Changes between Initial Version and Version 1 of Ticket #19396


Ignore:
Timestamp:
Nov 20, 2025, 8:58:00 AM (5 hours ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19396

    • Property Component Unassigned → DICOM
    • Property Owner set to Zach Pearson
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Orthoplanes: 'NoneType' object has no attribute 'image_colors'

  • Ticket #19396 – Description

    initial v1  
    2168216820 atoms, 21 bonds, 1 residue, 1 model selected 
    21692169
    2170 > select add #14/A:21
    2171 
    2172 42 atoms, 45 bonds, 2 residues, 1 model selected 
    2173 
    2174 > select #14/A:21
    2175 
    2176 22 atoms, 24 bonds, 1 residue, 1 model selected 
    2177 
    2178 > select #14/A:3-21
    2179 
    2180 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2181 
    2182 > select ~sel & ##selected
    2183 
    2184 264 atoms, 296 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2185 
    2186 > combine #14
    2187 
    2188 > hide #!15 models
    2189 
    2190 > select #14/A:3
    2191 
    2192 20 atoms, 21 bonds, 1 residue, 1 model selected 
    2193 
    2194 > select #14/A:3-21
    2195 
    2196 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2197 
    2198 > select ~sel & ##selected
    2199 
    2200 264 atoms, 296 bonds, 1 pseudobond, 12 residues, 2 models selected 
    2201 
    2202 > delete atoms (#!14 & sel)
    2203 
    2204 > delete bonds (#!14 & sel)
    2205 
    2206 > select add #14
    2207 
    2208 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2209 
    2210 > show #!11 models
    2211 
    2212 > view matrix models
    2213 > #14,0.57897,-0.40594,0.70711,218.89,-0.81422,-0.24219,0.52763,119.61,-0.042931,-0.88122,-0.47074,242
    2214 
    2215 > view matrix models
    2216 > #14,0.63527,-0.15383,0.75682,218.03,-0.75301,-0.341,0.56276,121.18,0.1715,-0.92739,-0.33246,245.5
    2217 
    2218 > view matrix models
    2219 > #14,0.6708,0.5424,0.50579,216.14,0.15706,-0.77042,0.61789,141.28,0.72481,-0.33504,-0.60199,254.52
    2220 
    2221 > view matrix models
    2222 > #14,-0.0096955,0.8583,0.51306,200.68,0.23548,-0.4967,0.83537,139.53,0.97183,0.12891,-0.19729,253.57
    2223 
    2224 > view matrix models
    2225 > #14,-0.043091,0.81466,0.57833,199.81,0.078596,-0.57431,0.81486,137.07,0.99597,0.080568,-0.039281,253.18
    2226 
    2227 > view matrix models
    2228 > #14,0.18371,0.80389,0.5657,204.48,0.48828,-0.5741,0.65726,146.38,0.85313,0.15548,-0.49799,253.26
    2229 
    2230 > view matrix models
    2231 > #14,0.31116,0.74123,0.59478,207.2,0.61668,-0.63367,0.46708,150.66,0.72311,0.22145,-0.65427,251.38
    2232 
    2233 > ui mousemode right "translate selected models"
    2234 
    2235 > view matrix models
    2236 > #14,0.31116,0.74123,0.59478,229.64,0.61668,-0.63367,0.46708,133.88,0.72311,0.22145,-0.65427,234.23
    2237 
    2238 > fitmap #14 inMap #11
    2239 
    2240 Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2241 (#14) to map volume difference_region_3016.mrc (#11) using 398 atoms 
    2242 average map value = 0.01366, steps = 164 
    2243 shifted from previous position = 9.19 
    2244 rotated from previous position = 25.9 degrees 
    2245 atoms outside contour = 159, contour level = 0.0039469 
    2246  
    2247 Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2248 (#14) relative to volume difference_region_3016.mrc (#11) coordinates: 
    2249 Matrix rotation and translation 
    2250 0.44237445 0.83737600 0.32110168 241.23365048 
    2251 0.43361643 -0.51311710 0.74073454 131.62595737 
    2252 0.78503609 -0.18844707 -0.59008988 240.44462097 
    2253 Axis -0.83388001 -0.41635093 -0.36234793 
    2254 Axis point 0.00000000 26.78409318 69.85789243 
    2255 Rotation angle (degrees) 146.14152143 
    2256 Shift along axis -343.08712124 
    2257  
    2258 
    2259 > fitmap #14 inMap #11
    2260 
    2261 Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2262 (#14) to map volume difference_region_3016.mrc (#11) using 398 atoms 
    2263 average map value = 0.01366, steps = 84 
    2264 shifted from previous position = 0.00107 
    2265 rotated from previous position = 0.0113 degrees 
    2266 atoms outside contour = 159, contour level = 0.0039469 
    2267  
    2268 Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2269 (#14) relative to volume difference_region_3016.mrc (#11) coordinates: 
    2270 Matrix rotation and translation 
    2271 0.44228295 0.83745750 0.32101517 241.23186129 
    2272 0.43378042 -0.51301909 0.74070641 131.62900073 
    2273 0.78499704 -0.18835172 -0.59017226 240.44261670 
    2274 Axis -0.83385383 -0.41643580 -0.36231067 
    2275 Axis point 0.00000000 26.77227104 69.86521066 
    2276 Rotation angle (degrees) 146.14542280 
    2277 Shift along axis -343.08206462 
    2278  
    2279 
    2280 > view matrix models
    2281 > #14,0.44228,0.83746,0.32102,238.12,0.43378,-0.51302,0.74071,130.3,0.785,-0.18835,-0.59017,241.33
    2282 
    2283 > view matrix models
    2284 > #14,0.44228,0.83746,0.32102,235.42,0.43378,-0.51302,0.74071,128.18,0.785,-0.18835,-0.59017,246.76
    2285 
    2286 > view matrix models
    2287 > #14,0.44228,0.83746,0.32102,241.38,0.43378,-0.51302,0.74071,132.34,0.785,-0.18835,-0.59017,237.24
    2288 
    2289 > ui mousemode right "rotate selected models"
    2290 
    2291 > view matrix models
    2292 > #14,0.65001,0.45793,0.60645,245.93,0.50956,-0.85469,0.099228,140.62,0.56377,0.24453,-0.7889,231.48
    2293 
    2294 > view matrix models
    2295 > #14,0.82543,0.02422,0.56398,252.52,0.43785,-0.65806,-0.61257,143.14,0.3563,0.75257,-0.55379,222.36
    2296 
    2297 > view matrix models
    2298 > #14,0.87475,-0.19216,0.44484,255.8,0.42474,-0.13785,-0.89476,141.48,0.23326,0.97163,-0.038966,214.76
    2299 
    2300 > view matrix models
    2301 > #14,0.86023,-0.29738,0.4142,256.41,0.47657,0.18003,-0.86051,140.25,0.18133,0.93763,0.29659,211.43
    2302 
    2303 > view matrix models
    2304 > #14,0.6592,-0.73696,0.14952,257.04,0.29733,0.072809,-0.95199,137.97,0.69069,0.67201,0.26711,223.64
    2305 
    2306 > view matrix models
    2307 > #14,0.42019,-0.90733,0.013617,254.31,0.16772,0.062905,-0.98383,135.64,0.8918,0.41568,0.17861,230.02
    2308 
    2309 > view matrix models
    2310 > #14,0.29225,-0.94377,-0.15453,253.25,0.5821,0.30375,-0.75425,140.71,0.75878,0.13048,0.63814,225.69
    2311 
    2312 > view matrix models
    2313 > #14,0.19583,-0.97443,-0.11021,251.22,0.65554,0.21366,-0.7243,142.51,0.72933,0.069595,0.68062,225.18
    2314 
    2315 > view matrix models
    2316 > #14,0.2664,-0.96386,-0.0034393,251.75,0.69404,0.1943,-0.69322,143.16,0.66883,0.18229,0.72072,222.97
    2317 
    2318 > fitmap #14 inMap #11
    2319 
    2320 Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2321 (#14) to map volume difference_region_3016.mrc (#11) using 398 atoms 
    2322 average map value = 0.01977, steps = 108 
    2323 shifted from previous position = 3.79 
    2324 rotated from previous position = 24.6 degrees 
    2325 atoms outside contour = 51, contour level = 0.0039469 
    2326  
    2327 Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2328 (#14) relative to volume difference_region_3016.mrc (#11) coordinates: 
    2329 Matrix rotation and translation 
    2330 0.20806683 -0.94482438 0.25301206 245.31730866 
    2331 0.49213996 -0.12241887 -0.86186536 140.91802461 
    2332 0.84528485 0.30384293 0.43951452 227.20931476 
    2333 Axis 0.60000999 -0.30485293 0.73963012 
    2334 Axis point -88.33522929 160.77013316 0.00000000 
    2335 Rotation angle (degrees) 103.73424325 
    2336 Shift along axis 272.28441377 
    2337  
    2338 
    2339 > fitmap #14 inMap #11
    2340 
    2341 Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2342 (#14) to map volume difference_region_3016.mrc (#11) using 398 atoms 
    2343 average map value = 0.01977, steps = 48 
    2344 shifted from previous position = 0.0218 
    2345 rotated from previous position = 0.0598 degrees 
    2346 atoms outside contour = 52, contour level = 0.0039469 
    2347  
    2348 Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2349 (#14) relative to volume difference_region_3016.mrc (#11) coordinates: 
    2350 Matrix rotation and translation 
    2351 0.20889893 -0.94456618 0.25329030 245.35231743 
    2352 0.49253493 -0.12213559 -0.86167990 140.92150924 
    2353 0.84484945 0.30475832 0.43971784 227.19009581 
    2354 Axis 0.60028626 -0.30443518 0.73957800 
    2355 Axis point -88.41121626 160.68071724 0.00000000 
    2356 Rotation angle (degrees) 103.69535646 
    2357 Shift along axis 272.40495819 
    2358  
    2359 
    2360 > fitmap #14 inMap #11
    2361 
    2362 Fit molecule copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2363 (#14) to map volume difference_region_3016.mrc (#11) using 398 atoms 
    2364 average map value = 0.01977, steps = 48 
    2365 shifted from previous position = 0.00476 
    2366 rotated from previous position = 0.00986 degrees 
    2367 atoms outside contour = 52, contour level = 0.0039469 
    2368  
    2369 Position of copy of fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif
    2370 (#14) relative to volume difference_region_3016.mrc (#11) coordinates: 
    2371 Matrix rotation and translation 
    2372 0.20890985 -0.94454457 0.25336187 245.35121844 
    2373 0.49267792 -0.12214409 -0.86159694 140.91961113 
    2374 0.84476337 0.30482188 0.43983915 227.18531334 
    2375 Axis 0.60026697 -0.30434933 0.73962900 
    2376 Axis point -88.38914790 160.65954736 0.00000000 
    2377 Rotation angle (degrees) 103.69170825 
    2378 Shift along axis 272.42028832 
    2379  
    2380 
    2381 > select subtract #14
    2382 
    2383 Nothing selected 
    2384 
    2385 > show #!15 models
    2386 
    2387 > hide #!15 models
    2388 
    2389 > show #12 models
    2390 
    2391 > hide #12 models
    2392 
    2393 > show #12 models
    2394 
    2395 > hide #12 models
    2396 
    2397 > hide #13 models
    2398 
    2399 > show #13 models
    2400 
    2401 > hide #13 models
    2402 
    2403 > show #13 models
    2404 
    2405 > hide #13 models
    2406 
    2407 > hide #!14 models
    2408 
    2409 > show #!14 models
    2410 
    2411 > show #13 models
    2412 
    2413 > show #!15 models
    2414 
    2415 > hide #!15 models
    2416 
    2417 > hide #!14 models
    2418 
    2419 > show #!14 models
    2420 
    2421 > hide #13 models
    2422 
    2423 > show #13 models
    2424 
    2425 > nucleotides #13#!14 atoms
    2426 
    2427 > style nucleic & #13#!14 stick
    2428 
    2429 Changed 1123 atom styles 
    2430 
    2431 > color #13#!14 bynucleotide
    2432 
    2433 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    2434 > Project/20251112 JT.cxs"
    2435 
    2436 ——— End of log from Wed Nov 12 18:34:04 2025 ———
    2437 
    2438 > view name session-start
    2439 
    2440 opened ChimeraX session 
    2441 Showing volume difference.seg - 190 regions, 190 surfaces 
    2442 
    2443 > hide #!6 models
    2444 
    2445 > select add #13
    2446 
    2447 725 atoms, 810 bonds, 34 residues, 1 model selected 
    2448 
    2449 > select add #14
    2450 
    2451 1123 atoms, 1253 bonds, 53 residues, 2 models selected 
    2452 
    2453 > color sel bynucleotide
    2454 
    2455 > nucleotides sel stubs
    2456 
    2457 > select subtract #13
    2458 
    2459 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2460 
    2461 > select subtract #14
    2462 
    2463 Nothing selected 
    2464 
    2465 > show #!15 models
    2466 
    2467 > select add #15
    2468 
    2469 662 atoms, 739 bonds, 1 pseudobond, 31 residues, 3 models selected 
    2470 
    2471 > nucleotides sel stubs
    2472 
    2473 > select subtract #15
    2474 
    2475 Nothing selected 
    2476 
    2477 > select add #15
    2478 
    2479 662 atoms, 739 bonds, 1 pseudobond, 31 residues, 3 models selected 
    2480 
    2481 > ui mousemode right "translate selected models"
    2482 
    2483 > view matrix models
    2484 > #15,0.92914,-0.28325,-0.23764,207.96,0.066616,-0.50395,0.86116,157.33,-0.36368,-0.81597,-0.44937,216.66
    2485 
    2486 > show #!4 models
    2487 
    2488 > hide #!4 models
    2489 
    2490 > ui mousemode right "rotate selected models"
    2491 
    2492 > view matrix models
    2493 > #15,-0.44033,0.86492,0.24087,198.66,-0.53009,-0.46698,0.70777,155,0.72464,0.18397,0.66411,216.96
    2494 
    2495 > view matrix models
    2496 > #15,-0.5898,0.76607,-0.25549,202.43,0.75019,0.40267,-0.52447,180.8,-0.2989,-0.501,-0.81219,222.37
    2497 
    2498 > ui mousemode right "translate selected models"
    2499 
    2500 > view matrix models
    2501 > #15,-0.5898,0.76607,-0.25549,228.3,0.75019,0.40267,-0.52447,106.18,-0.2989,-0.501,-0.81219,190.99
    2502 
    2503 > show #10 models
    2504 
    2505 > hide #10 models
    2506 
    2507 > view matrix models
    2508 > #15,-0.5898,0.76607,-0.25549,227.98,0.75019,0.40267,-0.52447,113.3,-0.2989,-0.501,-0.81219,261.42
    2509 
    2510 > ui mousemode right "rotate selected models"
    2511 
    2512 > view matrix models
    2513 > #15,-0.61037,0.75534,-0.23857,227.61,0.67906,0.65402,0.33337,104.89,0.40784,0.041476,-0.91211,269.82
    2514 
    2515 > ui mousemode right "translate selected models"
    2516 
    2517 > view matrix models
    2518 > #15,-0.61037,0.75534,-0.23857,226.14,0.67906,0.65402,0.33337,104.13,0.40784,0.041476,-0.91211,259.49
    2519 
    2520 > view matrix models
    2521 > #15,-0.61037,0.75534,-0.23857,235.37,0.67906,0.65402,0.33337,130.29,0.40784,0.041476,-0.91211,272.29
    2522 
    2523 > ui mousemode right "rotate selected models"
    2524 
    2525 > view matrix models
    2526 > #15,-0.15592,0.94238,-0.29597,239.97,0.88226,0.26761,0.38729,129.37,0.44418,-0.20074,-0.87316,271.02
    2527 
    2528 > view orient
    2529 
    2530 > ui mousemode right "translate selected models"
    2531 
    2532 > view matrix models
    2533 > #15,-0.15592,0.94238,-0.29597,229.73,0.88226,0.26761,0.38729,128.58,0.44418,-0.20074,-0.87316,248.19
    2534 
    2535 > select subtract #15
    2536 
    2537 Nothing selected 
    2538 
    2539 > select add #15/A:65
    2540 
    2541 22 atoms, 24 bonds, 1 residue, 1 model selected 
    2542 
    2543 > select up
    2544 
    2545 662 atoms, 739 bonds, 31 residues, 1 model selected 
    2546 
    2547 > select down
    2548 
    2549 22 atoms, 24 bonds, 1 residue, 1 model selected 
    2550 
    2551 > select add #15
    2552 
    2553 662 atoms, 739 bonds, 1 pseudobond, 31 residues, 3 models selected 
    2554 
    2555 > view matrix models
    2556 > #15,-0.15592,0.94238,-0.29597,206.87,0.88226,0.26761,0.38729,110.59,0.44418,-0.20074,-0.87316,221.39
    2557 
    2558 > select subtract #15
    2559 
    2560 Nothing selected 
    2561 Drag select of 8 residues, 19 shapes 
    2562 
    2563 > select ~sel & ##selected
    2564 
    2565 439 atoms, 488 bonds, 1 pseudobond, 21 residues, 2 models selected 
    2566 
    2567 > delete atoms (#!15 & sel)
    2568 
    2569 > delete bonds (#!15 & sel)
    2570 
    2571 > select add #15
    2572 
    2573 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2574 
    2575 > view matrix models
    2576 > #15,-0.15592,0.94238,-0.29597,230.07,0.88226,0.26761,0.38729,138.82,0.44418,-0.20074,-0.87316,231.95
    2577 
    2578 > view matrix models
    2579 > #15,-0.15592,0.94238,-0.29597,226.49,0.88226,0.26761,0.38729,128.37,0.44418,-0.20074,-0.87316,245.68
    2580 
    2581 > select subtract #15
    2582 
    2583 Nothing selected 
    2584 
    2585 > select add #15
    2586 
    2587 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2588 
    2589 > view matrix models
    2590 > #15,-0.15592,0.94238,-0.29597,225.61,0.88226,0.26761,0.38729,128.31,0.44418,-0.20074,-0.87316,246.98
    2591 
    2592 > view matrix models
    2593 > #15,-0.15592,0.94238,-0.29597,230.1,0.88226,0.26761,0.38729,129.09,0.44418,-0.20074,-0.87316,250.41
    2594 
    2595 > fitmap #15 inMap #11
    2596 
    2597 Fit molecule copy of copy of
    2598 fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) to map volume
    2599 difference_region_3016.mrc (#11) using 223 atoms 
    2600 average map value = 0.02543, steps = 132 
    2601 shifted from previous position = 5.25 
    2602 rotated from previous position = 16.9 degrees 
    2603 atoms outside contour = 1, contour level = 0.0039469 
    2604  
    2605 Position of copy of copy of
    2606 fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) relative to
    2607 volume difference_region_3016.mrc (#11) coordinates: 
    2608 Matrix rotation and translation 
    2609 -0.27108821 0.96021231 -0.06710817 231.36559527 
    2610 0.92731396 0.27922003 0.24924886 132.89262157 
    2611 0.25806976 0.00533809 -0.96611153 253.72195023 
    2612 Axis -0.59808743 -0.79736059 -0.08066921 
    2613 Axis point 50.82941084 0.00000000 124.85438837 
    2614 Rotation angle (degrees) 168.23436216 
    2615 Shift along axis -264.80774107 
    2616  
    2617 
    2618 > fitmap #15 inMap #11
    2619 
    2620 Fit molecule copy of copy of
    2621 fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) to map volume
    2622 difference_region_3016.mrc (#11) using 223 atoms 
    2623 average map value = 0.02543, steps = 100 
    2624 shifted from previous position = 0.00562 
    2625 rotated from previous position = 0.0243 degrees 
    2626 atoms outside contour = 1, contour level = 0.0039469 
    2627  
    2628 Position of copy of copy of
    2629 fold_2025_11_12_15_46_rna_phicb5_region_3016_model_0.cif (#15) relative to
    2630 volume difference_region_3016.mrc (#11) coordinates: 
    2631 Matrix rotation and translation 
    2632 -0.27095722 0.96024980 -0.06710071 231.36710944 
    2633 0.92745359 0.27909367 0.24887056 132.89784192 
    2634 0.25770528 0.00520048 -0.96620957 253.72893157 
    2635 Axis -0.59815543 -0.79732594 -0.08050733 
    2636 Axis point 50.83325559 0.00000000 124.86559187 
    2637 Rotation angle (degrees) 168.24749354 
    2638 Shift along axis -264.78342854 
    2639  
    2640 
    2641 > hide #!15 models
    2642 
    2643 > show #!15 models
    2644 
    2645 > select subtract #15
    2646 
    2647 Nothing selected 
    2648 
    2649 > select add #15
    2650 
    2651 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2652 
    2653 > select subtract #15
    2654 
    2655 Nothing selected 
    2656 
    2657 > select #14/A
    2658 
    2659 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2660 
    2661 > select clear
    2662 
    2663 [Repeated 2 time(s)]
    2664 
    2665 > select #14/A:3-13
    2666 
    2667 227 atoms, 251 bonds, 11 residues, 1 model selected 
    2668 
    2669 > select clear
    2670 
    2671 [Repeated 2 time(s)]
    2672 
    2673 > select #14/A:3-16
    2674 
    2675 289 atoms, 320 bonds, 14 residues, 1 model selected 
    2676 
    2677 > select clear
    2678 
    2679 [Repeated 1 time(s)]
    2680 
    2681 > color #13#!14-15 bynucleotide
    2682 
    2683 > ui tool show "Show Sequence Viewer"
    2684 
    2685 > sequence chain #13/A #14/A #15/A
    2686 
    2687 Alignment identifier is 1 
    2688 
    2689 > select clear
    2690 
    2691 > select #13/A #14/A #15/A
    2692 
    2693 1346 atoms, 1504 bonds, 63 residues, 3 models selected 
    2694 
    2695 > select subtract #13
    2696 
    2697 621 atoms, 694 bonds, 29 residues, 2 models selected 
    2698 
    2699 > select subtract #14
    2700 
    2701 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2702 
    2703 > select subtract #15
    2704 
    2705 Nothing selected 
    2706 
    2707 > select add #15
    2708 
    2709 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2710 
    2711 > select subtract #15
    2712 
    2713 Nothing selected 
    2714 
    2715 > hide #13 models
    2716 
    2717 > show #13 models
    2718 
    2719 > vop add #13-15
    2720 
    2721 > vop add #13,14,15
    2722 
    2723 > vop add #13 #14 #15
    2724 
    2725 > show #!6 models
    2726 
    2727 > transparency #6#11.1 0
    2728 
    2729 > transparency #6#11.1 50
    2730 
    2731 > hide #!11 models
    2732 
    2733 > show #!11 models
    2734 
    2735 > hide #!6 models
    2736 
    2737 > hide #!11 models
    2738 
    2739 > select clear
    2740 
    2741 [Repeated 1 time(s)]
    2742 
    2743 > select #14/A
    2744 
    2745 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2746 
    2747 > select clear
    2748 
    2749 > select #14/A
    2750 
    2751 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2752 
    2753 > select #14/A:3
    2754 
    2755 20 atoms, 21 bonds, 1 residue, 1 model selected 
    2756 
    2757 > select #14/A:3-5
    2758 
    2759 60 atoms, 65 bonds, 3 residues, 1 model selected 
    2760 
    2761 > show #!11 models
    2762 
    2763 > hide #13 models
    2764 
    2765 > show #13 models
    2766 
    2767 > hide #!14 models
    2768 
    2769 > show #!14 models
    2770 
    2771 > hide #!15 models
    2772 
    2773 > hide #13 models
    2774 
    2775 > show #13 models
    2776 
    2777 > hide #13 models
    2778 
    2779 > show #13 models
    2780 
    2781 > show #!15 models
    2782 
    2783 > select add #14
    2784 
    2785 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2786 
    2787 > select add #15
    2788 
    2789 621 atoms, 694 bonds, 29 residues, 2 models selected 
    2790 
    2791 > select subtract #14
    2792 
    2793 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2794 
    2795 > select subtract #15
    2796 
    2797 Nothing selected 
    2798 
    2799 > select clear
    2800 
    2801 [Repeated 1 time(s)]
    2802 
    2803 > select add #15
    2804 
    2805 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2806 
    2807 > select subtract #15.1
    2808 
