Changes between Initial Version and Version 1 of Ticket #17437


Ignore:
Timestamp:
Apr 21, 2025, 1:43:11 PM (6 months ago)
Author:
pett
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17437

    • 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 #17437 – Description

    initial v1  
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    1407     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
    1408     "name" : "_ribbons.cpython-311-darwin.so"
    1409   },
    1410   {
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    1412     "arch" : "arm64",
    1413     "base" : 6103613440,
    1414     "size" : 16384,
    1415     "uuid" : "c802abe8-4352-3827-8717-7d4c0f0892ff",
    1416     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
    1417     "name" : "_graphics.cpython-311-darwin.so"
    1418   },
    1419   {
    1420     "source" : "P",
    1421     "arch" : "arm64",
    1422     "base" : 6106398720,
    1423     "size" : 458752,
    1424     "uuid" : "6b6db01c-1280-3773-b08f-d693798baba7",
    1425     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
    1426     "name" : "mmcif.cpython-311-darwin.so"
    1427   },
    1428   {
    1429     "source" : "P",
    1430     "arch" : "arm64",
    1431     "base" : 6105006080,
    1432     "size" : 409600,
    1433     "uuid" : "f03f0cb6-82d1-33ee-a10b-cc8d92c14417",
    1434     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
    1435     "name" : "_mmcif.cpython-311-darwin.so"
    1436   },
    1437   {
    1438     "source" : "P",
    1439     "arch" : "arm64",
    1440     "base" : 6107693056,
    1441     "size" : 147456,
    1442     "uuid" : "96691a20-aa26-3905-98c4-0939edf5bdd4",
    1443     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
    1444     "name" : "_pdbio.cpython-311-darwin.so"
    1445   },
    1446   {
    1447     "source" : "P",
    1448     "arch" : "arm64",
    1449     "base" : 13715095552,
    1450     "size" : 4096000,
    1451     "uuid" : "3c92d9be-9b63-3d45-838a-e4fd342ddf46",
    1452     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
    1453     "name" : "etree.cpython-311-darwin.so"
    1454   },
    1455   {
    1456     "source" : "P",
    1457     "arch" : "arm64",
    1458     "base" : 13703462912,
    1459     "size" : 147456,
    1460     "uuid" : "0ee9ca02-13c3-3c35-99ec-fdcf207a8b79",
    1461     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    1462     "name" : "_elementpath.cpython-311-darwin.so"
    1463   },
    1464   {
    1465     "source" : "P",
    1466     "arch" : "arm64",
    1467     "base" : 13031866368,
    1468     "size" : 32768,
    1469     "uuid" : "f6112c45-e8b3-3787-a9ab-c7209e77530f",
    1470     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
    1471     "name" : "_imagingmath.cpython-311-darwin.so"
    1472   },
    1473   {
    1474     "source" : "P",
    1475     "arch" : "arm64",
    1476     "base" : 13322223616,
    1477     "size" : 32768,
    1478     "uuid" : "2c043e84-38d8-33d9-a9a4-ff18ae1f885f",
    1479     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
    1480     "name" : "_psutil_osx.abi3.so"
    1481   },
    1482   {
    1483     "source" : "P",
    1484     "arch" : "arm64",
    1485     "base" : 13139836928,
    1486     "size" : 16384,
    1487     "uuid" : "802f0c32-e7ad-3a81-ac8d-ae72c0022ae6",
    1488     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
    1489     "name" : "_psutil_posix.abi3.so"
    1490   },
    1491   {
    1492     "source" : "P",
    1493     "arch" : "arm64e",
    1494     "base" : 6734798848,
    1495     "size" : 241656,
    1496     "uuid" : "eee9d0d3-dffc-37cb-9ced-b27cd0286d8c",
    1497     "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    1498     "name" : "libsystem_kernel.dylib"
    1499   },
    1500   {
    1501     "source" : "P",
    1502     "arch" : "arm64e",
    1503     "base" : 6735040512,
    1504     "size" : 53248,
    1505     "uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
    1506     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1507     "name" : "libsystem_pthread.dylib"
    1508   },
    1509   {
    1510     "source" : "P",
    1511     "arch" : "arm64e",
    1512     "base" : 6733574144,
    1513     "size" : 532476,
    1514     "uuid" : "92699527-645f-3d8d-aed8-1cfb0c034e15",
    1515     "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    1516     "name" : "libsystem_c.dylib"
    1517   },
    1518   {
    1519     "source" : "P",
    1520     "arch" : "arm64e",
    1521     "base" : 6735278080,
    1522     "size" : 32748,
    1523     "uuid" : "984d08b8-f85c-36f5-9e17-5bff7fc779a3",
    1524     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1525     "name" : "libsystem_platform.dylib"
    1526   },
    1527   {
    1528     "source" : "P",
    1529     "arch" : "arm64e",
    1530     "base" : 6798127104,
    1531     "CFBundleShortVersionString" : "6.9",
    1532     "CFBundleIdentifier" : "com.apple.AppKit",
    1533     "size" : 21221376,
    1534     "uuid" : "b88a44c1-d617-33dc-90ed-b6ab417c428e",
    1535     "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    1536     "name" : "AppKit",
    1537     "CFBundleVersion" : "2575.40.6"
    1538   },
    1539   {
    1540     "source" : "P",
    1541     "arch" : "arm64e",
    1542     "base" : 6831747072,
    1543     "CFBundleShortVersionString" : "1.600.0",
    1544     "CFBundleIdentifier" : "com.apple.SkyLight",
    1545     "size" : 5427200,
    1546     "uuid" : "f66e0c94-99b5-3fcd-b726-3e3cbca668a3",
    1547     "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    1548     "name" : "SkyLight"
    1549   },
    1550   {
    1551     "source" : "P",
    1552     "arch" : "arm64e",
    1553     "base" : 6733271040,
    1554     "size" : 290816,
    1555     "uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
    1556     "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1557     "name" : "libdispatch.dylib"
    1558   },
    1559   {
    1560     "source" : "P",
    1561     "arch" : "arm64e",
    1562     "base" : 6735507456,
    1563     "CFBundleShortVersionString" : "6.9",
    1564     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    1565     "size" : 5197824,
    1566     "uuid" : "190e6a36-fcaa-3ea3-94bb-7009c44653da",
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    1568     "name" : "CoreFoundation",
    1569     "CFBundleVersion" : "3302.1.400"
    1570   },
    1571   {
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    1573     "arch" : "arm64e",
    1574     "base" : 6925164544,
    1575     "CFBundleShortVersionString" : "2.1.1",
    1576     "CFBundleIdentifier" : "com.apple.HIToolbox",
    1577     "size" : 3178496,
    1578     "uuid" : "950f1236-acaf-379d-819f-6c6b0b5deabd",
    1579     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    1580     "name" : "HIToolbox"
    1581   },
    1582   {
    1583     "source" : "P",
    1584     "arch" : "arm64e",
    1585     "base" : 6731374592,
    1586     "size" : 532288,
    1587     "uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
    1588     "path" : "\/usr\/lib\/dyld",
    1589     "name" : "dyld"
    1590   },
    1591   {
    1592     "size" : 0,
    1593     "source" : "A",
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    1595     "uuid" : "00000000-0000-0000-0000-000000000000"
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    1597   {
    1598     "source" : "P",
    1599     "arch" : "arm64e",
    1600     "base" : 6734106624,
    1601     "size" : 581628,
    1602     "uuid" : "bbab286c-2e51-3d64-9ae3-a4102935fe32",
    1603     "path" : "\/usr\/lib\/libc++.1.dylib",
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    1605   }
     72[deleted to fit within ticket limits]
     73
    160674],
    160775  "sharedCache" : {
    … …  
    2117585> view sel
    2118586
    2119 > open
    2120 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/note.txt
    2121 
    2122 Unrecognized file suffix '.txt' 
    2123 
    2124 > open
    2125 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/relion_locres_filtered.mrc
    2126 
    2127 Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
    2128 shown at level 0.00146, step 2, values float32 
    2129 
    2130 > color #3 #b2b2b296 models
    2131 
    2132 > volume #3 step 1
    2133 
    2134 > ui tool show "Side View"
    2135 
    2136 > volume #3 level 0.01472
    2137 
    2138 > select add #1
    2139 
    2140 3482 atoms, 3578 bonds, 1 pseudobond, 448 residues, 3 models selected 
    2141 
    2142 > show sel atoms
    2143 
    2144 JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
    2145 properties of undefined (reading 'id') 
    2146 
    2147 > hide #2.1-20 models
    2148 
    2149 > show #2.1 models
    2150 
    2151 > select clear
    2152 
    2153 > volume #3 level 0.01037
    2154 
    2155 > show #2.2 models
    2156 
    2157 > show #2.3 models
    2158 
    2159 > hide #2.2 models
    2160 
    2161 > hide #2.1 models
    2162 
    2163 > volume #3 level 0.009064
    2164 
    2165 > volume #3 level 0.009281
    2166 
    2167 > hide #2.3 models
    2168 
    2169 > show #2.4 models
    2170 
    2171 > hide #2.4 models
    2172 
    2173 > show #2.5 models
    2174 
    2175 > close #1
    2176 
    2177 > open
    2178 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    2179 > hOCT1-noVB1.pdb"
    2180 
    2181 Chain information for hOCT1-noVB1.pdb #1 
    2182 --- 
    2183 Chain | Description 
    2184 A | No description available 
    2185  
    2186 
    2187 > select add #1
    2188 
    2189 3461 atoms, 3556 bonds, 1 pseudobond, 447 residues, 2 models selected 
    2190 
    2191 > show sel atoms
    2192 
    2193 > select clear
    2194 
    2195 > hide #2.5 models
    2196 
    2197 > show #2.6 models
    2198 
    2199 > hide #2.6 models
    2200 
    2201 > show #2.7 models
    2202 
    2203 > hide #2.7 models
    2204 
    2205 > show #2.8 models
    2206 
    2207 > hide #2.8 models
    2208 
    2209 > show #2.9 models
    2210 
    2211 > hide #2.9 models
    2212 
    2213 > show #2.10 models
    2214 
    2215 > hide #2.10 models
    2216 
    2217 > show #2.10 models
    2218 
    2219 > hide #2.10 models
    2220 
    2221 > show #2.11 models
    2222 
    2223 > hide #2.11 models
    2224 
    2225 > show #2.12 models
    2226 
    2227 > save
    2228 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    2229 > includeMaps true
    2230 
    2231 > lighting soft
    2232 
    2233 > lighting simple
    2234 
    2235 > color #3 #b2b2b264 models
    2236 
    2237 > hide #2.12 models
    2238 
    2239 > show #2.13 models
    2240 
    2241 > hide #2.13 models
    2242 
    2243 > show #2.14 models
    2244 
    2245 > hide #2.14 models
    2246 
    2247 > show #2.15 models
    2248 
    2249 > hide #2.15 models
    2250 
    2251 > show #2.15 models
    2252 
    2253 > hide #2.15 models
    2254 
    2255 > show #2.16 models
    2256 
    2257 > hide #2.16 models
    2258 
    2259 > show #2.17 models
    2260 
    2261 > hide #2.17 models
    2262 
    2263 > show #2.18 models
    2264 
    2265 > hide #2.18 models
    2266 
    2267 > show #2.19 models
    2268 
    2269 > hide #2.19 models
    2270 
    2271 > show #2.20 models
    2272 
    2273 > hide #2.20 models
    2274 
    2275 > show #2.19 models
    2276 
    2277 > hide #2.19 models
    2278 
    2279 > show #2.20 models
    2280 
    2281 > hide #2.20 models
    2282 
    2283 > show #2.1 models
    2284 
    2285 > hide #2.1 models
    2286 
    2287 > show #2.2 models
    2288 
    2289 > hide #2.2 models
    2290 
    2291 > show #2.1 models
    2292 
    2293 > hide #2.1 models
    2294 
    2295 > show #2.2 models
    2296 
    2297 > hide #2.2 models
    2298 
    2299 > show #2.3 models
    2300 
    2301 > hide #2.3 models
    2302 
    2303 > show #2.3 models
    2304 
    2305 > hide #2.3 models
    2306 
    2307 > show #2.4 models
    2308 
    2309 > hide #2.4 models
    2310 
    2311 > show #2.5 models
    2312 
    2313 > hide #2.5 models
    2314 
    2315 > show #2.6 models
    2316 
    2317 > hide #2.6 models
    2318 
    2319 > show #2.7 models
    2320 
    2321 > hide #2.7 models
    2322 
    2323 > show #2.7 models
    2324 
    2325 > hide #2.7 models
    2326 
    2327 > show #2.8 models
    2328 
    2329 > hide #2.8 models
    2330 
    2331 > show #2.9 models
    2332 
    2333 > hide #2.9 models
    2334 
    2335 > show #2.10 models
    2336 
    2337 > select down
    2338 
    2339 Nothing selected 
    2340 
    2341 > hide #2.10 models
    2342 
    2343 > show #2.10 models
    2344 
    2345 > hide #2.10 models
    2346 
    2347 > show #2.11 models
    2348 
    2349 > hide #2.11 models
    2350 
    2351 > show #2.12 models
    2352 
    2353 > hide #2.12 models
    2354 
    2355 > show #2.13 models
    2356 
    2357 > hide #2.13 models
    2358 
    2359 > show #2.14 models
    2360 
    2361 > hide #2.14 models
    2362 
    2363 > show #2.15 models
    2364 
    2365 > hide #2.15 models
    2366 
    2367 > show #2.15 models
    2368 
    2369 > hide #2.15 models
    2370 
    2371 > show #2.15 models
    2372 
    2373 > hide #2.15 models
    2374 
    2375 > show #2.16 models
    2376 
    2377 > hide #2.16 models
    2378 
    2379 > show #2.16 models
    2380 
    2381 > hide #2.16 models
    2382 
    2383 > show #2.17 models
    2384 
    2385 > hide #2.17 models
    2386 
    2387 > show #2.17 models
    2388 
    2389 > hide #2.17 models
    2390 
    2391 > show #2.18 models
    2392 
    2393 > hide #2.18 models
    2394 
    2395 > show #2.19 models
    2396 
    2397 > hide #2.19 models
    2398 
    2399 > show #2.20 models
    2400 
    2401 > volume #3 level 0.01124
    2402 
    2403 > hide #2.20 models
    2404 
    2405 > show #2.20 models
    2406 
    2407 > hide #2.20 models
    2408 
    2409 > show #2.20 models
    2410 
    2411 > hide #2.20 models
    2412 
    2413 > show #2.19 models
    2414 
    2415 > hide #2.19 models
    2416 
    2417 > show #2.18 models
    2418 
    2419 > hide #2.18 models
    2420 
    2421 > show #2.19 models
    2422 
    2423 > hide #2.19 models
    2424 
    2425 > show #2.18 models
    2426 
    2427 > volume #3 level 0.008629
    2428 
    2429 > hide #2.18 models
    2430 
    2431 > show #2.18 models
    2432 
    2433 > hide #2.18 models
    2434 
    2435 > show #2.17 models
    2436 
    2437 > hide #2.17 models
    2438 
    2439 > show #2.16 models
    2440 
    2441 > hide #2.16 models
    2442 
    2443 > show #2.15 models
    2444 
    2445 > hide #2.15 models
    2446 
    2447 > show #2.14 models
    2448 
    2449 > hide #2.14 models
    2450 
    2451 > show #2.13 models
    2452 
    2453 > hide #2.13 models
    2454 
    2455 > show #2.12 models
    2456 
    2457 > hide #2.12 models
    2458 
    2459 > show #2.11 models
    2460 
    2461 > hide #2.11 models
    2462 
    2463 > show #2.10 models
    2464 
    2465 > hide #2.10 models
    2466 
    2467 > show #2.1 models
    2468 
    2469 > hide #2.1 models
    2470 
    2471 > show #2.1 models
    2472 
    2473 > hide #2.1 models
    2474 
    2475 > show #2.2 models
    2476 
    2477 > hide #2.2 models
    2478 
    2479 > show #2.3 models
    2480 
    2481 > hide #2.3 models
    2482 
    2483 > show #2.4 models
    2484 
    2485 > hide #2.4 models
    2486 
    2487 > show #2.5 models
    2488 
    2489 > hide #2.5 models
    2490 
    2491 > show #2.6 models
    2492 
    2493 > hide #2.6 models
    2494 
    2495 > show #2.7 models
    2496 
    2497 > hide #2.7 models
    2498 
    2499 > show #2.8 models
    2500 
    2501 > hide #2.8 models
    2502 
    2503 > show #2.9 models
    2504 
    2505 > hide #2.9 models
    2506 
    2507 > show #2.9 models
    2508 
    2509 > hide #2.9 models
    2510 
    2511 > show #2.9 models
    2512 
    2513 > hide #2.9 models
    2514 
    2515 > show #2.10 models
    2516 
    2517 > hide #2.10 models
    2518 
    2519 > show #2.11 models
    2520 
    2521 > hide #2.11 models
    2522 
    2523 > show #2.12 models
    2524 
    2525 > hide #2.12 models
    2526 
    2527 > show #2.13 models
    2528 
    2529 > hide #2.13 models
    2530 
    2531 > show #2.12 models
    2532 
    2533 > hide #2.12 models
    2534 
    2535 > show #2.1 models
    2536 
    2537 > hide #2.1 models
    2538 
    2539 > show #2.2 models
    2540 
    2541 > hide #2.2 models
    2542 
    2543 > show #2.3 models
    2544 
    2545 > hide #2.3 models
    2546 
    2547 > show #2.4 models
    2548 
    2549 > hide #2.4 models
    2550 
    2551 > show #2.5 models
    2552 
    2553 > hide #2.5 models
    2554 
    2555 > show #2.6 models
    2556 
    2557 > hide #2.6 models
    2558 
    2559 > show #2.7 models
    2560 
    2561 > hide #2.7 models
    2562 
    2563 > show #2.8 models
    2564 
    2565 > hide #2.8 models
    2566 
    2567 > show #2.8 models
    2568 
    2569 > hide #2.8 models
    2570 
    2571 > show #2.9 models
    2572 
    2573 > hide #2.9 models
    2574 
    2575 > show #2.10 models
    2576 
    2577 > hide #2.10 models
    2578 
    2579 > show #2.11 models
    2580 
    2581 > hide #2.11 models
    2582 
    2583 > show #2.12 models
    2584 
    2585 > hide #2.12 models
    2586 
    2587 > show #2.1 models
    2588 
    2589 > save
    2590 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    2591 > includeMaps true
    2592 
    2593 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35492, resource id:
    2594 35652978, major code: 40 (TranslateCoords), minor code: 0 
    2595 
    2596 > volume #3 level 0.009281
    2597 
    2598 > hide #2.1 models
    2599 
    2600 > show #2.2 models
    2601 
    2602 > hide #2.2 models
    2603 
    2604 > show #2.3 models
    2605 
    2606 > hide #2.3 models
    2607 
    2608 > show #2.4 models
    2609 
    2610 > show #2.5 models
    2611 
    2612 > hide #2.4 models
    2613 
    2614 > hide #2.5 models
    2615 
    2616 > show #2.18 models
    2617 
    2618 > hide #2.18 models
    2619 
    2620 > show #2.18 models
    2621 
    2622 > hide #2.18 models
    2623 
    2624 > show #2.17 models
    2625 
    2626 > hide #2.17 models
    2627 
    2628 > show #2.16 models
    2629 
    2630 > hide #2.16 models
    2631 
    2632 > show #2.15 models
    2633 
    2634 > hide #2.15 models
    2635 
    2636 > show #2.14 models
    2637 
    2638 > hide #2.14 models
    2639 
    2640 > show #2.13 models
    2641 
    2642 > hide #2.13 models
    2643 
    2644 > show #2.12 models
    2645 
    2646 > hide #2.12 models
    2647 
    2648 > show #2.12 models
    2649 
    2650 > hide #2.12 models
    2651 
    2652 > save
    2653 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    2654 > includeMaps true
    2655 
    2656 QXcbConnection: XCB error: 3 (BadWindow), sequence: 32670, resource id:
    2657 35652988, major code: 40 (TranslateCoords), minor code: 0 
    2658 
    2659 ——— End of log from Tue Dec 10 11:33:02 2024 ———
    2660 
    2661 opened ChimeraX session 
    2662 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    2663 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    2664 
    2665 > save
    2666 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    2667 > includeMaps true
    2668 
    2669 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7404, resource id:
    2670 35653140, major code: 40 (TranslateCoords), minor code: 0 
    2671 
    2672 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7416, resource id:
    2673 35653135, major code: 40 (TranslateCoords), minor code: 0 
    2674 
    2675 > show #2.11 models
    2676 
    2677 > hide #2.11 models
    2678 
    2679 > show #2.12 models
    2680 
    2681 > hide #2.12 models
    2682 
    2683 > save
    2684 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    2685 > includeMaps true
    2686 
    2687 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60442, resource id:
    2688 35653379, major code: 40 (TranslateCoords), minor code: 0 
    2689 
    2690 ——— End of log from Wed Dec 11 13:28:04 2024 ———
    2691 
    2692 opened ChimeraX session 
    2693 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    2694 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    2695 
    2696 > show #2.11 models
    2697 
    2698 > show #2.12 models
    2699 
    2700 > hide #2.11 models
    2701 
    2702 > open
    2703 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_7/hOCT1VB1007.pdb
    2704 
    2705 Chain information for hOCT1VB1007.pdb #4 
    2706 --- 
    2707 Chain | Description 
    2708 A | No description available 
    2709  
    2710 
    2711 > open
    2712 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_8/
    2713 > hOCT1-VB_Dock2_real_space_refined_008.pdb"
    2714 
    2715 Chain information for hOCT1-VB_Dock2_real_space_refined_008.pdb #5 
    2716 --- 
    2717 Chain | Description 
    2718 A | No description available 
    2719  
    2720 
    2721 QXcbConnection: XCB error: 3 (BadWindow), sequence: 17659, resource id:
    2722 35653657, major code: 40 (TranslateCoords), minor code: 0 
    2723 
    2724 > close session
    2725 
    2726 > open
    2727 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/P3_J149_fsc_iteration_010_after_fsc_mask_auto_tightening.pdf
    2728 
    2729 QXcbConnection: XCB error: 3 (BadWindow), sequence: 50929, resource id:
    2730 35654568, major code: 40 (TranslateCoords), minor code: 0 
    2731 
    2732 > open
    2733 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240.mrc
    2734 
    2735 Opened cryosparc_P3_J154__localfilter_240.mrc as #1, grid size 240,240,240,
    2736 pixel 0.553, shown at level 0.207, step 1, values float32 
    2737 
    2738 > open
    2739 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240_VB1.mrc
    2740 
    2741 Opened cryosparc_P3_J154__localfilter_240_VB1.mrc as #2, grid size
    2742 240,240,240, pixel 0.553, shown at level 0.000117, step 1, values float32 
    2743 
    2744 > volume #2 level 0.3318
    2745 
    2746 Drag select of 2 cryosparc_P3_J154__localfilter_240_VB1.mrc 
    2747 
    2748 > view orient
    2749 
    2750 > select clear
    2751 
    2752 > open
    2753 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb
    2754 
    2755 Summary of feedback from opening
    2756 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb 
    2757 --- 
    2758 warnings | Cannot find LINK/SSBOND residue CYS (50 ) 
    2759 Cannot find LINK/SSBOND residue CYS (62 ) 
    2760 Cannot find LINK/SSBOND residue CYS (89 ) 
    2761  
    2762 
    2763 > open
    2764 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb
    2765 
    2766 Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4 
    2767 --- 
    2768 Chain | Description 
    2769 A | No description available 
    2770  
    2771 
    2772 > open
    2773 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb
    2774 
    2775 Chain information for mOCT1-VB1_real_space_refined_014.pdb #5 
    2776 --- 
    2777 Chain | Description 
    2778 A | No description available 
    2779  
    2780 
    2781 > close #3#4
    2782 
    2783 > volume #2 color #ffffb296
    2784 
    2785 > volume #2 color #ffffb2c8
    2786 
    2787 > volume #2 level 0.4304
    2788 
    2789 > volume #2 level 0.3677
    2790 
    2791 > select /A:601@C15
    2792 
    2793 1 atom, 1 residue, 1 model selected 
    2794 
    2795 > select up
    2796 
    2797 18 atoms, 19 bonds, 1 residue, 1 model selected 
    2798 
    2799 > view sel
    2800 
    2801 > select clear
    2802 
    2803 > open
    2804 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb
    2805 
    2806 Chain information for mOCT1-ABC_real_space_refined_009.pdb #3 
    2807 --- 
    2808 Chain | Description 
    2809 A | No description available 
    2810  
    2811 
    2812 > open
    2813 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc
    2814 
    2815 Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240,
    2816 pixel 0.553, shown at level 0.229, step 1, values float32 
    2817 
    2818 > volume #4 level 0.7041
    2819 
    2820 > hide #!2 models
    2821 
    2822 > hide #!3 models
    2823 
    2824 > hide #!5 models
    2825 
    2826 > show #!3 models
    2827 
    2828 > select ::name="ABC"
    2829 
    2830 42 atoms, 48 bonds, 2 residues, 1 model selected 
    2831 
    2832 > view sel
    2833 
    2834 > volume #4 level 0.5273
    2835 
    2836 > hide #!4 models
    2837 
    2838 > show #!4 models
    2839 
    2840 > show #!1 models
    2841 
    2842 > hide #!3 models
    2843 
    2844 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    2845 > density.cxs" includeMaps true
    2846 
    2847 QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id:
    2848 35654641, major code: 40 (TranslateCoords), minor code: 0 
    2849 
    2850 > hide #!1 models
    2851 
    2852 > rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    2853 
    2854 > rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc
    2855 
    2856 > rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc
    2857 
    2858 > show #!3 models
    2859 
    2860 > select clear
    2861 
    2862 > hide #!4 models
    2863 
    2864 > select ::name="ABC"
    2865 
    2866 42 atoms, 48 bonds, 2 residues, 1 model selected 
    2867 
    2868 > select add #3
    2869 
    2870 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    2871 
    2872 > color (#!3 & sel) white
    2873 
    2874 > select clear
    2875 
    2876 > select ::name="ABC"
    2877 
    2878 42 atoms, 48 bonds, 2 residues, 1 model selected 
    2879 
    2880 > color sel red
    2881 
    2882 > show #!4 models
    2883 
    2884 > ui tool show "Color Zone"
    2885 
    2886 > color zone #4 near #3 distance 3.32
    2887 
    2888 > volume splitbyzone #4
    2889 
    2890 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size
    2891 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    2892 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size
    2893 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    2894 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size
    2895 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    2896 
    2897 > hide #!3 models
    2898 
    2899 > select add #3
    2900 
    2901 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    2902 
    2903 > select subtract #3
    2904 
    2905 Nothing selected 
    2906 
    2907 > hide #!6.1 models
    2908 
    2909 > hide #!6.3 models
    2910 
    2911 > show #!6.3 models
    2912 
    2913 > hide #!6.2 models
    2914 
    2915 > close #6.1-2
    2916 
    2917 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    2918 > density.cxs" includeMaps true
    2919 
    2920 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id:
    2921 35654647, major code: 40 (TranslateCoords), minor code: 0 
    2922 
    2923 > show #!3 models
    2924 
    2925 > color #3 #fffffbff
    2926 
    2927 > color #3 #ddddaaff
    2928 
    2929 > color #3 #dda0deff
    2930 
    2931 > color #3 plum
    2932 
    2933 > select add #3
    2934 
    2935 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    2936 
    2937 > color (#!3 & sel) byhetero
    2938 
    2939 > color #6.3 #ddddaaff models
    2940 
    2941 > color #6.3 plum models
    2942 
    2943 > color #6.3 #ffffb2ff models
    2944 
    2945 Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5
    2946 atoms, 5 residues, 5 bonds 
    2947 
    2948 > select clear
    2949 
    2950 > color #6.3 #ffffb2c8 models
    2951 
    2952 > select ::name="ABC"
    2953 
    2954 42 atoms, 48 bonds, 2 residues, 1 model selected 
    2955 
    2956 > view sel
    2957 
    2958 > select #3/A:234
    2959 
    2960 11 atoms, 10 bonds, 1 residue, 1 model selected 
    2961 
    2962 > color #6.3 #ffffb296 models
    2963 
    2964 > show #!2 models
    2965 
    2966 > hide #!2 models
    2967 
    2968 > show #!2 models
    2969 
    2970 > hide #!3 models
    2971 
    2972 > hide #!6 models
    2973 
    2974 > hide #!6.3 models
    2975 
    2976 > show #!4 models
    2977 
    2978 > hide #!4 models
    2979 
    2980 > show #!5 models
    2981 
    2982 > show #!3 models
    2983 
    2984 > hide #!3 models
    2985 
    2986 > select #5/A:36
    2987 
    2988 12 atoms, 12 bonds, 1 residue, 1 model selected 
    2989 
    2990 > show sel atoms
    2991 
    2992 > hide #!5 models
    2993 
    2994 > hide #!2 models
    2995 
    2996 > show #!1 models
    2997 
    2998 > view
    2999 
    3000 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3001 > density.cxs" includeMaps true
    3002 
    3003 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id:
    3004 35654673, major code: 40 (TranslateCoords), minor code: 0 
    3005 
    3006 > open
    3007 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc
    3008 
    3009 Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83,
    3010 shown at level 0.00144, step 2, values float32 
    3011 
    3012 > volume #7 level 0.01204
    3013 
    3014 > select add #7
    3015 
    3016 12 atoms, 12 bonds, 1 residue, 3 models selected 
    3017 
    3018 > select add #5
    3019 
    3020 3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected 
    3021 
    3022 > select subtract #5
    3023 
    3024 2 models selected 
    3025 
    3026 > ui mousemode right "translate selected models"
    3027 
    3028 > view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016
    3029 
    3030 > view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057
    3031 
    3032 > ui mousemode right "rotate selected models"
    3033 
    3034 > view matrix models
    3035 > #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495
    3036 
    3037 > ui mousemode right "translate selected models"
    3038 
    3039 > view matrix models
    3040 > #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226
    3041 
    3042 > view matrix models
    3043 > #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256
    3044 
    3045 > view matrix models
    3046 > #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175
    3047 
    3048 > ui tool show "Fit in Map"
    3049 
    3050 > fitmap #7 inMap #1
    3051 
    3052 Fit map relion_locres_filtered.mrc in map
    3053 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points 
    3054 correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07 
    3055 steps = 116, shift = 1.21, angle = 8.84 degrees 
    3056  
    3057 Position of relion_locres_filtered.mrc (#7) relative to
    3058 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3059 Matrix rotation and translation 
    3060 -0.36461695 0.73265397 0.57469351 -59.14787422 
    3061 -0.87490183 -0.48082660 0.05790126 236.29988230 
    3062 0.31874951 -0.48168862 0.81631784 -18.80617873 
    3063 Axis -0.31464704 0.14924672 -0.93740208 
    3064 Axis point 41.71559551 127.71968026 0.00000000 
    3065 Rotation angle (degrees) 120.96824033 
    3066 Shift along axis 71.50663710 
    3067  
    3068 
    3069 > rename #7 mOCT1-3TC
    3070 
    3071 > select clear
    3072 
    3073 [Repeated 1 time(s)]
    3074 
    3075 > rename #7 mOCT1-3TC.mrc
    3076 
    3077 > open
    3078 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC-
    3079 > coot-14_real_space_refined_006.pdb
    3080 
    3081 Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8 
    3082 --- 
    3083 Chain | Description 
    3084 A | No description available 
    3085  
    3086 
    3087 > ui tool show Matchmaker
    3088 
    3089 > matchmaker #!8 to #5
    3090 
    3091 Parameters 
    3092 --- 
    3093 Chain pairing | bb 
    3094 Alignment algorithm | Needleman-Wunsch 
    3095 Similarity matrix | BLOSUM-62 
    3096 SS fraction | 0.3 
    3097 Gap open (HH/SS/other) | 18/18/6 
    3098 Gap extend | 1 
    3099 SS matrix |  |  | H | S | O 
    3100 ---|---|---|--- 
    3101 H | 6 | -9 | -6 
    3102 S |  | 6 | -6 
    3103 O |  |  | 4 
    3104 Iteration cutoff | 2 
    3105  
    3106 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC-
    3107 coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score =
    3108 2352.2 
    3109 RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs:
    3110 0.409) 
    3111  
    3112 
    3113 > hide #!1 models
    3114 
    3115 > hide #!7 models
    3116 
    3117 > show #!1 models
    3118 
    3119 > hide #!8 models
    3120 
    3121 > show #!7 models
    3122 
    3123 > select add #7
    3124 
    3125 2 models selected 
    3126 
    3127 > ui mousemode right "rotate selected models"
    3128 
    3129 > view matrix models
    3130 > #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956
    3131 
    3132 > ui mousemode right "translate selected models"
    3133 
    3134 > view matrix models
    3135 > #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096
    3136 
    3137 > fitmap #7 inMap #1
    3138 
    3139 Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3140 using 3812 points 
    3141 correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08 
    3142 steps = 160, shift = 6.4, angle = 20.1 degrees 
    3143  
    3144 Position of mOCT1-3TC.mrc (#7) relative to
    3145 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3146 Matrix rotation and translation 
    3147 0.27009123 -0.75134279 -0.60210857 210.67160095 
    3148 0.83888334 0.49056205 -0.23584655 -78.20606144 
    3149 0.47257322 -0.44139877 0.76278546 -39.17036140 
    3150 Axis -0.10648785 -0.55674686 0.82382842 
    3151 Axis point 169.78551241 113.86943556 0.00000000 
    3152 Rotation angle (degrees) 74.82789173 
    3153 Shift along axis -11.16264322 
    3154  
    3155 
    3156 > fitmap #8 inMap #7
    3157 
    3158 Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map
    3159 mOCT1-3TC.mrc (#7) using 7048 atoms 
    3160 average map value = 0.01706, steps = 60 
    3161 shifted from previous position = 0.0823 
    3162 rotated from previous position = 0.357 degrees 
    3163 atoms outside contour = 4146, contour level = 0.012041 
    3164  
    3165 Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to
    3166 mOCT1-3TC.mrc (#7) coordinates: 
    3167 Matrix rotation and translation 
    3168 0.99999991 -0.00005602 -0.00043067 0.07339565 
    3169 0.00005621 0.99999991 0.00043709 -0.06044298 
    3170 0.00043064 -0.00043712 0.99999982 0.02180230 
    3171 Axis -0.70938425 -0.69891365 0.09106970 
    3172 Axis point 0.00000000 51.44490735 150.82453668 
    3173 Rotation angle (degrees) 0.03530433 
    3174 Shift along axis -0.00783577 
    3175  
    3176 
    3177 > show #!8 models
    3178 
    3179 > hide #!8 models
    3180 
    3181 > select subtract #7
    3182 
    3183 Nothing selected 
    3184 
    3185 > hide #!1 models
    3186 
    3187 > show #!8 models
    3188 
    3189 > select ::name="3TC"
    3190 
    3191 26 atoms, 27 bonds, 1 residue, 1 model selected 
    3192 
    3193 > select add #8
    3194 
    3195 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3196 
    3197 > color (#!8 & sel) white
    3198 
    3199 > select ::name="3TC"
    3200 
    3201 26 atoms, 27 bonds, 1 residue, 1 model selected 
    3202 
    3203 > color sel red
    3204 
    3205 > view sel
    3206 
    3207 > volume #7 step 1
    3208 
    3209 > color zone #7 near #8 distance 4.98
    3210 
    3211 > volume splitbyzone #7
    3212 
    3213 Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    3214 level 0.012, step 1, values float32 
    3215 Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    3216 level 0.012, step 1, values float32 
    3217 Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    3218 level 0.012, step 1, values float32 
    3219 
    3220 > close #9.2
    3221 
    3222 > close #9.1
    3223 
    3224 > color #9.3 white models
    3225 
    3226 > color #9.3 #ffffb2ff models
    3227 
    3228 > color #9.3 #ffffb296 models
    3229 
    3230 > select #8/A:447
    3231 
    3232 19 atoms, 18 bonds, 1 residue, 1 model selected 
    3233 
    3234 > select add #8
    3235 
    3236 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3237 
    3238 > color #8 #bb22ffff
    3239 
    3240 > color #8 #b2fffbff
    3241 
    3242 > color #8 #b2ffb2ff
    3243 
    3244 > color (#!8 & sel) byhetero
    3245 
    3246 > select clear
    3247 
    3248 [Repeated 1 time(s)]
    3249 
    3250 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3251 > density.cxs" includeMaps true
    3252 
    3253 > hide #!9.3 models
    3254 
    3255 > hide #!9 models
    3256 
    3257 > hide #!8 models
    3258 
    3259 > open
    3260 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc
    3261 
    3262 Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel
    3263 0.83, shown at level 0.00125, step 2, values float32 
    3264 
    3265 > show #!1 models
    3266 
    3267 > view
    3268 
    3269 > volume #1 level 0.3063
    3270 
    3271 > volume #10 step 1
    3272 
    3273 > volume #10 level 0.01019
    3274 
    3275 > rename #10 mOCT1-AZT.mrc
    3276 
    3277 > select add #10
    3278 
    3279 2 models selected 
    3280 
    3281 > view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093
    3282 
    3283 > view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826
    3284 
    3285 > ui mousemode right "rotate selected models"
    3286 
    3287 > view matrix models
    3288 > #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718
    3289 
    3290 > ui mousemode right "translate selected models"
    3291 
    3292 > view matrix models
    3293 > #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969
    3294 
    3295 > view matrix models
    3296 > #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609
    3297 
    3298 > fitmap #10 inMap #1
    3299 
    3300 Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3301 using 33175 points 
    3302 correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2 
    3303 steps = 172, shift = 3.01, angle = 24.4 degrees 
    3304  
    3305 Position of mOCT1-AZT.mrc (#10) relative to
    3306 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3307 Matrix rotation and translation 
    3308 0.17958596 0.98366820 0.01207312 -89.49221412 
    3309 -0.89232990 0.16805236 -0.41893408 218.60375344 
    3310 -0.41412105 0.06446147 0.90793639 -7.62218964 
    3311 Axis 0.24369569 0.21485858 -0.94575272 
    3312 Axis point 81.50821029 166.97786454 0.00000000 
    3313 Rotation angle (degrees) 82.65824965 
    3314 Shift along axis 32.36873253 
    3315  
    3316 
    3317 > view
    3318 
    3319 > view orient
    3320 
    3321 > ui tool show "Side View"
    3322 
    3323 > open
    3324 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb
    3325 
    3326 Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11 
    3327 --- 
    3328 Chain | Description 
    3329 A | No description available 
    3330  
    3331 
    3332 > ui tool show Matchmaker
    3333 
    3334 > matchmaker #!11 to #5
    3335 
    3336 Parameters 
    3337 --- 
    3338 Chain pairing | bb 
    3339 Alignment algorithm | Needleman-Wunsch 
    3340 Similarity matrix | BLOSUM-62 
    3341 SS fraction | 0.3 
    3342 Gap open (HH/SS/other) | 18/18/6 
    3343 Gap extend | 1 
    3344 SS matrix |  |  | H | S | O 
    3345 ---|---|---|--- 
    3346 H | 6 | -9 | -6 
    3347 S |  | 6 | -6 
    3348 O |  |  | 4 
    3349 Iteration cutoff | 2 
    3350  
    3351 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    3352 mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment
    3353 score = 2367.3 
    3354 RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs:
    3355 0.415) 
    3356  
    3357 
    3358 > fitmap #11 inMap #10
    3359 
    3360 Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map
    3361 mOCT1-AZT.mrc (#10) using 7017 atoms 
    3362 average map value = 0.01592, steps = 48 
    3363 shifted from previous position = 0.0651 
    3364 rotated from previous position = 0.278 degrees 
    3365 atoms outside contour = 3029, contour level = 0.010186 
    3366  
    3367 Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to
    3368 mOCT1-AZT.mrc (#10) coordinates: 
    3369 Matrix rotation and translation 
    3370 -0.89530533 -0.39092164 -0.21356179 331.89133766 
    3371 0.43778783 -0.68362766 -0.58394781 243.21431714 
    3372 0.08228108 -0.61630634 0.78319622 99.39179726 
    3373 Axis -0.03674901 -0.33598352 0.94115067 
    3374 Axis point 137.92729950 180.24940846 0.00000000 
    3375 Rotation angle (degrees) 153.87927506 
    3376 Shift along axis -0.37002346 
    3377  
    3378 
    3379 > hide #!1 models
    3380 
    3381 > select ::name="AZZ"
    3382 
    3383 19 atoms, 20 bonds, 1 residue, 1 model selected 
    3384 
    3385 > hide #!10 models
    3386 
    3387 > select add #11
    3388 
    3389 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    3390 
    3391 > select subtract #11
    3392 
    3393 Nothing selected 
    3394 
    3395 > select add #11
    3396 
    3397 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    3398 
    3399 > color (#!11 & sel) white
    3400 
    3401 > color #11 #aaaaffff
    3402 
    3403 > color (#!11 & sel) white
    3404 
    3405 > select ::name="AZZ"
    3406 
    3407 19 atoms, 20 bonds, 1 residue, 1 model selected 
    3408 
    3409 > color sel red
    3410 
    3411 > color zone #10 near #11 distance 4.98
    3412 
    3413 > show #!10 models
    3414 
    3415 > volume splitbyzone #10
    3416 
    3417 Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at
    3418 level 0.0102, step 1, values float32 
    3419 Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at
    3420 level 0.0102, step 1, values float32 
    3421 Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at
    3422 level 0.0102, step 1, values float32 
    3423 
    3424 > close #12.2
    3425 
    3426 > close #12.1
    3427 
    3428 > color #12.3 #ff0000fe models
    3429 
    3430 > color #12.3 #ff000096 models
    3431 
    3432 > color #12.3 #ffffff96 models
    3433 
    3434 > color #12.3 #ffffb296 models
    3435 
    3436 > color #11 #aaffffff
    3437 
    3438 > color #11 #aaaaffff
    3439 
    3440 > select add #11
    3441 
    3442 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    3443 
    3444 > color (#!11 & sel) byhetero
    3445 
    3446 > select clear
    3447 
    3448 > show #!3 models
    3449 
    3450 > hide #!3 models
    3451 
    3452 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3453 > density.cxs" includeMaps true
    3454 
    3455 > hide #!12.3 models
    3456 
    3457 > hide #!12 models
    3458 
    3459 > hide #!11 models
    3460 
    3461 > show #!1 models
    3462 
    3463 > open
    3464 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc
    3465 
    3466 Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at
    3467 level 0.00595, step 2, values float32 
    3468 
    3469 > volume #13 step 1
    3470 
    3471 > volume #13 level 0.02012
    3472 
    3473 > select add #13
    3474 
    3475 2 models selected 
    3476 
    3477 > view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565
    3478 
    3479 > ui mousemode right "rotate selected models"
    3480 
    3481 > view matrix models
    3482 > #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26
    3483 
    3484 > ui mousemode right "translate selected models"
    3485 
    3486 > view matrix models
    3487 > #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75
    3488 
    3489 > view matrix models
    3490 > #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86
    3491 
    3492 > rename #13 mOCT1-MTF.mrc
    3493 
    3494 > open
    3495 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF-
    3496 > coot-9_real_space_refined_003.pdb
    3497 
    3498 Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14 
    3499 --- 
    3500 Chain | Description 
    3501 A | No description available 
    3502  
    3503 
    3504 > fitmap #13 inMap #1
    3505 
    3506 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3507 using 17817 points 
    3508 correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29 
    3509 steps = 200, shift = 2.4, angle = 7.61 degrees 
    3510  
    3511 Position of mOCT1-MTF.mrc (#13) relative to
    3512 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3513 Matrix rotation and translation 
    3514 -0.05771312 -0.64461025 0.76232987 59.74942259 
    3515 -0.34050237 0.73052504 0.59193860 -66.21901607 
    3516 -0.93847075 -0.22541250 -0.26165220 256.68697920 
    3517 Axis -0.42762978 0.88984156 0.15910615 
    3518 Axis point 123.33045199 0.00000000 117.21732044 
    3519 Rotation angle (degrees) 107.12276965 
    3520 Shift along axis -43.63458901 
    3521  
    3522 
    3523 > select subtract #13
    3524 
    3525 Nothing selected 
    3526 
    3527 > select add #13
    3528 
    3529 2 models selected 
    3530 
    3531 > ui mousemode right "rotate selected models"
    3532 
    3533 > view matrix models
    3534 > #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29
    3535 
    3536 > ui mousemode right "translate selected models"
    3537 
    3538 > view matrix models
    3539 > #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18
    3540 
    3541 > view matrix models
    3542 > #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38
    3543 
    3544 > fitmap #13 inMap #1
    3545 
    3546 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3547 using 17817 points 
    3548 correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06 
    3549 steps = 120, shift = 2.59, angle = 4.72 degrees 
    3550  
    3551 Position of mOCT1-MTF.mrc (#13) relative to
    3552 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3553 Matrix rotation and translation 
    3554 0.43566959 0.38627366 -0.81300964 69.55864121 
    3555 -0.07375796 -0.88487887 -0.45994473 251.91510217 
    3556 -0.89707959 0.26034986 -0.35702406 194.41028021 
    3557 Axis 0.83873143 0.09789343 -0.53567385 
    3558 Axis point 0.00000000 97.27212052 153.57991582 
    3559 Rotation angle (degrees) 154.57081238 
    3560 Shift along axis -21.13865268 
    3561  
    3562 
    3563 > view matrix models
    3564 > #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15
    3565 
    3566 > ui mousemode right "rotate selected models"
    3567 
    3568 > view matrix models
    3569 > #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12
    3570 
    3571 > view matrix models
    3572 > #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42
    3573 
    3574 > ui mousemode right "translate selected models"
    3575 
    3576 > view matrix models
    3577 > #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11
    3578 
    3579 > fitmap #13 inMap #1
    3580 
    3581 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3582 using 17817 points 
    3583 correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72 
    3584 steps = 92, shift = 1.81, angle = 5.01 degrees 
    3585  
    3586 Position of mOCT1-MTF.mrc (#13) relative to
    3587 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3588 Matrix rotation and translation 
    3589 0.31415893 0.53789144 -0.78228958 53.81386032 
    3590 0.19698588 -0.84300825 -0.50053338 220.95415625 
    3591 -0.92870918 0.00314703 -0.37079559 234.49017112 
    3592 Axis 0.80514260 0.23405449 -0.54494394 
    3593 Axis point 0.00000000 81.07236056 158.23174632 
    3594 Rotation angle (degrees) 161.77257653 
    3595 Shift along axis -32.74085292 
    3596  
    3597 
    3598 > view matrix models
    3599 > #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22
    3600 
    3601 > fitmap #13 inMap #1
    3602 
    3603 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3604 using 17817 points 
    3605 correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5 
    3606 steps = 80, shift = 1.45, angle = 5.73 degrees 
    3607  
    3608 Position of mOCT1-MTF.mrc (#13) relative to
    3609 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3610 Matrix rotation and translation 
    3611 0.28419679 0.60053681 -0.74738728 50.81854511 
    3612 0.27816291 -0.79764719 -0.53514891 205.19579930 
    3613 -0.91752798 -0.05580782 -0.39373584 245.12613641 
    3614 Axis 0.79598780 0.28253351 -0.53533003 
    3615 Axis point 0.00000000 71.54715698 160.41463451 
    3616 Rotation angle (degrees) 162.47642045 
    3617 Shift along axis -32.79775064 
    3618  
    3619 
    3620 > view matrix models
    3621 > #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99
    3622 
    3623 > fitmap #13 inMap #1
    3624 
    3625 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3626 using 17817 points 
    3627 correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2 
    3628 steps = 88, shift = 2.33, angle = 2.34 degrees 
    3629  
    3630 Position of mOCT1-MTF.mrc (#13) relative to
    3631 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3632 Matrix rotation and translation 
    3633 0.29378487 0.57675594 -0.76226180 52.65591556 
    3634 0.29516509 -0.81321822 -0.50155130 203.18767751 
    3635 -0.90915787 -0.07764488 -0.40914943 245.95334709 
    3636 Axis 0.80029578 0.27732609 -0.53161726 
    3637 Axis point 0.00000000 73.19686532 158.33534093 
    3638 Rotation angle (degrees) 164.64234082 
    3639 Shift along axis -32.26349399 
    3640  
    3641 
    3642 > view matrix models
    3643 > #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78
    3644 
    3645 > fitmap #13 inMap #1
    3646 
    3647 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3648 using 17817 points 
    3649 correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6 
    3650 steps = 52, shift = 1.52, angle = 1.92 degrees 
    3651  
    3652 Position of mOCT1-MTF.mrc (#13) relative to
    3653 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3654 Matrix rotation and translation 
    3655 0.29574252 0.60146473 -0.74214321 45.38180479 
    3656 0.29484975 -0.79643687 -0.52796964 204.44935424 
    3657 -0.90862533 -0.06267767 -0.41288198 249.74597785 
    3658 Axis 0.80005949 0.28626242 -0.52721784 
    3659 Axis point 0.00000000 72.71544700 159.79227740 
    3660 Rotation angle (degrees) 163.09499009 
    3661 Shift along axis -36.83622428 
    3662  
    3663 
    3664 > ui tool show Matchmaker
    3665 
    3666 > matchmaker #!14 to #5
    3667 
    3668 Parameters 
    3669 --- 
    3670 Chain pairing | bb 
    3671 Alignment algorithm | Needleman-Wunsch 
    3672 Similarity matrix | BLOSUM-62 
    3673 SS fraction | 0.3 
    3674 Gap open (HH/SS/other) | 18/18/6 
    3675 Gap extend | 1 
    3676 SS matrix |  |  | H | S | O 
    3677 ---|---|---|--- 
    3678 H | 6 | -9 | -6 
    3679 S |  | 6 | -6 
    3680 O |  |  | 4 
    3681 Iteration cutoff | 2 
    3682  
    3683 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF-
    3684 coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score =
    3685 2355.8 
    3686 RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs:
    3687 0.377) 
    3688  
    3689 
    3690 > select add #14
    3691 
    3692 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    3693 
    3694 > select subtract #13
    3695 
    3696 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3697 
    3698 > hide #!1 models
    3699 
    3700 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3701 > density.cxs" includeMaps true
    3702 
    3703 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id:
    3704 35654810, major code: 40 (TranslateCoords), minor code: 0 
    3705 
    3706 > color #14 #95cacdff
    3707 
    3708 > select ::name="MF8"
    3709 
    3710 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3711 
    3712 > select add #14
    3713 
    3714 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3715 
    3716 > select subtract #14
    3717 
    3718 Nothing selected 
    3719 
    3720 > select add #14
    3721 
    3722 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3723 
    3724 > color (#!14 & sel) white
    3725 
    3726 > select ::name="MF8"
    3727 
    3728 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3729 
    3730 > color sel red
    3731 
    3732 > color zone #10 near #11 distance 4.98
    3733 
    3734 > color zone #13 near #14 distance 4.98
    3735 
    3736 > hide #!14 models
    3737 
    3738 > show #!14 models
    3739 
    3740 > volume #13 level 0.0238
    3741 
    3742 > volume #13 level 0.02122
    3743 
    3744 > volume #13 level 0.01423
    3745 
    3746 > volume splitbyzone #13
    3747 
    3748 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    3749 level 0.0142, step 1, values float32 
    3750 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    3751 level 0.0142, step 1, values float32 
    3752 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    3753 level 0.0142, step 1, values float32 
    3754 
    3755 > close #15.1
    3756 
    3757 > close #15.2
    3758 
    3759 > volume #15.3 level 0.009273
    3760 
    3761 > volume #15.3 level 0.01703
    3762 
    3763 > close #15#15.3
    3764 
    3765 > select add #14
    3766 
    3767 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3768 
    3769 > show #!13 models
    3770 
    3771 > color zone #13 near #14 distance 4.88
    3772 
    3773 > color zone #13 near #14 distance 4.78
    3774 
    3775 > color zone #13 near #14 distance 4.68
    3776 
    3777 > color zone #13 near #14 distance 4.58
    3778 
    3779 > color zone #13 near #14 distance 4.48
    3780 
    3781 > color zone #13 near #14 distance 4.38
    3782 
    3783 > color zone #13 near #14 distance 4.28
    3784 
    3785 > color zone #13 near #14 distance 4.18
    3786 
    3787 > color zone #13 near #14 distance 4.08
    3788 
    3789 > color zone #13 near #14 distance 3.98
    3790 
    3791 > color zone #13 near #14 distance 3.88
    3792 
    3793 > color zone #13 near #14 distance 3.78
    3794 
    3795 > color zone #13 near #14 distance 3.68
    3796 
    3797 > color zone #13 near #14 distance 3.58
    3798 
    3799 > color zone #13 near #14 distance 3.48
    3800 
    3801 > color zone #13 near #14 distance 3.38
    3802 
    3803 [Repeated 1 time(s)]
    3804 
    3805 > volume splitbyzone #13
    3806 
    3807 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    3808 level 0.0142, step 1, values float32 
    3809 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    3810 level 0.0142, step 1, values float32 
    3811 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    3812 level 0.0142, step 1, values float32 
    3813 
    3814 > close #15.1-2
    3815 
    3816 > volume #15.3 level 0.009634
    3817 
    3818 > color zone #13 near #14 distance 3.28
    3819 
    3820 > color zone #13 near #14 distance 3.18
    3821 
    3822 > color zone #13 near #14 distance 3.08
    3823 
    3824 > close #15#15.3
    3825 
    3826 > show #!13 models
    3827 
    3828 > select add #13
    3829 
    3830 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    3831 
    3832 > select subtract #13
    3833 
    3834 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3835 
    3836 > color zone #13 near #14 distance 2.98
    3837 
    3838 > color zone #13 near #14 distance 2.88
    3839 
    3840 > color zone #13 near #14 distance 2.78
    3841 
    3842 > color zone #13 near #14 distance 2.68
    3843 
    3844 > color zone #13 near #14 distance 2.58
    3845 
    3846 > color zone #13 near #14 distance 2.48
    3847 
    3848 > volume #13 level 0.01681
    3849 
    3850 > fitmap #14 inMap #13
    3851 
    3852 Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map
    3853 mOCT1-MTF.mrc (#13) using 7044 atoms 
    3854 average map value = 0.01572, steps = 48 
