Changes between Initial Version and Version 1 of Ticket #20338


Ignore:
Timestamp:
May 18, 2026, 11:13:59 AM (8 hours ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #20338

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

  • Ticket #20338 – Description

    initial v1  
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    1667     "name" : "_cmsgpack.cpython-311-darwin.so"
    1668   },
    1669   {
    1670     "source" : "P",
    1671     "arch" : "x86_64",
    1672     "base" : 7099645952,
    1673     "size" : 4210688,
    1674     "uuid" : "08a0cdf4-85d3-328a-98ac-8a7ec48356eb",
    1675     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
    1676     "name" : "etree.cpython-311-darwin.so"
    1677   },
    1678   {
    1679     "source" : "P",
    1680     "arch" : "x86_64",
    1681     "base" : 6039584768,
    1682     "size" : 147456,
    1683     "uuid" : "a66bb1e2-ecf4-3220-9c8e-a465d9305940",
    1684     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    1685     "name" : "_elementpath.cpython-311-darwin.so"
    1686   },
    1687   {
    1688     "source" : "P",
    1689     "arch" : "x86_64",
    1690     "base" : 6178029568,
    1691     "size" : 393216,
    1692     "uuid" : "b22060fb-029b-3fba-a262-ad22a0e78c84",
    1693     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/segment\/_segment.cpython-311-darwin.so",
    1694     "name" : "_segment.cpython-311-darwin.so"
    1695   },
    1696   {
    1697     "size" : 0,
    1698     "source" : "A",
    1699     "base" : 0,
    1700     "uuid" : "00000000-0000-0000-0000-000000000000"
    1701   },
    1702   {
    1703     "source" : "P",
    1704     "arch" : "x86_64",
    1705     "base" : 140703409131520,
    1706     "size" : 252184,
    1707     "uuid" : "62e8ef56-067e-397a-be4f-6cc00881a2ee",
    1708     "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    1709     "name" : "libsystem_kernel.dylib"
    1710   },
    1711   {
    1712     "source" : "P",
    1713     "arch" : "x86_64",
    1714     "base" : 140703409385472,
    1715     "size" : 49192,
    1716     "uuid" : "f9c81fc7-1abf-3b5e-a6b3-3113dad29577",
    1717     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1718     "name" : "libsystem_pthread.dylib"
    1719   },
    1720   {
    1721     "source" : "P",
    1722     "arch" : "x86_64",
    1723     "base" : 140703407898624,
    1724     "size" : 563448,
    1725     "uuid" : "b349e7c1-a14b-3991-b786-dbba5ee9d443",
    1726     "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    1727     "name" : "libsystem_c.dylib"
    1728   },
    1729   {
    1730     "source" : "P",
    1731     "arch" : "x86_64",
    1732     "base" : 140703409438720,
    1733     "size" : 40016,
    1734     "uuid" : "fc0c42b2-0b55-370b-8fc7-17bac96bb458",
    1735     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1736     "name" : "libsystem_platform.dylib"
    1737   },
    1738   {
    1739     "source" : "P",
    1740     "arch" : "x86_64",
    1741     "base" : 140703474651136,
    1742     "CFBundleShortVersionString" : "6.9",
    1743     "CFBundleIdentifier" : "com.apple.AppKit",
    1744     "size" : 25138887,
    1745     "uuid" : "81eb18f8-946d-373c-8622-6d1d5ad7c25d",
    1746     "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    1747     "name" : "AppKit",
    1748     "CFBundleVersion" : "2685.40.108"
    1749   },
    1750   {
    1751     "source" : "P",
    1752     "arch" : "x86_64",
    1753     "base" : 140703512731648,
    1754     "CFBundleShortVersionString" : "1.600.0",
    1755     "CFBundleIdentifier" : "com.apple.SkyLight",
    1756     "size" : 5549334,
    1757     "uuid" : "c4a0ebe2-9423-327e-8969-0d1873b3c7d8",
    1758     "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    1759     "name" : "SkyLight"
    1760   },
    1761   {
    1762     "source" : "P",
    1763     "arch" : "x86_64",
    1764     "base" : 140703409672192,
    1765     "CFBundleShortVersionString" : "6.9",
    1766     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    1767     "size" : 4956771,
    1768     "uuid" : "0dec7be2-3fd1-3ac1-9f83-7d1333f68ec3",
    1769     "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    1770     "name" : "CoreFoundation",
    1771     "CFBundleVersion" : "4302"
    1772   },
    1773   {
    1774     "source" : "P",
    1775     "arch" : "x86_64",
    1776     "base" : 140703625371648,
    1777     "CFBundleShortVersionString" : "2.1.1",
    1778     "CFBundleIdentifier" : "com.apple.HIToolbox",
    1779     "size" : 3007016,
    1780     "uuid" : "a50fbb92-900e-3d92-9ae8-49e3693fbbcb",
    1781     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    1782     "name" : "HIToolbox"
    1783   },
    1784   {
    1785     "source" : "P",
    1786     "arch" : "x86_64",
    1787     "base" : 140703408463872,
    1788     "size" : 566416,
    1789     "uuid" : "fad5093a-e81d-3a83-aabc-c23b2fa28ebe",
    1790     "path" : "\/usr\/lib\/libc++.1.dylib",
    1791     "name" : "libc++.1.dylib"
    1792   },
    1793   {
    1794     "source" : "P",
    1795     "arch" : "x86_64",
    1796     "base" : 140703407591424,
    1797     "size" : 293154,
    1798     "uuid" : "22d4457f-c2ab-36da-a743-e92bef816167",
    1799     "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1800     "name" : "libdispatch.dylib"
    1801   }
     142[deleted to fit within ticket limits]
     143
    1802144],
    1803145  "sharedCache" : {
    … …  
    2307649 
    2308650
    2309 > fitmap #8.1 inMap #2
    2310 
    2311 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points 
    2312 correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04 
    2313 steps = 44, shift = 0.018, angle = 0.0027 degrees 
    2314  
    2315 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2316 (#2) coordinates: 
    2317 Matrix rotation and translation 
    2318 -0.69926433 -0.23397681 -0.67548816 617.14637779 
    2319 0.16945124 0.86373748 -0.47459861 158.86627486 
    2320 0.69448951 -0.44633219 -0.56433315 343.06743005 
    2321 Axis 0.01978856 -0.95908408 0.28242900 
    2322 Axis point 232.39289702 0.00000000 330.28780285 
    2323 Rotation angle (degrees) 134.42138794 
    2324 Shift along axis -43.26148998 
    2325  
    2326 
    2327 > hide #!8.1 models
    2328 
    2329 > hide #!8 models
    2330 
    2331 > show #!7 models
    2332 
    2333 > show #!6 models
    2334 
    2335 > show #!5 models
    2336 
    2337 > show #!4 models
    2338 
    2339 > show #!2 models
    2340 
    2341 > volume #!2-7 showOutlineBox true
    2342 
    2343 > volume #!2-7 showOutlineBox false
    2344 
    2345 > merge #2-7
    2346 
    2347 Unknown command: merge #2-7 
    2348 
    2349 > fitmap #3 inMap #2
    2350 
    2351 Fit map S2b.map in map s2a.map using 127771 points 
    2352 correlation = 0.8481, correlation about mean = 0.7002, overlap = 2.246e+04 
    2353 steps = 76, shift = 0.14, angle = 0.136 degrees 
    2354  
    2355 Position of S2b.map (#3) relative to s2a.map (#2) coordinates: 
    2356 Matrix rotation and translation 
    2357 0.99999893 0.00046750 0.00138637 -0.48017172 
    2358 -0.00047010 0.99999813 0.00187416 -0.36067376 
    2359 -0.00138549 -0.00187481 0.99999728 0.77296866 
    2360 Axis -0.78830302 0.58284662 -0.19715010 
    2361 Axis point 0.00000000 413.67917942 197.80659664 
    2362 Rotation angle (degrees) 0.13624199 
    2363 Shift along axis 0.01591248 
    2364  
    2365 
    2366 > fitmap #4 inMap #2
    2367 
    2368 Fit map S2c.map in map s2a.map using 136539 points 
    2369 correlation = 0.8642, correlation about mean = 0.7029, overlap = 1.999e+04 
    2370 steps = 104, shift = 0.159, angle = 0.164 degrees 
    2371  
    2372 Position of S2c.map (#4) relative to s2a.map (#2) coordinates: 
    2373 Matrix rotation and translation 
    2374 0.99999665 -0.00085462 0.00244505 -0.42250571 
    2375 0.00085166 0.99999890 0.00121219 -0.51096848 
    2376 -0.00244609 -0.00121011 0.99999628 0.87778449 
    2377 Axis -0.42358399 0.85530631 0.29837514 
    2378 Axis point 358.12126580 0.00000000 172.62607561 
    2379 Rotation angle (degrees) 0.16382554 
    2380 Shift along axis 0.00384116 
    2381  
    2382 
    2383 > fitmap #5 inMap #2
    2384 
    2385 Fit map S2d.map in map s2a.map using 79890 points 
    2386 correlation = 0.9046, correlation about mean = 0.6581, overlap = 1.853e+04 
    2387 steps = 64, shift = 0.137, angle = 0.13 degrees 
    2388  
    2389 Position of S2d.map (#5) relative to s2a.map (#2) coordinates: 
    2390 Matrix rotation and translation 
    2391 0.99999863 0.00027462 0.00163284 -0.48201429 
    2392 -0.00027715 0.99999876 0.00155123 -0.31736122 
    2393 -0.00163241 -0.00155168 0.99999746 0.76429665 
    2394 Axis -0.68374678 0.71951844 -0.12158762 
    2395 Axis point 468.36598992 0.00000000 292.11829933 
    2396 Rotation angle (degrees) 0.13000708 
    2397 Shift along axis 0.00829947 
    2398  
    2399 
    2400 > fitmap #6 inMap #2
    2401 
    2402 Fit map S2e.map in map s2a.map using 79966 points 
    2403 correlation = 0.9225, correlation about mean = 0.5942, overlap = 1.213e+04 
    2404 steps = 36, shift = 0.0474, angle = 0.0524 degrees 
    2405  
    2406 Position of S2e.map (#6) relative to s2a.map (#2) coordinates: 
    2407 Matrix rotation and translation 
    2408 0.99999959 -0.00059609 0.00068859 -0.04583687 
    2409 0.00059603 0.99999982 0.00008012 -0.17163671 
    2410 -0.00068863 -0.00007971 0.99999976 0.17304490 
    2411 Axis -0.08741239 0.75319408 0.65196454 
    2412 Axis point 263.05002421 0.00000000 68.30544170 
    2413 Rotation angle (degrees) 0.05238292 
    2414 Shift along axis -0.01244990 
    2415  
    2416 
    2417 > fitmap #7 inMap #2
    2418 
    2419 Fit map S2f.map in map s2a.map using 79936 points 
    2420 correlation = 0.9348, correlation about mean = 0.6876, overlap = 1.07e+04 
    2421 steps = 48, shift = 0.0304, angle = 0.0769 degrees 
    2422  
    2423 Position of S2f.map (#7) relative to s2a.map (#2) coordinates: 
    2424 Matrix rotation and translation 
    2425 0.99999916 -0.00084681 0.00098555 -0.06122969 
    2426 0.00084714 0.99999958 -0.00033593 -0.14685155 
    2427 -0.00098527 0.00033677 0.99999946 0.17922134 
    2428 Axis 0.25059275 0.73416968 0.63102944 
    2429 Axis point 188.31364750 0.00000000 59.72966796 
    2430 Rotation angle (degrees) 0.07690306 
    2431 Shift along axis -0.01006373 
    2432  
    2433 
    2434 > morph #2-7
    2435 
    2436 Require at least 2 structures for morph 
    2437 
    2438 > morph #2,3,4,5,6,7
    2439 
    2440 Require at least 2 structures for morph 
    2441 
    2442 > morph #2,7
    2443 
    2444 Require at least 2 structures for morph 
    2445 
    2446 > morph #2-7
    2447 
    2448 Require at least 2 structures for morph 
    2449 
    2450 > morph #2 \- #7
    2451 
    2452 Expected a keyword 
    2453 
    2454 > morph #2,#7
    2455 
    2456 Missing or invalid "structures" argument: only initial part "#2" of atom
    2457 specifier valid 
    2458 
    2459 > morph #2-7
    2460 
    2461 Require at least 2 structures for morph 
    2462 
    2463 > morph #2
    2464 
    2465 Require at least 2 structures for morph 
    2466 
    2467 > show #!8.1 models
    2468 
    2469 > volume #8.1 level 0.4249
    2470 
    2471 > save /Users/haandrew/Desktop/image165.png supersample 3
    2472 
    2473 > volume #8.2 level 1.13
    2474 
    2475 > hide #!8.2 models
    2476 
    2477 > volume #8.1 level 0.255
    2478 
    2479 > hide #!7 models
    2480 
    2481 > hide #!6 models
    2482 
    2483 > hide #!5 models
    2484 
    2485 > hide #!4 models
    2486 
    2487 > hide #!3 models
    2488 
    2489 > hide #!2 models
    2490 
    2491 > hide #!8 models
    2492 
    2493 > show #!8 models
    2494 
    2495 > hide #!8 models
    2496 
    2497 > show #!3 models
    2498 
    2499 > volume #3 level 0.8318
    2500 
    2501 > volume #3 level 0.4964
    2502 
    2503 > volume #3 level 0.389
    2504 
    2505 > volume #3 level -0.04027
    2506 
    2507 > volume #3 level 0.1744
    2508 
    2509 > hide #!8.1 models
    2510 
    2511 > show #!8.1 models
    2512 
    2513 > volume #8.1 level 0.5949
    2514 
    2515 > hide #4.1 models
    2516 