    2809 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2810 
    2811 > select add #15.1
    2812 
    2813 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2814 
    2815 > select subtract #15.1
    2816 
    2817 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2818 
    2819 > select subtract #15
    2820 
    2821 Nothing selected 
    2822 
    2823 > select #14/A:12-14
    2824 
    2825 60 atoms, 65 bonds, 3 residues, 1 model selected 
    2826 
    2827 > select #14/A:12-18
    2828 
    2829 145 atoms, 160 bonds, 7 residues, 1 model selected 
    2830 
    2831 > select clear
    2832 
    2833 [Repeated 4 time(s)]
    2834 
    2835 > select #14/A:3-5
    2836 
    2837 60 atoms, 65 bonds, 3 residues, 1 model selected 
    2838 
    2839 > select add #14
    2840 
    2841 398 atoms, 443 bonds, 19 residues, 1 model selected 
    2842 
    2843 > select add #15
    2844 
    2845 621 atoms, 694 bonds, 29 residues, 2 models selected 
    2846 
    2847 > hide #13 models
    2848 
    2849 > hide #!14 models
    2850 
    2851 > hide #!15 models
    2852 
    2853 > select subtract #14
    2854 
    2855 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2856 
    2857 > show #!15 models
    2858 
    2859 > hide #!15 models
    2860 
    2861 > select subtract #15
    2862 
    2863 Nothing selected 
    2864 
    2865 > show #!9 models
    2866 
    2867 > hide #!9 models
    2868 
    2869 > show #!7 models
    2870 
    2871 > hide #!7 models
    2872 
    2873 > show #!6 models
    2874 
    2875 > rename #12 region_3016.cif
    2876 
    2877 > hide #!6 models
    2878 
    2879 > show #12 models
    2880 
    2881 > undo
    2882 
    2883 > show #12 models
    2884 
    2885 > color #12 bynucleotide
    2886 
    2887 > ui tool show "Show Sequence Viewer"
    2888 
    2889 > sequence chain #12/A
    2890 
    2891 Alignment identifier is 12/A 
    2892 
    2893 > rename #12 region_3016_80nu.cif
    2894 
    2895 > hide #!11 models
    2896 
    2897 > show #!11 models
    2898 
    2899 > hide #12 models
    2900 
    2901 > show #13 models
    2902 
    2903 > show #!14 models
    2904 
    2905 > show #!15 models
    2906 
    2907 > rename #15 region_3016_65nu_1
    2908 
    2909 > hide #!14 models
    2910 
    2911 > hide #13 models
    2912 
    2913 > show #13 models
    2914 
    2915 > rename #13 region_3016_65nu_2
    2916 
    2917 > rename #14 region_3016_65nu_3
    2918 
    2919 > hide #13 models
    2920 
    2921 > hide #!15 models
    2922 
    2923 > show #12 models
    2924 
    2925 > hide #12 models
    2926 
    2927 > show #13 models
    2928 
    2929 > show #!14 models
    2930 
    2931 > show #!15 models
    2932 
    2933 > ui tool show "Show Sequence Viewer"
    2934 
    2935 > sequence chain #13/A #14/A #15/A
    2936 
    2937 Alignment identifier is 1 
    2938 
    2939 > select clear
    2940 
    2941 [Repeated 1 time(s)]
    2942 
    2943 > select #13/A #14/A #15/A
    2944 
    2945 1346 atoms, 1504 bonds, 63 residues, 3 models selected 
    2946 
    2947 > select clear
    2948 
    2949 > select #13/A #14/A #15/A
    2950 
    2951 1346 atoms, 1504 bonds, 63 residues, 3 models selected 
    2952 
    2953 > select #15/A:62
    2954 
    2955 20 atoms, 21 bonds, 1 residue, 1 model selected 
    2956 
    2957 > select #15/A:62
    2958 
    2959 20 atoms, 21 bonds, 1 residue, 1 model selected 
    2960 
    2961 > select #13/A #14/A #15/A
    2962 
    2963 1346 atoms, 1504 bonds, 63 residues, 3 models selected 
    2964 
    2965 > select subtract #13
    2966 
    2967 621 atoms, 694 bonds, 29 residues, 2 models selected 
    2968 
    2969 > select subtract #14
    2970 
    2971 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2972 
    2973 > select subtract #15
    2974 
    2975 Nothing selected 
    2976 
    2977 > select add #15
    2978 
    2979 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2980 
    2981 > select subtract #15
    2982 
    2983 Nothing selected 
    2984 
    2985 > select add #13
    2986 
    2987 725 atoms, 810 bonds, 34 residues, 1 model selected 
    2988 
    2989 > select subtract #13
    2990 
    2991 Nothing selected 
    2992 
    2993 > select add #15
    2994 
    2995 223 atoms, 251 bonds, 10 residues, 1 model selected 
    2996 
    2997 > select add #14
    2998 
    2999 621 atoms, 694 bonds, 29 residues, 2 models selected 
    3000 
    3001 > select subtract #15
    3002 
    3003 398 atoms, 443 bonds, 19 residues, 1 model selected 
    3004 
    3005 > select #14/A:3
    3006 
    3007 20 atoms, 21 bonds, 1 residue, 1 model selected 
    3008 
    3009 > select #13/A #14/A #15/A
    3010 
    3011 1346 atoms, 1504 bonds, 63 residues, 3 models selected 
    3012 
    3013 > select #14/A:3
    3014 
    3015 20 atoms, 21 bonds, 1 residue, 1 model selected 
    3016 
    3017 > select #13/A #14/A #15/A
    3018 
    3019 1346 atoms, 1504 bonds, 63 residues, 3 models selected 
    3020 
    3021 > select #14/A:3
    3022 
    3023 20 atoms, 21 bonds, 1 residue, 1 model selected 
    3024 
    3025 > select #13/A #14/A #15/A
    3026 
    3027 1346 atoms, 1504 bonds, 63 residues, 3 models selected 
    3028 
    3029 > show #!9 models
    3030 
    3031 > hide #!9 models
    3032 
    3033 > show #!7 models
    3034 
    3035 > hide #!7 models
    3036 
    3037 > show #!6 models
    3038 
    3039 > select subtract #13
    3040 
    3041 621 atoms, 694 bonds, 29 residues, 2 models selected 
    3042 
    3043 > select subtract #14
    3044 
    3045 223 atoms, 251 bonds, 10 residues, 1 model selected 
    3046 
    3047 > select subtract #15
    3048 
    3049 Nothing selected 
    3050 
    3051 > ui tool show "Side View"
    3052 
    3053 > select add #6.152
    3054 
    3055 1 model selected 
    3056 
    3057 > select add #6.27
    3058 
    3059 2 models selected 
    3060 
    3061 > select add #6.148
    3062 
    3063 3 models selected 
    3064 
    3065 > hide #13#!14-15 surfaces
    3066 
    3067 > surface hidePatches #6.27,148,152
    3068 
    3069 > select add #6
    3070 
    3071 191 models selected 
    3072 
    3073 > select subtract #6
    3074 
    3075 Nothing selected 
    3076 
    3077 > show #5 models
    3078 
    3079 > hide #5 models
    3080 
    3081 > select add #6.188
    3082 
    3083 1 model selected 
    3084 
    3085 > hide #13#!14-15 surfaces
    3086 
    3087 > hide #6.188 models
    3088 
    3089 > hide #6.190 models
    3090 
    3091 > show #6.190 models
    3092 
    3093 > select add #6.189
    3094 
    3095 2 models selected 
    3096 
    3097 > select subtract #6.188
    3098 
    3099 1 model selected 
    3100 
    3101 > select add #6.188
    3102 
    3103 2 models selected 
    3104 
    3105 > hide #6.189 models
    3106 
    3107 > select subtract #6.189
    3108 
    3109 1 model selected 
    3110 
    3111 > select subtract #6.188
    3112 
    3113 Nothing selected 
    3114 
    3115 > select add #6.40
    3116 
    3117 1 model selected 
    3118 
    3119 > select add #6.141
    3120 
    3121 2 models selected 
    3122 
    3123 > hide #6.40 models
    3124 
    3125 > select subtract #6.40
    3126 
    3127 1 model selected 
    3128 
    3129 > hide #6.141 models
    3130 
    3131 > select subtract #6.141
    3132 
    3133 Nothing selected 
    3134 
    3135 > select add #6.46
    3136 
    3137 1 model selected 
    3138 
    3139 > select add #6.179
    3140 
    3141 2 models selected 
    3142 
    3143 > select add #6.138
    3144 
    3145 3 models selected 
    3146 
    3147 > hide #6.138 models
    3148 
    3149 > select subtract #6.138
    3150 
    3151 2 models selected 
    3152 
    3153 > hide #6.46 models
    3154 
    3155 > select subtract #6.46
    3156 
    3157 1 model selected 
    3158 
    3159 > select subtract #6.179
    3160 
    3161 Nothing selected 
    3162 
    3163 > hide #6.179 models
    3164 
    3165 > undo
    3166 
    3167 > select #6.90
    3168 
    3169 1 model selected 
    3170 
    3171 > undo
    3172 
    3173 [Repeated 6 time(s)]
    3174 
    3175 > hide #6.46 models
    3176 
    3177 > select subtract #6.46
    3178 
    3179 2 models selected 
    3180 
    3181 > select subtract #6.138
    3182 
    3183 1 model selected 
    3184 
    3185 > hide #6.138 models
    3186 
    3187 > hide #6.179 models
    3188 
    3189 > select subtract #6.179
    3190 
    3191 Nothing selected 
    3192 
    3193 > select add #6.90
    3194 
    3195 1 model selected 
    3196 
    3197 > select add #6.168
    3198 
    3199 2 models selected 
    3200 
    3201 > select subtract #6.90
    3202 
    3203 1 model selected 
    3204 
    3205 > ui tool show "Segment Map"
    3206 
    3207 Ungrouped to 6 regions 
    3208 
    3209 > select subtract #6.195
    3210 
    3211 5 models selected 
    3212 
    3213 > select add #6.195
    3214 
    3215 6 models selected 
    3216 
    3217 > select subtract #6.191
    3218 
    3219 5 models selected 
    3220 
    3221 > select add #6.49
    3222 
    3223 6 models selected 
    3224 
    3225 > select add #6.108
    3226 
    3227 7 models selected 
    3228 
    3229 > select subtract #6.108
    3230 
    3231 6 models selected 
    3232 
    3233 > select subtract #6.49
    3234 
    3235 5 models selected 
    3236 
    3237 > select subtract #6.194
    3238 
    3239 4 models selected 
    3240 
    3241 > select subtract #6.195
    3242 
    3243 3 models selected 
    3244 
    3245 > select subtract #6.196
    3246 
    3247 2 models selected 
    3248 
    3249 > select add #6.108
    3250 
    3251 3 models selected 
    3252 
    3253 > select subtract #6.108
    3254 
    3255 2 models selected 
    3256 
    3257 > select subtract #6.193
    3258 
    3259 1 model selected 
    3260 
    3261 > select subtract #6.192
    3262 
    3263 Nothing selected 
    3264 
    3265 > select add #6.90
    3266 
    3267 1 model selected 
    3268 
    3269 > select add #6.194
    3270 
    3271 2 models selected 
    3272 
    3273 > undo
    3274 
    3275 > select #6.193
    3276 
    3277 1 model selected 
    3278 
    3279 > undo
    3280 
    3281 [Repeated 9 time(s)]
    3282 
    3283 > select subtract #6.108
    3284 
    3285 2 models selected 
    3286 
    3287 > select add #6.108
    3288 
    3289 3 models selected 
    3290 
    3291 > select add #6.194
    3292 
    3293 4 models selected 
    3294 
    3295 > select add #6.195
    3296 
    3297 5 models selected 
    3298 
    3299 > select subtract #6.108
    3300 
    3301 4 models selected 
    3302 
    3303 > select add #6.185
    3304 
    3305 5 models selected 
    3306 
    3307 > select add #6.100
    3308 
    3309 6 models selected 
    3310 
    3311 > select add #6.129
    3312 
    3313 7 models selected 
    3314 Grouped 7 regions 
    3315 Saving 1 regions to mrc file... 
    3316 Opened region_3017.mrc as #16, grid size 83,94,52, pixel 1.12, shown at step
    3317 1, values float32 
    3318 Wrote region_3017.mrc 
    3319 
    3320 QWindowsWindow::setGeometry: Unable to set geometry 1920x1287+0+35 (frame:
    3321 1942x1343-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    3322 Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
    3323 11, 11 minimum size: 624x858 MINMAXINFO(maxSize=POINT(x=0, y=0),
    3324 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
    3325 y=1343))) 
    3326 
    3327 > hide #!6 models
    3328 
    3329 > volume #16 level 0.0135
    3330 
    3331 > hide #!11 models
    3332 
    3333 > show #!11 models
    3334 
    3335 > rename #11 region_3016.mrc
    3336 
    3337 > hide #!15 models
    3338 
    3339 > show #!15 models
    3340 
    3341 > volume #16 level 0.01566
    3342 
    3343 > show #!6 models
    3344 
    3345 > select add #6
    3346 
    3347 190 models selected 
    3348 
    3349 > select subtract #6
    3350 
    3351 Nothing selected 
    3352 
    3353 > show #!9 models
    3354 
    3355 > show #10 models
    3356 
    3357 > select subtract #9
    3358 
    3359 Nothing selected 
    3360 
    3361 > hide #!6 models
    3362 
    3363 > show #!6 models
    3364 
    3365 > hide #!6 models
    3366 
    3367 > show #!4 models
    3368 
    3369 > hide #!9 models
    3370 
    3371 > hide #!4 models
    3372 
    3373 > show #!8 models
    3374 
    3375 > hide #!8 models
    3376 
    3377 > show #!6 models
    3378 
    3379 > rename #5 region_1.pdb
    3380 
    3381 > rename #9 "volume difference_region_2.mrc"
    3382 
    3383 > rename #10 region_2.cif
    3384 
    3385 > rename #11 region_3.mrc
    3386 
    3387 > rename #12 region_3_80nu.cif
    3388 
    3389 > rename #13 region_3_65nu_2
    3390 
    3391 > rename #14 region_3_65nu_3
    3392 
    3393 > rename #15 region_3_65nu_1
    3394 
    3395 > rename #16 region_4.mrc
    3396 
    3397 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    3398 > Project/20251113 region_4 start.cxs"
    3399 
    3400 ——— End of log from Thu Nov 13 13:38:11 2025 ———
    3401 
    3402 > view name session-start
    3403 
    3404 opened ChimeraX session 
    3405 Showing volume difference.seg - 189 regions, 189 surfaces 
    3406 
    3407 > hide #!6 models
    3408 
    3409 > hide #13 models
    3410 
    3411 > hide #!14 models
    3412 
    3413 > hide #!15 models
    3414 
    3415 > hide #!16 models
    3416 
    3417 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    3418 > Project/20251113_rna_phicb5_region_3_75nu/fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif"
    3419 
    3420 Chain information for
    3421 fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif #17 
    3422 --- 
    3423 Chain | Description 
    3424 A | . 
    3425  
    3426 Computing secondary structure 
    3427 
    3428 > rename #17 region_3_75nu.cif
    3429 
    3430 > select add #17
    3431 
    3432 1594 atoms, 1781 bonds, 75 residues, 1 model selected 
    3433 
    3434 > ui mousemode right "translate selected models"
    3435 
    3436 > view matrix models #17,1,0,0,151.4,0,1,0,54.629,0,0,1,-7.9536
    3437 
    3438 > view matrix models #17,1,0,0,292.05,0,1,0,135.56,0,0,1,111.02
    3439 
    3440 > view matrix models #17,1,0,0,293.26,0,1,0,101.03,0,0,1,179.18
    3441 
    3442 > view matrix models #17,1,0,0,262.85,0,1,0,133.91,0,0,1,157.56
    3443 
    3444 > ui mousemode right "rotate selected models"
    3445 
    3446 > view matrix models
    3447 > #17,-0.315,0.88625,-0.3396,255.28,0.85381,0.10836,-0.50918,138.52,-0.41446,-0.45035,-0.79083,154.43
    3448 
    3449 > view matrix models
    3450 > #17,-0.94742,-0.070488,-0.31212,254.27,0.30877,0.054586,-0.94957,135.76,0.083971,-0.99602,-0.029951,158.4
    3451 
    3452 > view matrix models
    3453 > #17,-0.87941,-0.11639,-0.46163,254.47,0.47586,-0.18609,-0.85961,137.02,0.014142,-0.97562,0.21903,158.35
    3454 
    3455 > nucleotides sel stubs
    3456 
    3457 > combine #17
    3458 
    3459 [Repeated 1 time(s)]
    3460 
    3461 > rename #18 region_3_75nu.cif
    3462 
    3463 > rename #17 region_3_75nu_stem.cif
    3464 
    3465 > rename #18 region_3_stemloop_1.cif
    3466 
    3467 > rename #17 region_3_stem.cif
    3468 
    3469 > rename #19 region_3_stemloop_2.cif
    3470 
    3471 > select subtract #17
    3472 
    3473 Nothing selected 
    3474 
    3475 > select add #17
    3476 
    3477 1594 atoms, 1781 bonds, 75 residues, 1 model selected 
    3478 
    3479 > select add #18
    3480 
    3481 3188 atoms, 3562 bonds, 150 residues, 2 models selected 
    3482 
    3483 > select add #19
    3484 
    3485 4782 atoms, 5343 bonds, 225 residues, 3 models selected 
    3486 
    3487 > nucleotides sel stubs
    3488 
    3489 > select subtract #17
    3490 
    3491 3188 atoms, 3562 bonds, 150 residues, 2 models selected 
    3492 
    3493 > select subtract #18
    3494 
    3495 1594 atoms, 1781 bonds, 75 residues, 1 model selected 
    3496 
    3497 > select add #18
    3498 
    3499 3188 atoms, 3562 bonds, 150 residues, 2 models selected 
    3500 
    3501 > select add #17
    3502 
    3503 4782 atoms, 5343 bonds, 225 residues, 3 models selected 
    3504 
    3505 > ui tool show "Show Sequence Viewer"
    3506 
    3507 > sequence chain #17/A
    3508 
    3509 Alignment identifier is 17/A 
    3510 
    3511 > sequence chain #18/A
    3512 
    3513 Alignment identifier is 18/A 
    3514 
    3515 > sequence chain #19/A
    3516 
    3517 Alignment identifier is 19/A 
    3518 
    3519 QWindowsWindow::setGeometry: Unable to set geometry 1920x1134+0+35 (frame:
    3520 1942x1190-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    3521 Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
    3522 11, 11 minimum size: 624x756 MINMAXINFO(maxSize=POINT(x=0, y=0),
    3523 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
    3524 y=1190))) 
    3525 
    3526 > select subtract #19
    3527 
    3528 3188 atoms, 3562 bonds, 150 residues, 2 models selected 
    3529 
    3530 > select subtract #18
    3531 
    3532 1594 atoms, 1781 bonds, 75 residues, 1 model selected 
    3533 
    3534 > select subtract #17
    3535 
    3536 Nothing selected 
    3537 
    3538 > select #19/A:13
    3539 
    3540 20 atoms, 21 bonds, 1 residue, 1 model selected 
    3541 
    3542 > select #19/A:13-32
    3543 
    3544 420 atoms, 468 bonds, 20 residues, 1 model selected 
    3545 
    3546 > select ~sel & ##selected
    3547 
    3548 1174 atoms, 1313 bonds, 55 residues, 1 model selected 
    3549 
    3550 > delete atoms sel
    3551 
    3552 > delete bonds sel
    3553 
    3554 > select #18/A:33
    3555 
    3556 20 atoms, 21 bonds, 1 residue, 1 model selected 
    3557 
    3558 > select #18/A:33-59
    3559 
    3560 572 atoms, 638 bonds, 27 residues, 1 model selected 
    3561 
    3562 > select #18/A:33
    3563 
    3564 20 atoms, 21 bonds, 1 residue, 1 model selected 
    3565 
    3566 > select #18/A:33-63
    3567 
    3568 660 atoms, 737 bonds, 31 residues, 1 model selected 
    3569 
    3570 > select ~sel & ##selected
    3571 
    3572 934 atoms, 1044 bonds, 44 residues, 1 model selected 
    3573 
    3574 > delete atoms sel
    3575 
    3576 > delete bonds sel
    3577 
    3578 > select #17/A:12-13
    3579 
    3580 40 atoms, 43 bonds, 2 residues, 1 model selected 
    3581 
    3582 > select #17/A:12-63
    3583 
    3584 1100 atoms, 1228 bonds, 52 residues, 1 model selected 
    3585 
    3586 > delete atoms sel
    3587 
    3588 > delete bonds sel
    3589 
    3590 > select add #17
    3591 
    3592 494 atoms, 551 bonds, 1 pseudobond, 23 residues, 2 models selected 
    3593 
    3594 > select add #18
    3595 
    3596 1154 atoms, 1288 bonds, 1 pseudobond, 54 residues, 3 models selected 
    3597 
    3598 > select add #19
    3599 
    3600 1574 atoms, 1756 bonds, 1 pseudobond, 74 residues, 4 models selected 
    3601 
    3602 > select subtract #18
    3603 
    3604 914 atoms, 1019 bonds, 1 pseudobond, 43 residues, 3 models selected 
    3605 
    3606 > select subtract #19
    3607 
    3608 494 atoms, 551 bonds, 1 pseudobond, 23 residues, 2 models selected 
    3609 
    3610 > view matrix models
    3611 > #17,-0.33746,-0.0025218,-0.94134,251.56,0.92281,-0.19832,-0.33029,126.5,-0.18585,-0.98013,0.069253,162.3
    3612 
    3613 > ui mousemode right "translate selected models"
    3614 
    3615 > view matrix models
    3616 > #17,-0.33746,-0.0025218,-0.94134,221.15,0.92281,-0.19832,-0.33029,137.61,-0.18585,-0.98013,0.069253,230.68
    3617 
    3618 > fit#17 inmap #11
    3619 
    3620 Unknown command: fit#17 inmap #11 
    3621 
    3622 > fit#17 inmap #11
    3623 
    3624 Unknown command: fit#17 inmap #11 
    3625 
    3626 > fit#17 inmap #11
    3627 
    3628 Unknown command: fit#17 inmap #11 
    3629 
    3630 > fitmap #17 inMap #11
    3631 
    3632 Fit molecule region_3_stem.cif (#17) to map region_3.mrc (#11) using 494 atoms 
    3633 average map value = 0.02034, steps = 152 
    3634 shifted from previous position = 15.8 
    3635 rotated from previous position = 57.9 degrees 
    3636 atoms outside contour = 46, contour level = 0.0039469 
    3637  
    3638 Position of region_3_stem.cif (#17) relative to region_3.mrc (#11)
    3639 coordinates: 
    3640 Matrix rotation and translation 
    3641 -0.13072243 0.68750809 -0.71431383 230.67755924 
    3642 0.48701854 -0.58304173 -0.65028860 130.11432530 
    3643 -0.86355346 -0.43289139 -0.25861255 248.44280777 
    3644 Axis 0.65628298 0.45052750 -0.60524179 
    3645 Axis point 0.00000000 -32.19839622 237.14920419 
    3646 Rotation angle (degrees) 170.46630204 
    3647 Shift along axis 59.64186845 
    3648  
    3649 
    3650 > select subtract #17
    3651 
    3652 Nothing selected 
    3653 
    3654 > select add #18
    3655 
    3656 660 atoms, 737 bonds, 31 residues, 1 model selected 
    3657 
    3658 > view matrix models
    3659 > #18,-0.87941,-0.11639,-0.46163,240.73,0.47586,-0.18609,-0.85961,106.49,0.014142,-0.97562,0.21903,227.79
    3660 
    3661 > fitmap #18 inMap #11
    3662 
    3663 Fit molecule region_3_stemloop_1.cif (#18) to map region_3.mrc (#11) using 660
    3664 atoms 
    3665 average map value = 0.01098, steps = 180 
    3666 shifted from previous position = 18 
    3667 rotated from previous position = 29.1 degrees 
    3668 atoms outside contour = 340, contour level = 0.0039469 
    3669  
    3670 Position of region_3_stemloop_1.cif (#18) relative to region_3.mrc (#11)
    3671 coordinates: 
    3672 Matrix rotation and translation 
    3673 -0.74171820 0.34928190 -0.57258734 233.26637193 
    3674 0.51414519 -0.25212314 -0.81981012 120.84020558 
    3675 -0.43070736 -0.90246112 0.00742271 213.88373295 
    3676 Axis -0.35520974 -0.60975855 0.70853409 