    3855 shifted from previous position = 0.0765 
    3856 rotated from previous position = 0.266 degrees 
    3857 atoms outside contour = 4386, contour level = 0.016807 
    3858  
    3859 Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to
    3860 mOCT1-MTF.mrc (#13) coordinates: 
    3861 Matrix rotation and translation 
    3862 0.99946408 0.01781074 -0.02746495 0.87693504 
    3863 -0.01720783 0.99960910 0.02203450 -1.16466203 
    3864 0.02784666 -0.02155008 0.99937988 -1.14535630 
    3865 Axis -0.55418255 -0.70329295 -0.44526478 
    3866 Axis point 28.72708736 -0.00000000 48.38067452 
    3867 Rotation angle (degrees) 2.25364092 
    3868 Shift along axis 0.84310332 
    3869  
    3870 
    3871 > color zone #13 near #14 distance 2.48
    3872 
    3873 [Repeated 1 time(s)]
    3874 
    3875 > color single #13
    3876 
    3877 > color zone #13 near #14 distance 2.48
    3878 
    3879 > color zone #13 near #14 distance 2.38
    3880 
    3881 > color zone #13 near #14 distance 2.28
    3882 
    3883 > color zone #13 near #14 distance 2.18
    3884 
    3885 > color zone #13 near #14 distance 2.08
    3886 
    3887 > color zone #13 near #14 distance 1.98
    3888 
    3889 > color zone #13 near #14 distance 1.88
    3890 
    3891 > color zone #13 near #14 distance 1.78
    3892 
    3893 > color zone #13 near #14 distance 1.68
    3894 
    3895 > color zone #13 near #14 distance 1.58
    3896 
    3897 > color zone #13 near #14 distance 1.48
    3898 
    3899 > color zone #13 near #14 distance 1.38
    3900 
    3901 > color zone #13 near #14 distance 1.48
    3902 
    3903 > color zone #13 near #14 distance 1.58
    3904 
    3905 > color zone #13 near #14 distance 1.68
    3906 
    3907 > color zone #13 near #14 distance 1.78
    3908 
    3909 > color zone #13 near #14 distance 1.88
    3910 
    3911 > color zone #13 near #14 distance 1.98
    3912 
    3913 > volume #13 level 0.01957
    3914 
    3915 > color zone #13 near #14 distance 1.98
    3916 
    3917 > volume splitbyzone #13
    3918 
    3919 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    3920 level 0.0196, step 1, values float32 
    3921 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    3922 level 0.0196, step 1, values float32 
    3923 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    3924 level 0.0196, step 1, values float32 
    3925 
    3926 > close #15.1-2
    3927 
    3928 > color #15.3 yellow models
    3929 
    3930 > color #15.3 white models
    3931 
    3932 > color #15.3 #ffffb2ff models
    3933 
    3934 > color #15.3 #ffffb296 models
    3935 
    3936 > volume #15.3 level 0.01524
    3937 
    3938 > volume #15.3 level 0.0119
    3939 
    3940 > select subtract #14
    3941 
    3942 Nothing selected 
    3943 
    3944 > select add #14
    3945 
    3946 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3947 
    3948 > color #14 #55dd44ff
    3949 
    3950 > color #14 #5d42cdff
    3951 
    3952 > color #14 #5858cdff
    3953 
    3954 > color #14 #7d76cdff
    3955 
    3956 > color #14 #9d7bcdff
    3957 
    3958 > color #14 #cd75baff
    3959 
    3960 > color #14 #9381cdff
    3961 
    3962 > color (#!14 & sel) byhetero
    3963 
    3964 > select clear
    3965 
    3966 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3967 > density.cxs" includeMaps true
    3968 
    3969 > hide #!15.3 models
    3970 
    3971 > hide #!15 models
    3972 
    3973 > hide #!14 models
    3974 
    3975 > show #!1 models
    3976 
    3977 > open
    3978 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc
    3979 
    3980 Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83,
    3981 shown at level 0.00147, step 2, values float32 
    3982 
    3983 > volume #13 level 0.01846
    3984 
    3985 > volume #16 step 1
    3986 
    3987 > volume #16 level 0.01137
    3988 
    3989 > select add #16
    3990 
    3991 2 models selected 
    3992 
    3993 > ui mousemode right "rotate selected models"
    3994 
    3995 > view matrix models
    3996 > #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4
    3997 
    3998 > view matrix models
    3999 > #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203
    4000 
    4001 > view matrix models
    4002 > #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605
    4003 
    4004 > view matrix models
    4005 > #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74
    4006 
    4007 > view matrix models
    4008 > #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38
    4009 
    4010 > view matrix models
    4011 > #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16
    4012 
    4013 > ui mousemode right "translate selected models"
    4014 
    4015 > view matrix models
    4016 > #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09
    4017 
    4018 > view matrix models
    4019 > #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87
    4020 
    4021 > view matrix models
    4022 > #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08
    4023 
    4024 > view matrix models
    4025 > #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69
    4026 
    4027 > ui mousemode right "rotate selected models"
    4028 
    4029 > view matrix models
    4030 > #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76
    4031 
    4032 > view matrix models
    4033 > #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35
    4034 
    4035 > ui mousemode right "translate selected models"
    4036 
    4037 > view matrix models
    4038 > #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37
    4039 
    4040 > ui mousemode right "rotate selected models"
    4041 
    4042 > view matrix models
    4043 > #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3
    4044 
    4045 > rename #16 hOCT1-VB1.mrc
    4046 
    4047 > fitmap #16 inMap #1
    4048 
    4049 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4050 using 29501 points 
    4051 correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4 
    4052 steps = 148, shift = 3.34, angle = 5.64 degrees 
    4053  
    4054 Position of hOCT1-VB1.mrc (#16) relative to
    4055 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4056 Matrix rotation and translation 
    4057 -0.66774800 0.66848229 -0.32748134 111.59775010 
    4058 0.47076725 0.03845367 -0.88141903 115.78397104 
    4059 -0.57662015 -0.74273329 -0.34037693 282.67572866 
    4060 Axis 0.39969377 0.71802066 -0.56981683 
    4061 Axis point 39.62225841 0.00000000 179.67701786 
    4062 Rotation angle (degrees) 170.00920250 
    4063 Shift along axis -33.33317846 
    4064  
    4065 
    4066 > ui mousemode right "translate selected models"
    4067 
    4068 > view matrix models
    4069 > #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9
    4070 
    4071 > fitmap #16 inMap #1
    4072 
    4073 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4074 using 29501 points 
    4075 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    4076 steps = 60, shift = 1.34, angle = 1.92 degrees 
    4077  
    4078 Position of hOCT1-VB1.mrc (#16) relative to
    4079 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4080 Matrix rotation and translation 
    4081 -0.68896253 0.65809895 -0.30370448 111.90845021 
    4082 0.45027206 0.06027049 -0.89085495 116.65862228 
    4083 -0.56796628 -0.75051532 -0.33784768 287.44343290 
    4084 Axis 0.38522072 0.72537689 -0.57046767 
    4085 Axis point 41.86637964 0.00000000 181.62562393 
    4086 Rotation angle (degrees) 169.50470225 
    4087 Shift along axis -36.24626372 
    4088  
    4089 
    4090 > view matrix models
    4091 > #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46
    4092 
    4093 > fitmap #16 inMap #1
    4094 
    4095 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4096 using 29501 points 
    4097 correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7 
    4098 steps = 72, shift = 3.09, angle = 0.0182 degrees 
    4099  
    4100 Position of hOCT1-VB1.mrc (#16) relative to
    4101 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4102 Matrix rotation and translation 
    4103 -0.68902052 0.65795875 -0.30387662 111.96278841 
    4104 0.45022908 0.06002731 -0.89089309 116.69902951 
    4105 -0.56793001 -0.75065771 -0.33759222 287.41226501 
    4106 Axis 0.38519550 0.72529614 -0.57058737 
    4107 Axis point 41.87016659 0.00000000 181.64241189 
    4108 Rotation angle (degrees) 169.51189271 
    4109 Shift along axis -36.22489055 
    4110  
    4111 
    4112 > fitmap #16 inMap #1
    4113 
    4114 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4115 using 29501 points 
    4116 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    4117 steps = 36, shift = 0.00448, angle = 0.00722 degrees 
    4118  
    4119 Position of hOCT1-VB1.mrc (#16) relative to
    4120 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4121 Matrix rotation and translation 
    4122 -0.68898476 0.65802671 -0.30381055 111.93916561 
    4123 0.45024501 0.06010903 -0.89087953 116.68451889 
    4124 -0.56796077 -0.75059160 -0.33768744 287.42460080 
    4125 Axis 0.38521270 0.72532270 -0.57054198 
    4126 Axis point 41.86758112 0.00000000 181.63640339 
    4127 Rotation angle (degrees) 169.50839167 
    4128 Shift along axis -36.23348002 
    4129  
    4130 
    4131 > open
    4132 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb
    4133 
    4134 Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17 
    4135 --- 
    4136 Chain | Description 
    4137 A | No description available 
    4138  
    4139 
    4140 > ui tool show Matchmaker
    4141 
    4142 > matchmaker #!17 to #5
    4143 
    4144 Parameters 
    4145 --- 
    4146 Chain pairing | bb 
    4147 Alignment algorithm | Needleman-Wunsch 
    4148 Similarity matrix | BLOSUM-62 
    4149 SS fraction | 0.3 
    4150 Gap open (HH/SS/other) | 18/18/6 
    4151 Gap extend | 1 
    4152 SS matrix |  |  | H | S | O 
    4153 ---|---|---|--- 
    4154 H | 6 | -9 | -6 
    4155 S |  | 6 | -6 
    4156 O |  |  | 4 
    4157 Iteration cutoff | 2 
    4158  
    4159 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    4160 hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment
    4161 score = 1980 
    4162 RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs:
    4163 1.346) 
    4164  
    4165 
    4166 > fitmap #17 inMap #16
    4167 
    4168 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    4169 hOCT1-VB1.mrc (#16) using 3479 atoms 
    4170 average map value = 0.02025, steps = 64 
    4171 shifted from previous position = 0.153 
    4172 rotated from previous position = 0.521 degrees 
    4173 atoms outside contour = 1063, contour level = 0.011373 
    4174  
    4175 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    4176 hOCT1-VB1.mrc (#16) coordinates: 
    4177 Matrix rotation and translation 
    4178 0.99999651 0.00186028 0.00187897 -0.40239474 
    4179 -0.00185675 0.99999652 -0.00187607 0.55801929 
    4180 -0.00188246 0.00187257 0.99999648 0.09469763 
    4181 Axis 0.57831092 0.58028383 -0.57343453 
    4182 Axis point 61.09212114 0.00000000 225.59585813 
    4183 Rotation angle (degrees) 0.18569746 
    4184 Shift along axis 0.03679741 
    4185  
    4186 
    4187 > fitmap #17 inMap #16
    4188 
    4189 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    4190 hOCT1-VB1.mrc (#16) using 3479 atoms 
    4191 average map value = 0.02025, steps = 28 
    4192 shifted from previous position = 0.0153 
    4193 rotated from previous position = 0.0146 degrees 
    4194 atoms outside contour = 1064, contour level = 0.011373 
    4195  
    4196 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    4197 hOCT1-VB1.mrc (#16) coordinates: 
    4198 Matrix rotation and translation 
    4199 0.99999599 0.00211002 0.00188874 -0.43726655 
    4200 -0.00210638 0.99999592 -0.00192887 0.59237860 
    4201 -0.00189280 0.00192488 0.99999636 0.07510223 
    4202 Axis 0.56254941 0.55200867 -0.61548727 
    4203 Axis point 271.69369003 217.02489508 0.00000000 
    4204 Rotation angle (degrees) 0.19625280 
    4205 Shift along axis 0.03478962 
    4206  
    4207 
    4208 > hide #!1 models
    4209 
    4210 > select add #17
    4211 
    4212 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    4213 
    4214 > select subtract #16
    4215 
    4216 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4217 
    4218 > color (#!17 & sel) white
    4219 
    4220 > select clear
    4221 
    4222 > select ::name="VIB"
    4223 
    4224 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4225 
    4226 > color sel red
    4227 
    4228 > color zone #16 near #17 distance 4.98
    4229 
    4230 > color zone #16 near #17 distance 4.88
    4231 
    4232 > color zone #16 near #17 distance 4.78
    4233 
    4234 > color zone #16 near #17 distance 4.68
    4235 
    4236 > color zone #16 near #17 distance 4.58
    4237 
    4238 > color zone #16 near #17 distance 4.48
    4239 
    4240 > color zone #16 near #17 distance 4.38
    4241 
    4242 > color zone #16 near #17 distance 4.28
    4243 
    4244 > color zone #16 near #17 distance 4.18
    4245 
    4246 > color zone #16 near #17 distance 4.08
    4247 
    4248 > color zone #16 near #17 distance 3.98
    4249 
    4250 > color zone #16 near #17 distance 3.88
    4251 
    4252 > color zone #16 near #17 distance 3.78
    4253 
    4254 > color zone #16 near #17 distance 3.68
    4255 
    4256 > color zone #16 near #17 distance 3.58
    4257 
    4258 > color zone #16 near #17 distance 3.48
    4259 
    4260 > color zone #16 near #17 distance 3.38
    4261 
    4262 > color zone #16 near #17 distance 3.28
    4263 
    4264 > color sel white
    4265 
    4266 > select ::name="VIB"
    4267 
    4268 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4269 
    4270 > color sel red
    4271 
    4272 > select add #16
    4273 
    4274 18 atoms, 19 bonds, 1 residue, 3 models selected 
    4275 
    4276 > select add #17
    4277 
    4278 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    4279 
    4280 > select subtract #17
    4281 
    4282 2 models selected 
    4283 
    4284 > color #16.1 white
    4285 
    4286 > color zone #16 near #17 distance 3.28
    4287 
    4288 > color zone #16 near #17 distance 3.18
    4289 
    4290 > color zone #16 near #17 distance 3.08
    4291 
    4292 > color zone #16 near #17 distance 2.98
    4293 
    4294 > color zone #16 near #17 distance 2.88
    4295 
    4296 > color zone #16 near #17 distance 2.98
    4297 
    4298 > color zone #16 near #17 distance 3.08
    4299 
    4300 > color zone #16 near #17 distance 3.18
    4301 
    4302 > color zone #16 near #17 distance 3.28
    4303 
    4304 > color zone #16 near #17 distance 3.38
    4305 
    4306 [Repeated 1 time(s)]
    4307 
    4308 > volume splitbyzone #16
    4309 
    4310 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    4311 level 0.0114, step 1, values float32 
    4312 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    4313 level 0.0114, step 1, values float32 
    4314 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    4315 level 0.0114, step 1, values float32 
    4316 
    4317 > close #18.1-2
    4318 
    4319 > color #18.3 yellow models
    4320 
    4321 > color #18.3 white models
    4322 
    4323 > color #18.3 #ffffb2ff models
    4324 
    4325 > color #18.3 #ffffb296 models
    4326 
    4327 > select add #17
    4328 
    4329 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    4330 
    4331 > select subtract #16
    4332 
    4333 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4334 
    4335 > color #17 #6622bbff
    4336 
    4337 > color #17 #62be40ff
    4338 
    4339 > color (#!17 & sel) byhetero
    4340 
    4341 Drag select of 1 atoms, 1 bonds 
    4342 
    4343 > volume #18.3 level 0.006511
    4344 
    4345 > volume #18.3 level 0.01112
    4346 
    4347 > close #18#18.3
    4348 
    4349 > select add #17
    4350 
    4351 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4352 
    4353 > color (#!17 & sel) white
    4354 
    4355 > select ::name="VIB"
    4356 
    4357 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4358 
    4359 > color sel red
    4360 
    4361 > show #!16 models
    4362 
    4363 > color zone #16 near #17 distance 3.28
    4364 
    4365 > color zone #16 near #17 distance 3.18
    4366 
    4367 > color zone #16 near #17 distance 3.08
    4368 
    4369 > color zone #16 near #17 distance 2.98
    4370 
    4371 > color zone #16 near #17 distance 2.88
    4372 
    4373 > color zone #16 near #17 distance 2.78
    4374 
    4375 > color zone #16 near #17 distance 2.68
    4376 
    4377 > color zone #16 near #17 distance 2.58
    4378 
    4379 > color zone #16 near #17 distance 2.48
    4380 
    4381 > color zone #16 near #17 distance 2.38
    4382 
    4383 > color zone #16 near #17 distance 2.28
    4384 
    4385 > color zone #16 near #17 distance 2.18
    4386 
    4387 > color zone #16 near #17 distance 2.08
    4388 
    4389 > color zone #16 near #17 distance 1.98
    4390 
    4391 > color zone #16 near #17 distance 1.88
    4392 
    4393 > color zone #16 near #17 distance 1.78
    4394 
    4395 > color zone #16 near #17 distance 1.68
    4396 
    4397 > color zone #16 near #17 distance 1.78
    4398 
    4399 > color zone #16 near #17 distance 1.88
    4400 
    4401 > color zone #16 near #17 distance 1.98
    4402 
    4403 > color zone #16 near #17 distance 2.08
    4404 
    4405 > volume splitbyzone #16
    4406 
    4407 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    4408 level 0.0114, step 1, values float32 
    4409 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    4410 level 0.0114, step 1, values float32 
    4411 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    4412 level 0.0114, step 1, values float32 
    4413 
    4414 > close #18.1-2
    4415 
    4416 > color #18.3 white models
    4417 
    4418 > color #18.3 #ffffb2ff models
    4419 
    4420 > select add #18.3
    4421 
    4422 18 atoms, 19 bonds, 1 residue, 3 models selected 
    4423 
    4424 > color #18.3 #ffffb296 models
    4425 
    4426 > select subtract #18.3
    4427 
    4428 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4429 
    4430 > select add #17
    4431 
    4432 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4433 
    4434 > select subtract #17
    4435 
    4436 Nothing selected 
    4437 
    4438 > select add #17
    4439 
    4440 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4441 
    4442 > color #17 #6622bbff
    4443 
    4444 > color #17 #62be40ff
    4445 
    4446 > color (#!17 & sel) byhetero
    4447 
    4448 > view
    4449 
    4450 > hide #!18.3 models
    4451 
    4452 > hide #!18 models
    4453 
    4454 > hide #!17 models
    4455 
    4456 > select subtract #17
    4457 
    4458 Nothing selected 
    4459 
    4460 > show #!1 models
    4461 
    4462 > open
    4463 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc
    4464 
    4465 Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown
    4466 at level 2.83e-06, step 2, values float32 
    4467 
    4468 > volume #19 step 1
    4469 
    4470 > volume #19 level 0.0131
    4471 
    4472 > select add #19
    4473 
    4474 2 models selected 
    4475 
    4476 > ui mousemode right "rotate selected models"
    4477 
    4478 > view matrix models
    4479 > #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04
    4480 
    4481 > ui mousemode right "translate selected models"
    4482 
    4483 > view matrix models
    4484 > #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801
    4485 
    4486 > view matrix models
    4487 > #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027
    4488 
    4489 > view matrix models
    4490 > #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593
    4491 
    4492 > rename #19 hOCT1-AZT.mrc
    4493 
    4494 > fitmap #19 inMap #16
    4495 
    4496 Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points 
    4497 correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07 
    4498 steps = 112, shift = 2.59, angle = 19.3 degrees 
    4499  
    4500 Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates: 
    4501 Matrix rotation and translation 
    4502 0.86934918 -0.02079803 -0.49376051 87.20318527 
    4503 -0.45396874 0.36123943 -0.81450504 253.58267245 
    4504 0.19530587 0.93224113 0.30460154 -57.13169181 
    4505 Axis 0.90642923 -0.35757337 -0.22478286 
    4506 Axis point 0.00000000 185.25380563 166.58335969 
    4507 Rotation angle (degrees) 74.47879004 
    4508 Shift along axis 1.21133072 
    4509  
    4510 
    4511 > open
    4512 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT-
    4513 > coot-2_real_space_refined_006.pdb
    4514 
    4515 Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20 
    4516 --- 
    4517 Chain | Description 
    4518 A | No description available 
    4519  
    4520 
    4521 > ui tool show Matchmaker
    4522 
    4523 > matchmaker #!20 to #5
    4524 
    4525 Parameters 
    4526 --- 
    4527 Chain pairing | bb 
    4528 Alignment algorithm | Needleman-Wunsch 
    4529 Similarity matrix | BLOSUM-62 
    4530 SS fraction | 0.3 
    4531 Gap open (HH/SS/other) | 18/18/6 
    4532 Gap extend | 1 
    4533 SS matrix |  |  | H | S | O 
    4534 ---|---|---|--- 
    4535 H | 6 | -9 | -6 
    4536 S |  | 6 | -6 
    4537 O |  |  | 4 
    4538 Iteration cutoff | 2 
    4539  
    4540 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT-
    4541 coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score =
    4542 1978 
    4543 RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs:
    4544 1.482) 
    4545  
    4546 
    4547 > hide #!1 models
    4548 
    4549 > color #19 white models
    4550 
    4551 > select add #20
    4552 
    4553 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected 
    4554 
    4555 > color #20 white
    4556 
    4557 > hide #!19 models
    4558 
    4559 > select subtract #19
    4560 
    4561 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    4562 
    4563 > select up
    4564 
    4565 2 atoms, 1 bond, 1 residue, 1 model selected 
    4566 
    4567 > select up
    4568 
    4569 19 atoms, 20 bonds, 1 residue, 1 model selected 
    4570 
    4571 > color sel red
    4572 
    4573 > color zone #19 near #20 distance 4.98
    4574 
    4575 > show #!19 models
    4576 
    4577 > select add #19
    4578 
    4579 19 atoms, 20 bonds, 1 residue, 3 models selected 
    4580 
    4581 > select subtract #19
    4582 
    4583 19 atoms, 20 bonds, 1 residue, 1 model selected 
    4584 
    4585 > color zone #19 near #20 distance 4.88
    4586 
    4587 > color zone #19 near #20 distance 4.78
    4588 
    4589 > color zone #19 near #20 distance 4.68
    4590 
    4591 > color zone #19 near #20 distance 4.58
    4592 
    4593 > color zone #19 near #20 distance 4.48
    4594 
    4595 > color zone #19 near #20 distance 4.38
    4596 
    4597 > color zone #19 near #20 distance 4.28
    4598 
    4599 > color zone #19 near #20 distance 4.18
    4600 
    4601 > color zone #19 near #20 distance 4.08
    4602 
    4603 > color zone #19 near #20 distance 3.98
    4604 
    4605 > color zone #19 near #20 distance 3.88
    4606 
    4607 > color zone #19 near #20 distance 3.78
    4608 
    4609 > color zone #19 near #20 distance 3.68
    4610 
    4611 > color zone #19 near #20 distance 3.58
    4612 
    4613 > color zone #19 near #20 distance 3.48
    4614 
    4615 > volume #19 level 0.01039
    4616 
    4617 > color zone #19 near #20 distance 3.38
    4618 
    4619 > color zone #19 near #20 distance 3.28
    4620 
    4621 > color zone #19 near #20 distance 3.18
    4622 
    4623 > color zone #19 near #20 distance 3.08
    4624 
    4625 > color zone #19 near #20 distance 2.98
    4626 
    4627 > color zone #19 near #20 distance 2.88
    4628 
    4629 > color zone #19 near #20 distance 2.78
    4630 
    4631 > color zone #19 near #20 distance 2.68
    4632 
    4633 > color zone #19 near #20 distance 2.58
    4634 
    4635 > color zone #19 near #20 distance 2.48
    4636 
    4637 > color zone #19 near #20 distance 2.38
    4638 
    4639 > color zone #19 near #20 distance 2.28
    4640 
    4641 > color zone #19 near #20 distance 2.18
    4642 
    4643 > color zone #19 near #20 distance 2.08
    4644 
    4645 > color zone #19 near #20 distance 1.98
    4646 
    4647 > color zone #19 near #20 distance 1.88
    4648 
    4649 > color zone #19 near #20 distance 1.78
    4650 
    4651 > color zone #19 near #20 distance 1.88
    4652 
    4653 > color zone #19 near #20 distance 1.98
    4654 
    4655 > color zone #19 near #20 distance 2.08
    4656 
    4657 [Repeated 1 time(s)]
    4658 
    4659 > volume splitbyzone #19
    4660 
    4661 Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at
    4662 level 0.0104, step 1, values float32 
    4663 Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at
    4664 level 0.0104, step 1, values float32 
    4665 Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at
    4666 level 0.0104, step 1, values float32 
    4667 
    4668 > close #21.1-2
    4669 
    4670 > select add #20
    4671 
    4672 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    4673 
    4674 > select subtract #20
    4675 
    4676 Nothing selected 
    4677 
    4678 > select add #20
    4679 
    4680 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    4681 
    4682 > color #20 #773333ff
    4683 
    4684 > color #20 #733551ff
    4685 
    4686 > color (#!20 & sel) byhetero
    4687 
    4688 > select clear
    4689 
    4690 > color #21.3 #ff000096 models
    4691 
    4692 > color #21.3 #ffffff96 models
    4693 
    4694 > color #21.3 #ffffb296 models
    4695 
    4696 > volume #21.3 level 0.008896
    4697 
    4698 > hide #!21.3 models
    4699 
    4700 > hide #!21 models
    4701 
    4702 > hide #!20 models
    4703 
    4704 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    4705 > density.cxs" includeMaps true
    4706 
    4707 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id:
    4708 35654939, major code: 40 (TranslateCoords), minor code: 0 
    4709 
    4710 > show #!3 models
    4711 
    4712 > show #!6.3 models
    4713 
    4714 > select ::name="ABC"
    4715 
    4716 42 atoms, 48 bonds, 2 residues, 1 model selected 
    4717 
    4718 > view sel
    4719 
    4720 > select clear
    4721 
    4722 > hide #!6.3 models
    4723 
    4724 > hide #!6 models
    4725 
    4726 > hide #!3 models
    4727 
    4728 > show #!2 models
    4729 
    4730 > show #!5 models
    4731 
    4732 > hide #!5 models
    4733 
    4734 > hide #!2 models
    4735 
    4736 > show #!8 models
    4737 
    4738 > show #!9.3 models
    4739 
    4740 > hide #!9.3 models
    4741 
    4742 > hide #!9 models
    4743 
    4744 > hide #!8 models
    4745 
    4746 > show #!11 models
    4747 
    4748 > show #!12.3 models
    4749 
    4750 > hide #!12.3 models
    4751 
    4752 > hide #!12 models
    4753 
    4754 > hide #!11 models
    4755 
    4756 > show #!14 models
    4757 
    4758 > show #!15 models
    4759 
    4760 > hide #!15 models
    4761 
    4762 > show #!15.3 models
    4763 
    4764 > hide #!14 models
    4765 
    4766 > hide #!15 models
    4767 
    4768 > hide #!15.3 models
    4769 
    4770 > show #!17 models
    4771 
    4772 > show #!18.3 models
    4773 
    4774 > hide #!18.3 models
    4775 
    4776 > hide #!18 models
    4777 
    4778 > hide #!17 models
    4779 
    4780 > show #!20 models
    4781 
    4782 > show #!21.3 models
    4783 
    4784 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    4785 > density.cxs" includeMaps true
    4786 
    4787 > save
    4788 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs
    4789 > includeMaps true
    4790 
    4791 [Repeated 1 time(s)]
    4792 
    4793 > close session
    4794 
    4795 > open
    4796 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot-
    4797 > history.scm
    4798 
    4799 Unrecognized file suffix '.scm' 
    4800 
    4801 > open
    4802 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
    4803 
    4804 Summary of feedback from opening
    4805 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif 
    4806 --- 
    4807 warnings | Skipping chem_comp category: Missing column 'type' near line 187 
    4808 Missing entity information. Treating each chain as a separate entity. 
    4809 Bad residue range for struct_conf "3" near line 98 
    4810 Bad residue range for struct_conf "4" near line 99 
    4811 Bad residue range for struct_conf "5" near line 100 
    4812 Bad residue range for struct_conf "6" near line 101 
    4813 Bad residue range for struct_conf "7" near line 102 
    4814 15 messages similar to the above omitted 
    4815 Invalid sheet range for struct_sheet_range "2 1" near line 183 
    4816 Invalid sheet range for struct_sheet_range "3 1" near line 184 
    4817 Invalid sheet range for struct_sheet_range "4 1" near line 186 
    4818 Missing or incomplete sequence information. Inferred polymer connectivity. 
    4819 Skipping chem_comp category: Missing column 'type' near line 4361 
    4820  
    4821 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1 
    4822 --- 
    4823 Chain | Description 
    4824 A | No description available 
    4825  
    4826 
    4827 > close session
    4828 
    4829 > open
    4830 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb
    4831 
    4832 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1 
    4833 --- 
    4834 Chain | Description 
    4835 A | No description available 
    4836  
    4837 
    4838 QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id:
    4839 35655077, major code: 40 (TranslateCoords), minor code: 0 
    4840 
    4841 > open
    4842 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc
    4843 
    4844 Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    4845 level 0.00421, step 2, values float32 
    4846 
    4847 > rename #2 rOAT1-AZT.mrc
    4848 
    4849 > volume #2 step 1
    4850 
    4851 > volume #2 level 0.01415
    4852 
    4853 > save
    4854 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    4855 > includeMaps true
    4856 
    4857 > select add #1
    4858 
    4859 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    4860 
    4861 > ui mousemode right "rotate selected models"
    4862 
    4863 > view matrix models
    4864 > #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07
    4865 
    4866 > ui mousemode right "translate selected models"
    4867 
    4868 > view matrix models
    4869 > #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5
    4870 
    4871 > ui mousemode right "rotate selected models"
    4872 
    4873 > view matrix models
    4874 > #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33
    4875 
    4876 > ui mousemode right "translate selected models"
    4877 
    4878 > view matrix models
    4879 > #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34
    4880 
    4881 > view matrix models
    4882 > #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41
    4883 
    4884 > ui tool show "Fit in Map"
    4885 
    4886 > fitmap #1 inMap #2
    4887 
    4888 Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map
    4889 rOAT1-AZT.mrc (#2) using 3905 atoms 
    4890 average map value = 0.01965, steps = 108 
    4891 shifted from previous position = 2.32 
    4892 rotated from previous position = 12.8 degrees 
    4893 atoms outside contour = 1436, contour level = 0.014154 
    4894  
    4895 Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to
    4896 rOAT1-AZT.mrc (#2) coordinates: 
    4897 Matrix rotation and translation 
    4898 -0.62427498 -0.78041245 -0.03517318 323.27181278 
    4899 -0.15760640 0.16991691 -0.97277359 257.26632447 
    4900 0.76514114 -0.60173470 -0.22907287 142.60270901 
    4901 Axis 0.34360458 -0.74113973 0.57675627 
    4902 Axis point 193.37147122 0.00000000 235.15956508 
    4903 Rotation angle (degrees) 147.32171525 
    4904 Shift along axis 2.65438788 
    4905  
    4906 
    4907 > select subtract #1
    4908 
    4909 Nothing selected 
    4910 
    4911 > select add #1
    4912 
    4913 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    4914 
    4915 > color sel white
    4916 
    4917 > select ::name="AZZ"
    4918 
    4919 19 atoms, 20 bonds, 1 residue, 1 model selected 
    4920 
    4921 > color sel red
    4922 
    4923 > ui tool show "Color Zone"
    4924 
    4925 > color zone #2 near #1 distance 4.98
    4926 
    4927 > volume #2 level 0.0105
    4928 
    4929 > color zone #2 near #1 distance 4.88
    4930 
    4931 > color zone #2 near #1 distance 4.78
    4932 
    4933 > color zone #2 near #1 distance 4.68
    4934 
    4935 > color zone #2 near #1 distance 4.58
    4936 
    4937 > color zone #2 near #1 distance 4.48
    4938 
    4939 > color zone #2 near #1 distance 4.38
    4940 
    4941 > color zone #2 near #1 distance 4.28
    4942 
    4943 > color zone #2 near #1 distance 4.18
    4944 
    4945 > color zone #2 near #1 distance 4.08
    4946 
    4947 > color zone #2 near #1 distance 3.98
    4948 
    4949 > color zone #2 near #1 distance 3.88
    4950 
    4951 > color zone #2 near #1 distance 3.78
    4952 
    4953 > color zone #2 near #1 distance 3.68
    4954 
    4955 > color zone #2 near #1 distance 3.58
    4956 
    4957 > color zone #2 near #1 distance 3.48
    4958 
    4959 > color zone #2 near #1 distance 3.38
    4960 
    4961 > color zone #2 near #1 distance 3.28
    4962 
    4963 > color zone #2 near #1 distance 3.18
    4964 
    4965 > color zone #2 near #1 distance 3.08
    4966 
    4967 > color zone #2 near #1 distance 2.98
    4968 
    4969 > color zone #2 near #1 distance 2.88
    4970 
    4971 > color zone #2 near #1 distance 2.78
    4972 
    4973 > color zone #2 near #1 distance 2.68
    4974 
    4975 > color zone #2 near #1 distance 2.58
    4976 
    4977 > color zone #2 near #1 distance 2.48
    4978 
    4979 > color zone #2 near #1 distance 2.38
    4980 
    4981 > color zone #2 near #1 distance 2.28
    4982 
    4983 > color zone #2 near #1 distance 2.18
    4984 
    4985 > color zone #2 near #1 distance 2.08
    4986 
    4987 > color zone #2 near #1 distance 1.98
    4988 
    4989 > color zone #2 near #1 distance 1.88
    4990 
    4991 > color zone #2 near #1 distance 1.78
    4992 
    4993 > volume #2 level 0.008069
    4994 
    4995 > volume splitbyzone #2
    4996 
    4997 Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at
    4998 level 0.00807, step 1, values float32 
    4999 Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at
    5000 level 0.00807, step 1, values float32 
    5001 Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    5002 level 0.00807, step 1, values float32 
    5003 
    5004 > close #3.1-2
    5005 
    5006 > color #3.3 white models
    5007 
    5008 > color #3.3 #ffffb2ff models
    5009 
    5010 > select add #1
    5011 
    5012 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    5013 
    5014 > color #1 #dd22bbff
    5015 
    5016 > color #1 tan
    5017 
    5018 > color sel byhetero
    5019 
    5020 > color #3.3 #ffffb296 models
    5021 
    5022 > save
    5023 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5024 > includeMaps true
    5025 
    5026 QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id:
    5027 35655128, major code: 40 (TranslateCoords), minor code: 0 
    5028 
    5029 QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id:
    5030 35655123, major code: 40 (TranslateCoords), minor code: 0 
    5031 
    5032 > save
    5033 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5034 > includeMaps true
    5035 
    5036 QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id:
    5037 35655133, major code: 40 (TranslateCoords), minor code: 0 
    5038 
    5039 > rename #1 rOAT1-AZT_IF.pdb
    5040 
    5041 > rename #2 rOAT1-AZT_IF.mrc
    5042 
    5043 > rename #3 "rOAT1-AZT_IF.mrc split"
    5044 
    5045 > rename #3.3 "rOAT1-AZT_IF.mrc 2"
    5046 
    5047 > save
    5048 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5049 > includeMaps true
    5050 
    5051 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id:
    5052 35655148, major code: 40 (TranslateCoords), minor code: 0 
    5053 
    5054 > open
    5055 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc
    5056 
    5057 Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    5058 level 0.00134, step 2, values float32 
    5059 
    5060 > close #4
    5061 
    5062 > open
    5063 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    5064 
    5065 Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    5066 level 0.00459, step 2, values float32 
    5067 
    5068 > volume #4 step 1
    5069 
    5070 > volume #4 level 0.01366
    5071 
    5072 > rename #4 rOAT1-AZT_OF.mrc
    5073 
    5074 > open
    5075 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    5076 > coot-7_real_space_refined_008.pdb
    5077 
    5078 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5 
    5079 --- 
    5080 Chain | Description 
    5081 A | No description available 
    5082  
    5083 
    5084 > select subtract #1
    5085 
    5086 Nothing selected 
    5087 
    5088 > select add #5
    5089 
    5090 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5091 
    5092 > hide #!3 models
    5093 
    5094 > hide #!3.3 models
    5095 
    5096 > hide #1 models
    5097 
    5098 > view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632
    5099 
    5100 > view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95
    5101 
    5102 > fitmap #5 inMap #4
    5103 
    5104 Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map
    5105 rOAT1-AZT_OF.mrc (#4) using 3792 atoms 
    5106 average map value = 0.01938, steps = 84 
    5107 shifted from previous position = 0.803 
    5108 rotated from previous position = 4.35 degrees 
    5109 atoms outside contour = 1323, contour level = 0.013659 
    5110  
    5111 Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to
    5112 rOAT1-AZT_OF.mrc (#4) coordinates: 
    5113 Matrix rotation and translation 
    5114 0.99822969 -0.04531644 -0.03852150 72.45731875 
    5115 0.04345449 0.99790785 -0.04787105 67.21065914 
    5116 0.04061025 0.04611237 0.99811044 61.32293455 
    5117 Axis 0.62004547 -0.52206316 0.58565662 
    5118 Axis point 0.00000000 -669.59173064 1932.22009801 
    5119 Rotation angle (degrees) 4.34647273 
    5120 Shift along axis 45.75280586 
    5121  
    5122 
    5123 > save
    5124 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb
    5125 > models #5 relModel #4
    5126 
    5127 > save
    5128 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb
    5129 > models #1
    5130 
    5131 > close #5
    5132 
    5133 > open
    5134 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    5135 
    5136 Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at
    5137 level 0.00459, step 2, values float32 
    5138 
    5139 > close #5
    5140 
    5141 > open
    5142 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF-
    5143 > coot-0_real_space_refined_003.pdb
    5144 
    5145 Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5 
    5146 --- 
    5147 Chain | Description 
    5148 A | No description available 
    5149  
    5150 
    5151 > select add #4
    5152 
    5153 2 models selected 
    5154 
    5155 > select subtract #4
    5156 
    5157 Nothing selected 
    5158 
    5159 > select add #5
    5160 
    5161 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5162 
    5163 > select clear
    5164 
    5165 > select add #5
    5166 
    5167 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5168 
    5169 > color #5 white
    5170 
    5171 > color #4 white models
    5172 
    5173 > color #2 white models
    5174 
    5175 > select #5/A:601@O4
    5176 
    5177 1 atom, 1 residue, 1 model selected 
    5178 
    5179 > select up
    5180 
    5181 19 atoms, 20 bonds, 1 residue, 1 model selected 
    5182 
    5183 > color sel red
    5184 
    5185 > color zone #4 near #5 distance 4.98
    5186 
    5187 > color zone #4 near #5 distance 4.88
    5188 
    5189 > color zone #4 near #5 distance 4.78
    5190 
    5191 > color zone #4 near #5 distance 4.68
    5192 
    5193 > color zone #4 near #5 distance 4.58
    5194 
    5195 > color zone #4 near #5 distance 4.48
    5196 
    5197 > color zone #4 near #5 distance 4.38
    5198 
    5199 > color zone #4 near #5 distance 4.28
    5200 
    5201 > color zone #4 near #5 distance 4.18
    5202 
    5203 > color zone #4 near #5 distance 4.08
    5204 
    5205 > color zone #4 near #5 distance 3.98
    5206 
    5207 > color zone #4 near #5 distance 3.88
    5208 
    5209 > color zone #4 near #5 distance 3.78
    5210 
    5211 > color zone #4 near #5 distance 3.68
    5212 
    5213 > color zone #4 near #5 distance 3.58
    5214 
    5215 > color zone #4 near #5 distance 3.48
    5216 
    5217 > color zone #4 near #5 distance 3.38
    5218 
    5219 > color zone #4 near #5 distance 3.28
    5220 
    5221 > color zone #4 near #5 distance 3.18
    5222 
    5223 > color zone #4 near #5 distance 3.08
    5224 
    5225 > color zone #4 near #5 distance 2.98
    5226 
    5227 > color zone #4 near #5 distance 2.88
    5228 
    5229 > color zone #4 near #5 distance 2.78
    5230 
    5231 > color zone #4 near #5 distance 2.68
    5232 
    5233 > color zone #4 near #5 distance 2.58
    5234 
    5235 > color zone #4 near #5 distance 2.48
    5236 
    5237 > color zone #4 near #5 distance 2.38
    5238 
    5239 > color zone #4 near #5 distance 2.28
    5240 
    5241 > color zone #4 near #5 distance 2.18
    5242 
    5243 > color zone #4 near #5 distance 2.08
    5244 
    5245 > color zone #4 near #5 distance 1.98
    5246 
    5247 > color zone #4 near #5 distance 1.88
    5248 
    5249 > color zone #4 near #5 distance 1.78
    5250 
    5251 > color zone #4 near #5 distance 1.68
    5252 
    5253 > color zone #4 near #5 distance 1.58
    5254 
    5255 > color zone #4 near #5 distance 1.48
    5256 
    5257 > color zone #4 near #5 distance 1.58
    5258 
    5259 > color zone #4 near #5 distance 1.68
    5260 
    5261 > color zone #4 near #5 distance 1.78
    5262 
    5263 > color zone #4 near #5 distance 1.88
    5264 
    5265 > volume splitbyzone #4
    5266 
    5267 Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at
    5268 level 0.0137, step 1, values float32 
    5269 Opened rOAT1-AZT_OF.mrc 1 as #6.2, grid size 320,320,320, pixel 0.83, shown at
    5270 level 0.0137, step 1, values float32 
    5271 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    5272 level 0.0137, step 1, values float32 
    5273 
    5274 > close #6.1-2
    5275 
    5276 > volume #6.3 level 0.0116
    5277 
    5278 > select add #5
    5279 
    5280 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5281 
    5282 > select subtract #5
    5283 
    5284 Nothing selected 
    5285 
    5286 > color #6.3 yellow models
    5287 
    5288 > color #6.3 white models
    5289 
    5290 > color #6.3 #ffffb2ff models
    5291 
    5292 > select add #5
    5293 
    5294 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5295 
    5296 > color #5 #ffaa88ff
    5297 
    5298 > color #5 salmon
    5299 
    5300 > color (#!5 & sel) byhetero
    5301 
    5302 > color #6.3 #ffffb296 models
    5303 
    5304 > select clear
    5305 
    5306 > save
    5307 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5308 > includeMaps true
    5309 
    5310 > show #!2 models
    5311 
    5312 > hide #!5 models
    5313 
    5314 > hide #!6 models
    5315 
    5316 > hide #!6.3 models
    5317 
    5318 > volume #2 level 0.01456
    5319 
    5320 > color #2 #a5a5a5ff models
    5321 
    5322 > open
    5323 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc
    5324 
    5325 Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    5326 level 0.00408, step 2, values float32 
    5327 
    5328 > rename #7 rOAT1-PBD_IF.mrc
    5329 
    5330 > volume #2 level 0.01983
    5331 
    5332 > volume #2 level 0.0151
    5333 
    5334 > hide #!7 models
    5335 
    5336 > volume #7 level 0.01185
    5337 
    5338 > volume #7 step 1
    5339 
    5340 > volume #7 level 0.01094
    5341 
    5342 > hide #!2 models
    5343 
    5344 > open
    5345 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD-
    5346 > coot-6.pdb
    5347 
    5348 Chain information for rOAT1-PBD-coot-6.pdb #8 
    5349 --- 
    5350 Chain | Description 
    5351 A | No description available 
    5352  
    5353 
    5354 > select add #8
    5355 
    5356 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    5357 
    5358 > ui mousemode right "translate selected models"
    5359 
    5360 > view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702
    5361 
    5362 > view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973
    5363 
    5364 > fitmap #8 inMap #7
    5365 
    5366 Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912
    5367 atoms 
    5368 average map value = 0.02737, steps = 56 
    5369 shifted from previous position = 2.6 
    5370 rotated from previous position = 0.396 degrees 
    5371 atoms outside contour = 571, contour level = 0.010939 
    5372  
    5373 Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7)
    5374 coordinates: 
    5375 Matrix rotation and translation 
    5376 0.99998387 0.00531886 -0.00199304 66.36205660 
    5377 -0.00532668 0.99997806 -0.00393867 67.06308709 
    5378 0.00197205 0.00394922 0.99999026 65.65327743 
    5379 Axis 0.57034742 -0.28670293 -0.76974363 
    5380 Axis point 10937.66555565 -15865.74627304 0.00000000 
    5381 Rotation angle (degrees) 0.39620277 
    5382 Shift along axis -31.91394767 
    5383  
    5384 
    5385 > rename #8 rOAT1-PBD_IF.pdb
    5386 
    5387 > save
    5388 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5389 > includeMaps true
    5390 
    5391 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id:
    5392 35655645, major code: 40 (TranslateCoords), minor code: 0 
    5393 
    5394 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id:
    5395 35655640, major code: 40 (TranslateCoords), minor code: 0 
    5396 
    5397 > color #8 white
    5398 
    5399 > hide #!7 models
    5400 
    5401 > select up
    5402 
    5403 2 atoms, 1 bond, 1 residue, 1 model selected 
    5404 
    5405 > select up
    5406 
    5407 19 atoms, 19 bonds, 1 residue, 1 model selected 
    5408 
    5409 > color sel red
    5410 
    5411 > show #!7 models
    5412 
    5413 > color zone #7 near #8 distance 4.98
    5414 
    5415 > color zone #7 near #8 distance 4.88
    5416 
    5417 > color zone #7 near #8 distance 4.78
    5418 
    5419 > color zone #7 near #8 distance 4.68
    5420 
    5421 > color zone #7 near #8 distance 4.58
    5422 
    5423 > color zone #7 near #8 distance 4.48
    5424 
    5425 > color zone #7 near #8 distance 4.38
    5426 
    5427 > color zone #7 near #8 distance 4.28
    5428 
    5429 > color zone #7 near #8 distance 4.18
    5430 
    5431 > color zone #7 near #8 distance 4.08
    5432 
    5433 > color zone #7 near #8 distance 3.98
    5434 
    5435 > color zone #7 near #8 distance 3.88
    5436 
    5437 > color zone #7 near #8 distance 3.78
    5438 
    5439 > color zone #7 near #8 distance 3.68
    5440 
    5441 > volume #7 level 0.02515
    5442 
    5443 > volume #7 level 0.01677
    5444 
    5445 > volume #7 level 0.0124
    5446 
    5447 > volume #7 level 0.01476
    5448 
    5449 > color zone #7 near #8 distance 3.58
    5450 
    5451 > color zone #7 near #8 distance 3.48
    5452 
    5453 > color zone #7 near #8 distance 3.38
    5454 
    5455 > color zone #7 near #8 distance 3.28
    5456 
    5457 > color zone #7 near #8 distance 3.18
    5458 
    5459 > color zone #7 near #8 distance 3.08
    5460 
    5461 > color zone #7 near #8 distance 2.98
    5462 
    5463 > color zone #7 near #8 distance 2.88
    5464 
    5465 > color zone #7 near #8 distance 2.78
    5466 
    5467 > color zone #7 near #8 distance 2.68
    5468 
    5469 > color zone #7 near #8 distance 2.58
    5470 
    5471 > color zone #7 near #8 distance 2.48
    5472 
    5473 > color zone #7 near #8 distance 2.38
    5474 
    5475 > color zone #7 near #8 distance 2.28
    5476 
    5477 > volume #7 level 0.01112
    5478 
    5479 > color zone #7 near #8 distance 2.18
    5480 
    5481 > color zone #7 near #8 distance 2.08
    5482 
    5483 > color zone #7 near #8 distance 1.98
    5484 
    5485 > color zone #7 near #8 distance 1.88
    5486 
    5487 > color zone #7 near #8 distance 1.98
    5488 
    5489 > color zone #7 near #8 distance 2.08
    5490 
    5491 > volume splitbyzone #7
    5492 
    5493 Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    5494 level 0.0111, step 1, values float32 
    5495 Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    5496 level 0.0111, step 1, values float32 
    5497 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    5498 level 0.0111, step 1, values float32 
    5499 
    5500 > close #9.1-2
    5501 
    5502 > color #9.3 #ff000096 models
    5503 
    5504 > color #9.3 #ffff0096 models
    5505 
    5506 > color #9.3 #ffffff96 models
    5507 
    5508 > color #9.3 #ffffb296 models
    5509 
    5510 > select add #8
    5511 
    5512 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    5513 
    5514 > color #8 #ffffddff
    5515 
    5516 > color #8 gold
    5517 
    5518 > select clear
    5519 
    5520 > select add #8
    5521 
    5522 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    5523 
    5524 > color sel byhetero
    5525 
    5526 > select clear
    5527 
    5528 > save
    5529 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5530 > includeMaps true
    5531 
    5532 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id:
    5533 35655670, major code: 40 (TranslateCoords), minor code: 0 
    5534 
    5535 > open
    5536 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc
    5537 
    5538 Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    5539 level 0.00409, step 2, values float32 
    5540 
    5541 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id:
    5542 35655680, major code: 40 (TranslateCoords), minor code: 0 
    5543 
    5544 > open
    5545 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF-
    5546 > coot-0.pdb
    5547 
    5548 Chain information for rOAT1-PBD_OF-coot-0.pdb #11 
    5549 --- 
    5550 Chain | Description 
    5551 A | No description available 
    5552  
    5553 
    5554 > hide #!9 models
    5555 
    5556 > hide #8 models
    5557 
    5558 > rename #10 rOAT1-PBD_OF
    5559 
    5560 > rename #10 rOAT1-PBD_OF.mrc
    5561 
    5562 > show #!2 models
    5563 
    5564 > volume #10 level 0.004712
    5565 
    5566 > volume #10 step 1
    5567 
    5568 > volume #10 level 0.01128
    5569 
    5570 > hide #!2 models
    5571 
    5572 > select add #11
    5573 
    5574 3872 atoms, 3966 bonds, 500 residues, 1 model selected 
    5575 
    5576 > view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035
    5577 
    5578 > view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073
    5579 
    5580 > view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386
    5581 
    5582 > fitmap #11 inMap #10
    5583 
    5584 Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using
    5585 3872 atoms 
    5586 average map value = 0.01531, steps = 56 
    5587 shifted from previous position = 2.42 
    5588 rotated from previous position = 0.764 degrees 
    5589 atoms outside contour = 1505, contour level = 0.011277 
    5590  
    5591 Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10)
    5592 coordinates: 
    5593 Matrix rotation and translation 
    5594 0.99995211 0.00939248 0.00274947 65.65298070 
    5595 -0.00936721 0.99991506 -0.00906240 67.47749964 
    5596 -0.00283436 0.00903621 0.99995516 65.83404461 
    5597 Axis 0.67891074 0.20945939 -0.70370943 
    5598 Axis point 6981.74049553 -6059.62250131 0.00000000 
    5599 Rotation angle (degrees) 0.76372650 
    5600 Shift along axis 12.37827175 
    5601  
    5602 
    5603 > show sel atoms
    5604 
    5605 > hide #!10 models
    5606 
    5607 > show #!10 models
    5608 
    5609 > open
    5610 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    5611 > coot-7_real_space_refined_008.pdb
    5612 
    5613 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12 
    5614 --- 
    5615 Chain | Description 
    5616 A | No description available 
    5617  
    5618 
    5619 > ui tool show Matchmaker
    5620 
    5621 > matchmaker #!12 to #11
    5622 
    5623 Parameters 
    5624 --- 
    5625 Chain pairing | bb 
    5626 Alignment algorithm | Needleman-Wunsch 
    5627 Similarity matrix | BLOSUM-62 
    5628 SS fraction | 0.3 
    5629 Gap open (HH/SS/other) | 18/18/6 
    5630 Gap extend | 1 
    5631 SS matrix |  |  | H | S | O 
    5632 ---|---|---|--- 
    5633 H | 6 | -9 | -6 
    5634 S |  | 6 | -6 
    5635 O |  |  | 4 
    5636 Iteration cutoff | 2 
    5637  
    5638 Matchmaker rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF-
    5639 coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score =
    5640 2423.1 
    5641 RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs:
    5642 1.080) 
    5643  
    5644 
    5645 > hide #11 models
    5646 
    5647 > select subtract #11
    5648 
    5649 Nothing selected 
    5650 
    5651 > show #11 models
    5652 
    5653 > hide #!12 models
    5654 
    5655 > hide #!10 models
    5656 
    5657 > show #!12 models
    5658 
    5659 > close #11
    5660 
    5661 > color #12 #bb4455ff
    5662 
    5663 > color #12 #b4503bff
    5664 
    5665 QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id:
    5666 35655708, major code: 40 (TranslateCoords), minor code: 0 
    5667 
    5668 > show #!10 models
    5669 
    5670 > save
    5671 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5672 > includeMaps true
    5673 
    5674 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id:
    5675 35655718, major code: 40 (TranslateCoords), minor code: 0 
    5676 
    5677 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id:
    5678 35655713, major code: 40 (TranslateCoords), minor code: 0 
    5679 
    5680 > color #10 #ffb2ff96 models
    5681 
    5682 > volume #10 level 0.009218
    5683 
    5684 > volume #10 level 0.008059
    5685 
    5686 > color #10 #ffb2ffff models
    5687 
    5688 > select add #12
    5689 
    5690 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5691 
    5692 > hide #!10 models
    5693 
    5694 > color #12 white
    5695 
    5696 > select clear
    5697 
    5698 > select #12/B:601@C11
    5699 
    5700 1 atom, 1 residue, 1 model selected 
    5701 
    5702 > select up
    5703 
    5704 37 atoms, 37 bonds, 1 residue, 1 model selected 
    5705 
    5706 > color sel red
    5707 
    5708 > color #10 white models
    5709 
    5710 > select add #10
    5711 
    5712 37 atoms, 37 bonds, 1 residue, 3 models selected 
    5713 
    5714 > select subtract #10
    5715 
    5716 37 atoms, 37 bonds, 1 residue, 1 model selected 
    5717 
    5718 > show #!10 models
    5719 
    5720 > color zone #10 near #12 distance 2
    5721 
    5722 > color zone #10 near #12 distance 1.9
    5723 
    5724 > color zone #10 near #12 distance 1.8
    5725 
    5726 > color zone #10 near #12 distance 1.7
    5727 
    5728 > color zone #10 near #12 distance 1.8