    2517 > hide #!3 models
    2518 
    2519 > volume #8.1 level 0.9159
    2520 
    2521 > ui mousemode right "mark point"
    2522 
    2523 > marker #9 position 258,385.2,290.9 color yellow radius 1
    2524 
    2525 > ui mousemode right "mark point"
    2526 
    2527 > marker #9 position 331.1,315.9,301.1 color yellow radius 1
    2528 
    2529 > ui mousemode right "mark point"
    2530 
    2531 > marker #9 position 332.2,317,297.5 color yellow radius 1
    2532 
    2533 > hide #9 target m
    2534 
    2535 > close #9
    2536 
    2537 > marker #9 position 256.8,383.9,287.7 color yellow radius 5
    2538 
    2539 > marker change #9 color #d783ff
    2540 
    2541 > marker #9 position 332.3,301.8,314.7 color #d783ff radius 5
    2542 
    2543 > volume #8.2 level 1.07
    2544 
    2545 > hide #!8.2 models
    2546 
    2547 > volume #8.1 level 0.255
    2548 
    2549 > marker #9 position 282.7,424.7,385.4 color #d783ff radius 5
    2550 
    2551 > marker #9 position 394.3,321.1,386.7 color #d783ff radius 5
    2552 
    2553 > marker #9 position 399,325.4,392.8 color #d783ff radius 5
    2554 
    2555 > ui mousemode right "translate selected models"
    2556 
    2557 > view matrix models #9,1,0,0,3.3082,0,1,0,-2.3625,0,0,1,0.45069
    2558 
    2559 > ui mousemode right "translate selected models"
    2560 
    2561 > ui mousemode right "move picked models"
    2562 
    2563 > select add #9
    2564 
    2565 5 atoms, 5 residues, 1 model selected 
    2566 
    2567 > select subtract #9
    2568 
    2569 Nothing selected 
    2570 
    2571 > show #!4 models
    2572 
    2573 > hide #!4 models
    2574 
    2575 > volume #8.1 level 0.4123
    2576 
    2577 > morph #2
    2578 
    2579 Require at least 2 structures for morph 
    2580 
    2581 > show #!2 models
    2582 
    2583 > volume #2 level 0.0432
    2584 
    2585 > volume #2 level 0.1161
    2586 
    2587 > volume #2 level 0.1621
    2588 
    2589 > hide #!2 models
    2590 
    2591 > show #!3 models
    2592 
    2593 > flip vol #8.1
    2594 
    2595 Unknown command: flip vol #8.1 
    2596 
    2597 > volume flip #8.1
    2598 
    2599 Opened cryosparc_P1_J49_001_volume_map.mrc z flip as #10, grid size
    2600 128,128,128, pixel 3.32, shown at step 1, values float32 
    2601 
    2602 > hide #!8 models
    2603 
    2604 > select add #10
    2605 
    2606 2 models selected 
    2607 
    2608 > ui mousemode right "rotate selected models"
    2609 
    2610 > view matrix models
    2611 > #10,-0.47129,-0.87055,-0.14151,591.44,-0.4595,0.3793,-0.80311,459.48,0.75283,-0.31348,-0.57878,306.17
    2612 
    2613 > view matrix models
    2614 > #10,-0.80294,-0.59076,-0.079295,591.72,0.0014269,0.13113,-0.99136,450.75,0.59606,-0.79612,-0.10444,342.77
    2615 
    2616 > view matrix models
    2617 > #10,-0.91107,-0.36137,-0.19838,591.62,0.17443,0.098105,-0.97977,418.36,0.37353,-0.92725,-0.026347,401.35
    2618 
    2619 > volume #10 level 0.941
    2620 
    2621 > volume #3 level 0.6506
    2622 
    2623 > view matrix models
    2624 > #10,0.28057,-0.9398,0.19506,371,0.73095,0.077498,-0.67801,235.9,0.62208,0.33281,0.7087,-84.161
    2625 
    2626 > view matrix models
    2627 > #10,0.58555,-0.7054,0.39943,209.25,0.80357,0.44016,-0.40067,81.923,0.10682,0.55558,0.82457,-43.722
    2628 
    2629 > view matrix models
    2630 > #10,-0.13948,0.35124,0.92584,27.057,0.46669,-0.80131,0.37431,261.3,0.87336,0.48428,-0.052156,-10.494
    2631 
    2632 > view matrix models
    2633 > #10,-0.39737,0.88593,0.23922,113.78,-0.50672,-0.42917,0.7477,315.4,0.76507,0.1759,0.61946,-62.535
    2634 
    2635 > view matrix models
    2636 > #10,0.12655,0.75686,0.64121,-59.24,-0.8182,-0.28583,0.49885,405.86,0.56084,-0.58777,0.58309,156.41
    2637 
    2638 > hide #!3 models
    2639 
    2640 > view matrix models
    2641 > #10,0.79724,-0.39763,0.4542,83.944,0.0095689,0.76064,0.6491,-36.323,-0.60358,-0.51315,0.61022,391.09
    2642 
    2643 > view matrix models
    2644 > #10,0.16855,-0.93043,0.32542,365.9,0.84088,0.30798,0.44504,-77.634,-0.5143,0.19863,0.83429,168.81
    2645 
    2646 > view matrix models
    2647 > #10,0.19504,-0.7426,0.6407,252.05,0.72108,0.55137,0.41956,-98.759,-0.66483,0.38017,0.64302,203.22
    2648 
    2649 > show #!3 models
    2650 
    2651 > show #!2 models
    2652 
    2653 > volume #2 level 0.3039
    2654 
    2655 > volume #2 level 0.3614
    2656 
    2657 > view matrix models
    2658 > #10,0.19167,-0.75748,0.62408,259.57,0.73621,0.53147,0.41896,-97.637,-0.64904,0.37915,0.65954,196.44
    2659 
    2660 > hide #!3 models
    2661 
    2662 > hide #!10 models
    2663 
    2664 > select subtract #10
    2665 
    2666 Nothing selected 
    2667 
    2668 > show #!10 models
    2669 
    2670 > hide #!2 models
    2671 
    2672 > show #!3 models
    2673 
    2674 > hide #!3 models
    2675 
    2676 > show #!1 models
    2677 
    2678 > volume #1 level 0.4227
    2679 
    2680 > show #!2 models
    2681 
    2682 > show #!3 models
    2683 
    2684 > show #!4 models
    2685 
    2686 > show #!5 models
    2687 
    2688 > show #!6 models
    2689 
    2690 > show #!7 models
    2691 
    2692 > hide #!7 models
    2693 
    2694 > hide #!6 models
    2695 
    2696 > hide #!5 models
    2697 
    2698 > hide #!4 models
    2699 
    2700 > hide #!3 models
    2701 
    2702 > hide #!2 models
    2703 
    2704 > hide #!1 models
    2705 
    2706 > volume #10 level 0.3871
    2707 
    2708 > surface dust #10 size 33.2
    2709 
    2710 > show #!2 models
    2711 
    2712 > volume #2 level 0.2579
    2713 
    2714 > select add #2
    2715 
    2716 2 models selected 
    2717 
    2718 > ui mousemode right "translate selected models"
    2719 
    2720 > view matrix models #2,1,0,0,8.516,0,1,0,-10.038,0,0,1,4.9371
    2721 
    2722 > hide #!2 models
    2723 
    2724 > show #!2 models
    2725 
    2726 > select subtract #2
    2727 
    2728 Nothing selected 
    2729 
    2730 > hide #!10 models
    2731 
    2732 > show #!8.1 models
    2733 
    2734 > volume #8.1 level 0.6326
    2735 
    2736 > select add #8.1
    2737 
    2738 2 models selected 
    2739 
    2740 > view matrix models
    2741 > #8.1,-0.69926,-0.23398,-0.67549,627.13,0.16945,0.86374,-0.4746,149.85,0.69449,-0.44633,-0.56433,342.11
    2742 
    2743 > fitmap #8.1 inMap #2
    2744 
    2745 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2746 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2747 steps = 100, shift = 6.13, angle = 0.0502 degrees 
    2748  
    2749 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2750 (#2) coordinates: 
    2751 Matrix rotation and translation 
    2752 -0.69874496 -0.23441198 -0.67587462 617.22239177 
    2753 0.16965598 0.86353464 -0.47489449 158.94373547 
    2754 0.69496210 -0.44649631 -0.56362108 342.81711010 
    2755 Axis 0.01986679 -0.95900921 0.28267765 
    2756 Axis point 232.40643829 0.00000000 330.36090992 
    2757 Rotation angle (degrees) 134.38014463 
    2758 Shift along axis -43.25954537 
    2759  
    2760 
    2761 > fitmap #8.1 inMap #2
    2762 
    2763 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2764 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2765 steps = 28, shift = 0.021, angle = 0.00272 degrees 
    2766  
    2767 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2768 (#2) coordinates: 
    2769 Matrix rotation and translation 
    2770 -0.69871811 -0.23442448 -0.67589805 617.21079276 
    2771 0.16967932 0.86352299 -0.47490734 158.93421769 
    2772 0.69498341 -0.44651228 -0.56358216 342.79502680 
    2773 Axis 0.01986387 -0.95900497 0.28269224 
    2774 Axis point 232.40094538 0.00000000 330.35495830 
    2775 Rotation angle (degrees) 134.37797512 
    2776 Shift along axis -43.25301703 
    2777  
    2778 
    2779 > fitmap #8.1 inMap #2
    2780 
    2781 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2782 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2783 steps = 48, shift = 0.027, angle = 0.0111 degrees 
    2784  
    2785 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2786 (#2) coordinates: 
    2787 Matrix rotation and translation 
    2788 -0.69881107 -0.23452123 -0.67576836 617.22758681 
    2789 0.16960459 0.86346103 -0.47504667 159.01557909 
    2790 0.69490817 -0.44658129 -0.56362025 342.84803927 
    2791 Axis 0.01991569 -0.95898833 0.28274501 
    2792 Axis point 232.41512574 0.00000000 330.37919949 
    2793 Rotation angle (degrees) 134.38571197 
    2794 Shift along axis -43.26300177 
    2795  
    2796 
    2797 > fitmap #8.1 inMap #2
    2798 
    2799 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2800 correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04 
    2801 steps = 28, shift = 0.0098, angle = 0.00432 degrees 
    2802  
    2803 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2804 (#2) coordinates: 
    2805 Matrix rotation and translation 
    2806 -0.69881775 -0.23447655 -0.67577696 617.22412990 
    2807 0.16959206 0.86349747 -0.47498490 158.99998902 
    2808 0.69490452 -0.44653428 -0.56366200 342.85642338 
    2809 Axis 0.01990552 -0.95899966 0.28270730 
    2810 Axis point 232.41249284 0.00000000 330.37366254 
    2811 Rotation angle (degrees) 134.38619219 
    2812 Shift along axis -43.26675303 
    2813  
    2814 
    2815 > fitmap #8.1 inMap #2
    2816 
    2817 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2818 correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04 
    2819 steps = 28, shift = 0.0387, angle = 0.00738 degrees 
    2820  
    2821 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2822 (#2) coordinates: 
    2823 Matrix rotation and translation 
    2824 -0.69874430 -0.23446874 -0.67585562 617.20036926 
    2825 0.16958276 0.86354210 -0.47490708 158.94804993 
    2826 0.69498064 -0.44645207 -0.56363326 342.80268412 
    2827 Axis 0.01990659 -0.95901155 0.28266691 
    2828 Axis point 232.40326525 0.00000000 330.34801496 
    2829 Rotation angle (degrees) 134.38030701 
    2830 Shift along axis -43.24768257 
    2831  
    2832 
    2833 > fitmap #8.1 inMap #2
    2834 
    2835 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2836 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2837 steps = 44, shift = 0.0306, angle = 0.00758 degrees 
    2838  
    2839 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2840 (#2) coordinates: 
    2841 Matrix rotation and translation 
    2842 -0.69881703 -0.23448250 -0.67577564 617.22354689 
    2843 0.16959147 0.86349399 -0.47499143 158.99602998 
    2844 0.69490539 -0.44653788 -0.56365807 342.84475048 
    2845 Axis 0.01990756 -0.95899858 0.28271082 
    2846 Axis point 232.41487280 0.00000000 330.36774689 
    2847 Rotation angle (degrees) 134.38614530 
    2848 Shift along axis -43.26363325 
    2849  
    2850 
    2851 > fitmap #8.1 inMap #2
    2852 
    2853 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2854 correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04 
    2855 steps = 40, shift = 0.0185, angle = 0.0059 degrees 
    2856  
    2857 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2858 (#2) coordinates: 
    2859 Matrix rotation and translation 
    2860 -0.69875684 -0.23445023 -0.67584908 617.20999385 
    2861 0.16962641 0.86352141 -0.47492911 158.95405660 
    2862 0.69495738 -0.44650182 -0.56362254 342.81418427 
    2863 Axis 0.01988751 -0.95900547 0.28268885 
    2864 Axis point 232.40471427 0.00000000 330.35644302 
    2865 Rotation angle (degrees) 134.38120914 
    2866 Shift along axis -43.25328951 
    2867  
    2868 
    2869 > fitmap #8.1 inMap #2
    2870 
    2871 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2872 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2873 steps = 48, shift = 0.0213, angle = 0.00687 degrees 
    2874  
    2875 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2876 (#2) coordinates: 
    2877 Matrix rotation and translation 
    2878 -0.69880573 -0.23451361 -0.67577653 617.22504373 
    2879 0.16959431 0.86347540 -0.47502422 159.00993871 
    2880 0.69491605 -0.44655750 -0.56362938 342.84335997 
    2881 Axis 0.01991648 -0.95899261 0.28273044 
    2882 Axis point 232.41448747 0.00000000 330.37497003 
    2883 Rotation angle (degrees) 134.38528787 
    2884 Shift along axis -43.26415339 