    3677 Axis point 165.39454895 161.98845317 0.00000000 
    3678 Rotation angle (degrees) 173.31901522 
    3679 Shift along axis -4.99792143 
    3680  
    3681 
    3682 > ui mousemode right "rotate selected models"
    3683 
    3684 > view matrix models
    3685 > #18,-0.39586,-0.62219,-0.67541,235.16,0.49734,-0.76354,0.41189,126.2,-0.77198,-0.17286,0.6117,214.24
    3686 
    3687 > view matrix models
    3688 > #18,-0.42484,-0.89479,0.13738,238.41,0.18779,0.06135,0.98029,127.01,-0.88558,0.44226,0.14197,211.69
    3689 
    3690 > ui mousemode right "translate selected models"
    3691 
    3692 > view matrix models
    3693 > #18,-0.42484,-0.89479,0.13738,238.24,0.18779,0.06135,0.98029,134.21,-0.88558,0.44226,0.14197,221.15
    3694 
    3695 > fitmap #18 inMap #11
    3696 
    3697 Fit molecule region_3_stemloop_1.cif (#18) to map region_3.mrc (#11) using 660
    3698 atoms 
    3699 average map value = 0.02019, steps = 352 
    3700 shifted from previous position = 4.74 
    3701 rotated from previous position = 46.5 degrees 
    3702 atoms outside contour = 92, contour level = 0.0039469 
    3703  
    3704 Position of region_3_stemloop_1.cif (#18) relative to region_3.mrc (#11)
    3705 coordinates: 
    3706 Matrix rotation and translation 
    3707 -0.56096701 -0.77354279 -0.29486870 230.64413736 
    3708 0.47714143 -0.59319432 0.64842621 138.54664316 
    3709 -0.67649986 0.22305164 0.70185176 227.52913775 
    3710 Axis -0.30934926 0.27753732 0.90954718 
    3711 Axis point 134.25608165 96.84957985 0.00000000 
    3712 Rotation angle (degrees) 136.56499751 
    3713 Shift along axis 174.05075680 
    3714  
    3715 
    3716 > select subtract #18
    3717 
    3718 Nothing selected 
    3719 
    3720 > select add #19
    3721 
    3722 420 atoms, 468 bonds, 20 residues, 1 model selected 
    3723 
    3724 > view matrix models
    3725 > #19,-0.87941,-0.11639,-0.46163,239.74,0.47586,-0.18609,-0.85961,166.52,0.014142,-0.97562,0.21903,203.3
    3726 
    3727 > ui mousemode right "rotate selected models"
    3728 
    3729 > view matrix models
    3730 > #19,-0.71607,0.10544,0.69002,233.94,-0.38551,0.76435,-0.51686,156.57,-0.58191,-0.63612,-0.50669,202.47
    3731 
    3732 > ui mousemode right "translate selected models"
    3733 
    3734 > view matrix models
    3735 > #19,-0.71607,0.10544,0.69002,241.84,-0.38551,0.76435,-0.51686,125.89,-0.58191,-0.63612,-0.50669,254.33
    3736 
    3737 > view matrix models
    3738 > #19,-0.71607,0.10544,0.69002,242.44,-0.38551,0.76435,-0.51686,113.28,-0.58191,-0.63612,-0.50669,235.85
    3739 
    3740 > fitmap #19 inMap #11
    3741 
    3742 Fit molecule region_3_stemloop_2.cif (#19) to map region_3.mrc (#11) using 420
    3743 atoms 
    3744 average map value = 0.019, steps = 292 
    3745 shifted from previous position = 2.88 
    3746 rotated from previous position = 76.3 degrees 
    3747 atoms outside contour = 59, contour level = 0.0039469 
    3748  
    3749 Position of region_3_stemloop_2.cif (#19) relative to region_3.mrc (#11)
    3750 coordinates: 
    3751 Matrix rotation and translation 
    3752 0.09100647 -0.57474089 0.81325932 248.73552558 
    3753 -0.99242563 -0.12001126 0.02624228 137.70422521 
    3754 0.08251777 -0.80948761 -0.58130940 232.71669253 
    3755 Axis -0.70458946 0.61607560 -0.35214280 
    3756 Axis point 0.00000000 217.70064286 -2.66111062 
    3757 Rotation angle (degrees) 143.62542958 
    3758 Shift along axis -172.36972401 
    3759  
    3760 
    3761 > select subtract #19
    3762 
    3763 Nothing selected 
    3764 
    3765 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    3766 > Project/20251113 region_3.cxs"
    3767 
    3768 > close #12-16
    3769 
    3770 > hide #!11 models
    3771 
    3772 > hide #10 models
    3773 
    3774 > hide #!17 models
    3775 
    3776 > hide #18 models
    3777 
    3778 > show #18 models
    3779 
    3780 > show #!17 models
    3781 
    3782 > show #10 models
    3783 
    3784 > hide #10 models
    3785 
    3786 > show #5 models
    3787 
    3788 > show #10 models
    3789 
    3790 > nucleotides #5,10,18-19#!17 stubs
    3791 
    3792 > rename #17 id #12
    3793 
    3794 > rename #18 id #13
    3795 
    3796 > rename #19 id #14
    3797 
    3798 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    3799 > Project/20251113 region_3.cxs"
    3800 
    3801 ——— End of log from Thu Nov 13 15:31:54 2025 ———
    3802 
    3803 > view name session-start
    3804 
    3805 opened ChimeraX session 
    3806 Showing volume difference.seg - 189 regions, 189 surfaces 
    3807 
    3808 > show #!11 models
    3809 
    3810 > hide #!11 models
    3811 
    3812 > hide #!6 models
    3813 
    3814 > show #!6 models
    3815 
    3816 > select add #4
    3817 
    3818 3 models selected 
    3819 
    3820 > select subtract #4
    3821 
    3822 Nothing selected 
    3823 
    3824 > select add #6
    3825 
    3826 190 models selected 
    3827 
    3828 > transparency sel 0
    3829 
    3830 > transparency sel 50
    3831 
    3832 > select subtract #6
    3833 
    3834 Nothing selected 
    3835 
    3836 > select add #6.125
    3837 
    3838 1 model selected 
    3839 
    3840 > select add #6.108
    3841 
    3842 2 models selected 
    3843 
    3844 > select add #6.189
    3845 
    3846 3 models selected 
    3847 Grouped 3 regions 
    3848 
    3849 > transparency sel 0
    3850 
    3851 [Repeated 1 time(s)]
    3852 
    3853 > select add #6
    3854 
    3855 188 models selected 
    3856 
    3857 > select subtract #6
    3858 
    3859 Nothing selected 
    3860 
    3861 > select add #6.91
    3862 
    3863 1 model selected 
    3864 
    3865 > select add #6.108
    3866 
    3867 2 models selected 
    3868 Grouped 2 regions 
    3869 
    3870 > select add #6
    3871 
    3872 187 models selected 
    3873 
    3874 > select subtract #6
    3875 
    3876 Nothing selected 
    3877 
    3878 > hide #5 models
    3879 
    3880 > show #5 models
    3881 
    3882 > hide #6.188 models
    3883 
    3884 > hide #6.185 models
    3885 
    3886 > show #6.185 models
    3887 
    3888 > hide #6.187 models
    3889 
    3890 > select add #6.186
    3891 
    3892 1 model selected 
    3893 
    3894 > hide #6.186 models
    3895 
    3896 > select subtract #6.186
    3897 
    3898 Nothing selected 
    3899 
    3900 > select add #6.121
    3901 
    3902 1 model selected 
    3903 
    3904 > select add #6.50
    3905 
    3906 2 models selected 
    3907 
    3908 > select add #6.141
    3909 
    3910 3 models selected 
    3911 
    3912 > select add #6.40
    3913 
    3914 4 models selected 
    3915 
    3916 > select add #6.87
    3917 
    3918 5 models selected 
    3919 
    3920 > select add #6.83
    3921 
    3922 6 models selected 
    3923 
    3924 > undo
    3925 
    3926 > select #6.87
    3927 
    3928 1 model selected 
    3929 
    3930 > undo
    3931 
    3932 [Repeated 9 time(s)]
    3933 
    3934 > select #6.141
    3935 
    3936 1 model selected 
    3937 
    3938 > undo
    3939 
    3940 > select add #6.50
    3941 
    3942 2 models selected 
    3943 
    3944 > select add #6.43
    3945 
    3946 3 models selected 
    3947 
    3948 > select add #6.95
    3949 
    3950 4 models selected 
    3951 
    3952 > select add #6.172
    3953 
    3954 5 models selected 
    3955 
    3956 > select add #6.173
    3957 
    3958 6 models selected 
    3959 
    3960 > select add #6.61
    3961 
    3962 7 models selected 
    3963 
    3964 > select subtract #6.61
    3965 
    3966 6 models selected 
    3967 
    3968 > select add #6.91
    3969 
    3970 7 models selected 
    3971 Grouped 7 regions 
    3972 
    3973 > select add #6
    3974 
    3975 181 models selected 
    3976 
    3977 > select subtract #6
    3978 
    3979 Nothing selected 
    3980 
    3981 > select add #6
    3982 
    3983 181 models selected 
    3984 
    3985 > select subtract #6
    3986 
    3987 Nothing selected 
    3988 
    3989 > select add #6.43
    3990 
    3991 1 model selected 
    3992 
    3993 > select ~sel & ##selected
    3994 
    3995 Nothing selected 
    3996 
    3997 > select add #6.43
    3998 
    3999 1 model selected 
    4000 
    4001 > select ~sel & ##selected
    4002 
    4003 Nothing selected 
    4004 
    4005 > select add #6.43
    4006 
    4007 1 model selected 
    4008 Saving 1 regions to mrc file... 
    4009 Opened region_4_2.mrc as #15, grid size 108,100,92, pixel 1.12, shown at step
    4010 1, values float32 
    4011 Wrote region_4_2.mrc 
    4012 
    4013 > hide #5 models
    4014 
    4015 > show #5 models
    4016 
    4017 > hide #!6 models
    4018 
    4019 > volume #15 level 0.017
    4020 
    4021 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    4022 > Project/20251113_rna_phicb5_region_4_120nu/fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif"
    4023 
    4024 Chain information for
    4025 fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif #16 
    4026 --- 
    4027 Chain | Description 
    4028 A | . 
    4029  
    4030 Computing secondary structure 
    4031 
    4032 > rename #16 region_4_120nu_model_0.cif
    4033 
    4034 > rename #16 region_4_120nu.cif
    4035 
    4036 > view
    4037 
    4038 > select add #16
    4039 
    4040 2557 atoms, 2861 bonds, 120 residues, 2 models selected 
    4041 
    4042 > select add #5
    4043 
    4044 4892 atoms, 5464 bonds, 231 residues, 3 models selected 
    4045 
    4046 > select subtract #5
    4047 
    4048 2557 atoms, 2861 bonds, 120 residues, 2 models selected 
    4049 
    4050 > show #!6 models
    4051 
    4052 > view
    4053 
    4054 > ui mousemode right "translate selected models"
    4055 
    4056 > view matrix models
    4057 > #6.43,1,0,0,30.066,0,1,0,5.8403,0,0,1,14.045,#16,1,0,0,30.066,0,1,0,5.8403,0,0,1,14.045
    4058 
    4059 > undo
    4060 
    4061 > select add #6
    4062 
    4063 2557 atoms, 2861 bonds, 120 residues, 182 models selected 
    4064 
    4065 > select subtract #6
    4066 
    4067 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    4068 
    4069 > view matrix models #16,1,0,0,177.83,0,1,0,-26.18,0,0,1,219.9
    4070 
    4071 > select subtract #16
    4072 
    4073 Nothing selected 
    4074 
    4075 > hide #!6 models
    4076 
    4077 > select add #16
    4078 
    4079 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    4080 
    4081 > view matrix models #16,1,0,0,249.72,0,1,0,195.7,0,0,1,188.42
    4082 
    4083 > view matrix models #16,1,0,0,220.25,0,1,0,198.26,0,0,1,149.22
    4084 
    4085 > undo
    4086 
    4087 > select subtract #16
    4088 
    4089 Nothing selected 
    4090 
    4091 > ui mousemode right "rotate selected models"
    4092 
    4093 > select add #16
    4094 
    4095 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    4096 
    4097 > view matrix models
    4098 > #16,-0.57831,0.42398,0.69699,242.08,0.41526,0.88837,-0.19585,197.73,-0.70222,0.17617,-0.68982,192.83
    4099 
    4100 > view matrix models
    4101 > #16,-0.82518,0.42952,0.36686,242.66,0.49804,0.85966,0.11377,196.96,-0.26651,0.27659,-0.92329,194.2
    4102 
    4103 > select subtract #16
    4104 
    4105 Nothing selected 
    4106 
    4107 > ui mousemode right "translate selected models"
    4108 
    4109 > select add #16
    4110 
    4111 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    4112 
    4113 > view matrix models
    4114 > #16,-0.82518,0.42952,0.36686,186.47,0.49804,0.85966,0.11377,166.94,-0.26651,0.27659,-0.92329,233.94
    4115 
    4116 > ui mousemode right "move picked models"
    4117 
    4118 > ui mousemode right "rotate selected models"
    4119 
    4120 > view matrix models
    4121 > #16,-0.62712,0.76371,-0.1532,186.85,0.66899,0.62883,0.39626,166.67,0.39897,0.14601,-0.90527,236.05
    4122 
    4123 > view matrix models
    4124 > #16,-0.36789,0.88151,-0.29597,187.24,0.73741,0.47047,0.48464,167.3,0.56646,-0.039959,-0.82312,237.04
    4125 
    4126 > ui mousemode right "translate selected models"
    4127 
    4128 > view matrix models
    4129 > #16,-0.36789,0.88151,-0.29597,185.09,0.73741,0.47047,0.48464,181.43,0.56646,-0.039959,-0.82312,241.74
    4130 
    4131 > fitmap #16 inMap #15
    4132 
    4133 Fit molecule region_4_120nu.cif (#16) to map region_4_2.mrc (#15) using 2557
    4134 atoms 
    4135 average map value = 0.009566, steps = 120 
    4136 shifted from previous position = 7.67 
    4137 rotated from previous position = 5.26 degrees 
    4138 atoms outside contour = 1735, contour level = 0.017 
    4139  
    4140 Position of region_4_120nu.cif (#16) relative to region_4_2.mrc (#15)
    4141 coordinates: 
    4142 Matrix rotation and translation 
    4143 -0.28475396 0.91689579 -0.27967347 189.69488230 
    4144 0.76517002 0.39314944 0.50985129 176.45360329 
    4145 0.57743399 -0.06881558 -0.81353205 245.41255409 
    4146 Axis -0.55362547 -0.82001673 -0.14515994 
    4147 Axis point 0.19311164 -0.00000000 112.54517601 
    4148 Rotation angle (degrees) 148.49211885 
    4149 Shift along axis -285.33889665 
    4150  
    4151 
    4152 > hide #5 models
    4153 
    4154 > hide #10 models
    4155 
    4156 > hide #!12 models
    4157 
    4158 > hide #13 models
    4159 
    4160 > hide #14 models
    4161 
    4162 > show #!12 models
    4163 
    4164 > select subtract #16
    4165 
    4166 Nothing selected 
    4167 
    4168 > select add #16
    4169 
    4170 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    4171 
    4172 > view matrix models
    4173 > #16,-0.28475,0.9169,-0.27967,188.17,0.76517,0.39315,0.50985,171.38,0.57743,-0.068816,-0.81353,229.14
    4174 
    4175 > select subtract #16
    4176 
    4177 Nothing selected 
    4178 
    4179 > select add #16
    4180 
    4181 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    4182 
    4183 > ui mousemode right "rotate selected models"
    4184 
    4185 > view matrix models
    4186 > #16,-0.53508,0.57863,-0.61553,190.83,0.84344,0.32461,-0.42806,175.57,-0.047878,-0.74821,-0.66173,230.98
    4187 
    4188 > ui mousemode right "translate selected models"
    4189 
    4190 > view matrix models
    4191 > #16,-0.53508,0.57863,-0.61553,174.89,0.84344,0.32461,-0.42806,183.56,-0.047878,-0.74821,-0.66173,233.78
    4192 
    4193 > select subtract #16
    4194 
    4195 Nothing selected 
    4196 
    4197 > fitmap #16 inMap #15
    4198 
    4199 Fit molecule region_4_120nu.cif (#16) to map region_4_2.mrc (#15) using 2557
    4200 atoms 
    4201 average map value = 0.01117, steps = 168 
    4202 shifted from previous position = 11.1 
    4203 rotated from previous position = 6.6 degrees 
    4204 atoms outside contour = 1531, contour level = 0.017 
    4205  
    4206 Position of region_4_120nu.cif (#16) relative to region_4_2.mrc (#15)
    4207 coordinates: 
    4208 Matrix rotation and translation 
    4209 -0.61979660 0.50270893 -0.60260757 173.34699647 
    4210 0.78430487 0.37058243 -0.49752841 194.64245906 
    4211 -0.02679619 -0.78099446 -0.62396281 234.04968581 
    4212 Axis -0.40445326 -0.82157557 0.40178495 
    4213 Axis point 6.97144648 0.00000000 177.65200697 
    4214 Rotation angle (degrees) 159.48631031 
    4215 Shift along axis -135.98660569 
    4216  
    4217 
    4218 > hide #16 models
    4219 
    4220 > select add #15
    4221 
    4222 2 models selected 
    4223 
    4224 > ui tool show "Segment Map"
    4225 
    4226 Segmenting volume difference, density threshold 0.011922 
    4227 Showing 194 region surfaces 
    4228 2209 watershed regions, grouped to 194 regions 
    4229 Showing volume difference.seg - 194 regions, 194 surfaces 
    4230 
    4231 > hide #!6 models
    4232 
    4233 > select subtract #15
    4234 
    4235 Nothing selected 
    4236 
    4237 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    4238 > Project/20251113_rna_phicb5_region_4_stemloop_1/fold_2025_11_13_16_35_rna_phicb5_region_4_stemloop_1_model_0.cif"
    4239 
    4240 Chain information for
    4241 fold_2025_11_13_16_35_rna_phicb5_region_4_stemloop_1_model_0.cif #17 
    4242 --- 
    4243 Chain | Description 
    4244 A | . 
    4245  
    4246 Computing secondary structure 
    4247 
    4248 > rename #17 region_4_stemloop_1.cif
    4249 
    4250 > view
    4251 
    4252 > select add #17
    4253 
    4254 767 atoms, 855 bonds, 36 residues, 1 model selected 
    4255 
    4256 > view matrix models #17,1,0,0,60.502,0,1,0,261.29,0,0,1,93.386
    4257 
    4258 > select subtract #17
    4259 
    4260 Nothing selected 
    4261 
    4262 > select add #17
    4263 
    4264 767 atoms, 855 bonds, 36 residues, 1 model selected 
    4265 
    4266 > view matrix models #17,1,0,0,140.1,0,1,0,140.23,0,0,1,193.3
    4267 
    4268 > view matrix models #17,1,0,0,179.86,0,1,0,176.45,0,0,1,205
    4269 
    4270 > select subtract #17
    4271 
    4272 Nothing selected 
    4273 
    4274 > fitmap #17 inMap #15
    4275 
    4276 Fit molecule region_4_stemloop_1.cif (#17) to map region_4_2.mrc (#15) using
    4277 767 atoms 
    4278 average map value = 0.01573, steps = 196 
    4279 shifted from previous position = 16.3 
    4280 rotated from previous position = 62 degrees 
    4281 atoms outside contour = 352, contour level = 0.017 
    4282  
    4283 Position of region_4_stemloop_1.cif (#17) relative to region_4_2.mrc (#15)
    4284 coordinates: 
    4285 Matrix rotation and translation 
    4286 0.63718988 0.58570337 0.50093973 193.33216599 
    4287 -0.16123908 0.73689782 -0.65649339 179.93984192 
    4288 -0.75365178 0.33753988 0.56398211 215.41428826 
    4289 Axis 0.56275826 0.71026973 -0.42287120 
    4290 Axis point 349.66657078 0.00000000 30.77979180 
    4291 Rotation angle (degrees) 62.02833176 
    4292 Shift along axis 145.51259855 
    4293  
    4294 
    4295 > select add #17
    4296 
    4297 767 atoms, 855 bonds, 36 residues, 1 model selected 
    4298 
    4299 > view matrix models
    4300 > #17,0.63719,0.5857,0.50094,179.71,-0.16124,0.7369,-0.65649,134.47,-0.75365,0.33754,0.56398,204.32
    4301 
    4302 > view matrix models
    4303 > #17,0.63719,0.5857,0.50094,182.09,-0.16124,0.7369,-0.65649,226.47,-0.75365,0.33754,0.56398,203.71
    4304 
    4305 > ui mousemode right "rotate selected models"
    4306 
    4307 > view matrix models
    4308 > #17,0.81737,-0.41844,-0.39599,183.75,0.33938,0.90516,-0.25595,224.77,0.46553,0.074822,0.88186,201.01
    4309 
    4310 > select subtract #17
    4311 
    4312 Nothing selected 
    4313 
    4314 > ui mousemode right "translate selected models"
    4315 
    4316 > ui mousemode right "rotate selected models"
    4317 
    4318 > select add #17
    4319 
    4320 767 atoms, 855 bonds, 36 residues, 1 model selected 
    4321 
    4322 > view matrix models
    4323 > #17,0.57938,0.79297,-0.18846,182.94,-0.37806,0.056611,-0.92405,227.84,-0.72208,0.60662,0.33259,203.72
    4324 
    4325 > view matrix models
    4326 > #17,-0.88964,-0.12232,0.43997,185.89,-0.2621,-0.65218,-0.71131,227.92,0.37395,-0.74813,0.54814,202.34
    4327 
    4328 > select subtract #17
    4329 
    4330 Nothing selected 
    4331 
    4332 > select add #17
    4333 
    4334 767 atoms, 855 bonds, 36 residues, 1 model selected 
    4335 
    4336 > show #!6 models
    4337 
    4338 > hide #!6 models
    4339 
    4340 > show #!6 models
    4341 
    4342 > hide #!6 models
    4343 
    4344 > show #!6 models
    4345 
    4346 > select subtract #17
    4347 
    4348 Nothing selected 
    4349 
    4350 > hide #!15 models
    4351 
    4352 > show #!15 models
    4353 
    4354 > hide #!15 models
    4355 
    4356 > show #!15 models
    4357 
    4358 > transparency #6#15.1 50
    4359 
    4360 > show #10 models
    4361 
    4362 > show #5 models
    4363 
    4364 > hide #5 models
    4365 
    4366 > show #5 models
    4367 
    4368 > hide #5 models
    4369 
    4370 > hide #!6 models
    4371 
    4372 > hide #10 models
    4373 
    4374 > select add #17
    4375 
    4376 767 atoms, 855 bonds, 36 residues, 1 model selected 
    4377 
    4378 > view matrix models
    4379 > #17,-0.9658,-0.15764,0.20586,186.38,-0.032602,-0.71383,-0.69956,227.49,0.25723,-0.68235,0.68427,202.34
    4380 
    4381 > ui mousemode right "translate selected models"
    4382 
    4383 > view matrix models
    4384 > #17,-0.9658,-0.15764,0.20586,146.38,-0.032602,-0.71383,-0.69956,180.8,0.25723,-0.68235,0.68427,260.34
    4385 
    4386 > fitmap #17 inMap #15
    4387 
    4388 Fit molecule region_4_stemloop_1.cif (#17) to map region_4_2.mrc (#15) using
    4389 767 atoms 
    4390 average map value = 0.01913, steps = 88 
    4391 shifted from previous position = 4.9 
    4392 rotated from previous position = 15.8 degrees 
    4393 atoms outside contour = 301, contour level = 0.017 
    4394  
    4395 Position of region_4_stemloop_1.cif (#17) relative to region_4_2.mrc (#15)
    4396 coordinates: 
    4397 Matrix rotation and translation 
    4398 -0.86454611 -0.33525618 0.37438389 146.86140773 
    4399 -0.06548829 -0.66345498 -0.74534469 183.59063241 
    4400 0.49826829 -0.66890261 0.55163210 264.38738669 
    4401 Axis 0.24937242 -0.40414064 0.88004758 
    4402 Axis point 24.47750757 156.80350177 0.00000000 
    4403 Rotation angle (degrees) 171.18358655 
    4404 Shift along axis 195.10022874 
    4405  
    4406 
    4407 > color #17 red
    4408 
    4409 > undo
    4410 
    4411 > select subtract #17
    4412 
    4413 Nothing selected 
    4414 
    4415 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    4416 > Project/20251114 region_4_wip.cxs"
    4417 
    4418 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    4419 > Project/20251114_rna_phicb5_region_4_stemloop_2/fold_2025_11_14_08_10_rna_phicb5_region_4_stemloop_2_model_0.cif"
