoms, 38 bonds, 2 residues, 1 model selected 
    16930 
    16931 > select clear
    16932 
    16933 > hide cartoons
    16934 
    16935 > show cartoons
    16936 
    16937 > select H
    16938 
    16939 2402 atoms, 293 residues, 1 model selected 
    16940 
    16941 > hide sel atoms
    16942 
    16943 > hide sel cartoons
    16944 
    16945 > select clear
    16946 
    16947 Drag select of eraser sphere, 36 of 1000 triangles, 4 emd_33525_7xz5.map copy 
    16948 
    16949 > select clear
    16950 
    16951 > ui mousemode right "map eraser"
    16952 
    16953 > volume erase #4 center 99.191,131.76,90.892 radius 8.1396
    16954 
    16955 > volume erase #4 center 94.667,131.6,96.584 radius 8.1396
    16956 
    16957 > volume erase #4 center 87.721,132.18,90.667 radius 8.1396
    16958 
    16959 > volume erase #4 center 105.84,126.62,94.736 radius 8.1396
    16960 
    16961 > volume erase #4 center 102.4,128.73,80.393 radius 8.1396
    16962 
    16963 > volume erase #4 center 111.48,120.97,87.878 radius 8.1396
    16964 
    16965 > volume erase #4 center 115.93,111.85,82.092 radius 8.1396
    16966 
    16967 > volume erase #4 center 108.43,107.99,82.775 radius 8.1396
    16968 
    16969 > volume erase #4 center 107.73,105.23,74.587 radius 8.1396
    16970 
    16971 > volume erase #4 center 103.7,108.91,94.52 radius 8.1396
    16972 
    16973 > volume erase #4 center 104.47,110.59,96.834 radius 8.1396
    16974 
    16975 > volume erase #4 center 98.862,114.5,101.46 radius 8.1396
    16976 
    16977 > volume erase #4 center 102.29,112.11,98.729 radius 8.1396
    16978 
    16979 > volume erase #4 center 106.98,108.74,92.776 radius 8.1396
    16980 
    16981 > volume erase #4 center 106.52,109.07,93.154 radius 8.1396
    16982 
    16983 > volume erase #4 center 110.68,111.23,90.78 radius 8.1396
    16984 
    16985 > volume erase #4 center 109.85,112.4,90.895 radius 8.1396
    16986 
    16987 > volume erase #4 center 99.406,103.96,74.532 radius 8.1396
    16988 
    16989 > volume erase #4 center 100.92,103.19,85.616 radius 8.1396
    16990 
    16991 > volume erase #4 center 84.855,122.16,78.913 radius 8.1396
    16992 
    16993 > volume erase #4 center 89.051,127.71,86.6 radius 8.1396
    16994 
    16995 > volume erase #4 center 102.67,123.01,69.123 radius 8.1396
    16996 
    16997 > volume erase #4 center 101.56,117.63,61.877 radius 8.1396
    16998 
    16999 > volume erase #4 center 88.061,108.98,67.752 radius 8.1396
    17000 
    17001 > volume erase #4 center 83.589,109.07,77.579 radius 8.1396
    17002 
    17003 > volume erase #4 center 85.901,111.98,86.928 radius 8.1396
    17004 
    17005 > volume erase #4 center 88.734,108.51,81.138 radius 8.1396
    17006 
    17007 > volume erase #4 center 93.055,109.37,87.843 radius 8.1396
    17008 
    17009 > volume erase #4 center 92.726,112.25,90.113 radius 8.1396
    17010 
    17011 > volume erase #4 center 90.389,114.04,94.248 radius 8.1396
    17012 
    17013 > volume erase #4 center 97.076,112.95,95.797 radius 8.1396
    17014 
    17015 > volume erase #4 center 99.29,112.81,94.683 radius 8.1396
    17016 
    17017 > volume erase #4 center 92.138,113.44,97.971 radius 8.1396
    17018 
    17019 > volume erase #4 center 81.483,121.4,91.171 radius 8.1396
    17020 
    17021 > volume erase #4 center 83.924,123.87,93.478 radius 8.1396
    17022 
    17023 > volume erase #4 center 96.101,123.11,103.59 radius 8.1396
    17024 
    17025 > volume erase #4 center 102.62,117.7,98.5 radius 8.1396
    17026 
    17027 > volume erase #4 center 88.295,135.88,81.964 radius 8.1396
    17028 
    17029 > volume erase #4 center 100.86,140.07,77.596 radius 8.1396
    17030 
    17031 > volume erase #4 center 109.6,135.56,78.637 radius 8.1396
    17032 
    17033 > volume erase #4 center 112.37,133.91,79.144 radius 8.1396
    17034 
    17035 > volume erase #4 center 91.34,129.9,67.561 radius 8.1396
    17036 
    17037 > volume erase #4 center 80.069,119.6,71.426 radius 8.1396
    17038 
    17039 > volume erase #4 center 106.29,107.99,68.884 radius 8.1396
    17040 
    17041 > volume erase #4 center 100.02,106.7,84.175 radius 8.1396
    17042 
    17043 > volume erase #4 center 106.83,115.8,82.832 radius 3.3201
    17044 
    17045 > volume erase #4 center 105.28,116.49,85.129 radius 3.3201
    17046 
    17047 > volume erase #4 center 101.52,119.15,74.378 radius 3.3201
    17048 
    17049 > volume erase #4 center 92.6,113.6,79.794 radius 3.3201
    17050 
    17051 > volume erase #4 center 93.305,125.06,77.822 radius 3.3201
    17052 
    17053 > volume erase #4 center 93.427,111.51,73.545 radius 3.3201
    17054 
    17055 > volume erase #4 center 90.272,115.88,72.197 radius 3.3201
    17056 
    17057 > volume erase #4 center 90.042,119.19,72.194 radius 3.3201
    17058 
    17059 > show cartoons
    17060 
    17061 > hide cartoons
    17062 
    17063 > ui mousemode right "map eraser"
    17064 
    17065 > volume erase #4 center 99.848,120.7,81.785 radius 1.7633
    17066 
    17067 > show cartoons
    17068 
    17069 > ui tool show "Side View"
    17070 
    17071 > select head_H_bond
    17072 
    17073 67 atoms, 64 bonds, 4 residues, 1 model selected 
    17074 
    17075 > color sel #20113eff
    17076 
    17077 > color sel #22123fff
    17078 
    17079 > color sel #261342ff
    17080 
    17081 [Repeated 1 time(s)]
    17082 
    17083 > color sel #261240ff
    17084 
    17085 > color sel #251240ff
    17086 
    17087 > color sel #25123fff
    17088 
    17089 [Repeated 1 time(s)]
    17090 
    17091 > color sel #24123eff
    17092 
    17093 [Repeated 1 time(s)]
    17094 
    17095 > color sel #23123dff
    17096 
    17097 > color sel #221139ff
    17098 
    17099 > color sel #1e0f33ff
    17100 
    17101 > color sel #1d0e30ff
    17102 
    17103 > color sel #1d0e2fff
    17104 
    17105 [Repeated 1 time(s)]
    17106 
    17107 > color sel #1c0e2fff
    17108 
    17109 > color sel #1c0d2fff
    17110 
    17111 > color sel #1c0e2fff
    17112 
    17113 > color sel #1b0e2dff
    17114 
    17115 > color sel #1a0d2bff
    17116 
    17117 > color sel #1a0d2aff
    17118 
    17119 > color sel #180d28ff
    17120 
    17121 > color sel #160b24ff
    17122 
    17123 > color sel #150a23ff
    17124 
    17125 > color sel #140a20ff
    17126 
    17127 > color sel #130a20ff
    17128 
    17129 > color sel #12091cff
    17130 
    17131 [Repeated 1 time(s)]
    17132 
    17133 > color sel #11091cff
    17134 
    17135 > color sel #10081bff
    17136 
    17137 > color sel #0c081aff
    17138 
    17139 > color sel #0b091cff
    17140 
    17141 [Repeated 2 time(s)]
    17142 
    17143 > color sel #0b0a1dff
    17144 
    17145 > color sel #0b0a1cff
    17146 
    17147 > color sel #0b0a1dff
    17148 
    17149 [Repeated 1 time(s)]
    17150 
    17151 > color sel #0b091dff
    17152 
    17153 > color sel #0c091dff
    17154 
    17155 [Repeated 1 time(s)]
    17156 
    17157 > color sel #0c091eff
    17158 
    17159 > color sel #0c091fff
    17160 
    17161 [Repeated 1 time(s)]
    17162 
    17163 > color sel #0c0a20ff
    17164 
    17165 > color sel #0d0a21ff
    17166 
    17167 > color sel #0e0b24ff
    17168 
    17169 > color sel #110c29ff
    17170 
    17171 > color sel #140d2dff
    17172 
    17173 > color sel #160e30ff
    17174 
    17175 > color sel #170f31ff
    17176 
    17177 > color sel #180e32ff
    17178 
    17179 [Repeated 1 time(s)]
    17180 
    17181 > color sel #190f33ff
    17182 
    17183 [Repeated 1 time(s)]
    17184 
    17185 > color sel #1a1038ff
    17186 
    17187 > color sel #1a1039ff
    17188 
    17189 > color sel #1a113eff
    17190 
    17191 > color sel #151241ff
    17192 
    17193 > color sel #151242ff
    17194 
    17195 > color sel #141243ff
    17196 
    17197 > color sel #141242ff
    17198 
    17199 > color sel #141243ff
    17200 
    17201 [Repeated 2 time(s)]
    17202 
    17203 > color sel #141242ff
    17204 
    17205 > color sel #141141ff
    17206 
    17207 > color sel #13113eff
    17208 
    17209 > color sel #11113dff
    17210 
    17211 > color sel #11113cff
    17212 
    17213 > color sel #10113cff
    17214 
    17215 [Repeated 1 time(s)]
    17216 
    17217 > color sel #12113cff
    17218 
    17219 > color sel #15113bff
    17220 
    17221 > color sel #1b1139ff
    17222 
    17223 > color sel #1d1138ff
    17224 
    17225 > color sel #1e1037ff
    17226 
    17227 > color sel #1f1037ff
    17228 
    17229 > color sel #200f33ff
    17230 
    17231 > color sel #200e2fff
    17232 
    17233 > color sel #1f0e2dff
    17234 
    17235 > color sel #1e0d29ff
    17236 
    17237 [Repeated 1 time(s)]
    17238 
    17239 > color sel #1d0d28ff
    17240 
    17241 [Repeated 1 time(s)]
    17242 
    17243 > color sel #1d0d26ff
    17244 
    17245 > color sel #1b0c23ff
    17246 
    17247 > color sel #190b20ff
    17248 
    17249 > color sel #180a1eff
    17250 
    17251 > color sel #17091dff
    17252 
    17253 > color sel #16081aff
    17254 
    17255 > color sel #160819ff
    17256 
    17257 [Repeated 2 time(s)]
    17258 
    17259 > color sel #150819ff
    17260 
    17261 > color sel #150818ff
    17262 
    17263 > color sel #140917ff
    17264 
    17265 > color sel #130916ff
    17266 
    17267 [Repeated 2 time(s)]
    17268 
    17269 > color sel #130816ff
    17270 
    17271 [Repeated 1 time(s)]
    17272 
    17273 > color sel #a9a9a9ff
    17274 
    17275 > color sel #929292ff
    17276 
    17277 > color sel #5e5e5eff
    17278 
    17279 > color sel byhetero
    17280 
    17281 > ui mousemode right select
    17282 
    17283 > select clear
    17284 
    17285 [Repeated 1 time(s)]
    17286 
    17287 > select hydrophobic_cavity
    17288 
    17289 196 atoms, 195 bonds, 10 residues, 1 model selected 
    17290 
    17291 > color sel dim gray
    17292 
    17293 > color sel byhetero
    17294 
    17295 > select clear
    17296 
    17297 > select stacking_pocket
    17298 
    17299 97 atoms, 96 bonds, 5 residues, 1 model selected 
    17300 
    17301 > color sel dim gray
    17302 
    17303 > color sel byhetero
    17304 
    17305 > select clear
    17306 
    17307 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    17308 > chimera files and png files/Figure 4/Figure4A_119_LPC.cxs"
    17309 
    17310 ——— End of log from Mon Jun 10 00:01:24 2024 ———
    17311 
    17312 opened ChimeraX session 
    17313 
    17314 > close session
    17315 
    17316 > open 7Xv3
    17317 
    17318 Summary of feedback from opening 7Xv3 fetched from pdb 
    17319 --- 
    17320 notes | Fetching compressed mmCIF 7xv3 from http://files.rcsb.org/download/7xv3.cif 
    17321 Fetching CCD WJS from
    17322 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/WJS/WJS.cif 
    17323  
    17324 7xv3 title: 
    17325 Cryo-EM structure of LPS-bound GPR174 in complex with Gs protein [more
    17326 info...] 
    17327  
    17328 Chain information for 7xv3 #1 
    17329 --- 
    17330 Chain | Description | UniProt 
    17331 A | Engineered G protein subunit S (mini-Gs) |   
    17332 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    17333 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    17334 N | Nb35 |   
    17335 R | Probable G-protein coupled receptor 174 | GP174_HUMAN 1-333 
    17336  
    17337 Non-standard residues in 7xv3 #1 
    17338 --- 
    17339 WJS — (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-
    17340 propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid 
    17341  
    17342 
    17343 > hide atoms
    17344 
    17345 > show atoms
    17346 
    17347 > style stick
    17348 
    17349 Changed 8347 atom styles 
    17350 
    17351 > hide atoms
    17352 
    17353 > show cartoons
    17354 
    17355 > open 8IZB
    17356 
    17357 Summary of feedback from opening 8IZB fetched from pdb 
    17358 --- 
    17359 note | Fetching compressed mmCIF 8izb from http://files.rcsb.org/download/8izb.cif 
    17360  
    17361 8izb title: 