    2885  
    2886 
    2887 > fitmap #8.1 inMap #2
    2888 
    2889 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2890 correlation = 0.8397, correlation about mean = 0.4242, overlap = 1.75e+04 
    2891 steps = 40, shift = 0.0204, angle = 0.00921 degrees 
    2892  
    2893 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2894 (#2) coordinates: 
    2895 Matrix rotation and translation 
    2896 -0.69874150 -0.23443480 -0.67587029 617.20791351 
    2897 0.16962362 0.86354096 -0.47489455 158.94387015 
    2898 0.69497349 -0.44647209 -0.56362623 342.80570237 
    2899 Axis 0.01988370 -0.95901109 0.28267007 
    2900 Axis point 232.40321294 0.00000000 330.35187117 
    2901 Rotation angle (degrees) 134.37995827 
    2902 Shift along axis -43.25564335 
    2903  
    2904 
    2905 > fitmap #8.1 inMap #2
    2906 
    2907 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2908 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2909 steps = 48, shift = 0.022, angle = 0.011 degrees 
    2910  
    2911 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2912 (#2) coordinates: 
    2913 Matrix rotation and translation 
    2914 -0.69881149 -0.23453010 -0.67576485 617.22680423 
    2915 0.16959863 0.86345844 -0.47505351 159.02083701 
    2916 0.69490921 -0.44658164 -0.56361870 342.84747838 
    2917 Axis 0.01992025 -0.95898756 0.28274732 
    2918 Axis point 232.41522508 0.00000000 330.37970010 
    2919 Rotation angle (degrees) 134.38577029 
    2920 Shift along axis -43.26448705 
    2921  
    2922 
    2923 > fitmap #8.1 inMap #2
    2924 
    2925 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2926 correlation = 0.8397, correlation about mean = 0.4244, overlap = 1.75e+04 
    2927 steps = 28, shift = 0.0299, angle = 0.0112 degrees 
    2928  
    2929 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2930 (#2) coordinates: 
    2931 Matrix rotation and translation 
    2932 -0.69869919 -0.23449606 -0.67589277 617.21237616 
    2933 0.16961131 0.86352492 -0.47492812 158.95410121 
    2934 0.69501902 -0.44647095 -0.56357098 342.77441915 
    2935 Axis 0.01990688 -0.95900516 0.28268854 
    2936 Axis point 232.40766096 0.00000000 330.35224728 
    2937 Rotation angle (degrees) 134.37669155 
    2938 Shift along axis -43.25263287 
    2939  
    2940 
    2941 > fitmap #8.1 inMap #2
    2942 
    2943 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2944 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2945 steps = 60, shift = 0.0073, angle = 0.00392 degrees 
    2946  
    2947 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2948 (#2) coordinates: 
    2949 Matrix rotation and translation 
    2950 -0.69872462 -0.23443282 -0.67588842 617.20536810 
    2951 0.16964807 0.86353427 -0.47489799 158.93413447 
    2952 0.69498449 -0.44648609 -0.56360158 342.79735068 
    2953 Axis 0.01987585 -0.95900861 0.28267905 
    2954 Axis point 232.40042751 0.00000000 330.35137907 
    2955 Rotation angle (degrees) 134.37856240 
    2956 Shift along axis -43.25009391 
    2957  
    2958 
    2959 > fitmap #8.1 inMap #2
    2960 
    2961 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    2962 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    2963 steps = 48, shift = 0.026, angle = 0.00991 degrees 
    2964  
    2965 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    2966 (#2) coordinates: 
    2967 Matrix rotation and translation 
    2968 -0.69880627 -0.23451710 -0.67577476 617.22265617 
    2969 0.16958919 0.86347600 -0.47502496 159.00958018 
    2970 0.69491676 -0.44655452 -0.56363087 342.84207182 
    2971 Axis 0.01991911 -0.95899281 0.28272957 
    2972 Axis point 232.41399927 0.00000000 330.37347471 
    2973 Rotation angle (degrees) 134.38534512 
    2974 Shift along axis -43.26292776 
    2975  
    2976 
    2977 > fitmap #3 inMap #2
    2978 
    2979 Fit map S2b.map in map s2a.map using 29082 points 
    2980 correlation = 0.9342, correlation about mean = 0.5212, overlap = 1.526e+04 
    2981 steps = 128, shift = 14.1, angle = 0.0654 degrees 
    2982  
    2983 Position of S2b.map (#3) relative to s2a.map (#2) coordinates: 
    2984 Matrix rotation and translation 
    2985 0.99999674 0.00072788 0.00244726 -0.79686476 
    2986 -0.00073327 0.99999730 0.00220317 -0.36408256 
    2987 -0.00244565 -0.00220495 0.99999458 1.12112740 
    2988 Axis -0.65345277 0.72531714 -0.21659761 
    2989 Axis point 458.92492000 0.00000000 322.54051248 
    2990 Rotation angle (degrees) 0.19325574 
    2991 Shift along axis 0.01380465 
    2992  
    2993 
    2994 > hide #!8.1 models
    2995 
    2996 > hide #9 models
    2997 
    2998 > hide #!8 models
    2999 
    3000 > close #10
    3001 
    3002 > show #!3 models
    3003 
    3004 > volume #3 level 0.322
    3005 
    3006 > hide #!3 models
    3007 
    3008 > show #!4 models
    3009 
    3010 > volume #4 level 0.1096
    3011 
    3012 > volume #4 level 0.1415
    3013 
    3014 > select add #4
    3015 
    3016 4 models selected 
    3017 
    3018 > view matrix models
    3019 > #4,1,-0.00085462,0.0024451,7.9102,0.00085166,1,0.0012122,-8.7285,-0.0024461,-0.0012101,1,2.4362,#8.1,-0.69881,-0.23452,-0.67577,634.07,0.16959,0.86348,-0.47502,140.75,0.69492,-0.44655,-0.56363,349.34
    3020 
    3021 > fitmap #4 inMap #2
    3022 
    3023 Fit map S2c.map in map s2a.map using 265934 points 
    3024 correlation = 0.8025, correlation about mean = 0.7438, overlap = 2.071e+04 
    3025 steps = 80, shift = 3.86, angle = 0.0102 degrees 
    3026  
    3027 Position of S2c.map (#4) relative to s2a.map (#2) coordinates: 
    3028 Matrix rotation and translation 
    3029 0.99999700 -0.00080964 0.00231071 -0.39889512 
    3030 0.00080709 0.99999906 0.00110393 -0.47734111 
    3031 -0.00231160 -0.00110206 0.99999672 0.82316809 
    3032 Axis -0.41073484 0.86062944 0.30102136 
    3033 Axis point 355.75185755 0.00000000 172.94533004 
    3034 Rotation angle (degrees) 0.15386339 
    3035 Shift along axis 0.00081750 
    3036  
    3037 
    3038 > volume #4 level 0.2264
    3039 
    3040 > select subtract #4
    3041 
    3042 2 models selected 
    3043 
    3044 > hide #!4 models
    3045 
    3046 > show #!5 models
    3047 
    3048 > select add #5
    3049 
    3050 4 models selected 
    3051 
    3052 > view matrix models
    3053 > #5,1,0.00027462,0.0016328,9.8966,-0.00027715,1,0.0015512,-8.9945,-0.0016324,-0.0015517,1,3.5357,#8.1,-0.69881,-0.23452,-0.67577,644.45,0.16959,0.86348,-0.47502,132.08,0.69492,-0.44655,-0.56363,352.11
    3054 
    3055 > fitmap #5 inMap #2
    3056 
    3057 Fit map S2d.map in map s2a.map using 79890 points 
    3058 correlation = 0.9045, correlation about mean = 0.6579, overlap = 1.854e+04 
    3059 steps = 88, shift = 3.17, angle = 0.00302 degrees 
    3060  
    3061 Position of S2d.map (#5) relative to s2a.map (#2) coordinates: 
    3062 Matrix rotation and translation 
    3063 0.99999870 0.00024279 0.00159655 -0.46901772 
    3064 -0.00024523 0.99999880 0.00152998 -0.31838440 
    3065 -0.00159618 -0.00153037 0.99999756 0.75063976 
    3066 Axis -0.68780695 0.71755925 -0.10968282 
    3067 Axis point 470.64161925 0.00000000 289.06952343 
    3068 Rotation angle (degrees) 0.12746682 
    3069 Shift along axis 0.01180168 
    3070  
    3071 
    3072 > hide #!5 models
    3073 
    3074 > select subtract #5
    3075 
    3076 2 models selected 
    3077 
    3078 > show #!6 models
    3079 
    3080 > select add #6
    3081 
    3082 4 models selected 
    3083 
    3084 > view matrix models
    3085 > #6,1,-0.00059609,0.00068859,8.8296,0.00059603,1,8.0122e-05,-7.5921,-0.00068863,-7.9712e-05,1,2.5431,#8.1,-0.69881,-0.23452,-0.67577,653.33,0.16959,0.86348,-0.47502,124.66,0.69492,-0.44655,-0.56363,354.48
    3086 
    3087 > fitmap #6 inMap #2
    3088 
    3089 Fit map S2e.map in map s2a.map using 79966 points 
    3090 correlation = 0.9224, correlation about mean = 0.594, overlap = 1.214e+04 
    3091 steps = 60, shift = 3.69, angle = 0.00453 degrees 
    3092  
    3093 Position of S2e.map (#6) relative to s2a.map (#2) coordinates: 
    3094 Matrix rotation and translation 
    3095 0.99999960 -0.00052817 0.00071763 -0.07258225 
    3096 0.00052813 0.99999986 0.00005189 -0.14841263 
    3097 -0.00071766 -0.00005151 0.99999974 0.17218540 
    3098 Axis -0.05792234 0.80404761 0.59173680 
    3099 Axis point 250.80493083 0.00000000 102.34858623 
    3100 Rotation angle (degrees) 0.05113884 
    3101 Shift along axis -0.01323824 
    3102  
    3103 
    3104 > select subtract #6
    3105 
    3106 2 models selected 
    3107 
    3108 > hide #!6 models
    3109 
    3110 > show #!7 models
    3111 
    3112 > select add #7
    3113 
    3114 4 models selected 
    3115 
    3116 > view matrix models
    3117 > #7,1,-0.00084681,0.00098555,8.574,0.00084714,1,-0.00033593,-7.3665,-0.00098527,0.00033677,1,2.4851,#8.1,-0.69881,-0.23452,-0.67577,661.96,0.16959,0.86348,-0.47502,117.44,0.69492,-0.44655,-0.56363,356.79
    3118 
    3119 > fitmap #7 inMap #2
    3120 
    3121 Fit map S2f.map in map s2a.map using 79936 points 
    3122 correlation = 0.9349, correlation about mean = 0.6881, overlap = 1.07e+04 
    3123 steps = 56, shift = 3.85, angle = 0.00333 degrees 
    3124  
    3125 Position of S2f.map (#7) relative to s2a.map (#2) coordinates: 
    3126 Matrix rotation and translation 
    3127 0.99999912 -0.00090202 0.00096907 -0.04311830 
    3128 0.00090235 0.99999953 -0.00034387 -0.13683604 
    3129 -0.00096876 0.00034475 0.99999947 0.17988426 
    3130 Axis 0.25169858 0.70829650 0.65951793 
    3131 Axis point 178.26385524 0.00000000 47.47744818 
    3132 Rotation angle (degrees) 0.07837767 
    3133 Shift along axis 0.01086359 
    3134  
    3135 
    3136 > select subtract #8.1
    3137 
    3138 2 models selected 
    3139 
    3140 > select subtract #7
    3141 
    3142 Nothing selected 
    3143 
    3144 > hide #!7 models
    3145 
    3146 > show #!8.1 models
    3147 
    3148 > show #9 models
    3149 
    3150 > select add #8.1
    3151 
    3152 2 models selected 
    3153 
    3154 > view matrix models
    3155 > #8.1,-0.69881,-0.23452,-0.67577,637.6,0.16959,0.86348,-0.47502,156.18,0.69492,-0.44655,-0.56363,344.02
    3156 
    3157 > view matrix models
    3158 > #8.1,-0.69881,-0.23452,-0.67577,625.48,0.16959,0.86348,-0.47502,150.06,0.69492,-0.44655,-0.56363,348.14
    3159 
    3160 > fitmap #8.1 inMap #2
    3161 
    3162 Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 54616 points 
    3163 correlation = 0.8397, correlation about mean = 0.4243, overlap = 1.75e+04 
    3164 steps = 68, shift = 1.17, angle = 0.00408 degrees 
    3165  
    3166 Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
    3167 (#2) coordinates: 
    3168 Matrix rotation and translation 
    3169 -0.69876795 -0.23456240 -0.67579866 617.22993942 
    3170 0.16955256 0.86348500 -0.47502167 159.01545354 
    3171 0.69496423 -0.44651331 -0.56360498 342.81525378 
    3172 Axis 0.01994464 -0.95899467 0.28272147 
    3173 Axis point 232.42031979 0.00000000 330.37150411 
    3174 Rotation angle (degrees) 134.38241052 
    3175 Shift along axis -43.26331539 
    3176  
    3177 
    3178 > select subtract #8.1
    3179 
    3180 Nothing selected 
    3181 
    3182 > hide #!2 models
    3183 
    3184 > show #!3 models
    3185 
    3186 > volume #3 level 0.2951
    3187 
    3188 > volume #3 level 0.2482
    3189 
    3190 > hide #!3 models
    3191 
    3192 > show #!4 models
    3193 
    3194 > show #!5 models
    3195 
    3196 > hide #!4 models
    3197 
    3198 > hide #!5 models
    3199 
    3200 > show #!6 models
    3201 
    3202 > volume #6 level 0.1712
    3203 
    3204 > hide #!6 models
    3205 
    3206 > show #!5 models
    3207 
    3208 > hide #!5 models
    3209 
    3210 > show #!4 models
    3211 
    3212 > hide #!4 models
    3213 
    3214 > show #!3 models
    3215 
    3216 > hide #!3 models
    3217 
    3218 > show #!2 models
    3219 
    3220 > hide #!2 models
    3221 
    3222 > open /Users/haandrew/Downloads/8BN3.cif
    3223 
    3224 Summary of feedback from opening /Users/haandrew/Downloads/8BN3.cif 
    3225 --- 
    3226 note | Fetching CCD K from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif 
    3227  
    3228 8BN3.cif title: 