    4420 
    4421 Chain information for
    4422 fold_2025_11_14_08_10_rna_phicb5_region_4_stemloop_2_model_0.cif #18 
    4423 --- 
    4424 Chain | Description 
    4425 A | . 
    4426  
    4427 Computing secondary structure 
    4428 
    4429 > rename #18 region_4_stemloop_2.cif
    4430 
    4431 > view
    4432 
    4433 > select add #18
    4434 
    4435 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4436 
    4437 > view matrix models #18,1,0,0,49.192,0,1,0,188.78,0,0,1,201
    4438 
    4439 > view matrix models #18,1,0,0,110.09,0,1,0,184.21,0,0,1,241.09
    4440 
    4441 > select subtract #18
    4442 
    4443 Nothing selected 
    4444 
    4445 > select add #18
    4446 
    4447 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4448 
    4449 > view matrix models #18,1,0,0,97.509,0,1,0,167.14,0,0,1,280.39
    4450 
    4451 > ui mousemode right "rotate selected models"
    4452 
    4453 > view matrix models
    4454 > #18,-0.052861,-0.98425,0.16871,94.316,-0.57615,-0.10793,-0.81019,166.48,0.81563,-0.14003,-0.56137,283.87
    4455 
    4456 > view matrix models
    4457 > #18,0.84482,-0.45859,0.27565,96.502,0.32042,0.021036,-0.94704,169.08,0.4285,0.8884,0.16471,282.01
    4458 
    4459 > view matrix models
    4460 > #18,0.82385,-0.032425,0.56588,95.313,0.43211,0.68204,-0.59001,168.74,-0.36682,0.7306,0.57591,279.65
    4461 
    4462 > ui mousemode right "translate selected models"
    4463 
    4464 > view matrix models
    4465 > #18,0.82385,-0.032425,0.56588,141.44,0.43211,0.68204,-0.59001,223.97,-0.36682,0.7306,0.57591,241.28
    4466 
    4467 > view matrix models
    4468 > #18,0.82385,-0.032425,0.56588,158.67,0.43211,0.68204,-0.59001,229.63,-0.36682,0.7306,0.57591,249.19
    4469 
    4470 > select ~sel & ##selected
    4471 
    4472 Nothing selected 
    4473 
    4474 > fitmap #18 inMap #15
    4475 
    4476 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4477 1377 atoms 
    4478 average map value = 0.01171, steps = 156 
    4479 shifted from previous position = 13.7 
    4480 rotated from previous position = 18.9 degrees 
    4481 atoms outside contour = 808, contour level = 0.017 
    4482  
    4483 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4484 coordinates: 
    4485 Matrix rotation and translation 
    4486 0.65891515 -0.10922066 0.74424569 149.69902909 
    4487 0.68455489 0.49717458 -0.53310601 227.06790773 
    4488 -0.31179385 0.86074867 0.40236341 259.53256306 
    4489 Axis 0.72579569 0.54989158 0.41332779 
    4490 Axis point 0.00000000 -52.09164905 123.55093508 
    4491 Rotation angle (degrees) 73.78595041 
    4492 Shift along axis 340.78566210 
    4493  
    4494 
    4495 > select add #18
    4496 
    4497 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4498 
    4499 > view matrix models
    4500 > #18,0.65892,-0.10922,0.74425,160.76,0.68455,0.49717,-0.53311,225.24,-0.31179,0.86075,0.40236,254.97
    4501 
    4502 > select subtract #18
    4503 
    4504 Nothing selected 
    4505 
    4506 > select add #18
    4507 
    4508 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4509 
    4510 > view matrix models
    4511 > #18,0.65892,-0.10922,0.74425,168.78,0.68455,0.49717,-0.53311,220.49,-0.31179,0.86075,0.40236,253.38
    4512 
    4513 > select subtract #18
    4514 
    4515 Nothing selected 
    4516 
    4517 > fitmap #18 inMap #15
    4518 
    4519 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4520 1377 atoms 
    4521 average map value = 0.01678, steps = 504 
    4522 shifted from previous position = 8.77 
    4523 rotated from previous position = 83.5 degrees 
    4524 atoms outside contour = 508, contour level = 0.017 
    4525  
    4526 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4527 coordinates: 
    4528 Matrix rotation and translation 
    4529 -0.20973364 -0.21007278 0.95492472 161.58163537 
    4530 -0.00177812 0.97672709 0.21447852 213.89266455 
    4531 -0.97775694 0.04328539 -0.20522606 248.71601996 
    4532 Axis -0.08772847 0.99040901 0.10674128 
    4533 Axis point 181.08562946 0.00000000 39.59869629 
    4534 Rotation angle (degrees) 102.65713467 
    4535 Shift along axis 224.21417822 
    4536  
    4537 
    4538 > select add #18
    4539 
    4540 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4541 
    4542 > view matrix models
    4543 > #18,-0.20973,-0.21007,0.95492,155.21,-0.0017781,0.97673,0.21448,221.7,-0.97776,0.043285,-0.20523,251.09
    4544 
    4545 > select subtract #18
    4546 
    4547 Nothing selected 
    4548 
    4549 > fitmap #18 inMap #15
    4550 
    4551 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4552 1377 atoms 
    4553 average map value = 0.01681, steps = 116 
    4554 shifted from previous position = 9.59 
    4555 rotated from previous position = 10 degrees 
    4556 atoms outside contour = 519, contour level = 0.017 
    4557  
    4558 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4559 coordinates: 
    4560 Matrix rotation and translation 
    4561 -0.31825061 -0.28525117 0.90407317 160.86993562 
    4562 -0.12129700 0.95807110 0.25958967 214.22093133 
    4563 -0.94021464 -0.02704679 -0.33950683 248.95705007 
    4564 Axis -0.15298566 0.98434646 0.08750679 
    4565 Axis point 178.42765225 0.00000000 47.02600011 
    4566 Rotation angle (degrees) 110.47772294 
    4567 Shift along axis 208.04225418 
    4568  
    4569 
    4570 > ui mousemode right "translate selected models"
    4571 
    4572 > ui mousemode right "rotate selected models"
    4573 
    4574 > select add #18
    4575 
    4576 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4577 
    4578 > view matrix models
    4579 > #18,-0.58077,-0.67576,0.45393,160.77,-0.66279,0.71627,0.21831,212.79,-0.47266,-0.17407,-0.86388,250.94
    4580 
    4581 > ui mousemode right "translate selected models"
    4582 
    4583 > view matrix models
    4584 > #18,-0.58077,-0.67576,0.45393,151.73,-0.66279,0.71627,0.21831,220.69,-0.47266,-0.17407,-0.86388,256.92
    4585 
    4586 > fitmap #18 inMap #15
    4587 
    4588 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4589 1377 atoms 
    4590 average map value = 0.01667, steps = 524 
    4591 shifted from previous position = 12.1 
    4592 rotated from previous position = 26.3 degrees 
    4593 atoms outside contour = 531, contour level = 0.017 
    4594  
    4595 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4596 coordinates: 
    4597 Matrix rotation and translation 
    4598 -0.48377449 -0.45033190 0.75044213 159.41944458 
    4599 -0.39242340 0.87804702 0.27392938 214.32135991 
    4600 -0.78228262 -0.16197101 -0.60149753 249.82409578 
    4601 Axis -0.27336794 0.96122375 0.03631639 
    4602 Axis point 173.18356662 0.00000000 67.51007497 
    4603 Rotation angle (degrees) 127.12906500 
    4604 Shift along axis 171.50332538 
    4605  
    4606 
    4607 > select subtract #18
    4608 
    4609 Nothing selected 
    4610 
    4611 > show #!6 models
    4612 
    4613 > hide #!6 models
    4614 
    4615 > show #!7 models
    4616 
    4617 > hide #!7 models
    4618 
    4619 > show #!6 models
    4620 
    4621 > hide #!6 models
    4622 
    4623 > volume #15 level 0.015
    4624 
    4625 > volume #15 level 0.02
    4626 
    4627 > volume #15 level 0.017
    4628 
    4629 > volume #15 level 0.015
    4630 
    4631 > fitmap #18 inMap #15
    4632 
    4633 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4634 1377 atoms 
    4635 average map value = 0.01667, steps = 40 
    4636 shifted from previous position = 0.104 
    4637 rotated from previous position = 1.39 degrees 
    4638 atoms outside contour = 475, contour level = 0.015 
    4639  
    4640 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4641 coordinates: 
    4642 Matrix rotation and translation 
    4643 -0.47517140 -0.43900751 0.76255133 159.52208081 
    4644 -0.37535668 0.88496373 0.27558402 214.31145790 
    4645 -0.79581372 -0.15527909 -0.58529386 249.76369944 
    4646 Axis -0.26627981 0.96309275 0.03933716 
    4647 Axis point 173.65219894 0.00000000 66.06604205 
    4648 Rotation angle (degrees) 125.99755800 
    4649 Shift along axis 173.74929821 
    4650  
    4651 
    4652 > fitmap #18 inMap #15
    4653 
    4654 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4655 1377 atoms 
    4656 average map value = 0.01667, steps = 40 
    4657 shifted from previous position = 0.0346 
    4658 rotated from previous position = 0.505 degrees 
    4659 atoms outside contour = 475, contour level = 0.015 
    4660  
    4661 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4662 coordinates: 
    4663 Matrix rotation and translation 
    4664 -0.47191792 -0.43490924 0.76690769 159.55518190 
    4665 -0.36917760 0.88740807 0.27607030 214.30110182 
    4666 -0.80062560 -0.15284262 -0.57934253 249.75234606 
    4667 Axis -0.26370572 0.96375622 0.04041335 
    4668 Axis point 173.82598149 0.00000000 65.55170326 
    4669 Rotation angle (degrees) 125.58613536 
    4670 Shift along axis 174.55173573 
    4671  
    4672 
    4673 > select add #18
    4674 
    4675 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4676 
    4677 > view matrix models
    4678 > #18,-0.47192,-0.43491,0.76691,150.67,-0.36918,0.88741,0.27607,218.15,-0.80063,-0.15284,-0.57934,252.48
    4679 
    4680 > select subtract #18
    4681 
    4682 Nothing selected 
    4683 
    4684 > ui mousemode right "rotate selected models"
    4685 
    4686 > select add #18
    4687 
    4688 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4689 
    4690 > view matrix models
    4691 > #18,-0.63756,-0.14493,0.75664,150.29,-0.3077,0.94831,-0.077626,218.85,-0.70628,-0.28231,-0.6492,252.83
    4692 
    4693 > view matrix models
    4694 > #18,-0.5574,-0.6642,0.49813,150.78,-0.73589,0.67305,0.073978,217.35,-0.3844,-0.32534,-0.86394,254.06
    4695 
    4696 > view matrix models
    4697 > #18,0.20816,-0.96279,-0.17236,153.35,-0.96819,-0.17781,-0.17602,217.28,0.13883,0.20351,-0.96918,255.25
    4698 
    4699 > view matrix models
    4700 > #18,0.41964,-0.90726,0.027811,153.6,-0.86658,-0.40957,-0.28511,217.88,0.27006,0.095546,-0.95809,255.62
    4701 
    4702 > view matrix models
    4703 > #18,-0.55462,-0.74534,0.36995,150.8,-0.82247,0.55851,-0.10778,217.64,-0.12629,-0.36405,-0.92278,254.77
    4704 
    4705 > view matrix models
    4706 > #18,-0.040987,-0.98834,-0.14665,152.55,-0.96567,0.076864,-0.24813,217.56,0.25651,0.13144,-0.95756,255.58
    4707 
    4708 > ui mousemode right "translate selected models"
    4709 
    4710 > view matrix models
    4711 > #18,-0.040987,-0.98834,-0.14665,152.86,-0.96567,0.076864,-0.24813,224.01,0.25651,0.13144,-0.95756,256.67
    4712 
    4713 > fitmap #18 inMap #15
    4714 
    4715 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4716 1377 atoms 
    4717 average map value = 0.01667, steps = 1080 
    4718 shifted from previous position = 13.9 
    4719 rotated from previous position = 87.9 degrees 
    4720 atoms outside contour = 475, contour level = 0.015 
    4721  
    4722 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4723 coordinates: 
    4724 Matrix rotation and translation 
    4725 -0.48169283 -0.44710906 0.75370120 159.44262379 
    4726 -0.38754440 0.88006757 0.27439099 214.32321636 
    4727 -0.78599068 -0.15992051 -0.59719685 249.79458485 
    4728 Axis -0.27129501 0.96177681 0.03720739 
    4729 Axis point 173.27269554 0.00000000 67.11626704 
    4730 Rotation angle (degrees) 126.82772950 
    4731 Shift along axis 172.16931385 
    4732  
    4733 
    4734 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    4735 > Project/20251114_rna_phicb5_region_4_stemloop_2_2/fold_2025_11_14_08_25_rna_phicb5_region_4_stemloop_2_2_model_0.cif"
    4736 
    4737 Chain information for
    4738 fold_2025_11_14_08_25_rna_phicb5_region_4_stemloop_2_2_model_0.cif #19 
    4739 --- 
    4740 Chain | Description 
    4741 A | . 
    4742  
    4743 Computing secondary structure 
    4744 
    4745 > rename #19 region_4_stemloop_2_2.cif
    4746 
    4747 > select subtract #18
    4748 
    4749 Nothing selected 
    4750 
    4751 > hide #18 models
    4752 
    4753 > view
    4754 
    4755 > select add #19
    4756 
    4757 1475 atoms, 1648 bonds, 69 residues, 1 model selected 
    4758 
    4759 > view matrix models #19,1,0,0,-37.537,0,1,0,253.28,0,0,1,131.08
    4760 
    4761 > select subtract #19
    4762 
    4763 Nothing selected 
    4764 
    4765 > select add #19
    4766 
    4767 1475 atoms, 1648 bonds, 69 residues, 1 model selected 
    4768 
    4769 > view matrix models #19,1,0,0,200.89,0,1,0,228.69,0,0,1,233.87
    4770 
    4771 > select subtract #19
    4772 
    4773 Nothing selected 
    4774 
    4775 > nucleotides #17,19#!12 stubs
    4776 
    4777 > select add #19
    4778 
    4779 1475 atoms, 1648 bonds, 69 residues, 1 model selected 
    4780 
    4781 > nucleotides sel stubs
    4782 
    4783 > ui mousemode right "rotate selected models"
    4784 
    4785 > view matrix models
    4786 > #19,-0.67503,-0.73307,0.083312,202.62,0.46352,-0.50924,-0.72514,230,0.574,-0.45088,0.68354,233.46
    4787 
    4788 > view matrix models
    4789 > #19,-0.70302,-0.70777,-0.069474,202.96,0.41207,-0.32577,-0.85093,230.25,0.57963,-0.62684,0.52067,233.86
    4790 
    4791 > view matrix models
    4792 > #19,-0.96675,-0.21485,0.13868,202.69,0.25484,-0.76454,0.59206,227.82,-0.021181,0.60771,0.79387,233.57
    4793 
    4794 > ui mousemode right "translate selected models"
    4795 
    4796 > view matrix models
    4797 > #19,-0.96675,-0.21485,0.13868,164.99,0.25484,-0.76454,0.59206,224.56,-0.021181,0.60771,0.79387,256.15
    4798 
    4799 > select subtract #19
    4800 
    4801 Nothing selected 
    4802 
    4803 > fitmap #19 inMap #15
    4804 
    4805 Fit molecule region_4_stemloop_2_2.cif (#19) to map region_4_2.mrc (#15) using
    4806 1475 atoms 
    4807 average map value = 0.01361, steps = 328 
    4808 shifted from previous position = 15.4 
    4809 rotated from previous position = 30.7 degrees 
    4810 atoms outside contour = 732, contour level = 0.015 
    4811  
    4812 Position of region_4_stemloop_2_2.cif (#19) relative to region_4_2.mrc (#15)
    4813 coordinates: 
    4814 Matrix rotation and translation 
    4815 -0.80630916 -0.39740387 0.43810460 148.86026835 
    4816 0.51062823 -0.84149826 0.17646365 223.71740309 
    4817 0.29853693 0.36599284 0.88143343 256.30814112 
    4818 Axis 0.20204767 0.14878616 0.96800796 
    4819 Axis point 24.86292645 103.21513995 0.00000000 
    4820 Rotation angle (degrees) 152.02923384 
    4821 Shift along axis 311.47124518 
    4822  
    4823 
    4824 > show #18 models
    4825 
    4826 > hide #19 models
    4827 
    4828 > hide #18 models
    4829 
    4830 > show #19 models
    4831 
    4832 > rename #19 region_4_stemloop_1_2.cif
    4833 
    4834 > fitmap #19 inMap #15
    4835 
    4836 Fit molecule region_4_stemloop_1_2.cif (#19) to map region_4_2.mrc (#15) using
    4837 1475 atoms 
    4838 average map value = 0.0136, steps = 48 
    4839 shifted from previous position = 0.0389 
    4840 rotated from previous position = 0.599 degrees 
    4841 atoms outside contour = 731, contour level = 0.015 
    4842  
    4843 Position of region_4_stemloop_1_2.cif (#19) relative to region_4_2.mrc (#15)
    4844 coordinates: 
    4845 Matrix rotation and translation 
    4846 -0.80563603 -0.40394439 0.43333528 148.90231522 
    4847 0.51271950 -0.84186790 0.16845495 223.71798819 
    4848 0.29676464 0.35789284 0.88534932 256.28217507 
    4849 Axis 0.20026322 0.14437490 0.96904620 
    4850 Axis point 24.76080762 104.01914308 0.00000000 
    4851 Rotation angle (degrees) 151.77259501 
    4852 Shift along axis 310.46818550 
    4853  
    4854 
    4855 > select add #19
    4856 
    4857 1475 atoms, 1648 bonds, 69 residues, 1 model selected 
    4858 
    4859 > view matrix models
    4860 > #19,-0.80564,-0.40394,0.43334,157.73,0.51272,-0.84187,0.16845,219.64,0.29676,0.35789,0.88535,250.57
    4861 
    4862 > ui mousemode right "rotate selected models"
    4863 
    4864 > view matrix models
    4865 > #19,-0.54227,-0.81159,0.2174,157.9,0.78624,-0.5814,-0.20929,220.01,0.29626,0.057435,0.95338,250.47
    4866 
    4867 > view matrix models
    4868 > #19,-0.73866,-0.46243,0.49045,157.51,0.62572,-0.74099,0.24373,219.36,0.25071,0.48692,0.83669,250.69
    4869 
    4870 > view matrix models
    4871 > #19,-0.40629,-0.90496,0.12637,157.91,0.79755,-0.41871,-0.43427,220.41,0.44591,-0.075653,0.89187,250.46
    4872 
    4873 > view matrix models
    4874 > #19,-0.65527,-0.58174,0.48187,157.34,0.60575,-0.78578,-0.12492,220.11,0.45132,0.21004,0.86729,250.42
    4875 
    4876 > view matrix models
    4877 > #19,-0.59533,-0.77726,0.20359,157.89,0.53371,-0.57195,-0.62292,221.12,0.60062,-0.26218,0.75533,250.63
    4878 
    4879 > view matrix models
    4880 > #19,-0.615,-0.70875,0.34562,157.58,0.55275,-0.70008,-0.45205,220.8,0.56235,-0.086971,0.82231,250.45
    4881 
    4882 > view matrix models
    4883 > #19,-0.86921,0.49322,-0.034696,158.1,-0.044614,-0.0083526,0.99897,218.14,0.49242,0.86987,0.029265,251.91
    4884 
    4885 > view matrix models
    4886 > #19,-0.73828,0.57146,-0.35829,158.54,0.19235,0.68752,0.70023,218.35,0.64649,0.44805,-0.6175,252.9
    4887 
    4888 > fitmap #19 inMap #15
    4889 
    4890 Fit molecule region_4_stemloop_1_2.cif (#19) to map region_4_2.mrc (#15) using
    4891 1475 atoms 
    4892 average map value = 0.0145, steps = 408 
    4893 shifted from previous position = 8.2 
    4894 rotated from previous position = 42.2 degrees 
    4895 atoms outside contour = 641, contour level = 0.015 
    4896  
    4897 Position of region_4_stemloop_1_2.cif (#19) relative to region_4_2.mrc (#15)
    4898 coordinates: 
    4899 Matrix rotation and translation 
    4900 -0.44403872 0.56620002 -0.69444013 162.26647345 
    4901 0.56058655 0.78016444 0.27764382 211.87484894 
    4902 0.69897946 -0.26600920 -0.66382736 251.23346204 
    4903 Axis -0.36347002 -0.93159834 -0.00375300 
    4904 Axis point -20.57375469 0.00000000 141.77382209 
    4905 Rotation angle (degrees) 131.59422419 
    4906 Shift along axis -257.30413352 
    4907  
    4908 
    4909 > ui mousemode right "translate selected models"
    4910 
    4911 > ui mousemode right "rotate selected models"
    4912 
    4913 > view matrix models
    4914 > #19,-0.31267,-0.112,-0.94324,162.99,0.81877,0.47162,-0.3274,212.93,0.48152,-0.87466,-0.055761,250.56
    4915 
    4916 > ui mousemode right "translate selected models"
    4917 
    4918 > view matrix models
    4919 > #19,-0.31267,-0.112,-0.94324,159.61,0.81877,0.47162,-0.3274,216.47,0.48152,-0.87466,-0.055761,253.99
    4920 
    4921 > fitmap #19 inMap #15
    4922 
    4923 Fit molecule region_4_stemloop_1_2.cif (#19) to map region_4_2.mrc (#15) using
    4924 1475 atoms 
    4925 average map value = 0.01413, steps = 400 
    4926 shifted from previous position = 2.09 
    4927 rotated from previous position = 13.5 degrees 
    4928 atoms outside contour = 663, contour level = 0.015 
    4929  
    4930 Position of region_4_stemloop_1_2.cif (#19) relative to region_4_2.mrc (#15)
    4931 coordinates: 
    4932 Matrix rotation and translation 
    4933 -0.39953735 0.00014085 -0.91671688 160.85509232 
    4934 0.71533909 0.62541937 -0.31167375 215.76545376 
    4935 0.57328862 -0.78028873 -0.24997917 252.90594132 
    4936 Axis -0.27278156 -0.86733469 0.41631809 
    4937 Axis point -53.46619538 0.00000000 219.68205002 
    4938 Rotation angle (degrees) 120.80038147 
    4939 Shift along axis -125.72984834 
    4940  
    4941 
    4942 > select subtract #19
    4943 
    4944 Nothing selected 
    4945 
    4946 > hide #17 models
    4947 
    4948 > show #17 models
    4949 
    4950 > hide #17 models
    4951 
    4952 > show #18 models
    4953 
    4954 > select add #18
    4955 
    4956 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    4957 
    4958 > view matrix models
    4959 > #18,-0.48169,-0.44711,0.7537,124.68,-0.38754,0.88007,0.27439,194.18,-0.78599,-0.15992,-0.5972,208.39
    4960 
    4961 > view matrix models
    4962 > #18,-0.48169,-0.44711,0.7537,176.65,-0.38754,0.88007,0.27439,177.01,-0.78599,-0.15992,-0.5972,236
    4963 
    4964 > view matrix models
    4965 > #18,-0.48169,-0.44711,0.7537,175.44,-0.38754,0.88007,0.27439,167.65,-0.78599,-0.15992,-0.5972,258.91
    4966 
    4967 > ui mousemode right "rotate selected models"
    4968 
    4969 > view matrix models
    4970 > #18,-0.38549,-0.87302,0.29873,175.97,-0.22837,-0.22341,-0.94759,168.81,0.89401,-0.43351,-0.11325,262.34
    4971 
    4972 > view matrix models
    4973 > #18,0.32605,-0.94346,-0.059734,178.15,-0.6961,-0.19685,-0.69043,167.17,0.63964,0.26669,-0.72093,262.17
    4974 
    4975 > ui mousemode right "translate selected models"
    4976 
    4977 > view matrix models
    4978 > #18,0.32605,-0.94346,-0.059734,162.05,-0.6961,-0.19685,-0.69043,169.54,0.63964,0.26669,-0.72093,263.55
    4979 
    4980 > fitmap #18 inMap #15
    4981 
    4982 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    4983 1377 atoms 
    4984 average map value = 0.01176, steps = 272 
    4985 shifted from previous position = 14.4 
    4986 rotated from previous position = 25 degrees 
    4987 atoms outside contour = 799, contour level = 0.015 
    4988  
    4989 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    4990 coordinates: 
    4991 Matrix rotation and translation 
    4992 0.65910355 -0.74308173 0.11581037 164.04339614 
    4993 -0.53461222 -0.57125533 -0.62278175 182.00238429 
    4994 0.52893503 0.34856403 -0.77377700 255.99969199 
    4995 Axis 0.90278912 -0.38396672 0.19375593 
    4996 Axis point 0.00000000 88.50269799 147.75453533 
    4997 Rotation angle (degrees) 147.45448876 
    4998 Shift along axis 127.81519395 
    4999  
    5000 
    5001 > select subtract #18
    5002 
    5003 Nothing selected 
    5004 
    5005 > select add #18
    5006 
    5007 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    5008 
    5009 > ui mousemode right "rotate selected models"
    5010 
    5011 > view matrix models
    5012 > #18,-0.16968,-0.90099,0.39927,161.32,-0.71798,0.39055,0.57618,179.47,-0.67507,-0.1889,-0.71316,252.69
    5013 
    5014 > ui mousemode right "translate selected models"
    5015 
    5016 > view matrix models
    5017 > #18,-0.16968,-0.90099,0.39927,164.99,-0.71798,0.39055,0.57618,178.8,-0.67507,-0.1889,-0.71316,250.76
    5018 
    5019 > fitmap #18 inMap #15
    5020 
    5021 Fit molecule region_4_stemloop_2.cif (#18) to map region_4_2.mrc (#15) using
    5022 1377 atoms 
    5023 average map value = 0.01248, steps = 248 
    5024 shifted from previous position = 4.68 
    5025 rotated from previous position = 23.5 degrees 
    5026 atoms outside contour = 763, contour level = 0.015 
    5027  
    5028 Position of region_4_stemloop_2.cif (#18) relative to region_4_2.mrc (#15)
    5029 coordinates: 
    5030 Matrix rotation and translation 
    5031 -0.15124652 -0.85928512 0.48862416 168.73822316 
    5032 -0.38689683 0.50633479 0.77067237 181.49458118 
    5033 -0.90963472 -0.07248563 -0.40903606 248.57523535 
    5034 Axis -0.49604447 0.82261994 0.27791422 
    5035 Axis point 210.51992295 0.00000000 13.94496782 
    5036 Rotation angle (degrees) 121.80122035 
    5037 Shift along axis 134.68199153 
    5038  
    5039 
    5040 > select subtract #18
    5041 
    5042 Nothing selected 
    5043 
    5044 > select add #18
    5045 
    5046 1377 atoms, 1538 bonds, 65 residues, 1 model selected 
    5047 
    5048 > nucleotides sel stubs
    5049 
    5050 > select subtract #18
    5051 
    5052 Nothing selected 
    5053 
    5054 > hide #18 models
    5055 
    5056 > hide #19 models
    5057 
    5058 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    5059 > Project/20251113_rna_phicb5_region_4_120nu/fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif"