    17362 Lysophosphatidylserine receptor GPR174-Gs complex [more info...] 
    17363  
    17364 Chain information for 8izb #2 
    17365 --- 
    17366 Chain | Description | UniProt 
    17367 A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-66 205-394 
    17368 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    17369 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    17370 N | Nanobody35 |   
    17371 R | Probable G-protein coupled receptor 174 | GP174_HUMAN 1-309 
    17372  
    17373 Non-standard residues in 8izb #2 
    17374 --- 
    17375 CLR — cholesterol 
    17376 SER — serine 
    17377 UBL — [(2R)-2-oxidanyl-3-phosphonooxy-propyl] (Z)-octadec-9-enoate 
    17378  
    17379 
    17380 > style stick
    17381 
    17382 Changed 16669 atom styles 
    17383 
    17384 > hide atoms
    17385 
    17386 > show cartoons
    17387 
    17388 > ui tool show Matchmaker
    17389 
    17390 > matchmaker #!2 to #1
    17391 
    17392 Parameters 
    17393 --- 
    17394 Chain pairing | bb 
    17395 Alignment algorithm | Needleman-Wunsch 
    17396 Similarity matrix | BLOSUM-62 
    17397 SS fraction | 0.3 
    17398 Gap open (HH/SS/other) | 18/18/6 
    17399 Gap extend | 1 
    17400 SS matrix |  |  | H | S | O 
    17401 ---|---|---|--- 
    17402 H | 6 | -9 | -6 
    17403 S |  | 6 | -6 
    17404 O |  |  | 4 
    17405 Iteration cutoff | 2 
    17406  
    17407 Matchmaker 7xv3, chain B (#1) with 8izb, chain B (#2), sequence alignment
    17408 score = 1748.9 
    17409 RMSD between 338 pruned atom pairs is 0.870 angstroms; (across all 338 pairs:
    17410 0.870) 
    17411  
    17412 
    17413 > matchmaker #!2 to #1
    17414 
    17415 Parameters 
    17416 --- 
    17417 Chain pairing | bb 
    17418 Alignment algorithm | Needleman-Wunsch 
    17419 Similarity matrix | BLOSUM-62 
    17420 SS fraction | 0.3 
    17421 Gap open (HH/SS/other) | 18/18/6 
    17422 Gap extend | 1 
    17423 SS matrix |  |  | H | S | O 
    17424 ---|---|---|--- 
    17425 H | 6 | -9 | -6 
    17426 S |  | 6 | -6 
    17427 O |  |  | 4 
    17428 Iteration cutoff | 2 
    17429  
    17430 Matchmaker 7xv3, chain B (#1) with 8izb, chain B (#2), sequence alignment
    17431 score = 1748.9 
    17432 RMSD between 338 pruned atom pairs is 0.870 angstroms; (across all 338 pairs:
    17433 0.870) 
    17434  
    17435 
    17436 > select #1/R#2/R
    17437 
    17438 4742 atoms, 4879 bonds, 1 pseudobond, 579 residues, 3 models selected 
    17439 
    17440 > select ~sel
    17441 
    17442 11927 atoms, 12154 bonds, 2 pseudobonds, 1517 residues, 4 models selected 
    17443 
    17444 > delete atoms (#!1-2 & sel)
    17445 
    17446 > delete bonds (#!1-2 & sel)
    17447 
    17448 > ui tool show Matchmaker
    17449 
    17450 > matchmaker #!2 to #1
    17451 
    17452 Parameters 
    17453 --- 
    17454 Chain pairing | bb 
    17455 Alignment algorithm | Needleman-Wunsch 
    17456 Similarity matrix | BLOSUM-62 
    17457 SS fraction | 0.3 
    17458 Gap open (HH/SS/other) | 18/18/6 
    17459 Gap extend | 1 
    17460 SS matrix |  |  | H | S | O 
    17461 ---|---|---|--- 
    17462 H | 6 | -9 | -6 
    17463 S |  | 6 | -6 
    17464 O |  |  | 4 
    17465 Iteration cutoff | 2 
    17466  
    17467 Matchmaker 7xv3, chain R (#1) with 8izb, chain R (#2), sequence alignment
    17468 score = 1530.3 
    17469 RMSD between 275 pruned atom pairs is 0.891 angstroms; (across all 282 pairs:
    17470 0.952) 
    17471  
    17472 
    17473 > matchmaker #!2 to #1
    17474 
    17475 Parameters 
    17476 --- 
    17477 Chain pairing | bb 
    17478 Alignment algorithm | Needleman-Wunsch 
    17479 Similarity matrix | BLOSUM-62 
    17480 SS fraction | 0.3 
    17481 Gap open (HH/SS/other) | 18/18/6 
    17482 Gap extend | 1 
    17483 SS matrix |  |  | H | S | O 
    17484 ---|---|---|--- 
    17485 H | 6 | -9 | -6 
    17486 S |  | 6 | -6 
    17487 O |  |  | 4 
    17488 Iteration cutoff | 2 
    17489  
    17490 Matchmaker 7xv3, chain R (#1) with 8izb, chain R (#2), sequence alignment
    17491 score = 1530.3 
    17492 RMSD between 275 pruned atom pairs is 0.891 angstroms; (across all 282 pairs:
    17493 0.952) 
    17494  
    17495 
    17496 > color #1 #00f900ff
    17497 
    17498 > color #1 #73fa79ff
    17499 
    17500 > color #1 #8efa00ff
    17501 
    17502 > color #1 #008f00ff
    17503 
    17504 > color #1 #4f8f00ff
    17505 
    17506 > color #1 #71cd02ff
    17507 
    17508 > color #1 #5fac01ff
    17509 
    17510 > color #1 #62b102ff
    17511 
    17512 > color #1 #66b902ff
    17513 
    17514 > color #2 #ff9300ff
    17515 
    17516 > color #2 #ffd479ff
    17517 
    17518 > color #2 #fffc79ff
    17519 
    17520 > color #2 #ff8a76ff
    17521 
    17522 > color #2 #ff5b30ff
    17523 
    17524 > color #2 #ff6542ff
    17525 
    17526 > color #2 #ff694dff
    17527 
    17528 > color #2 #ff7e65ff
    17529 
    17530 > color #2 #ff7d61ff
    17531 
    17532 > select clear
    17533 
    17534 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    17535 > chimera files and png files/Figure 4/Figure4D_174.cxs"
    17536 
    17537 > hide #!2 models
    17538 
    17539 > show #!2 models
    17540 
    17541 > rename #1 GPR174_7XV3
    17542 
    17543 > rename #2 GPR174_8IZB
    17544 
    17545 > open /Users/dongju/Downloads/emd_33479_7XV3.map
    17546 
    17547 Opened emd_33479_7XV3.map as #3, grid size 256,256,256, pixel 1.1, shown at
    17548 level 0.36, step 1, values float32 
    17549 
    17550 > volume #3 level 1.405
    17551 
    17552 > volume #3 level 1.24
    17553 
    17554 > hide #!2 models
    17555 
    17556 > fitmap #1 inMap #3
    17557 
    17558 Fit molecule GPR174_7XV3 (#1) to map emd_33479_7XV3.map (#3) using 2405 atoms 
    17559 average map value = 1.557, steps = 40 
    17560 shifted from previous position = 0.0106 
    17561 rotated from previous position = 0.0257 degrees 
    17562 atoms outside contour = 1086, contour level = 1.2401 
    17563  
    17564 Position of GPR174_7XV3 (#1) relative to emd_33479_7XV3.map (#3) coordinates: 
    17565 Matrix rotation and translation 
    17566 0.99999993 -0.00006648 0.00036702 -0.03179555 
    17567 0.00006657 0.99999997 -0.00024767 0.02815569 
    17568 -0.00036701 0.00024769 0.99999990 0.02266206 
    17569 Axis 0.55317913 0.81970479 0.14858300 
    17570 Axis point 58.13526746 0.00000000 99.99218581 
    17571 Rotation angle (degrees) 0.02565375 
    17572 Shift along axis 0.00885791 
    17573  
    17574 
    17575 > select clear
    17576 
    17577 > ui tool show "Segment Map"
    17578 
    17579 Segmenting emd_33479_7XV3.map, density threshold 1.240100 
    17580 Showing 45 region surfaces 
    17581 1639 watershed regions, grouped to 45 regions 
    17582 Showing emd_33479_7XV3.seg - 45 regions, 45 surfaces 
    17583 
    17584 > volume #3 level 1.625
    17585 
    17586 > volume #3 level 1.515
    17587 
    17588 > select #4.5
    17589 
    17590 1 model selected 
    17591 
    17592 > select #4.9
    17593 
    17594 1 model selected 
    17595 
    17596 > select #4.33
    17597 
    17598 1 model selected 
    17599 
    17600 > select #4.25
    17601 
    17602 1 model selected 
    17603 
    17604 > select #4.42
    17605 
    17606 1 model selected 
    17607 
    17608 > select #4.32
    17609 
    17610 1 model selected 
    17611 
    17612 > select #4.40
    17613 
    17614 1 model selected 
    17615 
    17616 > select #4.24
    17617 
    17618 1 model selected 
    17619 
    17620 > volume style mesh
    17621 
    17622 > select ligand
    17623 
    17624 126 atoms, 130 bonds, 5 residues, 2 models selected 
    17625 
    17626 > show sel & #!1 atoms
    17627 
    17628 > select clear
    17629 
    17630 > ui tool show "Segment Map"
    17631 
    17632 > select clear
    17633 
    17634 Showing 45 region surfaces 
    17635 
    17636 > select #4.40
    17637 
    17638 1 model selected 
    17639 
    17640 > select clear
    17641 
    17642 > select #4.40
    17643 
    17644 1 model selected 
    17645 
    17646 > select add #4.32
    17647 
    17648 2 models selected 
    17649 
    17650 > select ligand
    17651 
    17652 126 atoms, 130 bonds, 5 residues, 2 models selected 
    17653 
    17654 > color (#!1 & sel) red
    17655 
    17656 > select #4.9
    17657 
    17658 1 model selected 
    17659 
    17660 > select #4.22
    17661 
    17662 1 model selected 
    17663 
    17664 > select #4.42
    17665 
    17666 1 model selected 
    17667 
    17668 > select #4.25
    17669 
    17670 1 model selected 
    17671 
    17672 > select #4.24
    17673 
    17674 1 model selected 
    17675 
    17676 > select #4.6
    17677 
    17678 1 model selected 
    17679 
    17680 > select #4.44
    17681 
    17682 1 model selected 
    17683 
    17684 > select #4.43
    17685 
    17686 1 model selected 
    17687 
    17688 > select #4.28
    17689 
    17690 1 model selected 
    17691 
    17692 > select #4.33
    17693 
    17694 1 model selected 
    17695 
    17696 > select #4.5
    17697 
    17698 1 model selected 
    17699 
    17700 > select clear
    17701 
    17702 > select #4.36
    17703 
    17704 1 model selected 
    17705 
    17706 > select add #4.5
    17707 
    17708 2 models selected 
    17709 
    17710 > select #4.36
    17711 
    17712 1 model selected 
    17713 
    17714 > select add #4.5
    17715 
    17716 2 models selected 
    17717 
    17718 > select #4.36
    17719 
    17720 1 model selected 
    17721 
    17722 > select add #4.21
    17723 
    17724 2 models selected 
    17725 
    17726 > select add #4.5
    17727 
    17728 3 models selected 
    17729 
    17730 > select clear
    17731 
    17732 > select #4.21
    17733 
    17734 1 model selected 
    17735 
    17736 > select #4.5
    17737 
    17738 1 model selected 
    17739 
    17740 > select clear
    17741 
    17742 > select #4.36
    17743 
    17744 1 model selected 
    17745 
    17746 > select clear
    17747 
    17748 Drag select of 2352, 2347, 2356, 2297, 2294, 2350, 2341, 2361, 2355, 2296,
    17749 2354, 2357, 2306, 2351, 2358, 2346, 2280, 2330, 2315, 2312, 2335, 2349, 2292,
    17750 2304, 2118, 2079, 2089, 2348, 2150, 1146, 65 residues, 3 emd_33479_7XV3.map 
    17751 
    17752 > select clear
    17753 
    17754 Drag select of 2352, 2347, 2356, 2297, 14670 of 14696 triangles, 2294, 12950
    17755 of 13052 triangles, 2350, 12861 of 12876 triangles, 2341, 2361, 2355, 11674 of
    17756 11720 triangles, 2296, 2354, 2357, 2306, 9815 of 9928 triangles, 2351, 2358,
    17757 2346, 2280, 2330, 2315, 5332 of 5700 triangles, 2312, 2335, 2349, 2292, 4192
    17758 of 4588 triangles, 2304, 2118, 2079, 2089, 2348, 2150, 1146, 1 residues, 3
    17759 emd_33479_7XV3.map 
    17760 
    17761 > select add #1/R:202
    17762 
    17763 17 atoms, 7 bonds, 2 residues, 33 models selected 
    17764 
    17765 > select subtract #1/R:202
    17766 
    17767 9 atoms, 1 residue, 31 models selected 
    17768 
    17769 > select #4.5
    17770 
    17771 1 model selected 
    17772 
    17773 > select add #4.36
    17774 
    17775 2 models selected 
    17776 
    17777 > hide #!3 models
    17778 
    17779 > select clear
    17780 
    17781 > select #4.5
    17782 
    17783 1 model selected 
    17784 
    17785 > select clear
    17786 
    17787 Drag select of 2353, 2333, 35 atoms, 196 residues, 34 bonds 
    17788 
    17789 > select clear
    17790 
    17791 Drag select of 2353, 2333, 35 atoms, 197 residues, 34 bonds 
    17792 
    17793 > select #1/R:40
    17794 
    17795 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17796 
    17797 > select #4.5
    17798 
    17799 1 model selected 
    17800 
    17801 > select add #4.36
    17802 
    17803 2 models selected 
    17804 Segmenting emd_33479_7XV3.map, density threshold 1.515058 
    17805 Showing 41 region surfaces 
    17806 1431 watershed regions, grouped to 41 regions 
    17807 Showing emd_33479_7XV3.seg - 41 regions, 41 surfaces 
    17808 
    17809 > undo
    17810 
    17811 [Repeated 1 time(s)]
    17812 
    17813 > show #!3 models
    17814 
    17815 > ui mousemode right "map eraser"
    17816 
    17817 > volume erase #3 center 140.58,139.71,106.28 radius 11.852 outside true
    17818 
    17819 Opened emd_33479_7XV3.map copy as #6, grid size 256,256,256, pixel 1.1, shown
    17820 at step 1, values float32 
    17821 
    17822 > volume erase #6 center 137.3,152.38,97.859 radius 11.827
    17823 
    17824 > volume erase #6 center 135.39,152.17,108.13 radius 11.827
    17825 
    17826 > volume erase #6 center 144.73,147.59,113.46 radius 11.827
    17827 
    17828 > volume erase #6 center 146.32,146.11,101.19 radius 5.4912
    17829 
    17830 > volume erase #6 center 152.41,143.39,102.84 radius 5.4912
    17831 
    17832 > volume erase #6 center 138.24,142.17,93.12 radius 5.4912
    17833 
    17834 > volume erase #6 center 136.41,143.11,98.222 radius 5.4912
    17835 
    17836 > volume erase #6 center 137.82,144.4,102.77 radius 5.4912
    17837 
    17838 > volume erase #6 center 131.31,145.4,113.23 radius 5.4912
    17839 
    17840 > volume erase #6 center 132.17,144.82,109.47 radius 5.4912
    17841 
    17842 > volume erase #6 center 131.37,144.07,111.4 radius 5.4912
    17843 
    17844 > volume erase #6 center 132.5,144.22,106.45 radius 5.4912
    17845 
    17846 > volume erase #6 center 130.12,143.49,107.79 radius 5.4912
    17847 
    17848 > volume erase #6 center 129.52,142.42,108.59 radius 5.4912
    17849 
    17850 > volume erase #6 center 129.08,142.98,101.33 radius 5.4912
    17851 
    17852 > volume erase #6 center 145.74,131.78,111.69 radius 5.4912
    17853 
    17854 > volume erase #6 center 150.8,133.41,107.81 radius 5.4912
    17855 
    17856 > volume erase #6 center 151.98,137.02,108.6 radius 5.4912
    17857 
    17858 > volume erase #6 center 143.1,131.49,103.53 radius 5.4912
    17859 
    17860 > undo
    17861 
    17862 [Repeated 1 time(s)]
    17863 
    17864 > show #!3 models
    17865 
    17866 > hide #!3 models
    17867 
    17868 > volume erase #6 center 142.48,134.18,95.914 radius 2.112
    17869 
    17870 > volume erase #6 center 143.41,137.35,104.66 radius 2.112
    17871 
    17872 > volume erase #6 center 142.13,136.54,106.85 radius 2.112
    17873 
    17874 > volume erase #6 center 138.06,135.9,104.81 radius 2.112
    17875 
    17876 > volume erase #6 center 136.16,130.41,103.82 radius 3.3792
    17877 
    17878 > volume erase #6 center 137,131.27,108.9 radius 3.3792
    17879 
    17880 > volume erase #6 center 136.49,131.45,109.31 radius 3.3792
    17881 
    17882 > volume erase #6 center 135.44,130.37,109.42 radius 3.3792
    17883 
    17884 > volume erase #6 center 138.2,132.73,114.96 radius 3.3792
    17885 
    17886 > volume erase #6 center 140.56,135.89,116.43 radius 3.3792
    17887 
    17888 > volume erase #6 center 138.76,138,109.25 radius 3.3792
    17889 
    17890 > volume erase #6 center 139.05,137.66,112.31 radius 3.3792
    17891 
    17892 > volume erase #6 center 142.67,137.36,109.71 radius 3.3792
    17893 
    17894 > volume erase #6 center 141.81,136.15,110.68 radius 3.3792
    17895 
    17896 > ui mousemode right select
    17897 
    17898 > color #4 #bfbb4dff
    17899 
    17900 > color #4 #bfb75cff
    17901 
    17902 > color #6 #8769bfff models
    17903 
    17904 > select clear
    17905 
    17906 > show #!2 models
    17907 
    17908 > hide #!4 models
    17909 
    17910 > hide #!6 models
    17911 