    5729 
    5730 > color zone #10 near #12 distance 1.9
    5731 
    5732 > color zone #10 near #12 distance 2
    5733 
    5734 [Repeated 1 time(s)]
    5735 
    5736 > volume splitbyzone #10
    5737 
    5738 Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown
    5739 at level 0.00806, step 1, values float32 
    5740 Opened rOAT1-PBD_OF.mrc 1 as #11.2, grid size 320,320,320, pixel 0.83, shown
    5741 at level 0.00806, step 1, values float32 
    5742 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    5743 at level 0.00806, step 1, values float32 
    5744 
    5745 > volume splitbyzone #10
    5746 
    5747 Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown
    5748 at level 0.00806, step 1, values float32 
    5749 Opened rOAT1-PBD_OF.mrc 1 as #13.2, grid size 320,320,320, pixel 0.83, shown
    5750 at level 0.00806, step 1, values float32 
    5751 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    5752 at level 0.00806, step 1, values float32 
    5753 
    5754 > close #11.1-2
    5755 
    5756 > hide #!12 models
    5757 
    5758 > hide #!11.3 models
    5759 
    5760 > hide #!11 models
    5761 
    5762 > select add #12
    5763 
    5764 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5765 
    5766 > select subtract #12
    5767 
    5768 Nothing selected 
    5769 
    5770 > close #13.1-2
    5771 
    5772 > show #!12 models
    5773 
    5774 > color #11.3 white models
    5775 
    5776 > color #11.3 #ffffb2ff models
    5777 
    5778 > color #13.3 white models
    5779 
    5780 > color #13.3 #ffffb2ff models
    5781 
    5782 > select add #12
    5783 
    5784 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5785 
    5786 > color #12 #bb4455ff
    5787 
    5788 > color #12 #b4503bff
    5789 
    5790 > color (#!12 & sel) byhetero
    5791 
    5792 > select #12/A:440
    5793 
    5794 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5795 
    5796 > select add #12
    5797 
    5798 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5799 
    5800 > select subtract #12
    5801 
    5802 Nothing selected 
    5803 
    5804 > save
    5805 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5806 > includeMaps true
    5807 
    5808 > hide #!13 models
    5809 
    5810 > hide #!13.3 models
    5811 
    5812 > hide #!12 models
    5813 
    5814 > open
    5815 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc
    5816 
    5817 Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    5818 level 0.00408, step 2, values float32 
    5819 
    5820 QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id:
    5821 35655778, major code: 40 (TranslateCoords), minor code: 0 
    5822 
    5823 > show #!2 models
    5824 
    5825 > hide #!2 models
    5826 
    5827 > rename #14 rOAT1-TFV_IF.mrc
    5828 
    5829 > show #1 models
    5830 
    5831 > hide #!14 models
    5832 
    5833 > save
    5834 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb
    5835 > models #1 relModel #14
    5836 
    5837 > open
    5838 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF-
    5839 > coot-2_real_space_refined_005.pdb
    5840 
    5841 Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15 
    5842 --- 
    5843 Chain | Description 
    5844 A | No description available 
    5845  
    5846 
    5847 > hide #1 models
    5848 
    5849 > show #!14 models
    5850 
    5851 > color #15 white
    5852 
    5853 > color #14 white models
    5854 
    5855 > select ::name="TFV"
    5856 
    5857 31 atoms, 32 bonds, 1 residue, 1 model selected 
    5858 
    5859 > color sel red
    5860 
    5861 > color zone #14 near #15 distance 4.68
    5862 
    5863 > color zone #14 near #15 distance 4.58
    5864 
    5865 > color zone #14 near #15 distance 4.48
    5866 
    5867 > color zone #14 near #15 distance 4.38
    5868 
    5869 > color zone #14 near #15 distance 4.28
    5870 
    5871 > color zone #14 near #15 distance 4.18
    5872 
    5873 > color zone #14 near #15 distance 4.08
    5874 
    5875 > color zone #14 near #15 distance 3.98
    5876 
    5877 > color zone #14 near #15 distance 3.88
    5878 
    5879 > color zone #14 near #15 distance 3.78
    5880 
    5881 > color zone #14 near #15 distance 3.68
    5882 
    5883 > color zone #14 near #15 distance 3.58
    5884 
    5885 > color zone #14 near #15 distance 3.48
    5886 
    5887 > color zone #14 near #15 distance 3.38
    5888 
    5889 > color zone #14 near #15 distance 3.28
    5890 
    5891 > color zone #14 near #15 distance 3.18
    5892 
    5893 > color zone #14 near #15 distance 3.08
    5894 
    5895 > color zone #14 near #15 distance 2.98
    5896 
    5897 > color zone #14 near #15 distance 2.88
    5898 
    5899 > color zone #14 near #15 distance 2.78
    5900 
    5901 > color zone #14 near #15 distance 2.68
    5902 
    5903 > volume #14 level 0.007613
    5904 
    5905 > color zone #14 near #15 distance 2.78
    5906 
    5907 > color zone #14 near #15 distance 2.88
    5908 
    5909 > color zone #14 near #15 distance 2.98
    5910 
    5911 > color zone #14 near #15 distance 2.88
    5912 
    5913 > color zone #14 near #15 distance 2.78
    5914 
    5915 > color zone #14 near #15 distance 2.68
    5916 
    5917 > color zone #14 near #15 distance 2.58
    5918 
    5919 > color zone #14 near #15 distance 2.48
    5920 
    5921 > color zone #14 near #15 distance 2.38
    5922 
    5923 > volume #14 level 0.005915
    5924 
    5925 > volume #14 level 0.005632
    5926 
    5927 > volume splitbyzone #14
    5928 
    5929 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    5930 at level 0.00563, step 1, values float32 
    5931 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    5932 at level 0.00563, step 1, values float32 
    5933 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    5934 at level 0.00563, step 1, values float32 
    5935 
    5936 > close #16.1-2
    5937 
    5938 > color zone #14 near #15 distance 2.09
    5939 
    5940 > close #16#16.3
    5941 
    5942 > show #!14 models
    5943 
    5944 > color zone #14 near #15 distance 1.99
    5945 
    5946 > color zone #14 near #15 distance 2.09
    5947 
    5948 > color zone #14 near #15 distance 2.19
    5949 
    5950 > color zone #14 near #15 distance 2.29
    5951 
    5952 > color zone #14 near #15 distance 2.39
    5953 
    5954 > color zone #14 near #15 distance 2.29
    5955 
    5956 > volume splitbyzone #14
    5957 
    5958 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    5959 at level 0.00563, step 1, values float32 
    5960 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    5961 at level 0.00563, step 1, values float32 
    5962 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    5963 at level 0.00563, step 1, values float32 
    5964 
    5965 > close #16.1-2
    5966 
    5967 > select add #15
    5968 
    5969 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    5970 
    5971 > color #16.3 #ff5500ff models
    5972 
    5973 > color #16.3 #aa0000ff models
    5974 
    5975 > color #16.3 #ff5500ff models
    5976 
    5977 > color #16.3 #ff557fff models
    5978 
    5979 > color #15 #ff557fff
    5980 
    5981 > color #16.3 white models
    5982 
    5983 > color #16.3 #ffffb2ff models
    5984 
    5985 > color #16.3 #ffffb296 models
    5986 
    5987 > open
    5988 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    5989 > coot-3.pdb
    5990 
    5991 Chain information for rOAT1-TFV_IF-coot-3.pdb #17 
    5992 --- 
    5993 Chain | Description 
    5994 A | No description available 
    5995  
    5996 
    5997 > close #17#16#16.3
    5998 
    5999 > close #15
    6000 
    6001 > open
    6002 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    6003 > coot-3.pdb
    6004 
    6005 Chain information for rOAT1-TFV_IF-coot-3.pdb #15 
    6006 --- 
    6007 Chain | Description 
    6008 A | No description available 
    6009  
    6010 
    6011 QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id:
    6012 35656402, major code: 40 (TranslateCoords), minor code: 0 
    6013 
    6014 > show #!14 models
    6015 
    6016 > select add #15
    6017 
    6018 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    6019 
    6020 > select subtract #15
    6021 
    6022 Nothing selected 
    6023 
    6024 > select add #15
    6025 
    6026 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    6027 
    6028 > color #15 white
    6029 
    6030 > color zone #14 near #15 distance 2.29
    6031 
    6032 > select ::name="TFV"
    6033 
    6034 31 atoms, 32 bonds, 1 residue, 1 model selected 
    6035 
    6036 > color sel red
    6037 
    6038 > color zone #14 near #15 distance 2.29
    6039 
    6040 > color zone #14 near #15 distance 2.19
    6041 
    6042 > color zone #14 near #15 distance 2.09
    6043 
    6044 > color zone #14 near #15 distance 1.99
    6045 
    6046 > color zone #14 near #15 distance 1.89
    6047 
    6048 > color zone #14 near #15 distance 1.79
    6049 
    6050 > color zone #14 near #15 distance 1.69
    6051 
    6052 > color zone #14 near #15 distance 1.59
    6053 
    6054 > color zone #14 near #15 distance 1.49
    6055 
    6056 > color zone #14 near #15 distance 1.39
    6057 
    6058 > color zone #14 near #15 distance 1.29
    6059 
    6060 > color zone #14 near #15 distance 1.19
    6061 
    6062 > color zone #14 near #15 distance 1.09
    6063 
    6064 > color zone #14 near #15 distance 1.19
    6065 
    6066 > color zone #14 near #15 distance 1.29
    6067 
    6068 > color zone #14 near #15 distance 1.39
    6069 
    6070 > color zone #14 near #15 distance 1.49
    6071 
    6072 > color zone #14 near #15 distance 1.59
    6073 
    6074 > color zone #14 near #15 distance 1.69
    6075 
    6076 > color zone #14 near #15 distance 1.79
    6077 
    6078 > color zone #14 near #15 distance 1.89
    6079 
    6080 > color zone #14 near #15 distance 1.99
    6081 
    6082 > color zone #14 near #15 distance 2.09
    6083 
    6084 [Repeated 1 time(s)]
    6085 
    6086 > volume splitbyzone #14
    6087 
    6088 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    6089 at level 0.00563, step 1, values float32 
    6090 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    6091 at level 0.00563, step 1, values float32 
    6092 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    6093 at level 0.00563, step 1, values float32 
    6094 
    6095 > close #16.1-2
    6096 
    6097 > color #16.3 white models
    6098 
    6099 > color #16.3 #ffffb2ff models
    6100 
    6101 > color #16.3 #ffffb296 models
    6102 
    6103 > color #15 #ff5500ff
    6104 
    6105 > color #15 #ff557fff
    6106 
    6107 > select add #15
    6108 
    6109 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    6110 
    6111 > color sel byhetero
    6112 
    6113 > select clear
    6114 
    6115 > save
    6116 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6117 > includeMaps true
    6118 
    6119 > open
    6120 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc
    6121 
    6122 Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    6123 level 0.00401, step 2, values float32 
    6124 
    6125 > rename #17 rOAT1-TVF_OF.mrc
    6126 
    6127 > hide #15 models
    6128 
    6129 > hide #!16 models
    6130 
    6131 > show #8 models
    6132 
    6133 > hide #8 models
    6134 
    6135 > show #!11.3 models
    6136 
    6137 > hide #!11 models
    6138 
    6139 > hide #!11.3 models
    6140 
    6141 > show #!12 models
    6142 
    6143 > volume #17 step 1
    6144 
    6145 > volume #17 level 0.01305
    6146 
    6147 > save
    6148 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    6149 > models #12 relModel #17
    6150 
    6151 > hide #!16.3 models
    6152 
    6153 > hide #!12 models
    6154 
    6155 > open
    6156 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    6157 
    6158 Chain information for rOAT1-TFV_OF.pdb #18 
    6159 --- 
    6160 Chain | Description 
    6161 A | No description available 
    6162  
    6163 
    6164 > save
    6165 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6166 > includeMaps true
    6167 
    6168 > close #18
    6169 
    6170 > open
    6171 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF-
    6172 > coot-1_real_space_refined_007.pdb
    6173 
    6174 Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18 
    6175 --- 
    6176 Chain | Description 
    6177 A | No description available 
    6178  
    6179 
    6180 > select add #18
    6181 
    6182 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6183 
    6184 > color #18 white
    6185 
    6186 > color #17 white models
    6187 
    6188 > select #18/A:601@H131
    6189 
    6190 1 atom, 1 residue, 1 model selected 
    6191 
    6192 > select up
    6193 
    6194 31 atoms, 32 bonds, 1 residue, 1 model selected 
    6195 
    6196 > color sel red
    6197 
    6198 > volume #17 level 0.011
    6199 
    6200 > color zone #17 near #18 distance 4.98
    6201 
    6202 > color zone #17 near #18 distance 4.88
    6203 
    6204 > color zone #17 near #18 distance 4.78
    6205 
    6206 > color zone #17 near #18 distance 4.68
    6207 
    6208 > color zone #17 near #18 distance 4.58
    6209 
    6210 > color zone #17 near #18 distance 4.48
    6211 
    6212 > color zone #17 near #18 distance 4.38
    6213 
    6214 > color zone #17 near #18 distance 4.28
    6215 
    6216 > color zone #17 near #18 distance 4.18
    6217 
    6218 > color zone #17 near #18 distance 4.08
    6219 
    6220 > color zone #17 near #18 distance 3.98
    6221 
    6222 > color zone #17 near #18 distance 3.88
    6223 
    6224 > color zone #17 near #18 distance 3.78
    6225 
    6226 > color zone #17 near #18 distance 3.68
    6227 
    6228 > color zone #17 near #18 distance 3.58
    6229 
    6230 > color zone #17 near #18 distance 3.48
    6231 
    6232 > color zone #17 near #18 distance 3.38
    6233 
    6234 > color zone #17 near #18 distance 3.28
    6235 
    6236 > color zone #17 near #18 distance 3.18
    6237 
    6238 > color zone #17 near #18 distance 3.08
    6239 
    6240 > color zone #17 near #18 distance 2.98
    6241 
    6242 > volume splitbyzone #17
    6243 
    6244 Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
    6245 at level 0.011, step 1, values float32 
    6246 Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
    6247 at level 0.011, step 1, values float32 
    6248 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    6249 at level 0.011, step 1, values float32 
    6250 
    6251 > close #19.1-2
    6252 
    6253 > color #19.3 white models
    6254 
    6255 > color #19.3 #ffffb2ff models
    6256 
    6257 > select add #18
    6258 
    6259 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6260 
    6261 > color #18 #337744ff
    6262 
    6263 > color #18 #374c02ff
    6264 
    6265 > color (#!18 & sel) byhetero
    6266 
    6267 > select clear
    6268 
    6269 > color #19.3 #ffffb296 models
    6270 
    6271 > save
    6272 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6273 > includeMaps true
    6274 
    6275 > open
    6276 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc
    6277 
    6278 Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    6279 level 0.00494, step 2, values float32 
    6280 
    6281 > volume #20 step 1
    6282 
    6283 > hide #!19 models
    6284 
    6285 > hide #!18 models
    6286 
    6287 > rename #20 rOAT1-AAI_IF.mrc
    6288 
    6289 > volume #20 level 0.0194
    6290 
    6291 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id:
    6292 35656688, major code: 40 (TranslateCoords), minor code: 0 
    6293 
    6294 > show #!2 models
    6295 
    6296 > hide #!2 models
    6297 
    6298 > show #1 models
    6299 
    6300 > save
    6301 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    6302 > models #1 relModel #20
    6303 
    6304 > hide #1 models
    6305 
    6306 > open
    6307 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    6308 
    6309 Chain information for rOAT1-AAI_IF.pdb #21 
    6310 --- 
    6311 Chain | Description 
    6312 A | No description available 
    6313  
    6314 
    6315 > close #21
    6316 
    6317 > open
    6318 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb
    6319 
    6320 Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21 
    6321 --- 
    6322 Chain | Description 
    6323 A | No description available 
    6324  
    6325 
    6326 QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id:
    6327 35656914, major code: 40 (TranslateCoords), minor code: 0 
    6328 
    6329 > close #21
    6330 
    6331 > open
    6332 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    6333 > coot-1_real_space_refined_003_initial.geo
    6334 
    6335 Unrecognized file suffix '.geo' 
    6336 
    6337 > open
    6338 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    6339 > coot-1_real_space_refined_003.pdb
    6340 
    6341 Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21 
    6342 --- 
    6343 Chain | Description 
    6344 A | No description available 
    6345  
    6346 
    6347 QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id:
    6348 35657106, major code: 40 (TranslateCoords), minor code: 0 
    6349 
    6350 > select add #21
    6351 
    6352 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    6353 
    6354 > color #21 white
    6355 
    6356 > color #20 white models
    6357 
    6358 > select clear
    6359 
    6360 > select #21/A:602@O24
    6361 
    6362 1 atom, 1 residue, 1 model selected 
    6363 
    6364 > select up
    6365 
    6366 35 atoms, 38 bonds, 1 residue, 1 model selected 
    6367 
    6368 > select #21/A:601@O20
    6369 
    6370 1 atom, 1 residue, 1 model selected 
    6371 
    6372 > select add #21/A:602@C23
    6373 
    6374 2 atoms, 2 residues, 1 model selected 
    6375 
    6376 > select up
    6377 
    6378 70 atoms, 76 bonds, 2 residues, 1 model selected 
    6379 
    6380 > color sel red
    6381 
    6382 > color zone #20 near #21 distance 4.98
    6383 
    6384 > color zone #20 near #21 distance 4.88
    6385 
    6386 > color zone #20 near #21 distance 4.78
    6387 
    6388 > color zone #20 near #21 distance 4.68
    6389 
    6390 > color zone #20 near #21 distance 4.58
    6391 
    6392 > color zone #20 near #21 distance 4.48
    6393 
    6394 > color zone #20 near #21 distance 4.38
    6395 
    6396 > color zone #20 near #21 distance 4.28
    6397 
    6398 > color zone #20 near #21 distance 4.18
    6399 
    6400 > color zone #20 near #21 distance 4.08
    6401 
    6402 > color zone #20 near #21 distance 3.98
    6403 
    6404 > color zone #20 near #21 distance 3.88
    6405 
    6406 > color zone #20 near #21 distance 3.78
    6407 
    6408 > color zone #20 near #21 distance 3.68
    6409 
    6410 > color zone #20 near #21 distance 3.58
    6411 
    6412 > color zone #20 near #21 distance 3.48
    6413 
    6414 > color zone #20 near #21 distance 3.38
    6415 
    6416 > color zone #20 near #21 distance 3.28
    6417 
    6418 > color zone #20 near #21 distance 3.18
    6419 
    6420 > color zone #20 near #21 distance 3.08
    6421 
    6422 > color zone #20 near #21 distance 2.98
    6423 
    6424 > color zone #20 near #21 distance 2.88
    6425 
    6426 > volume splitbyzone #20
    6427 
    6428 Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown
    6429 at level 0.0194, step 1, values float32 
    6430 Opened rOAT1-AAI_IF.mrc 1 as #22.2, grid size 320,320,320, pixel 0.83, shown
    6431 at level 0.0194, step 1, values float32 
    6432 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    6433 at level 0.0194, step 1, values float32 
    6434 
    6435 > close #22.1-2
    6436 
    6437 > color #22.3 yellow models
    6438 
    6439 > color #22.3 white models
    6440 
    6441 > color #22.3 #ffffb2ff models
    6442 
    6443 > color #22.3 #ffffb296 models
    6444 
    6445 > select add #21
    6446 
    6447 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    6448 
    6449 > color #21 #668855ff
    6450 
    6451 > color #21 #685d73ff
    6452 
    6453 > color sel byhetero
    6454 
    6455 > select clear
    6456 
    6457 [Repeated 1 time(s)]
    6458 
    6459 > save
    6460 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6461 > includeMaps true
    6462 
    6463 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id:
    6464 35657141, major code: 40 (TranslateCoords), minor code: 0 
    6465 
    6466 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id:
    6467 35657136, major code: 40 (TranslateCoords), minor code: 0 
    6468 
    6469 > hide #!22.3 models
    6470 
    6471 > hide #!22 models
    6472 
    6473 > hide #21 models
    6474 
    6475 > open
    6476 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc
    6477 
    6478 Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    6479 level 0.00494, step 2, values float32 
    6480 
    6481 > volume #23 level 0.01307
    6482 
    6483 > volume #23 step 1
    6484 
    6485 > volume #23 level 0.01684
    6486 
    6487 > show #1 models
    6488 
    6489 > hide #1 models
    6490 
    6491 > show #!5 models
    6492 
    6493 > rename #23 rOAT1-AAI_OF.mrc
    6494 
    6495 > save
    6496 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb
    6497 > models #5 relModel #23
    6498 
    6499 > open
    6500 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF-
    6501 > coot-1_real_space_refined_004.pdb
    6502 
    6503 Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24 
    6504 --- 
    6505 Chain | Description 
    6506 A | No description available 
    6507  
    6508 
    6509 > color #23 white models
    6510 
    6511 > color #24 white
    6512 
    6513 > hide #!5 models
    6514 
    6515 > select add #24/A:601@O24
    6516 
    6517 1 atom, 1 residue, 1 model selected 
    6518 
    6519 > select add #24/A:230@OH
    6520 
    6521 2 atoms, 2 residues, 1 model selected 
    6522 
    6523 > select clear
    6524 
    6525 > select add #24/A:601@O24
    6526 
    6527 1 atom, 1 residue, 1 model selected 
    6528 
    6529 > select up
    6530 
    6531 35 atoms, 38 bonds, 1 residue, 1 model selected 
    6532 
    6533 > color sel red
    6534 
    6535 > color zone #23 near #24 distance 4.98
    6536 
    6537 > volume splitbyzone #23
    6538 
    6539 Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown
    6540 at level 0.0168, step 1, values float32 
    6541 Opened rOAT1-AAI_OF.mrc 1 as #25.2, grid size 320,320,320, pixel 0.83, shown
    6542 at level 0.0168, step 1, values float32 
    6543 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    6544 at level 0.0168, step 1, values float32 
    6545 
    6546 > close #25.1-2
    6547 
    6548 > select add #24
    6549 
    6550 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6551 
    6552 > select subtract #24
    6553 
    6554 Nothing selected 
    6555 
    6556 > color #25.3 white models
    6557 
    6558 > color #25.3 #ffffb2ff models
    6559 
    6560 > select add #24
    6561 
    6562 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6563 
    6564 > color #24 #1177ccff
    6565 
    6566 > color #24 #17c127ff
    6567 
    6568 > color (#!24 & sel) byhetero
    6569 
    6570 > select #24/A:438@CE2
    6571 
    6572 1 atom, 1 residue, 1 model selected 
    6573 Drag select of 1 atoms, 1 bonds 
    6574 
    6575 > select clear
    6576 
    6577 > color #25.3 #ffffb296 models
    6578 
    6579 > select clear
    6580 
    6581 > save
    6582 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6583 > includeMaps true
    6584 
    6585 > open
    6586 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH-
    6587 > coot-7_real_space_refined_007.pdb
    6588 
    6589 Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26 
    6590 --- 
    6591 Chain | Description 
    6592 A | No description available 
    6593  
    6594 
    6595 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id:
    6596 35657291, major code: 40 (TranslateCoords), minor code: 0 
    6597 
    6598 > open
    6599 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc
    6600 
    6601 Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160,
    6602 pixel 0.83, shown at level 0.134, step 1, values float32 
    6603 
    6604 > hide #!24 models
    6605 
    6606 > hide #!25.3 models
    6607 
    6608 > hide #!25 models
    6609 
    6610 > view
    6611 
    6612 > show #!2 models
    6613 
    6614 > select add #26
    6615 
    6616 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    6617 
    6618 > select add #27
    6619 
    6620 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected 
    6621 
    6622 > view matrix models
    6623 > #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865
    6624 
    6625 > view matrix models
    6626 > #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563
    6627 
    6628 > rename #27 rOAT1-PAH
    6629 
    6630 > rename #27 rOAT1-PAH.mrc
    6631 
    6632 > view
    6633 
    6634 > fitmap #26 inMap #27
    6635 
    6636 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    6637 rOAT1-PAH.mrc (#27) using 3865 atoms 
    6638 average map value = 0.3441, steps = 44 
    6639 shifted from previous position = 0.0131 
    6640 rotated from previous position = 0.0158 degrees 
    6641 atoms outside contour = 699, contour level = 0.13428 
    6642  
    6643 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    6644 rOAT1-PAH.mrc (#27) coordinates: 
    6645 Matrix rotation and translation 
    6646 0.99999996 -0.00021122 0.00016567 0.00535685 
    6647 0.00021123 0.99999998 -0.00006568 0.00053709 
    6648 -0.00016566 0.00006571 0.99999998 -0.00148379 
    6649 Axis 0.23771757 0.59945172 0.76429575 
    6650 Axis point -1.23064203 24.84299856 0.00000000 
    6651 Rotation angle (degrees) 0.01583428 
    6652 Shift along axis 0.00046132 
    6653  
    6654 
    6655 > hide #!2 models
    6656 
    6657 > color #27 white models
    6658 
    6659 > color #26 white
    6660 
    6661 > hide #!26 models
    6662 
    6663 > select subtract #27
    6664 
    6665 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    6666 
    6667 > select subtract #26
    6668 
    6669 Nothing selected 
    6670 
    6671 > hide #!27 models
    6672 
    6673 > show #!26 models
    6674 
    6675 > select #26/B:601@C07
    6676 
    6677 1 atom, 1 residue, 1 model selected 
    6678 
    6679 > select up
    6680 
    6681 23 atoms, 23 bonds, 1 residue, 1 model selected 
    6682 
    6683 > color sel red
    6684 
    6685 > show #!27 models
    6686 
    6687 > color zone #27 near #26 distance 4.98
    6688 
    6689 > color zone #27 near #26 distance 4.88
    6690 
    6691 > color zone #27 near #26 distance 4.78
    6692 
    6693 > color zone #27 near #26 distance 4.68
    6694 
    6695 > color zone #27 near #26 distance 4.58
    6696 
    6697 > color zone #27 near #26 distance 4.48
    6698 
    6699 > color zone #27 near #26 distance 4.38
    6700 
    6701 > color zone #27 near #26 distance 4.28
    6702 
    6703 > color zone #27 near #26 distance 4.18
    6704 
    6705 > color zone #27 near #26 distance 4.08
    6706 
    6707 > color zone #27 near #26 distance 3.98
    6708 
    6709 > color zone #27 near #26 distance 3.88
    6710 
    6711 > color zone #27 near #26 distance 3.78
    6712 
    6713 > color zone #27 near #26 distance 3.68
    6714 
    6715 > color zone #27 near #26 distance 3.58
    6716 
    6717 > color zone #27 near #26 distance 3.48
    6718 
    6719 > color zone #27 near #26 distance 3.38
    6720 
    6721 > color zone #27 near #26 distance 3.28
    6722 
    6723 > color zone #27 near #26 distance 3.18
    6724 
    6725 > color zone #27 near #26 distance 3.08
    6726 
    6727 > color zone #27 near #26 distance 2.98
    6728 
    6729 > color zone #27 near #26 distance 2.88
    6730 
    6731 > color zone #27 near #26 distance 2.78
    6732 
    6733 > color zone #27 near #26 distance 2.68
    6734 
    6735 > color zone #27 near #26 distance 2.58
    6736 
    6737 > color zone #27 near #26 distance 2.48
    6738 
    6739 > color zone #27 near #26 distance 2.38
    6740 
    6741 > color zone #27 near #26 distance 2.28
    6742 
    6743 > volume #27 level 0.1207
    6744 
    6745 > color zone #27 near #26 distance 2.18
    6746 
    6747 > color zone #27 near #26 distance 2.08
    6748 
    6749 > hide #!27 models
    6750 
    6751 > show #!27 models
    6752 
    6753 > fitmap #26 inMap #27
    6754 
    6755 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    6756 rOAT1-PAH.mrc (#27) using 3865 atoms 
    6757 average map value = 0.3441, steps = 44 
    6758 shifted from previous position = 0.00509 
    6759 rotated from previous position = 0.0145 degrees 
    6760 atoms outside contour = 605, contour level = 0.12073 
    6761  
    6762 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    6763 rOAT1-PAH.mrc (#27) coordinates: 
    6764 Matrix rotation and translation 
    6765 1.00000000 -0.00003177 0.00004592 0.00408484 
    6766 0.00003177 1.00000000 0.00006809 -0.00110606 
    6767 -0.00004592 -0.00006809 1.00000000 0.00040828 
    6768 Axis -0.77323345 0.52146975 0.36080373 
    6769 Axis point 0.00000000 25.00840435 -11.23310139 
    6770 Rotation angle (degrees) 0.00504562 
    6771 Shift along axis -0.00358800 
    6772  
    6773 
    6774 > fitmap #26 inMap #27
    6775 
    6776 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    6777 rOAT1-PAH.mrc (#27) using 3865 atoms 
    6778 average map value = 0.3441, steps = 40 
    6779 shifted from previous position = 0.0153 
    6780 rotated from previous position = 0.0197 degrees 
    6781 atoms outside contour = 607, contour level = 0.12073 
    6782  
    6783 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    6784 rOAT1-PAH.mrc (#27) coordinates: 
    6785 Matrix rotation and translation 
    6786 0.99999998 -0.00017402 -0.00004728 0.01145050 
    6787 0.00017401 0.99999996 -0.00023139 -0.00012574 
    6788 0.00004732 0.00023138 0.99999997 -0.01696563 
    6789 Axis 0.78875519 -0.16123857 0.59318410 
    6790 Axis point 0.00000000 70.72803400 -1.26127659 
    6791 Rotation angle (degrees) 0.01680827 
    6792 Shift along axis -0.00101183 
    6793  
    6794 
    6795 > volume splitbyzone #27
    6796 
    6797 Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at
    6798 level 0.121, step 1, values float32 
    6799 Opened rOAT1-PAH.mrc 1 as #28.2, grid size 160,160,160, pixel 0.83, shown at
    6800 level 0.121, step 1, values float32 
    6801 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    6802 level 0.121, step 1, values float32 
    6803 
    6804 > close #28.1-2
    6805 
    6806 > volume #28.3 level 0.05463
    6807 
    6808 > color #28.3 white models
    6809 
    6810 > color #28.3 #ffffb2ff models
    6811 
    6812 > color #28.3 #ffffb296 models
    6813 
    6814 > select add #26
    6815 
    6816 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    6817 
    6818 > color #26 #bf3434ff
    6819 
    6820 > select subtract #26
    6821 
    6822 Nothing selected 
    6823 
    6824 > hide #!26 models
    6825 
    6826 > hide #!28 models
    6827 
    6828 > hide #!28.3 models
    6829 
    6830 > show #!28 models
    6831 
    6832 > show #!28.3 models
    6833 
    6834 > hide #!28 models
    6835 
    6836 > show #!28 models
    6837 
    6838 > show #!26 models
    6839 
    6840 > save
    6841 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6842 > includeMaps true
    6843 
    6844 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id:
    6845 35657337, major code: 40 (TranslateCoords), minor code: 0 
    6846 
    6847 > hide #!26 models
    6848 
    6849 > hide #!28 models
    6850 
    6851 > hide #!28.3 models
    6852 
    6853 > open
    6854 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc
    6855 
    6856 Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at
    6857 level 0.0068, step 2, values float32 
    6858 
    6859 > open
    6860 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb
    6861 
    6862 Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30 
    6863 --- 
    6864 Chain | Description 
    6865 A | No description available 
    6866  
    6867 
    6868 > show #!2 models
    6869 
    6870 > volume #29 step 1
    6871 
    6872 > volume #29 level 0.01695
    6873 
    6874 > select add #30
    6875 
    6876 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    6877 
    6878 > view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467
    6879 
    6880 > view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8
    6881 
    6882 > view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211
    6883 
    6884 > view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823
    6885 
    6886 > rename #29 rOAT1-FBP.mrc
    6887 
    6888 > fitmap #30 inMap #29
    6889 
    6890 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    6891 using 4327 atoms 
    6892 average map value = 0.02366, steps = 64 
    6893 shifted from previous position = 2.15 
    6894 rotated from previous position = 1.57 degrees 
    6895 atoms outside contour = 1497, contour level = 0.016951 
    6896  
    6897 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    6898 (#29) coordinates: 
    6899 Matrix rotation and translation 
    6900 0.99965949 -0.01809184 -0.01880406 69.16631575 
    6901 0.01825291 0.99979787 0.00842953 64.90387685 
    6902 0.01864775 -0.00876989 0.99978765 65.39100171 
    6903 Axis -0.31300664 -0.68157330 0.66142625 
    6904 Axis point -4271.01743380 0.00000000 3378.83285764 
    6905 Rotation angle (degrees) 1.57437238 
    6906 Shift along axis -22.63494048 
    6907  
    6908 
    6909 > fitmap #29 inMap #28.3
    6910 
    6911 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    6912 correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449 
    6913 steps = 2000, shift = 8.88, angle = 34.9 degrees 
    6914  
    6915 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    6916 coordinates: 
    6917 Matrix rotation and translation 
    6918 0.83021101 -0.04922054 -0.55527201 36.70411652 
    6919 0.13130357 0.98533433 0.10897540 -101.23145590 
    6920 0.54176475 -0.16338178 0.82449824 -98.97434819 
    6921 Axis -0.23793623 -0.95839145 0.15770918 
    6922 Axis point 214.13564799 0.00000000 31.76591481 
    6923 Rotation angle (degrees) 34.91302477 
    6924 Shift along axis 72.67695975 
    6925  
    6926 
    6927 > fitmap #29 inMap #28.3
    6928 
    6929 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    6930 correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215 
    6931 steps = 1976, shift = 9.79, angle = 47.5 degrees 
    6932  
    6933 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    6934 coordinates: 
    6935 Matrix rotation and translation 
    6936 0.44591506 0.03168285 -0.89451437 128.47676238 
    6937 -0.42572042 0.88660402 -0.18081879 31.25418163 
    6938 0.78735118 0.46144286 0.40883812 -156.17744024 
    6939 Axis 0.34576253 -0.90543486 -0.24624374 
    6940 Axis point 186.53313716 0.00000000 6.98625710 
    6941 Rotation angle (degrees) 68.24252592 
    6942 Shift along axis 54.58154231 
    6943  
    6944 
    6945 > fitmap #29 inMap #2
    6946 
    6947 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    6948 correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051 
    6949 steps = 232, shift = 3.32, angle = 8.56 degrees 
    6950  
    6951 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    6952 Matrix rotation and translation 
    6953 0.54964589 -0.00012465 -0.83539774 175.75622877 
    6954 -0.44507129 0.84621907 -0.29295875 119.06565669 
    6955 0.70696602 0.53283512 0.46506536 -99.09845418 
    6956 Axis 0.45744920 -0.85439368 -0.24647856 
    6957 Axis point 210.95352936 0.00000000 94.96801349 
    6958 Rotation angle (degrees) 64.50291620 
    6959 Shift along axis 3.09624573 
    6960  
    6961 
    6962 > select add #29
    6963 
    6964 4327 atoms, 4393 bonds, 591 residues, 3 models selected 
    6965 
    6966 > hide #!2 models
    6967 
    6968 > show #!2 models
    6969 
    6970 > hide #!2 models
    6971 
    6972 > show #!27 models
    6973 
    6974 > view matrix models
    6975 > #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312
    6976 
    6977 > select subtract #30
    6978 
    6979 2 models selected 
    6980 
    6981 > ui mousemode right "rotate selected models"
    6982 
    6983 > view matrix models
    6984 > #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4
    6985 
    6986 > view matrix models
    6987 > #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407
    6988 
    6989 > ui mousemode right "translate selected models"
    6990 
    6991 > view matrix models
    6992 > #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751
    6993 
    6994 > view matrix models
    6995 > #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331
    6996 
    6997 > fitmap #29 inMap #2
    6998 
    6999 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    7000 correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98 
    7001 steps = 260, shift = 2.93, angle = 16.7 degrees 
    7002  
    7003 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    7004 Matrix rotation and translation 
    7005 0.99338416 0.10541244 -0.04556454 -5.89234048 
    7006 -0.10461957 0.99432199 0.01945563 14.33237930 
    7007 0.04735669 -0.01455997 0.99877192 -4.89753719 
    7008 Axis -0.14650897 -0.40022199 -0.90463113 
    7009 Axis point 131.78683646 64.78395429 0.00000000 
    7010 Rotation angle (degrees) 6.66633138 
    7011 Shift along axis -0.44238796 
    7012  
    7013 
    7014 > fitmap #30 inMap #29
    7015 
    7016 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    7017 using 4327 atoms 
    7018 average map value = 0.02366, steps = 84 
    7019 shifted from previous position = 1.18 
    7020 rotated from previous position = 6.66 degrees 
    7021 atoms outside contour = 1496, contour level = 0.016951 
    7022  
    7023 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    7024 (#29) coordinates: 
    7025 Matrix rotation and translation 
    7026 0.99966027 -0.01808767 -0.01876641 69.16021058 
    7027 0.01824668 0.99979876 0.00833662 64.90031908 
    7028 0.01861185 -0.00867622 0.99978914 65.39198117 
    7029 Axis -0.31026139 -0.68166338 0.66262576 
    7030 Axis point -4271.35731029 0.00000000 3392.84555643 
    7031 Rotation angle (degrees) 1.57107230 
    7032 Shift along axis -22.36750269 
    7033  
    7034 
    7035 > select subtract #29
    7036 
    7037 Nothing selected 
    7038 
    7039 > hide #!27 models
    7040 
    7041 > color #29 white models
    7042 
    7043 > color #30 white
    7044 
    7045 > select ::name="FBP"
    7046 
    7047 18 atoms, 19 bonds, 1 residue, 1 model selected 
    7048 
    7049 > color sel red
    7050 
    7051 > color zone #29 near #30 distance 4.98
    7052 
    7053 > volume #29 level 0.01043
    7054 
    7055 > volume splitbyzone #29
    7056 
    7057 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    7058 level 0.0104, step 1, values float32 
    7059 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    7060 level 0.0104, step 1, values float32 
    7061 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    7062 level 0.0104, step 1, values float32 
    7063 
    7064 > close #31.1-2
    7065 
    7066 > volume #31.3 level 0.002491
    7067 
    7068 > volume #31.3 level 0.005476
    7069 
    7070 > close #31#31.3
    7071 
    7072 > show #!29 models
    7073 
    7074 > color zone #29 near #30 distance 2
    7075 
    7076 [Repeated 1 time(s)]
    7077 
    7078 > volume splitbyzone #29
    7079 
    7080 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    7081 level 0.0104, step 1, values float32 
    7082 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    7083 level 0.0104, step 1, values float32 
    7084 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    7085 level 0.0104, step 1, values float32 
    7086 
    7087 > close #31.1-2
    7088 
    7089 > volume #31.3 level 0.003802
    7090 
    7091 > color #31.3 white models
    7092 
    7093 > color #31.3 #ffffb2ff models
    7094 
    7095 > color #31.3 #ffffb20f models
    7096 
    7097 > color #31.3 #ffffb296 models
    7098 
    7099 > select add #30
    7100 
    7101 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    7102 
    7103 > color #30 #889944ff
    7104 
    7105 > color #30 #894a08ff
    7106 
    7107 > save
    7108 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    7109 > includeMaps true
    7110 
    7111 > hide #!31.3 models
    7112 
    7113 > hide #!31 models
    7114 
    7115 > select subtract #30
    7116 
    7117 Nothing selected 
    7118 
    7119 > hide #30 models
    7120 
    7121 > show #!2 models
    7122 
    7123 > open
    7124 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc
    7125 
    7126 Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at
    7127 level 0.00396, step 2, values float32 
    7128 
    7129 QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id:
    7130 35657387, major code: 40 (TranslateCoords), minor code: 0 
    7131 
    7132 > volume #32 step 1
    7133 
    7134 > volume #32 level 0.01186
    7135 
    7136 > rename #32 rOAT1-CFM.mrc
    7137 
    7138 > fitmap #31.3 inMap #32
    7139 
    7140 Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points 
    7141 correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643 
    7142 steps = 80, shift = 1.06, angle = 39.7 degrees 
    7143  
    7144 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32)
    7145 coordinates: 
    7146 Matrix rotation and translation 
    7147 0.74404465 0.65679786 0.12253212 -67.09990326 
    7148 -0.66239846 0.70118044 0.26376935 89.56606533 
    7149 0.08732602 -0.27742126 0.95677145 29.93219993 
    7150 Axis -0.37942983 0.02468307 -0.92489121 
    7151 Axis point 75.79903236 131.70903838 0.00000000 
    7152 Rotation angle (degrees) 45.49284979 
    7153 Shift along axis -0.01355792 
    7154  
    7155 
    7156 > fitmap #31.3 inMap #2
    7157 
    7158 Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points 
    7159 correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295 
    7160 steps = 76, shift = 0.987, angle = 35 degrees 
    7161  
    7162 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2)
    7163 coordinates: 
    7164 Matrix rotation and translation 
    7165 0.98357109 0.17790518 -0.03062105 -15.98050765 
    7166 -0.17592201 0.98266732 0.05844983 19.75924781 
    7167 0.04048883 -0.05210265 0.99782061 1.12732183 
    7168 Axis -0.29288928 -0.18839308 -0.93740275 
    7169 Axis point 102.41456930 99.44616144 0.00000000 
    7170 Rotation angle (degrees) 10.87852675 
    7171 Shift along axis -0.09874061 
    7172  
    7173 
    7174 > fitmap #32 inMap #2
    7175 
    7176 Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points 
    7177 correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57 
    7178 steps = 72, shift = 2.43, angle = 7.06 degrees 
    7179  
    7180 Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    7181 Matrix rotation and translation 
    7182 0.99240829 0.11776796 -0.03544703 -8.88787383 
    7183 -0.11778889 0.99303752 0.00150464 18.44106769 
    7184 0.03537743 0.00268205 0.99937042 -5.69387210 
    7185 Axis 0.00478670 -0.28793162 -0.95763901 
    7186 Axis point 151.76616064 85.25679566 0.00000000 
    7187 Rotation angle (degrees) 7.06459913 
    7188 Shift along axis 0.10036409 
    7189  
    7190 
    7191 > save
    7192 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    7193 > models #30 relModel #32
    7194 
    7195 > open
    7196 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    7197 
    7198 Chain information for rOAT1-CFM_IF.pdb #33 
    7199 --- 
    7200 Chain | Description 
    7201 A | No description available 
    7202  
    7203 
    7204 > color #33 #ffff7fff
    7205 
    7206 > color #33 #55aaffff
    7207 
    7208 > select add #33
    7209 
    7210 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    7211 
    7212 > view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224
    7213 
    7214 > view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924
    7215 
    7216 > view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036
    7217 
    7218 > fitmap #33 inMap #32
    7219 
    7220 Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327
    7221 atoms 
    7222 average map value = 0.0191, steps = 80 
    7223 shifted from previous position = 1.1 
    7224 rotated from previous position = 7.12 degrees 
    7225 atoms outside contour = 1362, contour level = 0.01186 
    7226  
    7227 Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32)
    7228 coordinates: 
    7229 Matrix rotation and translation 
    7230 0.99999299 -0.00023005 -0.00373680 -4.70643521 
    7231 0.00021365 0.99999035 -0.00438786 8.58155234 
    7232 0.00373777 0.00438703 0.99998339 -3.97966882 
    7233 Axis 0.76069466 -0.64796926 0.03846397 
    7234 Axis point 0.00000000 827.85989235 581.48051316 
    7235 Rotation angle (degrees) 0.33046593 
    7236 Shift along axis -9.29381608 
    7237  
    7238 
    7239 > save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb
    7240 > models #33 relModel #32
    7241 
    7242 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id:
    7243 35657459, major code: 40 (TranslateCoords), minor code: 0 
    7244 
    7245 > hide #33 models
    7246 
    7247 > hide #!32 models
    7248 
    7249 > select subtract #33
    7250 
    7251 Nothing selected 
    7252 
    7253 > show #!17 models
    7254 
    7255 > hide #!17 models
    7256 
    7257 > show #!17 models
    7258 
    7259 > hide #!2 models
    7260 
    7261 > open
    7262 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV-
    7263 > Cl_OF-coot-2.pdb
    7264 
    7265 Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34 
    7266 --- 
    7267 Chain | Description 
    7268 A | No description available 
    7269  
    7270 
    7271 > select ::name="CL"
    7272 
    7273 1 atom, 1 residue, 1 model selected 
    7274 
    7275 > hide #!17 models
    7276 
    7277 > show sel atoms
    7278 
    7279 > show #!17 models
    7280 
    7281 > style sel stick
    7282 
    7283 Changed 1 atom style 
    7284 
    7285 > color zone #17 near #34 distance 2.98
    7286 
    7287 > select add #34
    7288 
    7289 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7290 
    7291 > color #34 white
    7292 
    7293 > color zone #17 near #34 distance 2.98
    7294 
    7295 > select ::name="CL"
    7296 
    7297 1 atom, 1 residue, 1 model selected 
    7298 
    7299 > color sel red
    7300 
    7301 > color zone #17 near #34 distance 2.98
    7302 
    7303 > volume splitbyzone #17
    7304 
    7305 Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown
    7306 at level 0.011, step 1, values float32 
    7307 Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown
    7308 at level 0.011, step 1, values float32 
    7309 Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown
    7310 at level 0.011, step 1, values float32 
    7311 
    7312 > rename #35 "rOAT1-TVF-Cl_OF.mrc split"
    7313 
    7314 > close #35.1-2
    7315 
    7316 > rename #35.3 "rOAT1-TVF-Cl_OF.mrc 2"
    7317 
    7318 > hide #!35.3 models
    7319 
    7320 > select #34/B:1@CL
    7321 
    7322 1 atom, 1 residue, 1 model selected 
    7323 
    7324 > ui tool show Contacts
    7325 
    7326 > contacts sel interModel false ignoreHiddenModels true select true
    7327 
    7328 6 contacts 
    7329 
    7330 > ui tool show Contacts
    7331 
    7332 > contacts sel intraRes true ignoreHiddenModels true select true
    7333 
    7334 15 contacts 
    7335 
    7336 > show sel atoms
    7337 
    7338 > color #34 yellow
    7339 
    7340 > show sel atoms
    7341 
    7342 > close #36
    7343 
    7344 > select add #34
    7345 
    7346 3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected 
    7347 
    7348 > color #34 white
    7349 
    7350 > hide sel atoms
    7351 
    7352 > select ::name="CL"
    7353 
    7354 1 atom, 1 residue, 1 model selected 
    7355 
    7356 > show sel atoms
    7357 
    7358 > hide #35.3.1 models
    7359 
    7360 > show #35.3.1 models
    7361 
    7362 > close #34.2
    7363 
    7364 > hide #!35.3 models
    7365 
    7366 > hide #35.3.1 models
    7367 
    7368 > hide #!35 models
    7369 
    7370 > hide #34.1 models
    7371 
    7372 > select #34/B:1@CL
    7373 
    7374 1 atom, 1 residue, 1 model selected 
    7375 
    7376 > select #34/A:216
    7377 
    7378 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7379 
    7380 > show sel atoms
    7381 
    7382 > select #34/A:511
    7383 
    7384 7 atoms, 7 bonds, 1 residue, 1 model selected 
    7385 
    7386 > show sel atoms
    7387 
    7388 > select #34: 219
    7389 
    7390 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7391 
    7392 > show sel atoms
    7393 
    7394 > select #34: 273
    7395 
    7396 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7397 
    7398 > show sel atoms
    7399 
    7400 > select #34/A:4
    7401 
    7402 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7403 
    7404 > show sel atoms
    7405 
    7406 > select add #34/A:511
    7407 
    7408 15 atoms, 14 bonds, 2 residues, 1 model selected 
    7409 
    7410 > show sel atoms
    7411 
    7412 > select add #34/A:512
    7413 
    7414 23 atoms, 21 bonds, 3 residues, 1 model selected 
    7415 
    7416 > show sel atoms
    7417 
    7418 > select #34/B:1@CL
    7419 
    7420 1 atom, 1 residue, 1 model selected 
    7421 
    7422 > color sel lime
    7423 
    7424 > color #35.3.1 white
    7425 
    7426 > color #35.3.1 #ffffb2ff
    7427 
    7428 > color #35.3.1 #ffffb296
    7429 
    7430 > select #34/B:1@CL
    7431 
    7432 1 atom, 1 residue, 1 model selected 
    7433 
    7434 > select add #34
    7435 
    7436 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7437 
    7438 > color #34 #374c02ff
    7439 
    7440 > select #34/B:1@CL
    7441 
    7442 1 atom, 1 residue, 1 model selected 
    7443 
    7444 > color sel lime
    7445 
    7446 > select add #34
    7447 
    7448 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7449 
    7450 > color (#!34 & sel) byhetero
    7451 
    7452 > select #34/A:2
    7453 
    7454 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7455 
    7456 > show sel atoms
    7457 
    7458 > select #34/A:3
    7459 
    7460 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7461 
    7462 > show sel atoms
    7463 
    7464 > select add #34/A:215
    7465 
    7466 18 atoms, 18 bonds, 2 residues, 1 model selected 
    7467 
    7468 > show sel atoms
    7469 
    7470 > select #34/B:1@CL
    7471 
    7472 1 atom, 1 residue, 1 model selected 
    7473 
    7474 > show #35.3.1 models
    7475 
    7476 > view sel
    7477 
    7478 > hide #35.3.1 models
    7479 
    7480 > hide #!35.3 models
    7481 
    7482 > hide #!35 models
    7483 
    7484 > hide #!34 models
    7485 
    7486 > select add #34
    7487 
    7488 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7489 
    7490 > select subtract #34
    7491 
    7492 Nothing selected 
    7493 
    7494 > show #1 models
    7495 
    7496 > view
    7497 
    7498 > hide #1 models
    7499 
    7500 > show #21 models
    7501 
    7502 > select add #21/A:602@C12
    7503 
    7504 1 atom, 1 residue, 1 model selected 
    7505 
    7506 > select up
    7507 
    7508 3 atoms, 1 bond, 2 residues, 1 model selected 
    7509 
    7510 > select up
    7511 
    7512 44 atoms, 46 bonds, 2 residues, 1 model selected 
    7513 
    7514 > select clear
    7515 
    7516 > select #21/A:602@O14
    7517 
    7518 1 atom, 1 residue, 1 model selected 
    7519 
    7520 > select add #21/A:601@C04
    7521 
    7522 2 atoms, 2 residues, 1 model selected 
    7523 
    7524 > select up
    7525 
    7526 70 atoms, 76 bonds, 2 residues, 1 model selected 
    7527 
    7528 > view sel
    7529 
    7530 > show #!22.3 models
    7531 
    7532 > hide #!22.3 models
    7533 
    7534 > hide #!22 models
    7535 
    7536 > hide #21 models
    7537 
    7538 > select add #21
    7539 
    7540 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    7541 
    7542 > select subtract #21
    7543 
    7544 Nothing selected 
    7545 
    7546 > save
    7547 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    7548 > includeMaps true
    7549 
    7550 QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id:
    7551 35657669, major code: 40 (TranslateCoords), minor code: 0 
    7552 
    7553 > open
    7554 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc
    7555 
    7556 Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    7557 level 0.00418, step 2, values float32 
    7558 
    7559 > open
    7560 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    7561 
    7562 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    7563 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    7564 (Q4U2R8) [more info...] 
    7565  
    7566 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37 
    7567 --- 
    7568 Chain | Description | UniProt 
    7569 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    7570  
    7571 
    7572 > rename #36 hOAT1-TFV.mrc
    7573 
    7574 > volume #36 step 1
    7575 
    7576 > volume #36 level 0.008515
    7577 
    7578 > rename #37 hOAT1-TFV_IF.pdb
    7579 
    7580 > view
    7581 
    7582 > show #!2 models
    7583 
    7584 > hide #!2 models
    7585 
    7586 > ui tool show Matchmaker
    7587 
    7588 > matchmaker #37 to #1
    7589 
    7590 Parameters 
    7591 --- 
    7592 Chain pairing | bb 
    7593 Alignment algorithm | Needleman-Wunsch 
    7594 Similarity matrix | BLOSUM-62 
    7595 SS fraction | 0.3 
    7596 Gap open (HH/SS/other) | 18/18/6 
    7597 Gap extend | 1 
    7598 SS matrix |  |  | H | S | O 
    7599 ---|---|---|--- 
    7600 H | 6 | -9 | -6 
    7601 S |  | 6 | -6 
    7602 O |  |  | 4 
    7603 Iteration cutoff | 2 
    7604  
    7605 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    7606 (#37), sequence alignment score = 2359.6 
    7607 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    7608 0.862) 
    7609  
    7610 
    7611 > matchmaker #37 to #1
    7612 
    7613 Parameters 
    7614 --- 
    7615 Chain pairing | bb 
    7616 Alignment algorithm | Needleman-Wunsch 
    7617 Similarity matrix | BLOSUM-62 
    7618 SS fraction | 0.3 
    7619 Gap open (HH/SS/other) | 18/18/6 
    7620 Gap extend | 1 
    7621 SS matrix |  |  | H | S | O 
    7622 ---|---|---|--- 
    7623 H | 6 | -9 | -6 
    7624 S |  | 6 | -6 
    7625 O |  |  | 4 
    7626 Iteration cutoff | 2 
    7627  
    7628 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    7629 (#37), sequence alignment score = 2359.6 
    7630 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    7631 0.862) 
    7632  
    7633 
    7634 > save
    7635 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb
    7636 > models #37 relModel #36
    7637 
    7638 > rename #36 hOAT1-TFV_IF.mrc
    7639 
    7640 > hide #37 models
    7641 
    7642 > hide #!36 models
    7643 
    7644 > open
    7645 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    7646 
    7647 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    7648 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    7649 (Q4U2R8) [more info...] 