    5060 
    5061 Chain information for
    5062 fold_2025_11_13_17_24_rna_phicb5_region_4_120nu_model_0.cif #20 
    5063 --- 
    5064 Chain | Description 
    5065 A | . 
    5066  
    5067 Computing secondary structure 
    5068 
    5069 > rename #20 region_4_120nu.cif
    5070 
    5071 > view
    5072 
    5073 > select add #20
    5074 
    5075 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    5076 
    5077 > view matrix models #20,1,0,0,147.07,0,1,0,181.24,0,0,1,4.4982
    5078 
    5079 > view matrix models #20,1,0,0,187.8,0,1,0,234.51,0,0,1,225.19
    5080 
    5081 > ui mousemode right "rotate selected models"
    5082 
    5083 > view matrix models
    5084 > #20,0.97675,-0.13541,-0.16622,189.24,0.099309,0.97287,-0.20896,235.83,0.19,0.18759,0.9637,224.78
    5085 
    5086 > view matrix models
    5087 > #20,-0.15807,0.90623,-0.39212,182.32,0.82183,0.34088,0.45651,238.12,0.54737,-0.2501,-0.79865,234.44
    5088 
    5089 > view matrix models
    5090 > #20,-0.19588,0.75524,-0.62549,183.79,0.91929,0.36347,0.15098,239.23,0.34138,-0.54543,-0.76548,235.37
    5091 
    5092 > ui mousemode right "translate selected models"
    5093 
    5094 > view matrix models
    5095 > #20,-0.19588,0.75524,-0.62549,182.07,0.91929,0.36347,0.15098,183.49,0.34138,-0.54543,-0.76548,242.57
    5096 
    5097 > fitmap #20 inMap #15
    5098 
    5099 Fit molecule region_4_120nu.cif (#20) to map region_4_2.mrc (#15) using 2557
    5100 atoms 
    5101 average map value = 0.00965, steps = 344 
    5102 shifted from previous position = 10.6 
    5103 rotated from previous position = 7.82 degrees 
    5104 atoms outside contour = 1685, contour level = 0.015 
    5105  
    5106 Position of region_4_120nu.cif (#20) relative to region_4_2.mrc (#15)
    5107 coordinates: 
    5108 Matrix rotation and translation 
    5109 -0.09007301 0.72102720 -0.68702741 191.56672213 
    5110 0.91137050 0.33784720 0.23508107 179.93787550 
    5111 0.40161012 -0.60496205 -0.68755382 245.73283063 
    5112 Axis -0.60514132 -0.78422113 0.13711749 
    5113 Axis point -44.74841808 0.00000000 153.11243538 
    5114 Rotation angle (degrees) 136.04538342 
    5115 Shift along axis -223.34175502 
    5116  
    5117 
    5118 > select subtract #20
    5119 
    5120 Nothing selected 
    5121 
    5122 > select add #20
    5123 
    5124 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    5125 
    5126 > select subtract #20
    5127 
    5128 Nothing selected 
    5129 
    5130 > select add #20
    5131 
    5132 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    5133 
    5134 > ui mousemode right "rotate selected models"
    5135 
    5136 > view matrix models
    5137 > #20,-0.89361,-0.22926,0.38589,190.65,0.38581,-0.83168,0.39933,184.36,0.22938,0.50572,0.83164,233.95
    5138 
    5139 > ui mousemode right "translate selected models"
    5140 
    5141 > view matrix models
    5142 > #20,-0.89361,-0.22926,0.38589,172.21,0.38581,-0.83168,0.39933,179.76,0.22938,0.50572,0.83164,227.61
    5143 
    5144 > select subtract #20
    5145 
    5146 Nothing selected 
    5147 
    5148 > ui mousemode right "rotate selected models"
    5149 
    5150 > select add #20
    5151 
    5152 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    5153 
    5154 > view matrix models
    5155 > #20,-0.69753,0.50123,-0.51208,172.2,0.64421,0.75158,-0.14185,174.37,0.31377,-0.42883,-0.84714,238.66
    5156 
    5157 > select subtract #20
    5158 
    5159 Nothing selected 
    5160 
    5161 > fitmap #20 inMap #15
    5162 
    5163 Fit molecule region_4_120nu.cif (#20) to map region_4_2.mrc (#15) using 2557
    5164 atoms 
    5165 average map value = 0.009375, steps = 108 
    5166 shifted from previous position = 5.09 
    5167 rotated from previous position = 15.9 degrees 
    5168 atoms outside contour = 1687, contour level = 0.015 
    5169  
    5170 Position of region_4_120nu.cif (#20) relative to region_4_2.mrc (#15)
    5171 coordinates: 
    5172 Matrix rotation and translation 
    5173 -0.83371377 0.26403476 -0.48498145 174.66873272 
    5174 0.42572847 0.86668944 -0.26000902 177.13275157 
    5175 0.35167689 -0.42324351 -0.83497803 235.10372112 
    5176 Axis -0.18813765 -0.96429949 0.18636181 
    5177 Axis point 38.71073478 0.00000000 151.77758101 
    5178 Rotation angle (degrees) 154.28998074 
    5179 Shift along axis -159.85643138 
    5180  
    5181 
    5182 > hide #20 models
    5183 
    5184 > combine #6
    5185 
    5186 No structures specified 
    5187 
    5188 > show #!6 models
    5189 
    5190 > hide #!6 models
    5191 
    5192 > hide #!15 models
    5193 
    5194 > show #!6 models
    5195 
    5196 > show #10 models
    5197 
    5198 > show #5 models
    5199 
    5200 > hide #5 models
    5201 
    5202 > show #5 models
    5203 
    5204 > hide #5 models
    5205 
    5206 > show #!7 models
    5207 
    5208 > hide #!7 models
    5209 
    5210 > show #13 models
    5211 
    5212 > show #14 models
    5213 
    5214 > show #!15 models
    5215 
    5216 > hide #!15 models
    5217 
    5218 > hide #!6 models
    5219 
    5220 > show #!15 models
    5221 
    5222 > show #!9 models
    5223 
    5224 > hide #!9 models
    5225 
    5226 > show #!6 models
    5227 
    5228 > hide #!6 models
    5229 
    5230 > show #!6 models
    5231 
    5232 > hide #!6 models
    5233 
    5234 > show #!9 models
    5235 
    5236 > show #!11 models
    5237 
    5238 > show #!7 models
    5239 
    5240 > hide #!7 models
    5241 
    5242 > show #5 models
    5243 
    5244 > hide #5 models
    5245 
    5246 > show #!6 models
    5247 
    5248 > hide #!6 models
    5249 
    5250 > show #!6 models
    5251 
    5252 > hide #!6 models
    5253 
    5254 > show #!6 models
    5255 
    5256 > select add #6.190
    5257 
    5258 1 model selected 
    5259 
    5260 > select add #6.67
    5261 
    5262 2 models selected 
    5263 
    5264 > select add #6
    5265 
    5266 195 models selected 
    5267 
    5268 > select subtract #6
    5269 
    5270 Nothing selected 
    5271 
    5272 > select add #6.190
    5273 
    5274 1 model selected 
    5275 
    5276 > select add #6.2
    5277 
    5278 2 models selected 
    5279 
    5280 > ui tool show "Segment Map"
    5281 
    5282 Grouped 2 regions 
    5283 
    5284 > select add #6
    5285 
    5286 194 models selected 
    5287 
    5288 > select subtract #6
    5289 
    5290 Nothing selected 
    5291 
    5292 > hide #!6 models
    5293 
    5294 > show #!6 models
    5295 
    5296 > show #5 models
    5297 
    5298 > hide #5 models
    5299 
    5300 > hide #!6 models
    5301 
    5302 > show #!6 models
    5303 
    5304 > select add #6.147
    5305 
    5306 1 model selected 
    5307 
    5308 > select add #6.66
    5309 
    5310 2 models selected 
    5311 
    5312 > select add #6.187
    5313 
    5314 3 models selected 
    5315 
    5316 > ui tool show "Segment Map"
    5317 
    5318 > select add #6
    5319 
    5320 194 models selected 
    5321 
    5322 > select subtract #6
    5323 
    5324 Nothing selected 
    5325 
    5326 > select add #6.20
    5327 
    5328 1 model selected 
    5329 
    5330 > select add #6.46
    5331 
    5332 2 models selected 
    5333 
    5334 > select add #6.36
    5335 
    5336 3 models selected 
    5337 
    5338 > select add #6.136
    5339 
    5340 4 models selected 
    5341 
    5342 > select add #6.173
    5343 
    5344 5 models selected 
    5345 
    5346 > select add #6.60
    5347 
    5348 6 models selected 
    5349 
    5350 > select subtract #6.60
    5351 
    5352 5 models selected 
    5353 
    5354 > select subtract #6.136
    5355 
    5356 4 models selected 
    5357 
    5358 > select add #6
    5359 
    5360 194 models selected 
    5361 
    5362 > select subtract #6
    5363 
    5364 Nothing selected 
    5365 
    5366 > hide #!6 models
    5367 
    5368 > show #!6 models
    5369 
    5370 Showing 193 region surfaces 
    5371 
    5372 > select add #6.2
    5373 
    5374 1 model selected 
    5375 Region has 9 adjacent regions 
    5376 
    5377 > hide #!6 models
    5378 
    5379 > show #5 models
    5380 
    5381 > hide #5 models
    5382 
    5383 > show #!6 models
    5384 
    5385 > hide #!6 models
    5386 
    5387 > volume #15 level 0.02025
    5388 
    5389 > show #!6 models
    5390 
    5391 > hide #!6 models
    5392 
    5393 > show #!6 models
    5394 
    5395 > hide #!6 models
    5396 
    5397 > show #!6 models
    5398 
    5399 > hide #!6 models
    5400 
    5401 > show #!6 models
    5402 
    5403 > hide #!6 models
    5404 
    5405 > show #!6 models
    5406 
    5407 > hide #!6 models
    5408 
    5409 > show #!6 models
    5410 
    5411 > hide #!6 models
    5412 
    5413 > show #!6 models
    5414 
    5415 > select add #6.83
    5416 
    5417 1 model selected 
    5418 
    5419 > select add #6.2
    5420 
    5421 2 models selected 
    5422 
    5423 > select add #6.156
    5424 
    5425 3 models selected 
    5426 
    5427 > select add #6.57
    5428 
    5429 4 models selected 
    5430 
    5431 > select add #6.146
    5432 
    5433 5 models selected 
    5434 
    5435 > select add #6.184
    5436 
    5437 6 models selected 
    5438 
    5439 > select add #6.170
    5440 
    5441 7 models selected 
    5442 
    5443 > select subtract #6.170
    5444 
    5445 6 models selected 
    5446 
    5447 > select add #6.48
    5448 
    5449 7 models selected 
    5450 
    5451 > select subtract #6.48
    5452 
    5453 6 models selected 
    5454 
    5455 > select add #6
    5456 
    5457 194 models selected 
    5458 
    5459 > select subtract #6
    5460 
    5461 Nothing selected 
    5462 
    5463 > select add #6.46
    5464 
    5465 1 model selected 
    5466 
    5467 > select add #6.20
    5468 
    5469 2 models selected 
    5470 
    5471 > select add #6.173
    5472 
    5473 3 models selected 
    5474 
    5475 > select add #6.136
    5476 
    5477 4 models selected 
    5478 
    5479 > select add #6.60
    5480 
    5481 5 models selected 
    5482 
    5483 > select add #6.36
    5484 
    5485 6 models selected 
    5486 
    5487 > select add #6.179
    5488 
    5489 7 models selected 
    5490 
    5491 > select subtract #6.179
    5492 
    5493 6 models selected 
    5494 
    5495 > select add #6
    5496 
    5497 194 models selected 
    5498 
    5499 > hide #!6 models
    5500 
    5501 > select subtract #6
    5502 
    5503 Nothing selected 
    5504 
    5505 > show #!7 models
    5506 
    5507 > hide #!7 models
    5508 
    5509 > show #!8 models
    5510 
    5511 > select add #8
    5512 
    5513 2 models selected 
    5514 
    5515 > select subtract #8
    5516 
    5517 Nothing selected 
    5518 
    5519 > hide #!9 models
    5520 
    5521 > select add #7
    5522 
    5523 2 models selected 
    5524 
    5525 > select subtract #7
    5526 
    5527 Nothing selected 
    5528 
    5529 > select add #8
    5530 
    5531 2 models selected 
    5532 Segmenting volume difference, density threshold 0.011922 
    5533 Showing 194 region surfaces 
    5534 2209 watershed regions, grouped to 194 regions 
    5535 Showing volume difference.seg - 194 regions, 194 surfaces 
    5536 
    5537 > hide #!6 models
    5538 
    5539 > show #!6 models
    5540 
    5541 > hide #!6 models
    5542 
    5543 > select subtract #8
    5544 
    5545 Nothing selected 
    5546 
    5547 > select add #8
    5548 
    5549 2 models selected 
    5550 
    5551 > select subtract #8
    5552 
    5553 Nothing selected 
    5554 
    5555 > volume #8 level 0.0017
    5556 
    5557 > volume #8 level 0.017
    5558 
    5559 > select subtract #8
    5560 
    5561 Nothing selected 
    5562 
    5563 > show #!9 models
    5564 
    5565 > volume #4 level 0.017
    5566 
    5567 > volume #7 level 0.017
    5568 
    5569 > volume #9 level 0.017
    5570 
    5571 > hide #!8 models
    5572 
    5573 > show #!8 models
    5574 
    5575 > hide #!8 models
    5576 
    5577 > show #!8 models
    5578 
    5579 > volume #11 level 0.017
    5580 
    5581 > volume #15 level 0.017
    5582 
    5583 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    5584 > Project/20251114 region_4_wip.cxs"
    5585 
    5586 > vop subtract #8 #9
    5587 
    5588 Opened volume difference as #21, grid size 215,224,227, pixel 1.12,1.12,1.12,
    5589 shown at step 1, values float32 
    5590 
    5591 QWindowsWindow::setGeometry: Unable to set geometry 1920x1458+0+35 (frame:
    5592 1942x1514-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    5593 Resulting geometry: 1920x1166+0+34 (frame: 1942x1222-11-11) margins: 11, 45,
    5594 11, 11 minimum size: 624x972 MINMAXINFO(maxSize=POINT(x=0, y=0),
    5595 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
    5596 y=1514))) 
    5597 
    5598 > hide #!21 models
    5599 
    5600 > show #!6 models
    5601 
    5602 > show #!8 models
    5603 
    5604 > hide #!6 models
    5605 
    5606 > show #!9 models
    5607 
    5608 > hide #!9 models
    5609 
    5610 > hide #!8 models
    5611 
    5612 > show #!21 models
    5613 
    5614 > transparency #11.1#15.1#21.1 0
    5615 
    5616 > select add #21
    5617 
    5618 2 models selected 
    5619 
    5620 > transparency sel 50
    5621 
    5622 > select subtract #21
    5623 
    5624 Nothing selected 
    5625 
    5626 > vop subtract #21 #7
    5627 
    5628 Opened volume difference as #22, grid size 215,224,227, pixel 1.12,1.12,1.12,
    5629 shown at step 1, values float32 
    5630 
    5631 > vop subtract #22 #11
    5632 
    5633 Opened volume difference as #23, grid size 215,224,227, pixel 1.12,1.12,1.12,
    5634 shown at step 1, values float32 
    5635 
    5636 QWindowsWindow::setGeometry: Unable to set geometry 1920x1458+0+35 (frame:
    5637 1942x1514-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    5638 Resulting geometry: 1920x1166+0+34 (frame: 1942x1222-11-11) margins: 11, 45,
    5639 11, 11 minimum size: 624x972 MINMAXINFO(maxSize=POINT(x=0, y=0),
    5640 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
    5641 y=1514))) 
    5642 
    5643 > close #21-22
    5644 
    5645 > rename #23 "vol diff region_3"
    5646 
    5647 > rename #23 id #21
    5648 
    5649 > select add #21
    5650 
    5651 2 models selected 
    5652 
    5653 > transparency sel 50
    5654 
    5655 > show #5 models
    5656 
    5657 > select subtract #21
    5658 
    5659 Nothing selected 
    5660 Segmenting vol diff region_3, density threshold 0.017000 
    5661 Showing 199 region surfaces 
    5662 1931 watershed regions, grouped to 199 regions 
    5663 Showing vol diff region_3.seg - 199 regions, 199 surfaces 
    5664 
    5665 > select add #21
    5666 
    5667 2 models selected 
    5668 
    5669 > transparency sel 0
    5670 
    5671 > select subtract #21
    5672 
    5673 Nothing selected 
    5674 
    5675 > select add #21
    5676 
    5677 2 models selected 
    5678 
    5679 > transparency sel 50
    5680 
    5681 > select subtract #21
    5682 
    5683 Nothing selected 
    5684 
    5685 > hide #!21 models
    5686 
    5687 > show #!21 models
    5688 
    5689 > hide #!21 models
    5690 
    5691 > show #!9 models
    5692 
    5693 > hide #!9 models
    5694 
    5695 > rename #9 region_2.mrc
    5696 
    5697 > rename #7 region_1.mrc
    5698 
    5699 > select add #6
    5700 
    5701 200 models selected 
    5702 
    5703 > transparency sel 50
    5704 
    5705 > select subtract #6
    5706 
    5707 Nothing selected 
    5708 
    5709 > hide #!15 models
    5710 
    5711 > select add #6.2
    5712 
    5713 1 model selected 
    5714 
    5715 > select add #6.68
    5716 
    5717 2 models selected 
    5718 
    5719 > select add #6.11
    5720 
    5721 3 models selected 
    5722 
    5723 > select add #6.32
    5724 
    5725 4 models selected 
    5726 
    5727 > select add #6.42
    5728 
    5729 5 models selected 
    5730 
    5731 > select add #6.58
    5732 
    5733 6 models selected 
    5734 
    5735 > ui mousemode right translate
    5736 
    5737 > select add #6.66
    5738 
    5739 7 models selected 
    5740 
    5741 > select subtract #6.66
    5742 
    5743 6 models selected 
    5744 
    5745 > select add #6.66
    5746 
    5747 7 models selected 
    5748 
    5749 > select subtract #6.66
    5750 
    5751 6 models selected 
    5752 
    5753 > select add #6.39
    5754 
    5755 7 models selected 
    5756 
    5757 > select add #6.34
    5758 
    5759 8 models selected 
    5760 
    5761 > select add #6.145
    5762 
    5763 9 models selected 
    5764 
    5765 > select add #6.81
    5766 
    5767 10 models selected 
    5768 
    5769 > select add #6.61
    5770 
    5771 11 models selected 
    5772 
    5773 > select add #6.88
    5774 
    5775 12 models selected 
    5776 
    5777 > select add #6.7
    5778 
    5779 13 models selected 
    5780 
    5781 > select add #6.120
    5782 
    5783 14 models selected 
    5784 
    5785 > select add #6.148
    5786 
    5787 15 models selected 
    5788 
    5789 > select add #6.165
    5790 
    5791 16 models selected 
    5792 
    5793 > select add #6.96
    5794 
    5795 17 models selected 
    5796 
    5797 > select add #6.159
    5798 
    5799 18 models selected 
    5800 
    5801 > select add #6.18
    5802 
    5803 19 models selected 
    5804 
    5805 > select add #6.184
    5806 
    5807 20 models selected 
    5808 
    5809 > select add #6.25
    5810 
    5811 21 models selected 
    5812 
    5813 > select add #6.117
    5814 
    5815 22 models selected 
    5816 Saving 22 regions to mrc file... 
    5817 Opened region_4_jxn.mrc as #22, grid size 166,122,96, pixel 1.12,1.12,1.12,
    5818 shown at step 1, values float32 
    5819 Wrote region_4_jxn.mrc 
    5820 
    5821 QWindowsWindow::setGeometry: Unable to set geometry 1920x1458+0+35 (frame:
    5822 1942x1514-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
    5823 Resulting geometry: 1920x1166+0+34 (frame: 1942x1222-11-11) margins: 11, 45,
    5824 11, 11 minimum size: 624x972 MINMAXINFO(maxSize=POINT(x=0, y=0),
    5825 maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=958,
    5826 y=1514))) 
    5827 
    5828 > hide #!6 models
    5829 
    5830 > select add #6
    5831 
    5832 200 models selected 
    5833 
    5834 > select subtract #6
    5835 
    5836 Nothing selected 
    5837 
    5838 > select add #22
    5839 
    5840 2 models selected 
    5841 
    5842 > volume #22 level 0.017
    5843 
    5844 > select subtract #22
    5845 
    5846 Nothing selected 
    5847 
    5848 > volume #22 level 0.02478
    5849 
    5850 > volume #22 level 0.02235
    5851 
    5852 > volume #22 level 0.02429
    5853 
    5854 > volume #22 level 0.017
    5855 
    5856 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    5857 > Project/20251114_rna_phicb5_region_4_3/fold_2025_11_14_11_03_rna_phicb5_region_4_3_model_0.cif"