    17912 > hide #!2 models
    17913 
    17914 > hide #!1 models
    17915 
    17916 > show #!2 models
    17917 
    17918 > select ligand
    17919 
    17920 126 atoms, 130 bonds, 5 residues, 2 models selected 
    17921 
    17922 > show sel & #!2 atoms
    17923 
    17924 > color (#!2 & sel) cyan
    17925 
    17926 > color (#!2 & sel) byelement
    17927 
    17928 > color (#!2 & sel) cyan
    17929 
    17930 > color (#!2 & sel) byhetero
    17931 
    17932 > select clear
    17933 
    17934 > select ligand
    17935 
    17936 126 atoms, 130 bonds, 5 residues, 2 models selected 
    17937 
    17938 > select clear
    17939 
    17940 Drag select of 28 atoms, 14 residues, 31 bonds 
    17941 
    17942 > select subtract #2/R:107
    17943 
    17944 124 atoms, 31 bonds, 14 residues, 1 model selected 
    17945 
    17946 > select subtract #2/R:108
    17947 
    17948 113 atoms, 31 bonds, 13 residues, 1 model selected 
    17949 
    17950 > select subtract #2/R:104
    17951 
    17952 108 atoms, 31 bonds, 12 residues, 1 model selected 
    17953 
    17954 > select subtract #2/R:105
    17955 
    17956 102 atoms, 31 bonds, 11 residues, 1 model selected 
    17957 Drag select of 4 residues 
    17958 
    17959 > select subtract #2/R:285
    17960 
    17961 111 atoms, 31 bonds, 12 residues, 1 model selected 
    17962 
    17963 > select add #2/R:64
    17964 
    17965 116 atoms, 35 bonds, 13 residues, 1 model selected 
    17966 
    17967 > select subtract #2/R:65
    17968 
    17969 108 atoms, 35 bonds, 12 residues, 1 model selected 
    17970 
    17971 > select subtract #2/R:286
    17972 
    17973 102 atoms, 35 bonds, 11 residues, 1 model selected 
    17974 
    17975 > select subtract #2/R:64
    17976 
    17977 97 atoms, 31 bonds, 10 residues, 1 model selected 
    17978 
    17979 > select subtract #2/R:63
    17980 
    17981 89 atoms, 31 bonds, 9 residues, 1 model selected 
    17982 
    17983 > select subtract #2/R:61
    17984 
    17985 81 atoms, 31 bonds, 8 residues, 1 model selected 
    17986 
    17987 > select subtract #2/R:60
    17988 
    17989 73 atoms, 31 bonds, 7 residues, 1 model selected 
    17990 
    17991 > select subtract #2/R:59
    17992 
    17993 65 atoms, 31 bonds, 6 residues, 1 model selected 
    17994 
    17995 > select subtract #2/R:56
    17996 
    17997 57 atoms, 31 bonds, 5 residues, 1 model selected 
    17998 
    17999 > select subtract #2/R:54
    18000 
    18001 52 atoms, 31 bonds, 4 residues, 1 model selected 
    18002 
    18003 > hide sel atoms
    18004 
    18005 > select clear
    18006 
    18007 Drag select of 28 atoms, 43 residues, 31 bonds 
    18008 
    18009 > hide sel atoms
    18010 
    18011 > select clear
    18012 
    18013 > open /Users/dongju/Downloads/emd_35838_8IZB.map
    18014 
    18015 Opened emd_35838_8IZB.map as #5, grid size 192,192,192, pixel 1.07, shown at
    18016 level 0.109, step 1, values float32 
    18017 
    18018 > fitmap #2 inMap #5
    18019 
    18020 Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms 
    18021 average map value = 0.03112, steps = 212 
    18022 shifted from previous position = 22.3 
    18023 rotated from previous position = 24.7 degrees 
    18024 atoms outside contour = 2133, contour level = 0.10906 
    18025  
    18026 Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates: 
    18027 Matrix rotation and translation 
    18028 -0.75709552 0.55152368 0.35018282 113.97146734 
    18029 -0.50474698 -0.83411747 0.22243769 251.71856442 
    18030 0.41477326 -0.00834714 0.90988651 -4.43581388 
    18031 Axis -0.21307481 -0.05963389 -0.97521430 
    18032 Axis point 95.12709807 109.92648099 0.00000000 
    18033 Rotation angle (degrees) 147.21022229 
    18034 Shift along axis -34.96953558 
    18035  
    18036 
    18037 > volume #5 level 0.31
    18038 
    18039 > ui tool show "Fit in Map"
    18040 
    18041 > fitmap #2 inMap #5
    18042 
    18043 Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms 
    18044 average map value = 0.03115, steps = 48 
    18045 shifted from previous position = 0.025 
    18046 rotated from previous position = 0.0816 degrees 
    18047 atoms outside contour = 2259, contour level = 0.30999 
    18048  
    18049 Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates: 
    18050 Matrix rotation and translation 
    18051 -0.75634424 0.55270285 0.34994707 113.77452372 
    18052 -0.50587272 -0.83333500 0.22281287 251.71833289 
    18053 0.41477245 -0.00850545 0.90988542 -4.40405517 
    18054 Axis -0.21309999 -0.05971981 -0.97520354 
    18055 Axis point 95.12333021 109.91381983 0.00000000 
    18056 Rotation angle (degrees) 147.12923511 
    18057 Shift along axis -34.98307141 
    18058  
    18059 
    18060 > ui mousemode right "translate selected models"
    18061 
    18062 > select add #2
    18063 
    18064 2337 atoms, 2408 bonds, 1 pseudobond, 287 residues, 2 models selected 
    18065 
    18066 > view matrix models
    18067 > #2,-0.75634,0.5527,0.34995,100.77,-0.50587,-0.83333,0.22281,216.63,0.41477,-0.0085054,0.90989,-31.932
    18068 
    18069 > fitmap #2 inMap #5
    18070 
    18071 Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms 
    18072 average map value = 0.08239, steps = 112 
    18073 shifted from previous position = 2.02 
    18074 rotated from previous position = 15.7 degrees 
    18075 atoms outside contour = 2038, contour level = 0.30999 
    18076  
    18077 Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates: 
    18078 Matrix rotation and translation 
    18079 -0.62364597 0.74902223 0.22367702 77.87927936 
    18080 -0.66907043 -0.65943588 0.34276680 205.54528669 
    18081 0.40424060 0.06410946 0.91240315 -40.48325695 
    18082 Axis -0.19132671 -0.12397533 -0.97366535 
    18083 Axis point 88.49903660 88.11034294 0.00000000 
    18084 Rotation angle (degrees) 133.26230076 
    18085 Shift along axis -0.96578672 
    18086  
    18087 
    18088 > ui mousemode right "rotate selected models"
    18089 
    18090 > view matrix models
    18091 > #2,-0.70332,0.62636,0.33617,89.044,-0.54828,-0.77897,0.30429,208.47,0.45246,0.029698,0.89129,-40.182
    18092 
    18093 > view matrix models
    18094 > #2,-0.38844,0.53793,0.74816,33.249,-0.82947,-0.55777,-0.029626,241.38,0.40136,-0.63209,0.66285,49.269
    18095 
    18096 > view matrix models
    18097 > #2,-0.65242,0.24877,0.71586,91.091,-0.63219,-0.69958,-0.33305,260.16,0.41795,-0.66985,0.61369,55.325
    18098 
    18099 > view matrix models
    18100 > #2,-0.5867,0.50734,0.63118,65.537,-0.7995,-0.48686,-0.35181,257.2,0.12881,-0.71103,0.69126,82.133
    18101 
    18102 > ui mousemode right "translate selected models"
    18103 
    18104 > view matrix models
    18105 > #2,-0.5867,0.50734,0.63118,60.551,-0.7995,-0.48686,-0.35181,261.38,0.12881,-0.71103,0.69126,84.231
    18106 
    18107 > fitmap #2 inMap #5
    18108 
    18109 Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms 
    18110 average map value = 0.1085, steps = 92 
    18111 shifted from previous position = 0.937 
    18112 rotated from previous position = 10 degrees 
    18113 atoms outside contour = 1891, contour level = 0.30999 
    18114  
    18115 Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates: 
    18116 Matrix rotation and translation 
    18117 -0.62096528 0.36269632 0.69487660 72.83627793 
    18118 -0.76631836 -0.46729282 -0.44090089 263.50441797 
    18119 0.16479771 -0.80628084 0.56811347 99.96027181 
    18120 Axis -0.28113136 0.40785433 -0.86868867 
    18121 Axis point 76.22679670 139.73009413 0.00000000 
    18122 Rotation angle (degrees) 139.47057346 
    18123 Shift along axis 0.16050012 
    18124  
    18125 
    18126 > view matrix models
    18127 > #2,-0.62097,0.3627,0.69488,72.832,-0.76632,-0.46729,-0.4409,263.51,0.1648,-0.80628,0.56811,99.969
    18128 
    18129 > view matrix models
    18130 > #2,-0.62097,0.3627,0.69488,72.278,-0.76632,-0.46729,-0.4409,263.09,0.1648,-0.80628,0.56811,99.426
    18131 
    18132 > ui mousemode right "rotate selected models"
    18133 
    18134 > view matrix models
    18135 > #2,0.88734,-0.45949,0.038594,56.044,0.37767,0.77224,0.51089,-51.449,-0.26456,-0.43876,0.85878,82.396
    18136 
    18137 > view matrix models
    18138 > #2,0.68908,-0.72467,-0.004158,105.76,0.64997,0.61549,0.44576,-57.838,-0.32047,-0.30987,0.89514,72.218
    18139 
    18140 > view matrix models
    18141 > #2,0.55824,-0.82784,-0.05519,133.24,0.7659,0.48861,0.41792,-54.551,-0.319,-0.27557,0.90681,67.714
    18142 
    18143 > view matrix models
    18144 > #2,0.32974,-0.92787,-0.17416,175.64,0.90726,0.26044,0.33022,-38.902,-0.26104,-0.26689,0.9277,59.37
    18145 
    18146 > view matrix models
    18147 > #2,0.45763,-0.88555,-0.079857,151.04,0.84987,0.46205,-0.25344,-6.3646,0.26133,0.048115,0.96405,-27.233
    18148 
    18149 > view matrix models
    18150 > #2,0.49381,-0.86137,0.11913,129.02,0.8695,0.49087,-0.054935,-27.152,-0.011156,0.13071,0.99136,-10.394
    18151 
    18152 > ui mousemode right "translate selected models"
    18153 
    18154 > view matrix models
    18155 > #2,0.49381,-0.86137,0.11913,130.24,0.8695,0.49087,-0.054935,-27.912,-0.011156,0.13071,0.99136,-12.122
    18156 
    18157 > fitmap #2 inMap #5
    18158 
    18159 Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms 
    18160 average map value = 0.09425, steps = 80 
    18161 shifted from previous position = 2.89 
    18162 rotated from previous position = 5.57 degrees 
    18163 atoms outside contour = 1973, contour level = 0.30999 
    18164  
    18165 Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates: 
    18166 Matrix rotation and translation 
    18167 0.52515536 -0.85051680 0.02886199 134.01497851 
    18168 0.84977602 0.52227137 -0.07150763 -24.99386004 
    18169 0.04574465 0.06207884 0.99702239 -11.46111867 
    18170 Axis 0.07832154 -0.00989827 0.99687901 
    18171 Axis point 89.84006467 107.47382746 0.00000000 
    18172 Rotation angle (degrees) 58.51841098 
    18173 Shift along axis -0.68169319 
    18174  
    18175 
    18176 > view matrix models
    18177 > #2,0.52516,-0.85052,0.028862,134.03,0.84978,0.52227,-0.071508,-24.982,0.045745,0.062079,0.99702,-11.446
    18178 
    18179 > select subtract #2
    18180 
    18181 Nothing selected 
    18182 
    18183 > hide #!2 models
    18184 
    18185 > show #!2 models
    18186 
    18187 > open 8IZB
    18188 
    18189 8izb title: 
    18190 Lysophosphatidylserine receptor GPR174-Gs complex [more info...] 
    18191  
    18192 Chain information for 8izb #7 
    18193 --- 
    18194 Chain | Description | UniProt 
    18195 A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-66 205-394 
    18196 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    18197 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    18198 N | Nanobody35 |   
    18199 R | Probable G-protein coupled receptor 174 | GP174_HUMAN 1-309 
    18200  
    18201 Non-standard residues in 8izb #7 
    18202 --- 
    18203 CLR — cholesterol 
    18204 SER — serine 
    18205 UBL — [(2R)-2-oxidanyl-3-phosphonooxy-propyl] (Z)-octadec-9-enoate 
    18206  
    18207 
    18208 > show #!2,7 atoms
    18209 
    18210 > hide #!2,7 atoms
    18211 
    18212 > show #!2,7 cartoons
    18213 
    18214 > hide #!2 models
    18215 
    18216 > fitmap #7 inMap #5
    18217 
    18218 Fit molecule 8izb (#7) to map emd_35838_8IZB.map (#5) using 8322 atoms 
    18219 average map value = 0.528, steps = 48 
    18220 shifted from previous position = 0.00983 
    18221 rotated from previous position = 0.0346 degrees 
    18222 atoms outside contour = 2668, contour level = 0.30999 
    18223  
    18224 Position of 8izb (#7) relative to emd_35838_8IZB.map (#5) coordinates: 
    18225 Matrix rotation and translation 
    18226 0.99999990 -0.00043812 -0.00007167 0.05733242 
    18227 0.00043815 0.99999982 0.00040866 -0.10116588 
    18228 0.00007149 -0.00040870 0.99999991 0.03879010 
    18229 Axis -0.67728235 -0.11862354 0.72609715 
    18230 Axis point 230.58619138 132.87307402 0.00000000 
    18231 Rotation angle (degrees) 0.03457291 
    18232 Shift along axis 0.00133580 
    18233  
    18234 
    18235 > fitmap #7 inMap #5
    18236 
    18237 Fit molecule 8izb (#7) to map emd_35838_8IZB.map (#5) using 8322 atoms 
    18238 average map value = 0.528, steps = 40 
    18239 shifted from previous position = 0.0136 
    18240 rotated from previous position = 0.0126 degrees 
    18241 atoms outside contour = 2663, contour level = 0.30999 
    18242  
    18243 Position of 8izb (#7) relative to emd_35838_8IZB.map (#5) coordinates: 
    18244 Matrix rotation and translation 
    18245 0.99999989 -0.00041193 -0.00021360 0.07185299 
    18246 0.00041198 0.99999989 0.00024297 -0.07255698 
    18247 0.00021350 -0.00024306 0.99999995 -0.00480124 
    18248 Axis -0.46394690 -0.40768761 0.78647574 
    18249 Axis point 183.61588251 165.89958263 0.00000000 
    18250 Rotation angle (degrees) 0.03001154 
    18251 Shift along axis -0.00753145 
    18252  
    18253 
    18254 > select ligand
    18255 
    18256 217 atoms, 226 bonds, 9 residues, 3 models selected 
    18257 
    18258 > show sel & #!7 atoms
    18259 
    18260 > style sel & #!7 stick
    18261 
    18262 Changed 91 atom styles 
    18263 
    18264 > color (#!7 & sel) cyan
    18265 
    18266 > color (#!7 & sel) byhetero
    18267 
    18268 > ui mousemode right select
    18269 
    18270 > select clear
    18271 
    18272 > color #7 #e97925ff
    18273 
    18274 > select clear
    18275 
    18276 > ui mousemode right "map eraser"
    18277 
    18278 > hide #!5 models
    18279 
    18280 > select ligand
    18281 
    18282 217 atoms, 226 bonds, 9 residues, 3 models selected 
    18283 
    18284 > color (#!7 & sel) cyan
    18285 
    18286 > color (#!7 & sel) byhetero
    18287 
    18288 > ui mousemode right select
    18289 
    18290 > select clear
    18291 
    18292 Drag select of 28 atoms, 15 residues, 31 bonds 
    18293 
    18294 > hide sel atoms
    18295 
    18296 Drag select of 28 atoms, 36 residues, 31 bonds 
    18297 
    18298 > hide sel atoms
    18299 
    18300 > select clear
    18301 
    18302 > ui mousemode right "map eraser"
    18303 
    18304 > show #!5 models
    18305 
    18306 > volume erase #5 center 106.66,103.8,71.644 radius 14.586 outside true
    18307 
    18308 Opened emd_35838_8IZB.map copy as #9, grid size 192,192,192, pixel 1.07, shown
    18309 at step 1, values float32 
    18310 
    18311 > volume #!9 style mesh
    18312 
    18313 > volume erase #9 center 111.41,89.902,65.361 radius 14.586
    18314 
    18315 > volume erase #9 center 107.94,121.91,67.65 radius 14.586
    18316 
    18317 > volume erase #9 center 111.71,121.18,80.776 radius 14.586
    18318 
    18319 > show #!6 models
    18320 
    18321 > hide #!6 models
    18322 
    18323 > show #!5 models
    18324 
    18325 > hide #!5 models
    18326 
    18327 > hide #!9 models
    18328 
    18329 > show #!9 models
    18330 
    18331 > hide #!9 models
    18332 
    18333 > hide #!7 models
    18334 
    18335 > show #!7 models
    18336 
    18337 > select up
    18338 
    18339 2 atoms, 1 bond, 1 residue, 1 model selected 
    18340 
    18341 > select up
    18342 
    18343 28 atoms, 27 bonds, 1 residue, 1 model selected 
    18344 
    18345 > select up
    18346 
    18347 35 atoms, 34 bonds, 2 residues, 1 model selected 
    18348 
    18349 > select clear
    18350 
    18351 > select #7/R:501@CAL
    18352 
    18353 1 atom, 1 residue, 1 model selected 
    18354 