    3229 Yeast 80S, ES7s delta, eIF5A, Stm1 containing [more info...] 
    3230  
    3231 Chain information for 8BN3.cif #10 
    3232 --- 
    3233 Chain | Description | UniProt 
    3234 1 | 25S ribosomal RNA |   
    3235 2 | 18S ribosomal RNA |   
    3236 3 | 5S ribosomal RNA |   
    3237 4 | 5.8S ribosomal RNA |   
    3238 B | 60S ribosomal protein L1-A | RL1A_YEAST 1-217 
    3239 C0 | Small ribosomal subunit protein eS10A | RS10A_YEAST 1-96 
    3240 C1 | Small ribosomal subunit protein uS17A | RS11A_YEAST 2-156 
    3241 C3 | 40S ribosomal protein S13 | RS13_YEAST 2-151 
    3242 C4 | 40S ribosomal protein S14-B | RS14B_YEAST 11-137 
    3243 C5 | RPS15 isoform 1 | A0A6A5Q6F2_YEASX 8-131 
    3244 C6 | 40S ribosomal protein S16-A | RS16A_YEAST 3-143 
    3245 C7 | ES17 | A0A0J9X224_LACKL 2-126 
    3246 C8 | 40S ribosomal protein S18-A | RS18A_YEAST 2-146 
    3247 C9 | 40S ribosomal protein S19-A | RS19A_YEAST 2-144 
    3248 D0 | RPS20 isoform 1 | A0A6A5PVE9_YEASX 15-121 
    3249 D1 | Small ribosomal subunit protein eS21A | RS21A_YEAST 1-87 
    3250 D2 | RPS22A isoform 1 | A0A6A5PSE9_YEASX 2-130 
    3251 D3 | 40S ribosomal protein S23-A | RS23A_YEAST 2-145 
    3252 D4 | 40S ribosomal protein S24-A | RS24A_YEAST 2-135 
    3253 D5 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 36-105 
    3254 D6 | RPS26B isoform 1 | A0A6A5Q0E8_YEASX 2-98 
    3255 D7 | 40S ribosomal protein S27-A | RS27A_YEAST 2-82 
    3256 D8 | RPS28A isoform 1 | A0A6A5Q700_YEASX 5-67 
    3257 D9 | RPS29A isoform 1 | A0A6A5PV92_YEASX 4-56 
    3258 E0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-61 
    3259 E1 | RPS31 isoform 1 | A0A6A5PU37_YEASX 82-152 
    3260 L2 | 60S ribosomal protein L2-A | RL2A_YEAST 2-253 
    3261 L3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 2-387 
    3262 L4 | RPL4A isoform 1 | A0A6A5Q3W0_YEASX 2-362 
    3263 L5 | RPL5 isoform 1 | A0A6A5Q0W8_YEASX -2-296 
    3264 L6 | 60S ribosomal protein L6-A |   
    3265 L7 | 60S ribosomal protein L7-A | RL7A_YEAST 23-244 
    3266 L8 | 60S ribosomal protein L8-A | RL8A_YEAST 24-256 
    3267 L9 | RPL9A isoform 1 | A0A8H4FCT7_YEASX 1-189 
    3268 M0 | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 2-219 
    3269 M1 | RPL11B isoform 1 | A0A6A5PYM2_YEASX 6-173 
    3270 M3 | 60S ribosomal protein L13-A | RL13A_YEAST 2-194 
    3271 M4 | 60S ribosomal protein L14-A | RL14A_YEAST 3-138 
    3272 M5 | Ribosomal protein L15 | A0A8H4BX09_YEASX 2-203 
    3273 M6 | 60S ribosomal protein L16-A | RL16A_YEAST 3-199 
    3274 M7 | 60S ribosomal protein L17-A | RL17A_YEAST 2-184 
    3275 M8 | 60S ribosomal protein L18-A | RL18A_YEAST 2-186 
    3276 M9 | 60S ribosomal protein L19-A | RL19A_YEAST 2-189 
    3277 N0 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 
    3278 N1 | 60S ribosomal protein L21-A | RL21A_YEAST 2-160 
    3279 N2 | 60S ribosomal protein L22-A | RL22A_YEAST 9-108 
    3280 N3 | 60S ribosomal protein L23-A | RL23A_YEAST 2-137 
    3281 N4 | RPL24A isoform 1 | A0A6A5PY83_YEASX 1-98 
    3282 N5 | 60S ribosomal protein L25 | RL25_YEAST 22-142 
    3283 N6 | Large ribosomal subunit protein uL24A | RL26A_YEAST 2-127 
    3284 N7 | 60S ribosomal protein L27-A | RL27A_YEAST 2-136 
    3285 N8 | 60S ribosomal protein L28 | RL28_YEAST 2-149 
    3286 N9 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 2-57 
    3287 O0 | 60S ribosomal protein L30 | RL30_YEAST 9-105 
    3288 O1 | 60S ribosomal protein L31-A | RL31A_YEAST 4-112 
    3289 O2 | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 2-128 
    3290 O3 | 60S ribosomal protein L33-A | RL33A_YEAST 2-107 
    3291 O4 | Large ribosomal subunit protein eL34A | RL34A_YEAST 2-112 
    3292 O5 | 60S ribosomal protein L35-A | RL35A_YEAST 2-120 
    3293 O6 | 60S ribosomal protein L36-A | RL36A_YEAST 2-100 
    3294 O7 | Large ribosomal subunit protein eL37A | RL37A_YEAST 2-87 
    3295 O8 | RPL38 isoform 1 | A0A6A5PUL8_YEASX 2-78 
    3296 O9 | 60S ribosomal protein L39 | RL39_YEAST 2-51 
    3297 P | 60S ribosomal protein L41-A |   
    3298 Q0 | 60S ribosomal protein L40-A | RL40A_YEAST 77-128 
    3299 Q1 | Large ribosomal subunit protein eL41B | RL41B_YEAST 1-25 
    3300 Q2 | 60S ribosomal protein L42-A | RL44A_YEAST 2-106 
    3301 Q3 | 60S ribosomal protein L43-A | RL43A_YEAST 2-92 
    3302 S0 | Small ribosomal subunit protein uS2A | RSSA1_YEAST 2-252 
    3303 S1 | Small ribosomal subunit protein eS1 | A0A6A5PRY4_YEASX 20-233 
    3304 S2 | RPS2 isoform 1 | A0A6A5PWF7_YEASX 34-250 
    3305 S3 | 40S ribosomal protein S3 | A0A6A5Q3Q1_YEASX 3-225 
    3306 S4 | Small ribosomal subunit protein eS4A | RS4A_YEAST 2-261 
    3307 S5 | Rps5p | A0A1L4AA68_YEASX 20-225 
    3308 S6 | Small ribosomal subunit protein eS6A | RS6A_YEAST 1-226 
    3309 S7 | 40S ribosomal protein S7-A | RS7A_YEAST 4-187 
    3310 S8 | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-200 
    3311 S9 | Small ribosomal subunit protein uS4A | RS9A_YEAST 2-186 
    3312 SM | STM1 isoform 1 | A0A8H4FBL9_YEASX 21-138 
    3313 SR | Small ribosomal subunit protein RACK1 | GBLP_YEAST 2-319 
    3314 eI | Eukaryotic translation initiation factor 5A | A0A8H8ULI0_YEASX 10-154 
    3315  
    3316 Non-standard residues in 8BN3.cif #10 
    3317 --- 
    3318 3HE —
    3319 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione 
    3320 5CT — Hypusine (N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine) 
    3321 K — potassium ion 
    3322 MG — magnesium ion 
    3323 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    3324 ZN — zinc ion 
    3325  
    3326 11 atoms have alternate locations. Control/examine alternate locations with
    3327 Altloc Explorer [start tool...] or the altlocs command. 
    3328 
    3329 > select add #10
    3330 
    3331 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 4 models
    3332 selected 
    3333 
    3334 > view matrix models #10,1,0,0,-192.67,0,1,0,69.056,0,0,1,24.732
    3335 
    3336 > ui mousemode right "rotate selected models"
    3337 
    3338 > view matrix models
    3339 > #10,0.30897,0.92926,0.20252,-263.15,-0.65178,0.051814,0.75664,212.71,0.69262,-0.36578,0.62168,30.24
    3340 
    3341 > view matrix models
    3342 > #10,-0.40273,0.80951,-0.4272,13.021,-0.86332,-0.18088,0.47112,348.07,0.3041,0.55855,0.77172,-86.494
    3343 
    3344 > view matrix models
    3345 > #10,0.21937,0.97326,0.068145,-228.13,-0.57385,0.1852,-0.79774,472.75,-0.78903,0.13589,0.59913,227
    3346 
    3347 > view matrix models
    3348 > #10,0.91604,0.40069,-0.017607,-243.39,-0.22757,0.4831,-0.84548,364.44,-0.33027,0.7785,0.53372,40.634
    3349 
    3350 > view matrix models
    3351 > #10,0.96208,0.18482,0.20059,-256.23,0.25178,-0.31897,-0.91371,426.98,-0.10489,0.92957,-0.35341,141.77
    3352 
    3353 > view matrix models
    3354 > #10,0.27794,0.6918,0.66646,-304.79,-0.1769,-0.64506,0.74337,247.18,0.94417,-0.32451,-0.056911,105.62
    3355 
    3356 > view matrix models
    3357 > #10,0.05857,0.91413,0.40117,-251.28,-0.63838,-0.27466,0.71905,274.39,0.76749,-0.29822,0.56747,14.687
    3358 
    3359 > ui mousemode right "translate selected models"
    3360 
    3361 > view matrix models
    3362 > #10,0.05857,0.91413,0.40117,-255,-0.63838,-0.27466,0.71905,319.24,0.76749,-0.29822,0.56747,29.955
    3363 
    3364 > view matrix models
    3365 > #10,0.05857,0.91413,0.40117,8.6081,-0.63838,-0.27466,0.71905,349.16,0.76749,-0.29822,0.56747,-38.273
    3366 
    3367 > view matrix models
    3368 > #10,0.05857,0.91413,0.40117,-3.1339,-0.63838,-0.27466,0.71905,314.81,0.76749,-0.29822,0.56747,84.619
    3369 
    3370 > ui mousemode right "rotate selected models"
    3371 
    3372 > view matrix models
    3373 > #10,0.20197,0.56316,0.80128,-45.679,-0.70248,-0.48679,0.51919,402.28,0.68245,-0.66775,0.29729,217.02
    3374 
    3375 > ui mousemode right "translate selected models"
    3376 
    3377 > view matrix models
    3378 > #10,0.20197,0.56316,0.80128,-20.057,-0.70248,-0.48679,0.51919,401.18,0.68245,-0.66775,0.29729,214.26
    3379 
    3380 > view matrix models
    3381 > #10,0.20197,0.56316,0.80128,-198.99,-0.70248,-0.48679,0.51919,531.3,0.68245,-0.66775,0.29729,409.01
    3382 
    3383 > view matrix models
    3384 > #10,0.20197,0.56316,0.80128,-16.643,-0.70248,-0.48679,0.51919,355.78,0.68245,-0.66775,0.29729,323.43
    3385 
    3386 > view matrix models
    3387 > #10,0.20197,0.56316,0.80128,-13.859,-0.70248,-0.48679,0.51919,408.36,0.68245,-0.66775,0.29729,234.87
    3388 
    3389 > fitmap #10 inMap #8.1
    3390 
    3391 Fit molecule 8BN3.cif (#10) to map cryosparc_P1_J49_001_volume_map.mrc (#8.1)
    3392 using 201660 atoms 
    3393 average map value = 0.7505, steps = 180 
    3394 shifted from previous position = 16 
    3395 rotated from previous position = 39.3 degrees 
    3396 atoms outside contour = 70556, contour level = 0.63262 
    3397  
    3398 Position of 8BN3.cif (#10) relative to cryosparc_P1_J49_001_volume_map.mrc
    3399 (#8.1) coordinates: 
    3400 Matrix rotation and translation 
    3401 0.65613488 -0.74028800 0.14649469 202.25922708 
    3402 -0.72999412 -0.67183893 -0.12546326 501.80546349 
    3403 0.19129978 -0.02461944 -0.98122284 361.48342205 
    3404 Axis 0.90990948 -0.40427443 0.09288126 
    3405 Axis point 0.00000000 290.34778333 178.15544695 
    3406 Rotation angle (degrees) 176.82337291 
    3407 Shift along axis 14.74550438 
    3408  
    3409 
    3410 > view matrix models
    3411 > #10,-0.41654,0.69152,0.59017,175.18,-0.60996,-0.69395,0.38261,414.4,0.67412,-0.20061,0.71085,58.581
    3412 
    3413 > ui mousemode right "translate selected models"
    3414 
    3415 > select subtract #10
    3416 
    3417 Nothing selected 
    3418 
    3419 > sequence chain #10/SM
    3420 
    3421 Alignment identifier is 10/SM 
    3422 
    3423 > select #10/SM:21
    3424 
    3425 7 atoms, 7 bonds, 1 residue, 1 model selected 
    3426 
    3427 > select #10/SM
    3428 
    3429 893 atoms, 903 bonds, 118 residues, 1 model selected 
    3430 
    3431 > color sel red
    3432 
    3433 > sel~sel
    3434 
    3435 Unknown command: sel~sel 
    3436 
    3437 > select ~sel
    3438 
    3439 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 24 models
    3440 selected 
    3441 
    3442 > select subtract #1
    3443 
    3444 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 22 models
    3445 selected 
    3446 
    3447 > select subtract #2
    3448 
    3449 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 20 models
    3450 selected 
    3451 
    3452 > select subtract #3
    3453 
    3454 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 18 models
    3455 selected 
    3456 
    3457 > select subtract #4
    3458 
    3459 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 16 models
    3460 selected 
    3461 
    3462 > select subtract #5
    3463 
    3464 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 14 models
    3465 selected 
    3466 
    3467 > select subtract #6
    3468 
    3469 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 12 models
    3470 selected 
    3471 
    3472 > select subtract #7
    3473 
    3474 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 10 models
    3475 selected 
    3476 
    3477 > select subtract #8
    3478 
    3479 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 5 models
    3480 selected 
    3481 
    3482 > select add #8.1
    3483 
    3484 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 7 models
    3485 selected 
    3486 
    3487 > select add #8
    3488 
    3489 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 10 models
    3490 selected 
    3491 
    3492 > select subtract #8
    3493 
    3494 200772 atoms, 213303 bonds, 6055 pseudobonds, 18430 residues, 5 models
    3495 selected 
    3496 
    3497 > select subtract #9
    3498 
    3499 200767 atoms, 213303 bonds, 6055 pseudobonds, 18425 residues, 4 models
    3500 selected 
    3501 
    3502 > hide (#!10 & sel) target a