    5858 
    5859 Chain information for fold_2025_11_14_11_03_rna_phicb5_region_4_3_model_0.cif
    5860 #23 
    5861 --- 
    5862 Chain | Description 
    5863 A | . 
    5864  
    5865 Computing secondary structure 
    5866 
    5867 > rename #23 region_4_3.cif
    5868 
    5869 > view
    5870 
    5871 > ui mousemode right "translate selected models"
    5872 
    5873 > select add #23
    5874 
    5875 2096 atoms, 2348 bonds, 98 residues, 1 model selected 
    5876 
    5877 > view matrix models #23,1,0,0,-4.7303,0,1,0,-51.188,0,0,1,147.86
    5878 
    5879 > view matrix models #23,1,0,0,152.16,0,1,0,129.27,0,0,1,289.71
    5880 
    5881 > view matrix models #23,1,0,0,159.25,0,1,0,162.08,0,0,1,241.61
    5882 
    5883 > select subtract #23
    5884 
    5885 Nothing selected 
    5886 
    5887 > fitmap #23 inMap #22
    5888 
    5889 Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
    5890 atoms 
    5891 average map value = 0.009486, steps = 140 
    5892 shifted from previous position = 13.6 
    5893 rotated from previous position = 14.9 degrees 
    5894 atoms outside contour = 1443, contour level = 0.017 
    5895  
    5896 Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
    5897 coordinates: 
    5898 Matrix rotation and translation 
    5899 0.97814527 0.20472685 -0.03631444 152.26881265 
    5900 -0.20787309 0.96669438 -0.14930092 173.70692628 
    5901 0.00453906 0.15358678 0.98812474 242.02271617 
    5902 Axis 0.58988702 -0.07956398 -0.80355639 
    5903 Axis point 947.94058164 -983.94836323 0.00000000 
    5904 Rotation angle (degrees) 14.87633671 
    5905 Shift along axis -118.47831866 
    5906  
    5907 
    5908 > select add #23
    5909 
    5910 2096 atoms, 2348 bonds, 98 residues, 1 model selected 
    5911 
    5912 > view matrix models
    5913 > #23,0.97815,0.20473,-0.036314,114.29,-0.20787,0.96669,-0.1493,143.91,0.0045391,0.15359,0.98812,257.11
    5914 
    5915 > ui mousemode right "translate selected models"
    5916 
    5917 > ui mousemode right "rotate selected models"
    5918 
    5919 > view matrix models
    5920 > #23,0.71198,0.69496,-0.10061,114.76,0.23992,-0.3754,-0.89527,146.42,-0.65995,0.61328,-0.43401,263.04
    5921 
    5922 > view matrix models
    5923 > #23,0.17276,-0.9119,-0.37227,111.43,-0.57716,-0.39999,0.71196,136.14,-0.79815,0.091866,-0.59542,262.3
    5924 
    5925 > view matrix models
    5926 > #23,-0.69946,-0.7123,0.058216,107.21,-0.64537,0.66453,0.3767,139.76,-0.30701,0.22591,-0.92451,265.61
    5927 
    5928 > view matrix models
    5929 > #23,-0.95467,0.25968,0.14552,107.89,-0.11801,0.11865,-0.9859,147.08,-0.27328,-0.95838,-0.082624,259.32
    5930 
    5931 > view matrix models
    5932 > #23,0.10008,-0.54744,-0.83084,114.23,0.99495,0.061255,0.079483,145.05,0.0073802,-0.8346,0.55081,256.86
    5933 
    5934 > view matrix models
    5935 > #23,0.20676,-0.23089,0.95076,106.07,-0.95707,-0.24948,0.14755,138.63,0.20313,-0.94045,-0.27257,261.24
    5936 
    5937 > select subtract #23
    5938 
    5939 Nothing selected 
    5940 
    5941 > select add #23
    5942 
    5943 2096 atoms, 2348 bonds, 98 residues, 1 model selected 
    5944 
    5945 > nucleotides sel stubs
    5946 
    5947 > select subtract #23
    5948 
    5949 Nothing selected 
    5950 
    5951 > select add #23
    5952 
    5953 2096 atoms, 2348 bonds, 98 residues, 1 model selected 
    5954 
    5955 > view matrix models
    5956 > #23,-0.32679,0.51815,0.79039,106.87,-0.80197,-0.59452,0.058165,138.86,0.50004,-0.61487,0.60983,258.1
    5957 
    5958 > ui mousemode right "translate selected models"
    5959 
    5960 > view matrix models
    5961 > #23,-0.32679,0.51815,0.79039,173.31,-0.80197,-0.59452,0.058165,133.69,0.50004,-0.61487,0.60983,236.07
    5962 
    5963 > select subtract #23
    5964 
    5965 Nothing selected 
    5966 
    5967 > ui mousemode right "rotate selected models"
    5968 
    5969 > select add #23
    5970 
    5971 2096 atoms, 2348 bonds, 98 residues, 1 model selected 
    5972 
    5973 > view matrix models
    5974 > #23,0.018989,-0.98168,0.18958,174.29,0.78374,-0.10312,-0.61247,141.92,0.6208,0.16021,0.76742,237.07
    5975 
    5976 > view matrix models
    5977 > #23,-0.47548,-0.64194,-0.60152,177.71,0.58916,-0.74014,0.32416,135.59,-0.6533,-0.20026,0.73013,233.16
    5978 
    5979 > ui mousemode right "translate selected models"
    5980 
    5981 > view matrix models
    5982 > #23,-0.47548,-0.64194,-0.60152,222.45,0.58916,-0.74014,0.32416,188.56,-0.6533,-0.20026,0.73013,221.96
    5983 
    5984 > ui mousemode right "rotate selected models"
    5985 
    5986 > view matrix models
    5987 > #23,-0.0052927,-0.21665,-0.97624,226.33,0.96149,0.26718,-0.064505,193.35,0.2748,-0.93898,0.20689,225.63
    5988 
    5989 > view matrix models
    5990 > #23,0.52191,-0.56916,-0.63535,225.44,0.72683,0.68658,-0.017993,193.24,0.44646,-0.4524,0.77202,224.27
    5991 
    5992 > select subtract #23
    5993 
    5994 Nothing selected 
    5995 
    5996 > fitmap #23 inMap #22
    5997 
    5998 Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
    5999 atoms 
    6000 average map value = 0.00904, steps = 288 
    6001 shifted from previous position = 21 
    6002 rotated from previous position = 31.7 degrees 
    6003 atoms outside contour = 1443, contour level = 0.017 
    6004  
    6005 Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
    6006 coordinates: 
    6007 Matrix rotation and translation 
    6008 0.25376302 -0.42617964 -0.86831747 221.15007688 
    6009 0.93475318 0.33884393 0.10687037 174.37429887 
    6010 0.24867811 -0.83878227 0.48435881 232.59258539 
    6011 Axis -0.47317683 -0.55891180 0.68097084 
    6012 Axis point 76.96850905 335.60681404 0.00000000 
    6013 Rotation angle (degrees) 87.79454879 
    6014 Shift along axis -43.71417685 
    6015  
    6016 
    6017 > hide #23 models
    6018 
    6019 > show #20 models
    6020 
    6021 > select add #20
    6022 
    6023 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6024 
    6025 > view matrix models
    6026 > #20,0.70362,-0.71048,0.011774,180.93,0.19932,0.21325,0.95645,175.46,-0.68205,-0.67063,0.29166,230.04
    6027 
    6028 > ui mousemode right "translate selected models"
    6029 
    6030 > select subtract #20
    6031 
    6032 Nothing selected 
    6033 
    6034 > ui mousemode right "rotate selected models"
    6035 
    6036 > ui mousemode right "translate selected models"
    6037 
    6038 > select add #20
    6039 
    6040 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6041 
    6042 > view matrix models
    6043 > #20,0.70362,-0.71048,0.011774,219.95,0.19932,0.21325,0.95645,146.66,-0.68205,-0.67063,0.29166,224.09
    6044 
    6045 > view matrix models
    6046 > #20,0.70362,-0.71048,0.011774,304.94,0.19932,0.21325,0.95645,175.08,-0.68205,-0.67063,0.29166,220.99
    6047 
    6048 > ui mousemode right "rotate selected models"
    6049 
    6050 > view matrix models
    6051 > #20,0.94663,0.3122,-0.080152,300.46,0.28675,-0.70214,0.65174,181.08,0.14719,-0.63994,-0.75419,226.35
    6052 
    6053 > view matrix models
    6054 > #20,0.97694,0.20816,0.047473,300.48,-0.15108,0.51688,0.84262,172.81,0.15086,-0.83036,0.53641,222.4
    6055 
    6056 > view matrix models
    6057 > #20,0.97094,0.2032,0.12645,300.17,-0.16208,0.16949,0.97211,174.01,0.1761,-0.96435,0.1975,224.52
    6058 
    6059 > view matrix models
    6060 > #20,0.97995,0.16549,0.11093,300.43,-0.17688,0.46641,0.8667,172.95,0.091696,-0.86895,0.48634,222.75
    6061 
    6062 > ui mousemode right "translate selected models"
    6063 
    6064 > view matrix models
    6065 > #20,0.97995,0.16549,0.11093,247.65,-0.17688,0.46641,0.8667,138.87,0.091696,-0.86895,0.48634,234.14
    6066 
    6067 > select add #19
    6068 
    6069 4032 atoms, 4509 bonds, 189 residues, 2 models selected 
    6070 
    6071 > select subtract #19
    6072 
    6073 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6074 
    6075 > select subtract #20
    6076 
    6077 Nothing selected 
    6078 
    6079 > ui mousemode right "rotate selected models"
    6080 
    6081 > select add #20
    6082 
    6083 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6084 
    6085 > view matrix models
    6086 > #20,0.50696,-0.35054,0.78747,246.55,-0.85954,-0.13702,0.49237,141.85,-0.064698,-0.92647,-0.37076,237.46
    6087 
    6088 > ui mousemode right "translate selected models"
    6089 
    6090 > view matrix models
    6091 > #20,0.50696,-0.35054,0.78747,251.08,-0.85954,-0.13702,0.49237,157.1,-0.064698,-0.92647,-0.37076,243.22
    6092 
    6093 > fitmap #23 inMap #22
    6094 
    6095 Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
    6096 atoms 
    6097 average map value = 0.00904, steps = 80 
    6098 shifted from previous position = 0.00622 
    6099 rotated from previous position = 0.00572 degrees 
    6100 atoms outside contour = 1444, contour level = 0.017 
    6101  
    6102 Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
    6103 coordinates: 
    6104 Matrix rotation and translation 
    6105 0.25377019 -0.42608945 -0.86835964 221.14600498 
    6106 0.93474480 0.33885811 0.10689869 174.37359049 
    6107 0.24870228 -0.83882236 0.48427696 232.59719779 
    6108 Axis -0.47321051 -0.55894435 0.68092072 
    6109 Axis point 76.98468596 335.61635547 0.00000000 
    6110 Rotation angle (degrees) 87.79628314 
    6111 Shift along axis -43.73349350 
    6112  
    6113 
    6114 > select subtract #20
    6115 
    6116 Nothing selected 
    6117 
    6118 > select add #20
    6119 
    6120 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6121 
    6122 > ui mousemode right "rotate selected models"
    6123 
    6124 > ui mousemode right "translate selected models"
    6125 
    6126 > view matrix models
    6127 > #20,0.50696,-0.35054,0.78747,240.78,-0.85954,-0.13702,0.49237,167.31,-0.064698,-0.92647,-0.37076,226.7
    6128 
    6129 > select subtract #20
    6130 
    6131 Nothing selected 
    6132 
    6133 > fitmap #23 inMap #22
    6134 
    6135 Fit molecule region_4_3.cif (#23) to map region_4_jxn.mrc (#22) using 2096
    6136 atoms 
    6137 average map value = 0.00904, steps = 240 
    6138 shifted from previous position = 0.00241 
    6139 rotated from previous position = 0.00998 degrees 
    6140 atoms outside contour = 1444, contour level = 0.017 
    6141  
    6142 Position of region_4_3.cif (#23) relative to region_4_jxn.mrc (#22)
    6143 coordinates: 
    6144 Matrix rotation and translation 
    6145 0.25377471 -0.42622353 -0.86829251 221.14362591 
    6146 0.93477545 0.33876936 0.10691201 174.37387948 
    6147 0.24858246 -0.83879009 0.48439437 232.59784460 
    6148 Axis -0.47320132 -0.55885116 0.68100358 
    6149 Axis point 76.96439817 335.58572140 0.00000000 
    6150 Rotation angle (degrees) 87.79533221 
    6151 Shift along axis -43.69453628 
    6152  
    6153 
    6154 > hide #20 models
    6155 
    6156 > hide #!22 models
    6157 
    6158 > show #!22 models
    6159 
    6160 > show #20 models
    6161 
    6162 > select add #20
    6163 
    6164 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6165 
    6166 > view matrix models
    6167 > #20,0.50696,-0.35054,0.78747,185.24,-0.85954,-0.13702,0.49237,205.85,-0.064698,-0.92647,-0.37076,271.45
    6168 
    6169 > ui mousemode right "rotate selected models"
    6170 
    6171 > view matrix models
    6172 > #20,-0.78942,0.6136,0.017528,181.03,0.52874,0.66519,0.52721,204.15,0.31184,0.42546,-0.84955,267.25
    6173 
    6174 > select subtract #20
    6175 
    6176 Nothing selected 
    6177 
    6178 > select add #20
    6179 
    6180 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6181 
    6182 > view matrix models
    6183 > #20,-0.70492,-0.49301,0.50993,184.81,0.13073,-0.79692,-0.58977,215.72,0.69714,-0.34908,0.62621,265.74
    6184 
    6185 > ui mousemode right "translate selected models"
    6186 
    6187 > view matrix models
    6188 > #20,-0.70492,-0.49301,0.50993,183.36,0.13073,-0.79692,-0.58977,170.06,0.69714,-0.34908,0.62621,283.89
    6189 
    6190 > view matrix models
    6191 > #20,-0.70492,-0.49301,0.50993,169.04,0.13073,-0.79692,-0.58977,165.99,0.69714,-0.34908,0.62621,255.97
    6192 
    6193 > fitmap #20 inMap #22
    6194 
    6195 Fit molecule region_4_120nu.cif (#20) to map region_4_jxn.mrc (#22) using 2557
    6196 atoms 
    6197 average map value = 0.008799, steps = 324 
    6198 shifted from previous position = 3.4 
    6199 rotated from previous position = 16.2 degrees 
    6200 atoms outside contour = 1887, contour level = 0.017 
    6201  
    6202 Position of region_4_120nu.cif (#20) relative to region_4_jxn.mrc (#22)
    6203 coordinates: 
    6204 Matrix rotation and translation 
    6205 -0.87056475 -0.34586323 0.34999370 169.35578872 
    6206 0.06101407 -0.78167901 -0.62068926 169.43294108 
    6207 0.48825634 -0.51899567 0.70160473 256.11260362 
    6208 Axis 0.23028633 -0.31309737 0.92137845 
    6209 Axis point 38.17956596 135.40457455 0.00000000 
    6210 Rotation angle (degrees) 167.24408354 
    6211 Shift along axis 221.92794682 
    6212  
    6213 
    6214 > select subtract #20
    6215 
    6216 Nothing selected 
    6217 
    6218 > select add #20
    6219 
    6220 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6221 
    6222 > view matrix models
    6223 > #20,-0.87056,-0.34586,0.34999,165.45,0.061014,-0.78168,-0.62069,180.41,0.48826,-0.519,0.7016,236.99
    6224 
    6225 > select subtract #20
    6226 
    6227 Nothing selected 
    6228 
    6229 > select add #20
    6230 
    6231 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6232 
    6233 > view matrix models
    6234 > #20,-0.87056,-0.34586,0.34999,171.97,0.061014,-0.78168,-0.62069,153.98,0.48826,-0.519,0.7016,253.5
    6235 
    6236 > select subtract #20
    6237 
    6238 Nothing selected 
    6239 
    6240 > select add #20
    6241 
    6242 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6243 
    6244 > view matrix models
    6245 > #20,-0.87056,-0.34586,0.34999,203.54,0.061014,-0.78168,-0.62069,159.16,0.48826,-0.519,0.7016,172.2
    6246 
    6247 > view matrix models
    6248 > #20,-0.87056,-0.34586,0.34999,219.53,0.061014,-0.78168,-0.62069,153.58,0.48826,-0.519,0.7016,176.59
    6249 
    6250 > ui mousemode right "rotate selected models"
    6251 
    6252 > view matrix models
    6253 > #20,0.97107,-0.07579,0.22646,221.99,0.2165,0.6796,-0.7009,147.08,-0.10078,0.72965,0.67635,169.06
    6254 
    6255 > view matrix models
    6256 > #20,0.83288,0.054804,0.55073,219.79,-0.43356,0.6831,0.58771,140.72,-0.344,-0.72826,0.5927,176.28
    6257 
    6258 > view matrix models
    6259 > #20,0.69204,-0.13499,0.70913,219.77,-0.72186,-0.1306,0.6796,143.66,0.00087434,-0.9822,-0.18782,181.26
    6260 
    6261 > ui mousemode right "translate selected models"
    6262 
    6263 > select subtract #20
    6264 
    6265 Nothing selected 
    6266 
    6267 > select add #20
    6268 
    6269 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6270 
    6271 > view matrix models
    6272 > #20,0.69204,-0.13499,0.70913,257.11,-0.72186,-0.1306,0.6796,159.78,0.00087434,-0.9822,-0.18782,228.69
    6273 
    6274 > view matrix models
    6275 > #20,0.69204,-0.13499,0.70913,247,-0.72186,-0.1306,0.6796,154.61,0.00087434,-0.9822,-0.18782,241.57
    6276 
    6277 > fitmap #20 inMap #22
    6278 
    6279 Fit molecule region_4_120nu.cif (#20) to map region_4_jxn.mrc (#22) using 2557
    6280 atoms 
    6281 average map value = 0.01196, steps = 144 
    6282 shifted from previous position = 15 
    6283 rotated from previous position = 31.3 degrees 
    6284 atoms outside contour = 1450, contour level = 0.017 
    6285  
    6286 Position of region_4_120nu.cif (#20) relative to region_4_jxn.mrc (#22)
    6287 coordinates: 
    6288 Matrix rotation and translation 
    6289 0.40381856 -0.17730696 0.89749249 239.22167029 
    6290 -0.83503508 -0.47217257 0.28243488 161.59415747 
    6291 0.37369368 -0.86349019 -0.33872958 230.73733341 
    6292 Axis -0.80624696 0.36853300 -0.46276263 
    6293 Axis point 0.00000000 166.41989331 -17.98113275 
    6294 Rotation angle (degrees) 134.71185810 
    6295 Shift along axis -240.09558153 
    6296  
    6297 
    6298 > ui mousemode right "rotate selected models"
    6299 
    6300 > view matrix models
    6301 > #20,0.60599,-0.74258,-0.28522,247.26,-0.75472,-0.42343,-0.5011,164.49,0.25133,0.51893,-0.81704,224.75
    6302 
    6303 > select subtract #20
    6304 
    6305 Nothing selected 
    6306 
    6307 > select add #20
    6308 
    6309 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6310 
    6311 > view matrix models
    6312 > #20,0.89255,0.13974,0.42875,240.55,-0.44253,0.45425,0.77319,155.57,-0.086711,-0.87984,0.46728,227.17
    6313 
    6314 > fitmap #20 inMap #22
    6315 
    6316 Fit molecule region_4_120nu.cif (#20) to map region_4_jxn.mrc (#22) using 2557
    6317 atoms 
    6318 average map value = 0.01196, steps = 312 
    6319 shifted from previous position = 6.44 
    6320 rotated from previous position = 70.7 degrees 
    6321 atoms outside contour = 1454, contour level = 0.017 
    6322  
    6323 Position of region_4_120nu.cif (#20) relative to region_4_jxn.mrc (#22)
    6324 coordinates: 
    6325 Matrix rotation and translation 
    6326 0.40343918 -0.17723559 0.89767719 239.23864776 
    6327 -0.83512837 -0.47221021 0.28209590 161.59484487 
    6328 0.37389492 -0.86348426 -0.33852257 230.72581851 
    6329 Axis -0.80612223 0.36857529 -0.46294622 
    6330 Axis point 0.00000000 166.42117224 -18.03030287 
    6331 Rotation angle (degrees) 134.72032483 
    6332 Shift along axis -240.10937070 
    6333  
    6334 
    6335 > view matrix models
    6336 > #20,0.3608,-0.31595,0.8775,239.98,-0.86109,-0.47427,0.18329,161.88,0.35826,-0.82173,-0.44318,230.82
    6337 
    6338 > ui mousemode right "translate selected models"
    6339 
    6340 > view matrix models
    6341 > #20,0.3608,-0.31595,0.8775,279.66,-0.86109,-0.47427,0.18329,154.95,0.35826,-0.82173,-0.44318,205.96
    6342 
    6343 > ui mousemode right "rotate selected models"
    6344 
    6345 > view matrix models
    6346 > #20,0.56431,0.070729,0.82253,278.13,-0.79465,-0.22355,0.56441,152.35,0.22379,-0.97212,-0.069944,205.19
    6347 
    6348 > select subtract #20
    6349 
    6350 Nothing selected 
    6351 
    6352 > mcopy #20
    6353 
    6354 Missing required "to_atoms" argument 
    6355 
    6356 > combine #20
    6357 
    6358 > combine #24
    6359 
    6360 > combine #25
    6361 
    6362 > combine #26
    6363 
    6364 > hide #20 models
    6365 
    6366 > rename #24 region_4_stemloop_1nu.cif
    6367 
    6368 > rename #24 region_4_stemloop_1.cif
    6369 
    6370 > rename #25 region_4_stemloop_2.cif
    6371 
    6372 > rename #26 region_4_stemloop_3.cif
    6373 
    6374 > rename #27 region_4_end.cif
    6375 
    6376 > select add #25
    6377 
    6378 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6379 
    6380 > select add #24
    6381 
    6382 5114 atoms, 5722 bonds, 240 residues, 2 models selected 
    6383 
    6384 > select add #26
    6385 
    6386 7671 atoms, 8583 bonds, 360 residues, 3 models selected 
    6387 
    6388 > select add #27
    6389 
    6390 10228 atoms, 11444 bonds, 480 residues, 4 models selected 
    6391 
    6392 > nucleotides sel stubs
    6393 
    6394 > select subtract #24
    6395 
    6396 7671 atoms, 8583 bonds, 360 residues, 3 models selected 
    6397 
    6398 > select subtract #25
    6399 
    6400 5114 atoms, 5722 bonds, 240 residues, 2 models selected 
    6401 
    6402 > select subtract #26
    6403 
    6404 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6405 
    6406 > select subtract #27
    6407 
    6408 Nothing selected 
    6409 
    6410 > ui tool show "Show Sequence Viewer"
    6411 
    6412 > sequence chain #27/A
    6413 
    6414 Alignment identifier is 27/A 
    6415 
    6416 > sequence chain #24/A
    6417 
    6418 Alignment identifier is 24/A 
    6419 
    6420 > sequence chain #25/A
    6421 
    6422 Alignment identifier is 25/A 
    6423 
    6424 > sequence chain #26/A
    6425 
    6426 Alignment identifier is 26/A 
    6427 
    6428 > select add #24
    6429 
    6430 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6431 
    6432 > select subtract #24
    6433 
    6434 Nothing selected 
    6435 
    6436 > select add #24
    6437 
    6438 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6439 
    6440 > select subtract #24
    6441 
    6442 Nothing selected 
    6443 
    6444 > select #24/A:15
    6445 
    6446 20 atoms, 21 bonds, 1 residue, 1 model selected 
    6447 
    6448 > select #24/A:15-76
    6449 
    6450 1320 atoms, 1477 bonds, 62 residues, 1 model selected 
    6451 
    6452 > select add #24
    6453 
    6454 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6455 
    6456 > select subtract #24
    6457 
    6458 Nothing selected 
    6459 
    6460 > select #24/A:15
    6461 
    6462 20 atoms, 21 bonds, 1 residue, 1 model selected 
    6463 
    6464 > select #24/A:15-108
    6465 
    6466 2004 atoms, 2244 bonds, 94 residues, 1 model selected 
    6467 
    6468 > select add #24
    6469 
    6470 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6471 
    6472 > select subtract #24
    6473 
    6474 Nothing selected 
    6475 
    6476 > select subtract #24/A:109
    6477 
    6478 20 atoms, 1 residue, 1 model selected 
    6479 
    6480 > select add #24
    6481 
    6482 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6483 
    6484 > select subtract #24
    6485 
    6486 Nothing selected 
    6487 
    6488 > select add #24/A:107
    6489 
    6490 43 atoms, 21 bonds, 2 residues, 1 model selected 
    6491 
    6492 > select #24/A:70
    6493 
    6494 23 atoms, 25 bonds, 1 residue, 1 model selected 
    6495 
    6496 > select #24/A:70-107
    6497 
    6498 810 atoms, 906 bonds, 38 residues, 1 model selected 
    6499 
    6500 > select ~sel & ##selected
    6501 
    6502 1747 atoms, 1955 bonds, 82 residues, 1 model selected 
    6503 
    6504 > delete atoms sel
    6505 
    6506 > delete bonds sel
    6507 
    6508 > select #24/A:70
    6509 
    6510 23 atoms, 25 bonds, 1 residue, 1 model selected 
    6511 
    6512 > select #24/A
    6513 
    6514 810 atoms, 906 bonds, 38 residues, 1 model selected 
    6515 
    6516 > select subtract #24
    6517 
    6518 Nothing selected 
    6519 
    6520 > select add #25
    6521 
    6522 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6523 
    6524 > select subtract #25
    6525 
    6526 Nothing selected 
    6527 
    6528 > select add #25/A:69
    6529 
    6530 22 atoms, 24 bonds, 1 residue, 1 model selected 
    6531 
    6532 > select add #25/A:53
    6533 
    6534 44 atoms, 48 bonds, 2 residues, 1 model selected 
    6535 
    6536 > select #25/A:53
    6537 
    6538 22 atoms, 24 bonds, 1 residue, 1 model selected 
    6539 
    6540 > select #25/A:53-69
    6541 
    6542 364 atoms, 407 bonds, 17 residues, 1 model selected 
    6543 
    6544 > select ~sel & ##selected
    6545 
    6546 2193 atoms, 2454 bonds, 103 residues, 1 model selected 
    6547 
    6548 > delete atoms sel
    6549 
    6550 > delete bonds sel
    6551 
    6552 > ui tool show "Show Sequence Viewer"
    6553 
    6554 > sequence chain #26/A
    6555 
    6556 Destroying pre-existing alignment with identifier 26/A 
    6557 Alignment identifier is 26/A 
    6558 
    6559 > select add #25
    6560 
    6561 364 atoms, 407 bonds, 17 residues, 1 model selected 
    6562 
    6563 > select subtract #25
    6564 
    6565 Nothing selected 
    6566 
    6567 > select add #26
    6568 
    6569 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6570 
    6571 > select subtract #26
    6572 
    6573 Nothing selected 
    6574 
    6575 > select add #25
    6576 
    6577 364 atoms, 407 bonds, 17 residues, 1 model selected 
    6578 
    6579 > select subtract #25
    6580 
    6581 Nothing selected 
    6582 
    6583 > select add #26
    6584 
    6585 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6586 
    6587 > select subtract #26
    6588 
    6589 Nothing selected 
    6590 
    6591 > select add #26/A:52
    6592 
    6593 22 atoms, 24 bonds, 1 residue, 1 model selected 
    6594 
    6595 > select add #26/A:16
    6596 
    6597 44 atoms, 48 bonds, 2 residues, 1 model selected 
    6598 
    6599 > select #26/A:16
    6600 
    6601 22 atoms, 24 bonds, 1 residue, 1 model selected 
    6602 
    6603 > select #26/A:16-52
    6604 
    6605 787 atoms, 881 bonds, 37 residues, 1 model selected 
    6606 
    6607 > select ~sel & ##selected
    6608 
    6609 1770 atoms, 1980 bonds, 83 residues, 1 model selected 
    6610 
    6611 > delete atoms sel
    6612 
    6613 > delete bonds sel
    6614 
    6615 > select #26/A:16
    6616 
    6617 22 atoms, 24 bonds, 1 residue, 1 model selected 
    6618 
    6619 > select #26/A:16-17
    6620 
    6621 42 atoms, 46 bonds, 2 residues, 1 model selected 
    6622 
    6623 > select add #26
    6624 
    6625 787 atoms, 881 bonds, 37 residues, 1 model selected 
    6626 
    6627 > select subtract #26
    6628 
    6629 Nothing selected 
    6630 
    6631 > select add #26
    6632 
    6633 787 atoms, 881 bonds, 37 residues, 1 model selected 
    6634 
    6635 > select subtract #26
    6636 
    6637 Nothing selected 
    6638 
    6639 > select add #27
    6640 
    6641 2557 atoms, 2861 bonds, 120 residues, 1 model selected 
    6642 
    6643 > select clear
    6644 
    6645 > select #26/A:16-17
    6646 
    6647 42 atoms, 46 bonds, 2 residues, 1 model selected 
    6648 
    6649 > select add #26
    6650 
    6651 787 atoms, 881 bonds, 37 residues, 1 model selected 
    6652 
    6653 > select subtract #26
    6654 
    6655 Nothing selected 
    6656 
    6657 > select add #26
    6658 
    6659 787 atoms, 881 bonds, 37 residues, 1 model selected 
    6660 
    6661 > select subtract #26
    6662 
    6663 Nothing selected 
    6664 
    6665 > select #27/A:16
    6666 
    6667 22 atoms, 24 bonds, 1 residue, 1 model selected 
    6668 
    6669 > select #27/A:16-107
    6670 
    6671 1961 atoms, 2196 bonds, 92 residues, 1 model selected 
    6672 
    6673 > delete atoms sel
    6674 
    6675 > delete bonds sel
    6676 
    6677 > rename #27 region_4_stem.cif
    6678 
    6679 > select add #24
    6680 
    6681 810 atoms, 906 bonds, 38 residues, 1 model selected 
    6682 
    6683 > ui mousemode right "translate selected models"
    6684 
    6685 > view matrix models
    6686 > #24,0.56431,0.070729,0.82253,238.68,-0.79465,-0.22355,0.56441,151.88,0.22379,-0.97212,-0.069944,241.45
    6687 
    6688 > view matrix models
    6689 > #24,0.56431,0.070729,0.82253,245.91,-0.79465,-0.22355,0.56441,167.94,0.22379,-0.97212,-0.069944,241.64
    6690 
    6691 > fitmap #24 inMap #22
    6692 
    6693 Fit molecule region_4_stemloop_1.cif (#24) to map region_4_jxn.mrc (#22) using
    6694 810 atoms 
    6695 average map value = 0.01566, steps = 204 
    6696 shifted from previous position = 7.99 
    6697 rotated from previous position = 33 degrees 
    6698 atoms outside contour = 342, contour level = 0.017 
    6699  
    6700 Position of region_4_stemloop_1.cif (#24) relative to region_4_jxn.mrc (#22)
    6701 coordinates: 
    6702 Matrix rotation and translation 
    6703 0.47123954 -0.08935096 0.87746776 246.88743327 
    6704 -0.66257951 -0.69251904 0.28531695 155.89515151 
    6705 0.58216980 -0.71584481 -0.38554447 241.39349735 
    6706 Axis -0.84071397 0.24797304 -0.48136202 
    6707 Axis point 0.00000000 134.81009863 5.52368848 
    6708 Rotation angle (degrees) 143.45716939 
    6709 Shift along axis -285.10158049 
    6710  
    6711 
    6712 > select subtract #24
    6713 
    6714 Nothing selected 
    6715 
    6716 > ui mousemode right "rotate selected models"
    6717 
    6718 > ui mousemode right "translate selected models"
    6719 
    6720 > select add #24
    6721 
    6722 810 atoms, 906 bonds, 38 residues, 1 model selected 
    6723 
    6724 > view matrix models
    6725 > #24,0.47124,-0.089351,0.87747,249.48,-0.66258,-0.69252,0.28532,155.36,0.58217,-0.71584,-0.38554,242.94
    6726 
    6727 > select subtract #24
    6728 
    6729 Nothing selected 
    6730 
    6731 > select ~sel & ##selected
    6732 
    6733 Nothing selected 
    6734 
    6735 > fitmap #24 inMap #22
    6736 
    6737 Fit molecule region_4_stemloop_1.cif (#24) to map region_4_jxn.mrc (#22) using
    6738 810 atoms 
    6739 average map value = 0.01566, steps = 60 
    6740 shifted from previous position = 3.06 
    6741 rotated from previous position = 0.0469 degrees 
    6742 atoms outside contour = 341, contour level = 0.017 
    6743  
    6744 Position of region_4_stemloop_1.cif (#24) relative to region_4_jxn.mrc (#22)
    6745 coordinates: 
    6746 Matrix rotation and translation 
    6747 0.47149621 -0.08957195 0.87730734 246.88840698 
    6748 -0.66297302 -0.69200386 0.28565261 155.89647266 
    6749 0.58151362 -0.71631524 -0.38566098 241.39562421 
    6750 Axis -0.84076694 0.24820515 -0.48114983 
    6751 Axis point 0.00000000 134.87948807 5.51206275 
    6752 Rotation angle (degrees) 143.42565114 
    6753 Shift along axis -285.02876562 
    6754  
    6755 
    6756 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    6757 > Project/20251114 region_4_wip.cxs"
    6758 
    6759 ——— End of log from Fri Nov 14 11:51:38 2025 ———
    6760 
    6761 > view name session-start
    6762 
    6763 opened ChimeraX session 
    6764 Showing vol diff region_3.seg - 199 regions, 199 surfaces 
    6765 
    6766 > hide #5 models
    6767 
    6768 > hide #!6 models
    6769 
    6770 > hide #!27 models
    6771 
    6772 > hide #26 models
    6773 
    6774 > hide #25 models
    6775 
    6776 > hide #24 models
    6777 
    6778 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    6779 > Project/20251114_region_4_3_21/fold_2025_11_14_15_36_region_4_3_21_model_0.cif"