    18355 > select up
    18356 
    18357 28 atoms, 27 bonds, 1 residue, 1 model selected 
    18358 
    18359 > select up
    18360 
    18361 35 atoms, 34 bonds, 2 residues, 1 model selected 
    18362 
    18363 > ui tool show "Surface Zone"
    18364 
    18365 > surface zone #5 nearAtoms sel distance 6.42
    18366 
    18367 > show #!5 models
    18368 
    18369 > surface zone #5 nearAtoms sel distance 6.39
    18370 
    18371 > surface zone #5 nearAtoms sel distance 2.37
    18372 
    18373 > volume #!5 style mesh
    18374 
    18375 > select clear
    18376 
    18377 > hide #!5 models
    18378 
    18379 > select #7/R:501@CAL
    18380 
    18381 1 atom, 1 residue, 1 model selected 
    18382 
    18383 > select clear
    18384 
    18385 > hide #!7 cartoons
    18386 
    18387 > show #!5 models
    18388 
    18389 > show #!7 cartoons
    18390 
    18391 > surface dust #5 size 10.7
    18392 
    18393 [Repeated 1 time(s)]
    18394 
    18395 > show #!9 models
    18396 
    18397 > hide #!9 models
    18398 
    18399 > hide #!5 models
    18400 
    18401 > show #!5 models
    18402 
    18403 > hide #!5 models
    18404 
    18405 > select ~sel & ##selected
    18406 
    18407 Nothing selected 
    18408 
    18409 > select ~sel & ##selected
    18410 
    18411 Nothing selected 
    18412 
    18413 > select ~sel & ##selected
    18414 
    18415 Nothing selected 
    18416 
    18417 > select ligand
    18418 
    18419 217 atoms, 226 bonds, 9 residues, 3 models selected 
    18420 
    18421 > surface zone #5 nearAtoms sel distance 2.37
    18422 
    18423 > show #!5 models
    18424 
    18425 > surface zone #5 nearAtoms sel distance 2.19
    18426 
    18427 > surface zone #5 nearAtoms sel distance 1.98
    18428 
    18429 > surface zone #5 nearAtoms sel distance 1.92
    18430 
    18431 > surface zone #5 nearAtoms sel distance 2.84
    18432 
    18433 > volume erase #5 center 97.122,114.32,87.432 radius 15.824
    18434 
    18435 Opened emd_35838_8IZB.map copy as #10, grid size 192,192,192, pixel 1.07,
    18436 shown at step 1, values float32 
    18437 
    18438 > hide #8 models
    18439 
    18440 > hide #!7 models
    18441 
    18442 > show #!7 models
    18443 
    18444 > hide #!10 models
    18445 
    18446 > show #!9 models
    18447 
    18448 > show #!10 models
    18449 
    18450 > hide #!10 models
    18451 
    18452 > show #!10 models
    18453 
    18454 > surface zone #5 nearAtoms sel distance 2.88
    18455 
    18456 > surface zone #5 nearAtoms sel distance 3.51
    18457 
    18458 > surface zone #10 nearAtoms sel distance 6.42
    18459 
    18460 > surface zone #10 nearAtoms sel distance 7.4
    18461 
    18462 > surface zone #10 nearAtoms sel distance 2.98
    18463 
    18464 > surface zone #10 nearAtoms sel distance 2.84
    18465 
    18466 > surface zone #10 nearAtoms sel distance 1.07
    18467 
    18468 > surface zone #10 nearAtoms sel distance 1.14
    18469 
    18470 > surface zone #10 nearAtoms sel distance 1.46
    18471 
    18472 > hide #!9 models
    18473 
    18474 > hide #!10 models
    18475 
    18476 > show #!9 models
    18477 
    18478 > ui mousemode right "map eraser"
    18479 
    18480 > show #8 models
    18481 
    18482 > volume erase #9 center 114.38,92.324,58.232 radius 15.819
    18483 
    18484 > volume erase #9 center 111.49,87.981,63.612 radius 15.819
    18485 
    18486 [Repeated 2 time(s)]
    18487 
    18488 > volume erase #9 center 107.71,88.792,66.568 radius 15.819
    18489 
    18490 Drag select of eraser sphere, 12 of 1000 triangles, 1 residues 
    18491 
    18492 > volume erase #9 center 105.1,88.752,87.326 radius 15.819
    18493 
    18494 > select clear
    18495 
    18496 [Repeated 1 time(s)]Drag select of eraser sphere, 22 of 1000 triangles 
    18497 
    18498 > volume erase #9 center 91.499,94.95,81.957 radius 15.819
    18499 
    18500 > volume erase #9 center 85.413,90.487,70.998 radius 15.819
    18501 
    18502 > volume erase #9 center 86.636,92.277,71.444 radius 15.819
    18503 
    18504 Drag select of 3 residues 
    18505 
    18506 > volume erase #9 center 98.241,122.4,57.74 radius 15.819
    18507 
    18508 > volume erase #9 center 102.19,111.25,73.203 radius 5.855
    18509 
    18510 > volume erase #9 center 97.847,107.45,77.377 radius 5.855
    18511 
    18512 > volume erase #9 center 99.791,104.95,73.32 radius 4.2115
    18513 
    18514 > volume erase #9 center 99.143,106.95,70.195 radius 1.5408
    18515 
    18516 > volume erase #9 center 100.36,103.84,59.868 radius 1.5408
    18517 
    18518 > volume erase #9 center 99.493,104.67,62.092 radius 1.5408
    18519 
    18520 > volume erase #9 center 98.056,103.55,61.843 radius 1.5408
    18521 
    18522 > volume erase #9 center 101.99,103.77,60.872 radius 1.5408
    18523 
    18524 > volume erase #9 center 114.36,107.58,72.154 radius 1.5408
    18525 
    18526 > volume erase #9 center 114.63,103.19,73.152 radius 2.6707
    18527 
    18528 > volume erase #9 center 114.95,102.6,75.728 radius 2.6707
    18529 
    18530 > volume erase #9 center 111.11,100.72,76.519 radius 2.6707
    18531 
    18532 > volume erase #9 center 111.56,100.18,79.429 radius 2.6707
    18533 
    18534 > volume erase #9 center 112.28,99.226,83.652 radius 2.6707
    18535 
    18536 > volume erase #9 center 113.98,100.1,82.377 radius 2.6707
    18537 
    18538 > volume erase #9 center 108.54,103.62,85.176 radius 2.6707
    18539 
    18540 > volume erase #9 center 110.25,103.01,85.589 radius 2.6707
    18541 
    18542 > volume erase #9 center 109.53,104.43,84.971 radius 2.6707
    18543 
    18544 > volume erase #9 center 110.73,103.84,85.163 radius 2.6707
    18545 
    18546 > volume erase #9 center 111.12,105.18,86.48 radius 2.6707
    18547 
    18548 > volume erase #9 center 108.43,104.79,87.72 radius 2.6707
    18549 
    18550 > volume erase #9 center 107.37,105.83,85.436 radius 2.6707
    18551 
    18552 > volume erase #9 center 100.71,107.72,83.237 radius 2.6707
    18553 
    18554 > volume erase #9 center 104.99,107.2,81.964 radius 2.6707
    18555 
    18556 > volume erase #9 center 96.298,109.91,77.518 radius 2.6707
    18557 
    18558 > volume erase #9 center 98.754,113.88,76.858 radius 2.6707
    18559 
    18560 > volume erase #9 center 103.49,107.6,70.05 radius 2.6707
    18561 
    18562 > volume erase #9 center 105.05,107.56,75.06 radius 2.6707
    18563 
    18564 > volume erase #9 center 105.08,107.46,78.505 radius 2.6707
    18565 
    18566 > volume erase #9 center 104.93,106.09,79.592 radius 2.6707
    18567 
    18568 > volume erase #9 center 104.63,102.97,82.066 radius 2.6707
    18569 
    18570 > volume erase #9 center 104.29,106.6,79.002 radius 2.6707
    18571 
    18572 > volume erase #9 center 104.49,106.53,79.109 radius 3.1843
    18573 
    18574 > volume erase #9 center 105.6,106.44,76.099 radius 3.1843
    18575 
    18576 > volume erase #9 center 105.35,106.52,74.933 radius 3.1843
    18577 
    18578 > volume erase #9 center 104.88,103.13,76.405 radius 3.1843
    18579 
    18580 > volume erase #9 center 104.98,103.66,75.024 radius 3.1843
    18581 
    18582 > ui mousemode right select
    18583 
    18584 > select clear
    18585 
    18586 > transparency 80 ribbons
    18587 
    18588 > graphics silhouettes width 1.3 depthJump 0.1
    18589 
    18590 > select clear
    18591 
    18592 > color #9 #5884ffff models
    18593 
    18594 > color #9 #2f4688ff models
    18595 
    18596 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    18597 > chimera files and png files/Figure 4/Figure4D_GPR174_8izb.png" width 2000
    18598 > height 1253 supersample 3 transparentBackground true
    18599 
    18600 > show #!1 models
    18601 
    18602 > show #!6 models
    18603 
    18604 > hide #!7 models
    18605 
    18606 > show #!1 cartoons
    18607 
    18608 > hide #!9 models
    18609 
    18610 Drag select of 4 residues 
    18611 
    18612 > select clear
    18613 
    18614 > select lignad
    18615 
    18616 Expected an objects specifier or a keyword 
    18617 
    18618 > select ligand
    18619 
    18620 217 atoms, 226 bonds, 9 residues, 3 models selected 
    18621 
    18622 > color (#!1 & sel) byhetero
    18623 
    18624 > select clear
    18625 
    18626 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    18627 > chimera files and png files/Figure 4/Figure4D_GPR174_7xv3.png" width 2000
    18628 > height 1253 supersample 3 transparentBackground true
    18629 
    18630 [Repeated 5 time(s)]
    18631 
    18632 > ui tool show "Show Sequence Viewer"
    18633 
    18634 > sequence chain #1/R
    18635 
    18636 Alignment identifier is 1/R 
    18637 
    18638 > select #1/R:103-104
    18639 
    18640 17 atoms, 17 bonds, 2 residues, 1 model selected 
    18641 
    18642 > select #1/R:103-104
    18643 
    18644 17 atoms, 17 bonds, 2 residues, 1 model selected 
    18645 
    18646 > select #1/R:103
    18647 
    18648 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18649 
    18650 > select #1/R:103
    18651 
    18652 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18653 
    18654 > select #1/R:103,151
    18655 
    18656 20 atoms, 19 bonds, 2 residues, 1 model selected 
    18657 
    18658 > select #1/R:103,151-152
    18659 
    18660 31 atoms, 31 bonds, 3 residues, 1 model selected 
    18661 
    18662 > select #1/R:103,151-152,155
    18663 
    18664 39 atoms, 38 bonds, 4 residues, 1 model selected 
    18665 
    18666 > select #1/R:103,151-152,155,185-186
    18667 
    18668 55 atoms, 53 bonds, 6 residues, 1 model selected 
    18669 
    18670 > select #1/R:103,151-152,155,185-186
    18671 
    18672 55 atoms, 53 bonds, 6 residues, 1 model selected 
    18673 
    18674 > select #1/R:103,151-152,155,185-186
    18675 
    18676 55 atoms, 53 bonds, 6 residues, 1 model selected 
    18677 
    18678 > select #1/R:103,151-152,155,185-187
    18679 
    18680 62 atoms, 60 bonds, 7 residues, 1 model selected 
    18681 
    18682 > select #1/R:103,151-152,155,185-187
    18683 
    18684 62 atoms, 60 bonds, 7 residues, 1 model selected 
    18685 
    18686 > select #1/R:103,151-152,155,185-187
    18687 
    18688 62 atoms, 60 bonds, 7 residues, 1 model selected 
    18689 
    18690 > select clear
    18691 
    18692 > select #1/R:103
    18693 
    18694 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18695 
    18696 > select #1/R:103
    18697 
    18698 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18699 
    18700 > select #1/R:103,155-156
    18701 
    18702 31 atoms, 30 bonds, 3 residues, 1 model selected 
    18703 
    18704 > select #1/R:103,151-152,155-156
    18705 
    18706 50 atoms, 49 bonds, 5 residues, 1 model selected 
    18707 
    18708 > select #1/R:103,151-152,155-156,185
    18709 
    18710 58 atoms, 56 bonds, 6 residues, 1 model selected 
    18711 
    18712 > select #1/R:103,151-152,155-156,185,250
    18713 
    18714 69 atoms, 67 bonds, 7 residues, 1 model selected 
    18715 
    18716 > select #1/R:103,151-152,155-156,185,250,254
    18717 
    18718 80 atoms, 78 bonds, 8 residues, 1 model selected 
    18719 
    18720 > name frozen 1_hydrophobic_cleft sel
    18721 
    18722 Not registering illegal selector name "1_hydrophobic_cleft" 
    18723 
    18724 > show sel atoms
    18725 
    18726 > style sel stick
    18727 
    18728 Changed 80 atom styles 
    18729 
    18730 > color sel byhetero
    18731 
    18732 > select clear
    18733 
    18734 > select #1/R:18
    18735 
    18736 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18737 
    18738 > select #1/R:18
    18739 
    18740 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18741 
    18742 > select #1/R:18,75
    18743 
    18744 22 atoms, 20 bonds, 2 residues, 1 model selected 
    18745 
    18746 > select #1/R:18,75,79
    18747 
    18748 34 atoms, 32 bonds, 3 residues, 1 model selected 
    18749 
    18750 > select #1/R:18,75,79,98
    18751 
    18752 43 atoms, 40 bonds, 4 residues, 1 model selected 
    18753 
    18754 > select #1/R:18,75,79,98-99
    18755 
    18756 55 atoms, 53 bonds, 5 residues, 1 model selected 
    18757 
    18758 > select #1/R:18,75,79,98-99,156
    18759 
    18760 66 atoms, 63 bonds, 6 residues, 1 model selected 
    18761 
    18762 > select #1/R:18,75,79,98-99,156,246
    18763 
    18764 78 atoms, 75 bonds, 7 residues, 1 model selected 
    18765 
    18766 > select #1/R:18,75,79,98-99,156,246,257
    18767 
    18768 87 atoms, 83 bonds, 8 residues, 1 model selected 
    18769 
    18770 > name frozen 1_head_interact sel
    18771 
    18772 Not registering illegal selector name "1_head_interact" 
    18773 
    18774 > show sel atoms
    18775 
    18776 > style sel stick
    18777 
    18778 Changed 87 atom styles 
    18779 
    18780 > color sel byhetero
    18781 
    18782 > select clear
    18783 
    18784 > select #1/R:18,75,79,98-99,156,246,257-258
    18785 
    18786 93 atoms, 89 bonds, 9 residues, 1 model selected 
    18787 
    18788 > select #1/R:18,75,79,98-99,156,246,257-258
    18789 
    18790 93 atoms, 89 bonds, 9 residues, 1 model selected 
    18791 
    18792 > select #1/R:18,75,79,98-99,156,246,257-258
    18793 
    18794 93 atoms, 89 bonds, 9 residues, 1 model selected 
    18795 
    18796 > select #1/R:18,75,79,98-99,156,246,256-259
    18797 
    18798 108 atoms, 104 bonds, 11 residues, 1 model selected 
    18799 
    18800 > select #1/R:18,75,79,98-99,156,246,256-259
    18801 
    18802 108 atoms, 104 bonds, 11 residues, 1 model selected 
    18803 
    18804 > select #1/R:18
    18805 
    18806 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18807 
    18808 > select #1/R:18
    18809 
    18810 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18811 
    18812 > select #1/R:18,75
    18813 
    18814 22 atoms, 20 bonds, 2 residues, 1 model selected 
    18815 
    18816 > select #1/R:18,75,79
    18817 
    18818 34 atoms, 32 bonds, 3 residues, 1 model selected 
    18819 
    18820 > select #1/R:18,75,79,98
    18821 
    18822 43 atoms, 40 bonds, 4 residues, 1 model selected 
    18823 
    18824 > select #1/R:18,75,79,98-99
    18825 
    18826 55 atoms, 53 bonds, 5 residues, 1 model selected 
    18827 
    18828 > select #1/R:18,75,79,98-99,156
    18829 
    18830 66 atoms, 63 bonds, 6 residues, 1 model selected 
    18831 
    18832 > select #1/R:18,75,79,98-99,156,246
    18833 
    18834 78 atoms, 75 bonds, 7 residues, 1 model selected 
    18835 
    18836 > select #1/R:18,75,79,98-99,156,246,257
    18837 
    18838 87 atoms, 83 bonds, 8 residues, 1 model selected 
    18839 
    18840 > name frozen head_interact_1 sel
    18841 
    18842 > hide sel atoms
    18843 
    18844 > select clear
    18845 
    18846 > select #1/R:154
    18847 
    18848 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18849 
    18850 > select clear
    18851 
    18852 > select #1/R:155
    18853 
    18854 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18855 
    18856 > select add #1/R:151
    18857 
    18858 16 atoms, 14 bonds, 2 residues, 1 model selected 
    18859 
    18860 > select add #1/R:185
    18861 
    18862 24 atoms, 21 bonds, 3 residues, 1 model selected 
    18863 
    18864 > select add #1/R:152
    18865 
    18866 35 atoms, 32 bonds, 4 residues, 1 model selected 
    18867 
    18868 > select add #1/R:254
    18869 
    18870 46 atoms, 43 bonds, 5 residues, 1 model selected 
    18871 
    18872 > select add #1/R:250
    18873 
    18874 57 atoms, 54 bonds, 6 residues, 1 model selected 