    7650  
    7651 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38 
    7652 --- 
    7653 Chain | Description | UniProt 
    7654 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    7655  
    7656 
    7657 > close #38
    7658 
    7659 > close #37
    7660 
    7661 > open
    7662 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF-
    7663 > coot-1_real_space_refined_002.pdb
    7664 
    7665 Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37 
    7666 --- 
    7667 Chain | Description 
    7668 A | No description available 
    7669  
    7670 
    7671 > show #!36 models
    7672 
    7673 > color #36 white models
    7674 
    7675 > color #37 white
    7676 
    7677 > hide #!36 models
    7678 
    7679 > select up
    7680 
    7681 2 atoms, 1 bond, 1 residue, 1 model selected 
    7682 
    7683 > select #37/A:601@C08
    7684 
    7685 1 atom, 1 residue, 1 model selected 
    7686 
    7687 > select up
    7688 
    7689 31 atoms, 32 bonds, 1 residue, 1 model selected 
    7690 
    7691 > color sel red
    7692 
    7693 > show #!36 models
    7694 
    7695 > color zone #36 near #37 distance 4.98
    7696 
    7697 > color zone #36 near #37 distance 2
    7698 
    7699 [Repeated 1 time(s)]
    7700 
    7701 > color zone #36 near #37 distance 1.9
    7702 
    7703 > color zone #36 near #37 distance 1.8
    7704 
    7705 > color zone #36 near #37 distance 1.7
    7706 
    7707 > volume splitbyzone #36
    7708 
    7709 Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown
    7710 at level 0.00852, step 1, values float32 
    7711 Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown
    7712 at level 0.00852, step 1, values float32 
    7713 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    7714 at level 0.00852, step 1, values float32 
    7715 
    7716 > close #38.1-2
    7717 
    7718 > color #38.3 white models
    7719 
    7720 > color #38.3 #ffffb2ff models
    7721 
    7722 > color #38.3 #ffffb296 models
    7723 
    7724 > color #37 #aaff7fff
    7725 
    7726 > select add #37
    7727 
    7728 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    7729 
    7730 > color sel byhetero
    7731 
    7732 > save
    7733 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    7734 > includeMaps true
    7735 
    7736 QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id:
    7737 35657985, major code: 40 (TranslateCoords), minor code: 0 
    7738 
    7739 > hide #!38.3 models
    7740 
    7741 > hide #!38 models
    7742 
    7743 > select subtract #37
    7744 
    7745 Nothing selected 
    7746 
    7747 > show #!34 models
    7748 
    7749 Drag select of 25 atoms, 383 residues, 24 bonds 
    7750 
    7751 > select up
    7752 
    7753 2906 atoms, 2958 bonds, 383 residues, 2 models selected 
    7754 
    7755 > select clear
    7756 
    7757 > select add #37/A:326
    7758 
    7759 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7760 
    7761 > select clear
    7762 
    7763 > hide #!34 models
    7764 
    7765 > select add #37
    7766 
    7767 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    7768 
    7769 > select subtract #37
    7770 
    7771 Nothing selected 
    7772 
    7773 > save
    7774 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7775 
    7776 > save
    7777 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7778 > models #37 relModel #36
    7779 
    7780 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id:
    7781 35658005, major code: 40 (TranslateCoords), minor code: 0 
    7782 
    7783 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id:
    7784 35657995, major code: 40 (TranslateCoords), minor code: 0 
    7785 
    7786 > open
    7787 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc
    7788 
    7789 Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    7790 level 0.00436, step 2, values float32 
    7791 
    7792 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id:
    7793 35658010, major code: 40 (TranslateCoords), minor code: 0 
    7794 
    7795 > rename #39 hOAT1-TFV_OF.mrc
    7796 
    7797 > volume #39 step 1
    7798 
    7799 > volume #39 level 0.01031
    7800 
    7801 > hide #!39 models
    7802 
    7803 > open
    7804 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7805 
    7806 Chain information for hOAT1-TFV_OF.pdb #40 
    7807 --- 
    7808 Chain | Description 
    7809 A | No description available 
    7810  
    7811 
    7812 > hide #37 models
    7813 
    7814 > select #40: 320-600
    7815 
    7816 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    7817 
    7818 > hide sel cartoons
    7819 
    7820 [Repeated 1 time(s)]
    7821 
    7822 > show sel cartoons
    7823 
    7824 > ui tool show Matchmaker
    7825 
    7826 > matchmaker #40 & sel to #18
    7827 
    7828 Parameters 
    7829 --- 
    7830 Chain pairing | bb 
    7831 Alignment algorithm | Needleman-Wunsch 
    7832 Similarity matrix | BLOSUM-62 
    7833 SS fraction | 0.3 
    7834 Gap open (HH/SS/other) | 18/18/6 
    7835 Gap extend | 1 
    7836 SS matrix |  |  | H | S | O 
    7837 ---|---|---|--- 
    7838 H | 6 | -9 | -6 
    7839 S |  | 6 | -6 
    7840 O |  |  | 4 
    7841 Iteration cutoff | 2 
    7842  
    7843 Matchmaker rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with
    7844 hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1 
    7845 RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs:
    7846 7.198) 
    7847  
    7848 
    7849 > matchmaker #40 to #15
    7850 
    7851 Parameters 
    7852 --- 
    7853 Chain pairing | bb 
    7854 Alignment algorithm | Needleman-Wunsch 
    7855 Similarity matrix | BLOSUM-62 
    7856 SS fraction | 0.3 
    7857 Gap open (HH/SS/other) | 18/18/6 
    7858 Gap extend | 1 
    7859 SS matrix |  |  | H | S | O 
    7860 ---|---|---|--- 
    7861 H | 6 | -9 | -6 
    7862 S |  | 6 | -6 
    7863 O |  |  | 4 
    7864 Iteration cutoff | 2 
    7865  
    7866 Matchmaker rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain
    7867 A (#40), sequence alignment score = 2368.6 
    7868 RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs:
    7869 0.719) 
    7870  
    7871 
    7872 > show #!18 models
    7873 
    7874 > ui mousemode right "translate selected atoms"
    7875 
    7876 > ui mousemode right "rotate selected models"
    7877 
    7878 > view matrix models
    7879 > #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122
    7880 
    7881 > undo
    7882 
    7883 > ui mousemode right "move picked models"
    7884 
    7885 > view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987
    7886 
    7887 > undo
    7888 
    7889 > ui mousemode right pivot
    7890 
    7891 > ui tool show Matchmaker
    7892 
    7893 > matchmaker #40 & sel to #5 & sel
    7894 
    7895 No 'to' model specified 
    7896 
    7897 > select clear
    7898 
    7899 > hide #!18 models
    7900 
    7901 > show #!18 models
    7902 
    7903 > select #18,40: 320-600
    7904 
    7905 3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected 
    7906 
    7907 > ui tool show Matchmaker
    7908 
    7909 > matchmaker #40 & sel to #5 & sel
    7910 
    7911 No 'to' model specified 
    7912 
    7913 > matchmaker #40 & sel to #5 & sel
    7914 
    7915 No 'to' model specified 
    7916 
    7917 > matchmaker #40 & sel to #5 & sel
    7918 
    7919 No 'to' model specified 
    7920 
    7921 > ui mousemode right "translate selected atoms"
    7922 
    7923 > select #40: 320-600
    7924 
    7925 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    7926 
    7927 > hide #!18 models
    7928 
    7929 > show #!18 models
    7930 
    7931 > hide #40 models
    7932 
    7933 > hide #!18 models
    7934 
    7935 > show #40 models
    7936 
    7937 > save
    7938 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7939 > models #40 relModel #39
    7940 
    7941 QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id:
    7942 35658147, major code: 40 (TranslateCoords), minor code: 0 
    7943 
    7944 > fitmap #40 inMap #39
    7945 
    7946 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    7947 atoms 
    7948 average map value = 0.007219, steps = 88 
    7949 shifted from previous position = 0.909 
    7950 rotated from previous position = 8.49 degrees 
    7951 atoms outside contour = 2887, contour level = 0.010308 
    7952  
    7953 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    7954 coordinates: 
    7955 Matrix rotation and translation 
    7956 0.99019825 -0.07829950 -0.11565728 27.38037598 
    7957 0.07892080 0.99688057 0.00079533 -10.70816731 
    7958 0.11523422 -0.00991530 0.99328886 -13.08861468 
    7959 Axis -0.03831490 -0.82596303 0.56242070 
    7960 Axis point 128.86145300 0.00000000 225.96021530 
    7961 Rotation angle (degrees) 8.03460025 
    7962 Shift along axis 0.43416611 
    7963  
    7964 
    7965 > save
    7966 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7967 > models #40 relModel #39
    7968 
    7969 > undo
    7970 
    7971 > select clear
    7972 
    7973 > show #!39 models
    7974 
    7975 > fitmap #40 inMap #39
    7976 
    7977 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    7978 atoms 
    7979 average map value = 0.007218, steps = 28 
    7980 shifted from previous position = 0.0175 
    7981 rotated from previous position = 0.016 degrees 
    7982 atoms outside contour = 2888, contour level = 0.010308 
    7983  
    7984 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    7985 coordinates: 
    7986 Matrix rotation and translation 
    7987 0.99020256 -0.07845145 -0.11551732 27.36683659 
    7988 0.07909202 0.99686685 0.00096497 -10.76110579 
    7989 0.11507968 -0.01009202 0.99330500 -13.04322773 
    7990 Axis -0.03956067 -0.82505023 0.56367284 
    7991 Axis point 128.67057833 0.00000000 226.14572082 
    7992 Rotation angle (degrees) 8.03322105 
    7993 Shift along axis 0.44368911 
    7994  
    7995 
    7996 > fitmap #40 inMap #39
    7997 
    7998 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    7999 atoms 
    8000 average map value = 0.007219, steps = 44 
    8001 shifted from previous position = 0.00455 
    8002 rotated from previous position = 0.00258 degrees 
    8003 atoms outside contour = 2889, contour level = 0.010308 
    8004  
    8005 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8006 coordinates: 
    8007 Matrix rotation and translation 
    8008 0.99020340 -0.07846932 -0.11549800 27.37049731 
    8009 0.07911379 0.99686509 0.00099928 -10.76639922 
    8010 0.11505751 -0.01012698 0.99330721 -13.03687370 
    8011 Axis -0.03980982 -0.82492871 0.56383314 
    8012 Axis point 128.62890621 0.00000000 226.21984207 
    8013 Rotation angle (degrees) 8.03295687 
    8014 Shift along axis 0.44127588 
    8015  
    8016 
    8017 > select add #40
    8018 
    8019 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    8020 
    8021 > fitmap #40 inMap #39
    8022 
    8023 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    8024 atoms 
    8025 average map value = 0.007219, steps = 60 
    8026 shifted from previous position = 2.24 
    8027 rotated from previous position = 0.00666 degrees 
    8028 atoms outside contour = 2889, contour level = 0.010308 
    8029  
    8030 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8031 coordinates: 
    8032 Matrix rotation and translation 
    8033 0.99020164 -0.07840067 -0.11555975 25.97288245 
    8034 0.07903810 0.99687116 0.00093711 -9.32824593 
    8035 0.11512471 -0.01006155 0.99330009 -12.03377088 
    8036 Axis -0.03935047 -0.82533103 0.56327634 
    8037 Axis point 116.53468443 0.00000000 214.84157931 
    8038 Rotation angle (degrees) 8.03353574 
    8039 Shift along axis -0.10149276 
    8040  
    8041 
    8042 > show #!17 models
    8043 
    8044 > fitmap #39 inMap #19.3
    8045 
    8046 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    8047 correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206 
    8048 steps = 936, shift = 1.08, angle = 13.4 degrees 
    8049  
    8050 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    8051 coordinates: 
    8052 Matrix rotation and translation 
    8053 0.98280665 -0.13043667 -0.13068041 37.39205996 
    8054 0.11063752 0.98266445 -0.14876125 8.18112237 
    8055 0.14781892 0.13174539 0.98020035 -34.01816129 
    8056 Axis 0.60585490 -0.60151939 0.52068635 
    8057 Axis point 0.00000000 261.98069292 24.54762139 
    8058 Rotation angle (degrees) 13.38519605 
    8059 Shift along axis 0.02026683 
    8060  
    8061 
    8062 > fitmap #39 inMap #19.3
    8063 
    8064 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    8065 correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206 
    8066 steps = 48, shift = 0.0138, angle = 0.161 degrees 
    8067  
    8068 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    8069 coordinates: 
    8070 Matrix rotation and translation 
    8071 0.98301413 -0.12857767 -0.13096186 37.15798588 
    8072 0.10847145 0.98263409 -0.15054633 8.70610140 
    8073 0.14804449 0.13378355 0.97989019 -34.26954280 
    8074 Axis 0.61337235 -0.60188813 0.51137563 
    8075 Axis point -0.00000000 260.45263984 27.89398858 
    8076 Rotation angle (degrees) 13.40165031 
    8077 Shift along axis 0.02697294 
    8078  
    8079 
    8080 > fitmap #40 inMap #39
    8081 
    8082 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    8083 atoms 
    8084 average map value = 0.007219, steps = 132 
    8085 shifted from previous position = 0.778 
    8086 rotated from previous position = 13.4 degrees 
    8087 atoms outside contour = 2889, contour level = 0.010308 
    8088  
    8089 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8090 coordinates: 
    8091 Matrix rotation and translation 
    8092 0.99020454 -0.07852899 -0.11544767 25.97319443 
    8093 0.07917768 0.99685998 0.00103677 -9.35919916 
    8094 0.11500374 -0.01016749 0.99331302 -12.00484753 
    8095 Axis -0.04009077 -0.82459474 0.56430155 
    8096 Axis point 116.41047661 0.00000000 215.06686153 
    8097 Rotation angle (degrees) 8.03257950 
    8098 Shift along axis -0.09809308 
    8099  
    8100 
    8101 > hide #!17 models
    8102 
    8103 > hide #!39 models
    8104 
    8105 > close #40
    8106 
    8107 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    8108 > coot-1.pdb
    8109 
    8110 Chain information for hOAT1-TFV_OF-coot-1.pdb #40 
    8111 --- 
    8112 Chain | Description 
    8113 A | No description available 
    8114  
    8115 
    8116 > show #!39 models
    8117 
    8118 > color #39 white models
    8119 
    8120 > color #40 white
    8121 
    8122 > hide #!39 models
    8123 
    8124 > select up
    8125 
    8126 2 atoms, 1 bond, 1 residue, 1 model selected 
    8127 
    8128 > color sel red
    8129 
    8130 > select up
    8131 
    8132 31 atoms, 32 bonds, 1 residue, 1 model selected 
    8133 
    8134 > color sel red
    8135 
    8136 > show #!39 models
    8137 
    8138 > color zone #39 near #40 distance 4.98
    8139 
    8140 > color zone #39 near #40 distance 2
    8141 
    8142 [Repeated 1 time(s)]
    8143 
    8144 > volume #39 level 0.01241
    8145 
    8146 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    8147 > coot-2.pdb
    8148 
    8149 Chain information for hOAT1-TFV_OF-coot-2.pdb #41 
    8150 --- 
    8151 Chain | Description 
    8152 A | No description available 
    8153  
    8154 
    8155 > hide #!40 models
    8156 
    8157 > color #41 white
    8158 
    8159 > color zone #39 near #41 distance 2
    8160 
    8161 > select up
    8162 
    8163 2 atoms, 1 bond, 1 residue, 1 model selected 
    8164 
    8165 > select up
    8166 
    8167 31 atoms, 32 bonds, 1 residue, 1 model selected 
    8168 
    8169 > color sel red
    8170 
    8171 > color zone #39 near #41 distance 2
    8172 
    8173 > volume #39 level 0.01056
    8174 
    8175 > color zone #39 near #41 distance 2.1
    8176 
    8177 > color zone #39 near #41 distance 2.2
    8178 
    8179 > color zone #39 near #41 distance 2.3
    8180 
    8181 > color zone #39 near #41 distance 2.4
    8182 
    8183 > color zone #39 near #41 distance 2.5
    8184 
    8185 > color zone #39 near #41 distance 2.6
    8186 
    8187 > color zone #39 near #41 distance 2.7
    8188 
    8189 > color zone #39 near #41 distance 2.8
    8190 
    8191 > color zone #39 near #41 distance 2.9
    8192 
    8193 > color zone #39 near #41 distance 3
    8194 
    8195 > color zone #39 near #41 distance 2.9
    8196 
    8197 > color zone #39 near #41 distance 2.8
    8198 
    8199 > color zone #39 near #41 distance 2.7
    8200 
    8201 > color zone #39 near #41 distance 2.6
    8202 
    8203 > color zone #39 near #41 distance 2.5
    8204 
    8205 > color zone #39 near #41 distance 2.4
    8206 
    8207 > color zone #39 near #41 distance 2.3
    8208 
    8209 > color zone #39 near #41 distance 2.2
    8210 
    8211 > color zone #39 near #41 distance 2.1
    8212 
    8213 > color zone #39 near #41 distance 2
    8214 
    8215 > color zone #39 near #41 distance 1.9
    8216 
    8217 > color zone #39 near #41 distance 2
    8218 
    8219 > color zone #39 near #41 distance 2.1
    8220 
    8221 > color zone #39 near #41 distance 2.2
    8222 
    8223 > color zone #39 near #41 distance 2.3
    8224 
    8225 > color zone #39 near #41 distance 2.4
    8226 
    8227 > color zone #39 near #41 distance 2.5
    8228 
    8229 > volume splitbyzone #39
    8230 
    8231 Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown
    8232 at level 0.0106, step 1, values float32 
    8233 Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown
    8234 at level 0.0106, step 1, values float32 
    8235 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    8236 at level 0.0106, step 1, values float32 
    8237 
    8238 > close #42.1-2
    8239 
    8240 > color #42.3 white models
    8241 
    8242 > color #42.3 #ffffb2ff models
    8243 
    8244 > color #42.3 #ffffb296 models
    8245 
    8246 > volume #42.3 level 0.006989
    8247 
    8248 > select add #41
    8249 
    8250 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    8251 
    8252 > color #41 #aaffffff
    8253 
    8254 > color #41 blue
    8255 
    8256 > color #41 red
    8257 
    8258 > color #41 #aa00ffff
    8259 
    8260 > color #41 #0055ffff
    8261 
    8262 > color #41 #55557fff
    8263 
    8264 > color #41 #ff557fff
    8265 
    8266 > color #41 #ffaaffff
    8267 
    8268 > color (#!41 & sel) byhetero
    8269 
    8270 > save
    8271 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    8272 > includeMaps true
    8273 
    8274 > show #!34 models
    8275 
    8276 > hide #!41 models
    8277 
    8278 > hide #!42 models
    8279 
    8280 > hide #!42.3 models
    8281 
    8282 > select subtract #41
    8283 
    8284 Nothing selected 
    8285 
    8286 > hide #!34 models
    8287 
    8288 > show #1 models
    8289 
    8290 > show #!3.3 models
    8291 
    8292 > hide #!3.3 models
    8293 
    8294 > hide #!3 models
    8295 
    8296 > hide #1 models
    8297 
    8298 > show #!22.3 models
    8299 
    8300 > show #21 models
    8301 
    8302 > select add #21/A:601@O25
    8303 
    8304 1 atom, 1 bond, 1 residue, 1 model selected 
    8305 
    8306 > select up
    8307 
    8308 3 atoms, 1 bond, 2 residues, 1 model selected 
    8309 
    8310 > view sel
    8311 
    8312 > volume #22.3 level 0.01409
    8313 
    8314 > hide #!22.3 models
    8315 
    8316 > hide #!22 models
    8317 
    8318 > hide #21 models
    8319 
    8320 > show #!22.3 models
    8321 
    8322 > hide #!22.3 models
    8323 
    8324 > hide #!22 models
    8325 
    8326 > show #!23 models
    8327 
    8328 > hide #!23 models
    8329 
    8330 > show #!25.3 models
    8331 
    8332 > show #!24 models
    8333 
    8334 > hide #!25.3 models
    8335 
    8336 > hide #!25 models
    8337 
    8338 > hide #!24 models
    8339 
    8340 > show #1 models
    8341 
    8342 > show #!3.3 models
    8343 
    8344 > hide #!3.3 models
    8345 
    8346 > hide #!3 models
    8347 
    8348 > hide #1 models
    8349 
    8350 > show #!5 models
    8351 
    8352 > show #!6.3 models
    8353 
    8354 > hide #!6.3 models
    8355 
    8356 > hide #!6 models
    8357 
    8358 > hide #!5 models
    8359 
    8360 > show #8 models
    8361 
    8362 > show #!9.3 models
    8363 
    8364 > volume #9.3 level 0.003826
    8365 
    8366 > select #8/A:230
    8367 
    8368 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8369 
    8370 > show sel atoms
    8371 
    8372 > select #8/A:227
    8373 
    8374 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8375 
    8376 > show sel atoms
    8377 
    8378 > select clear
    8379 
    8380 > hide #!9.3 models
    8381 
    8382 > hide #!9 models
    8383 
    8384 > hide #8 models
    8385 
    8386 > show #!12 models
    8387 
    8388 > show #!11.3 models
    8389 
    8390 > color #11.3 #ffffb296 models
    8391 
    8392 > hide #!12 models
    8393 
    8394 > hide #!11.3 models
    8395 
    8396 > hide #!11 models
    8397 
    8398 > show #15 models
    8399 
    8400 > show #!16.3 models
    8401 
    8402 > hide #!16.3 models
    8403 
    8404 > hide #!16 models
    8405 
    8406 > hide #15 models
    8407 
    8408 > show #!18 models
    8409 
    8410 > show #!19.3 models
    8411 
    8412 > hide #!18 models
    8413 
    8414 > hide #!19 models
    8415 
    8416 > hide #!19.3 models
    8417 
    8418 > show #37 models
    8419 
    8420 > show #!38.3 models
    8421 
    8422 > hide #!38.3 models
    8423 
    8424 > hide #!38 models
    8425 
    8426 > hide #37 models
    8427 
    8428 > close #40
    8429 
    8430 > show #!41 models
    8431 
    8432 > show #!42.3 models
    8433 
    8434 > hide #!42.3 models
    8435 
    8436 > hide #!42 models
    8437 
    8438 > hide #!41 models
    8439 
    8440 > show #!26 models
    8441 
    8442 > show #!28.3 models
    8443 
    8444 > select #26/A:230
    8445 
    8446 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8447 
    8448 > show sel atoms
    8449 
    8450 > select #26/A:200
    8451 
    8452 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8453 
    8454 > show sel atoms
    8455 
    8456 > select add #26
    8457 
    8458 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    8459 
    8460 > color (#!26 & sel) byhetero
    8461 
    8462 > select clear
    8463 
    8464 > select #26/A:223
    8465 
    8466 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8467 
    8468 > show sel atoms
    8469 
    8470 > select #26/A:227
    8471 
    8472 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8473 
    8474 > show sel atoms
    8475 
    8476 > select #26/A:223
    8477 
    8478 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8479 
    8480 > show sel atoms
    8481 
    8482 > select #26/A:200
    8483 
    8484 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8485 
    8486 > show sel atoms
    8487 
    8488 > select #26/A:226
    8489 
    8490 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8491 
    8492 > show sel atoms
    8493 
    8494 > select #26/A:204
    8495 
    8496 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8497 
    8498 > show sel atoms
    8499 
    8500 > select clear
    8501 
    8502 > hide #!28.3 models
    8503 
    8504 > hide #!28 models
    8505 
    8506 > hide #!26 models
    8507 
    8508 > show #!31.3 models
    8509 
    8510 > show #30 models
    8511 
    8512 > select add #30
    8513 
    8514 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    8515 
    8516 > color sel byhetero
    8517 
    8518 > select clear
    8519 
    8520 > save
    8521 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    8522 > includeMaps true
    8523 
    8524 ——— End of log from Mon Feb 10 17:46:10 2025 ———
    8525 
    8526 opened ChimeraX session 
    8527 
    8528 > hide #!31.3 models
    8529 
    8530 > hide #!31 models
    8531 
    8532 > hide #30 models
    8533 
    8534 > show #!34 models
    8535 
    8536 > show #!35 models
    8537 
    8538 > show #!35.3 models
    8539 
    8540 > volume #35.3 level 0.01175
    8541 
    8542 > select #35.3
    8543 
    8544 2 models selected 
    8545 
    8546 > view sel
    8547 
    8548 > color #34 tan
    8549 
    8550 > ui tool show "Side View"
    8551 
    8552 > select add #34
    8553 
    8554 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected 
    8555 
    8556 > color (#!34 & sel) byhetero
    8557 
    8558 > select clear
    8559 
    8560 > select #34/A:447
    8561 
    8562 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8563 
    8564 > show sel atoms
    8565 
    8566 > select #34/A:507
    8567 
    8568 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8569 
    8570 > show sel atoms
    8571 
    8572 > select clear
    8573 
    8574 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    8575 
    8576 ——— End of log from Tue Mar 11 12:00:09 2025 ———
    8577 
    8578 opened ChimeraX session 
    8579 
    8580 > hide #!35.3 models
    8581 
    8582 > hide #!35 models
    8583 
    8584 > show #!17 models
    8585 
    8586 > color #17 #ffffb2ff models
    8587 
    8588 > color #17 #ffffb280 models
    8589 
    8590 > ui tool show "Side View"
    8591 
    8592 > color #17 #ffffb24d models
    8593 
    8594 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    8595 
    8596 ——— End of log from Thu Apr 10 14:06:06 2025 ———
    8597 
    8598 opened ChimeraX session 
    8599 
    8600 > movie record
    8601 
    8602 > turn y 2 180
    8603 
    8604 > wait 180
    8605 
    8606 > movie encode /Users/dout2/Desktop/movie1.mp4
    8607 
    8608 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    8609  
    8610 
    8611 > select add #34
    8612 
    8613 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    8614 
    8615 > show sel atoms
    8616 
    8617 > select clear
    8618 
    8619 > hide #!34 models
    8620 
    8621 > hide #!17 models
    8622 
    8623 > show #!6 models
    8624 
    8625 > show #1 models
    8626 
    8627 > view
    8628 
    8629 > select #1/A:463
    8630 
    8631 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8632 
    8633 > select #1/A:466
    8634 
    8635 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8636 
    8637 > select #1/A:228
    8638 
    8639 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8640 
    8641 > select #1/A:230
    8642 
    8643 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8644 
    8645 > select #1/A:231
    8646 
    8647 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8648 
    8649 > select #1/A:377
    8650 
    8651 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8652 
    8653 > select #1/A:378
    8654 
    8655 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8656 
    8657 > select #1/A:381
    8658 
    8659 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8660 
    8661 > select #1/A:225
    8662 
    8663 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8664 
    8665 > select #1/A:382
    8666 
    8667 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8668 
    8669 > show sel atoms
    8670 
    8671 > hide #!6 models
    8672 
    8673 > show #!6 models
    8674 
    8675 > hide #1 models
    8676 
    8677 > show #1 models
    8678 
    8679 > select add #1
    8680 
    8681 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    8682 
    8683 > select subtract #1
    8684 
    8685 Nothing selected 
    8686 
    8687 > hide #1 models
    8688 
    8689 > hide #!6 models
    8690 
    8691 > show #!18 models
    8692 
    8693 > hide #!18 models
    8694 
    8695 > show #1 models
    8696 
    8697 > select #1/A:228
    8698 
    8699 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8700 
    8701 > select #1/A:199
    8702 
    8703 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8704 
    8705 > select #1/A:257
    8706 
    8707 7 atoms, 7 bonds, 1 residue, 1 model selected 
    8708 
    8709 > select #1/A:145
    8710 
    8711 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8712 
    8713 > select #1/A:466
    8714 
    8715 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8716 
    8717 > show sel atoms
    8718 
    8719 > select #1/A:149
    8720 
    8721 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8722 
    8723 > select #1/A:146
    8724 
    8725 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8726 
    8727 > select #1/A:204
    8728 
    8729 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8730 
    8731 > select #1/A:150
    8732 
    8733 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8734 
    8735 > select #1/A:149
    8736 
    8737 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8738 
    8739 > select #1/A:203
    8740 
    8741 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8742 
    8743 > select #1/A:146
    8744 
    8745 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8746 
    8747 > select #1/A:149
    8748 
    8749 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8750 Drag select of 13 residues 
    8751 
    8752 > select #1/A:463
    8753 
    8754 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8755 
    8756 > show sel atoms
    8757 
    8758 > select #1/A:466@CZ
    8759 
    8760 1 atom, 1 residue, 1 model selected 
    8761 
    8762 > select up
    8763 
    8764 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8765 
    8766 > ui tool show Contacts
    8767 
    8768 > contacts sel intraRes true ignoreHiddenModels true select true
    8769 > makePseudobonds false reveal true
    8770 
    8771 26 contacts 
    8772 
    8773 > select clear
    8774 
    8775 > select : 382
    8776 
    8777 126 atoms, 112 bonds, 14 residues, 14 models selected 
    8778 
    8779 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    8780 
    8781 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    8782 
    8783 > show sel & #1 atoms
    8784 
    8785 > hide #!6 target m
    8786 
    8787 [Repeated 1 time(s)]
    8788 
    8789 > hide #!4 target m
    8790 
    8791 > select add #1
    8792 
    8793 5716 atoms, 5702 bonds, 714 residues, 14 models selected 
    8794 
    8795 > select subtract #1
    8796 
    8797 1811 atoms, 1716 bonds, 199 residues, 13 models selected 
    8798 
    8799 > select add #5
    8800 
    8801 5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected 
    8802 
    8803 > select subtract #5
    8804 
    8805 1672 atoms, 1584 bonds, 184 residues, 12 models selected 
    8806 
    8807 > select add #8
    8808 
    8809 5445 atoms, 5437 bonds, 691 residues, 12 models selected 
    8810 
    8811 > select subtract #8
    8812 
    8813 1533 atoms, 1452 bonds, 169 residues, 11 models selected 
    8814 
    8815 > select add #12
    8816 
    8817 5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected 
    8818 
    8819 > select subtract #12
    8820 
    8821 1394 atoms, 1320 bonds, 154 residues, 10 models selected 
    8822 
    8823 > hide #1 models
    8824 
    8825 > show #1 models
    8826 
    8827 > select add #15
    8828 
    8829 5172 atoms, 5186 bonds, 654 residues, 10 models selected 
    8830 
    8831 > select subtract #15
    8832 
    8833 1255 atoms, 1188 bonds, 139 residues, 9 models selected 
    8834 
    8835 > select add #18
    8836 
    8837 4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected 
    8838 
    8839 > select subtract #18
    8840 
    8841 1116 atoms, 1056 bonds, 124 residues, 8 models selected 
    8842 
    8843 > select add #21
    8844 
    8845 4933 atoms, 4966 bonds, 625 residues, 8 models selected 
    8846 
    8847 > select subtract #21
    8848 
    8849 977 atoms, 924 bonds, 109 residues, 7 models selected 
    8850 
    8851 > select add #24
    8852 
    8853 4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected 
    8854 
    8855 > select subtract #24
    8856 
    8857 838 atoms, 792 bonds, 94 residues, 6 models selected 
    8858 
    8859 > select add #26
    8860 
    8861 4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected 
    8862 
    8863 > select subtract #26
    8864 
    8865 699 atoms, 660 bonds, 79 residues, 5 models selected 
    8866 
    8867 > select add #30
    8868 
    8869 4885 atoms, 4921 bonds, 653 residues, 5 models selected 
    8870 
    8871 > select subtract #30
    8872 
    8873 558 atoms, 528 bonds, 62 residues, 4 models selected 
    8874 
    8875 > select add #33
    8876 
    8877 4744 atoms, 4789 bonds, 636 residues, 4 models selected 
    8878 
    8879 > select subtract #33
    8880 
    8881 417 atoms, 396 bonds, 45 residues, 3 models selected 
    8882 
    8883 > select add #34
    8884 
    8885 4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected 
    8886 
    8887 > select subtract #34
    8888 
    8889 278 atoms, 264 bonds, 30 residues, 2 models selected 
    8890 
    8891 > select add #37
    8892 
    8893 4514 atoms, 4613 bonds, 579 residues, 2 models selected 
    8894 
    8895 > select subtract #37
    8896 
    8897 139 atoms, 132 bonds, 15 residues, 1 model selected 
    8898 
    8899 > select add #41
    8900 
    8901 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    8902 
    8903 > select subtract #41
    8904 
    8905 Nothing selected 
    8906 
    8907 > show #!2 models
    8908 
    8909 > hide #!2 models
    8910 
    8911 > show #!3 models
    8912 
    8913 > show #!3.3 models
    8914 
    8915 > ui tool show "Side View"
    8916 
    8917 > select #1/A:35@CG
    8918 
    8919 1 atom, 1 residue, 1 model selected 
    8920 
    8921 > select : 35
    8922 
    8923 112 atoms, 98 bonds, 14 residues, 14 models selected 
    8924 
    8925 > hide sel & #1 atoms
    8926 
    8927 > select up
    8928 
    8929 2 atoms, 1 bond, 1 residue, 1 model selected 
    8930 
    8931 > select up
    8932 
    8933 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8934 
    8935 > hide sel atoms
    8936 
    8937 > select clear
    8938 
    8939 > select : 35
    8940 
    8941 112 atoms, 98 bonds, 14 residues, 14 models selected 
    8942 
    8943 > show sel & #1 atoms
    8944 
    8945 > select clear
    8946 
    8947 > select : 35
    8948 
    8949 112 atoms, 98 bonds, 14 residues, 14 models selected 
    8950 
    8951 > hide sel & #1 atoms
    8952 
    8953 > save /Users/dout2/Desktop/image1.png supersample 3
    8954 
    8955 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    8956 
    8957 > select add #1
    8958 
    8959 4009 atoms, 4077 bonds, 528 residues, 14 models selected 
    8960 
    8961 > select subtract #1
    8962 
    8963 104 atoms, 91 bonds, 13 residues, 13 models selected 
    8964 
    8965 > select add #5
    8966 
    8967 3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected 
    8968 
    8969 > select subtract #5
    8970 
    8971 96 atoms, 84 bonds, 12 residues, 12 models selected 
    8972 
    8973 > select add #8
    8974 
    8975 4000 atoms, 4062 bonds, 533 residues, 12 models selected 
    8976 
    8977 > select subtract #8
    8978 
    8979 88 atoms, 77 bonds, 11 residues, 11 models selected 
    8980 
    8981 > select add #12
    8982 
    8983 3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected 
    8984 
    8985 > select subtract #12
    8986 
    8987 80 atoms, 70 bonds, 10 residues, 10 models selected 
    8988 
    8989 > select add #21
    8990 
    8991 4028 atoms, 4105 bonds, 525 residues, 10 models selected 
    8992 
    8993 > select subtract #21
    8994 
    8995 72 atoms, 63 bonds, 9 residues, 9 models selected 
    8996 
    8997 > select add #18
    8998 
    8999 3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected 
    9000 
    9001 > select subtract #18
    9002 
    9003 64 atoms, 56 bonds, 8 residues, 8 models selected 
    9004 
    9005 > select add #24
    9006 
    9007 3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected 
    9008 
    9009 > select subtract #24
    9010 
    9011 56 atoms, 49 bonds, 7 residues, 7 models selected 
    9012 
    9013 > select add #26
    9014 
    9015 3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected 
    9016 
    9017 > select subtract #26
    9018 
    9019 48 atoms, 42 bonds, 6 residues, 6 models selected 
    9020 
    9021 > select add #30
    9022 
    9023 4367 atoms, 4428 bonds, 596 residues, 6 models selected 
    9024 
    9025 > select subtract #30
    9026 
    9027 40 atoms, 35 bonds, 5 residues, 5 models selected 
    9028 
    9029 > select add #33
    9030 
    9031 4359 atoms, 4421 bonds, 595 residues, 5 models selected 
    9032 
    9033 > select subtract #33
    9034 
    9035 32 atoms, 28 bonds, 4 residues, 4 models selected 
    9036 
    9037 > select add #34
    9038 
    9039 3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected 
    9040 
    9041 > select subtract #34
    9042 
    9043 24 atoms, 21 bonds, 3 residues, 3 models selected 
    9044 
    9045 > select add #37
    9046 
    9047 4391 atoms, 4495 bonds, 566 residues, 3 models selected 
    9048 
    9049 > select subtract #37
    9050 
    9051 16 atoms, 14 bonds, 2 residues, 2 models selected 
    9052 
    9053 > select add #41
    9054 
    9055 4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected 
    9056 
    9057 > select subtract #41
    9058 
    9059 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9060 
    9061 > hide #!3.3 models
    9062 
    9063 > hide #!3 models
    9064 
    9065 > hide #1 models
    9066 
    9067 > show #!5 models
    9068 
    9069 > show #!6.3 models
    9070 
    9071 > hide #!6.3 models
    9072 
    9073 > hide #!6 models
    9074 
    9075 > hide #!5 models
    9076 
    9077 > show #8 models
    9078 
    9079 > show #!9 models
    9080 
    9081 > show #!9.3 models
    9082 
    9083 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9084 
    9085 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9086 
    9087 > show sel & #8 atoms
    9088 
    9089 > select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9090 
    9091 Unknown command: select:
    9092 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 
    9093 
    9094 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9095 
    9096 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9097 
    9098 > show sel & #8 atoms
    9099 
    9100 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9101 
    9102 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9103 
    9104 > show sel & #8 atoms
    9105 
    9106 > select clear
    9107 
    9108 > volume #9.3 level 0.00516
    9109 
    9110 > save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3
    9111 
    9112 > hide #!9.3 models
    9113 
    9114 > hide #!9 models
    9115 
    9116 > hide #8 models
    9117 
    9118 > show #15 models
    9119 
    9120 > show #!16 models
    9121 
    9122 > show #!16.3 models
    9123 
    9124 > select #15/A:442
    9125 
    9126 11 atoms, 11 bonds, 1 residue, 1 model selected 
    9127 
    9128 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9129 
    9130 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9131 
    9132 > show sel & #15 atoms
    9133 
    9134 > select #1-50: 438
    9135 
    9136 154 atoms, 154 bonds, 14 residues, 14 models selected 
    9137 
    9138 > select clear
    9139 
    9140 > save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3
    9141 
    9142 > hide #!16.3 models
    9143 
    9144 > hide #!16 models
    9145 
    9146 > hide #15 models
    9147 
    9148 > show #21 models
    9149 
    9150 > show #!22 models
    9151 
    9152 > show #!22.3 models
    9153 
    9154 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9155 
    9156 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9157 
    9158 > show sel & #21 atoms
    9159 
    9160 > select clear
    9161 
    9162 > save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3
    9163 
    9164 > volume #22.3 level 0.0128
    9165 
    9166 > hide #!22.3 models
    9167 
    9168 > hide #!22 models
    9169 
    9170 > hide #21 models
    9171 
    9172 > show #!27 models
    9173 
    9174 > show #!28 models
    9175 
    9176 > hide #!27 models
    9177 
    9178 > show #!26 models
    9179 
    9180 > show #!28.3 models
    9181 
    9182 > volume #28.3 level 0.06828
    9183 
    9184 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9185 
    9186 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9187 
    9188 > show sel & #!26 atoms
    9189 
    9190 > select clear
    9191 
    9192 > save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3
    9193 
    9194 > hide #!28.3 models
    9195 
    9196 > hide #!28 models
    9197 
    9198 > hide #!26 models
    9199 
    9200 > show #30 models
    9201 
    9202 > show #!31 models
    9203 
    9204 > show #!31.3 models
    9205 
    9206 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9207 
    9208 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9209 
    9210 > show sel & #30 atoms
    9211 
    9212 > select clear
    9213 
    9214 > save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3
    9215 
    9216 > hide #!31.3 models
    9217 
    9218 > hide #!31 models
    9219 
    9220 > hide #30 models
    9221 
    9222 > show #37 models
    9223 
    9224 > show #!38 models
    9225 
    9226 > show #!38.3 models
    9227 
    9228 > select clear
    9229 
    9230 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9231 
    9232 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9233 
    9234 > show sel & #37 atoms
    9235 
    9236 > select clear
    9237 
    9238 > show #!36 models
    9239 
    9240 > hide #!36 models
    9241 
    9242 > show #!36 models
    9243 
    9244 > hide #!36 models
    9245 
    9246 > volume #38.3 level 0.006101
    9247 
    9248 > volume #38.3 level 0.006864
    9249 
    9250 > save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3
    9251 
    9252 > hide #!38.3 models
    9253 
    9254 > hide #!38 models
    9255 
    9256 > hide #37 models
    9257 
    9258 > show #!2 models
    9259 
    9260 > hide #!2 models
    9261 
    9262 > show #1 models
    9263 
    9264 > show #!3 models
    9265 
    9266 > show #!3.3 models
    9267 
    9268 > hide #!3.3 models
    9269 
    9270 > hide #!3 models
    9271 
    9272 > hide #1 models
    9273 
    9274 > show #!5 models
    9275 
    9276 > show #!6.3 models
    9277 
    9278 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9279 
    9280 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9281 
    9282 > show sel & #!5 atoms
    9283 
    9284 > select clear
    9285 
    9286 > select up
    9287 
    9288 2 atoms, 1 bond, 1 residue, 1 model selected 
    9289 
    9290 > select up
    9291 
    9292 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9293 
    9294 > hide sel atoms
    9295 
    9296 > select clear
    9297 
    9298 [Repeated 1 time(s)]
    9299 
    9300 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9301 
    9302 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9303 
    9304 > show sel & #!5 atoms
    9305 
    9306 > select clear
    9307 
    9308 > select up
    9309 
    9310 2 atoms, 1 bond, 1 residue, 1 model selected 
    9311 
    9312 > hide sel atoms
    9313 
    9314 > select up
    9315 
    9316 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9317 
    9318 > hide sel atoms
    9319 
    9320 > select clear
    9321 
    9322 > volume #6.3 level 0.0106
    9323 
    9324 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    9325 
    9326 > hide #!5 models
    9327 
    9328 > hide #!6 models
    9329 
    9330 > hide #!6.3 models
    9331 
    9332 > show #!11 models
    9333 
    9334 > show #!12 models
    9335 
    9336 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9337 
    9338 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9339 
    9340 > show sel & #!12 atoms
    9341 
    9342 > select clear
    9343 
    9344 > show #!11.3 models
    9345 
    9346 > select clear
    9347 
    9348 > volume #11.3 level 0.009777
    9349 
    9350 > select clear
    9351 
    9352 > show #!10 models
    9353 
    9354 > hide #!10 models
    9355 
    9356 > select clear
    9357 
    9358 > volume #11.3 level 0.01081
    9359 
    9360 > select clear
    9361 
    9362 > show #!10 models
    9363 
    9364 > hide #!10 models
    9365 
    9366 > save /Users/dout2/Desktop/rOAT1-PBD_OF_LigandDensity.png supersample 3
    9367 
    9368 > hide #!12 models
    9369 
    9370 > hide #!11 models
    9371 
    9372 > show #!18 models
    9373 
    9374 > show #!19 models
    9375 
    9376 > show #!19.3 models
    9377 
    9378 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9379 
    9380 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9381 
    9382 > show sel & #!18 atoms
    9383 
    9384 > select clear
    9385 
    9386 > save /Users/dout2/Desktop/rOAT1-TFV_OF_LigandDensity.png supersample 3
    9387 
    9388 > hide #!19 models
    9389 
    9390 > hide #!18 models
    9391 
    9392 > show #!24 models
    9393 
    9394 > show #!25 models
    9395 
    9396 > show #!25.3 models
    9397 
    9398 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9399 
    9400 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9401 
    9402 > show sel & #!24 atoms
    9403 
    9404 > select clear
    9405 
    9406 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    9407 
    9408 > hide #!25 models
    9409 
    9410 > hide #!24 models
    9411 
    9412 > show #!35 models
    9413 
    9414 > show #!34 models
    9415 
    9416 > show #!35.3 models
    9417 
    9418 > hide #!35.3 models
    9419 
    9420 > hide #!35 models
    9421 
    9422 > hide #!34 models
    9423 
    9424 > show #!41 models
    9425 
    9426 > show #!42 models
    9427 
    9428 > show #!42.3 models
    9429 
    9430 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    9431 
    9432 > hide #!41 models
    9433 
    9434 > hide #!42 models
    9435 
    9436 > hide #!42.3 models
    9437 
    9438 > show #!25 models
    9439 
    9440 > show #!24 models
    9441 
    9442 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    9443 
    9444 > hide #!24 models
    9445 
    9446 > hide #!25 models
    9447 
    9448 > show #!42.3 models
    9449 
    9450 > show #!41 models
    9451 
    9452 > select clear
    9453 
    9454 [Repeated 1 time(s)]
    9455 
    9456 > ui tool show Distances
    9457 
    9458 > select clear
    9459 
    9460 No distances to delete! 
    9461 
    9462 > save /Users/dout2/Desktop/hOAT1-TFV_OF_LigandDensity.png supersample 3
    9463 
    9464 > view
    9465 
    9466 > view orient
    9467 
    9468 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
    9469 > facing/postprocess.mrc
    9470 
    9471 Opened postprocess.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    9472 level 0.00432, step 2, values float32 
    9473 
    9474 > volume #40 step 1
    9475 
    9476 > volume #40 level 0.008916
    9477 
    9478 > hide #!41 models
    9479 
    9480 > hide #!40 models
    9481 
    9482 > select add #41
    9483 
    9484 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    9485 
    9486 > select subtract #41
    9487 
    9488 Nothing selected 
    9489 
    9490 > hide #!42 models
    9491 
    9492 > show #!40 models
    9493 
    9494 > rename #40 rOAT1-AKG_OF.mrc
    9495 
    9496 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
    9497 > facing/RealSpaceRefine_1/rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb
    9498 
    9499 Chain information for rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb #43 
    9500 --- 
    9501 Chain | Description 
    9502 A | No description available 
    9503  
    9504 
    9505 > select clear
    9506 
    9507 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
    9508 > occluded/postprocess.mrc
    9509 
    9510 Opened postprocess.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    9511 level 0.00378, step 2, values float32 
    9512 
    9513 > rename #44 rOAT1-AKG_OOC.mrc
    9514 
    9515 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
    9516 > occluded/RealSpaceRefine_3/rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb
    9517 
    9518 Chain information for rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb #45 
    9519 --- 
    9520 Chain | Description 
    9521 A | No description available 
    9522  
    9523 
    9524 > rename #45 rOAT1-AKG_OOC-coot-4_real_space_refined_003.pdb
    9525 
    9526 > hide #!43 models
    9527 
    9528 > hide #!40 models
    9529 
    9530 > volume #44 step 1
    9531 
    9532 > volume #44 level 0.01023
    9533 
    9534 > select ::name="AKG"
    9535 
    9536 20 atoms, 18 bonds, 2 residues, 2 models selected 
    9537 
    9538 > view sel
    9539 
    9540 > color #44 #ffffb24d models
    9541 
    9542 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9543 
    9544 2228 atoms, 2112 bonds, 244 residues, 16 models selected 
    9545 
    9546 > show sel & #!45 atoms
    9547 
    9548 > select clear
    9549 
    9550 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9551 
    9552 > color #44 #ffffb280 models
    9553 
    9554 > color #44 #ffffb266 models
    9555 
    9556 > color #44 #ffffb24d models
    9557 
    9558 > select clear
    9559 
    9560 > save /Users/dout2/Desktop/hOAT1-AKG_OOC_LigandDensity.png supersample 3
    9561 
    9562 > movie record
    9563 
    9564 > turn y 2 180
    9565 
    9566 > wait 180
    9567 
    9568 > movie encode /Users/dout2/Desktop/movie2.mp4
    9569 
    9570 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    9571  
    9572 
    9573 > movie record
    9574 
    9575 > turn y 2 180
    9576 
    9577 > wait 180
    9578 
    9579 > movie encode /Users/dout2/Desktop/movie3.mp4
    9580 
    9581 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    9582  
    9583 
    9584 > hide #!45 models
    9585 
    9586 > hide #!44 models
    9587 
    9588 > show #!43 models
    9589 
    9590 > show #!40 models
    9591 
    9592 > color #40 #b2b2b24d models
    9593 
    9594 > select clear
    9595 
    9596 > color #40 #ffffb24d models
    9597 
    9598 > select clear
    9599 
    9600 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9601 
    9602 2228 atoms, 2112 bonds, 244 residues, 16 models selected 
    9603 
    9604 > show sel & #!43 atoms
    9605 
    9606 > select clear
    9607 
    9608 [Repeated 1 time(s)]
    9609 
    9610 > volume #40 level 0.009283
    9611 
    9612 > save /Users/dout2/Desktop/rOAT1-AKG_OF_LigandDensity.png supersample 3
    9613 
    9614 > movie record
    9615 
    9616 > turn y 2 180
    9617 
    9618 > wait 180
    9619 
    9620 > movie encode /Users/dout2/Desktop/movie3.mp4
    9621 
    9622 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    9623  
    9624 
    9625 > volume #40 level 0.01222
    9626 
    9627 > movie record
    9628 
    9629 > turn y 2 180
    9630 
    9631 > wait 180
    9632 
    9633 > movie encode /Users/dout2/Desktop/movie4.mp4
    9634 
    9635 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    9636  
    9637 
    9638 > hide #!43 models
    9639 
    9640 > hide #!40 models
    9641 
    9642 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    9643 > occluded/postprocess_rescaled.mrc
    9644 
    9645 Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
    9646 shown at level 0.0038, step 2, values float32 
    9647 
    9648 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    9649 > occluded/RealSpaceRefine_1/rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb
    9650 
    9651 Chain information for rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb #47 
    9652 --- 
    9653 Chain | Description 
    9654 A | No description available 
    9655  
    9656 
    9657 > select #46
    9658 
    9659 4 models selected 
    9660 
    9661 > select clear
    9662 
    9663 > view
    9664 
    9665 > volume #46 step 1
    9666 
    9667 > volume #46 level 0.01147
    9668 
    9669 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9670 
    9671 2367 atoms, 2244 bonds, 259 residues, 17 models selected 
    9672 
    9673 > view sel
    9674 
    9675 > color #46 #b2ffff4d models
    9676 
    9677 > select #46
    9678 
    9679 4 models selected 
    9680 
    9681 > show #!47 atoms
    9682 
    9683 > select clear
    9684 
    9685 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9686 
    9687 > close #47
    9688 
    9689 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    9690 > occluded/RealSpaceRefine_2/rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb
    9691 
    9692 Chain information for rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb #47 
    9693 --- 
    9694 Chain | Description 
    9695 A | No description available 
    9696  
    9697 
    9698 > select add #46
    9699 
    9700 4 models selected 
    9701 
    9702 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9703 
    9704 2361 atoms, 2238 bonds, 259 residues, 17 models selected 
    9705 
    9706 > show sel & #!47 atoms
    9707 
    9708 > select clear
    9709 
    9710 > select #46
    9711 
    9712 4 models selected 
    9713 
    9714 > select clear
    9715 
    9716 > save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity.png supersample 3
    9717 
    9718 > movie record
    9719 
    9720 > turn y 2 180
    9721 
    9722 > wait 180
    9723 
    9724 > movie encode /Users/dout2/Desktop/movie4.mp4
    9725 
    9726 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    9727  
    9728 
    9729 > hide #!46 models
    9730 
    9731 > show #!46 models
    9732 
    9733 > save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity2.png supersample 3
    9734 
    9735 > movie record
    9736 
    9737 > turn y 2 180
    9738 
    9739 > wait 180
    9740 
    9741 > movie encode /Users/dout2/Desktop/movie4.mp4
    9742 
    9743 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    9744  
    9745 
    9746 > view
    9747 
    9748 > color #46 #b2ffffff models
    9749 
    9750 > color #46 #b2ffffab models
    9751 
    9752 > color #46 #b2ffffff models
    9753 
    9754 > select clear
    9755 
    9756 [Repeated 1 time(s)]
    9757 
    9758 > save /Users/dout2/Desktop/rOAT1-R466A_OF.png supersample 3
    9759 
    9760 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9761 
    9762 ——— End of log from Thu Apr 10 15:43:35 2025 ———
    9763 
    9764 opened ChimeraX session 
    9765 
    9766 > hide #!47 models
    9767 
    9768 > hide #!46 models
    9769 
    9770 > rename #46 rOAT1-R466A.mrc
    9771 
    9772 > open
    9773 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/J12_2.05A_clip-240/cryosparc_P4_J16__localfilter_240.mrc
    9774 
    9775 Opened cryosparc_P4_J16__localfilter_240.mrc as #48, grid size 240,240,240,
    9776 pixel 0.553, shown at level 0.238, step 1, values float32 
    9777 
    9778 > open
    9779 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/model/rOAT1-apo-
    9780 > coot-4_real_space_refined_004.pdb
    9781 
    9782 Chain information for rOAT1-apo-coot-4_real_space_refined_004.pdb #49 
    9783 --- 
    9784 Chain | Description 
    9785 A | No description available 
    9786  
    9787 
    9788 The cached device pixel ratio value was stale on window expose. Please file a
    9789 QTBUG which explains how to reproduce. 
    9790 
    9791 > rename #48 rOAT1-Apo.mrc
    9792 
    9793 > hide #49 models
    9794 
    9795 > hide #!48 models
    9796 
    9797 > hide #48.1 models
    9798 
    9799 > show #49 models
    9800 
    9801 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9802 
    9803 > select #49: 382, 353,438,230,442,466
    9804 
    9805 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9806 
    9807 > show sel atoms
    9808 
    9809 > size stickRadius 0.3
    9810 
    9811 Changed 72733 bond radii 
    9812 
    9813 > select add #49
    9814 
    9815 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    9816 
    9817 > hide sel cartoons
    9818 
    9819 > select clear
    9820 
    9821 Drag select of 10 atoms, 11 bonds 
    9822 Drag select of 6 atoms, 9 bonds 
    9823 Drag select of 8 atoms, 10 bonds 
    9824 Drag select of 4 atoms, 4 bonds 
    9825 
    9826 > select up
    9827 
    9828 36 atoms, 34 bonds, 4 residues, 1 model selected 
    9829 
    9830 > lighting flat
    9831 
    9832 > graphics silhouettes false
    9833 
    9834 > select clear
    9835 
    9836 > select #49: 382, 353,438,230,442,466
    9837 
    9838 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9839 
    9840 > select clear
    9841 
    9842 > select #49: 382, 353,438,230,442,466
    9843 
    9844 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9845 
    9846 > color sel orange
    9847 
    9848 > color sel purple
    9849 
    9850 > color sel hot pink
    9851 
    9852 > size stickRadius 0.5
    9853 
    9854 Changed 72733 bond radii 
    9855 
    9856 > size stickRadius 0.4
    9857 
    9858 Changed 72733 bond radii 
    9859 
    9860 > select clear
    9861 
    9862 > select add #49/A:466@CB
    9863 
    9864 1 atom, 1 residue, 1 model selected 
    9865 
    9866 > select add #49/A:382@NZ
    9867 
    9868 2 atoms, 2 residues, 1 model selected 
    9869 
    9870 > select up
    9871 
    9872 20 atoms, 18 bonds, 2 residues, 1 model selected 
    9873 
    9874 > select #49: 382, 353,438,230,442,466
    9875 
    9876 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9877 
    9878 > color sel lime
    9879 
    9880 > color sel purple
    9881 
    9882 > select clear
    9883 
    9884 > select add #49/A:382@NZ
    9885 
    9886 1 atom, 1 residue, 1 model selected 
    9887 
    9888 > select up
    9889 
    9890 3 atoms, 1 bond, 2 residues, 1 model selected 
    9891 
    9892 > select up
    9893 
    9894 20 atoms, 18 bonds, 2 residues, 1 model selected 
    9895 
    9896 > color sel byhetero
    9897 
    9898 > select #49: 382, 353,438,230,442,466
    9899 
    9900 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9901 
    9902 > color sel purple
    9903 
    9904 > select clear
    9905 
    9906 > select #49/A:382@NZ
    9907 
    9908 1 atom, 1 residue, 1 model selected 
    9909 
    9910 > select add #49/A:466@NH2
    9911 
    9912 2 atoms, 2 residues, 1 model selected 
    9913 
    9914 > select add #49/A:466@NH1
    9915 
    9916 3 atoms, 2 residues, 1 model selected 
    9917 
    9918 > select add #49/A:466@CZ
    9919 
    9920 4 atoms, 2 residues, 1 model selected 
    9921 
    9922 > select add #49/A:466@NE
    9923 
    9924 5 atoms, 2 residues, 1 model selected 
    9925 
    9926 > color sel byhetero
    9927 
    9928 > select clear
    9929 
    9930 > save /Users/dout2/Desktop/rOAT1-Apo_keyresidue.png supersample 3
    9931 > transparentBackground true
    9932 
    9933 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9934 
    9935 > select #49: 382, 353,438,230,442,466
    9936 
    9937 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9938 
    9939 > ui tool show "Color Actions"
    9940 
    9941 The cached device pixel ratio value was stale on window expose. Please file a
    9942 QTBUG which explains how to reproduce. 
    9943 
    9944 > select #49: 382, 353,438,230,442,466
    9945 
    9946 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9947 
    9948 > hide sel atoms
    9949 
    9950 > select add #49
    9951 
    9952 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    9953 
    9954 > show sel cartoons
    9955 
    9956 > select clear
    9957 
    9958 > view
    9959 
    9960 > select add #49
    9961 
    9962 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    9963 
    9964 > color sel gray
    9965 
    9966 > color sel light gray
    9967 
    9968 > color sel dark gray
    9969 
    9970 > surface sel
    9971 
    9972 > select clear
    9973 
    9974 > save /Users/dout2/Desktop/rOAT1-Apo_bg.png supersample 3
    9975 > transparentBackground true
    9976 
    9977 > open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
    9978 
    9979 Summary of feedback from opening
    9980 /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif 
    9981 --- 
    9982 warning | Unable to fetch template for 'LIG_B': will connect using distance criteria 
    9983  
    9984 Chain information for model.cif #50 
    9985 --- 
    9986 Chain | Description 
    9987 A | . 
    9988  
    9989 
    9990 No chain in structure corresponds to chain ID given in local score info (chain
    9991 'B') 
    9992 
    9993 > hide #!49 models
    9994 
    9995 > rename #50 rOAT1-AKG_IF_af3.cif
    9996 
    9997 > select add #50
    9998 
    9999 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10000 
    10001 > select clear
    10002 
    10003 > select #50: 382, 353,438,230,442,466
    10004 
    10005 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10006 
    10007 > show sel atoms
    10008 
    10009 > color sel purple
    10010 
    10011 > size stickRadius 0.4
    10012 
    10013 Changed 77114 bond radii 
    10014 
    10015 > select clear
    10016 
    10017 > select add #50
    10018 
    10019 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10020 
    10021 > hide sel cartoons
    10022 
    10023 > select clear
    10024 
    10025 [Repeated 1 time(s)]
    10026 
    10027 > select #50/A:354@CG
    10028 
    10029 1 atom, 1 residue, 1 model selected 
    10030 
    10031 > select up
    10032 
    10033 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10034 
    10035 > hide sel atoms
    10036 
    10037 > select #50/B:1@C4
    10038 
    10039 1 atom, 1 residue, 1 model selected 
    10040 
    10041 > select up
    10042 
    10043 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10044 
    10045 > color sel yellow
    10046 
    10047 > color sel byhetero
    10048 
    10049 > select #50/A:382@NZ
    10050 
    10051 1 atom, 1 residue, 1 model selected 
    10052 
    10053 > select add #50/A:466@NH1
    10054 
    10055 2 atoms, 2 residues, 1 model selected 
    10056 
    10057 > select add #50/A:466@NH2
    10058 
    10059 3 atoms, 2 residues, 1 model selected 
    10060 
    10061 > select add #50/A:466@NE
    10062 
    10063 4 atoms, 2 residues, 1 model selected 
    10064 
    10065 > color sel byhetero
    10066 
    10067 > select clear
    10068 
    10069 > save /Users/dout2/Desktop/rOAT1-AKG_keyresidue.png supersample 3
    10070 > transparentBackground true
    10071 
    10072 > select add #50
    10073 
    10074 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10075 
    10076 > hide sel atoms
    10077 
    10078 > show sel cartoons
    10079 
    10080 > surface sel
    10081 
    10082 > color (#!50 & sel) dark gray
    10083 
    10084 > select clear
    10085 
    10086 > save /Users/dout2/Desktop/rOAT1-AKG_bg.png supersample 3
    10087 > transparentBackground true
    10088 
    10089 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10090 
    10091 > hide #!50 models
    10092 
    10093 > show #!45 models
    10094 
    10095 > show #!44 models
    10096 
    10097 > hide #!44 models
    10098 
    10099 > view
    10100 
    10101 > view orient
    10102 
    10103 > hide #!45 models
    10104 
    10105 > show #!43 models
    10106 
    10107 > show #!45 models
    10108 
    10109 > hide #!45 models
    10110 
    10111 > select add #43
    10112 
    10113 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected 
    10114 
    10115 > color (#!43 & sel) dark gray
    10116 
    10117 > surface (#!43 & sel)
    10118 
    10119 > select clear
    10120 
    10121 > save /Users/dout2/Desktop/rOAT1-AKG_OF_bg.png supersample 3
    10122 > transparentBackground true
    10123 
    10124 > hide #43.2 models
    10125 
    10126 > hide #43.1 models
    10127 
    10128 > show #43.1 models
    10129 
    10130 > select #43: 382, 353,438,230,442,466
    10131 
    10132 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10133 
    10134 > select subtract #43.2
    10135 
    10136 1 model selected 
    10137 
    10138 > select add #43
    10139 
    10140 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected 
    10141 
    10142 > hide sel cartoons
    10143 
    10144 > select clear
    10145 
    10146 > select #43: 382, 353,438,230,442,466
    10147 
    10148 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10149 
    10150 > select add #43
    10151 
    10152 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 3 models selected 
    10153 
    10154 > hide sel atoms
    10155 
    10156 > select #43: 382, 353,438,230,442,466
    10157 
    10158 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10159 
    10160 > show sel atoms
    10161 
    10162 > select #43: akg
    10163 
    10164 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10165 
    10166 > show sel atoms
    10167 
    10168 > select clear
    10169 
    10170 > select #43/A:601@C2
    10171 
    10172 1 atom, 1 residue, 1 model selected 
    10173 
    10174 > select up
    10175 
    10176 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10177 
    10178 > color sel yellow
    10179 
    10180 > color sel byhetero
    10181 
    10182 > select clear
    10183 
    10184 > select #43/A:466@NH2
    10185 
    10186 1 atom, 1 residue, 1 model selected 
    10187 
    10188 > select add #43/A:466@NH1
    10189 
    10190 2 atoms, 1 residue, 2 models selected 
    10191 
    10192 > select add #43/A:466@NE
    10193 
    10194 3 atoms, 1 residue, 2 models selected 
    10195 
    10196 > select add #43/A:382@NZ
    10197 
    10198 4 atoms, 2 residues, 2 models selected 
    10199 
    10200 > color (#!43 & sel) byhetero
    10201 
    10202 > select clear
    10203 
    10204 > select #43: 382, 353,438,230,442,466
    10205 
    10206 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10207 
    10208 > color (#!43 & sel) purple
    10209 
    10210 > select subtract #43/A:382@NZ
    10211 
    10212 65 atoms, 63 bonds, 6 residues, 2 models selected 
    10213 
    10214 > select subtract #43/A:466@NH2
    10215 
    10216 64 atoms, 62 bonds, 6 residues, 2 models selected 
    10217 
    10218 > select subtract #43/A:466@NH1
    10219 
    10220 63 atoms, 61 bonds, 6 residues, 2 models selected 
    10221 
    10222 > select subtract #43/A:466@CD
    10223 
    10224 62 atoms, 59 bonds, 6 residues, 2 models selected 
    10225 
    10226 > color (#!43 & sel) byhetero
    10227 
    10228 > select #43: 382, 353,438,230,442,466
    10229 
    10230 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10231 
    10232 > color (#!43 & sel) purple
    10233 
    10234 > select subtract #43/A:382@NZ
    10235 
    10236 65 atoms, 63 bonds, 6 residues, 2 models selected 
    10237 
    10238 > select subtract #43/A:466@NH1
    10239 
    10240 64 atoms, 62 bonds, 6 residues, 2 models selected 
    10241 
    10242 > select subtract #43/A:466@NH2
    10243 
    10244 63 atoms, 61 bonds, 6 residues, 2 models selected 
    10245 
    10246 > select clear
    10247 
    10248 > select add #43/A:466@NH2
    10249 
    10250 1 atom, 1 residue, 1 model selected 
    10251 
    10252 > select add #43/A:466@NH1
    10253 
    10254 2 atoms, 1 residue, 2 models selected 
    10255 
    10256 > select add #43/A:382@NZ
    10257 
    10258 3 atoms, 2 residues, 2 models selected 
    10259 
    10260 > color (#!43 & sel) byhetero
    10261 
    10262 > select clear
    10263 
    10264 > save /Users/dout2/Desktop/rOAT1-AKG_OF_residue.png supersample 3
    10265 > transparentBackground true
    10266 
    10267 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10268 
    10269 > open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
    10270 
    10271 Summary of feedback from opening
    10272 /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif 
    10273 --- 
    10274 warning | Unable to fetch template for 'LIG_B': will connect using distance criteria 