    6780 
    6781 Chain information for fold_2025_11_14_15_36_region_4_3_21_model_0.cif #28 
    6782 --- 
    6783 Chain | Description 
    6784 A | . 
    6785 B | . 
    6786  
    6787 Computing secondary structure 
    6788 
    6789 > rename #28 region_4_3_21.cif
    6790 
    6791 > view
    6792 
    6793 > select add #28
    6794 
    6795 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    6796 
    6797 > ui mousemode right "rotate selected models"
    6798 
    6799 > show #!21 models
    6800 
    6801 > hide #!21 models
    6802 
    6803 > show #!21 models
    6804 
    6805 > hide #!22 models
    6806 
    6807 > hide #!21 models
    6808 
    6809 > show #!22 models
    6810 
    6811 > ui mousemode right "translate selected models"
    6812 
    6813 > view matrix models #28,1,0,0,28.55,0,1,0,160.57,0,0,1,291.63
    6814 
    6815 > view matrix models #28,1,0,0,273.37,0,1,0,231.32,0,0,1,263.01
    6816 
    6817 > view matrix models #28,1,0,0,237.63,0,1,0,157.4,0,0,1,253.66
    6818 
    6819 > select subtract #28
    6820 
    6821 Nothing selected 
    6822 
    6823 > select add #28
    6824 
    6825 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    6826 
    6827 > ui mousemode right "rotate selected models"
    6828 
    6829 > view matrix models
    6830 > #28,-0.70736,0.51396,-0.48527,247.22,0.31821,0.84456,0.43065,153.92,0.63118,0.15021,-0.76095,256.69
    6831 
    6832 > select add #27
    6833 
    6834 3176 atoms, 3549 bonds, 1 pseudobond, 149 residues, 3 models selected 
    6835 
    6836 > select subtract #27
    6837 
    6838 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    6839 
    6840 > select subtract #28
    6841 
    6842 Nothing selected 
    6843 
    6844 > select add #28
    6845 
    6846 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    6847 
    6848 > view matrix models
    6849 > #28,-0.8442,0.41085,-0.34427,247.78,0.095152,0.74693,0.65806,154.51,0.52751,0.52278,-0.66965,255.98
    6850 
    6851 > ui mousemode right "translate selected models"
    6852 
    6853 > view matrix models
    6854 > #28,-0.8442,0.41085,-0.34427,286.95,0.095152,0.74693,0.65806,141.41,0.52751,0.52278,-0.66965,188.35
    6855 
    6856 > select subtract #28
    6857 
    6858 Nothing selected 
    6859 
    6860 > select add #28
    6861 
    6862 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    6863 
    6864 > view matrix models
    6865 > #28,-0.8442,0.41085,-0.34427,248.01,0.095152,0.74693,0.65806,133.17,0.52751,0.52278,-0.66965,230.96
    6866 
    6867 > view matrix models
    6868 > #28,-0.8442,0.41085,-0.34427,251.51,0.095152,0.74693,0.65806,152.01,0.52751,0.52278,-0.66965,233.12
    6869 
    6870 > hide #14 models
    6871 
    6872 > hide #13 models
    6873 
    6874 > hide #!12 models
    6875 
    6876 > hide #10 models
    6877 
    6878 > fitmap #28 inMap #22
    6879 
    6880 Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
    6881 atoms 
    6882 average map value = 0.00902, steps = 212 
    6883 shifted from previous position = 14.1 
    6884 rotated from previous position = 26.1 degrees 
    6885 atoms outside contour = 1728, contour level = 0.017 
    6886  
    6887 Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
    6888 coordinates: 
    6889 Matrix rotation and translation 
    6890 -0.56696987 0.76211348 -0.31261502 246.06883011 
    6891 0.36457387 0.57247410 0.73441079 164.65241079 
    6892 0.73866840 0.30241754 -0.60242225 235.21080724 
    6893 Axis -0.35876909 -0.87308769 -0.33015545 
    6894 Axis point 63.71455261 0.00000000 112.34714572 
    6895 Rotation angle (degrees) 142.98320067 
    6896 Shift along axis -309.69401300 
    6897  
    6898 
    6899 > view matrix models
    6900 > #28,-0.56697,0.76211,-0.31262,252.48,0.36457,0.57247,0.73441,155.72,0.73867,0.30242,-0.60242,253.66
    6901 
    6902 > fitmap #28 inMap #22
    6903 
    6904 Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
    6905 atoms 
    6906 average map value = 0.00972, steps = 484 
    6907 shifted from previous position = 13 
    6908 rotated from previous position = 44.1 degrees 
    6909 atoms outside contour = 1689, contour level = 0.017 
    6910  
    6911 Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
    6912 coordinates: 
    6913 Matrix rotation and translation 
    6914 -0.77259137 0.39520601 -0.49690514 245.21759893 
    6915 0.42143324 0.90458405 0.06420011 151.75737818 
    6916 0.47486475 -0.15981188 -0.86542681 242.82459807 
    6917 Axis -0.22455089 -0.97410765 0.02629032 
    6918 Axis point 71.10413697 0.00000000 151.04087509 
    6919 Rotation angle (degrees) 150.07935587 
    6920 Shift along axis -196.50791772 
    6921  
    6922 
    6923 > fitmap #28 inMap #22
    6924 
    6925 Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
    6926 atoms 
    6927 average map value = 0.009721, steps = 44 
    6928 shifted from previous position = 0.025 
    6929 rotated from previous position = 0.0776 degrees 
    6930 atoms outside contour = 1695, contour level = 0.017 
    6931  
    6932 Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
    6933 coordinates: 
    6934 Matrix rotation and translation 
    6935 -0.77180971 0.39582846 -0.49762390 245.21078502 
    6936 0.42235445 0.90415899 0.06413395 151.73491890 
    6937 0.47531718 -0.16067446 -0.86501863 242.81558009 
    6938 Axis -0.22504970 -0.97398537 0.02655447 
    6939 Axis point 70.99979291 0.00000000 151.08781870 
    6940 Rotation angle (degrees) 150.03546065 
    6941 Shift along axis -196.52436630 
    6942  
    6943 
    6944 > undo
    6945 
    6946 > view matrix models
    6947 > #28,-0.56697,0.76211,-0.31262,295.07,0.36457,0.57247,0.73441,125.94,0.73867,0.30242,-0.60242,183.56
    6948 
    6949 > select add #21
    6950 
    6951 2580 atoms, 2886 bonds, 121 residues, 3 models selected 
    6952 
    6953 > select subtract #21
    6954 
    6955 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    6956 
    6957 > show #!21 models
    6958 
    6959 > select subtract #28
    6960 
    6961 Nothing selected 
    6962 
    6963 > hide #!22 models
    6964 
    6965 > hide #!21 models
    6966 
    6967 > show #!22 models
    6968 
    6969 > combine #28
    6970 
    6971 [Repeated 3 time(s)]
    6972 
    6973 > rename #29 region_4_stemloop_1.cif
    6974 
    6975 > rename #30 region_4_stemloop_2.cif
    6976 
    6977 > rename #31 region_4_stemloop_3.cif
    6978 
    6979 > rename #32 region_4_stem.cif
    6980 
    6981 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    6982 > Project/20251114 region_4_wip.cxs"
    6983 
    6984 ——— End of log from Fri Nov 14 16:00:29 2025 ———
    6985 
    6986 > view name session-start
    6987 
    6988 opened ChimeraX session 
    6989 Showing vol diff region_3.seg - 199 regions, 199 surfaces 
    6990 
    6991 > hide #32 models
    6992 
    6993 > hide #31 models
    6994 
    6995 > hide #30 models
    6996 
    6997 > hide #29 models
    6998 
    6999 > hide #28 models
    7000 
    7001 > hide #!22 models
    7002 
    7003 > show #!12 models
    7004 
    7005 > hide #!12 models
    7006 
    7007 > show #!11 models
    7008 
    7009 > hide #!6 models
    7010 
    7011 > open "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    7012 > Project/20251113_rna_phicb5_region_3_75nt_final/fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif"
    7013 
    7014 Chain information for
    7015 fold_2025_11_13_14_27_rna_phicb5_region_3_75nu_model_0.cif #33 
    7016 --- 
    7017 Chain | Description 
    7018 A | . 
    7019  
    7020 Computing secondary structure 
    7021 
    7022 > rename #33 region_3_FL.cif
    7023 
    7024 > combine #33
    7025 
    7026 [Repeated 3 time(s)]
    7027 
    7028 > close #37
    7029 
    7030 > select add #33
    7031 
    7032 1594 atoms, 1781 bonds, 75 residues, 1 model selected 
    7033 
    7034 > select add #34
    7035 
    7036 3188 atoms, 3562 bonds, 150 residues, 2 models selected 
    7037 
    7038 > select add #35
    7039 
    7040 4782 atoms, 5343 bonds, 225 residues, 3 models selected 
    7041 
    7042 > select add #36
    7043 
    7044 6376 atoms, 7124 bonds, 300 residues, 4 models selected 
    7045 
    7046 > view
    7047 
    7048 > ui mousemode right "rotate selected models"
    7049 
    7050 > ui mousemode right "translate selected models"
    7051 
    7052 > view matrix models
    7053 > #33,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58,#34,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58,#35,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58,#36,1,0,0,153.99,0,1,0,-20.827,0,0,1,210.58
    7054 
    7055 > view matrix models
    7056 > #33,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99,#34,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99,#35,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99,#36,1,0,0,155.59,0,1,0,86.615,0,0,1,226.99
    7057 
    7058 > nucleotides sel stubs
    7059 
    7060 > ui mousemode right "rotate selected models"
    7061 
    7062 > view matrix models
    7063 > #33,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76,#34,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76,#35,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76,#36,0.40008,-0.80967,-0.42938,153.72,0.34342,0.56683,-0.74885,87.802,0.8497,0.15214,0.50483,229.76
    7064 
    7065 > view matrix models
    7066 > #33,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57,#34,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57,#35,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57,#36,0.37008,-0.90078,-0.22722,153.99,0.266,0.33709,-0.90311,87.624,0.8901,0.27378,0.36436,229.57
    7067 
    7068 > ui mousemode right "translate selected models"
    7069 
    7070 > view matrix models
    7071 > #33,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77,#34,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77,#35,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77,#36,0.37008,-0.90078,-0.22722,148.71,0.266,0.33709,-0.90311,149.78,0.8901,0.27378,0.36436,194.77
    7072 
    7073 > select subtract #33
    7074 
    7075 4782 atoms, 5343 bonds, 225 residues, 3 models selected 
    7076 
    7077 > select subtract #34
    7078 
    7079 3188 atoms, 3562 bonds, 150 residues, 2 models selected 
    7080 
    7081 > select subtract #35
    7082 
    7083 1594 atoms, 1781 bonds, 75 residues, 1 model selected 
    7084 
    7085 > select subtract #36
    7086 
    7087 Nothing selected 
    7088 
    7089 > show #10 models
    7090 
    7091 > hide #10 models
    7092 
    7093 > show #10 models
    7094 
    7095 > hide #33 models
    7096 
    7097 > rename #34 region_3_stem.cif
    7098 
    7099 > rename #35 region_3_stemloop_1.cif
    7100 
    7101 > rename #36 region_3_stemloop_2.cif
    7102 
    7103 > hide #34 models
    7104 
    7105 > hide #36 models
    7106 
    7107 > select add #35
    7108 
    7109 1594 atoms, 1781 bonds, 75 residues, 1 model selected 
    7110 
    7111 > select subtract #35
    7112 
    7113 Nothing selected 
    7114 
    7115 > show #34 models
    7116 
    7117 > show #36 models
    7118 
    7119 > ui tool show "Show Sequence Viewer"