    18875 
    18876 > select add #1/R:103
    18877 
    18878 69 atoms, 66 bonds, 7 residues, 1 model selected 
    18879 
    18880 > name frozen tail_interact_1 sel
    18881 
    18882 > select clear
    18883 
    18884 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    18885 > chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_tail.png" width
    18886 > 2000 height 1253 supersample 3 transparentBackground true
    18887 
    18888 > select head_interact_1
    18889 
    18890 87 atoms, 83 bonds, 8 residues, 1 model selected 
    18891 
    18892 > hide sel atoms
    18893 
    18894 > select tail_interact_1
    18895 
    18896 69 atoms, 67 bonds, 7 residues, 1 model selected 
    18897 
    18898 > hide sel atoms
    18899 
    18900 > select head_interact_1
    18901 
    18902 87 atoms, 83 bonds, 8 residues, 1 model selected 
    18903 
    18904 > show sel atoms
    18905 
    18906 > select clear
    18907 
    18908 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    18909 > chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_head.png" width
    18910 > 2000 height 1253 supersample 3 transparentBackground true
    18911 
    18912 > show #!2 models
    18913 
    18914 > hide #!1 models
    18915 
    18916 > hide #!6 models
    18917 
    18918 > show #!9 models
    18919 
    18920 > hide #!2 models
    18921 
    18922 > show #!10 models
    18923 
    18924 > hide #!10 models
    18925 
    18926 > show #!5 models
    18927 
    18928 > hide #!5 models
    18929 
    18930 > show #!7 models
    18931 
    18932 > ui tool show "Show Sequence Viewer"
    18933 
    18934 > sequence chain #7/R
    18935 
    18936 Alignment identifier is 7/R 
    18937 
    18938 > select #7/R:103
    18939 
    18940 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18941 
    18942 > select #7/R:103
    18943 
    18944 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18945 
    18946 > select #7/R:103,151
    18947 
    18948 20 atoms, 19 bonds, 2 residues, 1 model selected 
    18949 
    18950 > select #7/R:103,151-153
    18951 
    18952 38 atoms, 39 bonds, 4 residues, 1 model selected 
    18953 
    18954 > select #7/R:103
    18955 
    18956 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18957 
    18958 > select #7/R:103
    18959 
    18960 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18961 
    18962 > select #7/R:152
    18963 
    18964 11 atoms, 11 bonds, 1 residue, 1 model selected 
    18965 
    18966 > select #7/R:151-152
    18967 
    18968 19 atoms, 19 bonds, 2 residues, 1 model selected 
    18969 
    18970 > select #7/R:103,151-152
    18971 
    18972 31 atoms, 31 bonds, 3 residues, 1 model selected 
    18973 
    18974 > select #7/R:103,151-152,185
    18975 
    18976 39 atoms, 38 bonds, 4 residues, 1 model selected 
    18977 
    18978 > select #7/R:103,151-152,185,250
    18979 
    18980 50 atoms, 49 bonds, 5 residues, 1 model selected 
    18981 
    18982 > select #7/R:103,151-152,185,250,254
    18983 
    18984 61 atoms, 60 bonds, 6 residues, 1 model selected 
    18985 
    18986 > select #7/R:103,151-152,155,185,250,254
    18987 
    18988 69 atoms, 67 bonds, 7 residues, 1 model selected 
    18989 
    18990 > name frozen tail_interact_2 sel
    18991 
    18992 > show sel atoms
    18993 
    18994 > style sel stick
    18995 
    18996 Changed 69 atom styles 
    18997 
    18998 > color sel byhetero
    18999 
    19000 > select clear
    19001 
    19002 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19003 > chimera files and png files/Figure 4/Figure4D_GPR174_8izb_tail.png" width
    19004 > 2000 height 1253 supersample 3 transparentBackground true
    19005 
    19006 > select tail_interact_2
    19007 
    19008 69 atoms, 67 bonds, 7 residues, 1 model selected 
    19009 
    19010 > hide sel atoms
    19011 
    19012 > select clear
    19013 
    19014 > select #7/R:18
    19015 
    19016 11 atoms, 10 bonds, 1 residue, 1 model selected 
    19017 
    19018 > select #7/R:18
    19019 
    19020 11 atoms, 10 bonds, 1 residue, 1 model selected 
    19021 
    19022 > select #7/R:18,75
    19023 
    19024 22 atoms, 20 bonds, 2 residues, 1 model selected 
    19025 
    19026 > select #7/R:18,75,79
    19027 
    19028 34 atoms, 32 bonds, 3 residues, 1 model selected 
    19029 
    19030 > select #7/R:18,75,79,98
    19031 
    19032 43 atoms, 40 bonds, 4 residues, 1 model selected 
    19033 
    19034 > select #7/R:18,75,79,98-99
    19035 
    19036 55 atoms, 53 bonds, 5 residues, 1 model selected 
    19037 
    19038 > select #7/R:18,75,79,98-99,156
    19039 
    19040 66 atoms, 63 bonds, 6 residues, 1 model selected 
    19041 
    19042 > select #7/R:18,75,79,98-99,156,246
    19043 
    19044 78 atoms, 75 bonds, 7 residues, 1 model selected 
    19045 
    19046 > select #7/R:18,75,79,98-99,156,246,257
    19047 
    19048 87 atoms, 83 bonds, 8 residues, 1 model selected 
    19049 
    19050 > name frozen head_interact_2 sel
    19051 
    19052 > show sel atoms
    19053 
    19054 > style sel stick
    19055 
    19056 Changed 87 atom styles 
    19057 
    19058 > color sel byhetero
    19059 
    19060 > select clear
    19061 
    19062 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19063 > chimera files and png files/Figure 4/Figure4D_GPR174_8izb_head.png" width
    19064 > 2000 height 1253 supersample 3 transparentBackground true
    19065 
    19066 > select clear
    19067 
    19068 > select #7/R:103
    19069 
    19070 12 atoms, 12 bonds, 1 residue, 1 model selected 
    19071 
    19072 > select #7/R:103
    19073 
    19074 12 atoms, 12 bonds, 1 residue, 1 model selected 
    19075 
    19076 > show sel atoms
    19077 
    19078 > style sel stick
    19079 
    19080 Changed 12 atom styles 
    19081 
    19082 > ui tool show H-Bonds
    19083 
    19084 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    19085 > false intraRes false select true reveal true log true
    19086    
    19087    
    19088     Finding intramodel H-bonds
    19089     Constraints relaxed by 0.4 angstroms and 20 degrees
    19090     Models used:
    19091         7 8izb
    19092    
    19093     0 H-bonds
    19094     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    19095    
    19096 
    19097  
    19098 0 hydrogen bonds found 
    19099 
    19100 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    19101 > false intraRes false select true reveal true log true
    19102 
    19103 Atom specifier selects no atoms 
    19104 
    19105 > select clear
    19106 
    19107 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19108 > chimera files and png files/Figure 4/Figure4D_GPR174_8izb_head.png" width
    19109 > 2000 height 1253 supersample 3 transparentBackground true
    19110 
    19111 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19112 > chimera files and png files/Figure 4/Figure4D_174_v2.cxs"
    19113 
    19114 > hide #!9 models
    19115 
    19116 > show #!9 models
    19117 
    19118 > ui mousemode right "map eraser"
    19119 
    19120 > volume erase #9 center 103.31,102.34,56.196 radius 2.9422
    19121 
    19122 > ui mousemode right select
    19123 
    19124 > hide #!9 models
    19125 
    19126 > show #!9 models
    19127 
    19128 > save /Users/dongju/Desktop/image1.png supersample 3
    19129 
    19130 > hide #!9 models
    19131 
    19132 > show #!9 models
    19133 
    19134 > select tail_interact_2
    19135 
    19136 69 atoms, 67 bonds, 7 residues, 1 model selected 
    19137 
    19138 > show sel atoms
    19139 
    19140 > select tail_interact_2
    19141 
    19142 69 atoms, 67 bonds, 7 residues, 1 model selected 
    19143 
    19144 > select head_interact_2
    19145 
    19146 87 atoms, 83 bonds, 8 residues, 1 model selected 
    19147 
    19148 > hide sel atoms
    19149 
    19150 > select clear
    19151 
    19152 > select head_interact_2
    19153 
    19154 87 atoms, 83 bonds, 8 residues, 1 model selected 
    19155 
    19156 > show sel atoms
    19157 
    19158 > show #!1 models
    19159 
    19160 > hide #!7 models
    19161 
    19162 > hide #!9 models
    19163 
    19164 > select tail_interact_1
    19165 
    19166 69 atoms, 67 bonds, 7 residues, 1 model selected 
    19167 
    19168 > show sel atoms
    19169 
    19170 > select clear
    19171 
    19172 > show #!2 models
    19173 
    19174 > show #!10 models
    19175 
    19176 > hide #!2 models
    19177 
    19178 > show #!7 models
    19179 
    19180 > hide #!10 models
    19181 
    19182 > show #!9 models
    19183 
    19184 > show #!6 models
    19185 
    19186 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19187 > chimera files and png files/Figure 4/Figure4D_174_v3.cxs"
    19188 
    19189 ——— End of log from Fri Jun 14 01:29:38 2024 ———
    19190 
    19191 opened ChimeraX session 
    19192 Showing emd_33479_7XV3.seg - 41 regions, 41 surfaces 
    19193 
    19194 > hide #!9 models
    19195 
    19196 > hide #!7 models
    19197 
    19198 > show #!7 models
    19199 
    19200 > show #!9 models
    19201 
    19202 > hide #!1 models
    19203 
    19204 > hide #!4 models
    19205 
    19206 > hide #!7 models
    19207 
    19208 > show #!7 models
    19209 
    19210 > hide #!6 models
    19211 
    19212 > ui mousemode right select
    19213 
    19214 > select #7/R:501@CAH
    19215 
    19216 1 atom, 1 residue, 1 model selected 
    19217 
    19218 > ui tool show H-Bonds
    19219 
    19220 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    19221 > false intraRes false select true reveal true log true
    19222    
    19223    
    19224     Finding intramodel H-bonds
    19225     Constraints relaxed by 0.4 angstroms and 20 degrees
    19226     Models used:
    19227         7 8izb
    19228    
    19229     0 H-bonds
    19230     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    19231    
    19232 
    19233  
    19234 0 hydrogen bonds found 
    19235 
    19236 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    19237 > false intraRes false select true reveal true log true
    19238 
    19239 Atom specifier selects no atoms 
    19240 
    19241 > cartoon style helix width 1.7 thickness 0.2
    19242 
    19243 > cartoon style helix width 1.5 thickness 0.2
    19244 
    19245 > cartoon style helix width 1.3 thickness 0.2
    19246 
    19247 > select #7/N
    19248 
    19249 973 atoms, 995 bonds, 128 residues, 1 model selected 
    19250 
    19251 > delete atoms sel
    19252 
    19253 > delete bonds sel
    19254 
    19255 > select #7/A
    19256 
    19257 1954 atoms, 1993 bonds, 1 pseudobond, 235 residues, 2 models selected 
    19258 
    19259 > delete atoms (#!7 & sel)
    19260 
    19261 > delete bonds (#!7 & sel)
    19262 
    19263 > select #7/C
    19264 
    19265 436 atoms, 442 bonds, 57 residues, 1 model selected 
    19266 
    19267 > delete atoms sel
    19268 
    19269 > delete bonds sel
    19270 
    19271 > select #7/B
    19272 
    19273 2622 atoms, 2669 bonds, 342 residues, 1 model selected 
    19274 
    19275 > delete atoms sel
    19276 
    19277 > delete bonds sel
    19278 
    19279 > transparency 0 ribbons
    19280 
    19281 > ui tool show "Side View"
    19282 
    19283 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19284 > chimera files and png files/Figure 4/Figure4D_GPR174_8izb_overall_v2.png"
    19285 > width 3000 height 2304 supersample 3 transparentBackground true
    19286 
    19287 > transparency 80 ribbons
    19288 
    19289 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19290 > chimera files and png files/Figure 4/Figure4D_GPR174_8izb_binding_v2.png"
    19291 > width 2000 height 1536 supersample 3 transparentBackground true
    19292 
    19293 > show #!1 models
    19294 
    19295 > show #!6 models
    19296 
    19297 > select ~sel & ##selected
    19298 
    19299 Nothing selected 
    19300 
    19301 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19302 > chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_binding_v2.png"
    19303 > width 2000 height 1536 supersample 3 transparentBackground true
    19304 
    19305 > hide #!1 models
    19306 
    19307 > hide #!6 models
    19308 
    19309 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19310 > chimera files and png files/Figure 4/Figure4D_GPR174_8izb_binding_v2.png"
    19311 > width 2000 height 1536 supersample 3 transparentBackground true
    19312 
    19313 > show #!1 models
    19314 
    19315 > hide #!7 models
    19316 
    19317 > hide #!9 models
    19318 
    19319 > show #!6 models
    19320 
    19321 > transparency 0 ribbons
    19322 
    19323 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19324 > chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_overall_v2.png"
    19325 > width 3000 height 2304 supersample 3 transparentBackground true
    19326 
    19327 [Repeated 1 time(s)]
    19328 
    19329 > show #!7 models
    19330 
    19331 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    19332 > chimera files and png files/Figure 4/Figure4D_174_v3.cxs"
    19333 
    19334 ——— End of log from Sun Jun 16 23:57:53 2024 ———
    19335 
    19336 opened ChimeraX session 
    19337 Showing emd_33479_7XV3.seg - 41 regions, 41 surfaces 
    19338 
    19339 > close session
    19340 
    19341 > open 8X2K
    19342 
    19343 Summary of feedback from opening 8X2K fetched from pdb 
    19344 --- 
    19345 note | Fetching compressed mmCIF 8x2k from http://files.rcsb.org/download/8x2k.cif 
    19346  
    19347 8x2k title: 
    19348 a lipid receptor complex structure [more info...] 
    19349  
    19350 Chain information for 8x2k #1 
    19351 --- 
    19352 Chain | Description | UniProt 
    19353 A | Soluble cytochrome b562,G-protein coupled receptor 3 | C562_ECOLX -105--1, GPR3_HUMAN 1-330 
    19354 B | Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 26-394 
    19355 C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    19356 D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    19357 E | scfv16 |   
    19358  
    19359 Non-standard residues in 8x2k #1 
    19360 --- 
    19361 5YM — (Z)-N-(2-hydroxyethyl)octadec-9-enamide 
    19362  
    19363 
    19364 > select ~sel & ##selected
    19365 
    19366 Nothing selected 
    19367 
    19368 > open 8WW2
    19369 
    19370 Summary of feedback from opening 8WW2 fetched from pdb 
    19371 --- 
    19372 note | Fetching compressed mmCIF 8ww2 from http://files.rcsb.org/download/8ww2.cif 
    19373  
    19374 8ww2 title: 
    19375 GPR3/Gs complex [more info...] 
    19376  
    19377 Chain information for 8ww2 #2 
    19378 --- 
    19379 Chain | Description | UniProt 
    19380 A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |   
    19381 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    19382 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 
    19383 N | Nb35 |   
    19384 R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330 
    19385  
    19386 Non-standard residues in 8ww2 #2 
    19387 --- 
    19388 OLA — oleic acid 
    19389 PLM — palmitic acid 
    19390 Y01 — cholesterol hemisuccinate 
    19391  
    19392 
    19393 > open 8U8F
    19394 
    19395 Summary of feedback from opening 8U8F fetched from pdb 
    19396 --- 
    19397 note | Fetching compressed mmCIF 8u8f from http://files.rcsb.org/download/8u8f.cif 
    19398  
    19399 8u8f title: 
    19400 GPR3 Orphan G-coupled Protein Receptor in complex with Dominant Negative Gs.
    19401 [more info...] 