    10275  
    10276 Chain information for model.cif #51 
    10277 --- 
    10278 Chain | Description 
    10279 A | . 
    10280  
    10281 
    10282 No chain in structure corresponds to chain ID given in local score info (chain
    10283 'B') 
    10284 
    10285 > hide #!43 models
    10286 
    10287 > hide #43.1 models
    10288 
    10289 > view
    10290 
    10291 > rename #51 rOAT1-AKG_IF_af3_model1.cif
    10292 
    10293 > rename #51 rOAT1-AKG_IF_af3_model1-1.cif
    10294 
    10295 > select add #51
    10296 
    10297 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10298 
    10299 > color sel dark gray
    10300 
    10301 > surface sel
    10302 
    10303 > select clear
    10304 
    10305 > save /Users/dout2/Desktop/rOAT1-AKG_IF_bg.png supersample 3
    10306 > transparentBackground true
    10307 
    10308 > hide #51.1 models
    10309 
    10310 > select add #51
    10311 
    10312 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10313 
    10314 > hide sel atoms
    10315 
    10316 > hide sel cartoons
    10317 
    10318 > select #51: 382, 353,438,230,442,466
    10319 
    10320 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10321 
    10322 > show sel atoms
    10323 
    10324 > color (#!51 & sel) purple
    10325 
    10326 > size stickRadius 0.4
    10327 
    10328 Changed 81495 bond radii 
    10329 
    10330 > select clear
    10331 
    10332 > select #51: AKG
    10333 
    10334 Nothing selected 
    10335 
    10336 > show #!51 atoms
    10337 
    10338 > undo
    10339 
    10340 > select add #51
    10341 
    10342 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10343 
    10344 > show sel atoms
    10345 
    10346 > select #51/B:1@C3
    10347 
    10348 1 atom, 1 residue, 1 model selected 
    10349 
    10350 > select up
    10351 
    10352 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10353 
    10354 > select add #51
    10355 
    10356 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10357 
    10358 > hide sel atoms
    10359 
    10360 > select #51/B
    10361 
    10362 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10363 
    10364 > show sel atoms
    10365 
    10366 > color sel yellow
    10367 
    10368 > color sel byhetero
    10369 
    10370 > select clear
    10371 
    10372 > select #51: 382, 353,438,230,442,466
    10373 
    10374 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10375 
    10376 > show sel atoms
    10377 
    10378 > select #51/A:382@NZ
    10379 
    10380 1 atom, 1 residue, 1 model selected 
    10381 
    10382 > select add #51/A:466@NH1
    10383 
    10384 2 atoms, 2 residues, 2 models selected 
    10385 
    10386 > select add #51/A:466@NH2
    10387 
    10388 3 atoms, 2 residues, 2 models selected 
    10389 
    10390 > color (#!51 & sel) byhetero
    10391 
    10392 > select #51/A:466@NE
    10393 
    10394 1 atom, 1 residue, 1 model selected 
    10395 
    10396 > color (#!51 & sel) byhetero
    10397 
    10398 > select clear
    10399 
    10400 > save /Users/dout2/Desktop/rOAT1-AKG_IF_residue.png supersample 3
    10401 > transparentBackground true
    10402 
    10403 > close #50
    10404 
    10405 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10406 
    10407 ——— End of log from Sat Apr 12 21:31:41 2025 ———
    10408 
    10409 opened ChimeraX session 
    10410 
    10411 > hide #!51 models
    10412 
    10413 > show #!2 models
    10414 
    10415 > show #1 models
    10416 
    10417 > view
    10418 
    10419 > lighting simple
    10420 
    10421 > lighting soft
    10422 
    10423 > lighting simple
    10424 
    10425 > hide #!2 models
    10426 
    10427 > select #1: 382, 353,438,230,442,466
    10428 
    10429 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10430 
    10431 > view sel
    10432 
    10433 > cofr sel
    10434 
    10435 > select clear
    10436 
    10437 > show #!2 models
    10438 
    10439 > color #2 #ffffb2ff models
    10440 
    10441 > color #2 #ffffb24f models
    10442 
    10443 > color #2 #ffffb24e models
    10444 
    10445 > color #2 #ffffb24d models
    10446 
    10447 > select clear
    10448 
    10449 > color #2 #a5ffb24d models
    10450 
    10451 > color #2 #9effb24d models
    10452 
    10453 > color #2 #9e43b24d models
    10454 
    10455 > color #2 #9effb24d models
    10456 
    10457 > color #2 #9effff4d models
    10458 
    10459 > select clear
    10460 
    10461 > size stickRadius 0.2
    10462 
    10463 Changed 77114 bond radii 
    10464 
    10465 > select clear
    10466 
    10467 > color #2 #942192ff models
    10468 
    10469 > color #2 #9421924d models
    10470 
    10471 > select clear
    10472 
    10473 > color #2 #aa7942ff models
    10474 
    10475 > color #2 #00fdffff models
    10476 
    10477 > color #2 #00fdff4e models
    10478 
    10479 > select clear
    10480 
    10481 > select up
    10482 
    10483 2 atoms, 1 bond, 1 residue, 1 model selected 
    10484 
    10485 > select up
    10486 
    10487 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10488 
    10489 > view sel
    10490 
    10491 > ui tool show "Side View"
    10492 
    10493 > volume #2 level 0.01002
    10494 
    10495 > select clear
    10496 
    10497 > select #1/A:223
    10498 
    10499 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10500 
    10501 > show sel atoms
    10502 
    10503 > select #1/A:207
    10504 
    10505 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10506 
    10507 > show sel atoms
    10508 
    10509 > hide #!2 models
    10510 
    10511 > select #1/A:36
    10512 
    10513 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10514 
    10515 > show sel atoms
    10516 
    10517 > show #!2 models
    10518 
    10519 > select clear
    10520 
    10521 > select #1/A:601@C4'
    10522 
    10523 1 atom, 1 residue, 1 model selected 
    10524 
    10525 > select up
    10526 
    10527 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10528 
    10529 > select up
    10530 
    10531 3891 atoms, 3986 bonds, 501 residues, 1 model selected 
    10532 
    10533 > select down
    10534 
    10535 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10536 
    10537 > cofr sel
    10538 
    10539 > movie record
    10540 
    10541 > turn y 2 180
    10542 
    10543 > wait 180
    10544 
    10545 > movie encode /Users/dout2/Desktop/movie1.mp4
    10546 
    10547 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    10548  
    10549 
    10550 > hide #!2 models
    10551 
    10552 > hide #1 models
    10553 
    10554 > select add #1
    10555 
    10556 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    10557 
    10558 > select subtract #1
    10559 
    10560 Nothing selected 
    10561 
    10562 > show #1 models
    10563 
    10564 > hide #1 models
    10565 
    10566 > show #!5 models
    10567 
    10568 > show #!4 models
    10569 
    10570 > select clear
    10571 
    10572 > volume #4 level 0.01053
    10573 
    10574 > color #4 #fffb00ff models
    10575 
    10576 > color #4 #ffffb2ff models
    10577 
    10578 > color #4 #ffffb24d models
    10579 
    10580 > select #4
    10581 
    10582 4 models selected 
    10583 
    10584 > select clear
    10585 
    10586 > select #1: 382, 353,438,230,442,466,207
    10587 
    10588 74 atoms, 71 bonds, 7 residues, 1 model selected 
    10589 
    10590 > show #!5 atoms
    10591 
    10592 > select add #5
    10593 
    10594 3848 atoms, 3935 bonds, 5 pseudobonds, 493 residues, 3 models selected 
    10595 
    10596 > hide sel & #!5 atoms
    10597 
    10598 > select #5: 382, 353,438,230,442,466,207,601
    10599 
    10600 93 atoms, 91 bonds, 8 residues, 1 model selected 
    10601 
    10602 > show sel atoms
    10603 
    10604 > select clear
    10605 
    10606 > select add #5
    10607 
    10608 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    10609 
    10610 > show sel atoms
    10611 
    10612 > select clear
    10613 
    10614 > select #5/A:601@O4
    10615 
    10616 1 atom, 1 residue, 1 model selected 
    10617 
    10618 > select up
    10619 
    10620 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10621 
    10622 > cofr sel
    10623 
    10624 > select #4
    10625 
    10626 4 models selected 
    10627 
    10628 > volume #4 level 0.01089
    10629 
    10630 > volume #4 level 0.01182
    10631 
    10632 > volume #4 level 0.01292
    10633 
    10634 > select clear
    10635 
    10636 > volume #4 level 0.01311
    10637 
    10638 > volume #4 level 0.01274
    10639 
    10640 > volume #4 level 0.01126
    10641 
    10642 > volume #4 level 0.01274
    10643 
    10644 > volume #4 level 0.012
    10645 
    10646 > movie record
    10647 
    10648 > turn y 2 180
    10649 
    10650 > wait 180
    10651 
    10652 > movie encode /Users/dout2/Desktop/movie2.mp4
    10653 
    10654 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    10655  
    10656 
    10657 > movie record
    10658 
    10659 > turn y 2 180
    10660 
    10661 > wait 180
    10662 
    10663 > movie encode /Users/dout2/Desktop/movie3.mp4
    10664 
    10665 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    10666  
    10667 
    10668 > view
    10669 
    10670 > hide #!4 models
    10671 
    10672 > select add #5
    10673 
    10674 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    10675 
    10676 > hide sel atoms
    10677 
    10678 > select #5: 382, 353,438,230,442,466,207,601
    10679 
    10680 93 atoms, 91 bonds, 8 residues, 1 model selected 
    10681 
    10682 > show sel atoms
    10683 
    10684 > select clear
    10685 
    10686 > show #!4 models
    10687 
    10688 > hide #!4 models
    10689 
    10690 > hide #!5 models
    10691 
    10692 > show #8 models
    10693 
    10694 > show #!7 models
    10695 
    10696 > hide #8 models
    10697 
    10698 > hide #!7 models
    10699 
    10700 > show #!10 models
    10701 
    10702 > show #!12 models
    10703 
    10704 > color #10 darkgrey models
    10705 
    10706 > color #10 silver models
    10707 
    10708 > color #10 #c0c0c04d models
    10709 
    10710 > select clear
    10711 
    10712 > hide #!12 models
    10713 
    10714 > show #!12 models
    10715 
    10716 > hide #!10 models
    10717 
    10718 > show #!10 models
    10719 
    10720 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10721 
    10722 > volume #10 level 0.0124
    10723 
    10724 > select up
    10725 
    10726 2 atoms, 1 bond, 1 residue, 1 model selected 
    10727 
    10728 > select up
    10729 
    10730 37 atoms, 37 bonds, 1 residue, 1 model selected 
    10731 
    10732 > select #12: 382, 353,438,230,442,466,207,601
    10733 
    10734 111 atoms, 108 bonds, 8 residues, 1 model selected 
    10735 
    10736 > show sel atoms
    10737 
    10738 > select up
    10739 
    10740 2 atoms, 1 bond, 1 residue, 1 model selected 
    10741 
    10742 > select H
    10743 
    10744 117 atoms, 10 residues, 9 models selected 
    10745 
    10746 > hide sel & #!12 atoms
    10747 
    10748 > select clear
    10749 
    10750 > select #12: 382, 353,438,230,442,466,207,601
    10751 
    10752 111 atoms, 108 bonds, 8 residues, 1 model selected 
    10753 
    10754 > view sel
    10755 
    10756 > cofr sel
    10757 
    10758 > volume #10 level 0.009894
    10759 
    10760 > volume #10 level 0.01073
    10761 
    10762 > select clear
    10763 
    10764 > select #12/B:601@C16
    10765 
    10766 1 atom, 1 residue, 1 model selected 
    10767 
    10768 > select up
    10769 
    10770 37 atoms, 37 bonds, 1 residue, 1 model selected 
    10771 
    10772 > view sel
    10773 
    10774 > select clear
    10775 
    10776 > movie record
    10777 
    10778 > turn y 2 180
    10779 
    10780 > wait 180
    10781 
    10782 > movie encode /Users/dout2/Desktop/movie4.mp4
    10783 
    10784 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    10785  
    10786 
    10787 > select #10
    10788 
    10789 4 models selected 
    10790 
    10791 > select clear
    10792 
    10793 > hide #!12 models
    10794 
    10795 > hide #!10 models
    10796 
    10797 > show #8 models
    10798 
    10799 > show #!7 models
    10800 
    10801 > select up
    10802 
    10803 2 atoms, 1 bond, 1 residue, 1 model selected 
    10804 
    10805 > color #7 #ff2f92ff models
    10806 
    10807 > color #7 #ff2f924d models
    10808 
    10809 > select #7
    10810 
    10811 4 models selected 
    10812 
    10813 > select clear
    10814 
    10815 > select #8: 382, 353,438,230,442,466,207,601
    10816 
    10817 93 atoms, 90 bonds, 8 residues, 1 model selected 
    10818 
    10819 > show sel atoms
    10820 
    10821 > select clear
    10822 
    10823 > open
    10824 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-PBD_20230217/cryosparc_P4_J55__localfilter_160.mrc
    10825 
    10826 Opened cryosparc_P4_J55__localfilter_160.mrc as #50, grid size 160,160,160,
    10827 pixel 0.83, shown at level 0.131, step 1, values float32 
    10828 
    10829 > movie record
    10830 
    10831 > turn y 2 180
    10832 
    10833 > wait 180
    10834 
    10835 > movie encode /Users/dout2/Desktop/movie1.mp4
    10836 
    10837 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    10838  
    10839 
    10840 > hide #!7 models
    10841 
    10842 > view
    10843 
    10844 > show #!7 models
    10845 
    10846 > rename #50 rOAT1-PBD_IF.mrc
    10847 
    10848 > select add #50
    10849 
    10850 2 models selected 
    10851 
    10852 > ui mousemode right "translate selected models"
    10853 
    10854 > view matrix models #50,1,0,0,82.163,0,1,0,34.821,0,0,1,72.008
    10855 
    10856 > view matrix models #50,1,0,0,78.322,0,1,0,71.965,0,0,1,68.805
    10857 
    10858 > view matrix models #50,1,0,0,68.336,0,1,0,66.309,0,0,1,66.361
    10859 
    10860 > ui tool show "Fit in Map"
    10861 
    10862 > fitmap #50 inMap #7
    10863 
    10864 Fit map rOAT1-PBD_IF.mrc in map rOAT1-PBD_IF.mrc using 40907 points 
    10865 correlation = 0.9052, correlation about mean = 0.7104, overlap = 318.4 
    10866 steps = 88, shift = 2.7, angle = 7.48 degrees 
    10867  
    10868 Position of rOAT1-PBD_IF.mrc (#50) relative to rOAT1-PBD_IF.mrc (#7)
    10869 coordinates: 
    10870 Matrix rotation and translation 
    10871 0.99182552 0.09586728 -0.08421166 67.85108178 
    10872 -0.09362983 0.99515083 0.03013765 73.24636935 
    10873 0.08669251 -0.02200656 0.99599203 61.03836799 
    10874 Axis -0.20020488 -0.65617735 -0.72756395 
    10875 Axis point 63.93693297 -480.82614561 -0.00000000 
    10876 Rotation angle (degrees) 7.48271681 
    10877 Shift along axis -106.05604184 
    10878  
    10879 
    10880 > hide #!7 models
    10881 
    10882 > color #50 #b2b2b24d models
    10883 
    10884 > select clear
    10885 
    10886 > ui mousemode right translate
    10887 
    10888 > select #8: 382, 353,438,230,442,466,207,601
    10889 
    10890 93 atoms, 90 bonds, 8 residues, 1 model selected 
    10891 
    10892 > view sel
    10893 
    10894 > cofr sel
    10895 
    10896 > volume #50 level 0.2404
    10897 
    10898 > select clear
    10899 
    10900 > select #8: 382, 353,438,230,442,466,207,601
    10901 
    10902 93 atoms, 90 bonds, 8 residues, 1 model selected 
    10903 
    10904 > show sel atoms
    10905 
    10906 > select clear
    10907 
    10908 > volume #50 level 0.2822
    10909 
    10910 > select clear
    10911 
    10912 > movie record
    10913 
    10914 > turn y 2 180
    10915 
    10916 > wait 180
    10917 
    10918 > movie encode /Users/dout2/Desktop/movie2.mp4
    10919 
    10920 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    10921  
    10922 
    10923 > hide #!50 models
    10924 
    10925 > view
    10926 
    10927 > hide #8 models
    10928 
    10929 > show #!20 models
    10930 
    10931 > show #21 models
    10932 
    10933 > color #20 #ffffb2ff models
    10934 
    10935 > color #20 #ffffb24d models
    10936 
    10937 > select clear
    10938 
    10939 > select #21: 382, 353,438,230,442,466,207,601
    10940 
    10941 109 atoms, 109 bonds, 8 residues, 1 model selected 
    10942 
    10943 > show sel atoms
    10944 
    10945 > select clear
    10946 
    10947 > select H
    10948 
    10949 117 atoms, 10 residues, 9 models selected 
    10950 
    10951 > hide sel & #21 atoms
    10952 
    10953 > select clear
    10954 
    10955 > select #21: 382, 353,438,230,442,466,207,601
    10956 
    10957 109 atoms, 109 bonds, 8 residues, 1 model selected 
    10958 
    10959 > view sel
    10960 
    10961 > select clear
    10962 
    10963 > color #20 #ffffb280 models
    10964 
    10965 > select clear
    10966 
    10967 > volume #20 level 0.01329
    10968 
    10969 > select #21/A:602@O24
    10970 
    10971 1 atom, 1 residue, 1 model selected 
    10972 
    10973 > select up
    10974 
    10975 35 atoms, 38 bonds, 1 residue, 1 model selected 
    10976 
    10977 > select clear
    10978 
    10979 > movie record
    10980 
    10981 > turn y 2 180
    10982 
    10983 > wait 180
    10984 
    10985 > movie encode /Users/dout2/Desktop/movie2.mp4
    10986 
    10987 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    10988  
    10989 
    10990 > select #21: 382, 353,438,230,442,466,207,601,602
    10991 
    10992 144 atoms, 147 bonds, 9 residues, 1 model selected 
    10993 
    10994 > select #20
    10995 
    10996 4 models selected 
    10997 
    10998 > select clear
    10999 
    11000 > movie record
    11001 
    11002 > turn y 2 180
    11003 
    11004 > wait 180
    11005 
    11006 > movie encode /Users/dout2/Desktop/movie3.mp4
    11007 
    11008 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    11009  
    11010 
    11011 > hide #!20 models
    11012 
    11013 > view
    11014 
    11015 > hide #21 models
    11016 
    11017 > show #!24 models
    11018 
    11019 > show #!23 models
    11020 
    11021 > color #23 #ffffb2ff models
    11022 
    11023 > select clear
    11024 
    11025 > hide #!23 models
    11026 
    11027 > show #!23 models
    11028 
    11029 > select #24: 382, 353,438,230,442,466,207,601,602
    11030 
    11031 109 atoms, 109 bonds, 8 residues, 1 model selected 
    11032 
    11033 > view sel
    11034 
    11035 > color #23 #ffffb280 models
    11036 
    11037 > select clear
    11038 
    11039 > select #24/A:601@O14
    11040 
    11041 1 atom, 1 residue, 1 model selected 
    11042 
    11043 > select up
    11044 
    11045 35 atoms, 38 bonds, 1 residue, 1 model selected 
    11046 
    11047 > cofr sel
    11048 
    11049 > select #23
    11050 
    11051 4 models selected 
    11052 
    11053 > movie record
    11054 
    11055 > turn y 2 180
    11056 
    11057 > wait 180
    11058 
    11059 > movie encode /Users/dout2/Desktop/movie3.mp4
    11060 
    11061 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    11062  
    11063 
    11064 > select clear
    11065 
    11066 > movie record
    11067 
    11068 > turn y 2 180
    11069 
    11070 > wait 180
    11071 
    11072 > movie encode /Users/dout2/Desktop/movie4.mp4
    11073 
    11074 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    11075  
    11076 
    11077 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    11078 
    11079 > close session
    11080 
    11081 > open /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs
    11082 
    11083 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    11084 level 0.0151, step 1, values float32 
    11085 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    11086 level 0.00807, step 1, values float32 
    11087 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    11088 level 0.0137, step 1, values float32 
    11089 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    11090 level 0.0106, step 1, values float32 
    11091 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    11092 level 0.0111, step 1, values float32 
    11093 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    11094 level 0.00516, step 1, values float32 
    11095 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    11096 level 0.00806, step 1, values float32 
    11097 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    11098 at level 0.0108, step 1, values float32 
    11099 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    11100 at level 0.00806, step 1, values float32 
    11101 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    11102 level 0.00563, step 2, values float32 
    11103 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    11104 at level 0.00563, step 1, values float32 
    11105 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    11106 level 0.011, step 1, values float32 
    11107 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    11108 at level 0.011, step 1, values float32 
    11109 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    11110 level 0.0194, step 1, values float32 
    11111 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    11112 at level 0.0128, step 1, values float32 
    11113 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    11114 level 0.0168, step 1, values float32 
    11115 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    11116 at level 0.0168, step 1, values float32 
    11117 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    11118 0.121, step 1, values float32 
    11119 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    11120 level 0.0683, step 1, values float32 
    11121 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    11122 0.0104, step 1, values float32 
    11123 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    11124 level 0.0038, step 1, values float32 
    11125 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    11126 0.0119, step 1, values float32 
    11127 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    11128 shown at level 0.0118, step 1, values float32 
    11129 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    11130 level 0.00852, step 1, values float32 
    11131 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    11132 at level 0.00686, step 1, values float32 
    11133 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    11134 level 0.0106, step 1, values float32 
    11135 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    11136 at level 0.00699, step 1, values float32 
    11137 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    11138 level 0.0122, step 1, values float32 
    11139 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    11140 level 0.0102, step 1, values float32 
    11141 Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
    11142 level 0.0115, step 1, values float32 
    11143 Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
    11144 1, values float32 
    11145 opened ChimeraX session 
    11146 
    11147 > hide #15 models
    11148 
    11149 > select subtract #15
    11150 
    11151 Nothing selected 
    11152 
    11153 > show #!49 models
    11154 
    11155 > hide #49.1 models
    11156 
    11157 > select #49: 382, 353,438,230,442,466,207,601,602
    11158 
    11159 74 atoms, 71 bonds, 7 residues, 1 model selected 
    11160 
    11161 > show sel atoms
    11162 
    11163 > select add #49
    11164 
    11165 3942 atoms, 3966 bonds, 570 residues, 2 models selected 
    11166 
    11167 > hide sel cartoons
    11168 
    11169 > select clear
    11170 
    11171 > size stickRadius 0.4
    11172 
    11173 Changed 77114 bond radii 
    11174 
    11175 > select add #49
    11176 
    11177 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    11178 
    11179 > show sel cartoons
    11180 
    11181 > hide sel cartoons
    11182 
    11183 > show sel atoms
    11184 
    11185 > hide sel atoms
    11186 
    11187 > show sel cartoons
    11188 
    11189 > select #49: 382, 353,438,230,442,466,207,601,602
    11190 
    11191 74 atoms, 71 bonds, 7 residues, 1 model selected 
    11192 
    11193 > show sel atoms
    11194 
    11195 > view
    11196 
    11197 > hide sel cartoons
    11198 
    11199 > select add #49
    11200 
    11201 3942 atoms, 3966 bonds, 570 residues, 2 models selected 
    11202 
    11203 > hide sel cartoons
    11204 
    11205 > color (#!49 & sel) purple
    11206 
    11207 > select clear
    11208 
    11209 > select add #49
    11210 
    11211 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    11212 
    11213 > show sel cartoons
    11214 
    11215 > select #49/A:223
    11216 
    11217 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11218 
    11219 > show sel atoms
    11220 
    11221 > select #49: 382, 353,438,230,442,466,207,601,602,203
    11222 
    11223 79 atoms, 75 bonds, 8 residues, 1 model selected 
    11224 
    11225 > hide sel cartoons
    11226 
    11227 > select add #49
    11228 
    11229 3942 atoms, 3966 bonds, 570 residues, 2 models selected 
    11230 
    11231 > hide sel cartoons
    11232 
    11233 > select #49/A:223@CA
    11234 
    11235 1 atom, 1 residue, 1 model selected 
    11236 
    11237 > select up
    11238 
    11239 4 atoms, 3 bonds, 1 residue, 2 models selected 
    11240 
    11241 > hide sel atoms
    11242 
    11243 > select add #49
    11244 
    11245 3942 atoms, 3966 bonds, 570 residues, 2 models selected 
    11246 
    11247 > show sel cartoons
    11248 
    11249 > select #49/A:223
    11250 
    11251 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11252 
    11253 > select clear
    11254 
    11255 > select #49/A:224
    11256 
    11257 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11258 
    11259 > select #49/A:223
    11260 
    11261 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11262 
    11263 > hide sel cartoons
    11264 
    11265 > select add #49
    11266 
    11267 3942 atoms, 3966 bonds, 570 residues, 2 models selected 
    11268 
    11269 > hide sel cartoons
    11270 
    11271 > select #49/A:382@NZ
    11272 
    11273 1 atom, 1 residue, 1 model selected 
    11274 
    11275 > select add #49/A:466@NH2
    11276 
    11277 2 atoms, 2 residues, 2 models selected 
    11278 
    11279 > select add #49/A:466@NH1
    11280 
    11281 3 atoms, 2 residues, 2 models selected 
    11282 
    11283 > select add #49/A:466@NE
    11284 
    11285 4 atoms, 2 residues, 2 models selected 
    11286 
    11287 > color (#!49 & sel) byhetero
    11288 
    11289 > select clear
    11290 
    11291 > save /Users/dout2/Desktop/rOAT1-Apo_residues.png supersample 3
    11292 > transparentBackground true
    11293 
    11294 > select clear
    11295 
    11296 > save /Users/dout2/Desktop/rOAT1-Apo_residues.png supersample 3
    11297 > transparentBackground true
    11298 
    11299 > hide #!49 models
    11300 
    11301 > show #!51 models
    11302 
    11303 > view
    11304 
    11305 > show #!51 atoms
    11306 
    11307 > select add #51
    11308 
    11309 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    11310 
    11311 > undo
    11312 
    11313 > select add #51
    11314 
    11315 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    11316 
    11317 > show sel atoms
    11318 
    11319 > select #51/A:207@CE
    11320 
    11321 1 atom, 1 residue, 1 model selected 
    11322 
    11323 > select up
    11324 
    11325 8 atoms, 7 bonds, 1 residue, 2 models selected 
    11326 
    11327 > undo
    11328 
    11329 > show sel cartoons
    11330 
    11331 > select #51/A:223
    11332 
    11333 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11334 
    11335 > select #51/A:208
    11336 
    11337 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11338 
    11339 > select clear
    11340 
    11341 > select #51/A:211
    11342 
    11343 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11344 
    11345 > select #51/A:207
    11346 
    11347 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11348 
    11349 > show sel atoms
    11350 
    11351 > color (#!51 & sel) purple
    11352 
    11353 > select #51: 382, 353,438,230,442,466,207,601,602,203
    11354 
    11355 79 atoms, 75 bonds, 8 residues, 1 model selected 
    11356 
    11357 > select add #51
    11358 
    11359 4280 atoms, 4381 bonds, 552 residues, 2 models selected 
    11360 
    11361 > hide sel cartoons
    11362 
    11363 > select clear
    11364 
    11365 > save /Users/dout2/Desktop/rOAT1-AKG_IF_residues.png supersample 3
    11366 > transparentBackground true
    11367 
    11368 > save /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs includeMaps true
    11369 
    11370 > hide #!51 models
    11371 
    11372 > show #!43 models
    11373 
    11374 > view
    11375 
    11376 > select #43: 382, 353,438,230,442,466,207,601,602
    11377 
    11378 84 atoms, 80 bonds, 8 residues, 1 model selected 
    11379 
    11380 > show sel atoms
    11381 
    11382 > select clear
    11383 
    11384 > select #43/A:207@CB
    11385 
    11386 1 atom, 1 residue, 1 model selected 
    11387 
    11388 > select up
    11389 
    11390 8 atoms, 7 bonds, 1 residue, 2 models selected 
    11391 
    11392 > color (#!43 & sel) purple
    11393 
    11394 > select clear
    11395 
    11396 > save /Users/dout2/Desktop/rOAT1-AKG_OF_residues.png supersample 3
    11397 > transparentBackground true
    11398 
    11399 > hide #!43 models
    11400 
    11401 > show #!18 models
    11402 
    11403 > select #18: 382, 353,438,230,442,466,207,601,602
    11404 
    11405 105 atoms, 103 bonds, 8 residues, 1 model selected 
    11406 
    11407 > show sel atoms
    11408 
    11409 > select clear
    11410 
    11411 > select #18/A:601@C05
    11412 
    11413 1 atom, 1 residue, 1 model selected 
    11414 
    11415 > select up
    11416 
    11417 31 atoms, 32 bonds, 1 residue, 1 model selected 
    11418 
    11419 > hide sel atoms
    11420 
    11421 > select #18/A:207@CB
    11422 
    11423 1 atom, 1 residue, 1 model selected 
    11424 
    11425 > select up
    11426 
    11427 8 atoms, 7 bonds, 1 residue, 2 models selected 
    11428 
    11429 > color (#!18 & sel) purple
    11430 
    11431 > select clear
    11432 
    11433 > save /Users/dout2/Desktop/rOAT1-Apo_OF_residues.png supersample 3
    11434 > transparentBackground true
    11435 
    11436 > select #18: 382, 353,438,230,442,466,207,601,602
    11437 
    11438 105 atoms, 103 bonds, 8 residues, 1 model selected 
    11439 
    11440 > show sel atoms
    11441 
    11442 > select #18/A:601@C05
    11443 
    11444 1 atom, 1 residue, 1 model selected 
    11445 
    11446 > select #18/A:601@H051
    11447 
    11448 1 atom, 1 residue, 1 model selected 
    11449 
    11450 > select up
    11451 
    11452 31 atoms, 32 bonds, 1 residue, 1 model selected 
    11453 
    11454 > select H
    11455 
    11456 117 atoms, 10 residues, 9 models selected 
    11457 
    11458 > hide sel & #!18 atoms
    11459 
    11460 > select clear
    11461 
    11462 > save /Users/dout2/Desktop/rOAT1-TFV_OF_residues.png supersample 3
    11463 > transparentBackground true
    11464 
    11465 > hide #!18 models
    11466 
    11467 > show #15 models
    11468 
    11469 > select #15: 382, 353,438,230,442,466,207,601,602
    11470 
    11471 105 atoms, 103 bonds, 8 residues, 1 model selected 
    11472 
    11473 > show sel atoms
    11474 
    11475 > select add #15
    11476 
    11477 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11478 
    11479 > hide sel cartoons
    11480 
    11481 > select clear
    11482 
    11483 > select add #15
    11484 
    11485 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11486 
    11487 > hide sel atoms
    11488 
    11489 > select #15: 382, 353,438,230,442,466,207,601,602
    11490 
    11491 105 atoms, 103 bonds, 8 residues, 1 model selected 
    11492 
    11493 > show sel atoms
    11494 
    11495 > select #15/A:601@C07
    11496 
    11497 1 atom, 1 residue, 1 model selected 
    11498 
    11499 > select up
    11500 
    11501 31 atoms, 32 bonds, 1 residue, 1 model selected 
    11502 
    11503 > select H
    11504 
    11505 117 atoms, 10 residues, 9 models selected 
    11506 
    11507 > hide sel & #15 atoms
    11508 
    11509 > select clear
    11510 
    11511 > select #15/A:601@O19
    11512 
    11513 1 atom, 1 residue, 1 model selected 
    11514 
    11515 > select up
    11516 
    11517 31 atoms, 32 bonds, 1 residue, 1 model selected 
    11518 
    11519 > select up
    11520 
    11521 3903 atoms, 3998 bonds, 501 residues, 1 model selected 
    11522 
    11523 > select down
    11524 
    11525 31 atoms, 32 bonds, 1 residue, 1 model selected 
    11526 
    11527 > color sel yellow
    11528 
    11529 > color sel byhetero
    11530 
    11531 > select clear
    11532 
    11533 > select #15: 382, 353,438,230,442,466,207
    11534 
    11535 74 atoms, 71 bonds, 7 residues, 1 model selected 
    11536 
    11537 > color sel purple
    11538 
    11539 > select clear
    11540 
    11541 > select #15/A:382@NZ
    11542 
    11543 1 atom, 1 residue, 1 model selected 
    11544 
    11545 > select add #15/A:466@NH2
    11546 
    11547 2 atoms, 2 residues, 1 model selected 
    11548 
    11549 > select add #15/A:466@NH1
    11550 
    11551 3 atoms, 2 residues, 1 model selected 
    11552 
    11553 > select add #15/A:466@NE
    11554 
    11555 4 atoms, 2 residues, 1 model selected 
    11556 
    11557 > color sel byhetero
    11558 
    11559 > select clear
    11560 
    11561 > select #15/A:601@N13
    11562 
    11563 1 atom, 1 residue, 1 model selected 
    11564 
    11565 > select up
    11566 
    11567 31 atoms, 32 bonds, 1 residue, 1 model selected 
    11568 
    11569 > color sel cyan
    11570 
    11571 > color sel byhetero
    11572 
    11573 > select clear
    11574 
    11575 > save /Users/dout2/Desktop/rOAT1-TFV_IF_residues.png supersample 3
    11576 > transparentBackground true
    11577 
    11578 > save /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs includeMaps true
    11579 
    11580 > select add #15
    11581 
    11582 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11583 
    11584 > show sel cartoons
    11585 
    11586 > select #15/A:227
    11587 
    11588 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11589 
    11590 > show sel atoms
    11591 
    11592 > select #15/A:223
    11593 
    11594 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11595 
    11596 > show sel atoms
    11597 
    11598 > hide sel cartoons
    11599 
    11600 > select add #15
    11601 
    11602 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11603 
    11604 > hide sel cartoons
    11605 
    11606 > select up
    11607 
    11608 2 atoms, 1 bond, 1 residue, 1 model selected 
    11609 
    11610 > select up
    11611 
    11612 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11613 
    11614 > hide sel atoms
    11615 
    11616 > undo
    11617 
    11618 > select add #15
    11619 
    11620 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11621 
    11622 > show sel cartoons
    11623 
    11624 > select #15/A:223
    11625 
    11626 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11627 
    11628 > select add #15
    11629 
    11630 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11631 
    11632 > select clear
    11633 
    11634 > select add #15
    11635 
    11636 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11637 
    11638 > hide sel cartoons
    11639 
    11640 > show sel cartoons
    11641 
    11642 > select #15/A:203
    11643 
    11644 5 atoms, 4 bonds, 1 residue, 1 model selected 
    11645 
    11646 > select #15/A:223
    11647 
    11648 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11649 
    11650 > select add #15
    11651 
    11652 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    11653 
    11654 > hide sel cartoons
    11655 
    11656 > select clear
    11657 
    11658 
    11659 ===== Log before crash end =====
    11660 
    11661 Log:
    11662 UCSF ChimeraX version: 1.8 (2024-06-10) 
    11663 © 2016-2024 Regents of the University of California. All rights reserved. 
    11664 
    11665 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    11666 
    11667 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    11668 level 0.01, step 1, values float32 
    11669 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    11670 level 0.00807, step 1, values float32 
    11671 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    11672 level 0.012, step 1, values float32 
    11673 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    11674 level 0.0106, step 1, values float32 
    11675 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    11676 level 0.0111, step 1, values float32 
    11677 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    11678 level 0.00516, step 1, values float32 
    11679 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    11680 level 0.0107, step 1, values float32 
    11681 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    11682 at level 0.0108, step 1, values float32 
    11683 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    11684 at level 0.00806, step 1, values float32 
    11685 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    11686 level 0.00563, step 2, values float32 
    11687 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    11688 at level 0.00563, step 1, values float32 
    11689 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    11690 level 0.011, step 1, values float32 
    11691 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    11692 at level 0.011, step 1, values float32 
    11693 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    11694 level 0.0133, step 1, values float32 
    11695 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    11696 at level 0.0128, step 1, values float32 
    11697 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    11698 level 0.0168, step 1, values float32 
    11699 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    11700 at level 0.0168, step 1, values float32 
    11701 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    11702 0.121, step 1, values float32 
    11703 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    11704 level 0.0683, step 1, values float32 
    11705 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    11706 0.0104, step 1, values float32 
    11707 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    11708 level 0.0038, step 1, values float32 
    11709 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    11710 0.0119, step 1, values float32 
    11711 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    11712 shown at level 0.0118, step 1, values float32 
    11713 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    11714 level 0.00852, step 1, values float32 
    11715 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    11716 at level 0.00686, step 1, values float32 
    11717 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    11718 level 0.0106, step 1, values float32 
    11719 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    11720 at level 0.00699, step 1, values float32 
    11721 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    11722 level 0.0122, step 1, values float32 
    11723 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    11724 level 0.0102, step 1, values float32 
    11725 Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
    11726 level 0.0115, step 1, values float32 
    11727 Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
    11728 1, values float32 
    11729 Opened rOAT1-PBD_IF.mrc as #50, grid size 160,160,160, pixel 0.83, shown at
    11730 level 0.282, step 1, values float32 
    11731 Log from Tue Apr 15 12:09:47 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    11732 © 2016-2024 Regents of the University of California. All rights reserved. 
    11733 
    11734 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    11735 
    11736 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    11737 level 0.0151, step 1, values float32 
    11738 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    11739 level 0.00807, step 1, values float32 
    11740 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    11741 level 0.0137, step 1, values float32 
    11742 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    11743 level 0.0106, step 1, values float32 
    11744 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    11745 level 0.0111, step 1, values float32 
    11746 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    11747 level 0.00516, step 1, values float32 
    11748 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    11749 level 0.00806, step 1, values float32 
    11750 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    11751 at level 0.0108, step 1, values float32 
    11752 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    11753 at level 0.00806, step 1, values float32 
    11754 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    11755 level 0.00563, step 2, values float32 
    11756 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    11757 at level 0.00563, step 1, values float32 
    11758 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    11759 level 0.011, step 1, values float32 
    11760 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    11761 at level 0.011, step 1, values float32 
    11762 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    11763 level 0.0194, step 1, values float32 
    11764 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    11765 at level 0.0128, step 1, values float32 
    11766 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    11767 level 0.0168, step 1, values float32 
    11768 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    11769 at level 0.0168, step 1, values float32 
    11770 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    11771 0.121, step 1, values float32 
    11772 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    11773 level 0.0683, step 1, values float32 
    11774 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    11775 0.0104, step 1, values float32 
    11776 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    11777 level 0.0038, step 1, values float32 
    11778 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    11779 0.0119, step 1, values float32 
    11780 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    11781 shown at level 0.0118, step 1, values float32 
    11782 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    11783 level 0.00852, step 1, values float32 
    11784 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    11785 at level 0.00686, step 1, values float32 
    11786 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    11787 level 0.0106, step 1, values float32 
    11788 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    11789 at level 0.00699, step 1, values float32 
    11790 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    11791 level 0.0122, step 1, values float32 
    11792 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    11793 level 0.0102, step 1, values float32 
    11794 Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
    11795 level 0.0115, step 1, values float32 
    11796 Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
    11797 1, values float32 
    11798 Log from Sat Apr 12 21:31:41 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    11799 © 2016-2024 Regents of the University of California. All rights reserved. 
    11800 
    11801 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    11802 
    11803 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    11804 level 0.0151, step 1, values float32 
    11805 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    11806 level 0.00807, step 1, values float32 
    11807 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    11808 level 0.0137, step 1, values float32 
    11809 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    11810 level 0.0106, step 1, values float32 
    11811 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    11812 level 0.0111, step 1, values float32 
    11813 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    11814 level 0.00516, step 1, values float32 
    11815 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    11816 level 0.00806, step 1, values float32 
    11817 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    11818 at level 0.0108, step 1, values float32 
    11819 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    11820 at level 0.00806, step 1, values float32 
    11821 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    11822 level 0.00563, step 2, values float32 
    11823 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    11824 at level 0.00563, step 1, values float32 
    11825 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    11826 level 0.011, step 1, values float32 
    11827 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    11828 at level 0.011, step 1, values float32 
    11829 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    11830 level 0.0194, step 1, values float32 
    11831 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    11832 at level 0.0128, step 1, values float32 
    11833 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    11834 level 0.0168, step 1, values float32 
    11835 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    11836 at level 0.0168, step 1, values float32 
    11837 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    11838 0.121, step 1, values float32 
    11839 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    11840 level 0.0683, step 1, values float32 
    11841 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    11842 0.0104, step 1, values float32 
    11843 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    11844 level 0.0038, step 1, values float32 
    11845 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    11846 0.0119, step 1, values float32 
    11847 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    11848 shown at level 0.0118, step 1, values float32 
    11849 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    11850 level 0.00852, step 1, values float32 
    11851 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    11852 at level 0.00686, step 1, values float32 
    11853 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    11854 level 0.0106, step 1, values float32 
    11855 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    11856 at level 0.00699, step 1, values float32 
    11857 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    11858 level 0.0122, step 1, values float32 
    11859 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    11860 level 0.0102, step 1, values float32 
    11861 Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
    11862 shown at level 0.0115, step 1, values float32 
    11863 Log from Thu Apr 10 15:43:35 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    11864 © 2016-2024 Regents of the University of California. All rights reserved. 
    11865 
    11866 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs format session
    11867 
    11868 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    11869 level 0.0151, step 1, values float32 
    11870 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    11871 level 0.00807, step 1, values float32 
    11872 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    11873 level 0.0137, step 1, values float32 
    11874 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    11875 level 0.0116, step 1, values float32 
    11876 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    11877 level 0.0111, step 1, values float32 
    11878 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    11879 level 0.00383, step 1, values float32 
    11880 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    11881 level 0.00806, step 1, values float32 
    11882 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    11883 at level 0.00806, step 1, values float32 
    11884 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    11885 at level 0.00806, step 1, values float32 
    11886 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    11887 level 0.00563, step 2, values float32 
    11888 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    11889 at level 0.00563, step 1, values float32 
    11890 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    11891 level 0.011, step 1, values float32 
    11892 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    11893 at level 0.011, step 1, values float32 
    11894 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    11895 level 0.0194, step 1, values float32 
    11896 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    11897 at level 0.0141, step 1, values float32 
    11898 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    11899 level 0.0168, step 1, values float32 
    11900 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    11901 at level 0.0168, step 1, values float32 
    11902 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    11903 0.121, step 1, values float32 
    11904 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    11905 level 0.0546, step 1, values float32 
    11906 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    11907 0.0104, step 1, values float32 
    11908 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    11909 level 0.0038, step 1, values float32 
    11910 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    11911 0.0119, step 1, values float32 
    11912 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    11913 shown at level 0.0118, step 1, values float32 
    11914 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    11915 level 0.00852, step 1, values float32 
    11916 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    11917 at level 0.00852, step 1, values float32 
    11918 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    11919 level 0.0106, step 1, values float32 
    11920 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    11921 at level 0.00699, step 1, values float32 
    11922 Log from Thu Apr 10 14:06:06 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    11923 © 2016-2024 Regents of the University of California. All rights reserved. 
    11924 
    11925 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    11926 
    11927 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    11928 level 0.0151, step 1, values float32 
    11929 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    11930 level 0.00807, step 1, values float32 
    11931 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    11932 level 0.0137, step 1, values float32 
    11933 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    11934 level 0.0116, step 1, values float32 
    11935 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    11936 level 0.0111, step 1, values float32 
    11937 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    11938 level 0.00383, step 1, values float32 
    11939 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    11940 level 0.00806, step 1, values float32 
    11941 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    11942 at level 0.00806, step 1, values float32 
    11943 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    11944 at level 0.00806, step 1, values float32 
    11945 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    11946 level 0.00563, step 2, values float32 
    11947 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    11948 at level 0.00563, step 1, values float32 
    11949 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    11950 level 0.011, step 1, values float32 
    11951 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    11952 at level 0.011, step 1, values float32 
    11953 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    11954 level 0.0194, step 1, values float32 
    11955 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    11956 at level 0.0141, step 1, values float32 
    11957 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    11958 level 0.0168, step 1, values float32 
    11959 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    11960 at level 0.0168, step 1, values float32 
    11961 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    11962 0.121, step 1, values float32 
    11963 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    11964 level 0.0546, step 1, values float32 
    11965 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    11966 0.0104, step 1, values float32 
    11967 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    11968 level 0.0038, step 1, values float32 
    11969 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    11970 0.0119, step 1, values float32 
    11971 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    11972 shown at level 0.0118, step 1, values float32 
    11973 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    11974 level 0.00852, step 1, values float32 
    11975 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    11976 at level 0.00852, step 1, values float32 
    11977 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    11978 level 0.0106, step 1, values float32 
    11979 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    11980 at level 0.00699, step 1, values float32 
    11981 Log from Tue Mar 11 12:00:09 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    11982 © 2016-2024 Regents of the University of California. All rights reserved. 
    11983 
    11984 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    11985 
    11986 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    11987 level 0.0151, step 1, values float32 
    11988 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    11989 level 0.00807, step 1, values float32 
    11990 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    11991 level 0.0137, step 1, values float32 
    11992 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    11993 level 0.0116, step 1, values float32 
    11994 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    11995 level 0.0111, step 1, values float32 
    11996 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    11997 level 0.00383, step 1, values float32 
    11998 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    11999 level 0.00806, step 1, values float32 
    12000 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    12001 at level 0.00806, step 1, values float32 
    12002 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    12003 at level 0.00806, step 1, values float32 
    12004 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    12005 level 0.00563, step 2, values float32 
    12006 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    12007 at level 0.00563, step 1, values float32 
    12008 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    12009 level 0.011, step 1, values float32 
    12010 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    12011 at level 0.011, step 1, values float32 
    12012 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    12013 level 0.0194, step 1, values float32 
    12014 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    12015 at level 0.0141, step 1, values float32 
    12016 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    12017 level 0.0168, step 1, values float32 
    12018 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    12019 at level 0.0168, step 1, values float32 
    12020 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    12021 0.121, step 1, values float32 
    12022 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    12023 level 0.0546, step 1, values float32 
    12024 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    12025 0.0104, step 1, values float32 
    12026 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    12027 level 0.0038, step 1, values float32 
    12028 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    12029 0.0119, step 1, values float32 
    12030 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    12031 shown at step 1, values float32 
    12032 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    12033 level 0.00852, step 1, values float32 
    12034 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    12035 at level 0.00852, step 1, values float32 
    12036 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    12037 level 0.0106, step 1, values float32 
    12038 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    12039 at level 0.00699, step 1, values float32 
    12040 Log from Mon Feb 10 17:46:10 2025UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    12041 © 2016-2023 Regents of the University of California. All rights reserved. 
    12042 
    12043 > open
    12044 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    12045 
    12046 Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
    12047 shown at level 0.00928, step 1, values float32 
    12048 Log from Wed Dec 11 13:28:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    12049 © 2016-2023 Regents of the University of California. All rights reserved. 
    12050 
    12051 > open
    12052 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    12053 > format session
    12054 
    12055 Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
    12056 shown at level 0.00928, step 1, values float32 
    12057 Log from Tue Dec 10 11:33:02 2024 Startup Messages 
    12058 --- 
    12059 warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 
    12060 Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
    12061 that from NMRSTAR bundle 
    12062  
    12063 UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    12064 © 2016-2023 Regents of the University of California. All rights reserved. 
    12065 How to cite UCSF ChimeraX 
    12066 
    12067 > open
    12068 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    12069 > hOCT1-VB1_3_real_space_refined_002.pdb"
    12070 
    12071 Chain information for hOCT1-VB1_3_real_space_refined_002.pdb #1 
    12072 --- 
    12073 Chain | Description 
    12074 A | No description available 
    12075  
    12076 
    12077 QXcbConnection: XCB error: 3 (BadWindow), sequence: 1650, resource id:
    12078 35652789, major code: 40 (TranslateCoords), minor code: 0 
    12079 
    12080 > select ::name="VIB"
    12081 
    12082 18 atoms, 19 bonds, 1 residue, 1 model selected 
    12083 
    12084 > delete atoms sel
    12085 
    12086 > delete bonds sel
    12087 
    12088 > save
    12089 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    12090 > hOCT1-noVB1.pdb" relModel #1
    12091 
    12092 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7992, resource id:
    12093 35652794, major code: 40 (TranslateCoords), minor code: 0 
    12094 
    12095 > close session
    12096 
    12097 > open
    12098 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    12099 > hOCT1-noVB1.pdb"
    12100 
    12101 Chain information for hOCT1-noVB1.pdb #1 
    12102 --- 
    12103 Chain | Description 
    12104 A | No description available 
    12105  
    12106 
    12107 > open
    12108 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
    12109 
    12110 Summary of feedback from opening
    12111 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt 
    12112 --- 
    12113 warnings | Ignored bad PDB record found on line 1 
    12114 REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1 
    12115  
    12116 Ignored bad PDB record found on line 2 
    12117 REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13 
    12118  
    12119 Ignored bad PDB record found on line 3 
    12120 REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19 
    12121  
    12122 Ignored bad PDB record found on line 4 
    12123 REMARK H PARENT 13 10 17 20 17 21 
    12124  
    12125 Ignored bad PDB record found on line 5 
    12126 REMARK Flexibility Score: inf 
    12127  
    12128 15 messages similar to the above omitted 
    12129  
    12130 Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds) 
    12131 
    12132 > open
    12133 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
    12134 
    12135 Summary of feedback from opening
    12136 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt 
    12137 --- 
    12138 warnings | Ignored bad PDB record found on line 1 
    12139 REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1 
    12140  
    12141 Ignored bad PDB record found on line 2 
    12142 REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13 
    12143  
    12144 Ignored bad PDB record found on line 3 
    12145 REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19 
    12146  
    12147 Ignored bad PDB record found on line 4 
    12148 REMARK H PARENT 13 10 17 20 17 21 
    12149  
    12150 Ignored bad PDB record found on line 5 
    12151 REMARK Flexibility Score: inf 
    12152  
    12153 15 messages similar to the above omitted 
    12154  
    12155 Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds) 
    12156 
    12157 QXcbConnection: XCB error: 3 (BadWindow), sequence: 6676, resource id:
    12158 35652851, major code: 40 (TranslateCoords), minor code: 0 
    12159 
    12160 > hide #3 models
    12161 
    12162 > show #3 models
    12163 
    12164 > hide #3 models
    12165 
    12166 > close #2-3
    12167 
    12168 > open
    12169 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
    12170 
    12171 Summary of feedback from opening
    12172 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt 
    12173 --- 
    12174 warnings | Ignored bad PDB record found on line 2 
    12175 REMARK VINA RESULT: -6.139 0.000 0.000 
    12176  
    12177 Ignored bad PDB record found on line 3 
    12178 REMARK INTER + INTRA: -8.396 
    12179  
    12180 Ignored bad PDB record found on line 4 
    12181 REMARK INTER: -7.934 
    12182  
    12183 Ignored bad PDB record found on line 5 
    12184 REMARK INTRA: -0.463 
    12185  
    12186 Ignored bad PDB record found on line 6 
    12187 REMARK UNBOUND: -0.463 
    12188  
    12189 495 messages similar to the above omitted 
    12190  
    12191 Opened vina_dock.pdbqt containing 20 structures (420 atoms, 440 bonds) 
    12192 
    12193 > viewdockx #2.1-20
    12194 
    12195 > set bgColor white
    12196 
    12197 > select #2.9/?:1@@serial_number=16
    12198 
    12199 1 atom, 1 residue, 1 model selected 
    12200 
    12201 > select up
    12202 
    12203 21 atoms, 22 bonds, 1 residue, 1 model selected 
    12204 
    12205 > view sel
    12206 
    12207 > open
    12208 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/note.txt
    12209 
    12210 Unrecognized file suffix '.txt' 
    12211 
    12212 > open
    12213 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/relion_locres_filtered.mrc
    12214 
    12215 Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
    12216 shown at level 0.00146, step 2, values float32 
    12217 
    12218 > color #3 #b2b2b296 models
    12219 
    12220 > volume #3 step 1
    12221 
    12222 > ui tool show "Side View"
    12223 
    12224 > volume #3 level 0.01472
    12225 
    12226 > select add #1
    12227 
    12228 3482 atoms, 3578 bonds, 1 pseudobond, 448 residues, 3 models selected 
    12229 
    12230 > show sel atoms
    12231 
    12232 JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
    12233 properties of undefined (reading 'id') 
    12234 
    12235 > hide #2.1-20 models
    12236 
    12237 > show #2.1 models
    12238 
    12239 > select clear
    12240 
    12241 > volume #3 level 0.01037
    12242 
    12243 > show #2.2 models
    12244 
    12245 > show #2.3 models
    12246 
    12247 > hide #2.2 models
    12248 
    12249 > hide #2.1 models
    12250 
    12251 > volume #3 level 0.009064
    12252 
    12253 > volume #3 level 0.009281
    12254 
    12255 > hide #2.3 models
    12256 
    12257 > show #2.4 models
    12258 
    12259 > hide #2.4 models
    12260 
    12261 > show #2.5 models
    12262 
    12263 > close #1
    12264 
    12265 > open
    12266 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    12267 > hOCT1-noVB1.pdb"
    12268 
    12269 Chain information for hOCT1-noVB1.pdb #1 
    12270 --- 
    12271 Chain | Description 
    12272 A | No description available 
    12273  
    12274 
    12275 > select add #1
    12276 
    12277 3461 atoms, 3556 bonds, 1 pseudobond, 447 residues, 2 models selected 
    12278 
    12279 > show sel atoms
    12280 
    12281 > select clear
    12282 
    12283 > hide #2.5 models
    12284 
    12285 > show #2.6 models
    12286 
    12287 > hide #2.6 models
    12288 
    12289 > show #2.7 models
    12290 
    12291 > hide #2.7 models
    12292 
    12293 > show #2.8 models
    12294 
    12295 > hide #2.8 models
    12296 
    12297 > show #2.9 models
    12298 
    12299 > hide #2.9 models
    12300 
    12301 > show #2.10 models
    12302 
    12303 > hide #2.10 models
    12304 
    12305 > show #2.10 models
    12306 
    12307 > hide #2.10 models
    12308 
    12309 > show #2.11 models
    12310 
    12311 > hide #2.11 models
    12312 
    12313 > show #2.12 models
    12314 
    12315 > save
    12316 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    12317 > includeMaps true
    12318 
    12319 > lighting soft
    12320 
    12321 > lighting simple
    12322 
    12323 > color #3 #b2b2b264 models
    12324 
    12325 > hide #2.12 models
    12326 
    12327 > show #2.13 models
    12328 
    12329 > hide #2.13 models
    12330 
    12331 > show #2.14 models
    12332 
    12333 > hide #2.14 models
    12334 
    12335 > show #2.15 models
    12336 
    12337 > hide #2.15 models
    12338 
    12339 > show #2.15 models
    12340 
    12341 > hide #2.15 models
    12342 
    12343 > show #2.16 models
    12344 
    12345 > hide #2.16 models
    12346 
    12347 > show #2.17 models
    12348 
    12349 > hide #2.17 models
    12350 
    12351 > show #2.18 models
    12352 
    12353 > hide #2.18 models
    12354 
    12355 > show #2.19 models
    12356 
    12357 > hide #2.19 models
    12358 
    12359 > show #2.20 models
    12360 
    12361 > hide #2.20 models
    12362 
    12363 > show #2.19 models
    12364 
    12365 > hide #2.19 models
    12366 
    12367 > show #2.20 models
    12368 
    12369 > hide #2.20 models
    12370 
    12371 > show #2.1 models
    12372 
    12373 > hide #2.1 models
    12374 
    12375 > show #2.2 models
    12376 
    12377 > hide #2.2 models
    12378 
    12379 > show #2.1 models
    12380 
    12381 > hide #2.1 models
    12382 
    12383 > show #2.2 models
    12384 
    12385 > hide #2.2 models
    12386 
    12387 > show #2.3 models
    12388 
    12389 > hide #2.3 models
    12390 
    12391 > show #2.3 models
    12392 
    12393 > hide #2.3 models
    12394 
    12395 > show #2.4 models
    12396 
    12397 > hide #2.4 models
    12398 
    12399 > show #2.5 models
    12400 
    12401 > hide #2.5 models
    12402 
    12403 > show #2.6 models
    12404 
    12405 > hide #2.6 models
    12406 
    12407 > show #2.7 models
    12408 
    12409 > hide #2.7 models
    12410 
    12411 > show #2.7 models
    12412 
    12413 > hide #2.7 models
    12414 
    12415 > show #2.8 models
    12416 
    12417 > hide #2.8 models
    12418 
    12419 > show #2.9 models
    12420 
    12421 > hide #2.9 models
    12422 
    12423 > show #2.10 models
    12424 
    12425 > select down
    12426 
    12427 Nothing selected 
    12428 
    12429 > hide #2.10 models
    12430 
    12431 > show #2.10 models
    12432 
    12433 > hide #2.10 models
    12434 
    12435 > show #2.11 models
    12436 
    12437 > hide #2.11 models
    12438 
    12439 > show #2.12 models
    12440 
    12441 > hide #2.12 models
    12442 
    12443 > show #2.13 models
    12444 
    12445 > hide #2.13 models
    12446 
    12447 > show #2.14 models
    12448 
    12449 > hide #2.14 models
    12450 
    12451 > show #2.15 models
    12452 
    12453 > hide #2.15 models
    12454 
    12455 > show #2.15 models
    12456 
    12457 > hide #2.15 models
    12458 
    12459 > show #2.15 models
    12460 
    12461 > hide #2.15 models
    12462 
    12463 > show #2.16 models
    12464 
    12465 > hide #2.16 models
    12466 
    12467 > show #2.16 models
    12468 
    12469 > hide #2.16 models
    12470 
    12471 > show #2.17 models
    12472 
    12473 > hide #2.17 models
    12474 
    12475 > show #2.17 models
    12476 
    12477 > hide #2.17 models
    12478 
    12479 > show #2.18 models
    12480 
    12481 > hide #2.18 models
    12482 
    12483 > show #2.19 models
    12484 
    12485 > hide #2.19 models
    12486 
    12487 > show #2.20 models
    12488 
    12489 > volume #3 level 0.01124
    12490 
    12491 > hide #2.20 models
    12492 
    12493 > show #2.20 models
    12494 
    12495 > hide #2.20 models
    12496 
    12497 > show #2.20 models
    12498 
    12499 > hide #2.20 models
    12500 
    12501 > show #2.19 models
    12502 
    12503 > hide #2.19 models
    12504 
    12505 > show #2.18 models
    12506 
    12507 > hide #2.18 models
    12508 
    12509 > show #2.19 models
    12510 
    12511 > hide #2.19 models
    12512 
    12513 > show #2.18 models
    12514 
    12515 > volume #3 level 0.008629
    12516 
    12517 > hide #2.18 models
    12518 
    12519 > show #2.18 models
    12520 
    12521 > hide #2.18 models
    12522 
    12523 > show #2.17 models
    12524 
    12525 > hide #2.17 models
    12526 
    12527 > show #2.16 models
    12528 
    12529 > hide #2.16 models
    12530 
    12531 > show #2.15 models
    12532 
    12533 > hide #2.15 models
    12534 
    12535 > show #2.14 models
    12536 
    12537 > hide #2.14 models
    12538 
    12539 > show #2.13 models
    12540 
    12541 > hide #2.13 models
    12542 
    12543 > show #2.12 models
    12544 
    12545 > hide #2.12 models
    12546 
    12547 > show #2.11 models
    12548 
    12549 > hide #2.11 models
    12550 
    12551 > show #2.10 models
    12552 
    12553 > hide #2.10 models
    12554 
    12555 > show #2.1 models
    12556 
    12557 > hide #2.1 models
    12558 
    12559 > show #2.1 models
    12560 
    12561 > hide #2.1 models
    12562 
    12563 > show #2.2 models
    12564 
    12565 > hide #2.2 models
    12566 
    12567 > show #2.3 models
    12568 
    12569 > hide #2.3 models
    12570 
    12571 > show #2.4 models
    12572 
    12573 > hide #2.4 models
    12574 
    12575 > show #2.5 models
    12576 
    12577 > hide #2.5 models
    12578 
    12579 > show #2.6 models
    12580 
    12581 > hide #2.6 models
    12582 
    12583 > show #2.7 models
    12584 
    12585 > hide #2.7 models