    3503 
    3504 > ~select
    3505 
    3506 Nothing selected 
    3507 
    3508 > hide #!8 models
    3509 
    3510 > show #!8 models
    3511 
    3512 > hide #9 models
    3513 
    3514 > volume #8.1 level 0.3242
    3515 
    3516 > ui tool show "Side View"
    3517 
    3518 > volume #8.1 level 0.8277
    3519 
    3520 > volume #8.1 level 0.1794
    3521 
    3522 > open /Users/haandrew/Documents/progress/2025/Cryo-
    3523 > EM/20250506_scRibso_SND1/maps/apo_cryosparc_P2_J306_004_volume_map_sharp.mrc
    3524 
    3525 Opened apo_cryosparc_P2_J306_004_volume_map_sharp.mrc as #11, grid size
    3526 400,400,400, pixel 0.86, shown at level 0.214, step 2, values float32 
    3527 
    3528 > volume #11 level 0.2598
    3529 
    3530 > select add #11
    3531 
    3532 3 models selected 
    3533 
    3534 > view matrix models #11,1,0,0,-108.12,0,1,0,44.884,0,0,1,6.4872
    3535 
    3536 > volume #11 level 0.4262
    3537 
    3538 > select subtract #11
    3539 
    3540 Nothing selected 
    3541 
    3542 > close #11
    3543 
    3544 > open /Users/haandrew/Documents/progress/2025/Cryo-
    3545 > EM/20250506_scRibso_SND1/maps/cryosparc_P1_J25_mask.mrc
    3546 
    3547 Opened cryosparc_P1_J25_mask.mrc as #11, grid size 128,128,128, pixel 3.35,
    3548 shown at level 5e-05, step 1, values float32 
    3549 
    3550 > select add #11
    3551 
    3552 2 models selected 
    3553 
    3554 > close #11
    3555 
    3556 > open /Users/haandrew/Documents/progress/2025/Cryo-
    3557 > EM/20250506_scRibso_SND1/maps/apo_cryosparc_P2_J306_004_volume_map_sharp.mrc
    3558 
    3559 Opened apo_cryosparc_P2_J306_004_volume_map_sharp.mrc as #11, grid size
    3560 400,400,400, pixel 0.86, shown at level 0.214, step 2, values float32 
    3561 
    3562 > select add #11
    3563 
    3564 3 models selected 
    3565 
    3566 > view matrix models #11,1,0,0,-101.94,0,1,0,-61.742,0,0,1,66.111
    3567 
    3568 > volume #11 level -0.3903
    3569 
    3570 > close #11
    3571 
    3572 > open /Users/haandrew/Documents/progress/2025/Cryo-
    3573 > EM/20250506_scRibso_SND1/maps/NU_cryosparc_P1_J23_002_volume_map_sharp.mrc
    3574 
    3575 Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc as #11, grid size
    3576 128,128,128, pixel 3.35, shown at level 1.87, step 1, values float32 
    3577 
    3578 > select add #11
    3579 
    3580 2 models selected 
    3581 
    3582 > view matrix models #11,1,0,0,-62.35,0,1,0,-108.99,0,0,1,88.193
    3583 
    3584 > view matrix models #11,1,0,0,-80.234,0,1,0,-139.87,0,0,1,104.88
    3585 
    3586 > volume #11 level 0.5448
    3587 
    3588 > ui mousemode right "rotate selected models"
    3589 
    3590 > view matrix models
    3591 > #11,-0.77355,-0.26162,0.57722,257.19,-0.18669,-0.77633,-0.60205,415.96,0.60562,-0.57347,0.55169,186.86
    3592 
    3593 > view matrix models
    3594 > #11,-0.79278,0.50799,0.33681,148.41,-0.5134,-0.85439,0.080198,359.22,0.32851,-0.10934,0.93815,66.506
    3595 
    3596 > ui mousemode right "translate selected models"
    3597 
    3598 > view matrix models
    3599 > #11,-0.79278,0.50799,0.33681,99.56,-0.5134,-0.85439,0.080198,303.42,0.32851,-0.10934,0.93815,75.073
    3600 
    3601 > volume #11 level 1.757
    3602 
    3603 > ui mousemode right "rotate selected models"
    3604 
    3605 > view matrix models
    3606 > #11,-0.28671,0.83043,-0.47769,97.568,-0.47714,0.30861,0.82286,-106.26,0.83074,0.46385,0.30775,-17.872
    3607 
    3608 > view matrix models
    3609 > #11,-0.24518,0.96618,0.079905,-58.11,0.95394,0.22573,0.19759,-259.09,0.17287,0.12467,-0.97702,465.39
    3610 
    3611 > show #9 models
    3612 
    3613 > ui mousemode right "translate selected models"
    3614 
    3615 > view matrix models
    3616 > #11,-0.24518,0.96618,0.079905,-19.501,0.95394,0.22573,0.19759,-191.18,0.17287,0.12467,-0.97702,238.18
    3617 
    3618 > ui mousemode right "rotate selected models"
    3619 
    3620 > view matrix models
    3621 > #11,-0.44466,0.86193,0.24364,9.8808,0.43509,0.44561,-0.78238,80.482,-0.78293,-0.24189,-0.57316,431.83
    3622 
    3623 > view matrix models
    3624 > #11,-0.18798,0.93156,-0.31122,58.69,-0.76591,-0.3374,-0.54731,449.37,-0.61485,0.13548,0.77692,30.371
    3625 
    3626 > view matrix models
    3627 > #11,0.33453,0.89427,0.29728,-173.26,-0.90067,0.21057,0.38008,165.9,0.27729,-0.3949,0.87588,-68.074
    3628 
    3629 > view matrix models
    3630 > #11,-0.023396,0.72365,0.68977,-144.95,-0.75877,-0.4621,0.45906,260.43,0.65094,-0.51264,0.5599,-55.367
    3631 
    3632 > select add #8.1
    3633 
    3634 5 models selected 
    3635 
    3636 > select subtract #8.1
    3637 
    3638 2 models selected 
    3639 
    3640 > volume #8.1 level 0.8214
    3641 
    3642 > view matrix models
    3643 > #11,-0.25849,0.86303,0.434,-70.173,-0.92617,-0.34911,0.14259,339.31,0.27457,-0.3651,0.88956,-76.664
    3644 
    3645 > view matrix models
    3646 > #11,-0.2556,0.76987,0.58479,-83.218,-0.66743,-0.57812,0.46937,263.28,0.69943,-0.27033,0.6616,-138.13
    3647 
    3648 > ui mousemode right "translate selected models"
    3649 
    3650 > view matrix models
    3651 > #11,-0.2556,0.76987,0.58479,37.46,-0.66743,-0.57812,0.46937,405.92,0.69943,-0.27033,0.6616,74.829
    3652 
    3653 > view matrix models
    3654 > #11,-0.2556,0.76987,0.58479,-61.132,-0.66743,-0.57812,0.46937,246.04,0.69943,-0.27033,0.6616,168.26
    3655 
    3656 > vlo flip #11
    3657 
    3658 Unknown command: vlo flip #11 
    3659 
    3660 > volume flip #11
    3661 
    3662 Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip as #12, grid size
    3663 128,128,128, pixel 3.35, shown at step 1, values float32 
    3664 
    3665 > select subtract #11
    3666 
    3667 Nothing selected 
    3668 
    3669 > select add #12
    3670 
    3671 2 models selected 
    3672 
    3673 > view matrix models
    3674 > #12,-0.2556,0.76987,0.58479,-43.002,-0.66743,-0.57812,0.46937,298.27,0.69943,-0.27033,0.6616,-194.26
    3675 
    3676 > ui mousemode right "rotate selected models"
    3677 
    3678 > view matrix models
    3679 > #12,0.92577,0.31188,-0.21375,-26.853,0.27852,-0.94484,-0.17233,311.69,-0.25571,0.10001,-0.96157,275.75
    3680 
    3681 > view matrix models
    3682 > #12,0.62393,0.48527,-0.61256,85.536,0.17958,-0.8519,-0.49196,381.16,-0.76057,0.19695,-0.61866,289.25
    3683 
    3684 > ui mousemode right "translate selected models"
    3685 
    3686 > view matrix models
    3687 > #12,0.62393,0.48527,-0.61256,188.72,0.17958,-0.8519,-0.49196,497.09,-0.76057,0.19695,-0.61866,541.82
    3688 
    3689 > fitmap #11 inMap #8.1
    3690 
    3691 Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc in map
    3692 cryosparc_P1_J49_001_volume_map.mrc using 23893 points 
    3693 correlation = 0.01935, correlation about mean = -0.01646, overlap = 1.348 
    3694 steps = 2000, shift = 45.8, angle = 16.9 degrees 
    3695  
    3696 Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc (#11) relative to
    3697 cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates: 
    3698 Matrix rotation and translation 
    3699 0.76596209 -0.63078757 0.12413352 322.16906811 
    3700 -0.63024789 -0.77487124 -0.04860213 313.54152615 
    3701 0.12684511 -0.04100750 -0.99107452 517.38272158 
    3702 Axis 0.93967044 -0.33550078 0.06677342 
    3703 Axis point 0.00000000 213.74492934 247.66543738 
    3704 Rotation angle (degrees) 179.76846061 
    3705 Shift along axis 232.08674081 
    3706  
    3707 
    3708 > view matrix models
    3709 > #12,0.62393,0.48527,-0.61256,175.9,0.17958,-0.8519,-0.49196,515.24,-0.76057,0.19695,-0.61866,538.55
    3710 
    3711 > fitmap #11 inMap #8.1
    3712 
    3713 Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc in map
    3714 cryosparc_P1_J49_001_volume_map.mrc using 23893 points 
    3715 correlation = 0.02243, correlation about mean = -0.02075, overlap = 1.595 
    3716 steps = 2000, shift = 2.98, angle = 1.59 degrees 
    3717  
    3718 Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc (#11) relative to
    3719 cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates: 
    3720 Matrix rotation and translation 
    3721 0.76039117 -0.63772002 0.12295710 323.96547670 
    3722 -0.63353104 -0.77000069 -0.07574545 319.50905901 
    3723 0.14298144 -0.02030097 -0.98951715 511.69616259 
    3724 Axis 0.93817345 -0.33883092 0.07088153 
    3725 Axis point 0.00000000 214.35569589 246.74521785 
    3726 Rotation angle (degrees) 178.30671110 
    3727 Shift along axis 231.94606760 
    3728  
    3729 
    3730 > fitmap #11 inMap #8.1
    3731 
    3732 Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc in map
    3733 cryosparc_P1_J49_001_volume_map.mrc using 23893 points 
    3734 correlation = 0.02113, correlation about mean = -0.01959, overlap = 1.58 
    3735 steps = 2000, shift = 1.67, angle = 0.811 degrees 
    3736  
    3737 Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc (#11) relative to
    3738 cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates: 
    3739 Matrix rotation and translation 
    3740 0.75875117 -0.64007885 0.12081283 325.17547265 
    3741 -0.63770232 -0.76773938 -0.06254596 316.26964319 
    3742 0.13278712 -0.02958580 -0.99070292 514.78491310 
    3743 Axis 0.93774531 -0.34067882 0.06761421 
    3744 Axis point 0.00000000 214.86367769 247.52162959 
    3745 Rotation angle (degrees) 178.99302339 
    3746 Shift along axis 231.99217871 
    3747  
    3748 
    3749 > select subtract #12
    3750 
    3751 Nothing selected 
    3752 
    3753 > volume #8.1 level 0.2738
    3754 
    3755 > volume #11 level 2.705
    3756 
    3757 > fitmap #12 inMap #8.1
    3758 
    3759 Fit map NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip in map
    3760 cryosparc_P1_J49_001_volume_map.mrc using 23893 points 
    3761 correlation = 0.9682, correlation about mean = 0.4313, overlap = 5.764e+04 
    3762 steps = 76, shift = 6.77, angle = 9.6 degrees 
    3763  
    3764 Position of NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip (#12) relative
    3765 to cryosparc_P1_J49_001_volume_map.mrc (#8.1) coordinates: 
    3766 Matrix rotation and translation 
    3767 -0.97709476 -0.21259809 -0.00937515 470.84629512 
    3768 0.21276995 -0.97519050 -0.06109367 392.99085428 
    3769 0.00384584 -0.06168906 0.99808801 9.67927862 
    3770 Axis -0.00139902 -0.03106627 0.99951635 
    3771 Axis point 214.27703954 221.99548795 0.00000000 
    3772 Rotation angle (degrees) 167.71427589 
    3773 Shift along axis -3.19288320 
    3774  
    3775 
    3776 > hide #!11 models
    3777 
    3778 > volume #12 level 0.45
    3779 
    3780 > hide #9 models
    3781 
    3782 > hide #!8.1 models
    3783 
    3784 > ui tool show "Side View"
    3785 
    3786 > volume #7 level 0.04281
    3787 
    3788 > hide #!7 models
    3789 
    3790 > show #!8.1 models
    3791 
    3792 Traceback (most recent call last): 
    3793 File
    3794 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3795 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    3796 self.status(self._last_message, self._last_color) 
    3797 File
    3798 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3799 packages/chimerax/ui/statusbar.py", line 150, in status 
    3800 r.draw_background() 
    3801 File
    3802 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3803 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    3804 GL.glClear(flags) 
    3805 File "src/errorchecker.pyx", line 58, in
    3806 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3807 OpenGL.error.GLError: GLError( 
    3808 err = 1286, 
    3809 description = b'invalid framebuffer operation', 
    3810 baseOperation = glClear, 
    3811 cArguments = (16640,) 
    3812 ) 
    3813  
    3814 OpenGL.error.GLError: GLError( 
    3815 err = 1286, 
    3816 description = b'invalid framebuffer operation', 
    3817 baseOperation = glClear, 
    3818 cArguments = (16640,) 
    3819 ) 