    19402  
    19403 Chain information for 8u8f #3 
    19404 --- 
    19405 Chain | Description | UniProt 
    19406 A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-394 
    19407 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 
    19408 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 5-62 
    19409 R | G-protein coupled receptor 3 | GPR3_HUMAN 2-330 
    19410  
    19411 Non-standard residues in 8u8f #3 
    19412 --- 
    19413 PLM — palmitic acid 
    19414  
    19415 
    19416 > style stick
    19417 
    19418 Changed 30268 atom styles 
    19419 
    19420 > hide atoms
    19421 
    19422 > show cartoons
    19423 
    19424 > ui tool show Matchmaker
    19425 
    19426 > matchmaker #!2-3 to #1
    19427 
    19428 Parameters 
    19429 --- 
    19430 Chain pairing | bb 
    19431 Alignment algorithm | Needleman-Wunsch 
    19432 Similarity matrix | BLOSUM-62 
    19433 SS fraction | 0.3 
    19434 Gap open (HH/SS/other) | 18/18/6 
    19435 Gap extend | 1 
    19436 SS matrix |  |  | H | S | O 
    19437 ---|---|---|--- 
    19438 H | 6 | -9 | -6 
    19439 S |  | 6 | -6 
    19440 O |  |  | 4 
    19441 Iteration cutoff | 2 
    19442  
    19443 Matchmaker 8x2k, chain C (#1) with 8ww2, chain B (#2), sequence alignment
    19444 score = 1641.5 
    19445 RMSD between 337 pruned atom pairs is 0.626 angstroms; (across all 338 pairs:
    19446 0.643) 
    19447  
    19448 Matchmaker 8x2k, chain C (#1) with 8u8f, chain B (#3), sequence alignment
    19449 score = 1614.3 
    19450 RMSD between 336 pruned atom pairs is 0.784 angstroms; (across all 337 pairs:
    19451 0.791) 
    19452  
    19453 
    19454 > matchmaker #!2-3 to #1
    19455 
    19456 Parameters 
    19457 --- 
    19458 Chain pairing | bb 
    19459 Alignment algorithm | Needleman-Wunsch 
    19460 Similarity matrix | BLOSUM-62 
    19461 SS fraction | 0.3 
    19462 Gap open (HH/SS/other) | 18/18/6 
    19463 Gap extend | 1 
    19464 SS matrix |  |  | H | S | O 
    19465 ---|---|---|--- 
    19466 H | 6 | -9 | -6 
    19467 S |  | 6 | -6 
    19468 O |  |  | 4 
    19469 Iteration cutoff | 2 
    19470  
    19471 Matchmaker 8x2k, chain C (#1) with 8ww2, chain B (#2), sequence alignment
    19472 score = 1641.5 
    19473 RMSD between 337 pruned atom pairs is 0.626 angstroms; (across all 338 pairs:
    19474 0.643) 
    19475  
    19476 Matchmaker 8x2k, chain C (#1) with 8u8f, chain B (#3), sequence alignment
    19477 score = 1614.3 
    19478 RMSD between 336 pruned atom pairs is 0.784 angstroms; (across all 337 pairs:
    19479 0.791) 
    19480  
    19481 
    19482 > select ligand
    19483 
    19484 143 atoms, 142 bonds, 5 residues, 3 models selected 
    19485 
    19486 > show sel atoms
    19487 
    19488 > select clear
    19489 
    19490 [Repeated 2 time(s)]
    19491 
    19492 > hide #!3 models
    19493 
    19494 > hide #!2 models
    19495 
    19496 > show #!2 models
    19497 
    19498 > hide #!1 models
    19499 
    19500 > show #!3 models
    19501 
    19502 > hide #!2 models
    19503 
    19504 > hide #!3 models
    19505 
    19506 > show #!2 models
    19507 
    19508 > show #!1 models
    19509 
    19510 > hide #!2 models
    19511 
    19512 > show #!3 models
    19513 
    19514 > hide #!1 models
    19515 
    19516 > hide #!3 models
    19517 
    19518 > show #!1 models
    19519 
    19520 > show #!2 models
    19521 
    19522 > show #!3 models
    19523 
    19524 > color #1 #fff39bff
    19525 
    19526 > color #1 #b2ffa8ff
    19527 
    19528 > color #2 #edba84ff
    19529 
    19530 > color #2 #edd86aff
    19531 
    19532 > color #2 #6bacedff
    19533 
    19534 > color #3 #e581a5ff
    19535 
    19536 > color #3 #e5728bff
    19537 
    19538 > select ligand
    19539 
    19540 143 atoms, 142 bonds, 5 residues, 3 models selected 
    19541 
    19542 > color sel byhetero
    19543 
    19544 > select clear
    19545 
    19546 > cartoon style helix width 1.4 thickness 0.2
    19547 
    19548 > cartoon style helix width 1.4 thickness 0.4
    19549 
    19550 > select #1/D#2/G#3/G
    19551 
    19552 1721 atoms, 1739 bonds, 169 residues, 3 models selected 
    19553 
    19554 > delete atoms sel
    19555 
    19556 > delete bonds sel
    19557 
    19558 > select #1/C#2/B#3/B
    19559 
    19560 10266 atoms, 10407 bonds, 1016 residues, 3 models selected 
    19561 
    19562 > delete atoms sel
    19563 
    19564 > delete bonds sel
    19565 
    19566 > select #2/A#3/A
    19567 
    19568 5608 atoms, 5678 bonds, 4 pseudobonds, 460 residues, 4 models selected 
    19569 
    19570 > delete atoms (#!2-3 & sel)
    19571 
    19572 > delete bonds (#!2-3 & sel)
    19573 
    19574 > select #1/B
    19575 
    19576 1795 atoms, 1828 bonds, 4 pseudobonds, 218 residues, 2 models selected 
    19577 
    19578 > delete atoms (#!1 & sel)
    19579 
    19580 > delete bonds (#!1 & sel)
    19581 
    19582 > select #1/E
    19583 
    19584 1803 atoms, 1849 bonds, 1 pseudobond, 236 residues, 2 models selected 
    19585 
    19586 > delete atoms (#!1 & sel)
    19587 
    19588 > delete bonds (#!1 & sel)
    19589 
    19590 > select #2/N
    19591 
    19592 965 atoms, 987 bonds, 128 residues, 1 model selected 
    19593 
    19594 > delete atoms sel
    19595 
    19596 > delete bonds sel
    19597 
    19598 > select clear
    19599 
    19600 [Repeated 1 time(s)]
    19601 
    19602 > ui tool show Matchmaker
    19603 
    19604 > matchmaker #!2-3 to #1
    19605 
    19606 Parameters 
    19607 --- 
    19608 Chain pairing | bb 
    19609 Alignment algorithm | Needleman-Wunsch 
    19610 Similarity matrix | BLOSUM-62 
    19611 SS fraction | 0.3 
    19612 Gap open (HH/SS/other) | 18/18/6 
    19613 Gap extend | 1 
    19614 SS matrix |  |  | H | S | O 
    19615 ---|---|---|--- 
    19616 H | 6 | -9 | -6 
    19617 S |  | 6 | -6 
    19618 O |  |  | 4 
    19619 Iteration cutoff | 2 
    19620  
    19621 Matchmaker 8x2k, chain A (#1) with 8ww2, chain R (#2), sequence alignment
    19622 score = 1513.5 
    19623 RMSD between 254 pruned atom pairs is 0.631 angstroms; (across all 260 pairs:
    19624 0.821) 
    19625  
    19626 Matchmaker 8x2k, chain A (#1) with 8u8f, chain R (#3), sequence alignment
    19627 score = 1558.7 
    19628 RMSD between 251 pruned atom pairs is 0.795 angstroms; (across all 259 pairs:
    19629 0.961) 
    19630  
    19631 
    19632 > matchmaker #!2-3 to #1
    19633 
    19634 Parameters 
    19635 --- 
    19636 Chain pairing | bb 
    19637 Alignment algorithm | Needleman-Wunsch 
    19638 Similarity matrix | BLOSUM-62 
    19639 SS fraction | 0.3 
    19640 Gap open (HH/SS/other) | 18/18/6 
    19641 Gap extend | 1 
    19642 SS matrix |  |  | H | S | O 
    19643 ---|---|---|--- 
    19644 H | 6 | -9 | -6 
    19645 S |  | 6 | -6 
    19646 O |  |  | 4 
    19647 Iteration cutoff | 2 
    19648  
    19649 Matchmaker 8x2k, chain A (#1) with 8ww2, chain R (#2), sequence alignment
    19650 score = 1513.5 
    19651 RMSD between 254 pruned atom pairs is 0.631 angstroms; (across all 260 pairs:
    19652 0.821) 
    19653  
    19654 Matchmaker 8x2k, chain A (#1) with 8u8f, chain R (#3), sequence alignment
    19655 score = 1558.7 
    19656 RMSD between 251 pruned atom pairs is 0.795 angstroms; (across all 259 pairs:
    19657 0.961) 
    19658  
    19659 
    19660 > color #3 #eca5acff
    19661 
    19662 > color #3 #ec626dff
    19663 
    19664 > color #2 #4a8ff1ff
    19665 
    19666 > color #2 #4c86f1ff
    19667 
    19668 > color #2 #f1c847ff
    19669 
    19670 > color #2 #38a8f1ff
    19671 
    19672 > color #1 #fce991ff
    19673 
    19674 > select clear
    19675 
    19676 > select ligand
    19677 
    19678 143 atoms, 142 bonds, 5 residues, 3 models selected 
    19679 
    19680 > color sel byhetero
    19681 
    19682 > select clear
    19683 
    19684 > select ligand
    19685 
    19686 143 atoms, 142 bonds, 5 residues, 3 models selected 
    19687 
    19688 > select add #2
    19689 
    19690 2118 atoms, 2158 bonds, 1 pseudobond, 275 residues, 4 models selected 
    19691 
    19692 > select subtract #2
    19693 
    19694 70 atoms, 68 bonds, 2 residues, 2 models selected 
    19695 
    19696 > select add #3
    19697 
    19698 4164 atoms, 4209 bonds, 1 pseudobond, 267 residues, 3 models selected 
    19699 
    19700 > select subtract #3
    19701 
    19702 23 atoms, 22 bonds, 1 residue, 1 model selected 
    19703 
    19704 > color sel medium blue
    19705 
    19706 > color sel byhetero
    19707 
    19708 > color sel dim gray
    19709 
    19710 > color sel byhetero
    19711 
    19712 > select clear
    19713 
    19714 > select ligand
    19715 
    19716 143 atoms, 142 bonds, 5 residues, 3 models selected 
    19717 
    19718 > select add #1
    19719 
    19720 2041 atoms, 2076 bonds, 1 pseudobond, 267 residues, 4 models selected 
    19721 
    19722 > select subtract #1
    19723 
    19724 120 atoms, 120 bonds, 4 residues, 2 models selected 
    19725 
    19726 > select add #3
    19727 
    19728 4214 atoms, 4261 bonds, 1 pseudobond, 269 residues, 3 models selected 
    19729 
    19730 > select subtract #3
    19731 
    19732 73 atoms, 74 bonds, 3 residues, 1 model selected 
    19733 
    19734 > color sel orange
    19735 
    19736 > color sel byhetero
    19737 
    19738 > select clear
    19739 
    19740 > select ligand
    19741 
    19742 143 atoms, 142 bonds, 5 residues, 3 models selected 
    19743 
    19744 > select add #1
    19745 
    19746 2041 atoms, 2076 bonds, 1 pseudobond, 267 residues, 4 models selected 
    19747 
    19748 > select subtract #1
    19749 
    19750 120 atoms, 120 bonds, 4 residues, 2 models selected 
    19751 
    19752 > select add #2
    19753 
    19754 2095 atoms, 2136 bonds, 1 pseudobond, 274 residues, 3 models selected 
    19755 
    19756 > select subtract #2
    19757 
    19758 47 atoms, 46 bonds, 1 residue, 1 model selected 
    19759 
    19760 > color sel #fc6739ff
    19761 
    19762 > color sel #fc6336ff
    19763 
    19764 > color sel #fc6134ff
    19765 
    19766 > color sel #fc5f32ff
    19767 
    19768 > color sel #fc5529ff
    19769 
    19770 > color sel #fc5328ff
    19771 
    19772 > color sel #fc5227ff
    19773 
    19774 > color sel #fc4f25ff
    19775 
    19776 > color sel #fc4e24ff
    19777 
    19778 > color sel #fc4d23ff
    19779 
    19780 > color sel #fc4b1fff
    19781 
    19782 > color sel #fc4a1eff
    19783 
    19784 > color sel #fc4a1dff
    19785 
    19786 [Repeated 1 time(s)]
    19787 
    19788 > color sel #fc4a1cff
    19789 
    19790 > color sel #fc4a1bff
    19791 
    19792 > color sel #fc4919ff
    19793 
    19794 > color sel #fc4917ff
    19795 
    19796 > color sel #fc4812ff
    19797 
    19798 > color sel #fc4811ff
    19799 
    19800 > color sel #fc470fff
    19801 
    19802 > color sel #fc460eff
    19803 
    19804 > color sel #fc440bff
    19805 
    19806 > color sel #fc4309ff
    19807 
    19808 > color sel #fc4208ff
    19809 
    19810 > color sel #fc3f04ff
    19811 
    19812 > color sel #fc3e03ff
    19813 
    19814 > color sel #fc3d02ff
    19815 
    19816 [Repeated 2 time(s)]
    19817 
    19818 > color sel #fc3c02ff
    19819 
    19820 > color sel #fc3901ff
    19821 
    19822 > color sel #fc3801ff
    19823 
    19824 > color sel #fc3702ff
    19825 
    19826 > color sel #fc3602ff
    19827 
    19828 [Repeated 1 time(s)]
    19829 
    19830 > color sel #fc3504ff
    19831 
    19832 > color sel #fc3505ff
    19833 
    19834 > color sel #fc3605ff
    19835 
    19836 > color sel #fc3606ff
    19837 
    19838 > color sel #fc3706ff
    19839 
    19840 > color sel #fc3808ff
    19841 
    19842 > color sel #fc3a0aff
    19843 
    19844 > color sel #fc3d0cff
    19845 
    19846 > color sel #fc3f0eff
    19847 
    19848 > color sel #fc4211ff
    19849 
    19850 > color sel #fc4613ff
    19851 
    19852 > color sel #fc4916ff
    19853 
    19854 > color sel #fc4c19ff
    19855 
    19856 > color sel #fc4e1aff
    19857 
    19858 > color sel #fc501bff
    19859 
    19860 [Repeated 1 time(s)]
    19861 
    19862 > color sel #fc501cff
    19863 
    19864 > color sel #fc511cff
    19865 
    19866 [Repeated 1 time(s)]
    19867 
    19868 > color sel #fc511dff
    19869 
    19870 [Repeated 2 time(s)]
    19871 
    19872 > color sel #fc511eff
    19873 
    19874 [Repeated 1 time(s)]
    19875 
    19876 > color sel #fc511fff
    19877 
    19878 > color sel #fc5323ff
    19879 
    19880 > color sel #fc5424ff
    19881 
    19882 > color sel #fc5426ff
    19883 
    19884 > color sel #fc5528ff
    19885 
    19886 > color sel #fc5629ff
    19887 
    19888 > color sel #fc562aff
    19889 
    19890 > color sel #fc562bff
    19891 
    19892 > color sel #fc562dff
    19893 
    19894 > color sel #fc562eff
    19895 
    19896 > color sel #fc562fff
    19897 
    19898 > color sel #fc552fff
    19899 
    19900 [Repeated 1 time(s)]
    19901 
    19902 > color sel #fc542fff
    19903 
    19904 > color sel #fc532fff
    19905 
    19906 [Repeated 1 time(s)]
    19907 
    19908 > color sel #fc4f30ff
    19909 
    19910 > color sel #fc4e31ff
    19911 
    19912 > color sel #fc4a34ff
    19913 
    19914 > color sel #fc4037ff
    19915 
    19916 > color sel #fc3d38ff
    19917 
    19918 > color sel #fc3b38ff
    19919 
    19920 > color sel #fc3839ff
    19921 
    19922 > color sel #fc3942ff
    19923 
    19924 > color sel #fc3845ff
    19925 
    19926 > color sel #fc3847ff
    19927 
    19928 > color sel #fc3849ff
    19929 
    19930 > color sel #fc384bff
    19931 
    19932 > color sel #fc384dff
    19933 
    19934 > color sel #fc3754ff
    19935 
    19936 > color sel #fc3656ff
    19937 
    19938 > color sel #fc3659ff
    19939 
    19940 > color sel #fc365cff
    19941 
    19942 > color sel #fc355dff
    19943 
    19944 > color sel #fc355fff
    19945 
    19946 > color sel #fc3463ff
    19947 
    19948 > color sel #fc3364ff
    19949 
    19950 > color sel #fc3366ff
    19951 
    19952 > color sel #fc326aff
    19953 
    19954 > color sel #fc326bff
    19955 
    19956 > color sel #fc326dff
    19957 
    19958 > color sel #fc316dff
    19959 
    19960 [Repeated 1 time(s)]
    19961 
    19962 > color sel #fc316eff
    19963 
    19964 > color sel #fc326eff
    19965 
    19966 [Repeated 1 time(s)]
    19967 
    19968 > color sel #fc326fff
    19969 
    19970 [Repeated 1 time(s)]
    19971 
    19972 > color sel #fc3370ff
    19973 
    19974 > color sel #fc3d80ff
    19975 
    19976 > color sel #fc438aff