    12586 
    12587 > show #2.8 models
    12588 
    12589 > hide #2.8 models
    12590 
    12591 > show #2.9 models
    12592 
    12593 > hide #2.9 models
    12594 
    12595 > show #2.9 models
    12596 
    12597 > hide #2.9 models
    12598 
    12599 > show #2.9 models
    12600 
    12601 > hide #2.9 models
    12602 
    12603 > show #2.10 models
    12604 
    12605 > hide #2.10 models
    12606 
    12607 > show #2.11 models
    12608 
    12609 > hide #2.11 models
    12610 
    12611 > show #2.12 models
    12612 
    12613 > hide #2.12 models
    12614 
    12615 > show #2.13 models
    12616 
    12617 > hide #2.13 models
    12618 
    12619 > show #2.12 models
    12620 
    12621 > hide #2.12 models
    12622 
    12623 > show #2.1 models
    12624 
    12625 > hide #2.1 models
    12626 
    12627 > show #2.2 models
    12628 
    12629 > hide #2.2 models
    12630 
    12631 > show #2.3 models
    12632 
    12633 > hide #2.3 models
    12634 
    12635 > show #2.4 models
    12636 
    12637 > hide #2.4 models
    12638 
    12639 > show #2.5 models
    12640 
    12641 > hide #2.5 models
    12642 
    12643 > show #2.6 models
    12644 
    12645 > hide #2.6 models
    12646 
    12647 > show #2.7 models
    12648 
    12649 > hide #2.7 models
    12650 
    12651 > show #2.8 models
    12652 
    12653 > hide #2.8 models
    12654 
    12655 > show #2.8 models
    12656 
    12657 > hide #2.8 models
    12658 
    12659 > show #2.9 models
    12660 
    12661 > hide #2.9 models
    12662 
    12663 > show #2.10 models
    12664 
    12665 > hide #2.10 models
    12666 
    12667 > show #2.11 models
    12668 
    12669 > hide #2.11 models
    12670 
    12671 > show #2.12 models
    12672 
    12673 > hide #2.12 models
    12674 
    12675 > show #2.1 models
    12676 
    12677 > save
    12678 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    12679 > includeMaps true
    12680 
    12681 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35492, resource id:
    12682 35652978, major code: 40 (TranslateCoords), minor code: 0 
    12683 
    12684 > volume #3 level 0.009281
    12685 
    12686 > hide #2.1 models
    12687 
    12688 > show #2.2 models
    12689 
    12690 > hide #2.2 models
    12691 
    12692 > show #2.3 models
    12693 
    12694 > hide #2.3 models
    12695 
    12696 > show #2.4 models
    12697 
    12698 > show #2.5 models
    12699 
    12700 > hide #2.4 models
    12701 
    12702 > hide #2.5 models
    12703 
    12704 > show #2.18 models
    12705 
    12706 > hide #2.18 models
    12707 
    12708 > show #2.18 models
    12709 
    12710 > hide #2.18 models
    12711 
    12712 > show #2.17 models
    12713 
    12714 > hide #2.17 models
    12715 
    12716 > show #2.16 models
    12717 
    12718 > hide #2.16 models
    12719 
    12720 > show #2.15 models
    12721 
    12722 > hide #2.15 models
    12723 
    12724 > show #2.14 models
    12725 
    12726 > hide #2.14 models
    12727 
    12728 > show #2.13 models
    12729 
    12730 > hide #2.13 models
    12731 
    12732 > show #2.12 models
    12733 
    12734 > hide #2.12 models
    12735 
    12736 > show #2.12 models
    12737 
    12738 > hide #2.12 models
    12739 
    12740 > save
    12741 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    12742 > includeMaps true
    12743 
    12744 QXcbConnection: XCB error: 3 (BadWindow), sequence: 32670, resource id:
    12745 35652988, major code: 40 (TranslateCoords), minor code: 0 
    12746 
    12747 ——— End of log from Tue Dec 10 11:33:02 2024 ———
    12748 
    12749 opened ChimeraX session 
    12750 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    12751 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    12752 
    12753 > save
    12754 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    12755 > includeMaps true
    12756 
    12757 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7404, resource id:
    12758 35653140, major code: 40 (TranslateCoords), minor code: 0 
    12759 
    12760 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7416, resource id:
    12761 35653135, major code: 40 (TranslateCoords), minor code: 0 
    12762 
    12763 > show #2.11 models
    12764 
    12765 > hide #2.11 models
    12766 
    12767 > show #2.12 models
    12768 
    12769 > hide #2.12 models
    12770 
    12771 > save
    12772 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    12773 > includeMaps true
    12774 
    12775 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60442, resource id:
    12776 35653379, major code: 40 (TranslateCoords), minor code: 0 
    12777 
    12778 ——— End of log from Wed Dec 11 13:28:04 2024 ———
    12779 
    12780 opened ChimeraX session 
    12781 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    12782 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    12783 
    12784 > show #2.11 models
    12785 
    12786 > show #2.12 models
    12787 
    12788 > hide #2.11 models
    12789 
    12790 > open
    12791 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_7/hOCT1VB1007.pdb
    12792 
    12793 Chain information for hOCT1VB1007.pdb #4 
    12794 --- 
    12795 Chain | Description 
    12796 A | No description available 
    12797  
    12798 
    12799 > open
    12800 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_8/
    12801 > hOCT1-VB_Dock2_real_space_refined_008.pdb"
    12802 
    12803 Chain information for hOCT1-VB_Dock2_real_space_refined_008.pdb #5 
    12804 --- 
    12805 Chain | Description 
    12806 A | No description available 
    12807  
    12808 
    12809 QXcbConnection: XCB error: 3 (BadWindow), sequence: 17659, resource id:
    12810 35653657, major code: 40 (TranslateCoords), minor code: 0 
    12811 
    12812 > close session
    12813 
    12814 > open
    12815 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/P3_J149_fsc_iteration_010_after_fsc_mask_auto_tightening.pdf
    12816 
    12817 QXcbConnection: XCB error: 3 (BadWindow), sequence: 50929, resource id:
    12818 35654568, major code: 40 (TranslateCoords), minor code: 0 
    12819 
    12820 > open
    12821 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240.mrc
    12822 
    12823 Opened cryosparc_P3_J154__localfilter_240.mrc as #1, grid size 240,240,240,
    12824 pixel 0.553, shown at level 0.207, step 1, values float32 
    12825 
    12826 > open
    12827 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240_VB1.mrc
    12828 
    12829 Opened cryosparc_P3_J154__localfilter_240_VB1.mrc as #2, grid size
    12830 240,240,240, pixel 0.553, shown at level 0.000117, step 1, values float32 
    12831 
    12832 > volume #2 level 0.3318
    12833 
    12834 Drag select of 2 cryosparc_P3_J154__localfilter_240_VB1.mrc 
    12835 
    12836 > view orient
    12837 
    12838 > select clear
    12839 
    12840 > open
    12841 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb
    12842 
    12843 Summary of feedback from opening
    12844 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb 
    12845 --- 
    12846 warnings | Cannot find LINK/SSBOND residue CYS (50 ) 
    12847 Cannot find LINK/SSBOND residue CYS (62 ) 
    12848 Cannot find LINK/SSBOND residue CYS (89 ) 
    12849  
    12850 
    12851 > open
    12852 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb
    12853 
    12854 Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4 
    12855 --- 
    12856 Chain | Description 
    12857 A | No description available 
    12858  
    12859 
    12860 > open
    12861 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb
    12862 
    12863 Chain information for mOCT1-VB1_real_space_refined_014.pdb #5 
    12864 --- 
    12865 Chain | Description 
    12866 A | No description available 
    12867  
    12868 
    12869 > close #3#4
    12870 
    12871 > volume #2 color #ffffb296
    12872 
    12873 > volume #2 color #ffffb2c8
    12874 
    12875 > volume #2 level 0.4304
    12876 
    12877 > volume #2 level 0.3677
    12878 
    12879 > select /A:601@C15
    12880 
    12881 1 atom, 1 residue, 1 model selected 
    12882 
    12883 > select up
    12884 
    12885 18 atoms, 19 bonds, 1 residue, 1 model selected 
    12886 
    12887 > view sel
    12888 
    12889 > select clear
    12890 
    12891 > open
    12892 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb
    12893 
    12894 Chain information for mOCT1-ABC_real_space_refined_009.pdb #3 
    12895 --- 
    12896 Chain | Description 
    12897 A | No description available 
    12898  
    12899 
    12900 > open
    12901 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc
    12902 
    12903 Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240,
    12904 pixel 0.553, shown at level 0.229, step 1, values float32 
    12905 
    12906 > volume #4 level 0.7041
    12907 
    12908 > hide #!2 models
    12909 
    12910 > hide #!3 models
    12911 
    12912 > hide #!5 models
    12913 
    12914 > show #!3 models
    12915 
    12916 > select ::name="ABC"
    12917 
    12918 42 atoms, 48 bonds, 2 residues, 1 model selected 
    12919 
    12920 > view sel
    12921 
    12922 > volume #4 level 0.5273
    12923 
    12924 > hide #!4 models
    12925 
    12926 > show #!4 models
    12927 
    12928 > show #!1 models
    12929 
    12930 > hide #!3 models
    12931 
    12932 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    12933 > density.cxs" includeMaps true
    12934 
    12935 QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id:
    12936 35654641, major code: 40 (TranslateCoords), minor code: 0 
    12937 
    12938 > hide #!1 models
    12939 
    12940 > rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    12941 
    12942 > rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc
    12943 
    12944 > rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc
    12945 
    12946 > show #!3 models
    12947 
    12948 > select clear
    12949 
    12950 > hide #!4 models
    12951 
    12952 > select ::name="ABC"
    12953 
    12954 42 atoms, 48 bonds, 2 residues, 1 model selected 
    12955 
    12956 > select add #3
    12957 
    12958 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    12959 
    12960 > color (#!3 & sel) white
    12961 
    12962 > select clear
    12963 
    12964 > select ::name="ABC"
    12965 
    12966 42 atoms, 48 bonds, 2 residues, 1 model selected 
    12967 
    12968 > color sel red
    12969 
    12970 > show #!4 models
    12971 
    12972 > ui tool show "Color Zone"
    12973 
    12974 > color zone #4 near #3 distance 3.32
    12975 
    12976 > volume splitbyzone #4
    12977 
    12978 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size
    12979 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    12980 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size
    12981 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    12982 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size
    12983 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    12984 
    12985 > hide #!3 models
    12986 
    12987 > select add #3
    12988 
    12989 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    12990 
    12991 > select subtract #3
    12992 
    12993 Nothing selected 
    12994 
    12995 > hide #!6.1 models
    12996 
    12997 > hide #!6.3 models
    12998 
    12999 > show #!6.3 models
    13000 
    13001 > hide #!6.2 models
    13002 
    13003 > close #6.1-2
    13004 
    13005 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    13006 > density.cxs" includeMaps true
    13007 
    13008 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id:
    13009 35654647, major code: 40 (TranslateCoords), minor code: 0 
    13010 
    13011 > show #!3 models
    13012 
    13013 > color #3 #fffffbff
    13014 
    13015 > color #3 #ddddaaff
    13016 
    13017 > color #3 #dda0deff
    13018 
    13019 > color #3 plum
    13020 
    13021 > select add #3
    13022 
    13023 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    13024 
    13025 > color (#!3 & sel) byhetero
    13026 
    13027 > color #6.3 #ddddaaff models
    13028 
    13029 > color #6.3 plum models
    13030 
    13031 > color #6.3 #ffffb2ff models
    13032 
    13033 Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5
    13034 atoms, 5 residues, 5 bonds 
    13035 
    13036 > select clear
    13037 
    13038 > color #6.3 #ffffb2c8 models
    13039 
    13040 > select ::name="ABC"
    13041 
    13042 42 atoms, 48 bonds, 2 residues, 1 model selected 
    13043 
    13044 > view sel
    13045 
    13046 > select #3/A:234
    13047 
    13048 11 atoms, 10 bonds, 1 residue, 1 model selected 
    13049 
    13050 > color #6.3 #ffffb296 models
    13051 
    13052 > show #!2 models
    13053 
    13054 > hide #!2 models
    13055 
    13056 > show #!2 models
    13057 
    13058 > hide #!3 models
    13059 
    13060 > hide #!6 models
    13061 
    13062 > hide #!6.3 models
    13063 
    13064 > show #!4 models
    13065 
    13066 > hide #!4 models
    13067 
    13068 > show #!5 models
    13069 
    13070 > show #!3 models
    13071 
    13072 > hide #!3 models
    13073 
    13074 > select #5/A:36
    13075 
    13076 12 atoms, 12 bonds, 1 residue, 1 model selected 
    13077 
    13078 > show sel atoms
    13079 
    13080 > hide #!5 models
    13081 
    13082 > hide #!2 models
    13083 
    13084 > show #!1 models
    13085 
    13086 > view
    13087 
    13088 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    13089 > density.cxs" includeMaps true
    13090 
    13091 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id:
    13092 35654673, major code: 40 (TranslateCoords), minor code: 0 
    13093 
    13094 > open
    13095 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc
    13096 
    13097 Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83,
    13098 shown at level 0.00144, step 2, values float32 
    13099 
    13100 > volume #7 level 0.01204
    13101 
    13102 > select add #7
    13103 
    13104 12 atoms, 12 bonds, 1 residue, 3 models selected 
    13105 
    13106 > select add #5
    13107 
    13108 3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected 
    13109 
    13110 > select subtract #5
    13111 
    13112 2 models selected 
    13113 
    13114 > ui mousemode right "translate selected models"
    13115 
    13116 > view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016
    13117 
    13118 > view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057
    13119 
    13120 > ui mousemode right "rotate selected models"
    13121 
    13122 > view matrix models
    13123 > #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495
    13124 
    13125 > ui mousemode right "translate selected models"
    13126 
    13127 > view matrix models
    13128 > #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226
    13129 
    13130 > view matrix models
    13131 > #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256
    13132 
    13133 > view matrix models
    13134 > #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175
    13135 
    13136 > ui tool show "Fit in Map"
    13137 
    13138 > fitmap #7 inMap #1
    13139 
    13140 Fit map relion_locres_filtered.mrc in map
    13141 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points 
    13142 correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07 
    13143 steps = 116, shift = 1.21, angle = 8.84 degrees 
    13144  
    13145 Position of relion_locres_filtered.mrc (#7) relative to
    13146 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13147 Matrix rotation and translation 
    13148 -0.36461695 0.73265397 0.57469351 -59.14787422 
    13149 -0.87490183 -0.48082660 0.05790126 236.29988230 
    13150 0.31874951 -0.48168862 0.81631784 -18.80617873 
    13151 Axis -0.31464704 0.14924672 -0.93740208 
    13152 Axis point 41.71559551 127.71968026 0.00000000 
    13153 Rotation angle (degrees) 120.96824033 
    13154 Shift along axis 71.50663710 
    13155  
    13156 
    13157 > rename #7 mOCT1-3TC
    13158 
    13159 > select clear
    13160 
    13161 [Repeated 1 time(s)]
    13162 
    13163 > rename #7 mOCT1-3TC.mrc
    13164 
    13165 > open
    13166 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC-
    13167 > coot-14_real_space_refined_006.pdb
    13168 
    13169 Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8 
    13170 --- 
    13171 Chain | Description 
    13172 A | No description available 
    13173  
    13174 
    13175 > ui tool show Matchmaker
    13176 
    13177 > matchmaker #!8 to #5
    13178 
    13179 Parameters 
    13180 --- 
    13181 Chain pairing | bb 
    13182 Alignment algorithm | Needleman-Wunsch 
    13183 Similarity matrix | BLOSUM-62 
    13184 SS fraction | 0.3 
    13185 Gap open (HH/SS/other) | 18/18/6 
    13186 Gap extend | 1 
    13187 SS matrix |  |  | H | S | O 
    13188 ---|---|---|--- 
    13189 H | 6 | -9 | -6 
    13190 S |  | 6 | -6 
    13191 O |  |  | 4 
    13192 Iteration cutoff | 2 
    13193  
    13194 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC-
    13195 coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score =
    13196 2352.2 
    13197 RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs:
    13198 0.409) 
    13199  
    13200 
    13201 > hide #!1 models
    13202 
    13203 > hide #!7 models
    13204 
    13205 > show #!1 models
    13206 
    13207 > hide #!8 models
    13208 
    13209 > show #!7 models
    13210 
    13211 > select add #7
    13212 
    13213 2 models selected 
    13214 
    13215 > ui mousemode right "rotate selected models"
    13216 
    13217 > view matrix models
    13218 > #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956
    13219 
    13220 > ui mousemode right "translate selected models"
    13221 
    13222 > view matrix models
    13223 > #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096
    13224 
    13225 > fitmap #7 inMap #1
    13226 
    13227 Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13228 using 3812 points 
    13229 correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08 
    13230 steps = 160, shift = 6.4, angle = 20.1 degrees 
    13231  
    13232 Position of mOCT1-3TC.mrc (#7) relative to
    13233 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13234 Matrix rotation and translation 
    13235 0.27009123 -0.75134279 -0.60210857 210.67160095 
    13236 0.83888334 0.49056205 -0.23584655 -78.20606144 
    13237 0.47257322 -0.44139877 0.76278546 -39.17036140 
    13238 Axis -0.10648785 -0.55674686 0.82382842 
    13239 Axis point 169.78551241 113.86943556 0.00000000 
    13240 Rotation angle (degrees) 74.82789173 
    13241 Shift along axis -11.16264322 
    13242  
    13243 
    13244 > fitmap #8 inMap #7
    13245 
    13246 Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map
    13247 mOCT1-3TC.mrc (#7) using 7048 atoms 
    13248 average map value = 0.01706, steps = 60 
    13249 shifted from previous position = 0.0823 
    13250 rotated from previous position = 0.357 degrees 
    13251 atoms outside contour = 4146, contour level = 0.012041 
    13252  
    13253 Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to
    13254 mOCT1-3TC.mrc (#7) coordinates: 
    13255 Matrix rotation and translation 
    13256 0.99999991 -0.00005602 -0.00043067 0.07339565 
    13257 0.00005621 0.99999991 0.00043709 -0.06044298 
    13258 0.00043064 -0.00043712 0.99999982 0.02180230 
    13259 Axis -0.70938425 -0.69891365 0.09106970 
    13260 Axis point 0.00000000 51.44490735 150.82453668 
    13261 Rotation angle (degrees) 0.03530433 
    13262 Shift along axis -0.00783577 
    13263  
    13264 
    13265 > show #!8 models
    13266 
    13267 > hide #!8 models
    13268 
    13269 > select subtract #7
    13270 
    13271 Nothing selected 
    13272 
    13273 > hide #!1 models
    13274 
    13275 > show #!8 models
    13276 
    13277 > select ::name="3TC"
    13278 
    13279 26 atoms, 27 bonds, 1 residue, 1 model selected 
    13280 
    13281 > select add #8
    13282 
    13283 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    13284 
    13285 > color (#!8 & sel) white
    13286 
    13287 > select ::name="3TC"
    13288 
    13289 26 atoms, 27 bonds, 1 residue, 1 model selected 
    13290 
    13291 > color sel red
    13292 
    13293 > view sel
    13294 
    13295 > volume #7 step 1
    13296 
    13297 > color zone #7 near #8 distance 4.98
    13298 
    13299 > volume splitbyzone #7
    13300 
    13301 Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    13302 level 0.012, step 1, values float32 
    13303 Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    13304 level 0.012, step 1, values float32 
    13305 Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    13306 level 0.012, step 1, values float32 
    13307 
    13308 > close #9.2
    13309 
    13310 > close #9.1
    13311 
    13312 > color #9.3 white models
    13313 
    13314 > color #9.3 #ffffb2ff models
    13315 
    13316 > color #9.3 #ffffb296 models
    13317 
    13318 > select #8/A:447
    13319 
    13320 19 atoms, 18 bonds, 1 residue, 1 model selected 
    13321 
    13322 > select add #8
    13323 
    13324 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    13325 
    13326 > color #8 #bb22ffff
    13327 
    13328 > color #8 #b2fffbff
    13329 
    13330 > color #8 #b2ffb2ff
    13331 
    13332 > color (#!8 & sel) byhetero
    13333 
    13334 > select clear
    13335 
    13336 [Repeated 1 time(s)]
    13337 
    13338 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    13339 > density.cxs" includeMaps true
    13340 
    13341 > hide #!9.3 models
    13342 
    13343 > hide #!9 models
    13344 
    13345 > hide #!8 models
    13346 
    13347 > open
    13348 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc
    13349 
    13350 Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel
    13351 0.83, shown at level 0.00125, step 2, values float32 
    13352 
    13353 > show #!1 models
    13354 
    13355 > view
    13356 
    13357 > volume #1 level 0.3063
    13358 
    13359 > volume #10 step 1
    13360 
    13361 > volume #10 level 0.01019
    13362 
    13363 > rename #10 mOCT1-AZT.mrc
    13364 
    13365 > select add #10
    13366 
    13367 2 models selected 
    13368 
    13369 > view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093
    13370 
    13371 > view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826
    13372 
    13373 > ui mousemode right "rotate selected models"
    13374 
    13375 > view matrix models
    13376 > #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718
    13377 
    13378 > ui mousemode right "translate selected models"
    13379 
    13380 > view matrix models
    13381 > #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969
    13382 
    13383 > view matrix models
    13384 > #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609
    13385 
    13386 > fitmap #10 inMap #1
    13387 
    13388 Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13389 using 33175 points 
    13390 correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2 
    13391 steps = 172, shift = 3.01, angle = 24.4 degrees 
    13392  
    13393 Position of mOCT1-AZT.mrc (#10) relative to
    13394 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13395 Matrix rotation and translation 
    13396 0.17958596 0.98366820 0.01207312 -89.49221412 
    13397 -0.89232990 0.16805236 -0.41893408 218.60375344 
    13398 -0.41412105 0.06446147 0.90793639 -7.62218964 
    13399 Axis 0.24369569 0.21485858 -0.94575272 
    13400 Axis point 81.50821029 166.97786454 0.00000000 
    13401 Rotation angle (degrees) 82.65824965 
    13402 Shift along axis 32.36873253 
    13403  
    13404 
    13405 > view
    13406 
    13407 > view orient
    13408 
    13409 > ui tool show "Side View"
    13410 
    13411 > open
    13412 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb
    13413 
    13414 Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11 
    13415 --- 
    13416 Chain | Description 
    13417 A | No description available 
    13418  
    13419 
    13420 > ui tool show Matchmaker
    13421 
    13422 > matchmaker #!11 to #5
    13423 
    13424 Parameters 
    13425 --- 
    13426 Chain pairing | bb 
    13427 Alignment algorithm | Needleman-Wunsch 
    13428 Similarity matrix | BLOSUM-62 
    13429 SS fraction | 0.3 
    13430 Gap open (HH/SS/other) | 18/18/6 
    13431 Gap extend | 1 
    13432 SS matrix |  |  | H | S | O 
    13433 ---|---|---|--- 
    13434 H | 6 | -9 | -6 
    13435 S |  | 6 | -6 
    13436 O |  |  | 4 
    13437 Iteration cutoff | 2 
    13438  
    13439 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    13440 mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment
    13441 score = 2367.3 
    13442 RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs:
    13443 0.415) 
    13444  
    13445 
    13446 > fitmap #11 inMap #10
    13447 
    13448 Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map
    13449 mOCT1-AZT.mrc (#10) using 7017 atoms 
    13450 average map value = 0.01592, steps = 48 
    13451 shifted from previous position = 0.0651 
    13452 rotated from previous position = 0.278 degrees 
    13453 atoms outside contour = 3029, contour level = 0.010186 
    13454  
    13455 Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to
    13456 mOCT1-AZT.mrc (#10) coordinates: 
    13457 Matrix rotation and translation 
    13458 -0.89530533 -0.39092164 -0.21356179 331.89133766 
    13459 0.43778783 -0.68362766 -0.58394781 243.21431714 
    13460 0.08228108 -0.61630634 0.78319622 99.39179726 
    13461 Axis -0.03674901 -0.33598352 0.94115067 
    13462 Axis point 137.92729950 180.24940846 0.00000000 
    13463 Rotation angle (degrees) 153.87927506 
    13464 Shift along axis -0.37002346 
    13465  
    13466 
    13467 > hide #!1 models
    13468 
    13469 > select ::name="AZZ"
    13470 
    13471 19 atoms, 20 bonds, 1 residue, 1 model selected 
    13472 
    13473 > hide #!10 models
    13474 
    13475 > select add #11
    13476 
    13477 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    13478 
    13479 > select subtract #11
    13480 
    13481 Nothing selected 
    13482 
    13483 > select add #11
    13484 
    13485 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    13486 
    13487 > color (#!11 & sel) white
    13488 
    13489 > color #11 #aaaaffff
    13490 
    13491 > color (#!11 & sel) white
    13492 
    13493 > select ::name="AZZ"
    13494 
    13495 19 atoms, 20 bonds, 1 residue, 1 model selected 
    13496 
    13497 > color sel red
    13498 
    13499 > color zone #10 near #11 distance 4.98
    13500 
    13501 > show #!10 models
    13502 
    13503 > volume splitbyzone #10
    13504 
    13505 Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at
    13506 level 0.0102, step 1, values float32 
    13507 Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at
    13508 level 0.0102, step 1, values float32 
    13509 Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at
    13510 level 0.0102, step 1, values float32 
    13511 
    13512 > close #12.2
    13513 
    13514 > close #12.1
    13515 
    13516 > color #12.3 #ff0000fe models
    13517 
    13518 > color #12.3 #ff000096 models
    13519 
    13520 > color #12.3 #ffffff96 models
    13521 
    13522 > color #12.3 #ffffb296 models
    13523 
    13524 > color #11 #aaffffff
    13525 
    13526 > color #11 #aaaaffff
    13527 
    13528 > select add #11
    13529 
    13530 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    13531 
    13532 > color (#!11 & sel) byhetero
    13533 
    13534 > select clear
    13535 
    13536 > show #!3 models
    13537 
    13538 > hide #!3 models
    13539 
    13540 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    13541 > density.cxs" includeMaps true
    13542 
    13543 > hide #!12.3 models
    13544 
    13545 > hide #!12 models
    13546 
    13547 > hide #!11 models
    13548 
    13549 > show #!1 models
    13550 
    13551 > open
    13552 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc
    13553 
    13554 Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at
    13555 level 0.00595, step 2, values float32 
    13556 
    13557 > volume #13 step 1
    13558 
    13559 > volume #13 level 0.02012
    13560 
    13561 > select add #13
    13562 
    13563 2 models selected 
    13564 
    13565 > view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565
    13566 
    13567 > ui mousemode right "rotate selected models"
    13568 
    13569 > view matrix models
    13570 > #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26
    13571 
    13572 > ui mousemode right "translate selected models"
    13573 
    13574 > view matrix models
    13575 > #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75
    13576 
    13577 > view matrix models
    13578 > #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86
    13579 
    13580 > rename #13 mOCT1-MTF.mrc
    13581 
    13582 > open
    13583 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF-
    13584 > coot-9_real_space_refined_003.pdb
    13585 
    13586 Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14 
    13587 --- 
    13588 Chain | Description 
    13589 A | No description available 
    13590  
    13591 
    13592 > fitmap #13 inMap #1
    13593 
    13594 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13595 using 17817 points 
    13596 correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29 
    13597 steps = 200, shift = 2.4, angle = 7.61 degrees 
    13598  
    13599 Position of mOCT1-MTF.mrc (#13) relative to
    13600 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13601 Matrix rotation and translation 
    13602 -0.05771312 -0.64461025 0.76232987 59.74942259 
    13603 -0.34050237 0.73052504 0.59193860 -66.21901607 
    13604 -0.93847075 -0.22541250 -0.26165220 256.68697920 
    13605 Axis -0.42762978 0.88984156 0.15910615 
    13606 Axis point 123.33045199 0.00000000 117.21732044 
    13607 Rotation angle (degrees) 107.12276965 
    13608 Shift along axis -43.63458901 
    13609  
    13610 
    13611 > select subtract #13
    13612 
    13613 Nothing selected 
    13614 
    13615 > select add #13
    13616 
    13617 2 models selected 
    13618 
    13619 > ui mousemode right "rotate selected models"
    13620 
    13621 > view matrix models
    13622 > #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29
    13623 
    13624 > ui mousemode right "translate selected models"
    13625 
    13626 > view matrix models
    13627 > #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18
    13628 
    13629 > view matrix models
    13630 > #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38
    13631 
    13632 > fitmap #13 inMap #1
    13633 
    13634 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13635 using 17817 points 
    13636 correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06 
    13637 steps = 120, shift = 2.59, angle = 4.72 degrees 
    13638  
    13639 Position of mOCT1-MTF.mrc (#13) relative to
    13640 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13641 Matrix rotation and translation 
    13642 0.43566959 0.38627366 -0.81300964 69.55864121 
    13643 -0.07375796 -0.88487887 -0.45994473 251.91510217 
    13644 -0.89707959 0.26034986 -0.35702406 194.41028021 
    13645 Axis 0.83873143 0.09789343 -0.53567385 
    13646 Axis point 0.00000000 97.27212052 153.57991582 
    13647 Rotation angle (degrees) 154.57081238 
    13648 Shift along axis -21.13865268 
    13649  
    13650 
    13651 > view matrix models
    13652 > #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15
    13653 
    13654 > ui mousemode right "rotate selected models"
    13655 
    13656 > view matrix models
    13657 > #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12
    13658 
    13659 > view matrix models
    13660 > #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42
    13661 
    13662 > ui mousemode right "translate selected models"
    13663 
    13664 > view matrix models
    13665 > #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11
    13666 
    13667 > fitmap #13 inMap #1
    13668 
    13669 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13670 using 17817 points 
    13671 correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72 
    13672 steps = 92, shift = 1.81, angle = 5.01 degrees 
    13673  
    13674 Position of mOCT1-MTF.mrc (#13) relative to
    13675 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13676 Matrix rotation and translation 
    13677 0.31415893 0.53789144 -0.78228958 53.81386032 
    13678 0.19698588 -0.84300825 -0.50053338 220.95415625 
    13679 -0.92870918 0.00314703 -0.37079559 234.49017112 
    13680 Axis 0.80514260 0.23405449 -0.54494394 
    13681 Axis point 0.00000000 81.07236056 158.23174632 
    13682 Rotation angle (degrees) 161.77257653 
    13683 Shift along axis -32.74085292 
    13684  
    13685 
    13686 > view matrix models
    13687 > #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22
    13688 
    13689 > fitmap #13 inMap #1
    13690 
    13691 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13692 using 17817 points 
    13693 correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5 
    13694 steps = 80, shift = 1.45, angle = 5.73 degrees 
    13695  
    13696 Position of mOCT1-MTF.mrc (#13) relative to
    13697 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13698 Matrix rotation and translation 
    13699 0.28419679 0.60053681 -0.74738728 50.81854511 
    13700 0.27816291 -0.79764719 -0.53514891 205.19579930 
    13701 -0.91752798 -0.05580782 -0.39373584 245.12613641 
    13702 Axis 0.79598780 0.28253351 -0.53533003 
    13703 Axis point 0.00000000 71.54715698 160.41463451 
    13704 Rotation angle (degrees) 162.47642045 
    13705 Shift along axis -32.79775064 
    13706  
    13707 
    13708 > view matrix models
    13709 > #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99
    13710 
    13711 > fitmap #13 inMap #1
    13712 
    13713 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13714 using 17817 points 
    13715 correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2 
    13716 steps = 88, shift = 2.33, angle = 2.34 degrees 
    13717  
    13718 Position of mOCT1-MTF.mrc (#13) relative to
    13719 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13720 Matrix rotation and translation 
    13721 0.29378487 0.57675594 -0.76226180 52.65591556 
    13722 0.29516509 -0.81321822 -0.50155130 203.18767751 
    13723 -0.90915787 -0.07764488 -0.40914943 245.95334709 
    13724 Axis 0.80029578 0.27732609 -0.53161726 
    13725 Axis point 0.00000000 73.19686532 158.33534093 
    13726 Rotation angle (degrees) 164.64234082 
    13727 Shift along axis -32.26349399 
    13728  
    13729 
    13730 > view matrix models
    13731 > #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78
    13732 
    13733 > fitmap #13 inMap #1
    13734 
    13735 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    13736 using 17817 points 
    13737 correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6 
    13738 steps = 52, shift = 1.52, angle = 1.92 degrees 
    13739  
    13740 Position of mOCT1-MTF.mrc (#13) relative to
    13741 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    13742 Matrix rotation and translation 
    13743 0.29574252 0.60146473 -0.74214321 45.38180479 
    13744 0.29484975 -0.79643687 -0.52796964 204.44935424 
    13745 -0.90862533 -0.06267767 -0.41288198 249.74597785 
    13746 Axis 0.80005949 0.28626242 -0.52721784 
    13747 Axis point 0.00000000 72.71544700 159.79227740 
    13748 Rotation angle (degrees) 163.09499009 
    13749 Shift along axis -36.83622428 
    13750  
    13751 
    13752 > ui tool show Matchmaker
    13753 
    13754 > matchmaker #!14 to #5
    13755 
    13756 Parameters 
    13757 --- 
    13758 Chain pairing | bb 
    13759 Alignment algorithm | Needleman-Wunsch 
    13760 Similarity matrix | BLOSUM-62 
    13761 SS fraction | 0.3 
    13762 Gap open (HH/SS/other) | 18/18/6 
    13763 Gap extend | 1 
    13764 SS matrix |  |  | H | S | O 
    13765 ---|---|---|--- 
    13766 H | 6 | -9 | -6 
    13767 S |  | 6 | -6 
    13768 O |  |  | 4 
    13769 Iteration cutoff | 2 
    13770  
    13771 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF-
    13772 coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score =
    13773 2355.8 
    13774 RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs:
    13775 0.377) 
    13776  
    13777 
    13778 > select add #14
    13779 
    13780 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    13781 
    13782 > select subtract #13
    13783 
    13784 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    13785 
    13786 > hide #!1 models
    13787 
    13788 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    13789 > density.cxs" includeMaps true
    13790 
    13791 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id:
    13792 35654810, major code: 40 (TranslateCoords), minor code: 0 
    13793 
    13794 > color #14 #95cacdff
    13795 
    13796 > select ::name="MF8"
    13797 
    13798 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13799 
    13800 > select add #14
    13801 
    13802 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    13803 
    13804 > select subtract #14
    13805 
    13806 Nothing selected 
    13807 
    13808 > select add #14
    13809 
    13810 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    13811 
    13812 > color (#!14 & sel) white
    13813 
    13814 > select ::name="MF8"
    13815 
    13816 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13817 
    13818 > color sel red
    13819 
    13820 > color zone #10 near #11 distance 4.98
    13821 
    13822 > color zone #13 near #14 distance 4.98
    13823 
    13824 > hide #!14 models
    13825 
    13826 > show #!14 models
    13827 
    13828 > volume #13 level 0.0238
    13829 
    13830 > volume #13 level 0.02122
    13831 
    13832 > volume #13 level 0.01423
    13833 
    13834 > volume splitbyzone #13
    13835 
    13836 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    13837 level 0.0142, step 1, values float32 
    13838 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    13839 level 0.0142, step 1, values float32 
    13840 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    13841 level 0.0142, step 1, values float32 
    13842 
    13843 > close #15.1
    13844 
    13845 > close #15.2
    13846 
    13847 > volume #15.3 level 0.009273
    13848 
    13849 > volume #15.3 level 0.01703
    13850 
    13851 > close #15#15.3
    13852 
    13853 > select add #14
    13854 
    13855 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    13856 
    13857 > show #!13 models
    13858 
    13859 > color zone #13 near #14 distance 4.88
    13860 
    13861 > color zone #13 near #14 distance 4.78
    13862 
    13863 > color zone #13 near #14 distance 4.68
    13864 
    13865 > color zone #13 near #14 distance 4.58
    13866 
    13867 > color zone #13 near #14 distance 4.48
    13868 
    13869 > color zone #13 near #14 distance 4.38
    13870 
    13871 > color zone #13 near #14 distance 4.28
    13872 
    13873 > color zone #13 near #14 distance 4.18
    13874 
    13875 > color zone #13 near #14 distance 4.08
    13876 
    13877 > color zone #13 near #14 distance 3.98
    13878 
    13879 > color zone #13 near #14 distance 3.88
    13880 
    13881 > color zone #13 near #14 distance 3.78
    13882 
    13883 > color zone #13 near #14 distance 3.68
    13884 
    13885 > color zone #13 near #14 distance 3.58
    13886 
    13887 > color zone #13 near #14 distance 3.48
    13888 
    13889 > color zone #13 near #14 distance 3.38
    13890 
    13891 [Repeated 1 time(s)]
    13892 
    13893 > volume splitbyzone #13
    13894 
    13895 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    13896 level 0.0142, step 1, values float32 
    13897 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    13898 level 0.0142, step 1, values float32 
    13899 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    13900 level 0.0142, step 1, values float32 
    13901 
    13902 > close #15.1-2
    13903 
    13904 > volume #15.3 level 0.009634
    13905 
    13906 > color zone #13 near #14 distance 3.28
    13907 
    13908 > color zone #13 near #14 distance 3.18
    13909 
    13910 > color zone #13 near #14 distance 3.08
    13911 
    13912 > close #15#15.3
    13913 
    13914 > show #!13 models
    13915 
    13916 > select add #13
    13917 
    13918 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    13919 
    13920 > select subtract #13
    13921 
    13922 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    13923 
    13924 > color zone #13 near #14 distance 2.98
    13925 
    13926 > color zone #13 near #14 distance 2.88
    13927 
    13928 > color zone #13 near #14 distance 2.78
    13929 
    13930 > color zone #13 near #14 distance 2.68
    13931 
    13932 > color zone #13 near #14 distance 2.58
    13933 
    13934 > color zone #13 near #14 distance 2.48
    13935 
    13936 > volume #13 level 0.01681
    13937 
    13938 > fitmap #14 inMap #13
    13939 
    13940 Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map
    13941 mOCT1-MTF.mrc (#13) using 7044 atoms 
    13942 average map value = 0.01572, steps = 48 
    13943 shifted from previous position = 0.0765 
    13944 rotated from previous position = 0.266 degrees 
    13945 atoms outside contour = 4386, contour level = 0.016807 
    13946  
    13947 Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to
    13948 mOCT1-MTF.mrc (#13) coordinates: 
    13949 Matrix rotation and translation 
    13950 0.99946408 0.01781074 -0.02746495 0.87693504 
    13951 -0.01720783 0.99960910 0.02203450 -1.16466203 
    13952 0.02784666 -0.02155008 0.99937988 -1.14535630 
    13953 Axis -0.55418255 -0.70329295 -0.44526478 
    13954 Axis point 28.72708736 -0.00000000 48.38067452 
    13955 Rotation angle (degrees) 2.25364092 
    13956 Shift along axis 0.84310332 
    13957  
    13958 
    13959 > color zone #13 near #14 distance 2.48
    13960 
    13961 [Repeated 1 time(s)]
    13962 
    13963 > color single #13
    13964 
    13965 > color zone #13 near #14 distance 2.48
    13966 
    13967 > color zone #13 near #14 distance 2.38
    13968 
    13969 > color zone #13 near #14 distance 2.28
    13970 
    13971 > color zone #13 near #14 distance 2.18
    13972 
    13973 > color zone #13 near #14 distance 2.08
    13974 
    13975 > color zone #13 near #14 distance 1.98
    13976 
    13977 > color zone #13 near #14 distance 1.88
    13978 
    13979 > color zone #13 near #14 distance 1.78
    13980 
    13981 > color zone #13 near #14 distance 1.68
    13982 
    13983 > color zone #13 near #14 distance 1.58
    13984 
    13985 > color zone #13 near #14 distance 1.48
    13986 
    13987 > color zone #13 near #14 distance 1.38
    13988 
    13989 > color zone #13 near #14 distance 1.48
    13990 
    13991 > color zone #13 near #14 distance 1.58
    13992 
    13993 > color zone #13 near #14 distance 1.68
    13994 
    13995 > color zone #13 near #14 distance 1.78
    13996 
    13997 > color zone #13 near #14 distance 1.88
    13998 
    13999 > color zone #13 near #14 distance 1.98
    14000 
    14001 > volume #13 level 0.01957
    14002 
    14003 > color zone #13 near #14 distance 1.98
    14004 
    14005 > volume splitbyzone #13
    14006 
    14007 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    14008 level 0.0196, step 1, values float32 
    14009 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    14010 level 0.0196, step 1, values float32 
    14011 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    14012 level 0.0196, step 1, values float32 
    14013 
    14014 > close #15.1-2
    14015 
    14016 > color #15.3 yellow models
    14017 
    14018 > color #15.3 white models
    14019 
    14020 > color #15.3 #ffffb2ff models
    14021 
    14022 > color #15.3 #ffffb296 models
    14023 
    14024 > volume #15.3 level 0.01524
    14025 
    14026 > volume #15.3 level 0.0119
    14027 
    14028 > select subtract #14
    14029 
    14030 Nothing selected 
    14031 
    14032 > select add #14
    14033 
    14034 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    14035 
    14036 > color #14 #55dd44ff
    14037 
    14038 > color #14 #5d42cdff
    14039 
    14040 > color #14 #5858cdff
    14041 
    14042 > color #14 #7d76cdff
    14043 
    14044 > color #14 #9d7bcdff
    14045 
    14046 > color #14 #cd75baff
    14047 
    14048 > color #14 #9381cdff
    14049 
    14050 > color (#!14 & sel) byhetero
    14051 
    14052 > select clear
    14053 
    14054 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    14055 > density.cxs" includeMaps true
    14056 
    14057 > hide #!15.3 models
    14058 
    14059 > hide #!15 models
    14060 
    14061 > hide #!14 models
    14062 
    14063 > show #!1 models
    14064 
    14065 > open
    14066 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc
    14067 
    14068 Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83,
    14069 shown at level 0.00147, step 2, values float32 
    14070 
    14071 > volume #13 level 0.01846
    14072 
    14073 > volume #16 step 1
    14074 
    14075 > volume #16 level 0.01137
    14076 
    14077 > select add #16
    14078 
    14079 2 models selected 
    14080 
    14081 > ui mousemode right "rotate selected models"
    14082 
    14083 > view matrix models
    14084 > #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4
    14085 
    14086 > view matrix models
    14087 > #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203
    14088 
    14089 > view matrix models
    14090 > #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605
    14091 
    14092 > view matrix models
    14093 > #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74
    14094 
    14095 > view matrix models
    14096 > #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38
    14097 
    14098 > view matrix models
    14099 > #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16
    14100 
    14101 > ui mousemode right "translate selected models"
    14102 
    14103 > view matrix models
    14104 > #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09
    14105 
    14106 > view matrix models
    14107 > #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87
    14108 
    14109 > view matrix models
    14110 > #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08
    14111 
    14112 > view matrix models
    14113 > #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69
    14114 
    14115 > ui mousemode right "rotate selected models"
    14116 
    14117 > view matrix models
    14118 > #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76
    14119 
    14120 > view matrix models
    14121 > #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35
    14122 
    14123 > ui mousemode right "translate selected models"
    14124 
    14125 > view matrix models
    14126 > #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37
    14127 
    14128 > ui mousemode right "rotate selected models"
    14129 
    14130 > view matrix models
    14131 > #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3
    14132 
    14133 > rename #16 hOCT1-VB1.mrc
    14134 
    14135 > fitmap #16 inMap #1
    14136 
    14137 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    14138 using 29501 points 
    14139 correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4 
    14140 steps = 148, shift = 3.34, angle = 5.64 degrees 
    14141  
    14142 Position of hOCT1-VB1.mrc (#16) relative to
    14143 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    14144 Matrix rotation and translation 
    14145 -0.66774800 0.66848229 -0.32748134 111.59775010 
    14146 0.47076725 0.03845367 -0.88141903 115.78397104 
    14147 -0.57662015 -0.74273329 -0.34037693 282.67572866 
    14148 Axis 0.39969377 0.71802066 -0.56981683 
    14149 Axis point 39.62225841 0.00000000 179.67701786 
    14150 Rotation angle (degrees) 170.00920250 
    14151 Shift along axis -33.33317846 
    14152  
    14153 
    14154 > ui mousemode right "translate selected models"
    14155 
    14156 > view matrix models
    14157 > #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9
    14158 
    14159 > fitmap #16 inMap #1
    14160 
    14161 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    14162 using 29501 points 
    14163 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    14164 steps = 60, shift = 1.34, angle = 1.92 degrees 
    14165  
    14166 Position of hOCT1-VB1.mrc (#16) relative to
    14167 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    14168 Matrix rotation and translation 
    14169 -0.68896253 0.65809895 -0.30370448 111.90845021 
    14170 0.45027206 0.06027049 -0.89085495 116.65862228 
    14171 -0.56796628 -0.75051532 -0.33784768 287.44343290 
    14172 Axis 0.38522072 0.72537689 -0.57046767 
    14173 Axis point 41.86637964 0.00000000 181.62562393 
    14174 Rotation angle (degrees) 169.50470225 
    14175 Shift along axis -36.24626372 
    14176  
    14177 
    14178 > view matrix models
    14179 > #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46
    14180 
    14181 > fitmap #16 inMap #1
    14182 
    14183 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    14184 using 29501 points 
    14185 correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7 
    14186 steps = 72, shift = 3.09, angle = 0.0182 degrees 
    14187  
    14188 Position of hOCT1-VB1.mrc (#16) relative to
    14189 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    14190 Matrix rotation and translation 
    14191 -0.68902052 0.65795875 -0.30387662 111.96278841 
    14192 0.45022908 0.06002731 -0.89089309 116.69902951 
    14193 -0.56793001 -0.75065771 -0.33759222 287.41226501 
    14194 Axis 0.38519550 0.72529614 -0.57058737 
    14195 Axis point 41.87016659 0.00000000 181.64241189 
    14196 Rotation angle (degrees) 169.51189271 
    14197 Shift along axis -36.22489055 
    14198  
    14199 
    14200 > fitmap #16 inMap #1
    14201 
    14202 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    14203 using 29501 points 
    14204 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    14205 steps = 36, shift = 0.00448, angle = 0.00722 degrees 
    14206  
    14207 Position of hOCT1-VB1.mrc (#16) relative to
    14208 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    14209 Matrix rotation and translation 
    14210 -0.68898476 0.65802671 -0.30381055 111.93916561 
    14211 0.45024501 0.06010903 -0.89087953 116.68451889 
    14212 -0.56796077 -0.75059160 -0.33768744 287.42460080 
    14213 Axis 0.38521270 0.72532270 -0.57054198 
    14214 Axis point 41.86758112 0.00000000 181.63640339 
    14215 Rotation angle (degrees) 169.50839167 
    14216 Shift along axis -36.23348002 
    14217  
    14218 
    14219 > open
    14220 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb
    14221 
    14222 Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17 
    14223 --- 
    14224 Chain | Description 
    14225 A | No description available 
    14226  
    14227 
    14228 > ui tool show Matchmaker
    14229 
    14230 > matchmaker #!17 to #5
    14231 
    14232 Parameters 
    14233 --- 
    14234 Chain pairing | bb 
    14235 Alignment algorithm | Needleman-Wunsch 
    14236 Similarity matrix | BLOSUM-62 
    14237 SS fraction | 0.3 
    14238 Gap open (HH/SS/other) | 18/18/6 
    14239 Gap extend | 1 
    14240 SS matrix |  |  | H | S | O 
    14241 ---|---|---|--- 
    14242 H | 6 | -9 | -6 
    14243 S |  | 6 | -6 
    14244 O |  |  | 4 
    14245 Iteration cutoff | 2 
    14246  
    14247 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    14248 hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment
    14249 score = 1980 
    14250 RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs:
    14251 1.346) 
    14252  
    14253 
    14254 > fitmap #17 inMap #16
    14255 
    14256 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    14257 hOCT1-VB1.mrc (#16) using 3479 atoms 
    14258 average map value = 0.02025, steps = 64 
    14259 shifted from previous position = 0.153 
    14260 rotated from previous position = 0.521 degrees 
    14261 atoms outside contour = 1063, contour level = 0.011373 
    14262  
    14263 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    14264 hOCT1-VB1.mrc (#16) coordinates: 
    14265 Matrix rotation and translation 
    14266 0.99999651 0.00186028 0.00187897 -0.40239474 
    14267 -0.00185675 0.99999652 -0.00187607 0.55801929 
    14268 -0.00188246 0.00187257 0.99999648 0.09469763 
    14269 Axis 0.57831092 0.58028383 -0.57343453 
    14270 Axis point 61.09212114 0.00000000 225.59585813 
    14271 Rotation angle (degrees) 0.18569746 
    14272 Shift along axis 0.03679741 
    14273  
    14274 
    14275 > fitmap #17 inMap #16
    14276 
    14277 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    14278 hOCT1-VB1.mrc (#16) using 3479 atoms 
    14279 average map value = 0.02025, steps = 28 
    14280 shifted from previous position = 0.0153 
    14281 rotated from previous position = 0.0146 degrees 
    14282 atoms outside contour = 1064, contour level = 0.011373 
    14283  
    14284 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    14285 hOCT1-VB1.mrc (#16) coordinates: 
    14286 Matrix rotation and translation 
    14287 0.99999599 0.00211002 0.00188874 -0.43726655 
    14288 -0.00210638 0.99999592 -0.00192887 0.59237860 
    14289 -0.00189280 0.00192488 0.99999636 0.07510223 
    14290 Axis 0.56254941 0.55200867 -0.61548727 
    14291 Axis point 271.69369003 217.02489508 0.00000000 
    14292 Rotation angle (degrees) 0.19625280 
    14293 Shift along axis 0.03478962 
    14294  
    14295 
    14296 > hide #!1 models
    14297 
    14298 > select add #17
    14299 
    14300 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    14301 
    14302 > select subtract #16
    14303 
    14304 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    14305 
    14306 > color (#!17 & sel) white
    14307 
    14308 > select clear
    14309 
    14310 > select ::name="VIB"
    14311 
    14312 18 atoms, 19 bonds, 1 residue, 1 model selected 
    14313 
    14314 > color sel red
    14315 
    14316 > color zone #16 near #17 distance 4.98
    14317 
    14318 > color zone #16 near #17 distance 4.88
    14319 
    14320 > color zone #16 near #17 distance 4.78
    14321 
    14322 > color zone #16 near #17 distance 4.68
    14323 
    14324 > color zone #16 near #17 distance 4.58
    14325 
    14326 > color zone #16 near #17 distance 4.48
    14327 
    14328 > color zone #16 near #17 distance 4.38
    14329 
    14330 > color zone #16 near #17 distance 4.28
    14331 
    14332 > color zone #16 near #17 distance 4.18
    14333 
    14334 > color zone #16 near #17 distance 4.08
    14335 
    14336 > color zone #16 near #17 distance 3.98
    14337 
    14338 > color zone #16 near #17 distance 3.88
    14339 
    14340 > color zone #16 near #17 distance 3.78
    14341 
    14342 > color zone #16 near #17 distance 3.68
    14343 
    14344 > color zone #16 near #17 distance 3.58
    14345 
    14346 > color zone #16 near #17 distance 3.48
    14347 
    14348 > color zone #16 near #17 distance 3.38
    14349 
    14350 > color zone #16 near #17 distance 3.28
    14351 
    14352 > color sel white
    14353 
    14354 > select ::name="VIB"
    14355 
    14356 18 atoms, 19 bonds, 1 residue, 1 model selected 
    14357 
    14358 > color sel red
    14359 
    14360 > select add #16
    14361 
    14362 18 atoms, 19 bonds, 1 residue, 3 models selected 
    14363 
    14364 > select add #17
    14365 
    14366 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    14367 
    14368 > select subtract #17
    14369 
    14370 2 models selected 
    14371 
    14372 > color #16.1 white
    14373 
    14374 > color zone #16 near #17 distance 3.28
    14375 
    14376 > color zone #16 near #17 distance 3.18
    14377 
    14378 > color zone #16 near #17 distance 3.08
    14379 
    14380 > color zone #16 near #17 distance 2.98
    14381 
    14382 > color zone #16 near #17 distance 2.88
    14383 
    14384 > color zone #16 near #17 distance 2.98
    14385 
    14386 > color zone #16 near #17 distance 3.08
    14387 
    14388 > color zone #16 near #17 distance 3.18
    14389 
    14390 > color zone #16 near #17 distance 3.28
    14391 
    14392 > color zone #16 near #17 distance 3.38
    14393 
    14394 [Repeated 1 time(s)]
    14395 
    14396 > volume splitbyzone #16
    14397 
    14398 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    14399 level 0.0114, step 1, values float32 
    14400 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    14401 level 0.0114, step 1, values float32 
    14402 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    14403 level 0.0114, step 1, values float32 
    14404 
    14405 > close #18.1-2
    14406 
    14407 > color #18.3 yellow models
    14408 
    14409 > color #18.3 white models
    14410 
    14411 > color #18.3 #ffffb2ff models
    14412 
    14413 > color #18.3 #ffffb296 models
    14414 
    14415 > select add #17
    14416 
    14417 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    14418 
    14419 > select subtract #16
    14420 
    14421 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    14422 
    14423 > color #17 #6622bbff
    14424 
    14425 > color #17 #62be40ff
    14426 
    14427 > color (#!17 & sel) byhetero
    14428 
    14429 Drag select of 1 atoms, 1 bonds 
    14430 
    14431 > volume #18.3 level 0.006511
    14432 
    14433 > volume #18.3 level 0.01112
    14434 
    14435 > close #18#18.3
    14436 
    14437 > select add #17
    14438 
    14439 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    14440 
    14441 > color (#!17 & sel) white
    14442 
    14443 > select ::name="VIB"
    14444 
    14445 18 atoms, 19 bonds, 1 residue, 1 model selected 
    14446 
    14447 > color sel red
    14448 
    14449 > show #!16 models
    14450 
    14451 > color zone #16 near #17 distance 3.28
    14452 
    14453 > color zone #16 near #17 distance 3.18
    14454 
    14455 > color zone #16 near #17 distance 3.08
    14456 
    14457 > color zone #16 near #17 distance 2.98
    14458 
    14459 > color zone #16 near #17 distance 2.88
    14460 
    14461 > color zone #16 near #17 distance 2.78
    14462 
    14463 > color zone #16 near #17 distance 2.68
    14464 
    14465 > color zone #16 near #17 distance 2.58
    14466 
    14467 > color zone #16 near #17 distance 2.48
    14468 
    14469 > color zone #16 near #17 distance 2.38
    14470 
    14471 > color zone #16 near #17 distance 2.28
    14472 
    14473 > color zone #16 near #17 distance 2.18
    14474 
    14475 > color zone #16 near #17 distance 2.08
    14476 
    14477 > color zone #16 near #17 distance 1.98
    14478 
    14479 > color zone #16 near #17 distance 1.88
    14480 
    14481 > color zone #16 near #17 distance 1.78
    14482 
    14483 > color zone #16 near #17 distance 1.68
    14484 
    14485 > color zone #16 near #17 distance 1.78
    14486 
    14487 > color zone #16 near #17 distance 1.88
    14488 
    14489 > color zone #16 near #17 distance 1.98
    14490 
    14491 > color zone #16 near #17 distance 2.08
    14492 
    14493 > volume splitbyzone #16
    14494 
    14495 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    14496 level 0.0114, step 1, values float32 
    14497 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    14498 level 0.0114, step 1, values float32 
    14499 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    14500 level 0.0114, step 1, values float32 
    14501 
    14502 > close #18.1-2
    14503 
    14504 > color #18.3 white models
    14505 
    14506 > color #18.3 #ffffb2ff models
    14507 
    14508 > select add #18.3
    14509 
    14510 18 atoms, 19 bonds, 1 residue, 3 models selected 
    14511 
    14512 > color #18.3 #ffffb296 models
    14513 
    14514 > select subtract #18.3
    14515 
    14516 18 atoms, 19 bonds, 1 residue, 1 model selected 
    14517 
    14518 > select add #17
    14519 
    14520 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    14521 
    14522 > select subtract #17
    14523 
    14524 Nothing selected 
    14525 
    14526 > select add #17
    14527 
    14528 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    14529 
    14530 > color #17 #6622bbff
    14531 
    14532 > color #17 #62be40ff
    14533 
    14534 > color (#!17 & sel) byhetero
    14535 
    14536 > view
    14537 
    14538 > hide #!18.3 models
    14539 
    14540 > hide #!18 models
    14541 
    14542 > hide #!17 models
    14543 
    14544 > select subtract #17
    14545 
    14546 Nothing selected 
    14547 
    14548 > show #!1 models
    14549 
    14550 > open
    14551 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc
    14552 
    14553 Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown
    14554 at level 2.83e-06, step 2, values float32 
    14555 
    14556 > volume #19 step 1
    14557 
    14558 > volume #19 level 0.0131
    14559 
    14560 > select add #19
    14561 
    14562 2 models selected 
    14563 
    14564 > ui mousemode right "rotate selected models"
    14565 
    14566 > view matrix models
    14567 > #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04
    14568 
    14569 > ui mousemode right "translate selected models"
    14570 
    14571 > view matrix models
    14572 > #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801
    14573 
    14574 > view matrix models
    14575 > #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027
    14576 
    14577 > view matrix models
    14578 > #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593
    14579 
    14580 > rename #19 hOCT1-AZT.mrc
    14581 
    14582 > fitmap #19 inMap #16
    14583 
    14584 Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points 
    14585 correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07 
    14586 steps = 112, shift = 2.59, angle = 19.3 degrees 
    14587  
    14588 Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates: 
    14589 Matrix rotation and translation 
    14590 0.86934918 -0.02079803 -0.49376051 87.20318527 
    14591 -0.45396874 0.36123943 -0.81450504 253.58267245 
    14592 0.19530587 0.93224113 0.30460154 -57.13169181 
    14593 Axis 0.90642923 -0.35757337 -0.22478286 
    14594 Axis point 0.00000000 185.25380563 166.58335969 
    14595 Rotation angle (degrees) 74.47879004 
    14596 Shift along axis 1.21133072 
    14597  
    14598 
    14599 > open
    14600 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT-
    14601 > coot-2_real_space_refined_006.pdb
    14602 
    14603 Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20 
    14604 --- 
    14605 Chain | Description 
    14606 A | No description available 
    14607  
    14608 
    14609 > ui tool show Matchmaker
    14610 
    14611 > matchmaker #!20 to #5
    14612 
    14613 Parameters 
    14614 --- 
    14615 Chain pairing | bb 
    14616 Alignment algorithm | Needleman-Wunsch 
    14617 Similarity matrix | BLOSUM-62 
    14618 SS fraction | 0.3 
    14619 Gap open (HH/SS/other) | 18/18/6 
    14620 Gap extend | 1 
    14621 SS matrix |  |  | H | S | O 
    14622 ---|---|---|--- 
    14623 H | 6 | -9 | -6 
    14624 S |  | 6 | -6 
    14625 O |  |  | 4 
    14626 Iteration cutoff | 2 
    14627  
    14628 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT-
    14629 coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score =
    14630 1978 
    14631 RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs:
    14632 1.482) 
    14633  
    14634 
    14635 > hide #!1 models
    14636 
    14637 > color #19 white models
    14638 
    14639 > select add #20
    14640 
    14641 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected 
    14642 
    14643 > color #20 white
    14644 
    14645 > hide #!19 models
    14646 
    14647 > select subtract #19
    14648 
    14649 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    14650 
    14651 > select up
    14652 
    14653 2 atoms, 1 bond, 1 residue, 1 model selected 
    14654 
    14655 > select up
    14656 
    14657 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14658 
    14659 > color sel red
    14660 
    14661 > color zone #19 near #20 distance 4.98
    14662 
    14663 > show #!19 models
    14664 
    14665 > select add #19
    14666 
    14667 19 atoms, 20 bonds, 1 residue, 3 models selected 
    14668 
    14669 > select subtract #19
    14670 
    14671 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14672 
    14673 > color zone #19 near #20 distance 4.88
    14674 
    14675 > color zone #19 near #20 distance 4.78
    14676 
    14677 > color zone #19 near #20 distance 4.68
    14678 
    14679 > color zone #19 near #20 distance 4.58
    14680 
    14681 > color zone #19 near #20 distance 4.48
    14682 
    14683 > color zone #19 near #20 distance 4.38
    14684 
    14685 > color zone #19 near #20 distance 4.28
    14686 
    14687 > color zone #19 near #20 distance 4.18
    14688 
    14689 > color zone #19 near #20 distance 4.08
    14690 
    14691 > color zone #19 near #20 distance 3.98
    14692 
    14693 > color zone #19 near #20 distance 3.88
    14694 
    14695 > color zone #19 near #20 distance 3.78
    14696 
    14697 > color zone #19 near #20 distance 3.68
    14698 
    14699 > color zone #19 near #20 distance 3.58
    14700 
    14701 > color zone #19 near #20 distance 3.48
    14702 
    14703 > volume #19 level 0.01039
    14704 
    14705 > color zone #19 near #20 distance 3.38
    14706 
    14707 > color zone #19 near #20 distance 3.28
    14708 
    14709 > color zone #19 near #20 distance 3.18
    14710 
    14711 > color zone #19 near #20 distance 3.08
    14712 
    14713 > color zone #19 near #20 distance 2.98
    14714 
    14715 > color zone #19 near #20 distance 2.88
    14716 
    14717 > color zone #19 near #20 distance 2.78
    14718 
    14719 > color zone #19 near #20 distance 2.68
    14720 
    14721 > color zone #19 near #20 distance 2.58
    14722 
    14723 > color zone #19 near #20 distance 2.48
    14724 
    14725 > color zone #19 near #20 distance 2.38
    14726 
    14727 > color zone #19 near #20 distance 2.28
    14728 
    14729 > color zone #19 near #20 distance 2.18
    14730 
    14731 > color zone #19 near #20 distance 2.08
    14732 
    14733 > color zone #19 near #20 distance 1.98
    14734 
    14735 > color zone #19 near #20 distance 1.88
    14736 
    14737 > color zone #19 near #20 distance 1.78
    14738 
    14739 > color zone #19 near #20 distance 1.88
    14740 
    14741 > color zone #19 near #20 distance 1.98
    14742 
    14743 > color zone #19 near #20 distance 2.08
    14744 
    14745 [Repeated 1 time(s)]
    14746 
    14747 > volume splitbyzone #19
    14748 
    14749 Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at
    14750 level 0.0104, step 1, values float32 
    14751 Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at
    14752 level 0.0104, step 1, values float32 
    14753 Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at
    14754 level 0.0104, step 1, values float32 
    14755 
    14756 > close #21.1-2
    14757 
    14758 > select add #20
    14759 
    14760 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    14761 
    14762 > select subtract #20
    14763 
    14764 Nothing selected 
    14765 
    14766 > select add #20
    14767 
    14768 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    14769 
    14770 > color #20 #773333ff
    14771 
    14772 > color #20 #733551ff
    14773 
    14774 > color (#!20 & sel) byhetero
    14775 
    14776 > select clear
    14777 
    14778 > color #21.3 #ff000096 models
    14779 
    14780 > color #21.3 #ffffff96 models
    14781 
    14782 > color #21.3 #ffffb296 models
    14783 
    14784 > volume #21.3 level 0.008896
    14785 
    14786 > hide #!21.3 models
    14787 
    14788 > hide #!21 models
    14789 
    14790 > hide #!20 models
    14791 
    14792 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    14793 > density.cxs" includeMaps true
    14794 
    14795 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id:
    14796 35654939, major code: 40 (TranslateCoords), minor code: 0 
    14797 
    14798 > show #!3 models
    14799 
    14800 > show #!6.3 models
    14801 
    14802 > select ::name="ABC"
    14803 
    14804 42 atoms, 48 bonds, 2 residues, 1 model selected 
    14805 
    14806 > view sel
    14807 
    14808 > select clear
    14809 
    14810 > hide #!6.3 models
    14811 
    14812 > hide #!6 models
    14813 
    14814 > hide #!3 models
    14815 
    14816 > show #!2 models
    14817 
    14818 > show #!5 models
    14819 
    14820 > hide #!5 models
    14821 
    14822 > hide #!2 models
    14823 
    14824 > show #!8 models
    14825 
    14826 > show #!9.3 models
    14827 
    14828 > hide #!9.3 models
    14829 
    14830 > hide #!9 models
    14831 
    14832 > hide #!8 models
    14833 
    14834 > show #!11 models
    14835 
    14836 > show #!12.3 models
    14837 
    14838 > hide #!12.3 models
    14839 
    14840 > hide #!12 models
    14841 
    14842 > hide #!11 models
    14843 
    14844 > show #!14 models
    14845 
    14846 > show #!15 models
    14847 
    14848 > hide #!15 models
    14849 
    14850 > show #!15.3 models
    14851 
    14852 > hide #!14 models
    14853 
    14854 > hide #!15 models
    14855 
    14856 > hide #!15.3 models
    14857 
    14858 > show #!17 models
    14859 
    14860 > show #!18.3 models
    14861 
    14862 > hide #!18.3 models
    14863 
    14864 > hide #!18 models
    14865 
    14866 > hide #!17 models
    14867 
    14868 > show #!20 models
    14869 
    14870 > show #!21.3 models
    14871 
    14872 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    14873 > density.cxs" includeMaps true
    14874 
    14875 > save
    14876 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs
    14877 > includeMaps true
    14878 
    14879 [Repeated 1 time(s)]
    14880 
    14881 > close session
    14882 
    14883 > open
    14884 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot-
    14885 > history.scm
    14886 
    14887 Unrecognized file suffix '.scm' 
    14888 
    14889 > open
    14890 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
    14891 
    14892 Summary of feedback from opening
    14893 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif 
    14894 --- 
    14895 warnings | Skipping chem_comp category: Missing column 'type' near line 187 