    7120 
    7121 > sequence chain #34/A
    7122 
    7123 Alignment identifier is 34/A 
    7124 
    7125 > sequence chain #35/A
    7126 
    7127 Alignment identifier is 35/A 
    7128 
    7129 > sequence chain #36/A
    7130 
    7131 Alignment identifier is 36/A 
    7132 
    7133 > select #35/A:32-33
    7134 
    7135 42 atoms, 46 bonds, 2 residues, 1 model selected 
    7136 
    7137 > select #35/A:33-44
    7138 
    7139 252 atoms, 280 bonds, 12 residues, 1 model selected 
    7140 
    7141 > select #35/A:33-44
    7142 
    7143 252 atoms, 280 bonds, 12 residues, 1 model selected 
    7144 
    7145 > select #35/A:33-44
    7146 
    7147 252 atoms, 280 bonds, 12 residues, 1 model selected 
    7148 
    7149 > select #35/A:33
    7150 
    7151 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7152 
    7153 > select #35/A:33-63
    7154 
    7155 660 atoms, 737 bonds, 31 residues, 1 model selected 
    7156 
    7157 > select ~sel & ##selected
    7158 
    7159 934 atoms, 1044 bonds, 44 residues, 1 model selected 
    7160 
    7161 > delete atoms sel
    7162 
    7163 > delete bonds sel
    7164 
    7165 > select #36/A:21
    7166 
    7167 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7168 
    7169 > select #36/A:21-32
    7170 
    7171 253 atoms, 282 bonds, 12 residues, 1 model selected 
    7172 
    7173 > select #36/A:13
    7174 
    7175 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7176 
    7177 > select #36/A:13-32
    7178 
    7179 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7180 
    7181 > select ~sel & ##selected
    7182 
    7183 1174 atoms, 1313 bonds, 55 residues, 1 model selected 
    7184 
    7185 > delete atoms sel
    7186 
    7187 > delete bonds sel
    7188 
    7189 > select #34/A:13
    7190 
    7191 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7192 
    7193 > select #34/A:13-63
    7194 
    7195 1080 atoms, 1206 bonds, 51 residues, 1 model selected 
    7196 
    7197 > delete atoms sel
    7198 
    7199 > delete bonds sel
    7200 
    7201 > undo
    7202 
    7203 Undo failed, probably because structures have been modified. 
    7204 
    7205 > close #34
    7206 
    7207 > combine #33
    7208 
    7209 > rename #34 region_3_stem.cif
    7210 
    7211 > nucleotides #10,34-36 stubs
    7212 
    7213 > ui tool show "Show Sequence Viewer"
    7214 
    7215 > sequence chain #34/A
    7216 
    7217 Alignment identifier is 34/A 
    7218 
    7219 > select #34/A:13
    7220 
    7221 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7222 
    7223 > select #34/A:13-63
    7224 
    7225 1080 atoms, 1206 bonds, 51 residues, 1 model selected 
    7226 
    7227 > delete atoms sel
    7228 
    7229 > delete bonds sel
    7230 
    7231 > hide #!34 models
    7232 
    7233 > show #!34 models
    7234 
    7235 > hide #35 models
    7236 
    7237 > show #35 models
    7238 
    7239 > hide #36 models
    7240 
    7241 > show #36 models
    7242 
    7243 > ui tool show "Show Sequence Viewer"
    7244 
    7245 > sequence chain #34/A
    7246 
    7247 Alignment identifier is 34/A 
    7248 
    7249 > sequence chain #35/A
    7250 
    7251 Alignment identifier is 35/A 
    7252 
    7253 > sequence chain #36/A
    7254 
    7255 Alignment identifier is 36/A 
    7256 
    7257 > select clear
    7258 
    7259 > select add #34
    7260 
    7261 514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected 
    7262 
    7263 > select subtract #34
    7264 
    7265 Nothing selected 
    7266 
    7267 > select add #34
    7268 
    7269 514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected 
    7270 
    7271 > select subtract #34
    7272 
    7273 Nothing selected 
    7274 
    7275 > select add #35
    7276 
    7277 660 atoms, 737 bonds, 31 residues, 1 model selected 
    7278 
    7279 > select subtract #35
    7280 
    7281 Nothing selected 
    7282 
    7283 > select add #36
    7284 
    7285 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7286 
    7287 > select subtract #36
    7288 
    7289 Nothing selected 
    7290 
    7291 > select add #34
    7292 
    7293 514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected 
    7294 
    7295 > select add #35
    7296 
    7297 1174 atoms, 1310 bonds, 1 pseudobond, 55 residues, 3 models selected 
    7298 
    7299 > select add #36
    7300 
    7301 1594 atoms, 1778 bonds, 1 pseudobond, 75 residues, 4 models selected 
    7302 
    7303 > ui tool show "Show Sequence Viewer"
    7304 
    7305 > sequence chain #34/A
    7306 
    7307 Alignment identifier is 34/A 
    7308 
    7309 > sequence chain #35/A
    7310 
    7311 Alignment identifier is 35/A 
    7312 
    7313 > sequence chain #36/A
    7314 
    7315 Alignment identifier is 36/A 
    7316 
    7317 > select subtract #34
    7318 
    7319 1080 atoms, 1205 bonds, 51 residues, 2 models selected 
    7320 
    7321 > select subtract #35
    7322 
    7323 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7324 
    7325 > select subtract #36
    7326 
    7327 Nothing selected 
    7328 
    7329 > close #12-14
    7330 
    7331 > rename #34 id #12
    7332 
    7333 > rename #35 id #13
    7334 
    7335 > rename #36 id #14
    7336 
    7337 > hide #!12 models
    7338 
    7339 > show #!12 models
    7340 
    7341 > select add #12
    7342 
    7343 514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected 
    7344 
    7345 > select add #13
    7346 
    7347 1174 atoms, 1310 bonds, 1 pseudobond, 55 residues, 3 models selected 
    7348 
    7349 > select add #14
    7350 
    7351 1594 atoms, 1778 bonds, 1 pseudobond, 75 residues, 4 models selected 
    7352 
    7353 > ui mousemode right "rotate selected models"
    7354 
    7355 > view matrix models
    7356 > #12,0.28393,0.95753,0.050275,150.24,-0.63519,0.14855,0.75794,140.25,0.71828,-0.24714,0.65039,185.37,#13,0.28393,0.95753,0.050275,150.24,-0.63519,0.14855,0.75794,140.25,0.71828,-0.24714,0.65039,185.37,#14,0.28393,0.95753,0.050275,150.24,-0.63519,0.14855,0.75794,140.25,0.71828,-0.24714,0.65039,185.37
    7357 
    7358 > view matrix models
    7359 > #12,-0.22185,0.96905,0.10827,148.24,-0.76762,-0.24204,0.59345,140.95,0.60128,0.04855,0.79756,184.03,#13,-0.22185,0.96905,0.10827,148.24,-0.76762,-0.24204,0.59345,140.95,0.60128,0.04855,0.79756,184.03,#14,-0.22185,0.96905,0.10827,148.24,-0.76762,-0.24204,0.59345,140.95,0.60128,0.04855,0.79756,184.03
    7360 
    7361 > select subtract #12
    7362 
    7363 1080 atoms, 1205 bonds, 51 residues, 2 models selected 
    7364 
    7365 > select subtract #13
    7366 
    7367 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7368 
    7369 > select subtract #14
    7370 
    7371 Nothing selected 
    7372 
    7373 > select add #12
    7374 
    7375 514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected 
    7376 
    7377 > ui mousemode right "translate selected models"
    7378 
    7379 > view matrix models
    7380 > #12,-0.22185,0.96905,0.10827,208.19,-0.76762,-0.24204,0.59345,106.42,0.60128,0.04855,0.79756,209.44
    7381 
    7382 > view matrix models
    7383 > #12,-0.22185,0.96905,0.10827,212.73,-0.76762,-0.24204,0.59345,145.2,0.60128,0.04855,0.79756,208.63
    7384 
    7385 > view matrix models
    7386 > #12,-0.22185,0.96905,0.10827,224.03,-0.76762,-0.24204,0.59345,143.99,0.60128,0.04855,0.79756,226.46
    7387 
    7388 > fitmap #12 inMap #11
    7389 
    7390 Fit molecule region_3_stem.cif (#12) to map region_3.mrc (#11) using 514 atoms 
    7391 average map value = 0.01856, steps = 332 
    7392 shifted from previous position = 4.24 
    7393 rotated from previous position = 92.1 degrees 
    7394 atoms outside contour = 165, contour level = 0.017 
    7395  
    7396 Position of region_3_stem.cif (#12) relative to region_3.mrc (#11)
    7397 coordinates: 
    7398 Matrix rotation and translation 
    7399 -0.67024334 0.57228792 -0.47250439 232.01849271 
    7400 -0.31171341 -0.79487891 -0.52057878 143.13229758 
    7401 -0.67350472 -0.20162850 0.71115212 240.73699862 
    7402 Axis 0.33188197 0.20914980 -0.91984277 
    7403 Axis point 182.68893013 61.35992766 0.00000000 
    7404 Rotation angle (degrees) 151.28078526 
    7405 Shift along axis -114.50134148 
    7406  
    7407 
    7408 > select add #11
    7409 
    7410 514 atoms, 573 bonds, 1 pseudobond, 24 residues, 4 models selected 
    7411 
    7412 > transparency sel 50
    7413 
    7414 > select subtract #11
    7415 
    7416 514 atoms, 573 bonds, 1 pseudobond, 24 residues, 2 models selected 
    7417 
    7418 > show #!7 models
    7419 
    7420 > hide #!7 models
    7421 
    7422 > show #!6 models
    7423 
    7424 > select subtract #12
    7425 
    7426 Nothing selected 
    7427 
    7428 > hide #!6 models
    7429 
    7430 > select add #13
    7431 
    7432 660 atoms, 737 bonds, 31 residues, 1 model selected 
    7433 
    7434 > select subtract #13
    7435 
    7436 Nothing selected 
    7437 
    7438 > select add #13
    7439 
    7440 660 atoms, 737 bonds, 31 residues, 1 model selected 
    7441 
    7442 > select subtract #13
    7443 
    7444 Nothing selected 
    7445 
    7446 > select add #14
    7447 
    7448 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7449 
    7450 > select subtract #14
    7451 
    7452 Nothing selected 
    7453 
    7454 > select add #13
    7455 
    7456 660 atoms, 737 bonds, 31 residues, 1 model selected 
    7457 
    7458 > view matrix models
    7459 > #13,-0.22185,0.96905,0.10827,252.13,-0.76762,-0.24204,0.59345,117.19,0.60128,0.04855,0.79756,253.51
    7460 
    7461 > ui mousemode right "rotate selected models"
    7462 
    7463 > view matrix models
    7464 > #13,-0.23797,-0.95608,-0.17115,243.27,0.74968,-0.29284,0.59349,143.26,-0.61754,0.012927,0.78644,232.24
    7465 
    7466 > fitmap #13 inMap #11
    7467 
    7468 Fit molecule region_3_stemloop_1.cif (#13) to map region_3.mrc (#11) using 660
    7469 atoms 
    7470 average map value = 0.0207, steps = 96 
    7471 shifted from previous position = 6.17 
    7472 rotated from previous position = 22.7 degrees 
    7473 atoms outside contour = 174, contour level = 0.017 
    7474  
    7475 Position of region_3_stemloop_1.cif (#13) relative to region_3.mrc (#11)
    7476 coordinates: 
    7477 Matrix rotation and translation 
    7478 -0.47098154 -0.78844909 -0.39563167 232.97818477 
    7479 0.70742252 -0.60551307 0.36456453 139.47240894 
    7480 -0.52700072 -0.10817559 0.84295212 230.51979068 
    7481 Axis -0.30028880 0.08344681 0.95019117 
    7482 Axis point 120.61892566 131.66491710 0.00000000 
    7483 Rotation angle (degrees) 128.08073496 
    7484 Shift along axis 160.71565780 
    7485  
    7486 
    7487 > select subtract #13
    7488 
    7489 Nothing selected 
    7490 
    7491 > select add #14
    7492 
    7493 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7494 
    7495 > ui mousemode right "translate selected models"
    7496 
    7497 > view matrix models
    7498 > #14,-0.22185,0.96905,0.10827,201.68,-0.76762,-0.24204,0.59345,130.17,0.60128,0.04855,0.79756,226.4
    7499 
    7500 > select subtract #14
    7501 
    7502 Nothing selected 
    7503 
    7504 > ui mousemode right "rotate selected models"
    7505 
    7506 > select add #14
    7507 
    7508 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7509 
    7510 > view matrix models
    7511 > #14,0.84509,-0.51135,-0.15605,221.02,-0.17224,-0.53671,0.826,129.76,-0.50613,-0.67116,-0.54164,254.01
    7512 
    7513 > view matrix models
    7514 > #14,0.79924,-0.5273,-0.2884,221.81,-0.22377,-0.70643,0.67148,133.87,-0.5578,-0.47214,-0.6826,250.29
    7515 
    7516 > select subtract #14
    7517 
    7518 Nothing selected 
    7519 
    7520 > ui mousemode right "translate selected models"
    7521 
    7522 > select add #14
    7523 
    7524 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7525 
    7526 > view matrix models
    7527 > #14,0.79924,-0.5273,-0.2884,231.33,-0.22377,-0.70643,0.67148,151.74,-0.5578,-0.47214,-0.6826,238.69
    7528 
    7529 > select subtract #14
    7530 
    7531 Nothing selected 
    7532 
    7533 > fitmap #14 inMap #11
    7534 
    7535 Fit molecule region_3_stemloop_2.cif (#14) to map region_3.mrc (#11) using 420
    7536 atoms 
    7537 average map value = 0.01729, steps = 120 
    7538 shifted from previous position = 8.45 
    7539 rotated from previous position = 51.2 degrees 
    7540 atoms outside contour = 157, contour level = 0.017 
    7541  
    7542 Position of region_3_stemloop_2.cif (#14) relative to region_3.mrc (#11)
    7543 coordinates: 
    7544 Matrix rotation and translation 
    7545 0.38535596 -0.92153920 0.04760545 251.94606474 
    7546 -0.13162435 -0.00383197 0.99129226 131.01134564 
    7547 -0.91333226 -0.38826641 -0.12277367 243.37850942 
    7548 Axis -0.74267035 0.51731032 0.42524204 
    7549 Axis point 0.00000000 267.35951271 130.31083100 
    7550 Rotation angle (degrees) 111.75415824 
    7551 Shift along axis -15.84457702 
    7552  
    7553 
    7554 > select add #14
    7555 
    7556 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7557 
    7558 > view matrix models
    7559 > #14,0.38536,-0.92154,0.047605,248.34,-0.13162,-0.003832,0.99129,117.85,-0.91333,-0.38827,-0.12277,239.61
    7560 
    7561 > select subtract #14
    7562 
    7563 Nothing selected 
    7564 
    7565 > select add #14
    7566 
    7567 420 atoms, 468 bonds, 20 residues, 1 model selected 
    7568 
    7569 > ui mousemode right "rotate selected models"
    7570 
    7571 > view matrix models
    7572 > #14,0.95819,-0.28542,-0.020102,227.89,-0.012417,-0.11167,0.99367,118.73,-0.28586,-0.95187,-0.11054,244.45
    7573 
    7574 > view matrix models
    7575 > #14,0.91501,-0.23497,0.32793,227.5,-0.2214,0.38705,0.89508,110.46,-0.33724,-0.89162,0.30213,243.98
    7576 
    7577 > view matrix models
    7578 > #14,0.068816,-0.55322,0.83019,244.42,-0.1128,0.82251,0.55745,99.562,-0.99123,-0.13201,-0.0058028,234.75
    7579 
    7580 > view matrix models
    7581 > #14,0.96827,0.0098179,0.24972,221.67,-0.22252,-0.421,0.87934,127.97,0.11377,-0.90701,-0.40546,238.69
    7582 
    7583 > view matrix models
    7584 > #14,0.73434,0.10252,0.67099,222.54,-0.67776,0.056552,0.73311,122.82,0.03721,-0.99312,0.11101,241.63
    7585 
    7586 > select subtract #14
    7587 
    7588 Nothing selected 
    7589 
    7590 > fitmap #14 inMap #11
    7591 
    7592 Fit molecule region_3_stemloop_2.cif (#14) to map region_3.mrc (#11) using 420
    7593 atoms 
    7594 average map value = 0.019, steps = 152 
    7595 shifted from previous position = 9.9 
    7596 rotated from previous position = 60.6 degrees 
    7597 atoms outside contour = 135, contour level = 0.017 
    7598  
    7599 Position of region_3_stemloop_2.cif (#14) relative to region_3.mrc (#11)
    7600 coordinates: 
    7601 Matrix rotation and translation 
    7602 0.09053332 -0.57439805 0.81355429 248.73407833 
    7603 -0.99249506 -0.11946733 0.02609792 137.69637743 
    7604 0.08220257 -0.80981135 -0.58090301 232.72316657 
    7605 Axis -0.70435616 0.61625359 -0.35229805 
    7606 Axis point 0.00000000 217.80260526 -2.76245318 
    7607 Rotation angle (degrees) 143.60238616 
    7608 Shift along axis -172.32940869 
    7609  
    7610 
    7611 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    7612 > Project/20251113 region_3.cxs"
    7613 
    7614 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    7615 > Project/20251114 region_4_wip.cxs"
    7616 
    7617 > hide #!11 models
    7618 
    7619 > show #!22 models
    7620 
    7621 > show #29 models
    7622 
    7623 > show #30 models
    7624 
    7625 > show #31 models
    7626 
    7627 > show #32 models
    7628 
    7629 > select add #32
    7630 
    7631 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7632 
    7633 > select add #31
    7634 
    7635 5160 atoms, 5772 bonds, 242 residues, 2 models selected 
    7636 
    7637 > select add #30
    7638 
    7639 7740 atoms, 8658 bonds, 363 residues, 3 models selected 
    7640 
    7641 > select add #29
    7642 
    7643 10320 atoms, 11544 bonds, 484 residues, 4 models selected 
    7644 
    7645 > nucleotides sel stubs
    7646 
    7647 > select subtract #29
    7648 
    7649 7740 atoms, 8658 bonds, 363 residues, 3 models selected 
    7650 
    7651 > select subtract #30
    7652 
    7653 5160 atoms, 5772 bonds, 242 residues, 2 models selected 
    7654 
    7655 > select subtract #31
    7656 
    7657 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7658 
    7659 > select subtract #32
    7660 
    7661 Nothing selected 
    7662 
    7663 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    7664 > Project/20251114 region_4_wip.cxs"
    7665 
    7666 > hide #29 models
    7667 
    7668 > hide #30 models
    7669 
    7670 > hide #31 models
    7671 
    7672 > hide #32 models
    7673 
    7674 > show #29 models
    7675 
    7676 > show #30 models
    7677 
    7678 > show #31 models
    7679 
    7680 > select add #29
    7681 
    7682 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7683 
    7684 > select add #30
    7685 
    7686 5160 atoms, 5772 bonds, 242 residues, 2 models selected 
    7687 
    7688 > select add #31
    7689 
    7690 7740 atoms, 8658 bonds, 363 residues, 3 models selected 
    7691 
    7692 > show #32 models
    7693 
    7694 > select add #32
    7695 
    7696 10320 atoms, 11544 bonds, 484 residues, 4 models selected 
    7697 
    7698 > ui tool show "Show Sequence Viewer"
    7699 
    7700 > select subtract #29
    7701 
    7702 7740 atoms, 8658 bonds, 363 residues, 3 models selected 
    7703 
    7704 > select subtract #30
    7705 
    7706 5160 atoms, 5772 bonds, 242 residues, 2 models selected 
    7707 
    7708 > select subtract #31
    7709 
    7710 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7711 
    7712 > select subtract #32
    7713 
    7714 Nothing selected 
    7715 
    7716 > ui tool show "Show Sequence Viewer"
    7717 
    7718 [Repeated 1 time(s)]
    7719 
    7720 > sequence chain #29/A
    7721 
    7722 Alignment identifier is 29/A 
    7723 
    7724 > sequence chain #30/A
    7725 
    7726 Alignment identifier is 30/A 
    7727 
    7728 > sequence chain #31/A
    7729 
    7730 Alignment identifier is 31/A 
    7731 
    7732 > sequence chain #32/A
    7733 
    7734 Alignment identifier is 32/A 
    7735 
    7736 > select #31/A:14
    7737 
    7738 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7739 
    7740 > select #31/A:14-50
    7741 
    7742 787 atoms, 881 bonds, 37 residues, 1 model selected 
    7743 
    7744 > select #31/A:14
    7745 
    7746 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7747 
    7748 > select #31/A:14-47
    7749 
    7750 723 atoms, 809 bonds, 34 residues, 1 model selected 
    7751 
    7752 > select add #31
    7753 
    7754 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7755 
    7756 > select subtract #31
    7757 
    7758 Nothing selected 
    7759 
    7760 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    7761 > Project/20251114 region_4_wip.cxs"
    7762 
    7763 > hide #29 models
    7764 
    7765 > hide #30 models
    7766 
    7767 > hide #31 models
    7768 
    7769 > hide #32 models
    7770 
    7771 > show #28 models
    7772 
    7773 > select add #22
    7774 
    7775 2 models selected 
    7776 
    7777 > transparency sel 50
    7778 
    7779 > select subtract #22
    7780 
    7781 Nothing selected 
    7782 
    7783 > select add #28
    7784 
    7785 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7786 
    7787 > ui mousemode right "translate selected models"
    7788 
    7789 > view matrix models
    7790 > #28,-0.56697,0.76211,-0.31262,265.75,0.36457,0.57247,0.73441,172.72,0.73867,0.30242,-0.60242,241.18
    7791 
    7792 > select subtract #28
    7793 
    7794 Nothing selected 
    7795 
    7796 > select add #28
    7797 
    7798 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7799 
    7800 > select subtract #28
    7801 
    7802 Nothing selected 
    7803 
    7804 > select add #28
    7805 
    7806 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7807 
    7808 > view matrix models
    7809 > #28,-0.56697,0.76211,-0.31262,253.23,0.36457,0.57247,0.73441,155.29,0.73867,0.30242,-0.60242,254.21
    7810 
    7811 > select subtract #28
    7812 
    7813 Nothing selected 
    7814 
    7815 > select add #28
    7816 
    7817 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
    7818 
    7819 > view matrix models
    7820 > #28,-0.56697,0.76211,-0.31262,259.51,0.36457,0.57247,0.73441,150.54,0.73867,0.30242,-0.60242,248.11
    7821 
    7822 > select subtract #28
    7823 
    7824 Nothing selected 
    7825 
    7826 > fitmap #28 inMap #22
    7827 
    7828 Fit molecule region_4_3_21.cif (#28) to map region_4_jxn.mrc (#22) using 2580
    7829 atoms 
    7830 average map value = 0.005419, steps = 128 
    7831 shifted from previous position = 8.73 
    7832 rotated from previous position = 14.1 degrees 
    7833 atoms outside contour = 2088, contour level = 0.017 
    7834  
    7835 Position of region_4_3_21.cif (#28) relative to region_4_jxn.mrc (#22)
    7836 coordinates: 
    7837 Matrix rotation and translation 
    7838 -0.69253716 0.58630432 -0.42028497 255.21353005 
    7839 0.25319026 0.74309928 0.61943367 156.05085047 
    7840 0.67549013 0.32256879 -0.66307044 253.54901589 
    7841 Axis -0.25091303 -0.92615958 -0.28155119 
    7842 Axis point 75.57428244 0.00000000 135.75975715 
    7843 Rotation angle (degrees) 143.73155176 
    7844 Shift along axis -279.95141943 
    7845  
    7846 
    7847 > hide #28 models
    7848 
    7849 > show #29 models
    7850 
    7851 > show #30 models
    7852 
    7853 > hide #30 models
    7854 
    7855 > hide #29 models
    7856 
    7857 > show #29 models
    7858 
    7859 > show #30 models
    7860 
    7861 > show #31 models
    7862 
    7863 > show #32 models
    7864 
    7865 > ui tool show "Show Sequence Viewer"
    7866 
    7867 > sequence chain #29/A
    7868 
    7869 Alignment identifier is 29/A 
    7870 
    7871 > sequence chain #29/B
    7872 
    7873 Alignment identifier is 29/B 
    7874 
    7875 > sequence chain #30/A
    7876 
    7877 Alignment identifier is 30/A 
    7878 
    7879 > sequence chain #30/B
    7880 
    7881 Alignment identifier is 30/B 
    7882 
    7883 > sequence chain #31/A
    7884 
    7885 Alignment identifier is 31/A 
    7886 
    7887 > sequence chain #31/B
    7888 
    7889 Alignment identifier is 31/B 
    7890 
    7891 > sequence chain #32/A
    7892 
    7893 Alignment identifier is 32/A 
    7894 
    7895 > sequence chain #32/B
    7896 
    7897 Alignment identifier is 32/B 
    7898 
    7899 > select #31/B:1
    7900 
    7901 21 atoms, 22 bonds, 1 residue, 1 model selected 
    7902 
    7903 > select #31/B
    7904 
    7905 1458 atoms, 1633 bonds, 68 residues, 1 model selected 
    7906 
    7907 > delete atoms sel
    7908 
    7909 > delete bonds sel
    7910 
    7911 > select #30/B:1
    7912 
    7913 21 atoms, 22 bonds, 1 residue, 1 model selected 
    7914 
    7915 > select #30/B:1-9
    7916 
    7917 193 atoms, 215 bonds, 9 residues, 1 model selected 
    7918 
    7919 > select #30/B:1
    7920 
    7921 21 atoms, 22 bonds, 1 residue, 1 model selected 
    7922 
    7923 > select #30/B:1-14
    7924 
    7925 303 atoms, 339 bonds, 14 residues, 1 model selected 
    7926 
    7927 > select ~sel & ##selected
    7928 
    7929 2277 atoms, 2547 bonds, 107 residues, 1 model selected 
    7930 
    7931 > delete atoms sel
    7932 
    7933 > delete bonds sel
    7934 
    7935 > select #29/B:15
    7936 
    7937 23 atoms, 25 bonds, 1 residue, 1 model selected 
    7938 
    7939 > select #29/B:15-52
    7940 
    7941 810 atoms, 906 bonds, 38 residues, 1 model selected 
    7942 
    7943 > select ~sel
    7944 
    7945 200707 atoms, 207188 bonds, 2 pseudobonds, 23630 residues, 245 models selected 
    7946 
    7947 > select subtract #32
    7948 
    7949 198127 atoms, 204302 bonds, 2 pseudobonds, 23509 residues, 244 models selected 
    7950 
    7951 > select add #32
    7952 
    7953 200707 atoms, 207188 bonds, 2 pseudobonds, 23630 residues, 245 models selected 
    7954 
    7955 > select subtract #33
    7956 
    7957 199113 atoms, 205407 bonds, 2 pseudobonds, 23555 residues, 244 models selected 
    7958 
    7959 > select subtract #32
    7960 
    7961 196533 atoms, 202521 bonds, 2 pseudobonds, 23434 residues, 243 models selected 
    7962 
    7963 > select subtract #31
    7964 
    7965 195411 atoms, 201268 bonds, 2 pseudobonds, 23381 residues, 242 models selected 
    7966 
    7967 > select subtract #30
    7968 
    7969 195108 atoms, 200929 bonds, 2 pseudobonds, 23367 residues, 241 models selected 
    7970 
    7971 > select add #29
    7972 
    7973 195918 atoms, 201837 bonds, 2 pseudobonds, 23405 residues, 241 models selected 
    7974 
    7975 > select subtract #28
    7976 
    7977 193338 atoms, 198951 bonds, 2 pseudobonds, 23284 residues, 240 models selected 
    7978 
    7979 > select subtract #29
    7980 
    7981 190758 atoms, 196065 bonds, 2 pseudobonds, 23163 residues, 239 models selected 
    7982 
    7983 > select subtract #27
    7984 
    7985 190162 atoms, 195402 bonds, 1 pseudobond, 23135 residues, 237 models selected 
    7986 
    7987 > select subtract #26
    7988 
    7989 189375 atoms, 194521 bonds, 1 pseudobond, 23098 residues, 236 models selected 
    7990 
    7991 > select subtract #25
    7992 
    7993 189011 atoms, 194114 bonds, 1 pseudobond, 23081 residues, 235 models selected 
    7994 
    7995 > select subtract #24
    7996 
    7997 188201 atoms, 193208 bonds, 1 pseudobond, 23043 residues, 234 models selected 
    7998 
    7999 > select subtract #1
    8000 
    8001 188201 atoms, 193208 bonds, 1 pseudobond, 23043 residues, 232 models selected 
    8002 
    8003 > select subtract #2
    8004 
    8005 15288 atoms, 17082 bonds, 1 pseudobond, 719 residues, 231 models selected 
    8006 
    8007 > select subtract #3
    8008 
    8009 15288 atoms, 17082 bonds, 1 pseudobond, 719 residues, 229 models selected 
    8010 
    8011 > select subtract #4
    8012 
    8013 15288 atoms, 17082 bonds, 1 pseudobond, 719 residues, 226 models selected 
    8014 
    8015 > select subtract #5
    8016 
    8017 12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 225 models selected 
    8018 
    8019 > select subtract #6
    8020 
    8021 12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 25 models selected 
    8022 
    8023 > select subtract #7
    8024 
    8025 12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 23 models selected 
    8026 
    8027 > select subtract #8
    8028 
    8029 12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 21 models selected 
    8030 
    8031 > select subtract #9
    8032 
    8033 12953 atoms, 14479 bonds, 1 pseudobond, 608 residues, 19 models selected 
    8034 
    8035 > select subtract #10
    8036 
    8037 12423 atoms, 13889 bonds, 1 pseudobond, 583 residues, 18 models selected 
    8038 
    8039 > select subtract #11
    8040 
    8041 12423 atoms, 13889 bonds, 1 pseudobond, 583 residues, 16 models selected 
    8042 
    8043 > select subtract #12
    8044 
    8045 11909 atoms, 13316 bonds, 559 residues, 14 models selected 
    8046 
    8047 > select subtract #13
    8048 
    8049 11249 atoms, 12579 bonds, 528 residues, 13 models selected 
    8050 
    8051 > select subtract #14
    8052 
    8053 10829 atoms, 12111 bonds, 508 residues, 12 models selected 
    8054 
    8055 > select subtract #15
    8056 
    8057 10829 atoms, 12111 bonds, 508 residues, 10 models selected 
    8058 
    8059 > select subtract #16
    8060 
    8061 8272 atoms, 9250 bonds, 388 residues, 9 models selected 
    8062 
    8063 > select subtract #17
    8064 
    8065 7505 atoms, 8395 bonds, 352 residues, 8 models selected 
    8066 
    8067 > select subtract #18
    8068 
    8069 6128 atoms, 6857 bonds, 287 residues, 7 models selected 
    8070 
    8071 > select subtract #19
    8072 
    8073 4653 atoms, 5209 bonds, 218 residues, 6 models selected 
    8074 
    8075 > select subtract #20
    8076 
    8077 2096 atoms, 2348 bonds, 98 residues, 5 models selected 
    8078 
    8079 > select subtract #21
    8080 
    8081 2096 atoms, 2348 bonds, 98 residues, 3 models selected 
    8082 
    8083 > select subtract #22
    8084 
    8085 2096 atoms, 2348 bonds, 98 residues, 1 model selected 
    8086 
    8087 > select subtract #23
    8088 
    8089 Nothing selected 
    8090 
    8091 > ui tool show "Show Sequence Viewer"
    8092 
    8093 > sequence chain #32/B
    8094 
    8095 Alignment identifier is 32/B 
    8096 
    8097 > select #29/B:15
    8098 
    8099 23 atoms, 25 bonds, 1 residue, 1 model selected 
    8100 
    8101 > select #29/B:15-52
    8102 
    8103 810 atoms, 906 bonds, 38 residues, 1 model selected 
    8104 
    8105 > select ~sel & ##selected
    8106 
    8107 1770 atoms, 1980 bonds, 83 residues, 1 model selected 
    8108 
    8109 > delete atoms sel
    8110 
    8111 > delete bonds sel
    8112 
    8113 > select #32/B:53
    8114 
    8115 23 atoms, 25 bonds, 1 residue, 1 model selected 
    8116 
    8117 > select #32/B:53-68
    8118 
    8119 345 atoms, 386 bonds, 16 residues, 1 model selected 
    8120 
    8121 > select ~sel & ##selected
    8122 
    8123 2235 atoms, 2500 bonds, 105 residues, 1 model selected 
    8124 
    8125 > delete atoms sel
    8126 
    8127 > delete bonds sel
    8128 
    8129 > save "C:/Users/TAMU/OneDrive - Texas A&M University/BICH 603/BICH 603
    8130 > Project/20251114 region_4_wip.cxs"
    8131 
    8132 > ui tool show "Show Sequence Viewer"
    8133 
    8134 > sequence chain #31/A
    8135 
    8136 Alignment identifier is 31/A 
    8137 
    8138 > hide #29 models
    8139 
    8140 > hide #30 models
    8141 
    8142 > hide #31 models
    8143 
    8144 > show #31 models
    8145 
    8146 > select #31/A:14
    8147 
    8148 22 atoms, 24 bonds, 1 residue, 1 model selected 
    8149 
    8150 > select #31/A:14-53
    8151 
    8152 849 atoms, 950 bonds, 40 residues, 1 model selected 
    8153 
    8154 > select #31/A:14
    8155 
    8156 22 atoms, 24 bonds, 1 residue, 1 model selected 
    8157 
    8158 > select #31/A:14-50
    8159 
    8160 787 atoms, 881 bonds, 37 residues, 1 model selected 
    8161 
    8162 > select ~sel & ##selected
    8163 
    8164 335 atoms, 372 bonds, 16 residues, 1 model selected 
    8165 
    8166 > delete atoms sel
    8167 
    8168 > delete bonds sel
    8169 
    8170 > hide #31 models
    8171 
    8172 > show #31 models
    8173 
    8174 > hide #32 models
    8175 
    8176 > show #32 models
    8177 
    8178 > combine #28
    8179 
    8180 > nucleotides #10,13-14,31-32,34#!12 stubs
    8181 
    8182 > select add #34
    8183 
    8184 2580 atoms, 2886 bonds, 121 residues, 1 model selected 
     2170[deleted to fit within ticket limits]
     2171
    81852172
    81862173> view matrix models