    3820  
    3821 File "src/errorchecker.pyx", line 58, in
    3822 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3823  
    3824 See log for complete Python traceback. 
    3825  
    3826 Traceback (most recent call last): 
    3827 File
    3828 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3829 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    3830 self.status(self._last_message, self._last_color) 
    3831 File
    3832 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3833 packages/chimerax/ui/statusbar.py", line 150, in status 
    3834 r.draw_background() 
    3835 File
    3836 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3837 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    3838 GL.glClear(flags) 
    3839 File "src/errorchecker.pyx", line 58, in
    3840 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3841 OpenGL.error.GLError: GLError( 
    3842 err = 1286, 
    3843 description = b'invalid framebuffer operation', 
    3844 baseOperation = glClear, 
    3845 cArguments = (16640,) 
    3846 ) 
    3847  
    3848 OpenGL.error.GLError: GLError( 
    3849 err = 1286, 
    3850 description = b'invalid framebuffer operation', 
    3851 baseOperation = glClear, 
    3852 cArguments = (16640,) 
    3853 ) 
    3854  
    3855 File "src/errorchecker.pyx", line 58, in
    3856 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3857  
    3858 See log for complete Python traceback. 
    3859  
    3860 Traceback (most recent call last): 
    3861 File
    3862 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3863 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    3864 self.status(self._last_message, self._last_color) 
    3865 File
    3866 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3867 packages/chimerax/ui/statusbar.py", line 150, in status 
    3868 r.draw_background() 
    3869 File
    3870 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3871 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    3872 GL.glClear(flags) 
    3873 File "src/errorchecker.pyx", line 58, in
    3874 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3875 OpenGL.error.GLError: GLError( 
    3876 err = 1286, 
    3877 description = b'invalid framebuffer operation', 
    3878 baseOperation = glClear, 
    3879 cArguments = (16640,) 
    3880 ) 
    3881  
    3882 OpenGL.error.GLError: GLError( 
    3883 err = 1286, 
    3884 description = b'invalid framebuffer operation', 
    3885 baseOperation = glClear, 
    3886 cArguments = (16640,) 
    3887 ) 
    3888  
    3889 File "src/errorchecker.pyx", line 58, in
    3890 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3891  
    3892 See log for complete Python traceback. 
    3893  
    3894 Traceback (most recent call last): 
    3895 File
    3896 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3897 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    3898 self.status(self._last_message, self._last_color) 
    3899 File
    3900 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3901 packages/chimerax/ui/statusbar.py", line 150, in status 
    3902 r.draw_background() 
    3903 File
    3904 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3905 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    3906 GL.glClear(flags) 
    3907 File "src/errorchecker.pyx", line 58, in
    3908 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3909 OpenGL.error.GLError: GLError( 
    3910 err = 1286, 
    3911 description = b'invalid framebuffer operation', 
    3912 baseOperation = glClear, 
    3913 cArguments = (16640,) 
    3914 ) 
    3915  
    3916 OpenGL.error.GLError: GLError( 
    3917 err = 1286, 
    3918 description = b'invalid framebuffer operation', 
    3919 baseOperation = glClear, 
    3920 cArguments = (16640,) 
    3921 ) 
    3922  
    3923 File "src/errorchecker.pyx", line 58, in
    3924 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3925  
    3926 See log for complete Python traceback. 
    3927  
    3928 Traceback (most recent call last): 
    3929 File
    3930 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3931 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    3932 self.status(self._last_message, self._last_color) 
    3933 File
    3934 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3935 packages/chimerax/ui/statusbar.py", line 150, in status 
    3936 r.draw_background() 
    3937 File
    3938 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3939 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    3940 GL.glClear(flags) 
    3941 File "src/errorchecker.pyx", line 58, in
    3942 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3943 OpenGL.error.GLError: GLError( 
    3944 err = 1286, 
    3945 description = b'invalid framebuffer operation', 
    3946 baseOperation = glClear, 
    3947 cArguments = (16640,) 
    3948 ) 
    3949  
    3950 OpenGL.error.GLError: GLError( 
    3951 err = 1286, 
    3952 description = b'invalid framebuffer operation', 
    3953 baseOperation = glClear, 
    3954 cArguments = (16640,) 
    3955 ) 
    3956  
    3957 File "src/errorchecker.pyx", line 58, in
    3958 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3959  
    3960 See log for complete Python traceback. 
    3961  
    3962 Traceback (most recent call last): 
    3963 File
    3964 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3965 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    3966 self.status(self._last_message, self._last_color) 
    3967 File
    3968 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3969 packages/chimerax/ui/statusbar.py", line 150, in status 
    3970 r.draw_background() 
    3971 File
    3972 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3973 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    3974 GL.glClear(flags) 
    3975 File "src/errorchecker.pyx", line 58, in
    3976 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3977 OpenGL.error.GLError: GLError( 
    3978 err = 1286, 
    3979 description = b'invalid framebuffer operation', 
    3980 baseOperation = glClear, 
    3981 cArguments = (16640,) 
    3982 ) 
    3983  
    3984 OpenGL.error.GLError: GLError( 
    3985 err = 1286, 
    3986 description = b'invalid framebuffer operation', 
    3987 baseOperation = glClear, 
    3988 cArguments = (16640,) 
    3989 ) 
    3990  
    3991 File "src/errorchecker.pyx", line 58, in
    3992 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3993  
    3994 See log for complete Python traceback. 
    3995  
    3996 Traceback (most recent call last): 
    3997 File
    3998 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3999 packages/chimerax/core/triggerset.py", line 149, in invoke 
    4000 return self._func(self._name, data) 
    4001 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4002 File
    4003 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4004 packages/chimerax/sideview/tool.py", line 113, in _redraw 
    4005 self.render() 
    4006 File
    4007 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4008 packages/chimerax/sideview/tool.py", line 143, in render 
    4009 mvwin = self.view.render.use_shared_context(self) 
    4010 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4011 File
    4012 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4013 packages/chimerax/graphics/opengl.py", line 579, in use_shared_context 
    4014 self.make_current() 
    4015 File
    4016 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4017 packages/chimerax/graphics/opengl.py", line 550, in make_current 
    4018 return self._opengl_context.make_current() 
    4019 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4020 File
    4021 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4022 packages/chimerax/graphics/opengl.py", line 123, in make_current 
    4023 raise OpenGLError("Could not make graphics context current") 
    4024 chimerax.graphics.opengl.OpenGLError: Could not make graphics context current 
    4025  
    4026 Error processing trigger "frame drawn": 
    4027 chimerax.graphics.opengl.OpenGLError: Could not make graphics context current 
    4028  
    4029 File
    4030 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4031 packages/chimerax/graphics/opengl.py", line 123, in make_current 
    4032 raise OpenGLError("Could not make graphics context current") 
    4033  
    4034 See log for complete Python traceback. 
    4035  
    4036 
    4037 The cached device pixel ratio value was stale on window expose. Please file a
    4038 QTBUG which explains how to reproduce. 
    4039 
    4040 > hide #!8 models
    4041 
    4042 The cached device pixel ratio value was stale on window expose. Please file a
    4043 QTBUG which explains how to reproduce. 
    4044 
    4045 > ui tool show "Side View"
    4046 
    4047 The cached device pixel ratio value was stale on window expose. Please file a
    4048 QTBUG which explains how to reproduce. 
    4049 
    4050 > save "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
    4051 > and exit focus mask /NU/scribo comp apo rotat.tif" width 864 height 590
    4052 > supersample 3
    4053 
    4054 > show #!8.2 models
    4055 
    4056 > hide #!8.2 models
    4057 
    4058 > save "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
    4059 > and exit focus mask /NU/J49 comp.tif" width 864 height 587 supersample 3
    4060 
    4061 > close session
    4062 
    4063 Traceback (most recent call last): 
    4064 File
    4065 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4066 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4067 self.status(self._last_message, self._last_color) 
    4068 File
    4069 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4070 packages/chimerax/ui/statusbar.py", line 150, in status 
    4071 r.draw_background() 
    4072 File
    4073 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4074 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4075 GL.glClear(flags) 
    4076 File "src/errorchecker.pyx", line 58, in
    4077 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4078 OpenGL.error.GLError: GLError( 
    4079 err = 1286, 
    4080 description = b'invalid framebuffer operation', 
    4081 baseOperation = glClear, 
    4082 cArguments = (16640,) 
    4083 ) 
    4084  
    4085 OpenGL.error.GLError: GLError( 
    4086 err = 1286, 
    4087 description = b'invalid framebuffer operation', 
    4088 baseOperation = glClear, 
    4089 cArguments = (16640,) 
    4090 ) 
    4091  
    4092 File "src/errorchecker.pyx", line 58, in
    4093 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4094  
    4095 See log for complete Python traceback. 
    4096  
    4097 Traceback (most recent call last): 
    4098 File
    4099 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4100 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4101 self.status(self._last_message, self._last_color) 
    4102 File
    4103 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4104 packages/chimerax/ui/statusbar.py", line 150, in status 
    4105 r.draw_background() 
    4106 File
    4107 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4108 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4109 GL.glClear(flags) 
    4110 File "src/errorchecker.pyx", line 58, in
    4111 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4112 OpenGL.error.GLError: GLError( 
    4113 err = 1286, 
    4114 description = b'invalid framebuffer operation', 
    4115 baseOperation = glClear, 
    4116 cArguments = (16640,) 
    4117 ) 
    4118  
    4119 OpenGL.error.GLError: GLError( 
    4120 err = 1286, 
    4121 description = b'invalid framebuffer operation', 
    4122 baseOperation = glClear, 
    4123 cArguments = (16640,) 
    4124 ) 
    4125  
    4126 File "src/errorchecker.pyx", line 58, in
    4127 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4128  
    4129 See log for complete Python traceback. 
    4130  
    4131 Traceback (most recent call last): 
    4132 File
    4133 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4134 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4135 self.status(self._last_message, self._last_color) 
    4136 File
    4137 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4138 packages/chimerax/ui/statusbar.py", line 150, in status 
    4139 r.draw_background() 
    4140 File
    4141 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4142 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4143 GL.glClear(flags) 
    4144 File "src/errorchecker.pyx", line 58, in
    4145 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4146 OpenGL.error.GLError: GLError( 
    4147 err = 1286, 
    4148 description = b'invalid framebuffer operation', 
    4149 baseOperation = glClear, 
    4150 cArguments = (16640,) 
    4151 ) 
    4152  
    4153 OpenGL.error.GLError: GLError( 
    4154 err = 1286, 
    4155 description = b'invalid framebuffer operation', 
    4156 baseOperation = glClear, 
    4157 cArguments = (16640,) 
    4158 ) 
    4159  
    4160 File "src/errorchecker.pyx", line 58, in
    4161 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4162  
    4163 See log for complete Python traceback. 
    4164  
    4165 Traceback (most recent call last): 
    4166 File
    4167 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4168 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4169 self.status(self._last_message, self._last_color) 
    4170 File
    4171 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4172 packages/chimerax/ui/statusbar.py", line 150, in status 
    4173 r.draw_background() 
    4174 File
    4175 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4176 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4177 GL.glClear(flags) 
    4178 File "src/errorchecker.pyx", line 58, in
    4179 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4180 OpenGL.error.GLError: GLError( 
    4181 err = 1286, 
    4182 description = b'invalid framebuffer operation', 
    4183 baseOperation = glClear, 
    4184 cArguments = (16640,) 
    4185 ) 
    4186  
    4187 OpenGL.error.GLError: GLError( 
    4188 err = 1286, 
    4189 description = b'invalid framebuffer operation', 
    4190 baseOperation = glClear, 
    4191 cArguments = (16640,) 
    4192 ) 
    4193  
    4194 File "src/errorchecker.pyx", line 58, in
    4195 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4196  
    4197 See log for complete Python traceback. 
    4198  
    4199 
    4200 The cached device pixel ratio value was stale on window expose. Please file a
    4201 QTBUG which explains how to reproduce. 
    4202 
    4203 Traceback (most recent call last): 
    4204 File
    4205 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4206 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4207 self.status(self._last_message, self._last_color) 
    4208 File
    4209 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4210 packages/chimerax/ui/statusbar.py", line 150, in status 
    4211 r.draw_background() 
    4212 File
    4213 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4214 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4215 GL.glClear(flags) 
    4216 File "src/errorchecker.pyx", line 58, in
    4217 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4218 OpenGL.error.GLError: GLError( 
    4219 err = 1286, 
    4220 description = b'invalid framebuffer operation', 
    4221 baseOperation = glClear, 
    4222 cArguments = (16640,) 
    4223 ) 
    4224  
    4225 OpenGL.error.GLError: GLError( 
    4226 err = 1286, 
    4227 description = b'invalid framebuffer operation', 
    4228 baseOperation = glClear, 
    4229 cArguments = (16640,) 
    4230 ) 