    14896 Missing entity information. Treating each chain as a separate entity. 
    14897 Bad residue range for struct_conf "3" near line 98 
    14898 Bad residue range for struct_conf "4" near line 99 
    14899 Bad residue range for struct_conf "5" near line 100 
    14900 Bad residue range for struct_conf "6" near line 101 
    14901 Bad residue range for struct_conf "7" near line 102 
    14902 15 messages similar to the above omitted 
    14903 Invalid sheet range for struct_sheet_range "2 1" near line 183 
    14904 Invalid sheet range for struct_sheet_range "3 1" near line 184 
    14905 Invalid sheet range for struct_sheet_range "4 1" near line 186 
    14906 Missing or incomplete sequence information. Inferred polymer connectivity. 
    14907 Skipping chem_comp category: Missing column 'type' near line 4361 
    14908  
    14909 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1 
    14910 --- 
    14911 Chain | Description 
    14912 A | No description available 
    14913  
    14914 
    14915 > close session
    14916 
    14917 > open
    14918 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb
    14919 
    14920 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1 
    14921 --- 
    14922 Chain | Description 
    14923 A | No description available 
    14924  
    14925 
    14926 QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id:
    14927 35655077, major code: 40 (TranslateCoords), minor code: 0 
    14928 
    14929 > open
    14930 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc
    14931 
    14932 Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    14933 level 0.00421, step 2, values float32 
    14934 
    14935 > rename #2 rOAT1-AZT.mrc
    14936 
    14937 > volume #2 step 1
    14938 
    14939 > volume #2 level 0.01415
    14940 
    14941 > save
    14942 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    14943 > includeMaps true
    14944 
    14945 > select add #1
    14946 
    14947 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    14948 
    14949 > ui mousemode right "rotate selected models"
    14950 
    14951 > view matrix models
    14952 > #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07
    14953 
    14954 > ui mousemode right "translate selected models"
    14955 
    14956 > view matrix models
    14957 > #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5
    14958 
    14959 > ui mousemode right "rotate selected models"
    14960 
    14961 > view matrix models
    14962 > #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33
    14963 
    14964 > ui mousemode right "translate selected models"
    14965 
    14966 > view matrix models
    14967 > #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34
    14968 
    14969 > view matrix models
    14970 > #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41
    14971 
    14972 > ui tool show "Fit in Map"
    14973 
    14974 > fitmap #1 inMap #2
    14975 
    14976 Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map
    14977 rOAT1-AZT.mrc (#2) using 3905 atoms 
    14978 average map value = 0.01965, steps = 108 
    14979 shifted from previous position = 2.32 
    14980 rotated from previous position = 12.8 degrees 
    14981 atoms outside contour = 1436, contour level = 0.014154 
    14982  
    14983 Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to
    14984 rOAT1-AZT.mrc (#2) coordinates: 
    14985 Matrix rotation and translation 
    14986 -0.62427498 -0.78041245 -0.03517318 323.27181278 
    14987 -0.15760640 0.16991691 -0.97277359 257.26632447 
    14988 0.76514114 -0.60173470 -0.22907287 142.60270901 
    14989 Axis 0.34360458 -0.74113973 0.57675627 
    14990 Axis point 193.37147122 0.00000000 235.15956508 
    14991 Rotation angle (degrees) 147.32171525 
    14992 Shift along axis 2.65438788 
    14993  
    14994 
    14995 > select subtract #1
    14996 
    14997 Nothing selected 
    14998 
    14999 > select add #1
    15000 
    15001 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    15002 
    15003 > color sel white
    15004 
    15005 > select ::name="AZZ"
    15006 
    15007 19 atoms, 20 bonds, 1 residue, 1 model selected 
    15008 
    15009 > color sel red
    15010 
    15011 > ui tool show "Color Zone"
    15012 
    15013 > color zone #2 near #1 distance 4.98
    15014 
    15015 > volume #2 level 0.0105
    15016 
    15017 > color zone #2 near #1 distance 4.88
    15018 
    15019 > color zone #2 near #1 distance 4.78
    15020 
    15021 > color zone #2 near #1 distance 4.68
    15022 
    15023 > color zone #2 near #1 distance 4.58
    15024 
    15025 > color zone #2 near #1 distance 4.48
    15026 
    15027 > color zone #2 near #1 distance 4.38
    15028 
    15029 > color zone #2 near #1 distance 4.28
    15030 
    15031 > color zone #2 near #1 distance 4.18
    15032 
    15033 > color zone #2 near #1 distance 4.08
    15034 
    15035 > color zone #2 near #1 distance 3.98
    15036 
    15037 > color zone #2 near #1 distance 3.88
    15038 
    15039 > color zone #2 near #1 distance 3.78
    15040 
    15041 > color zone #2 near #1 distance 3.68
    15042 
    15043 > color zone #2 near #1 distance 3.58
    15044 
    15045 > color zone #2 near #1 distance 3.48
    15046 
    15047 > color zone #2 near #1 distance 3.38
    15048 
    15049 > color zone #2 near #1 distance 3.28
    15050 
    15051 > color zone #2 near #1 distance 3.18
    15052 
    15053 > color zone #2 near #1 distance 3.08
    15054 
    15055 > color zone #2 near #1 distance 2.98
    15056 
    15057 > color zone #2 near #1 distance 2.88
    15058 
    15059 > color zone #2 near #1 distance 2.78
    15060 
    15061 > color zone #2 near #1 distance 2.68
    15062 
    15063 > color zone #2 near #1 distance 2.58
    15064 
    15065 > color zone #2 near #1 distance 2.48
    15066 
    15067 > color zone #2 near #1 distance 2.38
    15068 
    15069 > color zone #2 near #1 distance 2.28
    15070 
    15071 > color zone #2 near #1 distance 2.18
    15072 
    15073 > color zone #2 near #1 distance 2.08
    15074 
    15075 > color zone #2 near #1 distance 1.98
    15076 
    15077 > color zone #2 near #1 distance 1.88
    15078 
    15079 > color zone #2 near #1 distance 1.78
    15080 
    15081 > volume #2 level 0.008069
    15082 
    15083 > volume splitbyzone #2
    15084 
    15085 Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at
    15086 level 0.00807, step 1, values float32 
    15087 Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at
    15088 level 0.00807, step 1, values float32 
    15089 Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    15090 level 0.00807, step 1, values float32 
    15091 
    15092 > close #3.1-2
    15093 
    15094 > color #3.3 white models
    15095 
    15096 > color #3.3 #ffffb2ff models
    15097 
    15098 > select add #1
    15099 
    15100 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    15101 
    15102 > color #1 #dd22bbff
    15103 
    15104 > color #1 tan
    15105 
    15106 > color sel byhetero
    15107 
    15108 > color #3.3 #ffffb296 models
    15109 
    15110 > save
    15111 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15112 > includeMaps true
    15113 
    15114 QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id:
    15115 35655128, major code: 40 (TranslateCoords), minor code: 0 
    15116 
    15117 QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id:
    15118 35655123, major code: 40 (TranslateCoords), minor code: 0 
    15119 
    15120 > save
    15121 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15122 > includeMaps true
    15123 
    15124 QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id:
    15125 35655133, major code: 40 (TranslateCoords), minor code: 0 
    15126 
    15127 > rename #1 rOAT1-AZT_IF.pdb
    15128 
    15129 > rename #2 rOAT1-AZT_IF.mrc
    15130 
    15131 > rename #3 "rOAT1-AZT_IF.mrc split"
    15132 
    15133 > rename #3.3 "rOAT1-AZT_IF.mrc 2"
    15134 
    15135 > save
    15136 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15137 > includeMaps true
    15138 
    15139 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id:
    15140 35655148, major code: 40 (TranslateCoords), minor code: 0 
    15141 
    15142 > open
    15143 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc
    15144 
    15145 Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    15146 level 0.00134, step 2, values float32 
    15147 
    15148 > close #4
    15149 
    15150 > open
    15151 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    15152 
    15153 Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    15154 level 0.00459, step 2, values float32 
    15155 
    15156 > volume #4 step 1
    15157 
    15158 > volume #4 level 0.01366
    15159 
    15160 > rename #4 rOAT1-AZT_OF.mrc
    15161 
    15162 > open
    15163 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    15164 > coot-7_real_space_refined_008.pdb
    15165 
    15166 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5 
    15167 --- 
    15168 Chain | Description 
    15169 A | No description available 
    15170  
    15171 
    15172 > select subtract #1
    15173 
    15174 Nothing selected 
    15175 
    15176 > select add #5
    15177 
    15178 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15179 
    15180 > hide #!3 models
    15181 
    15182 > hide #!3.3 models
    15183 
    15184 > hide #1 models
    15185 
    15186 > view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632
    15187 
    15188 > view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95
    15189 
    15190 > fitmap #5 inMap #4
    15191 
    15192 Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map
    15193 rOAT1-AZT_OF.mrc (#4) using 3792 atoms 
    15194 average map value = 0.01938, steps = 84 
    15195 shifted from previous position = 0.803 
    15196 rotated from previous position = 4.35 degrees 
    15197 atoms outside contour = 1323, contour level = 0.013659 
    15198  
    15199 Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to
    15200 rOAT1-AZT_OF.mrc (#4) coordinates: 
    15201 Matrix rotation and translation 
    15202 0.99822969 -0.04531644 -0.03852150 72.45731875 
    15203 0.04345449 0.99790785 -0.04787105 67.21065914 
    15204 0.04061025 0.04611237 0.99811044 61.32293455 
    15205 Axis 0.62004547 -0.52206316 0.58565662 
    15206 Axis point 0.00000000 -669.59173064 1932.22009801 
    15207 Rotation angle (degrees) 4.34647273 
    15208 Shift along axis 45.75280586 
    15209  
    15210 
    15211 > save
    15212 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb
    15213 > models #5 relModel #4
    15214 
    15215 > save
    15216 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb
    15217 > models #1
    15218 
    15219 > close #5
    15220 
    15221 > open
    15222 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    15223 
    15224 Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at
    15225 level 0.00459, step 2, values float32 
    15226 
    15227 > close #5
    15228 
    15229 > open
    15230 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF-
    15231 > coot-0_real_space_refined_003.pdb
    15232 
    15233 Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5 
    15234 --- 
    15235 Chain | Description 
    15236 A | No description available 
    15237  
    15238 
    15239 > select add #4
    15240 
    15241 2 models selected 
    15242 
    15243 > select subtract #4
    15244 
    15245 Nothing selected 
    15246 
    15247 > select add #5
    15248 
    15249 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15250 
    15251 > select clear
    15252 
    15253 > select add #5
    15254 
    15255 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15256 
    15257 > color #5 white
    15258 
    15259 > color #4 white models
    15260 
    15261 > color #2 white models
    15262 
    15263 > select #5/A:601@O4
    15264 
    15265 1 atom, 1 residue, 1 model selected 
    15266 
    15267 > select up
    15268 
    15269 19 atoms, 20 bonds, 1 residue, 1 model selected 
    15270 
    15271 > color sel red
    15272 
    15273 > color zone #4 near #5 distance 4.98
    15274 
    15275 > color zone #4 near #5 distance 4.88
    15276 
    15277 > color zone #4 near #5 distance 4.78
    15278 
    15279 > color zone #4 near #5 distance 4.68
    15280 
    15281 > color zone #4 near #5 distance 4.58
    15282 
    15283 > color zone #4 near #5 distance 4.48
    15284 
    15285 > color zone #4 near #5 distance 4.38
    15286 
    15287 > color zone #4 near #5 distance 4.28
    15288 
    15289 > color zone #4 near #5 distance 4.18
    15290 
    15291 > color zone #4 near #5 distance 4.08
    15292 
    15293 > color zone #4 near #5 distance 3.98
    15294 
    15295 > color zone #4 near #5 distance 3.88
    15296 
    15297 > color zone #4 near #5 distance 3.78
    15298 
    15299 > color zone #4 near #5 distance 3.68
    15300 
    15301 > color zone #4 near #5 distance 3.58
    15302 
    15303 > color zone #4 near #5 distance 3.48
    15304 
    15305 > color zone #4 near #5 distance 3.38
    15306 
    15307 > color zone #4 near #5 distance 3.28
    15308 
    15309 > color zone #4 near #5 distance 3.18
    15310 
    15311 > color zone #4 near #5 distance 3.08
    15312 
    15313 > color zone #4 near #5 distance 2.98
    15314 
    15315 > color zone #4 near #5 distance 2.88
    15316 
    15317 > color zone #4 near #5 distance 2.78
    15318 
    15319 > color zone #4 near #5 distance 2.68
    15320 
    15321 > color zone #4 near #5 distance 2.58
    15322 
    15323 > color zone #4 near #5 distance 2.48
    15324 
    15325 > color zone #4 near #5 distance 2.38
    15326 
    15327 > color zone #4 near #5 distance 2.28
    15328 
    15329 > color zone #4 near #5 distance 2.18
    15330 
    15331 > color zone #4 near #5 distance 2.08
    15332 
    15333 > color zone #4 near #5 distance 1.98
    15334 
    15335 > color zone #4 near #5 distance 1.88
    15336 
    15337 > color zone #4 near #5 distance 1.78
    15338 
    15339 > color zone #4 near #5 distance 1.68
    15340 
    15341 > color zone #4 near #5 distance 1.58
    15342 
    15343 > color zone #4 near #5 distance 1.48
    15344 
    15345 > color zone #4 near #5 distance 1.58
    15346 
    15347 > color zone #4 near #5 distance 1.68
    15348 
    15349 > color zone #4 near #5 distance 1.78
    15350 
    15351 > color zone #4 near #5 distance 1.88
    15352 
    15353 > volume splitbyzone #4
    15354 
    15355 Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at
    15356 level 0.0137, step 1, values float32 
    15357 Opened rOAT1-AZT_OF.mrc 1 as #6.2, grid size 320,320,320, pixel 0.83, shown at
    15358 level 0.0137, step 1, values float32 
    15359 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    15360 level 0.0137, step 1, values float32 
    15361 
    15362 > close #6.1-2
    15363 
    15364 > volume #6.3 level 0.0116
    15365 
    15366 > select add #5
    15367 
    15368 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15369 
    15370 > select subtract #5
    15371 
    15372 Nothing selected 
    15373 
    15374 > color #6.3 yellow models
    15375 
    15376 > color #6.3 white models
    15377 
    15378 > color #6.3 #ffffb2ff models
    15379 
    15380 > select add #5
    15381 
    15382 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15383 
    15384 > color #5 #ffaa88ff
    15385 
    15386 > color #5 salmon
    15387 
    15388 > color (#!5 & sel) byhetero
    15389 
    15390 > color #6.3 #ffffb296 models
    15391 
    15392 > select clear
    15393 
    15394 > save
    15395 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15396 > includeMaps true
    15397 
    15398 > show #!2 models
    15399 
    15400 > hide #!5 models
    15401 
    15402 > hide #!6 models
    15403 
    15404 > hide #!6.3 models
    15405 
    15406 > volume #2 level 0.01456
    15407 
    15408 > color #2 #a5a5a5ff models
    15409 
    15410 > open
    15411 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc
    15412 
    15413 Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    15414 level 0.00408, step 2, values float32 
    15415 
    15416 > rename #7 rOAT1-PBD_IF.mrc
    15417 
    15418 > volume #2 level 0.01983
    15419 
    15420 > volume #2 level 0.0151
    15421 
    15422 > hide #!7 models
    15423 
    15424 > volume #7 level 0.01185
    15425 
    15426 > volume #7 step 1
    15427 
    15428 > volume #7 level 0.01094
    15429 
    15430 > hide #!2 models
    15431 
    15432 > open
    15433 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD-
    15434 > coot-6.pdb
    15435 
    15436 Chain information for rOAT1-PBD-coot-6.pdb #8 
    15437 --- 
    15438 Chain | Description 
    15439 A | No description available 
    15440  
    15441 
    15442 > select add #8
    15443 
    15444 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    15445 
    15446 > ui mousemode right "translate selected models"
    15447 
    15448 > view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702
    15449 
    15450 > view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973
    15451 
    15452 > fitmap #8 inMap #7
    15453 
    15454 Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912
    15455 atoms 
    15456 average map value = 0.02737, steps = 56 
    15457 shifted from previous position = 2.6 
    15458 rotated from previous position = 0.396 degrees 
    15459 atoms outside contour = 571, contour level = 0.010939 
    15460  
    15461 Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7)
    15462 coordinates: 
    15463 Matrix rotation and translation 
    15464 0.99998387 0.00531886 -0.00199304 66.36205660 
    15465 -0.00532668 0.99997806 -0.00393867 67.06308709 
    15466 0.00197205 0.00394922 0.99999026 65.65327743 
    15467 Axis 0.57034742 -0.28670293 -0.76974363 
    15468 Axis point 10937.66555565 -15865.74627304 0.00000000 
    15469 Rotation angle (degrees) 0.39620277 
    15470 Shift along axis -31.91394767 
    15471  
    15472 
    15473 > rename #8 rOAT1-PBD_IF.pdb
    15474 
    15475 > save
    15476 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15477 > includeMaps true
    15478 
    15479 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id:
    15480 35655645, major code: 40 (TranslateCoords), minor code: 0 
    15481 
    15482 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id:
    15483 35655640, major code: 40 (TranslateCoords), minor code: 0 
    15484 
    15485 > color #8 white
    15486 
    15487 > hide #!7 models
    15488 
    15489 > select up
    15490 
    15491 2 atoms, 1 bond, 1 residue, 1 model selected 
    15492 
    15493 > select up
    15494 
    15495 19 atoms, 19 bonds, 1 residue, 1 model selected 
    15496 
    15497 > color sel red
    15498 
    15499 > show #!7 models
    15500 
    15501 > color zone #7 near #8 distance 4.98
    15502 
    15503 > color zone #7 near #8 distance 4.88
    15504 
    15505 > color zone #7 near #8 distance 4.78
    15506 
    15507 > color zone #7 near #8 distance 4.68
    15508 
    15509 > color zone #7 near #8 distance 4.58
    15510 
    15511 > color zone #7 near #8 distance 4.48
    15512 
    15513 > color zone #7 near #8 distance 4.38
    15514 
    15515 > color zone #7 near #8 distance 4.28
    15516 
    15517 > color zone #7 near #8 distance 4.18
    15518 
    15519 > color zone #7 near #8 distance 4.08
    15520 
    15521 > color zone #7 near #8 distance 3.98
    15522 
    15523 > color zone #7 near #8 distance 3.88
    15524 
    15525 > color zone #7 near #8 distance 3.78
    15526 
    15527 > color zone #7 near #8 distance 3.68
    15528 
    15529 > volume #7 level 0.02515
    15530 
    15531 > volume #7 level 0.01677
    15532 
    15533 > volume #7 level 0.0124
    15534 
    15535 > volume #7 level 0.01476
    15536 
    15537 > color zone #7 near #8 distance 3.58
    15538 
    15539 > color zone #7 near #8 distance 3.48
    15540 
    15541 > color zone #7 near #8 distance 3.38
    15542 
    15543 > color zone #7 near #8 distance 3.28
    15544 
    15545 > color zone #7 near #8 distance 3.18
    15546 
    15547 > color zone #7 near #8 distance 3.08
    15548 
    15549 > color zone #7 near #8 distance 2.98
    15550 
    15551 > color zone #7 near #8 distance 2.88
    15552 
    15553 > color zone #7 near #8 distance 2.78
    15554 
    15555 > color zone #7 near #8 distance 2.68
    15556 
    15557 > color zone #7 near #8 distance 2.58
    15558 
    15559 > color zone #7 near #8 distance 2.48
    15560 
    15561 > color zone #7 near #8 distance 2.38
    15562 
    15563 > color zone #7 near #8 distance 2.28
    15564 
    15565 > volume #7 level 0.01112
    15566 
    15567 > color zone #7 near #8 distance 2.18
    15568 
    15569 > color zone #7 near #8 distance 2.08
    15570 
    15571 > color zone #7 near #8 distance 1.98
    15572 
    15573 > color zone #7 near #8 distance 1.88
    15574 
    15575 > color zone #7 near #8 distance 1.98
    15576 
    15577 > color zone #7 near #8 distance 2.08
    15578 
    15579 > volume splitbyzone #7
    15580 
    15581 Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    15582 level 0.0111, step 1, values float32 
    15583 Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    15584 level 0.0111, step 1, values float32 
    15585 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    15586 level 0.0111, step 1, values float32 
    15587 
    15588 > close #9.1-2
    15589 
    15590 > color #9.3 #ff000096 models
    15591 
    15592 > color #9.3 #ffff0096 models
    15593 
    15594 > color #9.3 #ffffff96 models
    15595 
    15596 > color #9.3 #ffffb296 models
    15597 
    15598 > select add #8
    15599 
    15600 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    15601 
    15602 > color #8 #ffffddff
    15603 
    15604 > color #8 gold
    15605 
    15606 > select clear
    15607 
    15608 > select add #8
    15609 
    15610 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    15611 
    15612 > color sel byhetero
    15613 
    15614 > select clear
    15615 
    15616 > save
    15617 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15618 > includeMaps true
    15619 
    15620 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id:
    15621 35655670, major code: 40 (TranslateCoords), minor code: 0 
    15622 
    15623 > open
    15624 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc
    15625 
    15626 Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    15627 level 0.00409, step 2, values float32 
    15628 
    15629 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id:
    15630 35655680, major code: 40 (TranslateCoords), minor code: 0 
    15631 
    15632 > open
    15633 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF-
    15634 > coot-0.pdb
    15635 
    15636 Chain information for rOAT1-PBD_OF-coot-0.pdb #11 
    15637 --- 
    15638 Chain | Description 
    15639 A | No description available 
    15640  
    15641 
    15642 > hide #!9 models
    15643 
    15644 > hide #8 models
    15645 
    15646 > rename #10 rOAT1-PBD_OF
    15647 
    15648 > rename #10 rOAT1-PBD_OF.mrc
    15649 
    15650 > show #!2 models
    15651 
    15652 > volume #10 level 0.004712
    15653 
    15654 > volume #10 step 1
    15655 
    15656 > volume #10 level 0.01128
    15657 
    15658 > hide #!2 models
    15659 
    15660 > select add #11
    15661 
    15662 3872 atoms, 3966 bonds, 500 residues, 1 model selected 
    15663 
    15664 > view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035
    15665 
    15666 > view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073
    15667 
    15668 > view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386
    15669 
    15670 > fitmap #11 inMap #10
    15671 
    15672 Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using
    15673 3872 atoms 
    15674 average map value = 0.01531, steps = 56 
    15675 shifted from previous position = 2.42 
    15676 rotated from previous position = 0.764 degrees 
    15677 atoms outside contour = 1505, contour level = 0.011277 
    15678  
    15679 Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10)
    15680 coordinates: 
    15681 Matrix rotation and translation 
    15682 0.99995211 0.00939248 0.00274947 65.65298070 
    15683 -0.00936721 0.99991506 -0.00906240 67.47749964 
    15684 -0.00283436 0.00903621 0.99995516 65.83404461 
    15685 Axis 0.67891074 0.20945939 -0.70370943 
    15686 Axis point 6981.74049553 -6059.62250131 0.00000000 
    15687 Rotation angle (degrees) 0.76372650 
    15688 Shift along axis 12.37827175 
    15689  
    15690 
    15691 > show sel atoms
    15692 
    15693 > hide #!10 models
    15694 
    15695 > show #!10 models
    15696 
    15697 > open
    15698 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    15699 > coot-7_real_space_refined_008.pdb
    15700 
    15701 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12 
    15702 --- 
    15703 Chain | Description 
    15704 A | No description available 
    15705  
    15706 
    15707 > ui tool show Matchmaker
    15708 
    15709 > matchmaker #!12 to #11
    15710 
    15711 Parameters 
    15712 --- 
    15713 Chain pairing | bb 
    15714 Alignment algorithm | Needleman-Wunsch 
    15715 Similarity matrix | BLOSUM-62 
    15716 SS fraction | 0.3 
    15717 Gap open (HH/SS/other) | 18/18/6 
    15718 Gap extend | 1 
    15719 SS matrix |  |  | H | S | O 
    15720 ---|---|---|--- 
    15721 H | 6 | -9 | -6 
    15722 S |  | 6 | -6 
    15723 O |  |  | 4 
    15724 Iteration cutoff | 2 
    15725  
    15726 Matchmaker rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF-
    15727 coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score =
    15728 2423.1 
    15729 RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs:
    15730 1.080) 
    15731  
    15732 
    15733 > hide #11 models
    15734 
    15735 > select subtract #11
    15736 
    15737 Nothing selected 
    15738 
    15739 > show #11 models
    15740 
    15741 > hide #!12 models
    15742 
    15743 > hide #!10 models
    15744 
    15745 > show #!12 models
    15746 
    15747 > close #11
    15748 
    15749 > color #12 #bb4455ff
    15750 
    15751 > color #12 #b4503bff
    15752 
    15753 QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id:
    15754 35655708, major code: 40 (TranslateCoords), minor code: 0 
    15755 
    15756 > show #!10 models
    15757 
    15758 > save
    15759 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15760 > includeMaps true
    15761 
    15762 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id:
    15763 35655718, major code: 40 (TranslateCoords), minor code: 0 
    15764 
    15765 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id:
    15766 35655713, major code: 40 (TranslateCoords), minor code: 0 
    15767 
    15768 > color #10 #ffb2ff96 models
    15769 
    15770 > volume #10 level 0.009218
    15771 
    15772 > volume #10 level 0.008059
    15773 
    15774 > color #10 #ffb2ffff models
    15775 
    15776 > select add #12
    15777 
    15778 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15779 
    15780 > hide #!10 models
    15781 
    15782 > color #12 white
    15783 
    15784 > select clear
    15785 
    15786 > select #12/B:601@C11
    15787 
    15788 1 atom, 1 residue, 1 model selected 
    15789 
    15790 > select up
    15791 
    15792 37 atoms, 37 bonds, 1 residue, 1 model selected 
    15793 
    15794 > color sel red
    15795 
    15796 > color #10 white models
    15797 
    15798 > select add #10
    15799 
    15800 37 atoms, 37 bonds, 1 residue, 3 models selected 
    15801 
    15802 > select subtract #10
    15803 
    15804 37 atoms, 37 bonds, 1 residue, 1 model selected 
    15805 
    15806 > show #!10 models
    15807 
    15808 > color zone #10 near #12 distance 2
    15809 
    15810 > color zone #10 near #12 distance 1.9
    15811 
    15812 > color zone #10 near #12 distance 1.8
    15813 
    15814 > color zone #10 near #12 distance 1.7
    15815 
    15816 > color zone #10 near #12 distance 1.8
    15817 
    15818 > color zone #10 near #12 distance 1.9
    15819 
    15820 > color zone #10 near #12 distance 2
    15821 
    15822 [Repeated 1 time(s)]
    15823 
    15824 > volume splitbyzone #10
    15825 
    15826 Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown
    15827 at level 0.00806, step 1, values float32 
    15828 Opened rOAT1-PBD_OF.mrc 1 as #11.2, grid size 320,320,320, pixel 0.83, shown
    15829 at level 0.00806, step 1, values float32 
    15830 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    15831 at level 0.00806, step 1, values float32 
    15832 
    15833 > volume splitbyzone #10
    15834 
    15835 Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown
    15836 at level 0.00806, step 1, values float32 
    15837 Opened rOAT1-PBD_OF.mrc 1 as #13.2, grid size 320,320,320, pixel 0.83, shown
    15838 at level 0.00806, step 1, values float32 
    15839 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    15840 at level 0.00806, step 1, values float32 
    15841 
    15842 > close #11.1-2
    15843 
    15844 > hide #!12 models
    15845 
    15846 > hide #!11.3 models
    15847 
    15848 > hide #!11 models
    15849 
    15850 > select add #12
    15851 
    15852 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15853 
    15854 > select subtract #12
    15855 
    15856 Nothing selected 
    15857 
    15858 > close #13.1-2
    15859 
    15860 > show #!12 models
    15861 
    15862 > color #11.3 white models
    15863 
    15864 > color #11.3 #ffffb2ff models
    15865 
    15866 > color #13.3 white models
    15867 
    15868 > color #13.3 #ffffb2ff models
    15869 
    15870 > select add #12
    15871 
    15872 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15873 
    15874 > color #12 #bb4455ff
    15875 
    15876 > color #12 #b4503bff
    15877 
    15878 > color (#!12 & sel) byhetero
    15879 
    15880 > select #12/A:440
    15881 
    15882 6 atoms, 5 bonds, 1 residue, 1 model selected 
    15883 
    15884 > select add #12
    15885 
    15886 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    15887 
    15888 > select subtract #12
    15889 
    15890 Nothing selected 
    15891 
    15892 > save
    15893 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    15894 > includeMaps true
    15895 
    15896 > hide #!13 models
    15897 
    15898 > hide #!13.3 models
    15899 
    15900 > hide #!12 models
    15901 
    15902 > open
    15903 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc
    15904 
    15905 Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    15906 level 0.00408, step 2, values float32 
    15907 
    15908 QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id:
    15909 35655778, major code: 40 (TranslateCoords), minor code: 0 
    15910 
    15911 > show #!2 models
    15912 
    15913 > hide #!2 models
    15914 
    15915 > rename #14 rOAT1-TFV_IF.mrc
    15916 
    15917 > show #1 models
    15918 
    15919 > hide #!14 models
    15920 
    15921 > save
    15922 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb
    15923 > models #1 relModel #14
    15924 
    15925 > open
    15926 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF-
    15927 > coot-2_real_space_refined_005.pdb
    15928 
    15929 Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15 
    15930 --- 
    15931 Chain | Description 
    15932 A | No description available 
    15933  
    15934 
    15935 > hide #1 models
    15936 
    15937 > show #!14 models
    15938 
    15939 > color #15 white
    15940 
    15941 > color #14 white models
    15942 
    15943 > select ::name="TFV"
    15944 
    15945 31 atoms, 32 bonds, 1 residue, 1 model selected 
    15946 
    15947 > color sel red
    15948 
    15949 > color zone #14 near #15 distance 4.68
    15950 
    15951 > color zone #14 near #15 distance 4.58
    15952 
    15953 > color zone #14 near #15 distance 4.48
    15954 
    15955 > color zone #14 near #15 distance 4.38
    15956 
    15957 > color zone #14 near #15 distance 4.28
    15958 
    15959 > color zone #14 near #15 distance 4.18
    15960 
    15961 > color zone #14 near #15 distance 4.08
    15962 
    15963 > color zone #14 near #15 distance 3.98
    15964 
    15965 > color zone #14 near #15 distance 3.88
    15966 
    15967 > color zone #14 near #15 distance 3.78
    15968 
    15969 > color zone #14 near #15 distance 3.68
    15970 
    15971 > color zone #14 near #15 distance 3.58
    15972 
    15973 > color zone #14 near #15 distance 3.48
    15974 
    15975 > color zone #14 near #15 distance 3.38
    15976 
    15977 > color zone #14 near #15 distance 3.28
    15978 
    15979 > color zone #14 near #15 distance 3.18
    15980 
    15981 > color zone #14 near #15 distance 3.08
    15982 
    15983 > color zone #14 near #15 distance 2.98
    15984 
    15985 > color zone #14 near #15 distance 2.88
    15986 
    15987 > color zone #14 near #15 distance 2.78
    15988 
    15989 > color zone #14 near #15 distance 2.68
    15990 
    15991 > volume #14 level 0.007613
    15992 
    15993 > color zone #14 near #15 distance 2.78
    15994 
    15995 > color zone #14 near #15 distance 2.88
    15996 
    15997 > color zone #14 near #15 distance 2.98
    15998 
    15999 > color zone #14 near #15 distance 2.88
    16000 
    16001 > color zone #14 near #15 distance 2.78
    16002 
    16003 > color zone #14 near #15 distance 2.68
    16004 
    16005 > color zone #14 near #15 distance 2.58
    16006 
    16007 > color zone #14 near #15 distance 2.48
    16008 
    16009 > color zone #14 near #15 distance 2.38
    16010 
    16011 > volume #14 level 0.005915
    16012 
    16013 > volume #14 level 0.005632
    16014 
    16015 > volume splitbyzone #14
    16016 
    16017 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    16018 at level 0.00563, step 1, values float32 
    16019 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    16020 at level 0.00563, step 1, values float32 
    16021 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    16022 at level 0.00563, step 1, values float32 
    16023 
    16024 > close #16.1-2
    16025 
    16026 > color zone #14 near #15 distance 2.09
    16027 
    16028 > close #16#16.3
    16029 
    16030 > show #!14 models
    16031 
    16032 > color zone #14 near #15 distance 1.99
    16033 
    16034 > color zone #14 near #15 distance 2.09
    16035 
    16036 > color zone #14 near #15 distance 2.19
    16037 
    16038 > color zone #14 near #15 distance 2.29
    16039 
    16040 > color zone #14 near #15 distance 2.39
    16041 
    16042 > color zone #14 near #15 distance 2.29
    16043 
    16044 > volume splitbyzone #14
    16045 
    16046 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    16047 at level 0.00563, step 1, values float32 
    16048 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    16049 at level 0.00563, step 1, values float32 
    16050 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    16051 at level 0.00563, step 1, values float32 
    16052 
    16053 > close #16.1-2
    16054 
    16055 > select add #15
    16056 
    16057 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    16058 
    16059 > color #16.3 #ff5500ff models
    16060 
    16061 > color #16.3 #aa0000ff models
    16062 
    16063 > color #16.3 #ff5500ff models
    16064 
    16065 > color #16.3 #ff557fff models
    16066 
    16067 > color #15 #ff557fff
    16068 
    16069 > color #16.3 white models
    16070 
    16071 > color #16.3 #ffffb2ff models
    16072 
    16073 > color #16.3 #ffffb296 models
    16074 
    16075 > open
    16076 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    16077 > coot-3.pdb
    16078 
    16079 Chain information for rOAT1-TFV_IF-coot-3.pdb #17 
    16080 --- 
    16081 Chain | Description 
    16082 A | No description available 
    16083  
    16084 
    16085 > close #17#16#16.3
    16086 
    16087 > close #15
    16088 
    16089 > open
    16090 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    16091 > coot-3.pdb
    16092 
    16093 Chain information for rOAT1-TFV_IF-coot-3.pdb #15 
    16094 --- 
    16095 Chain | Description 
    16096 A | No description available 
    16097  
    16098 
    16099 QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id:
    16100 35656402, major code: 40 (TranslateCoords), minor code: 0 
    16101 
    16102 > show #!14 models
    16103 
    16104 > select add #15
    16105 
    16106 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    16107 
    16108 > select subtract #15
    16109 
    16110 Nothing selected 
    16111 
    16112 > select add #15
    16113 
    16114 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    16115 
    16116 > color #15 white
    16117 
    16118 > color zone #14 near #15 distance 2.29
    16119 
    16120 > select ::name="TFV"
    16121 
    16122 31 atoms, 32 bonds, 1 residue, 1 model selected 
    16123 
    16124 > color sel red
    16125 
    16126 > color zone #14 near #15 distance 2.29
    16127 
    16128 > color zone #14 near #15 distance 2.19
    16129 
    16130 > color zone #14 near #15 distance 2.09
    16131 
    16132 > color zone #14 near #15 distance 1.99
    16133 
    16134 > color zone #14 near #15 distance 1.89
    16135 
    16136 > color zone #14 near #15 distance 1.79
    16137 
    16138 > color zone #14 near #15 distance 1.69
    16139 
    16140 > color zone #14 near #15 distance 1.59
    16141 
    16142 > color zone #14 near #15 distance 1.49
    16143 
    16144 > color zone #14 near #15 distance 1.39
    16145 
    16146 > color zone #14 near #15 distance 1.29
    16147 
    16148 > color zone #14 near #15 distance 1.19
    16149 
    16150 > color zone #14 near #15 distance 1.09
    16151 
    16152 > color zone #14 near #15 distance 1.19
    16153 
    16154 > color zone #14 near #15 distance 1.29
    16155 
    16156 > color zone #14 near #15 distance 1.39
    16157 
    16158 > color zone #14 near #15 distance 1.49
    16159 
    16160 > color zone #14 near #15 distance 1.59
    16161 
    16162 > color zone #14 near #15 distance 1.69
    16163 
    16164 > color zone #14 near #15 distance 1.79
    16165 
    16166 > color zone #14 near #15 distance 1.89
    16167 
    16168 > color zone #14 near #15 distance 1.99
    16169 
    16170 > color zone #14 near #15 distance 2.09
    16171 
    16172 [Repeated 1 time(s)]
    16173 
    16174 > volume splitbyzone #14
    16175 
    16176 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    16177 at level 0.00563, step 1, values float32 
    16178 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    16179 at level 0.00563, step 1, values float32 
    16180 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    16181 at level 0.00563, step 1, values float32 
    16182 
    16183 > close #16.1-2
    16184 
    16185 > color #16.3 white models
    16186 
    16187 > color #16.3 #ffffb2ff models
    16188 
    16189 > color #16.3 #ffffb296 models
    16190 
    16191 > color #15 #ff5500ff
    16192 
    16193 > color #15 #ff557fff
    16194 
    16195 > select add #15
    16196 
    16197 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    16198 
    16199 > color sel byhetero
    16200 
    16201 > select clear
    16202 
    16203 > save
    16204 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    16205 > includeMaps true
    16206 
    16207 > open
    16208 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc
    16209 
    16210 Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    16211 level 0.00401, step 2, values float32 
    16212 
    16213 > rename #17 rOAT1-TVF_OF.mrc
    16214 
    16215 > hide #15 models
    16216 
    16217 > hide #!16 models
    16218 
    16219 > show #8 models
    16220 
    16221 > hide #8 models
    16222 
    16223 > show #!11.3 models
    16224 
    16225 > hide #!11 models
    16226 
    16227 > hide #!11.3 models
    16228 
    16229 > show #!12 models
    16230 
    16231 > volume #17 step 1
    16232 
    16233 > volume #17 level 0.01305
    16234 
    16235 > save
    16236 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    16237 > models #12 relModel #17
    16238 
    16239 > hide #!16.3 models
    16240 
    16241 > hide #!12 models
    16242 
    16243 > open
    16244 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    16245 
    16246 Chain information for rOAT1-TFV_OF.pdb #18 
    16247 --- 
    16248 Chain | Description 
    16249 A | No description available 
    16250  
    16251 
    16252 > save
    16253 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    16254 > includeMaps true
    16255 
    16256 > close #18
    16257 
    16258 > open
    16259 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF-
    16260 > coot-1_real_space_refined_007.pdb
    16261 
    16262 Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18 
    16263 --- 
    16264 Chain | Description 
    16265 A | No description available 
    16266  
    16267 
    16268 > select add #18
    16269 
    16270 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    16271 
    16272 > color #18 white
    16273 
    16274 > color #17 white models
    16275 
    16276 > select #18/A:601@H131
    16277 
    16278 1 atom, 1 residue, 1 model selected 
    16279 
    16280 > select up
    16281 
    16282 31 atoms, 32 bonds, 1 residue, 1 model selected 
    16283 
    16284 > color sel red
    16285 
    16286 > volume #17 level 0.011
    16287 
    16288 > color zone #17 near #18 distance 4.98
    16289 
    16290 > color zone #17 near #18 distance 4.88
    16291 
    16292 > color zone #17 near #18 distance 4.78
    16293 
    16294 > color zone #17 near #18 distance 4.68
    16295 
    16296 > color zone #17 near #18 distance 4.58
    16297 
    16298 > color zone #17 near #18 distance 4.48
    16299 
    16300 > color zone #17 near #18 distance 4.38
    16301 
    16302 > color zone #17 near #18 distance 4.28
    16303 
    16304 > color zone #17 near #18 distance 4.18
    16305 
    16306 > color zone #17 near #18 distance 4.08
    16307 
    16308 > color zone #17 near #18 distance 3.98
    16309 
    16310 > color zone #17 near #18 distance 3.88
    16311 
    16312 > color zone #17 near #18 distance 3.78
    16313 
    16314 > color zone #17 near #18 distance 3.68
    16315 
    16316 > color zone #17 near #18 distance 3.58
    16317 
    16318 > color zone #17 near #18 distance 3.48
    16319 
    16320 > color zone #17 near #18 distance 3.38
    16321 
    16322 > color zone #17 near #18 distance 3.28
    16323 
    16324 > color zone #17 near #18 distance 3.18
    16325 
    16326 > color zone #17 near #18 distance 3.08
    16327 
    16328 > color zone #17 near #18 distance 2.98
    16329 
    16330 > volume splitbyzone #17
    16331 
    16332 Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
    16333 at level 0.011, step 1, values float32 
    16334 Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
    16335 at level 0.011, step 1, values float32 
    16336 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    16337 at level 0.011, step 1, values float32 
    16338 
    16339 > close #19.1-2
    16340 
    16341 > color #19.3 white models
    16342 
    16343 > color #19.3 #ffffb2ff models
    16344 
    16345 > select add #18
    16346 
    16347 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    16348 
    16349 > color #18 #337744ff
    16350 
    16351 > color #18 #374c02ff
    16352 
    16353 > color (#!18 & sel) byhetero
    16354 
    16355 > select clear
    16356 
    16357 > color #19.3 #ffffb296 models
    16358 
    16359 > save
    16360 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    16361 > includeMaps true
    16362 
    16363 > open
    16364 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc
    16365 
    16366 Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    16367 level 0.00494, step 2, values float32 
    16368 
    16369 > volume #20 step 1
    16370 
    16371 > hide #!19 models
    16372 
    16373 > hide #!18 models
    16374 
    16375 > rename #20 rOAT1-AAI_IF.mrc
    16376 
    16377 > volume #20 level 0.0194
    16378 
    16379 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id:
    16380 35656688, major code: 40 (TranslateCoords), minor code: 0 
    16381 
    16382 > show #!2 models
    16383 
    16384 > hide #!2 models
    16385 
    16386 > show #1 models
    16387 
    16388 > save
    16389 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    16390 > models #1 relModel #20
    16391 
    16392 > hide #1 models
    16393 
    16394 > open
    16395 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    16396 
    16397 Chain information for rOAT1-AAI_IF.pdb #21 
    16398 --- 
    16399 Chain | Description 
    16400 A | No description available 
    16401  
    16402 
    16403 > close #21
    16404 
    16405 > open
    16406 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb
    16407 
    16408 Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21 
    16409 --- 
    16410 Chain | Description 
    16411 A | No description available 
    16412  
    16413 
    16414 QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id:
    16415 35656914, major code: 40 (TranslateCoords), minor code: 0 
    16416 
    16417 > close #21
    16418 
    16419 > open
    16420 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    16421 > coot-1_real_space_refined_003_initial.geo
    16422 
    16423 Unrecognized file suffix '.geo' 
    16424 
    16425 > open
    16426 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    16427 > coot-1_real_space_refined_003.pdb
    16428 
    16429 Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21 
    16430 --- 
    16431 Chain | Description 
    16432 A | No description available 
    16433  
    16434 
    16435 QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id:
    16436 35657106, major code: 40 (TranslateCoords), minor code: 0 
    16437 
    16438 > select add #21
    16439 
    16440 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    16441 
    16442 > color #21 white
    16443 
    16444 > color #20 white models
    16445 
    16446 > select clear
    16447 
    16448 > select #21/A:602@O24
    16449 
    16450 1 atom, 1 residue, 1 model selected 
    16451 
    16452 > select up
    16453 
    16454 35 atoms, 38 bonds, 1 residue, 1 model selected 
    16455 
    16456 > select #21/A:601@O20
    16457 
    16458 1 atom, 1 residue, 1 model selected 
    16459 
    16460 > select add #21/A:602@C23
    16461 
    16462 2 atoms, 2 residues, 1 model selected 
    16463 
    16464 > select up
    16465 
    16466 70 atoms, 76 bonds, 2 residues, 1 model selected 
    16467 
    16468 > color sel red
    16469 
    16470 > color zone #20 near #21 distance 4.98
    16471 
    16472 > color zone #20 near #21 distance 4.88
    16473 
    16474 > color zone #20 near #21 distance 4.78
    16475 
    16476 > color zone #20 near #21 distance 4.68
    16477 
    16478 > color zone #20 near #21 distance 4.58
    16479 
    16480 > color zone #20 near #21 distance 4.48
    16481 
    16482 > color zone #20 near #21 distance 4.38
    16483 
    16484 > color zone #20 near #21 distance 4.28
    16485 
    16486 > color zone #20 near #21 distance 4.18
    16487 
    16488 > color zone #20 near #21 distance 4.08
    16489 
    16490 > color zone #20 near #21 distance 3.98
    16491 
    16492 > color zone #20 near #21 distance 3.88
    16493 
    16494 > color zone #20 near #21 distance 3.78
    16495 
    16496 > color zone #20 near #21 distance 3.68
    16497 
    16498 > color zone #20 near #21 distance 3.58
    16499 
    16500 > color zone #20 near #21 distance 3.48
    16501 
    16502 > color zone #20 near #21 distance 3.38
    16503 
    16504 > color zone #20 near #21 distance 3.28
    16505 
    16506 > color zone #20 near #21 distance 3.18
    16507 
    16508 > color zone #20 near #21 distance 3.08
    16509 
    16510 > color zone #20 near #21 distance 2.98
    16511 
    16512 > color zone #20 near #21 distance 2.88
    16513 
    16514 > volume splitbyzone #20
    16515 
    16516 Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown
    16517 at level 0.0194, step 1, values float32 
    16518 Opened rOAT1-AAI_IF.mrc 1 as #22.2, grid size 320,320,320, pixel 0.83, shown
    16519 at level 0.0194, step 1, values float32 
    16520 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    16521 at level 0.0194, step 1, values float32 
    16522 
    16523 > close #22.1-2
    16524 
    16525 > color #22.3 yellow models
    16526 
    16527 > color #22.3 white models
    16528 
    16529 > color #22.3 #ffffb2ff models
    16530 
    16531 > color #22.3 #ffffb296 models
    16532 
    16533 > select add #21
    16534 
    16535 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    16536 
    16537 > color #21 #668855ff
    16538 
    16539 > color #21 #685d73ff
    16540 
    16541 > color sel byhetero
    16542 
    16543 > select clear
    16544 
    16545 [Repeated 1 time(s)]
    16546 
    16547 > save
    16548 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    16549 > includeMaps true
    16550 
    16551 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id:
    16552 35657141, major code: 40 (TranslateCoords), minor code: 0 
    16553 
    16554 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id:
    16555 35657136, major code: 40 (TranslateCoords), minor code: 0 
    16556 
    16557 > hide #!22.3 models
    16558 
    16559 > hide #!22 models
    16560 
    16561 > hide #21 models
    16562 
    16563 > open
    16564 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc
    16565 
    16566 Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    16567 level 0.00494, step 2, values float32 
    16568 
    16569 > volume #23 level 0.01307
    16570 
    16571 > volume #23 step 1
    16572 
    16573 > volume #23 level 0.01684
    16574 
    16575 > show #1 models
    16576 
    16577 > hide #1 models
    16578 
    16579 > show #!5 models
    16580 
    16581 > rename #23 rOAT1-AAI_OF.mrc
    16582 
    16583 > save
    16584 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb
    16585 > models #5 relModel #23
    16586 
    16587 > open
    16588 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF-
    16589 > coot-1_real_space_refined_004.pdb
    16590 
    16591 Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24 
    16592 --- 
    16593 Chain | Description 
    16594 A | No description available 
    16595  
    16596 
    16597 > color #23 white models
    16598 
    16599 > color #24 white
    16600 
    16601 > hide #!5 models
    16602 
    16603 > select add #24/A:601@O24
    16604 
    16605 1 atom, 1 residue, 1 model selected 
    16606 
    16607 > select add #24/A:230@OH
    16608 
    16609 2 atoms, 2 residues, 1 model selected 
    16610 
    16611 > select clear
    16612 
    16613 > select add #24/A:601@O24
    16614 
    16615 1 atom, 1 residue, 1 model selected 
    16616 
    16617 > select up
    16618 
    16619 35 atoms, 38 bonds, 1 residue, 1 model selected 
    16620 
    16621 > color sel red
    16622 
    16623 > color zone #23 near #24 distance 4.98
    16624 
    16625 > volume splitbyzone #23
    16626 
    16627 Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown
    16628 at level 0.0168, step 1, values float32 
    16629 Opened rOAT1-AAI_OF.mrc 1 as #25.2, grid size 320,320,320, pixel 0.83, shown
    16630 at level 0.0168, step 1, values float32 
    16631 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    16632 at level 0.0168, step 1, values float32 
    16633 
    16634 > close #25.1-2
    16635 
    16636 > select add #24
    16637 
    16638 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    16639 
    16640 > select subtract #24
    16641 
    16642 Nothing selected 
    16643 
    16644 > color #25.3 white models
    16645 
    16646 > color #25.3 #ffffb2ff models
    16647 
    16648 > select add #24
    16649 
    16650 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    16651 
    16652 > color #24 #1177ccff
    16653 
    16654 > color #24 #17c127ff
    16655 
    16656 > color (#!24 & sel) byhetero
    16657 
    16658 > select #24/A:438@CE2
    16659 
    16660 1 atom, 1 residue, 1 model selected 
    16661 Drag select of 1 atoms, 1 bonds 
    16662 
    16663 > select clear
    16664 
    16665 > color #25.3 #ffffb296 models
    16666 
    16667 > select clear
    16668 
    16669 > save
    16670 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    16671 > includeMaps true
    16672 
    16673 > open
    16674 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH-
    16675 > coot-7_real_space_refined_007.pdb
    16676 
    16677 Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26 
    16678 --- 
    16679 Chain | Description 
    16680 A | No description available 
    16681  
    16682 
    16683 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id:
    16684 35657291, major code: 40 (TranslateCoords), minor code: 0 
    16685 
    16686 > open
    16687 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc
    16688 
    16689 Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160,
    16690 pixel 0.83, shown at level 0.134, step 1, values float32 
    16691 
    16692 > hide #!24 models
    16693 
    16694 > hide #!25.3 models
    16695 
    16696 > hide #!25 models
    16697 
    16698 > view
    16699 
    16700 > show #!2 models
    16701 
    16702 > select add #26
    16703 
    16704 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    16705 
    16706 > select add #27
    16707 
    16708 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected 
    16709 
    16710 > view matrix models
    16711 > #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865
    16712 
    16713 > view matrix models
    16714 > #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563
    16715 
    16716 > rename #27 rOAT1-PAH
    16717 
    16718 > rename #27 rOAT1-PAH.mrc
    16719 
    16720 > view
    16721 
    16722 > fitmap #26 inMap #27
    16723 
    16724 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    16725 rOAT1-PAH.mrc (#27) using 3865 atoms 
    16726 average map value = 0.3441, steps = 44 
    16727 shifted from previous position = 0.0131 
    16728 rotated from previous position = 0.0158 degrees 
    16729 atoms outside contour = 699, contour level = 0.13428 
    16730  
    16731 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    16732 rOAT1-PAH.mrc (#27) coordinates: 
    16733 Matrix rotation and translation 
    16734 0.99999996 -0.00021122 0.00016567 0.00535685 
    16735 0.00021123 0.99999998 -0.00006568 0.00053709 
    16736 -0.00016566 0.00006571 0.99999998 -0.00148379 
    16737 Axis 0.23771757 0.59945172 0.76429575 
    16738 Axis point -1.23064203 24.84299856 0.00000000 
    16739 Rotation angle (degrees) 0.01583428 
    16740 Shift along axis 0.00046132 
    16741  
    16742 
    16743 > hide #!2 models
    16744 
    16745 > color #27 white models
    16746 
    16747 > color #26 white
    16748 
    16749 > hide #!26 models
    16750 
    16751 > select subtract #27
    16752 
    16753 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    16754 
    16755 > select subtract #26
    16756 
    16757 Nothing selected 
    16758 
    16759 > hide #!27 models
    16760 
    16761 > show #!26 models
    16762 
    16763 > select #26/B:601@C07
    16764 
    16765 1 atom, 1 residue, 1 model selected 
    16766 
    16767 > select up
    16768 
    16769 23 atoms, 23 bonds, 1 residue, 1 model selected 
    16770 
    16771 > color sel red
    16772 
    16773 > show #!27 models
    16774 
    16775 > color zone #27 near #26 distance 4.98
    16776 
    16777 > color zone #27 near #26 distance 4.88
    16778 
    16779 > color zone #27 near #26 distance 4.78
    16780 
    16781 > color zone #27 near #26 distance 4.68
    16782 
    16783 > color zone #27 near #26 distance 4.58
    16784 
    16785 > color zone #27 near #26 distance 4.48
    16786 
    16787 > color zone #27 near #26 distance 4.38
    16788 
    16789 > color zone #27 near #26 distance 4.28
    16790 
    16791 > color zone #27 near #26 distance 4.18
    16792 
    16793 > color zone #27 near #26 distance 4.08
    16794 
    16795 > color zone #27 near #26 distance 3.98
    16796 
    16797 > color zone #27 near #26 distance 3.88
    16798 
    16799 > color zone #27 near #26 distance 3.78
    16800 
    16801 > color zone #27 near #26 distance 3.68
    16802 
    16803 > color zone #27 near #26 distance 3.58
    16804 
    16805 > color zone #27 near #26 distance 3.48
    16806 
    16807 > color zone #27 near #26 distance 3.38
    16808 
    16809 > color zone #27 near #26 distance 3.28
    16810 
    16811 > color zone #27 near #26 distance 3.18
    16812 
    16813 > color zone #27 near #26 distance 3.08
    16814 
    16815 > color zone #27 near #26 distance 2.98
    16816 
    16817 > color zone #27 near #26 distance 2.88
    16818 
    16819 > color zone #27 near #26 distance 2.78
    16820 
    16821 > color zone #27 near #26 distance 2.68
    16822 
    16823 > color zone #27 near #26 distance 2.58
    16824 
    16825 > color zone #27 near #26 distance 2.48
    16826 
    16827 > color zone #27 near #26 distance 2.38
    16828 
    16829 > color zone #27 near #26 distance 2.28
    16830 
    16831 > volume #27 level 0.1207
    16832 
    16833 > color zone #27 near #26 distance 2.18
    16834 
    16835 > color zone #27 near #26 distance 2.08
    16836 
    16837 > hide #!27 models
    16838 
    16839 > show #!27 models
    16840 
    16841 > fitmap #26 inMap #27
    16842 
    16843 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    16844 rOAT1-PAH.mrc (#27) using 3865 atoms 
    16845 average map value = 0.3441, steps = 44 
    16846 shifted from previous position = 0.00509 
    16847 rotated from previous position = 0.0145 degrees 
    16848 atoms outside contour = 605, contour level = 0.12073 
    16849  
    16850 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    16851 rOAT1-PAH.mrc (#27) coordinates: 
    16852 Matrix rotation and translation 
    16853 1.00000000 -0.00003177 0.00004592 0.00408484 
    16854 0.00003177 1.00000000 0.00006809 -0.00110606 
    16855 -0.00004592 -0.00006809 1.00000000 0.00040828 
    16856 Axis -0.77323345 0.52146975 0.36080373 
    16857 Axis point 0.00000000 25.00840435 -11.23310139 
    16858 Rotation angle (degrees) 0.00504562 
    16859 Shift along axis -0.00358800 
    16860  
    16861 
    16862 > fitmap #26 inMap #27
    16863 
    16864 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    16865 rOAT1-PAH.mrc (#27) using 3865 atoms 
    16866 average map value = 0.3441, steps = 40 
    16867 shifted from previous position = 0.0153 
    16868 rotated from previous position = 0.0197 degrees 
    16869 atoms outside contour = 607, contour level = 0.12073 
    16870  
    16871 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    16872 rOAT1-PAH.mrc (#27) coordinates: 
    16873 Matrix rotation and translation 
    16874 0.99999998 -0.00017402 -0.00004728 0.01145050 
    16875 0.00017401 0.99999996 -0.00023139 -0.00012574 
    16876 0.00004732 0.00023138 0.99999997 -0.01696563 
    16877 Axis 0.78875519 -0.16123857 0.59318410 
    16878 Axis point 0.00000000 70.72803400 -1.26127659 
    16879 Rotation angle (degrees) 0.01680827 
    16880 Shift along axis -0.00101183 
    16881  
    16882 
    16883 > volume splitbyzone #27
    16884 
    16885 Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at
    16886 level 0.121, step 1, values float32 
    16887 Opened rOAT1-PAH.mrc 1 as #28.2, grid size 160,160,160, pixel 0.83, shown at
    16888 level 0.121, step 1, values float32 
    16889 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    16890 level 0.121, step 1, values float32 
    16891 
    16892 > close #28.1-2
    16893 
    16894 > volume #28.3 level 0.05463
    16895 
    16896 > color #28.3 white models
    16897 
    16898 > color #28.3 #ffffb2ff models
    16899 
    16900 > color #28.3 #ffffb296 models
    16901 
    16902 > select add #26
    16903 
    16904 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    16905 
    16906 > color #26 #bf3434ff
    16907 
    16908 > select subtract #26
    16909 
    16910 Nothing selected 
    16911 
    16912 > hide #!26 models
    16913 
    16914 > hide #!28 models
    16915 
    16916 > hide #!28.3 models
    16917 
    16918 > show #!28 models
    16919 
    16920 > show #!28.3 models
    16921 
    16922 > hide #!28 models
    16923 
    16924 > show #!28 models
    16925 
    16926 > show #!26 models
    16927 
    16928 > save
    16929 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    16930 > includeMaps true
    16931 
    16932 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id:
    16933 35657337, major code: 40 (TranslateCoords), minor code: 0 
    16934 
    16935 > hide #!26 models
    16936 
    16937 > hide #!28 models
    16938 
    16939 > hide #!28.3 models
    16940 
    16941 > open
    16942 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc
    16943 
    16944 Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at
    16945 level 0.0068, step 2, values float32 
    16946 
    16947 > open
    16948 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb
    16949 
    16950 Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30 
    16951 --- 
    16952 Chain | Description 
    16953 A | No description available 
    16954  
    16955 
    16956 > show #!2 models
    16957 
    16958 > volume #29 step 1
    16959 
    16960 > volume #29 level 0.01695
    16961 
    16962 > select add #30
    16963 
    16964 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    16965 
    16966 > view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467
    16967 
    16968 > view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8
    16969 
    16970 > view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211
    16971 
    16972 > view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823
    16973 
    16974 > rename #29 rOAT1-FBP.mrc
    16975 
    16976 > fitmap #30 inMap #29
    16977 
    16978 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    16979 using 4327 atoms 
    16980 average map value = 0.02366, steps = 64 
    16981 shifted from previous position = 2.15 
    16982 rotated from previous position = 1.57 degrees 
    16983 atoms outside contour = 1497, contour level = 0.016951 
    16984  
    16985 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    16986 (#29) coordinates: 
    16987 Matrix rotation and translation 
    16988 0.99965949 -0.01809184 -0.01880406 69.16631575 
    16989 0.01825291 0.99979787 0.00842953 64.90387685 
    16990 0.01864775 -0.00876989 0.99978765 65.39100171 
    16991 Axis -0.31300664 -0.68157330 0.66142625 
    16992 Axis point -4271.01743380 0.00000000 3378.83285764 
    16993 Rotation angle (degrees) 1.57437238 
    16994 Shift along axis -22.63494048 
    16995  
    16996 
    16997 > fitmap #29 inMap #28.3
    16998 
    16999 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    17000 correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449 
    17001 steps = 2000, shift = 8.88, angle = 34.9 degrees 
    17002  
    17003 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    17004 coordinates: 
    17005 Matrix rotation and translation 
    17006 0.83021101 -0.04922054 -0.55527201 36.70411652 
    17007 0.13130357 0.98533433 0.10897540 -101.23145590 
    17008 0.54176475 -0.16338178 0.82449824 -98.97434819 
    17009 Axis -0.23793623 -0.95839145 0.15770918 
    17010 Axis point 214.13564799 0.00000000 31.76591481 
    17011 Rotation angle (degrees) 34.91302477 
    17012 Shift along axis 72.67695975 
    17013  
    17014 
    17015 > fitmap #29 inMap #28.3
    17016 
    17017 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    17018 correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215 
    17019 steps = 1976, shift = 9.79, angle = 47.5 degrees 
    17020  
    17021 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    17022 coordinates: 
    17023 Matrix rotation and translation 
    17024 0.44591506 0.03168285 -0.89451437 128.47676238 
    17025 -0.42572042 0.88660402 -0.18081879 31.25418163 
    17026 0.78735118 0.46144286 0.40883812 -156.17744024 
    17027 Axis 0.34576253 -0.90543486 -0.24624374 
    17028 Axis point 186.53313716 0.00000000 6.98625710 
    17029 Rotation angle (degrees) 68.24252592 
    17030 Shift along axis 54.58154231 
    17031  
    17032 
    17033 > fitmap #29 inMap #2
    17034 
    17035 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    17036 correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051 
    17037 steps = 232, shift = 3.32, angle = 8.56 degrees 
    17038  
    17039 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    17040 Matrix rotation and translation 
    17041 0.54964589 -0.00012465 -0.83539774 175.75622877 
    17042 -0.44507129 0.84621907 -0.29295875 119.06565669 
    17043 0.70696602 0.53283512 0.46506536 -99.09845418 
    17044 Axis 0.45744920 -0.85439368 -0.24647856 
    17045 Axis point 210.95352936 0.00000000 94.96801349 
    17046 Rotation angle (degrees) 64.50291620 
    17047 Shift along axis 3.09624573 
    17048  
    17049 
    17050 > select add #29
    17051 
    17052 4327 atoms, 4393 bonds, 591 residues, 3 models selected 
    17053 
    17054 > hide #!2 models
    17055 
    17056 > show #!2 models
    17057 
    17058 > hide #!2 models
    17059 
    17060 > show #!27 models
    17061 
    17062 > view matrix models
    17063 > #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312
    17064 
    17065 > select subtract #30
    17066 
    17067 2 models selected 
    17068 
    17069 > ui mousemode right "rotate selected models"
    17070 
    17071 > view matrix models
    17072 > #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4
    17073 
    17074 > view matrix models
    17075 > #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407
    17076 
    17077 > ui mousemode right "translate selected models"
    17078 
    17079 > view matrix models
    17080 > #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751
    17081 
    17082 > view matrix models
    17083 > #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331
    17084 
    17085 > fitmap #29 inMap #2
    17086 
    17087 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    17088 correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98 
    17089 steps = 260, shift = 2.93, angle = 16.7 degrees 
    17090  
    17091 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    17092 Matrix rotation and translation 
    17093 0.99338416 0.10541244 -0.04556454 -5.89234048 
    17094 -0.10461957 0.99432199 0.01945563 14.33237930 
    17095 0.04735669 -0.01455997 0.99877192 -4.89753719 
    17096 Axis -0.14650897 -0.40022199 -0.90463113 
    17097 Axis point 131.78683646 64.78395429 0.00000000 
    17098 Rotation angle (degrees) 6.66633138 
    17099 Shift along axis -0.44238796 
    17100  
    17101 
    17102 > fitmap #30 inMap #29
    17103 
    17104 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    17105 using 4327 atoms 
    17106 average map value = 0.02366, steps = 84 
    17107 shifted from previous position = 1.18 
    17108 rotated from previous position = 6.66 degrees 
    17109 atoms outside contour = 1496, contour level = 0.016951 
    17110  
    17111 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    17112 (#29) coordinates: 
    17113 Matrix rotation and translation 
    17114 0.99966027 -0.01808767 -0.01876641 69.16021058 
    17115 0.01824668 0.99979876 0.00833662 64.90031908 
    17116 0.01861185 -0.00867622 0.99978914 65.39198117 
    17117 Axis -0.31026139 -0.68166338 0.66262576 
    17118 Axis point -4271.35731029 0.00000000 3392.84555643 
    17119 Rotation angle (degrees) 1.57107230 
    17120 Shift along axis -22.36750269 
    17121  
    17122 
    17123 > select subtract #29
    17124 
    17125 Nothing selected 
    17126 
    17127 > hide #!27 models
    17128 
    17129 > color #29 white models
    17130 
    17131 > color #30 white
    17132 
    17133 > select ::name="FBP"
    17134 
    17135 18 atoms, 19 bonds, 1 residue, 1 model selected 
    17136 
    17137 > color sel red
    17138 
    17139 > color zone #29 near #30 distance 4.98
    17140 
    17141 > volume #29 level 0.01043
    17142 
    17143 > volume splitbyzone #29
    17144 
    17145 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    17146 level 0.0104, step 1, values float32 
    17147 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    17148 level 0.0104, step 1, values float32 
    17149 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    17150 level 0.0104, step 1, values float32 
    17151 
    17152 > close #31.1-2
    17153 
    17154 > volume #31.3 level 0.002491
    17155 
    17156 > volume #31.3 level 0.005476
    17157 
    17158 > close #31#31.3
    17159 
    17160 > show #!29 models
    17161 
    17162 > color zone #29 near #30 distance 2
    17163 
    17164 [Repeated 1 time(s)]
    17165 
    17166 > volume splitbyzone #29
    17167 
    17168 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    17169 level 0.0104, step 1, values float32 
    17170 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    17171 level 0.0104, step 1, values float32 
    17172 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    17173 level 0.0104, step 1, values float32 
    17174 
    17175 > close #31.1-2
    17176 
    17177 > volume #31.3 level 0.003802
    17178 
    17179 > color #31.3 white models
    17180 
    17181 > color #31.3 #ffffb2ff models
    17182 
    17183 > color #31.3 #ffffb20f models
    17184 
    17185 > color #31.3 #ffffb296 models
    17186 
    17187 > select add #30
    17188 
    17189 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    17190 
    17191 > color #30 #889944ff
    17192 
    17193 > color #30 #894a08ff
    17194 
    17195 > save
    17196 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    17197 > includeMaps true
    17198 
    17199 > hide #!31.3 models
    17200 
    17201 > hide #!31 models
    17202 
    17203 > select subtract #30
    17204 
    17205 Nothing selected 
    17206 
    17207 > hide #30 models
    17208 
    17209 > show #!2 models
    17210 
    17211 > open
    17212 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc
    17213 
    17214 Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at
    17215 level 0.00396, step 2, values float32 
    17216 
    17217 QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id:
    17218 35657387, major code: 40 (TranslateCoords), minor code: 0 
    17219 
    17220 > volume #32 step 1
    17221 
    17222 > volume #32 level 0.01186
    17223 
    17224 > rename #32 rOAT1-CFM.mrc
    17225 
    17226 > fitmap #31.3 inMap #32
    17227 
    17228 Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points 
    17229 correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643 
    17230 steps = 80, shift = 1.06, angle = 39.7 degrees 
    17231  
    17232 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32)
    17233 coordinates: 
    17234 Matrix rotation and translation 
    17235 0.74404465 0.65679786 0.12253212 -67.09990326 
    17236 -0.66239846 0.70118044 0.26376935 89.56606533 
    17237 0.08732602 -0.27742126 0.95677145 29.93219993 
    17238 Axis -0.37942983 0.02468307 -0.92489121 
    17239 Axis point 75.79903236 131.70903838 0.00000000 
    17240 Rotation angle (degrees) 45.49284979 
    17241 Shift along axis -0.01355792 
    17242  
    17243 
    17244 > fitmap #31.3 inMap #2
    17245 
    17246 Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points 
    17247 correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295 
    17248 steps = 76, shift = 0.987, angle = 35 degrees 
    17249  
    17250 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2)
    17251 coordinates: 
    17252 Matrix rotation and translation 
    17253 0.98357109 0.17790518 -0.03062105 -15.98050765 
    17254 -0.17592201 0.98266732 0.05844983 19.75924781 
    17255 0.04048883 -0.05210265 0.99782061 1.12732183 
    17256 Axis -0.29288928 -0.18839308 -0.93740275 
    17257 Axis point 102.41456930 99.44616144 0.00000000 
    17258 Rotation angle (degrees) 10.87852675 
    17259 Shift along axis -0.09874061 
    17260  
    17261 
    17262 > fitmap #32 inMap #2
    17263 
    17264 Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points 
    17265 correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57 
    17266 steps = 72, shift = 2.43, angle = 7.06 degrees 
    17267  
    17268 Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    17269 Matrix rotation and translation 
    17270 0.99240829 0.11776796 -0.03544703 -8.88787383 
    17271 -0.11778889 0.99303752 0.00150464 18.44106769 
    17272 0.03537743 0.00268205 0.99937042 -5.69387210 
    17273 Axis 0.00478670 -0.28793162 -0.95763901 
    17274 Axis point 151.76616064 85.25679566 0.00000000 
    17275 Rotation angle (degrees) 7.06459913 
    17276 Shift along axis 0.10036409 
    17277  
    17278 
    17279 > save
    17280 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    17281 > models #30 relModel #32
    17282 
    17283 > open
    17284 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    17285 
    17286 Chain information for rOAT1-CFM_IF.pdb #33 
    17287 --- 
    17288 Chain | Description 
    17289 A | No description available 
    17290  
    17291 
    17292 > color #33 #ffff7fff
    17293 
    17294 > color #33 #55aaffff
    17295 
    17296 > select add #33
    17297 
    17298 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    17299 
    17300 > view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224
    17301 
    17302 > view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924
    17303 
    17304 > view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036
    17305 
    17306 > fitmap #33 inMap #32
    17307 
    17308 Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327
    17309 atoms 
    17310 average map value = 0.0191, steps = 80 
    17311 shifted from previous position = 1.1 
    17312 rotated from previous position = 7.12 degrees 
    17313 atoms outside contour = 1362, contour level = 0.01186 
    17314  
    17315 Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32)
    17316 coordinates: 
    17317 Matrix rotation and translation 
    17318 0.99999299 -0.00023005 -0.00373680 -4.70643521 
    17319 0.00021365 0.99999035 -0.00438786 8.58155234 
    17320 0.00373777 0.00438703 0.99998339 -3.97966882 
    17321 Axis 0.76069466 -0.64796926 0.03846397 
    17322 Axis point 0.00000000 827.85989235 581.48051316 
    17323 Rotation angle (degrees) 0.33046593 
    17324 Shift along axis -9.29381608 
    17325  
    17326 
    17327 > save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb
    17328 > models #33 relModel #32
    17329 
    17330 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id:
    17331 35657459, major code: 40 (TranslateCoords), minor code: 0 
    17332 
    17333 > hide #33 models
    17334 
    17335 > hide #!32 models
    17336 
    17337 > select subtract #33
    17338 
    17339 Nothing selected 
    17340 
    17341 > show #!17 models
    17342 
    17343 > hide #!17 models
    17344 
    17345 > show #!17 models
    17346 
    17347 > hide #!2 models
    17348 
    17349 > open
    17350 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV-
    17351 > Cl_OF-coot-2.pdb
    17352 
    17353 Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34 
    17354 --- 
    17355 Chain | Description 
    17356 A | No description available 
    17357  
    17358 
    17359 > select ::name="CL"
    17360 
    17361 1 atom, 1 residue, 1 model selected 
    17362 
    17363 > hide #!17 models
    17364 
    17365 > show sel atoms
    17366 
    17367 > show #!17 models
    17368 
    17369 > style sel stick
    17370 
    17371 Changed 1 atom style 
    17372 
    17373 > color zone #17 near #34 distance 2.98
    17374 
    17375 > select add #34
    17376 
    17377 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    17378 
    17379 > color #34 white
    17380 
    17381 > color zone #17 near #34 distance 2.98
    17382 
    17383 > select ::name="CL"
    17384 
    17385 1 atom, 1 residue, 1 model selected 
    17386 
    17387 > color sel red
    17388 
    17389 > color zone #17 near #34 distance 2.98
    17390 
    17391 > volume splitbyzone #17
    17392 
    17393 Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown
    17394 at level 0.011, step 1, values float32 
    17395 Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown
    17396 at level 0.011, step 1, values float32 
    17397 Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown
    17398 at level 0.011, step 1, values float32 
    17399 
    17400 > rename #35 "rOAT1-TVF-Cl_OF.mrc split"
    17401 
    17402 > close #35.1-2
    17403 
    17404 > rename #35.3 "rOAT1-TVF-Cl_OF.mrc 2"
    17405 
    17406 > hide #!35.3 models
    17407 
    17408 > select #34/B:1@CL
    17409 
    17410 1 atom, 1 residue, 1 model selected 
    17411 
    17412 > ui tool show Contacts
    17413 
    17414 > contacts sel interModel false ignoreHiddenModels true select true
    17415 
    17416 6 contacts 
    17417 
    17418 > ui tool show Contacts
    17419 
    17420 > contacts sel intraRes true ignoreHiddenModels true select true
    17421 
    17422 15 contacts 
    17423 
    17424 > show sel atoms
    17425 
    17426 > color #34 yellow
    17427 
    17428 > show sel atoms
    17429 
    17430 > close #36
    17431 
    17432 > select add #34
    17433 
    17434 3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected 
    17435 
    17436 > color #34 white
    17437 
    17438 > hide sel atoms
    17439 
    17440 > select ::name="CL"
    17441 
    17442 1 atom, 1 residue, 1 model selected 
    17443 
    17444 > show sel atoms
    17445 
    17446 > hide #35.3.1 models
    17447 
    17448 > show #35.3.1 models
    17449 
    17450 > close #34.2
    17451 
    17452 > hide #!35.3 models
    17453 
    17454 > hide #35.3.1 models
    17455 
    17456 > hide #!35 models
    17457 
    17458 > hide #34.1 models
    17459 
    17460 > select #34/B:1@CL
    17461 
    17462 1 atom, 1 residue, 1 model selected 
    17463 
    17464 > select #34/A:216
    17465 
    17466 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17467 
    17468 > show sel atoms
    17469 
    17470 > select #34/A:511
    17471 
    17472 7 atoms, 7 bonds, 1 residue, 1 model selected 
    17473 
    17474 > show sel atoms
    17475 
    17476 > select #34: 219
    17477 
    17478 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17479 
    17480 > show sel atoms
    17481 
    17482 > select #34: 273
    17483 
    17484 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17485 
    17486 > show sel atoms
    17487 
    17488 > select #34/A:4
    17489 
    17490 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17491 
    17492 > show sel atoms
    17493 
    17494 > select add #34/A:511
    17495 
    17496 15 atoms, 14 bonds, 2 residues, 1 model selected 
    17497 
    17498 > show sel atoms
    17499 
    17500 > select add #34/A:512
    17501 
    17502 23 atoms, 21 bonds, 3 residues, 1 model selected 
    17503 
    17504 > show sel atoms
    17505 
    17506 > select #34/B:1@CL
    17507 
    17508 1 atom, 1 residue, 1 model selected 
    17509 
    17510 > color sel lime
    17511 
    17512 > color #35.3.1 white
    17513 
    17514 > color #35.3.1 #ffffb2ff
    17515 
    17516 > color #35.3.1 #ffffb296
    17517 
    17518 > select #34/B:1@CL
    17519 
    17520 1 atom, 1 residue, 1 model selected 
    17521 
    17522 > select add #34
    17523 
    17524 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    17525 
    17526 > color #34 #374c02ff
    17527 
    17528 > select #34/B:1@CL
    17529 
    17530 1 atom, 1 residue, 1 model selected 
    17531 
    17532 > color sel lime
    17533 
    17534 > select add #34
    17535 
    17536 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    17537 
    17538 > color (#!34 & sel) byhetero
    17539 
    17540 > select #34/A:2
    17541 
    17542 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17543 
    17544 > show sel atoms
    17545 
    17546 > select #34/A:3
    17547 
    17548 11 atoms, 11 bonds, 1 residue, 1 model selected 
    17549 
    17550 > show sel atoms
    17551 
    17552 > select add #34/A:215
    17553 
    17554 18 atoms, 18 bonds, 2 residues, 1 model selected 
    17555 
    17556 > show sel atoms
    17557 
    17558 > select #34/B:1@CL
    17559 
    17560 1 atom, 1 residue, 1 model selected 
    17561 
    17562 > show #35.3.1 models
    17563 
    17564 > view sel
    17565 
    17566 > hide #35.3.1 models
    17567 
    17568 > hide #!35.3 models
    17569 
    17570 > hide #!35 models
    17571 
    17572 > hide #!34 models
    17573 
    17574 > select add #34
    17575 
    17576 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    17577 
    17578 > select subtract #34
    17579 
    17580 Nothing selected 
    17581 
    17582 > show #1 models
    17583 
    17584 > view
    17585 
    17586 > hide #1 models
    17587 
    17588 > show #21 models
    17589 
    17590 > select add #21/A:602@C12
    17591 
    17592 1 atom, 1 residue, 1 model selected 
    17593 
    17594 > select up
    17595 
    17596 3 atoms, 1 bond, 2 residues, 1 model selected 
    17597 
    17598 > select up
    17599 
    17600 44 atoms, 46 bonds, 2 residues, 1 model selected 
    17601 
    17602 > select clear
    17603 
    17604 > select #21/A:602@O14
    17605 
    17606 1 atom, 1 residue, 1 model selected 
    17607 
    17608 > select add #21/A:601@C04
    17609 
    17610 2 atoms, 2 residues, 1 model selected 
    17611 
    17612 > select up
    17613 
    17614 70 atoms, 76 bonds, 2 residues, 1 model selected 
    17615 
    17616 > view sel
    17617 
    17618 > show #!22.3 models
    17619 
    17620 > hide #!22.3 models
    17621 
    17622 > hide #!22 models
    17623 
    17624 > hide #21 models
    17625 
    17626 > select add #21
    17627 
    17628 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    17629 
    17630 > select subtract #21
    17631 
    17632 Nothing selected 
    17633 
    17634 > save
    17635 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    17636 > includeMaps true
    17637 
    17638 QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id:
    17639 35657669, major code: 40 (TranslateCoords), minor code: 0 
    17640 
    17641 > open
    17642 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc
    17643 
    17644 Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    17645 level 0.00418, step 2, values float32 
    17646 
    17647 > open
    17648 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    17649 
    17650 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    17651 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    17652 (Q4U2R8) [more info...] 