    19977 
    19978 > color sel #fc4999ff
    19979 
    19980 > color sel #fc4aa1ff
    19981 
    19982 > color sel #fc4aa2ff
    19983 
    19984 > color sel #fc49a5ff
    19985 
    19986 > color sel #fc46afff
    19987 
    19988 > color sel #fc44b3ff
    19989 
    19990 > color sel #fc43b7ff
    19991 
    19992 > color sel #fc3ebfff
    19993 
    19994 > color sel #fc3ec0ff
    19995 
    19996 [Repeated 1 time(s)]
    19997 
    19998 > color sel #fc3dc2ff
    19999 
    20000 [Repeated 1 time(s)]
    20001 
    20002 > color sel #fc3dc3ff
    20003 
    20004 > color sel #fc3dc5ff
    20005 
    20006 > color sel #fc3dc7ff
    20007 
    20008 > color sel #fc3dc9ff
    20009 
    20010 > color sel #fc3dceff
    20011 
    20012 > color sel #fc3ecfff
    20013 
    20014 > color sel #fc3ed1ff
    20015 
    20016 > color sel #fc3fd2ff
    20017 
    20018 > color sel #fc3fd3ff
    20019 
    20020 > color sel #fc40d6ff
    20021 
    20022 > color sel #fc46dfff
    20023 
    20024 > color sel #fc49e5ff
    20025 
    20026 > color sel #fc4debff
    20027 
    20028 > color sel #fc53f6ff
    20029 
    20030 > color sel #fc53f7ff
    20031 
    20032 [Repeated 1 time(s)]
    20033 
    20034 > color sel #fc54f7ff
    20035 
    20036 [Repeated 1 time(s)]
    20037 
    20038 > color sel #fc55efff
    20039 
    20040 > color sel #fc54e9ff
    20041 
    20042 > color sel #fc53e3ff
    20043 
    20044 > color sel #fc51dcff
    20045 
    20046 > color sel #fc50d6ff
    20047 
    20048 > color sel #fc4ed0ff
    20049 
    20050 > color sel #fc4bcaff
    20051 
    20052 > color sel #fc47c3ff
    20053 
    20054 > color sel #fc3dacff
    20055 
    20056 > color sel #fc39a5ff
    20057 
    20058 > color sel #fc349bff
    20059 
    20060 > color sel #fc3193ff
    20061 
    20062 > color sel #fc3091ff
    20063 
    20064 > color sel #fc2e8cff
    20065 
    20066 > color sel #fc2c89ff
    20067 
    20068 > color sel #fc267cff
    20069 
    20070 > color sel #fc2478ff
    20071 
    20072 > color sel #fc2272ff
    20073 
    20074 > color sel #fc2171ff
    20075 
    20076 > color sel #fc2373ff
    20077 
    20078 > color sel #fc2776ff
    20079 
    20080 > color sel #fc3988ff
    20081 
    20082 > color sel #fc66b8ff
    20083 
    20084 > color sel #fc95f0ff
    20085 
    20086 > color sel #d6a9fcff
    20087 
    20088 > color sel #cea9fcff
    20089 
    20090 > color sel #caa8fcff
    20091 
    20092 > color sel #c5a7fcff
    20093 
    20094 > color sel #c0a6fcff
    20095 
    20096 > color sel #b7a4fcff
    20097 
    20098 > color sel #9999fcff
    20099 
    20100 > color sel #959bfcff
    20101 
    20102 > color sel #919cfcff
    20103 
    20104 > color sel #869efcff
    20105 
    20106 > color sel #859efcff
    20107 
    20108 [Repeated 1 time(s)]
    20109 
    20110 > color sel #859ffcff
    20111 
    20112 > color sel #829ffcff
    20113 
    20114 > color sel #78a0fcff
    20115 
    20116 > color sel #719ffcff
    20117 
    20118 > color sel #619efcff
    20119 
    20120 > color sel #499dfcff
    20121 
    20122 > color sel #469cfcff
    20123 
    20124 > color sel #439cfcff
    20125 
    20126 > color sel #3b9bfcff
    20127 
    20128 > color sel #399bfcff
    20129 
    20130 > color sel #389bfcff
    20131 
    20132 [Repeated 2 time(s)]
    20133 
    20134 > color sel #389cfcff
    20135 
    20136 > color sel #3fabfcff
    20137 
    20138 > color sel #43b6fcff
    20139 
    20140 > color sel #48d4fcff
    20141 
    20142 > color sel #48dafcff
    20143 
    20144 > color sel #48defcff
    20145 
    20146 > color sel #47e1fcff
    20147 
    20148 > color sel #47e4fcff
    20149 
    20150 > color sel #47e5fcff
    20151 
    20152 > color sel #46e8fcff
    20153 
    20154 > color sel #46eafcff
    20155 
    20156 > color sel #45ecfcff
    20157 
    20158 > color sel #44f9fcff
    20159 
    20160 > color sel #43fcfcff
    20161 
    20162 > color sel #43fcfaff
    20163 
    20164 > color sel #42fcf5ff
    20165 
    20166 > color sel #42fcf4ff
    20167 
    20168 > color sel #42fcf2ff
    20169 
    20170 > color sel #4efce4ff
    20171 
    20172 > color sel #56fcddff
    20173 
    20174 > color sel #5efcd5ff
    20175 
    20176 > color sel #67fccdff
    20177 
    20178 > color sel #6efcc4ff
    20179 
    20180 > color sel #72fcbbff
    20181 
    20182 > color sel #7cfca1ff
    20183 
    20184 > color sel #7dfc9aff
    20185 
    20186 > color sel #7cfc83ff
    20187 
    20188 > color sel #78fc79ff
    20189 
    20190 > color sel #76fc75ff
    20191 
    20192 > color sel #75fc73ff
    20193 
    20194 > color sel #71fc67ff
    20195 
    20196 > color sel #70fc66ff
    20197 
    20198 > color sel #70fc65ff
    20199 
    20200 > color sel #70fc64ff
    20201 
    20202 > color sel #6efc62ff
    20203 
    20204 > color sel #6efc61ff
    20205 
    20206 > color sel #6dfc5fff
    20207 
    20208 > color sel #6dfc5dff
    20209 
    20210 > color sel #6bfc58ff
    20211 
    20212 > color sel #6bfc57ff
    20213 
    20214 > color sel #6bfc56ff
    20215 
    20216 > color sel #6cfc56ff
    20217 
    20218 [Repeated 1 time(s)]
    20219 
    20220 > color sel #6dfc55ff
    20221 
    20222 [Repeated 2 time(s)]
    20223 
    20224 > color sel #6ffc54ff
    20225 
    20226 [Repeated 1 time(s)]
    20227 
    20228 > color sel #70fc54ff
    20229 
    20230 > color sel #70fc53ff
    20231 
    20232 > color sel #71fc53ff
    20233 
    20234 > color sel #72fc53ff
    20235 
    20236 > color sel #74fc52ff
    20237 
    20238 > color sel #75fc51ff
    20239 
    20240 [Repeated 1 time(s)]
    20241 
    20242 > color sel #75fc50ff
    20243 
    20244 > color sel #6cfc49ff
    20245 
    20246 > color sel #68fc47ff
    20247 
    20248 > color sel #63fc44ff
    20249 
    20250 > color sel #5ffc42ff
    20251 
    20252 > color sel #57fc3dff
    20253 
    20254 > color sel #54fc3cff
    20255 
    20256 > color sel #51fc3bff
    20257 
    20258 > color sel #4efc3aff
    20259 
    20260 > color sel #4bfc39ff
    20261 
    20262 > color sel #47fc38ff
    20263 
    20264 > color sel #40fc35ff
    20265 
    20266 > color sel #3ffc35ff
    20267 
    20268 > color sel #3dfc35ff
    20269 
    20270 > color sel #39fc33ff
    20271 
    20272 [Repeated 1 time(s)]
    20273 
    20274 > color sel #39fb33ff
    20275 
    20276 > color sel #33e22eff
    20277 
    20278 > color sel #30d72cff
    20279 
    20280 > color sel #2fcf2aff
    20281 
    20282 > color sel #2dc829ff
    20283 
    20284 > color sel #2cc428ff
    20285 
    20286 > color sel #2cc328ff
    20287 
    20288 > color sel #2bc127ff
    20289 
    20290 > color sel #2bc027ff
    20291 
    20292 [Repeated 1 time(s)]
    20293 
    20294 > color sel #2bbf27ff
    20295 
    20296 > color sel #28b224ff
    20297 
    20298 > color sel #27ad23ff
    20299 
    20300 > color sel #26ab23ff
    20301 
    20302 > color sel #26aa23ff
    20303 
    20304 > color sel #26a922ff
    20305 
    20306 > color sel #26a722ff
    20307 
    20308 [Repeated 1 time(s)]
    20309 
    20310 > color sel byhetero
    20311 
    20312 > select clear
    20313 
    20314 > select ligand
    20315 
    20316 143 atoms, 142 bonds, 5 residues, 3 models selected 
    20317 
    20318 > select add #1
    20319 
    20320 2041 atoms, 2076 bonds, 1 pseudobond, 267 residues, 4 models selected 
    20321 
    20322 > select subtract #1
    20323 
    20324 120 atoms, 120 bonds, 4 residues, 2 models selected 
    20325 
    20326 > select add #2
    20327 
    20328 2095 atoms, 2136 bonds, 1 pseudobond, 274 residues, 3 models selected 
    20329 
    20330 > select subtract #2
    20331 
    20332 47 atoms, 46 bonds, 1 residue, 1 model selected 
    20333 
    20334 > select H
    20335 
    20336 2121 atoms, 266 residues, 1 model selected 
    20337 
    20338 > hide sel atoms
    20339 
    20340 > select clear
    20341 
    20342 > select ::name="HOH"
    20343 
    20344 4 atoms, 4 residues, 2 models selected 
    20345 
    20346 > show sel atoms
    20347 
    20348 > style sel sphere
    20349 
    20350 Changed 4 atom styles 
    20351 
    20352 > color sel byhetero
    20353 
    20354 > select clear
    20355 
    20356 [Repeated 4 time(s)]
    20357 
    20358 > select HOH
    20359 
    20360 Expected an objects specifier or a keyword 
    20361 
    20362 > select HOH atoms
    20363 
    20364 Expected an objects specifier or a keyword 
    20365 
    20366 > select ::name="HOH"
    20367 
    20368 4 atoms, 4 residues, 2 models selected 
    20369 
    20370 > select add #2
    20371 
    20372 2050 atoms, 2090 bonds, 1 pseudobond, 275 residues, 3 models selected 
    20373 
    20374 > select subtract #2
    20375 
    20376 2 atoms, 2 residues, 1 model selected 
    20377 
    20378 > select ::name="HOH"
    20379 
    20380 4 atoms, 4 residues, 2 models selected 
    20381 
    20382 > ui tool show H-Bonds
    20383 
    20384 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    20385 > false intraRes false select true reveal true log true
    20386    
    20387    
    20388     Finding intramodel H-bonds
    20389     Constraints relaxed by 0.4 angstroms and 20 degrees
    20390     Models used:
    20391         1 8x2k
    20392         2 8ww2
    20393    
    20394     8 H-bonds
    20395     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    20396     8x2k #1/A HOH 501 O   8x2k #1/A TYR 280 OH  no hydrogen  3.217  N/A
    20397     8ww2 #2/R HIS 96 NE2  8ww2 #2/R HOH 701 O   no hydrogen  3.304  N/A
    20398     8ww2 #2/R TYR 280 OH  8ww2 #2/R HOH 702 O   no hydrogen  2.982  N/A
    20399     8ww2 #2/R HOH 701 O   8ww2 #2/R HIS 96 NE2  no hydrogen  3.304  N/A
    20400     8ww2 #2/R HOH 701 O   8ww2 #2/R OLA 601 O2  no hydrogen  2.722  N/A
    20401     8ww2 #2/R HOH 702 O   8ww2 #2/R TYR 280 OH  no hydrogen  2.982  N/A
    20402     8ww2 #2/R HOH 702 O   8ww2 #2/R OLA 601 O1  no hydrogen  2.993  N/A
    20403     8ww2 #2/R HOH 702 O   8ww2 #2/R OLA 601 O2  no hydrogen  3.443  N/A
    20404    
    20405 
    20406  
    20407 8 hydrogen bonds found 
    20408 
    20409 > hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
    20410 > false intraRes false select true reveal true log true
    20411    
    20412    
    20413     Finding intramodel H-bonds
    20414     Constraints relaxed by 0.4 angstroms and 20 degrees
    20415     Models used:
    20416         1 8x2k
    20417         2 8ww2
    20418    
    20419     8 H-bonds
    20420     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    20421     8x2k #1/A HOH 501 O   8x2k #1/A TYR 280 OH  no hydrogen  3.217  N/A
    20422     8ww2 #2/R HIS 96 NE2  8ww2 #2/R HOH 701 O   no hydrogen  3.304  N/A
    20423     8ww2 #2/R TYR 280 OH  8ww2 #2/R HOH 702 O   no hydrogen  2.982  N/A
    20424     8ww2 #2/R HOH 701 O   8ww2 #2/R HIS 96 NE2  no hydrogen  3.304  N/A
    20425     8ww2 #2/R HOH 701 O   8ww2 #2/R OLA 601 O2  no hydrogen  2.722  N/A
    20426     8ww2 #2/R HOH 702 O   8ww2 #2/R TYR 280 OH  no hydrogen  2.982  N/A
    20427     8ww2 #2/R HOH 702 O   8ww2 #2/R OLA 601 O1  no hydrogen  2.993  N/A
    20428     8ww2 #2/R HOH 702 O   8ww2 #2/R OLA 601 O2  no hydrogen  3.443  N/A
    20429    
    20430 
    20431  
    20432 8 hydrogen bonds found 
    20433 
    20434 > select clear
    20435 
    20436 > select ::name="HOH"
    20437 
    20438 4 atoms, 4 residues, 2 models selected 
    20439 
    20440 > style sel ball
    20441 
    20442 Changed 4 atom styles 
    20443 
    20444 > select clear
    20445 
    20446 [Repeated 2 time(s)]
    20447 
    20448 > hide #!2 models
    20449 
    20450 > hide #!3 models
    20451 
    20452 > select clear
    20453 
    20454 > show #!2 models
    20455 
    20456 > hide #!1 models
    20457 
    20458 > show #!1 models
    20459 
    20460 > show #!3 models
    20461 
    20462 > select add #3
    20463 
    20464 4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected 
    20465 
    20466 > select add #2
    20467 
    20468 6189 atoms, 6277 bonds, 9 pseudobonds, 539 residues, 5 models selected 
    20469 
    20470 > select add #1
    20471 
    20472 8110 atoms, 8233 bonds, 11 pseudobonds, 802 residues, 8 models selected 
    20473 
    20474 > select subtract #2
    20475 
    20476 6062 atoms, 6143 bonds, 3 pseudobonds, 529 residues, 5 models selected 
    20477 
    20478 > select subtract #1
    20479 
    20480 4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected 
    20481 
    20482 > select subtract #3
    20483 
    20484 Nothing selected 
    20485 
    20486 > select clear
    20487 
    20488 > open /Users/dongju/Downloads/emd_38015_8X2K.map
    20489 
    20490 Opened emd_38015_8X2K.map as #4, grid size 320,320,320, pixel 0.85, shown at
    20491 level 0.177, step 2, values float32 
    20492 
    20493 > volume #4 level 0.4238
    20494 
    20495 > hide #!2 models
    20496 
    20497 > hide #!3 models
    20498 
    20499 > color #4 #bf8883ff models
    20500 
    20501 > transparency 50
    20502 
    20503 > volume #4 level 0.5886
    20504 
    20505 > volume #4 level 0.465
    20506 
    20507 > fitmap #1 inMap #4
    20508 
    20509 Fit molecule 8x2k (#1) to map emd_38015_8X2K.map (#4) using 1921 atoms 
    20510 average map value = 0.907, steps = 48 
    20511 shifted from previous position = 0.015 
    20512 rotated from previous position = 0.0873 degrees 
    20513 atoms outside contour = 588, contour level = 0.465 
    20514  
    20515 Position of 8x2k (#1) relative to emd_38015_8X2K.map (#4) coordinates: 
    20516 Matrix rotation and translation 
    20517 0.99999891 -0.00055264 0.00136564 -0.14152221 
    20518 0.00055318 0.99999977 -0.00038973 -0.02175877 
    20519 -0.00136542 0.00039048 0.99999899 0.14489849 
    20520 Axis 0.25597560 0.89601911 0.36280330 
    20521 Axis point 106.88170121 0.00000000 103.12500396 
    20522 Rotation angle (degrees) 0.08731843 
    20523 Shift along axis -0.00315286 
    20524  
    20525 
    20526 > volume #4 level 0.3963
    20527 
    20528 > ui mousemode right "map eraser"
    20529 
    20530 > volume erase #4 center 127.51,123.25,165.71 radius 18.278 outside true
    20531 
    20532 Opened emd_38015_8X2K.map copy as #6, grid size 320,320,320, pixel 0.85, shown
    20533 at step 1, values float32 
    20534 
    20535 Window position QRect(1505,961 543x106) outside any known screen, using
    20536 primary screen 
    20537 
    20538 QDockWidget failed to find relevant screen info. screenFrom:
    20539 QScreen(0x600002333a20, name="P24h-2L") screenTo: QScreen(0x600002333a20,