    4231  
    4232 File "src/errorchecker.pyx", line 58, in
    4233 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4234  
    4235 See log for complete Python traceback. 
    4236  
    4237 Traceback (most recent call last): 
    4238 File
    4239 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4240 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4241 self.status(self._last_message, self._last_color) 
    4242 File
    4243 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4244 packages/chimerax/ui/statusbar.py", line 150, in status 
    4245 r.draw_background() 
    4246 File
    4247 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4248 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4249 GL.glClear(flags) 
    4250 File "src/errorchecker.pyx", line 58, in
    4251 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4252 OpenGL.error.GLError: GLError( 
    4253 err = 1286, 
    4254 description = b'invalid framebuffer operation', 
    4255 baseOperation = glClear, 
    4256 cArguments = (16640,) 
    4257 ) 
    4258  
    4259 OpenGL.error.GLError: GLError( 
    4260 err = 1286, 
    4261 description = b'invalid framebuffer operation', 
    4262 baseOperation = glClear, 
    4263 cArguments = (16640,) 
    4264 ) 
    4265  
    4266 File "src/errorchecker.pyx", line 58, in
    4267 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4268  
    4269 See log for complete Python traceback. 
    4270  
    4271 Traceback (most recent call last): 
    4272 File
    4273 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4274 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4275 self.status(self._last_message, self._last_color) 
    4276 File
    4277 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4278 packages/chimerax/ui/statusbar.py", line 150, in status 
    4279 r.draw_background() 
    4280 File
    4281 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4282 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4283 GL.glClear(flags) 
    4284 File "src/errorchecker.pyx", line 58, in
    4285 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4286 OpenGL.error.GLError: GLError( 
    4287 err = 1286, 
    4288 description = b'invalid framebuffer operation', 
    4289 baseOperation = glClear, 
    4290 cArguments = (16640,) 
    4291 ) 
    4292  
    4293 OpenGL.error.GLError: GLError( 
    4294 err = 1286, 
    4295 description = b'invalid framebuffer operation', 
    4296 baseOperation = glClear, 
    4297 cArguments = (16640,) 
    4298 ) 
    4299  
    4300 File "src/errorchecker.pyx", line 58, in
    4301 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4302  
    4303 See log for complete Python traceback. 
    4304  
    4305 Traceback (most recent call last): 
    4306 File
    4307 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4308 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4309 self.status(self._last_message, self._last_color) 
    4310 File
    4311 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4312 packages/chimerax/ui/statusbar.py", line 150, in status 
    4313 r.draw_background() 
    4314 File
    4315 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4316 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4317 GL.glClear(flags) 
    4318 File "src/errorchecker.pyx", line 58, in
    4319 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4320 OpenGL.error.GLError: GLError( 
    4321 err = 1286, 
    4322 description = b'invalid framebuffer operation', 
    4323 baseOperation = glClear, 
    4324 cArguments = (16640,) 
    4325 ) 
    4326  
    4327 OpenGL.error.GLError: GLError( 
    4328 err = 1286, 
    4329 description = b'invalid framebuffer operation', 
    4330 baseOperation = glClear, 
    4331 cArguments = (16640,) 
    4332 ) 
    4333  
    4334 File "src/errorchecker.pyx", line 58, in
    4335 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4336  
    4337 See log for complete Python traceback. 
    4338  
    4339 Traceback (most recent call last): 
    4340 File
    4341 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4342 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4343 self.status(self._last_message, self._last_color) 
    4344 File
    4345 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4346 packages/chimerax/ui/statusbar.py", line 150, in status 
    4347 r.draw_background() 
    4348 File
    4349 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4350 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4351 GL.glClear(flags) 
    4352 File "src/errorchecker.pyx", line 58, in
    4353 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4354 OpenGL.error.GLError: GLError( 
    4355 err = 1286, 
    4356 description = b'invalid framebuffer operation', 
    4357 baseOperation = glClear, 
    4358 cArguments = (16640,) 
    4359 ) 
    4360  
    4361 OpenGL.error.GLError: GLError( 
    4362 err = 1286, 
    4363 description = b'invalid framebuffer operation', 
    4364 baseOperation = glClear, 
    4365 cArguments = (16640,) 
    4366 ) 
    4367  
    4368 File "src/errorchecker.pyx", line 58, in
    4369 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4370  
    4371 See log for complete Python traceback. 
    4372  
    4373 Traceback (most recent call last): 
    4374 File
    4375 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4376 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4377 self.status(self._last_message, self._last_color) 
    4378 File
    4379 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4380 packages/chimerax/ui/statusbar.py", line 150, in status 
    4381 r.draw_background() 
    4382 File
    4383 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4384 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4385 GL.glClear(flags) 
    4386 File "src/errorchecker.pyx", line 58, in
    4387 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4388 OpenGL.error.GLError: GLError( 
    4389 err = 1286, 
    4390 description = b'invalid framebuffer operation', 
    4391 baseOperation = glClear, 
    4392 cArguments = (16640,) 
    4393 ) 
    4394  
    4395 OpenGL.error.GLError: GLError( 
    4396 err = 1286, 
    4397 description = b'invalid framebuffer operation', 
    4398 baseOperation = glClear, 
    4399 cArguments = (16640,) 
    4400 ) 
    4401  
    4402 File "src/errorchecker.pyx", line 58, in
    4403 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4404  
    4405 See log for complete Python traceback. 
    4406  
    4407 Traceback (most recent call last): 
    4408 File
    4409 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4410 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4411 self.status(self._last_message, self._last_color) 
    4412 File
    4413 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4414 packages/chimerax/ui/statusbar.py", line 150, in status 
    4415 r.draw_background() 
    4416 File
    4417 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4418 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4419 GL.glClear(flags) 
    4420 File "src/errorchecker.pyx", line 58, in
    4421 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4422 OpenGL.error.GLError: GLError( 
    4423 err = 1286, 
    4424 description = b'invalid framebuffer operation', 
    4425 baseOperation = glClear, 
    4426 cArguments = (16640,) 
    4427 ) 
    4428  
    4429 OpenGL.error.GLError: GLError( 
    4430 err = 1286, 
    4431 description = b'invalid framebuffer operation', 
    4432 baseOperation = glClear, 
    4433 cArguments = (16640,) 
    4434 ) 
    4435  
    4436 File "src/errorchecker.pyx", line 58, in
    4437 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4438  
    4439 See log for complete Python traceback. 
    4440  
    4441 Traceback (most recent call last): 
    4442 File
    4443 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4444 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4445 self.status(self._last_message, self._last_color) 
    4446 File
    4447 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4448 packages/chimerax/ui/statusbar.py", line 150, in status 
    4449 r.draw_background() 
    4450 File
    4451 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4452 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4453 GL.glClear(flags) 
    4454 File "src/errorchecker.pyx", line 58, in
    4455 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4456 OpenGL.error.GLError: GLError( 
    4457 err = 1286, 
    4458 description = b'invalid framebuffer operation', 
    4459 baseOperation = glClear, 
    4460 cArguments = (16640,) 
    4461 ) 
    4462  
    4463 OpenGL.error.GLError: GLError( 
    4464 err = 1286, 
    4465 description = b'invalid framebuffer operation', 
    4466 baseOperation = glClear, 
    4467 cArguments = (16640,) 
    4468 ) 
    4469  
    4470 File "src/errorchecker.pyx", line 58, in
    4471 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4472  
    4473 See log for complete Python traceback. 
    4474  
    4475 Traceback (most recent call last): 
    4476 File
    4477 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4478 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4479 self.status(self._last_message, self._last_color) 
    4480 File
    4481 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4482 packages/chimerax/ui/statusbar.py", line 150, in status 
    4483 r.draw_background() 
    4484 File
    4485 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4486 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4487 GL.glClear(flags) 
    4488 File "src/errorchecker.pyx", line 58, in
    4489 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4490 OpenGL.error.GLError: GLError( 
    4491 err = 1286, 
    4492 description = b'invalid framebuffer operation', 
    4493 baseOperation = glClear, 
    4494 cArguments = (16640,) 
    4495 ) 
    4496  
    4497 OpenGL.error.GLError: GLError( 
    4498 err = 1286, 
    4499 description = b'invalid framebuffer operation', 
    4500 baseOperation = glClear, 
    4501 cArguments = (16640,) 
    4502 ) 
    4503  
    4504 File "src/errorchecker.pyx", line 58, in
    4505 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4506  
    4507 See log for complete Python traceback. 
    4508  
    4509 Traceback (most recent call last): 
    4510 File
    4511 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4512 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4513 self.status(self._last_message, self._last_color) 
    4514 File
    4515 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4516 packages/chimerax/ui/statusbar.py", line 150, in status 
    4517 r.draw_background() 
    4518 File
    4519 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4520 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4521 GL.glClear(flags) 
    4522 File "src/errorchecker.pyx", line 58, in
    4523 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4524 OpenGL.error.GLError: GLError( 
    4525 err = 1286, 
    4526 description = b'invalid framebuffer operation', 
    4527 baseOperation = glClear, 
    4528 cArguments = (16640,) 
    4529 ) 
    4530  
    4531 OpenGL.error.GLError: GLError( 
    4532 err = 1286, 
    4533 description = b'invalid framebuffer operation', 
    4534 baseOperation = glClear, 
    4535 cArguments = (16640,) 
    4536 ) 
    4537  
    4538 File "src/errorchecker.pyx", line 58, in
    4539 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4540  
    4541 See log for complete Python traceback. 
    4542  
    4543 Traceback (most recent call last): 
    4544 File
    4545 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4546 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4547 self.status(self._last_message, self._last_color) 
    4548 File
    4549 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4550 packages/chimerax/ui/statusbar.py", line 150, in status 
    4551 r.draw_background() 
    4552 File
    4553 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4554 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4555 GL.glClear(flags) 
    4556 File "src/errorchecker.pyx", line 58, in
    4557 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4558 OpenGL.error.GLError: GLError( 
    4559 err = 1286, 
    4560 description = b'invalid framebuffer operation', 
    4561 baseOperation = glClear, 
    4562 cArguments = (16640,) 
    4563 ) 
    4564  
    4565 OpenGL.error.GLError: GLError( 
    4566 err = 1286, 
    4567 description = b'invalid framebuffer operation', 
    4568 baseOperation = glClear, 
    4569 cArguments = (16640,) 
    4570 ) 
    4571  
    4572 File "src/errorchecker.pyx", line 58, in
    4573 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4574  
    4575 See log for complete Python traceback. 
    4576  
    4577 Traceback (most recent call last): 
    4578 File
    4579 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4580 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4581 self.status(self._last_message, self._last_color) 
    4582 File
    4583 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4584 packages/chimerax/ui/statusbar.py", line 150, in status 
    4585 r.draw_background() 
    4586 File
    4587 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4588 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4589 GL.glClear(flags) 
    4590 File "src/errorchecker.pyx", line 58, in
    4591 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4592 OpenGL.error.GLError: GLError( 
    4593 err = 1286, 
    4594 description = b'invalid framebuffer operation', 
    4595 baseOperation = glClear, 
    4596 cArguments = (16640,) 
    4597 ) 
    4598  
    4599 OpenGL.error.GLError: GLError( 
    4600 err = 1286, 
    4601 description = b'invalid framebuffer operation', 
    4602 baseOperation = glClear, 
    4603 cArguments = (16640,) 
    4604 ) 
    4605  
    4606 File "src/errorchecker.pyx", line 58, in
    4607 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4608  
    4609 See log for complete Python traceback. 
    4610  
    4611 Traceback (most recent call last): 
    4612 File
    4613 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4614 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4615 self.status(self._last_message, self._last_color) 
    4616 File
    4617 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4618 packages/chimerax/ui/statusbar.py", line 150, in status 
    4619 r.draw_background() 
    4620 File
    4621 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4622 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4623 GL.glClear(flags) 
    4624 File "src/errorchecker.pyx", line 58, in
    4625 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4626 OpenGL.error.GLError: GLError( 
    4627 err = 1286, 
    4628 description = b'invalid framebuffer operation', 
    4629 baseOperation = glClear, 
    4630 cArguments = (16640,) 
    4631 ) 
    4632  
    4633 OpenGL.error.GLError: GLError( 
    4634 err = 1286, 
    4635 description = b'invalid framebuffer operation', 
    4636 baseOperation = glClear, 
    4637 cArguments = (16640,) 
    4638 ) 
    4639  
    4640 File "src/errorchecker.pyx", line 58, in
    4641 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4642  
    4643 See log for complete Python traceback. 
    4644  
    4645 Traceback (most recent call last): 
    4646 File
    4647 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4648 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4649 self.status(self._last_message, self._last_color) 
    4650 File
    4651 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4652 packages/chimerax/ui/statusbar.py", line 150, in status 
    4653 r.draw_background() 
    4654 File
    4655 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4656 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4657 GL.glClear(flags) 
    4658 File "src/errorchecker.pyx", line 58, in
    4659 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4660 OpenGL.error.GLError: GLError( 
    4661 err = 1286, 
    4662 description = b'invalid framebuffer operation', 
    4663 baseOperation = glClear, 
    4664 cArguments = (16640,) 
    4665 ) 
    4666  
    4667 OpenGL.error.GLError: GLError( 
    4668 err = 1286, 
    4669 description = b'invalid framebuffer operation', 
    4670 baseOperation = glClear, 
    4671 cArguments = (16640,) 
    4672 ) 
    4673  
    4674 File "src/errorchecker.pyx", line 58, in
    4675 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4676  
    4677 See log for complete Python traceback. 
    4678  
    4679 Traceback (most recent call last): 
    4680 File
    4681 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4682 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4683 self.status(self._last_message, self._last_color) 
    4684 File
    4685 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4686 packages/chimerax/ui/statusbar.py", line 150, in status 
    4687 r.draw_background() 
    4688 File
    4689 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4690 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4691 GL.glClear(flags) 
    4692 File "src/errorchecker.pyx", line 58, in
    4693 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4694 OpenGL.error.GLError: GLError( 
    4695 err = 1286, 
    4696 description = b'invalid framebuffer operation', 
    4697 baseOperation = glClear, 
    4698 cArguments = (16640,) 
    4699 ) 
    4700  
    4701 OpenGL.error.GLError: GLError( 
    4702 err = 1286, 
    4703 description = b'invalid framebuffer operation', 
    4704 baseOperation = glClear, 
    4705 cArguments = (16640,) 
    4706 ) 