    17653  
    17654 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37 
    17655 --- 
    17656 Chain | Description | UniProt 
    17657 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    17658  
    17659 
    17660 > rename #36 hOAT1-TFV.mrc
    17661 
    17662 > volume #36 step 1
    17663 
    17664 > volume #36 level 0.008515
    17665 
    17666 > rename #37 hOAT1-TFV_IF.pdb
    17667 
    17668 > view
    17669 
    17670 > show #!2 models
    17671 
    17672 > hide #!2 models
    17673 
    17674 > ui tool show Matchmaker
    17675 
    17676 > matchmaker #37 to #1
    17677 
    17678 Parameters 
    17679 --- 
    17680 Chain pairing | bb 
    17681 Alignment algorithm | Needleman-Wunsch 
    17682 Similarity matrix | BLOSUM-62 
    17683 SS fraction | 0.3 
    17684 Gap open (HH/SS/other) | 18/18/6 
    17685 Gap extend | 1 
    17686 SS matrix |  |  | H | S | O 
    17687 ---|---|---|--- 
    17688 H | 6 | -9 | -6 
    17689 S |  | 6 | -6 
    17690 O |  |  | 4 
    17691 Iteration cutoff | 2 
    17692  
    17693 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    17694 (#37), sequence alignment score = 2359.6 
    17695 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    17696 0.862) 
    17697  
    17698 
    17699 > matchmaker #37 to #1
    17700 
    17701 Parameters 
    17702 --- 
    17703 Chain pairing | bb 
    17704 Alignment algorithm | Needleman-Wunsch 
    17705 Similarity matrix | BLOSUM-62 
    17706 SS fraction | 0.3 
    17707 Gap open (HH/SS/other) | 18/18/6 
    17708 Gap extend | 1 
    17709 SS matrix |  |  | H | S | O 
    17710 ---|---|---|--- 
    17711 H | 6 | -9 | -6 
    17712 S |  | 6 | -6 
    17713 O |  |  | 4 
    17714 Iteration cutoff | 2 
    17715  
    17716 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    17717 (#37), sequence alignment score = 2359.6 
    17718 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    17719 0.862) 
    17720  
    17721 
    17722 > save
    17723 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb
    17724 > models #37 relModel #36
    17725 
    17726 > rename #36 hOAT1-TFV_IF.mrc
    17727 
    17728 > hide #37 models
    17729 
    17730 > hide #!36 models
    17731 
    17732 > open
    17733 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    17734 
    17735 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    17736 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    17737 (Q4U2R8) [more info...] 
    17738  
    17739 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38 
    17740 --- 
    17741 Chain | Description | UniProt 
    17742 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    17743  
    17744 
    17745 > close #38
    17746 
    17747 > close #37
    17748 
    17749 > open
    17750 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF-
    17751 > coot-1_real_space_refined_002.pdb
    17752 
    17753 Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37 
    17754 --- 
    17755 Chain | Description 
    17756 A | No description available 
    17757  
    17758 
    17759 > show #!36 models
    17760 
    17761 > color #36 white models
    17762 
    17763 > color #37 white
    17764 
    17765 > hide #!36 models
    17766 
    17767 > select up
    17768 
    17769 2 atoms, 1 bond, 1 residue, 1 model selected 
    17770 
    17771 > select #37/A:601@C08
    17772 
    17773 1 atom, 1 residue, 1 model selected 
    17774 
    17775 > select up
    17776 
    17777 31 atoms, 32 bonds, 1 residue, 1 model selected 
    17778 
    17779 > color sel red
    17780 
    17781 > show #!36 models
    17782 
    17783 > color zone #36 near #37 distance 4.98
    17784 
    17785 > color zone #36 near #37 distance 2
    17786 
    17787 [Repeated 1 time(s)]
    17788 
    17789 > color zone #36 near #37 distance 1.9
    17790 
    17791 > color zone #36 near #37 distance 1.8
    17792 
    17793 > color zone #36 near #37 distance 1.7
    17794 
    17795 > volume splitbyzone #36
    17796 
    17797 Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown
    17798 at level 0.00852, step 1, values float32 
    17799 Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown
    17800 at level 0.00852, step 1, values float32 
    17801 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    17802 at level 0.00852, step 1, values float32 
    17803 
    17804 > close #38.1-2
    17805 
    17806 > color #38.3 white models
    17807 
    17808 > color #38.3 #ffffb2ff models
    17809 
    17810 > color #38.3 #ffffb296 models
    17811 
    17812 > color #37 #aaff7fff
    17813 
    17814 > select add #37
    17815 
    17816 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    17817 
    17818 > color sel byhetero
    17819 
    17820 > save
    17821 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    17822 > includeMaps true
    17823 
    17824 QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id:
    17825 35657985, major code: 40 (TranslateCoords), minor code: 0 
    17826 
    17827 > hide #!38.3 models
    17828 
    17829 > hide #!38 models
    17830 
    17831 > select subtract #37
    17832 
    17833 Nothing selected 
    17834 
    17835 > show #!34 models
    17836 
    17837 Drag select of 25 atoms, 383 residues, 24 bonds 
    17838 
    17839 > select up
    17840 
    17841 2906 atoms, 2958 bonds, 383 residues, 2 models selected 
    17842 
    17843 > select clear
    17844 
    17845 > select add #37/A:326
    17846 
    17847 5 atoms, 4 bonds, 1 residue, 1 model selected 
    17848 
    17849 > select clear
    17850 
    17851 > hide #!34 models
    17852 
    17853 > select add #37
    17854 
    17855 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    17856 
    17857 > select subtract #37
    17858 
    17859 Nothing selected 
    17860 
    17861 > save
    17862 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    17863 
    17864 > save
    17865 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    17866 > models #37 relModel #36
    17867 
    17868 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id:
    17869 35658005, major code: 40 (TranslateCoords), minor code: 0 
    17870 
    17871 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id:
    17872 35657995, major code: 40 (TranslateCoords), minor code: 0 
    17873 
    17874 > open
    17875 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc
    17876 
    17877 Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    17878 level 0.00436, step 2, values float32 
    17879 
    17880 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id:
    17881 35658010, major code: 40 (TranslateCoords), minor code: 0 
    17882 
    17883 > rename #39 hOAT1-TFV_OF.mrc
    17884 
    17885 > volume #39 step 1
    17886 
    17887 > volume #39 level 0.01031
    17888 
    17889 > hide #!39 models
    17890 
    17891 > open
    17892 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    17893 
    17894 Chain information for hOAT1-TFV_OF.pdb #40 
    17895 --- 
    17896 Chain | Description 
    17897 A | No description available 
    17898  
    17899 
    17900 > hide #37 models
    17901 
    17902 > select #40: 320-600
    17903 
    17904 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    17905 
    17906 > hide sel cartoons
    17907 
    17908 [Repeated 1 time(s)]
    17909 
    17910 > show sel cartoons
    17911 
    17912 > ui tool show Matchmaker
    17913 
    17914 > matchmaker #40 & sel to #18
    17915 
    17916 Parameters 
    17917 --- 
    17918 Chain pairing | bb 
    17919 Alignment algorithm | Needleman-Wunsch 
    17920 Similarity matrix | BLOSUM-62 
    17921 SS fraction | 0.3 
    17922 Gap open (HH/SS/other) | 18/18/6 
    17923 Gap extend | 1 
    17924 SS matrix |  |  | H | S | O 
    17925 ---|---|---|--- 
    17926 H | 6 | -9 | -6 
    17927 S |  | 6 | -6 
    17928 O |  |  | 4 
    17929 Iteration cutoff | 2 
    17930  
    17931 Matchmaker rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with
    17932 hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1 
    17933 RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs:
    17934 7.198) 
    17935  
    17936 
    17937 > matchmaker #40 to #15
    17938 
    17939 Parameters 
    17940 --- 
    17941 Chain pairing | bb 
    17942 Alignment algorithm | Needleman-Wunsch 
    17943 Similarity matrix | BLOSUM-62 
    17944 SS fraction | 0.3 
    17945 Gap open (HH/SS/other) | 18/18/6 
    17946 Gap extend | 1 
    17947 SS matrix |  |  | H | S | O 
    17948 ---|---|---|--- 
    17949 H | 6 | -9 | -6 
    17950 S |  | 6 | -6 
    17951 O |  |  | 4 
    17952 Iteration cutoff | 2 
    17953  
    17954 Matchmaker rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain
    17955 A (#40), sequence alignment score = 2368.6 
    17956 RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs:
    17957 0.719) 
    17958  
    17959 
    17960 > show #!18 models
    17961 
    17962 > ui mousemode right "translate selected atoms"
    17963 
    17964 > ui mousemode right "rotate selected models"
    17965 
    17966 > view matrix models
    17967 > #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122
    17968 
    17969 > undo
    17970 
    17971 > ui mousemode right "move picked models"
    17972 
    17973 > view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987
    17974 
    17975 > undo
    17976 
    17977 > ui mousemode right pivot
    17978 
    17979 > ui tool show Matchmaker
    17980 
    17981 > matchmaker #40 & sel to #5 & sel
    17982 
    17983 No 'to' model specified 
    17984 
    17985 > select clear
    17986 
    17987 > hide #!18 models
    17988 
    17989 > show #!18 models
    17990 
    17991 > select #18,40: 320-600
    17992 
    17993 3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected 
    17994 
    17995 > ui tool show Matchmaker
    17996 
    17997 > matchmaker #40 & sel to #5 & sel
    17998 
    17999 No 'to' model specified 
    18000 
    18001 > matchmaker #40 & sel to #5 & sel
    18002 
    18003 No 'to' model specified 
    18004 
    18005 > matchmaker #40 & sel to #5 & sel
    18006 
    18007 No 'to' model specified 
    18008 
    18009 > ui mousemode right "translate selected atoms"
    18010 
    18011 > select #40: 320-600
    18012 
    18013 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    18014 
    18015 > hide #!18 models
    18016 
    18017 > show #!18 models
    18018 
    18019 > hide #40 models
    18020 
    18021 > hide #!18 models
    18022 
    18023 > show #40 models
    18024 
    18025 > save
    18026 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    18027 > models #40 relModel #39
    18028 
    18029 QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id:
    18030 35658147, major code: 40 (TranslateCoords), minor code: 0 
    18031 
    18032 > fitmap #40 inMap #39
    18033 
    18034 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    18035 atoms 
    18036 average map value = 0.007219, steps = 88 
    18037 shifted from previous position = 0.909 
    18038 rotated from previous position = 8.49 degrees 
    18039 atoms outside contour = 2887, contour level = 0.010308 
    18040  
    18041 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    18042 coordinates: 
    18043 Matrix rotation and translation 
    18044 0.99019825 -0.07829950 -0.11565728 27.38037598 
    18045 0.07892080 0.99688057 0.00079533 -10.70816731 
    18046 0.11523422 -0.00991530 0.99328886 -13.08861468 
    18047 Axis -0.03831490 -0.82596303 0.56242070 
    18048 Axis point 128.86145300 0.00000000 225.96021530 
    18049 Rotation angle (degrees) 8.03460025 
    18050 Shift along axis 0.43416611 
    18051  
    18052 
    18053 > save
    18054 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    18055 > models #40 relModel #39
    18056 
    18057 > undo
    18058 
    18059 > select clear
    18060 
    18061 > show #!39 models
    18062 
    18063 > fitmap #40 inMap #39
    18064 
    18065 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    18066 atoms 
    18067 average map value = 0.007218, steps = 28 
    18068 shifted from previous position = 0.0175 
    18069 rotated from previous position = 0.016 degrees 
    18070 atoms outside contour = 2888, contour level = 0.010308 
    18071  
    18072 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    18073 coordinates: 
    18074 Matrix rotation and translation 
    18075 0.99020256 -0.07845145 -0.11551732 27.36683659 
    18076 0.07909202 0.99686685 0.00096497 -10.76110579 
    18077 0.11507968 -0.01009202 0.99330500 -13.04322773 
    18078 Axis -0.03956067 -0.82505023 0.56367284 
    18079 Axis point 128.67057833 0.00000000 226.14572082 
    18080 Rotation angle (degrees) 8.03322105 
    18081 Shift along axis 0.44368911 
    18082  
    18083 
    18084 > fitmap #40 inMap #39
    18085 
    18086 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    18087 atoms 
    18088 average map value = 0.007219, steps = 44 
    18089 shifted from previous position = 0.00455 
    18090 rotated from previous position = 0.00258 degrees 
    18091 atoms outside contour = 2889, contour level = 0.010308 
    18092  
    18093 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    18094 coordinates: 
    18095 Matrix rotation and translation 
    18096 0.99020340 -0.07846932 -0.11549800 27.37049731 
    18097 0.07911379 0.99686509 0.00099928 -10.76639922 
    18098 0.11505751 -0.01012698 0.99330721 -13.03687370 
    18099 Axis -0.03980982 -0.82492871 0.56383314 
    18100 Axis point 128.62890621 0.00000000 226.21984207 
    18101 Rotation angle (degrees) 8.03295687 
    18102 Shift along axis 0.44127588 
    18103  
    18104 
    18105 > select add #40
    18106 
    18107 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    18108 
    18109 > fitmap #40 inMap #39
    18110 
    18111 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    18112 atoms 
    18113 average map value = 0.007219, steps = 60 
    18114 shifted from previous position = 2.24 
    18115 rotated from previous position = 0.00666 degrees 
    18116 atoms outside contour = 2889, contour level = 0.010308 
    18117  
    18118 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    18119 coordinates: 
    18120 Matrix rotation and translation 
    18121 0.99020164 -0.07840067 -0.11555975 25.97288245 
    18122 0.07903810 0.99687116 0.00093711 -9.32824593 
    18123 0.11512471 -0.01006155 0.99330009 -12.03377088 
    18124 Axis -0.03935047 -0.82533103 0.56327634 
    18125 Axis point 116.53468443 0.00000000 214.84157931 
    18126 Rotation angle (degrees) 8.03353574 
    18127 Shift along axis -0.10149276 
    18128  
    18129 
    18130 > show #!17 models
    18131 
    18132 > fitmap #39 inMap #19.3
    18133 
    18134 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    18135 correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206 
    18136 steps = 936, shift = 1.08, angle = 13.4 degrees 
    18137  
    18138 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    18139 coordinates: 
    18140 Matrix rotation and translation 
    18141 0.98280665 -0.13043667 -0.13068041 37.39205996 
    18142 0.11063752 0.98266445 -0.14876125 8.18112237 
    18143 0.14781892 0.13174539 0.98020035 -34.01816129 
    18144 Axis 0.60585490 -0.60151939 0.52068635 
    18145 Axis point 0.00000000 261.98069292 24.54762139 
    18146 Rotation angle (degrees) 13.38519605 
    18147 Shift along axis 0.02026683 
    18148  
    18149 
    18150 > fitmap #39 inMap #19.3
    18151 
    18152 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    18153 correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206 
    18154 steps = 48, shift = 0.0138, angle = 0.161 degrees 
    18155  
    18156 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    18157 coordinates: 
    18158 Matrix rotation and translation 
    18159 0.98301413 -0.12857767 -0.13096186 37.15798588 
    18160 0.10847145 0.98263409 -0.15054633 8.70610140 
    18161 0.14804449 0.13378355 0.97989019 -34.26954280 
    18162 Axis 0.61337235 -0.60188813 0.51137563 
    18163 Axis point -0.00000000 260.45263984 27.89398858 
    18164 Rotation angle (degrees) 13.40165031 
    18165 Shift along axis 0.02697294 
    18166  
    18167 
    18168 > fitmap #40 inMap #39
    18169 
    18170 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    18171 atoms 
    18172 average map value = 0.007219, steps = 132 
    18173 shifted from previous position = 0.778 
    18174 rotated from previous position = 13.4 degrees 
    18175 atoms outside contour = 2889, contour level = 0.010308 
    18176  
    18177 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    18178 coordinates: 
    18179 Matrix rotation and translation 
    18180 0.99020454 -0.07852899 -0.11544767 25.97319443 
    18181 0.07917768 0.99685998 0.00103677 -9.35919916 
    18182 0.11500374 -0.01016749 0.99331302 -12.00484753 
    18183 Axis -0.04009077 -0.82459474 0.56430155 
    18184 Axis point 116.41047661 0.00000000 215.06686153 
    18185 Rotation angle (degrees) 8.03257950 
    18186 Shift along axis -0.09809308 
    18187  
    18188 
    18189 > hide #!17 models
    18190 
    18191 > hide #!39 models
    18192 
    18193 > close #40
    18194 
    18195 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    18196 > coot-1.pdb
    18197 
    18198 Chain information for hOAT1-TFV_OF-coot-1.pdb #40 
    18199 --- 
    18200 Chain | Description 
    18201 A | No description available 
    18202  
    18203 
    18204 > show #!39 models
    18205 
    18206 > color #39 white models
    18207 
    18208 > color #40 white
    18209 
    18210 > hide #!39 models
    18211 
    18212 > select up
    18213 
    18214 2 atoms, 1 bond, 1 residue, 1 model selected 
    18215 
    18216 > color sel red
    18217 
    18218 > select up
    18219 
    18220 31 atoms, 32 bonds, 1 residue, 1 model selected 
    18221 
    18222 > color sel red
    18223 
    18224 > show #!39 models
    18225 
    18226 > color zone #39 near #40 distance 4.98
    18227 
    18228 > color zone #39 near #40 distance 2
    18229 
    18230 [Repeated 1 time(s)]
    18231 
    18232 > volume #39 level 0.01241
    18233 
    18234 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    18235 > coot-2.pdb
    18236 
    18237 Chain information for hOAT1-TFV_OF-coot-2.pdb #41 
    18238 --- 
    18239 Chain | Description 
    18240 A | No description available 
    18241  
    18242 
    18243 > hide #!40 models
    18244 
    18245 > color #41 white
    18246 
    18247 > color zone #39 near #41 distance 2
    18248 
    18249 > select up
    18250 
    18251 2 atoms, 1 bond, 1 residue, 1 model selected 
    18252 
    18253 > select up
    18254 
    18255 31 atoms, 32 bonds, 1 residue, 1 model selected 
    18256 
    18257 > color sel red
    18258 
    18259 > color zone #39 near #41 distance 2
    18260 
    18261 > volume #39 level 0.01056
    18262 
    18263 > color zone #39 near #41 distance 2.1
    18264 
    18265 > color zone #39 near #41 distance 2.2
    18266 
    18267 > color zone #39 near #41 distance 2.3
    18268 
    18269 > color zone #39 near #41 distance 2.4
    18270 
    18271 > color zone #39 near #41 distance 2.5
    18272 
    18273 > color zone #39 near #41 distance 2.6
    18274 
    18275 > color zone #39 near #41 distance 2.7
    18276 
    18277 > color zone #39 near #41 distance 2.8
    18278 
    18279 > color zone #39 near #41 distance 2.9
    18280 
    18281 > color zone #39 near #41 distance 3
    18282 
    18283 > color zone #39 near #41 distance 2.9
    18284 
    18285 > color zone #39 near #41 distance 2.8
    18286 
    18287 > color zone #39 near #41 distance 2.7
    18288 
    18289 > color zone #39 near #41 distance 2.6
    18290 
    18291 > color zone #39 near #41 distance 2.5
    18292 
    18293 > color zone #39 near #41 distance 2.4
    18294 
    18295 > color zone #39 near #41 distance 2.3
    18296 
    18297 > color zone #39 near #41 distance 2.2
    18298 
    18299 > color zone #39 near #41 distance 2.1
    18300 
    18301 > color zone #39 near #41 distance 2
    18302 
    18303 > color zone #39 near #41 distance 1.9
    18304 
    18305 > color zone #39 near #41 distance 2
    18306 
    18307 > color zone #39 near #41 distance 2.1
    18308 
    18309 > color zone #39 near #41 distance 2.2
    18310 
    18311 > color zone #39 near #41 distance 2.3
    18312 
    18313 > color zone #39 near #41 distance 2.4
    18314 
    18315 > color zone #39 near #41 distance 2.5
    18316 
    18317 > volume splitbyzone #39
    18318 
    18319 Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown
    18320 at level 0.0106, step 1, values float32 
    18321 Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown
    18322 at level 0.0106, step 1, values float32 
    18323 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    18324 at level 0.0106, step 1, values float32 
    18325 
    18326 > close #42.1-2
    18327 
    18328 > color #42.3 white models
    18329 
    18330 > color #42.3 #ffffb2ff models
    18331 
    18332 > color #42.3 #ffffb296 models
    18333 
    18334 > volume #42.3 level 0.006989
    18335 
    18336 > select add #41
    18337 
    18338 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    18339 
    18340 > color #41 #aaffffff
    18341 
    18342 > color #41 blue
    18343 
    18344 > color #41 red
    18345 
    18346 > color #41 #aa00ffff
    18347 
    18348 > color #41 #0055ffff
    18349 
    18350 > color #41 #55557fff
    18351 
    18352 > color #41 #ff557fff
    18353 
    18354 > color #41 #ffaaffff
    18355 
    18356 > color (#!41 & sel) byhetero
    18357 
    18358 > save
    18359 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18360 > includeMaps true
    18361 
    18362 > show #!34 models
    18363 
    18364 > hide #!41 models
    18365 
    18366 > hide #!42 models
    18367 
    18368 > hide #!42.3 models
    18369 
    18370 > select subtract #41
    18371 
    18372 Nothing selected 
    18373 
    18374 > hide #!34 models
    18375 
    18376 > show #1 models
    18377 
    18378 > show #!3.3 models
    18379 
    18380 > hide #!3.3 models
    18381 
    18382 > hide #!3 models
    18383 
    18384 > hide #1 models
    18385 
    18386 > show #!22.3 models
    18387 
    18388 > show #21 models
    18389 
    18390 > select add #21/A:601@O25
    18391 
    18392 1 atom, 1 bond, 1 residue, 1 model selected 
    18393 
    18394 > select up
    18395 
    18396 3 atoms, 1 bond, 2 residues, 1 model selected 
    18397 
    18398 > view sel
    18399 
    18400 > volume #22.3 level 0.01409
    18401 
    18402 > hide #!22.3 models
    18403 
    18404 > hide #!22 models
    18405 
    18406 > hide #21 models
    18407 
    18408 > show #!22.3 models
    18409 
    18410 > hide #!22.3 models
    18411 
    18412 > hide #!22 models
    18413 
    18414 > show #!23 models
    18415 
    18416 > hide #!23 models
    18417 
    18418 > show #!25.3 models
    18419 
    18420 > show #!24 models
    18421 
    18422 > hide #!25.3 models
    18423 
    18424 > hide #!25 models
    18425 
    18426 > hide #!24 models
    18427 
    18428 > show #1 models
    18429 
    18430 > show #!3.3 models
    18431 
    18432 > hide #!3.3 models
    18433 
    18434 > hide #!3 models
    18435 
    18436 > hide #1 models
    18437 
    18438 > show #!5 models
    18439 
    18440 > show #!6.3 models
    18441 
    18442 > hide #!6.3 models
    18443 
    18444 > hide #!6 models
    18445 
    18446 > hide #!5 models
    18447 
    18448 > show #8 models
    18449 
    18450 > show #!9.3 models
    18451 
    18452 > volume #9.3 level 0.003826
    18453 
    18454 > select #8/A:230
    18455 
    18456 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18457 
    18458 > show sel atoms
    18459 
    18460 > select #8/A:227
    18461 
    18462 4 atoms, 3 bonds, 1 residue, 1 model selected 
    18463 
    18464 > show sel atoms
    18465 
    18466 > select clear
    18467 
    18468 > hide #!9.3 models
    18469 
    18470 > hide #!9 models
    18471 
    18472 > hide #8 models
    18473 
    18474 > show #!12 models
    18475 
    18476 > show #!11.3 models
    18477 
    18478 > color #11.3 #ffffb296 models
    18479 
    18480 > hide #!12 models
    18481 
    18482 > hide #!11.3 models
    18483 
    18484 > hide #!11 models
    18485 
    18486 > show #15 models
    18487 
    18488 > show #!16.3 models
    18489 
    18490 > hide #!16.3 models
    18491 
    18492 > hide #!16 models
    18493 
    18494 > hide #15 models
    18495 
    18496 > show #!18 models
    18497 
    18498 > show #!19.3 models
    18499 
    18500 > hide #!18 models
    18501 
    18502 > hide #!19 models
    18503 
    18504 > hide #!19.3 models
    18505 
    18506 > show #37 models
    18507 
    18508 > show #!38.3 models
    18509 
    18510 > hide #!38.3 models
    18511 
    18512 > hide #!38 models
    18513 
    18514 > hide #37 models
    18515 
    18516 > close #40
    18517 
    18518 > show #!41 models
    18519 
    18520 > show #!42.3 models
    18521 
    18522 > hide #!42.3 models
    18523 
    18524 > hide #!42 models
    18525 
    18526 > hide #!41 models
    18527 
    18528 > show #!26 models
    18529 
    18530 > show #!28.3 models
    18531 
    18532 > select #26/A:230
    18533 
    18534 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18535 
    18536 > show sel atoms
    18537 
    18538 > select #26/A:200
    18539 
    18540 5 atoms, 4 bonds, 1 residue, 1 model selected 
    18541 
    18542 > show sel atoms
    18543 
    18544 > select add #26
    18545 
    18546 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    18547 
    18548 > color (#!26 & sel) byhetero
    18549 
    18550 > select clear
    18551 
    18552 > select #26/A:223
    18553 
    18554 4 atoms, 3 bonds, 1 residue, 1 model selected 
    18555 
    18556 > show sel atoms
    18557 
    18558 > select #26/A:227
    18559 
    18560 4 atoms, 3 bonds, 1 residue, 1 model selected 
    18561 
    18562 > show sel atoms
    18563 
    18564 > select #26/A:223
    18565 
    18566 4 atoms, 3 bonds, 1 residue, 1 model selected 
    18567 
    18568 > show sel atoms
    18569 
    18570 > select #26/A:200
    18571 
    18572 5 atoms, 4 bonds, 1 residue, 1 model selected 
    18573 
    18574 > show sel atoms
    18575 
    18576 > select #26/A:226
    18577 
    18578 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18579 
    18580 > show sel atoms
    18581 
    18582 > select #26/A:204
    18583 
    18584 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18585 
    18586 > show sel atoms
    18587 
    18588 > select clear
    18589 
    18590 > hide #!28.3 models
    18591 
    18592 > hide #!28 models
    18593 
    18594 > hide #!26 models
    18595 
    18596 > show #!31.3 models
    18597 
    18598 > show #30 models
    18599 
    18600 > select add #30
    18601 
    18602 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    18603 
    18604 > color sel byhetero
    18605 
    18606 > select clear
    18607 
    18608 > save
    18609 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18610 > includeMaps true
    18611 
    18612 ——— End of log from Mon Feb 10 17:46:10 2025 ———
    18613 
    18614 opened ChimeraX session 
    18615 
    18616 > hide #!31.3 models
    18617 
    18618 > hide #!31 models
    18619 
    18620 > hide #30 models
    18621 
    18622 > show #!34 models
    18623 
    18624 > show #!35 models
    18625 
    18626 > show #!35.3 models
    18627 
    18628 > volume #35.3 level 0.01175
    18629 
    18630 > select #35.3
    18631 
    18632 2 models selected 
    18633 
    18634 > view sel
    18635 
    18636 > color #34 tan
    18637 
    18638 > ui tool show "Side View"
    18639 
    18640 > select add #34
    18641 
    18642 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected 
    18643 
    18644 > color (#!34 & sel) byhetero
    18645 
    18646 > select clear
    18647 
    18648 > select #34/A:447
    18649 
    18650 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18651 
    18652 > show sel atoms
    18653 
    18654 > select #34/A:507
    18655 
    18656 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18657 
    18658 > show sel atoms
    18659 
    18660 > select clear
    18661 
    18662 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    18663 
    18664 ——— End of log from Tue Mar 11 12:00:09 2025 ———
    18665 
    18666 opened ChimeraX session 
    18667 
    18668 > hide #!35.3 models
    18669 
    18670 > hide #!35 models
    18671 
    18672 > show #!17 models
    18673 
    18674 > color #17 #ffffb2ff models
    18675 
    18676 > color #17 #ffffb280 models
    18677 
    18678 > ui tool show "Side View"
    18679 
    18680 > color #17 #ffffb24d models
    18681 
    18682 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    18683 
    18684 ——— End of log from Thu Apr 10 14:06:06 2025 ———
    18685 
    18686 opened ChimeraX session 
    18687 
    18688 > movie record
    18689 
    18690 > turn y 2 180
    18691 
    18692 > wait 180
    18693 
    18694 > movie encode /Users/dout2/Desktop/movie1.mp4
    18695 
    18696 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    18697  
    18698 
    18699 > select add #34
    18700 
    18701 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    18702 
    18703 > show sel atoms
    18704 
    18705 > select clear
    18706 
    18707 > hide #!34 models
    18708 
    18709 > hide #!17 models
    18710 
    18711 > show #!6 models
    18712 
    18713 > show #1 models
    18714 
    18715 > view
    18716 
    18717 > select #1/A:463
    18718 
    18719 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18720 
    18721 > select #1/A:466
    18722 
    18723 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18724 
    18725 > select #1/A:228
    18726 
    18727 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18728 
    18729 > select #1/A:230
    18730 
    18731 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18732 
    18733 > select #1/A:231
    18734 
    18735 6 atoms, 5 bonds, 1 residue, 1 model selected 
    18736 
    18737 > select #1/A:377
    18738 
    18739 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18740 
    18741 > select #1/A:378
    18742 
    18743 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18744 
    18745 > select #1/A:381
    18746 
    18747 5 atoms, 4 bonds, 1 residue, 1 model selected 
    18748 
    18749 > select #1/A:225
    18750 
    18751 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18752 
    18753 > select #1/A:382
    18754 
    18755 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18756 
    18757 > show sel atoms
    18758 
    18759 > hide #!6 models
    18760 
    18761 > show #!6 models
    18762 
    18763 > hide #1 models
    18764 
    18765 > show #1 models
    18766 
    18767 > select add #1
    18768 
    18769 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    18770 
    18771 > select subtract #1
    18772 
    18773 Nothing selected 
    18774 
    18775 > hide #1 models
    18776 
    18777 > hide #!6 models
    18778 
    18779 > show #!18 models
    18780 
    18781 > hide #!18 models
    18782 
    18783 > show #1 models
    18784 
    18785 > select #1/A:228
    18786 
    18787 12 atoms, 12 bonds, 1 residue, 1 model selected 
    18788 
    18789 > select #1/A:199
    18790 
    18791 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18792 
    18793 > select #1/A:257
    18794 
    18795 7 atoms, 7 bonds, 1 residue, 1 model selected 
    18796 
    18797 > select #1/A:145
    18798 
    18799 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18800 
    18801 > select #1/A:466
    18802 
    18803 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18804 
    18805 > show sel atoms
    18806 
    18807 > select #1/A:149
    18808 
    18809 5 atoms, 4 bonds, 1 residue, 1 model selected 
    18810 
    18811 > select #1/A:146
    18812 
    18813 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18814 
    18815 > select #1/A:204
    18816 
    18817 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18818 
    18819 > select #1/A:150
    18820 
    18821 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18822 
    18823 > select #1/A:149
    18824 
    18825 5 atoms, 4 bonds, 1 residue, 1 model selected 
    18826 
    18827 > select #1/A:203
    18828 
    18829 5 atoms, 4 bonds, 1 residue, 1 model selected 
    18830 
    18831 > select #1/A:146
    18832 
    18833 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18834 
    18835 > select #1/A:149
    18836 
    18837 5 atoms, 4 bonds, 1 residue, 1 model selected 
    18838 Drag select of 13 residues 
    18839 
    18840 > select #1/A:463
    18841 
    18842 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18843 
    18844 > show sel atoms
    18845 
    18846 > select #1/A:466@CZ
    18847 
    18848 1 atom, 1 residue, 1 model selected 
    18849 
    18850 > select up
    18851 
    18852 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18853 
    18854 > ui tool show Contacts
    18855 
    18856 > contacts sel intraRes true ignoreHiddenModels true select true
    18857 > makePseudobonds false reveal true
    18858 
    18859 26 contacts 
    18860 
    18861 > select clear
    18862 
    18863 > select : 382
    18864 
    18865 126 atoms, 112 bonds, 14 residues, 14 models selected 
    18866 
    18867 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    18868 
    18869 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    18870 
    18871 > show sel & #1 atoms
    18872 
    18873 > hide #!6 target m
    18874 
    18875 [Repeated 1 time(s)]
    18876 
    18877 > hide #!4 target m
    18878 
    18879 > select add #1
    18880 
    18881 5716 atoms, 5702 bonds, 714 residues, 14 models selected 
    18882 
    18883 > select subtract #1
    18884 
    18885 1811 atoms, 1716 bonds, 199 residues, 13 models selected 
    18886 
    18887 > select add #5
    18888 
    18889 5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected 
    18890 
    18891 > select subtract #5
    18892 
    18893 1672 atoms, 1584 bonds, 184 residues, 12 models selected 
    18894 
    18895 > select add #8
    18896 
    18897 5445 atoms, 5437 bonds, 691 residues, 12 models selected 
    18898 
    18899 > select subtract #8
    18900 
    18901 1533 atoms, 1452 bonds, 169 residues, 11 models selected 
    18902 
    18903 > select add #12
    18904 
    18905 5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected 
    18906 
    18907 > select subtract #12
    18908 
    18909 1394 atoms, 1320 bonds, 154 residues, 10 models selected 
    18910 
    18911 > hide #1 models
    18912 
    18913 > show #1 models
    18914 
    18915 > select add #15
    18916 
    18917 5172 atoms, 5186 bonds, 654 residues, 10 models selected 
    18918 
    18919 > select subtract #15
    18920 
    18921 1255 atoms, 1188 bonds, 139 residues, 9 models selected 
    18922 
    18923 > select add #18
    18924 
    18925 4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected 
    18926 
    18927 > select subtract #18
    18928 
    18929 1116 atoms, 1056 bonds, 124 residues, 8 models selected 
    18930 
    18931 > select add #21
    18932 
    18933 4933 atoms, 4966 bonds, 625 residues, 8 models selected 
    18934 
    18935 > select subtract #21
    18936 
    18937 977 atoms, 924 bonds, 109 residues, 7 models selected 
    18938 
    18939 > select add #24
    18940 
    18941 4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected 
    18942 
    18943 > select subtract #24
    18944 
    18945 838 atoms, 792 bonds, 94 residues, 6 models selected 
    18946 
    18947 > select add #26
    18948 
    18949 4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected 
    18950 
    18951 > select subtract #26
    18952 
    18953 699 atoms, 660 bonds, 79 residues, 5 models selected 
    18954 
    18955 > select add #30
    18956 
    18957 4885 atoms, 4921 bonds, 653 residues, 5 models selected 
    18958 
    18959 > select subtract #30
    18960 
    18961 558 atoms, 528 bonds, 62 residues, 4 models selected 
    18962 
    18963 > select add #33
    18964 
    18965 4744 atoms, 4789 bonds, 636 residues, 4 models selected 
    18966 
    18967 > select subtract #33
    18968 
    18969 417 atoms, 396 bonds, 45 residues, 3 models selected 
    18970 
    18971 > select add #34
    18972 
    18973 4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected 
    18974 
    18975 > select subtract #34
    18976 
    18977 278 atoms, 264 bonds, 30 residues, 2 models selected 
    18978 
    18979 > select add #37
    18980 
    18981 4514 atoms, 4613 bonds, 579 residues, 2 models selected 
    18982 
    18983 > select subtract #37
    18984 
    18985 139 atoms, 132 bonds, 15 residues, 1 model selected 
    18986 
    18987 > select add #41
    18988 
    18989 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    18990 
    18991 > select subtract #41
    18992 
    18993 Nothing selected 
    18994 
    18995 > show #!2 models
    18996 
    18997 > hide #!2 models
    18998 
    18999 > show #!3 models
    19000 
    19001 > show #!3.3 models
    19002 
    19003 > ui tool show "Side View"
    19004 
    19005 > select #1/A:35@CG
    19006 
    19007 1 atom, 1 residue, 1 model selected 
    19008 
    19009 > select : 35
    19010 
    19011 112 atoms, 98 bonds, 14 residues, 14 models selected 
    19012 
    19013 > hide sel & #1 atoms
    19014 
    19015 > select up
    19016 
    19017 2 atoms, 1 bond, 1 residue, 1 model selected 
    19018 
    19019 > select up
    19020 
    19021 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19022 
    19023 > hide sel atoms
    19024 
    19025 > select clear
    19026 
    19027 > select : 35
    19028 
    19029 112 atoms, 98 bonds, 14 residues, 14 models selected 
    19030 
    19031 > show sel & #1 atoms
    19032 
    19033 > select clear
    19034 
    19035 > select : 35
    19036 
    19037 112 atoms, 98 bonds, 14 residues, 14 models selected 
    19038 
    19039 > hide sel & #1 atoms
    19040 
    19041 > save /Users/dout2/Desktop/image1.png supersample 3
    19042 
    19043 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    19044 
    19045 > select add #1
    19046 
    19047 4009 atoms, 4077 bonds, 528 residues, 14 models selected 
    19048 
    19049 > select subtract #1
    19050 
    19051 104 atoms, 91 bonds, 13 residues, 13 models selected 
    19052 
    19053 > select add #5
    19054 
    19055 3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected 
    19056 
    19057 > select subtract #5
    19058 
    19059 96 atoms, 84 bonds, 12 residues, 12 models selected 
    19060 
    19061 > select add #8
    19062 
    19063 4000 atoms, 4062 bonds, 533 residues, 12 models selected 
    19064 
    19065 > select subtract #8
    19066 
    19067 88 atoms, 77 bonds, 11 residues, 11 models selected 
    19068 
    19069 > select add #12
    19070 
    19071 3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected 
    19072 
    19073 > select subtract #12
    19074 
    19075 80 atoms, 70 bonds, 10 residues, 10 models selected 
    19076 
    19077 > select add #21
    19078 
    19079 4028 atoms, 4105 bonds, 525 residues, 10 models selected 
    19080 
    19081 > select subtract #21
    19082 
    19083 72 atoms, 63 bonds, 9 residues, 9 models selected 
    19084 
    19085 > select add #18
    19086 
    19087 3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected 
    19088 
    19089 > select subtract #18
    19090 
    19091 64 atoms, 56 bonds, 8 residues, 8 models selected 
    19092 
    19093 > select add #24
    19094 
    19095 3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected 
    19096 
    19097 > select subtract #24
    19098 
    19099 56 atoms, 49 bonds, 7 residues, 7 models selected 
    19100 
    19101 > select add #26
    19102 
    19103 3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected 
    19104 
    19105 > select subtract #26
    19106 
    19107 48 atoms, 42 bonds, 6 residues, 6 models selected 
    19108 
    19109 > select add #30
    19110 
    19111 4367 atoms, 4428 bonds, 596 residues, 6 models selected 
    19112 
    19113 > select subtract #30
    19114 
    19115 40 atoms, 35 bonds, 5 residues, 5 models selected 
    19116 
    19117 > select add #33
    19118 
    19119 4359 atoms, 4421 bonds, 595 residues, 5 models selected 
    19120 
    19121 > select subtract #33
    19122 
    19123 32 atoms, 28 bonds, 4 residues, 4 models selected 
    19124 
    19125 > select add #34
    19126 
    19127 3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected 
    19128 
    19129 > select subtract #34
    19130 
    19131 24 atoms, 21 bonds, 3 residues, 3 models selected 
    19132 
    19133 > select add #37
    19134 
    19135 4391 atoms, 4495 bonds, 566 residues, 3 models selected 
    19136 
    19137 > select subtract #37
    19138 
    19139 16 atoms, 14 bonds, 2 residues, 2 models selected 
    19140 
    19141 > select add #41
    19142 
    19143 4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected 
    19144 
    19145 > select subtract #41
    19146 
    19147 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19148 
    19149 > hide #!3.3 models
    19150 
    19151 > hide #!3 models
    19152 
    19153 > hide #1 models
    19154 
    19155 > show #!5 models
    19156 
    19157 > show #!6.3 models
    19158 
    19159 > hide #!6.3 models
    19160 
    19161 > hide #!6 models
    19162 
    19163 > hide #!5 models
    19164 
    19165 > show #8 models
    19166 
    19167 > show #!9 models
    19168 
    19169 > show #!9.3 models
    19170 
    19171 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19172 
    19173 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19174 
    19175 > show sel & #8 atoms
    19176 
    19177 > select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19178 
    19179 Unknown command: select:
    19180 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 
    19181 
    19182 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19183 
    19184 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19185 
    19186 > show sel & #8 atoms
    19187 
    19188 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19189 
    19190 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19191 
    19192 > show sel & #8 atoms
    19193 
    19194 > select clear
    19195 
    19196 > volume #9.3 level 0.00516
    19197 
    19198 > save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3
    19199 
    19200 > hide #!9.3 models
    19201 
    19202 > hide #!9 models
    19203 
    19204 > hide #8 models
    19205 
    19206 > show #15 models
    19207 
    19208 > show #!16 models
    19209 
    19210 > show #!16.3 models
    19211 
    19212 > select #15/A:442
    19213 
    19214 11 atoms, 11 bonds, 1 residue, 1 model selected 
    19215 
    19216 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19217 
    19218 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19219 
    19220 > show sel & #15 atoms
    19221 
    19222 > select #1-50: 438
    19223 
    19224 154 atoms, 154 bonds, 14 residues, 14 models selected 
    19225 
    19226 > select clear
    19227 
    19228 > save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3
    19229 
    19230 > hide #!16.3 models
    19231 
    19232 > hide #!16 models
    19233 
    19234 > hide #15 models
    19235 
    19236 > show #21 models
    19237 
    19238 > show #!22 models
    19239 
    19240 > show #!22.3 models
    19241 
    19242 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19243 
    19244 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19245 
    19246 > show sel & #21 atoms
    19247 
    19248 > select clear
    19249 
    19250 > save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3
    19251 
    19252 > volume #22.3 level 0.0128
    19253 
    19254 > hide #!22.3 models
    19255 
    19256 > hide #!22 models
    19257 
    19258 > hide #21 models
    19259 
    19260 > show #!27 models
    19261 
    19262 > show #!28 models
    19263 
    19264 > hide #!27 models
    19265 
    19266 > show #!26 models
    19267 
    19268 > show #!28.3 models
    19269 
    19270 > volume #28.3 level 0.06828
    19271 
    19272 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19273 
    19274 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19275 
    19276 > show sel & #!26 atoms
    19277 
    19278 > select clear
    19279 
    19280 > save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3
    19281 
    19282 > hide #!28.3 models
    19283 
    19284 > hide #!28 models
    19285 
    19286 > hide #!26 models
    19287 
    19288 > show #30 models
    19289 
    19290 > show #!31 models
    19291 
    19292 > show #!31.3 models
    19293 
    19294 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19295 
    19296 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19297 
    19298 > show sel & #30 atoms
    19299 
    19300 > select clear
    19301 
    19302 > save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3
    19303 
    19304 > hide #!31.3 models
    19305 
    19306 > hide #!31 models
    19307 
    19308 > hide #30 models
    19309 
    19310 > show #37 models
    19311 
    19312 > show #!38 models
    19313 
    19314 > show #!38.3 models
    19315 
    19316 > select clear
    19317 
    19318 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19319 
    19320 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19321 
    19322 > show sel & #37 atoms
    19323 
    19324 > select clear
    19325 
    19326 > show #!36 models
    19327 
    19328 > hide #!36 models
    19329 
    19330 > show #!36 models
    19331 
    19332 > hide #!36 models
    19333 
    19334 > volume #38.3 level 0.006101
    19335 
    19336 > volume #38.3 level 0.006864
    19337 
    19338 > save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3
    19339 
    19340 > hide #!38.3 models
    19341 
    19342 > hide #!38 models
    19343 
    19344 > hide #37 models
    19345 
    19346 > show #!2 models
    19347 
    19348 > hide #!2 models
    19349 
    19350 > show #1 models
    19351 
    19352 > show #!3 models
    19353 
    19354 > show #!3.3 models
    19355 
    19356 > hide #!3.3 models
    19357 
    19358 > hide #!3 models
    19359 
    19360 > hide #1 models
    19361 
    19362 > show #!5 models
    19363 
    19364 > show #!6.3 models
    19365 
    19366 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19367 
    19368 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19369 
    19370 > show sel & #!5 atoms
    19371 
    19372 > select clear
    19373 
    19374 > select up
    19375 
    19376 2 atoms, 1 bond, 1 residue, 1 model selected 
    19377 
    19378 > select up
    19379 
    19380 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19381 
    19382 > hide sel atoms
    19383 
    19384 > select clear
    19385 
    19386 [Repeated 1 time(s)]
    19387 
    19388 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19389 
    19390 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19391 
    19392 > show sel & #!5 atoms
    19393 
    19394 > select clear
    19395 
    19396 > select up
    19397 
    19398 2 atoms, 1 bond, 1 residue, 1 model selected 
    19399 
    19400 > hide sel atoms
    19401 
    19402 > select up
    19403 
    19404 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19405 
    19406 > hide sel atoms
    19407 
    19408 > select clear
    19409 
    19410 > volume #6.3 level 0.0106
    19411 
    19412 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    19413 
    19414 > hide #!5 models
    19415 
    19416 > hide #!6 models
    19417 
    19418 > hide #!6.3 models
    19419 
    19420 > show #!11 models
    19421 
    19422 > show #!12 models
    19423 
    19424 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    19425 
    19426 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    19427 
    19428 > show sel & #!12 atoms
    19429 
    19430 > select clear
    19431 
    19432 > show #!11.3 models
    19433 
    19434 > select clear
    19435 
    19436 > volume #11.3 level 0.009777
     587[deleted to fit within ticket limits]
     588
    19437589
    19438590> select clear