    20540 name="P24h-2L") wdgScreen: QScreen(0x600002333a20, name="P24h-2L")
    20541 orgWdgScreen QScreen(0x0) 
    20542 
    20543 [Repeated 29 time(s)]
    20544 
    20545 > volume erase #6 center 142,114.56,175.19 radius 8.024
    20546 
    20547 > volume erase #6 center 136.19,104.28,165.16 radius 8.024
    20548 
    20549 > volume erase #6 center 128.24,98.937,169.56 radius 8.024
    20550 
    20551 > volume erase #6 center 126.39,104.21,161.15 radius 8.024
    20552 
    20553 > volume erase #6 center 115.72,109.49,164.49 radius 8.024
    20554 
    20555 > volume erase #6 center 132.54,123.1,182.79 radius 8.024
    20556 
    20557 > volume erase #6 center 125.6,122.84,182.82 radius 8.024
    20558 
    20559 > volume erase #6 center 129.85,131.24,173.66 radius 8.024
    20560 
    20561 > volume erase #6 center 112.27,123.76,168.47 radius 8.024
    20562 
    20563 > volume erase #6 center 115.5,115.26,169.04 radius 8.024
    20564 
    20565 > undo
    20566 
    20567 > ui mousemode right "map eraser"
    20568 
    20569 Window position QRect(1505,961 543x106) outside any known screen, using
    20570 primary screen 
    20571 
    20572 QDockWidget failed to find relevant screen info. screenFrom:
    20573 QScreen(0x600002333a20, name="P24h-2L") screenTo: QScreen(0x600002333a20,
    20574 name="P24h-2L") wdgScreen: QScreen(0x600002333a20, name="P24h-2L")
    20575 orgWdgScreen QScreen(0x0) 
    20576 
    20577 [Repeated 31 time(s)]
    20578 
    20579 > volume erase #6 center 116.48,128.87,176.5 radius 9.5658
    20580 
    20581 > volume erase #6 center 123.67,132.4,168.66 radius 9.5658
    20582 
    20583 > volume erase #6 center 123.1,126.91,155.3 radius 9.5658
    20584 
    20585 > volume erase #6 center 125.01,117.12,159.44 radius 9.5658
    20586 
    20587 > volume erase #6 center 136.08,107.51,167.69 radius 9.5658
    20588 
    20589 > volume erase #6 center 123.64,103.8,167.02 radius 9.5658
    20590 
    20591 > volume erase #6 center 136.62,115.75,158.76 radius 9.5658
    20592 
    20593 > hide #!1 cartoons
    20594 
    20595 > volume erase #6 center 130.23,127.73,158.64 radius 9.5658
    20596 
    20597 > volume erase #6 center 131.66,131.14,153.87 radius 9.5658
    20598 
    20599 > volume erase #6 center 140.88,132.78,176.18 radius 9.5658
    20600 
    20601 > volume erase #6 center 142.88,137.99,164.91 radius 9.5658
    20602 
    20603 > volume erase #6 center 129.75,139.75,165.34 radius 9.5658
    20604 
    20605 > volume erase #6 center 128.93,134.45,168.38 radius 9.5658
    20606 
    20607 > volume erase #6 center 134.52,113.7,179.21 radius 9.5658
    20608 
    20609 > volume erase #6 center 132.74,109.33,180.49 radius 9.5658
    20610 
    20611 > volume erase #6 center 132.82,122.81,156.79 radius 9.5658
    20612 
    20613 > volume erase #6 center 122.17,117.24,157.44 radius 9.5658
    20614 
    20615 > volume erase #6 center 120.58,131.5,164.85 radius 9.5658
    20616 
    20617 > volume erase #6 center 115.75,128.65,163.98 radius 9.5658
    20618 
    20619 > volume erase #6 center 139.63,135.19,156.83 radius 9.5658
    20620 
    20621 > volume erase #6 center 136.82,136.03,161.61 radius 9.5658
    20622 
    20623 > volume erase #6 center 135.65,122.9,180.03 radius 9.5658
    20624 
    20625 > volume erase #6 center 127.19,136.49,183.98 radius 9.5658
    20626 
    20627 > volume erase #6 center 126.46,115.47,154.19 radius 9.5658
    20628 
    20629 > volume erase #6 center 141.41,122.41,149.22 radius 9.5658
    20630 
    20631 > volume erase #6 center 140.71,109.81,171.26 radius 9.5658
    20632 
    20633 > volume erase #6 center 131.13,114.42,168.7 radius 3.5872
    20634 
    20635 > volume erase #6 center 129.51,115.56,167.48 radius 3.5872
    20636 
    20637 > volume erase #6 center 143.93,119.91,165 radius 3.5872
    20638 
    20639 > volume erase #6 center 147.72,123.04,164 radius 3.5872
    20640 
    20641 > volume erase #6 center 141.43,120.71,170.51 radius 3.5872
    20642 
    20643 > volume erase #6 center 139.15,121.13,170.31 radius 3.5872
    20644 
    20645 > volume erase #6 center 139.59,120.06,162.9 radius 3.5872
    20646 
    20647 > volume erase #6 center 144.6,126.91,169.16 radius 3.5872
    20648 
    20649 > volume erase #6 center 142.9,123.29,172.77 radius 3.5872
    20650 
    20651 > volume erase #6 center 135.18,116.13,148.01 radius 3.5872
    20652 
    20653 > volume erase #6 center 127.53,122.57,149.89 radius 3.5872
    20654 
    20655 > volume erase #6 center 142.81,125.98,172.3 radius 3.5872
    20656 
    20657 > volume erase #6 center 125.5,111.69,182.44 radius 3.5872
    20658 
    20659 > volume erase #6 center 119.49,113.64,177.23 radius 3.5872
    20660 
    20661 > volume erase #6 center 141.1,118.59,171.25 radius 3.5872
    20662 
    20663 > volume erase #6 center 119.87,112.45,173.34 radius 3.5872
    20664 
    20665 > volume erase #6 center 121.27,112.17,169.3 radius 3.5872
    20666 
    20667 > volume erase #6 center 122.64,117.8,167.35 radius 3.5872
    20668 
    20669 > volume erase #6 center 140.15,123.5,171.95 radius 3.3695
    20670 
    20671 > show #!1 cartoons
    20672 
    20673 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    20674 > chimera files and png files/Figure 4/Figure4F_GPR3.cxs"
    20675 
    20676 > lighting flat
    20677 
    20678 > lighting soft
    20679 
    20680 > lighting shadows true intensity 0.5
    20681 
    20682 > ui mousemode right select
    20683 
    20684 > select clear
    20685 
    20686 [Repeated 2 time(s)]
    20687 
    20688 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    20689 > chimera files and png files/Figure 4/Figure4F_8X2K_overall.png" width 3000
    20690 > height 1903 supersample 3 transparentBackground true
    20691 
    20692 > hide #!1 models
    20693 
    20694 > show #!1 models
    20695 
    20696 > hide #!1 cartoons
    20697 
    20698 > select add #6
    20699 
    20700 2 models selected 
    20701 
    20702 > volume sel style mesh
    20703 
    20704 > select clear
    20705 
    20706 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    20707 > chimera files and png files/Figure 4/Figure4F_8X2K_ligand_mesh.png" width
    20708 > 2000 height 1269 supersample 3 transparentBackground true
    20709 
    20710 > select add #6
    20711 
    20712 2 models selected 
    20713 
    20714 > volume sel style surface
    20715 
    20716 > select clear
    20717 
    20718 > save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
    20719 > chimera files and png files/Figure 4/Figure4F_8X2K_ligand_surface.png" width
    20720 > 2000 height 1269 supersample 3 transparentBackground true
    20721 
    20722 > hide #!1 models
    20723 
    20724 > show #!1 models
    20725 
    20726 > hide #!6 models
    20727 
    20728 > show #!6 models
    20729 
    20730 > select add #1
    20731 
    20732 1921 atoms, 1956 bonds, 2 pseudobonds, 263 residues, 3 models selected 
    20733 
    20734 > show sel cartoons
    20735 
    20736 > select clear
    20737 
    20738 > show #!2 models
    20739 
    20740 > hide #!1 models
    20741 
    20742 > hide #!6 models
    20743 
    20744 > open /Users/dongju/Downloads/emd_37881_8WW2.map
    20745 
    20746 Opened emd_37881_8WW2.map as #5, grid size 256,256,256, pixel 1.1, shown at
    20747 level 0.322, step 1, values float32 
    20748 
    20749 > ui tool show "Volume Viewer"
    20750 
    20751 > volume #5 level 1.109
    20752 
    20753 > ui tool show "Fit in Map"
    20754 
    20755 > fitmap #2 inMap #5
    20756 
    20757 Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms 
    20758 average map value = 0.2273, steps = 108 
    20759 shifted from previous position = 1.3 
    20760 rotated from previous position = 5.34 degrees 
    20761 atoms outside contour = 1882, contour level = 1.1093 
    20762  
    20763 Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates: 
    20764 Matrix rotation and translation 
    20765 0.93399282 0.35338446 0.05269577 -53.98910026 
    20766 -0.25181302 0.75569361 -0.60458033 160.37968845 
    20767 -0.25347115 0.55140420 0.79479921 -8.76457449 
    20768 Axis 0.86250634 0.22843810 -0.45155160 
    20769 Axis point 0.00000000 104.61289764 225.25740459 
    20770 Rotation angle (degrees) 42.07717898 
    20771 Shift along axis -5.97145309 
    20772  
    20773 
    20774 > select add #5
    20775 
    20776 4 models selected 
    20777 
    20778 > ui mousemode right "translate selected models"
    20779 
    20780 > view matrix models #5,1,0,0,-7.105,0,1,0,-3.3134,0,0,1,-1.3607
    20781 
    20782 > ui mousemode right "rotate selected models"
    20783 
    20784 > view matrix models
    20785 > #5,0.95945,0.0019066,-0.28188,36.818,-0.040684,0.99044,-0.13178,21.749,0.27893,0.13791,0.95036,-53.242
    20786 
    20787 > ui mousemode right "translate selected models"
    20788 
    20789 > view matrix models
    20790 > #5,0.95945,0.0019066,-0.28188,42.412,-0.040684,0.99044,-0.13178,24.246,0.27893,0.13791,0.95036,-50.7
    20791 
    20792 > view matrix models
    20793 > #5,0.95945,0.0019066,-0.28188,43.465,-0.040684,0.99044,-0.13178,19.488,0.27893,0.13791,0.95036,-49.071
    20794 
    20795 > ui mousemode right "rotate selected models"
    20796 
    20797 > view matrix models
    20798 > #5,0.94577,0.15382,-0.28611,24.668,-0.20098,0.96905,-0.14337,46.665,0.25521,0.1931,0.94741,-53.064
    20799 
    20800 > view matrix models
    20801 > #5,0.9292,0.10856,-0.35328,42.518,-0.16119,0.97922,-0.12305,36.856,0.33258,0.17128,0.92739,-58.179
    20802 
    20803 > view matrix models
    20804 > #5,0.92379,-0.065525,-0.37724,70.964,-0.13791,0.86218,-0.48747,99.73,0.35719,0.50235,0.78744,-88.974
    20805 
    20806 > view matrix models
    20807 > #5,0.8279,0.50151,-0.25112,-12.256,-0.55781,0.68954,-0.46192,179.64,-0.058502,0.52251,0.85063,-41.831
    20808 
    20809 > view matrix models
    20810 > #5,0.89237,0.36679,-0.26293,-0.83787,-0.44914,0.77876,-0.43797,148.54,0.044116,0.50892,0.85968,-55.627
    20811 
    20812 > view matrix models
    20813 > #5,0.8829,0.3169,-0.3465,18.9,-0.44818,0.78885,-0.42053,144.61,0.14007,0.52658,0.83851,-68.738
    20814 
    20815 > view matrix models
    20816 > #5,0.91961,0.31846,-0.23,-2.3946,-0.39005,0.80976,-0.43835,135.92,0.046645,0.49282,0.86888,-54.981
    20817 
    20818 > view matrix models
    20819 > #5,0.95245,0.15168,-0.26425,21.041,-0.25161,0.88066,-0.40142,101.42,0.17183,0.44882,0.87695,-67.556
    20820 
    20821 > view matrix models
    20822 > #5,0.96202,0.071376,-0.2635,30.853,-0.21539,0.79147,-0.57199,132.1,0.16773,0.60702,0.77678,-75.493
    20823 
    20824 > ui mousemode right "translate selected models"
    20825 
    20826 > view matrix models
    20827 > #5,0.96202,0.071376,-0.2635,30.813,-0.21539,0.79147,-0.57199,138.5,0.16773,0.60702,0.77678,-71.707
    20828 
    20829 > ui mousemode right "rotate selected models"
    20830 
    20831 > view matrix models
    20832 > #5,0.95807,0.19822,-0.20693,5.8585,-0.28402,0.75269,-0.59396,156.61,0.038016,0.62783,0.77743,-56.428
    20833 
    20834 > view matrix models
    20835 > #5,0.94976,0.24396,-0.19605,-0.87055,-0.31295,0.73323,-0.60368,164.74,-0.0035254,0.63471,0.77274,-50.899
    20836 
    20837 > ui mousemode right "translate selected models"
    20838 
    20839 > view matrix models
    20840 > #5,0.94976,0.24396,-0.19605,-1.0075,-0.31295,0.73323,-0.60368,166.12,-0.0035254,0.63471,0.77274,-49.751
    20841 
    20842 > fitmap #2 inMap #5
    20843 
    20844 Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms 
    20845 average map value = 0.329, steps = 76 
    20846 shifted from previous position = 1.39 
    20847 rotated from previous position = 8.43 degrees 
    20848 atoms outside contour = 1708, contour level = 1.1093 
    20849  
    20850 Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates: 
    20851 Matrix rotation and translation 
    20852 0.91950152 0.12557835 0.37248763 -66.96689278 
    20853 -0.16246606 0.98428326 0.06921873 17.35756690 
    20854 -0.35794097 -0.12416333 0.92545218 75.38744531 
    20855 Axis -0.23914600 0.90328481 -0.35621024 
    20856 Axis point 170.94087250 0.00000000 213.61763802 
    20857 Rotation angle (degrees) 23.84839592 
    20858 Shift along axis 4.83991131 
    20859  
    20860 
    20861 > view matrix models
    20862 > #5,0.94976,0.24396,-0.19605,-1.0108,-0.31295,0.73323,-0.60368,166.07,-0.0035254,0.63471,0.77274,-49.77
    20863 
    20864 > select subtract #5
    20865 
    20866 Nothing selected 
    20867 
    20868 > volume #5 level 1.488
    20869 
    20870 > select add #5
    20871 
    20872 4 models selected 
    20873 
    20874 > view matrix models
    20875 > #5,0.94976,0.24396,-0.19605,-0.8891,-0.31295,0.73323,-0.60368,166,-0.0035254,0.63471,0.77274,-49.393
    20876 
    20877 > ui mousemode right "rotate selected models"
    20878 
    20879 > view matrix models
    20880 > #5,0.90637,0.30351,-0.29389,10.083,-0.41806,0.74462,-0.52036,168.02,0.060903,0.5945,0.80178,-56.771
    20881 
    20882 > view matrix models
    20883 > #5,0.92471,0.31681,-0.21105,-5.5286,-0.38013,0.79797,-0.46771,148.1,0.020234,0.51272,0.85832,-47.203
    20884 
    20885 > view matrix models
    20886 > #5,0.87818,0.44033,-0.18683,-19.512,-0.47312,0.74212,-0.47477,169.99,-0.070402,0.50533,0.86005,-33.611
    20887 
    20888 > view matrix models
    20889 > #5,0.96541,0.15763,-0.20769,10.555,-0.24143,0.84124,-0.48377,124.63,0.098463,0.51718,0.8502,-57.772
    20890 
    20891 > volume #5 level 0.7885
    20892 
    20893 > volume #5 step 2
    20894 
    20895 > volume #5 step 1
    20896 
    20897 > view matrix models
    20898 > #5,0.90157,0.39956,-0.16591,-21.23,-0.42572,0.75103,-0.5047,167.3,-0.077056,0.52565,0.8472,-33.228
    20899 
    20900 > view matrix models
    20901 > #5,0.91439,0.404,0.025785,-48.997,-0.36846,0.85696,-0.36036,124.44,-0.16768,0.32001,0.93246,-1.1627
    20902 
    20903 > view matrix models
    20904 > #5,0.90443,0.4027,-0.14084,-25.409,-0.41738,0.76692,-0.48747,161.49,-0.088297,0.49967,0.8617,-29.699
    20905 
    20906 > ui mousemode right "translate selected models"
    20907 
    20908 > view matrix models
    20909 > #5,0.90443,0.4027,-0.14084,-26.413,-0.41738,0.76692,-0.48747,161.95,-0.088297,0.49967,0.8617,-32.605
    20910 
    20911 > view matrix models
    20912 > #5,0.90443,0.4027,-0.14084,-25.849,-0.41738,0.76692,-0.48747,162.3,-0.088297,0.49967,0.8617,-32.466
     469[deleted to fit within ticket limits]
    20913470
    20914471> ui mousemode right "rotate selected models"