    4707  
    4708 File "src/errorchecker.pyx", line 58, in
    4709 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4710  
    4711 See log for complete Python traceback. 
    4712  
    4713 Traceback (most recent call last): 
    4714 File
    4715 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4716 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4717 self.status(self._last_message, self._last_color) 
    4718 File
    4719 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4720 packages/chimerax/ui/statusbar.py", line 150, in status 
    4721 r.draw_background() 
    4722 File
    4723 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4724 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4725 GL.glClear(flags) 
    4726 File "src/errorchecker.pyx", line 58, in
    4727 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4728 OpenGL.error.GLError: GLError( 
    4729 err = 1286, 
    4730 description = b'invalid framebuffer operation', 
    4731 baseOperation = glClear, 
    4732 cArguments = (16640,) 
    4733 ) 
    4734  
    4735 OpenGL.error.GLError: GLError( 
    4736 err = 1286, 
    4737 description = b'invalid framebuffer operation', 
    4738 baseOperation = glClear, 
    4739 cArguments = (16640,) 
    4740 ) 
    4741  
    4742 File "src/errorchecker.pyx", line 58, in
    4743 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4744  
    4745 See log for complete Python traceback. 
    4746  
    4747 Traceback (most recent call last): 
    4748 File
    4749 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4750 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4751 self.status(self._last_message, self._last_color) 
    4752 File
    4753 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4754 packages/chimerax/ui/statusbar.py", line 150, in status 
    4755 r.draw_background() 
    4756 File
    4757 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4758 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4759 GL.glClear(flags) 
    4760 File "src/errorchecker.pyx", line 58, in
    4761 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4762 OpenGL.error.GLError: GLError( 
    4763 err = 1286, 
    4764 description = b'invalid framebuffer operation', 
    4765 baseOperation = glClear, 
    4766 cArguments = (16640,) 
    4767 ) 
    4768  
    4769 OpenGL.error.GLError: GLError( 
    4770 err = 1286, 
    4771 description = b'invalid framebuffer operation', 
    4772 baseOperation = glClear, 
    4773 cArguments = (16640,) 
    4774 ) 
    4775  
    4776 File "src/errorchecker.pyx", line 58, in
    4777 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4778  
    4779 See log for complete Python traceback. 
    4780  
    4781 Traceback (most recent call last): 
    4782 File
    4783 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4784 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4785 self.status(self._last_message, self._last_color) 
    4786 File
    4787 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4788 packages/chimerax/ui/statusbar.py", line 150, in status 
    4789 r.draw_background() 
    4790 File
    4791 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4792 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4793 GL.glClear(flags) 
    4794 File "src/errorchecker.pyx", line 58, in
    4795 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4796 OpenGL.error.GLError: GLError( 
    4797 err = 1286, 
    4798 description = b'invalid framebuffer operation', 
    4799 baseOperation = glClear, 
    4800 cArguments = (16640,) 
    4801 ) 
    4802  
    4803 OpenGL.error.GLError: GLError( 
    4804 err = 1286, 
    4805 description = b'invalid framebuffer operation', 
    4806 baseOperation = glClear, 
    4807 cArguments = (16640,) 
    4808 ) 
    4809  
    4810 File "src/errorchecker.pyx", line 58, in
    4811 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4812  
    4813 See log for complete Python traceback. 
    4814  
    4815 Traceback (most recent call last): 
    4816 File
    4817 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4818 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4819 self.status(self._last_message, self._last_color) 
    4820 File
    4821 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4822 packages/chimerax/ui/statusbar.py", line 150, in status 
    4823 r.draw_background() 
    4824 File
    4825 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4826 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4827 GL.glClear(flags) 
    4828 File "src/errorchecker.pyx", line 58, in
    4829 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4830 OpenGL.error.GLError: GLError( 
    4831 err = 1286, 
    4832 description = b'invalid framebuffer operation', 
    4833 baseOperation = glClear, 
    4834 cArguments = (16640,) 
    4835 ) 
    4836  
    4837 OpenGL.error.GLError: GLError( 
    4838 err = 1286, 
    4839 description = b'invalid framebuffer operation', 
    4840 baseOperation = glClear, 
    4841 cArguments = (16640,) 
    4842 ) 
    4843  
    4844 File "src/errorchecker.pyx", line 58, in
    4845 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4846  
    4847 See log for complete Python traceback. 
    4848  
    4849 Traceback (most recent call last): 
    4850 File
    4851 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4852 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4853 self.status(self._last_message, self._last_color) 
    4854 File
    4855 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4856 packages/chimerax/ui/statusbar.py", line 150, in status 
    4857 r.draw_background() 
    4858 File
    4859 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4860 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4861 GL.glClear(flags) 
    4862 File "src/errorchecker.pyx", line 58, in
    4863 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4864 OpenGL.error.GLError: GLError( 
    4865 err = 1286, 
    4866 description = b'invalid framebuffer operation', 
    4867 baseOperation = glClear, 
    4868 cArguments = (16640,) 
    4869 ) 
    4870  
    4871 OpenGL.error.GLError: GLError( 
    4872 err = 1286, 
    4873 description = b'invalid framebuffer operation', 
    4874 baseOperation = glClear, 
    4875 cArguments = (16640,) 
    4876 ) 
    4877  
    4878 File "src/errorchecker.pyx", line 58, in
    4879 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4880  
    4881 See log for complete Python traceback. 
    4882  
    4883 Traceback (most recent call last): 
    4884 File
    4885 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4886 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4887 self.status(self._last_message, self._last_color) 
    4888 File
    4889 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4890 packages/chimerax/ui/statusbar.py", line 150, in status 
    4891 r.draw_background() 
    4892 File
    4893 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4894 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4895 GL.glClear(flags) 
    4896 File "src/errorchecker.pyx", line 58, in
    4897 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4898 OpenGL.error.GLError: GLError( 
    4899 err = 1286, 
    4900 description = b'invalid framebuffer operation', 
    4901 baseOperation = glClear, 
    4902 cArguments = (16640,) 
    4903 ) 
    4904  
    4905 OpenGL.error.GLError: GLError( 
    4906 err = 1286, 
    4907 description = b'invalid framebuffer operation', 
    4908 baseOperation = glClear, 
    4909 cArguments = (16640,) 
    4910 ) 
    4911  
    4912 File "src/errorchecker.pyx", line 58, in
    4913 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4914  
    4915 See log for complete Python traceback. 
    4916  
    4917 Traceback (most recent call last): 
    4918 File
    4919 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4920 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4921 self.status(self._last_message, self._last_color) 
    4922 File
    4923 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4924 packages/chimerax/ui/statusbar.py", line 150, in status 
    4925 r.draw_background() 
    4926 File
    4927 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4928 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4929 GL.glClear(flags) 
    4930 File "src/errorchecker.pyx", line 58, in
    4931 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4932 OpenGL.error.GLError: GLError( 
    4933 err = 1286, 
    4934 description = b'invalid framebuffer operation', 
    4935 baseOperation = glClear, 
    4936 cArguments = (16640,) 
    4937 ) 
    4938  
    4939 OpenGL.error.GLError: GLError( 
    4940 err = 1286, 
    4941 description = b'invalid framebuffer operation', 
    4942 baseOperation = glClear, 
    4943 cArguments = (16640,) 
    4944 ) 
    4945  
    4946 File "src/errorchecker.pyx", line 58, in
    4947 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4948  
    4949 See log for complete Python traceback. 
    4950  
    4951 Traceback (most recent call last): 
    4952 File
    4953 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4954 packages/chimerax/ui/statusbar.py", line 84, in _expose_event 
    4955 self.status(self._last_message, self._last_color) 
    4956 File
    4957 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4958 packages/chimerax/ui/statusbar.py", line 150, in status 
    4959 r.draw_background() 
    4960 File
    4961 "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4962 packages/chimerax/graphics/opengl.py", line 1220, in draw_background 
    4963 GL.glClear(flags) 
    4964 File "src/errorchecker.pyx", line 58, in
    4965 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4966 OpenGL.error.GLError: GLError( 
    4967 err = 1286, 
    4968 description = b'invalid framebuffer operation', 
    4969 baseOperation = glClear, 
    4970 cArguments = (16640,) 
    4971 ) 
    4972  
    4973 OpenGL.error.GLError: GLError( 
    4974 err = 1286, 
    4975 description = b'invalid framebuffer operation', 
    4976 baseOperation = glClear, 
    4977 cArguments = (16640,) 
    4978 ) 
    4979  
    4980 File "src/errorchecker.pyx", line 58, in
    4981 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4982  
    4983 See log for complete Python traceback. 
    4984  
    4985 
    4986 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    4987 > 1/NU-refinement /cryosparc_P1_J103_001_volume_map_sharp.mrc"
    4988 
    4989 Opened cryosparc_P1_J103_001_volume_map_sharp.mrc as #1, grid size
    4990 128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32 
    4991 
    4992 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    4993 > 1/NU-refinement /cryosparc_P1_J103_001_volume_map.mrc"
    4994 
    4995 Opened cryosparc_P1_J103_001_volume_map.mrc as #2, grid size 128,128,128,
    4996 pixel 3.32, shown at level 1.04, step 1, values float32 
    4997 
    4998 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    4999 > 1/NU-refinement /cryosparc_P1_J104_001_volume_map_sharp.mrc"
    5000 
    5001 Opened cryosparc_P1_J104_001_volume_map_sharp.mrc as #3, grid size
    5002 128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32 
    5003 
    5004 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5005 > 1/NU-refinement /cryosparc_P1_J104_001_volume_map.mrc"
    5006 
    5007 Opened cryosparc_P1_J104_001_volume_map.mrc as #4, grid size 128,128,128,
    5008 pixel 3.32, shown at level 1.04, step 1, values float32 
    5009 
    5010 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5011 > 1/NU-refinement /cryosparc_P1_J108_001_volume_map_sharp.mrc"
    5012 
    5013 Opened cryosparc_P1_J108_001_volume_map_sharp.mrc as #5, grid size
    5014 128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32 
    5015 
    5016 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5017 > 1/NU-refinement /cryosparc_P1_J108_001_volume_map.mrc"
    5018 
    5019 Opened cryosparc_P1_J108_001_volume_map.mrc as #6, grid size 128,128,128,
    5020 pixel 3.32, shown at level 0.863, step 1, values float32 
    5021 
    5022 > hide #!1 models
    5023 
    5024 > hide #!2 models
    5025 
    5026 > hide #!3 models
    5027 
    5028 > hide #!4 models
    5029 
    5030 > hide #!5 models
    5031 
    5032 > hide #!6 models
    5033 
    5034 > show #!2 models
    5035 
    5036 > show #!1 models
    5037 
    5038 > volume #1 level 0.4865
    5039 
    5040 > surface dust #1 size 33.2
    5041 
    5042 > surface dust #2 size 33.2
    5043 
    5044 > volume #2 level 0.1316
    5045 
    5046 > hide #!2 models
    5047 
    5048 > hide #!1 models
    5049 
    5050 > show #!2 models
    5051 
    5052 > show #!1 models
    5053 
    5054 > hide #!2 models
    5055 
    5056 > open "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /100625_allmaps
    5057 > overlay w NU 2.cxs"
    5058 
    5059 restore_snapshot for "Volume" returned None 
    5060 
    5061 restore_snapshot for "VolumeSurface" returned None 
    5062 
    5063 Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1, grid size
    5064 128,128,128, pixel 3.35, shown at level 0.86, step 1, values float32 
    5065 Opened cryosparc_P1_J21_class_04_00082_volume.mrc as #2, grid size
    5066 128,128,128, pixel 3.32, shown at level 0.34, step 1, values float32 
    5067 Opened cryosparc_P1_J21_class_03_00082_volume.mrc as #3, grid size
    5068 128,128,128, pixel 3.32, shown at level 0.108, step 1, values float32 
    5069 Opened cryosparc_P1_J21_class_02_00082_volume.mrc as #4, grid size
    5070 128,128,128, pixel 3.32, shown at level 0.0537, step 1, values float32 
    5071 Opened cryosparc_P1_J21_class_01_00082_volume.mrc as #5, grid size
    5072 128,128,128, pixel 3.32, shown at level 0.59, step 1, values float32 
    5073 Opened cryosparc_P1_J21_class_00_00082_volume.mrc as #6, grid size
    5074 128,128,128, pixel 3.32, shown at level 0.249, step 1, values float32 
    5075 Opened cryosparc_P1_J21_class_00_00082_volume.mrc z flip as #7, grid size
    5076 128,128,128, pixel 3.32, shown at level 0.618, step 1, values float32 
    5077 Opened cryosparc_P1_J21_class_01_00082_volume.mrc z flip as #8, grid size
    5078 128,128,128, pixel 3.32, shown at level 0.498, step 1, values float32 
    5079 Opened cryosparc_P1_J24_001_volume_map.mrc z flip as #10, grid size
    5080 128,128,128, pixel 3.32, shown at level -0.0329, step 1, values float32 
    5081 Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc as #11, grid size
    5082 128,128,128, pixel 3.35, shown at level 0.147, step 1, values float32 
    5083 Opened NU_cryosparc_P1_J23_002_volume_map_sharp.mrc z flip as #12, grid size
    5084 128,128,128, pixel 3.35, shown at level 0.223, step 1, values float32 
    5085 opened ChimeraX session 
    5086 
    5087 > close session
    5088 
    5089 > open /Users/haandrew/Documents/progress/2025/Cryo-
    5090 > EM/20250506_scRibso_SND1/maps/apo_cryosparc_P2_J306_004_volume_map_sharp.mrc
    5091 > format mrc
    5092 
    5093 Opened apo_cryosparc_P2_J306_004_volume_map_sharp.mrc as #1, grid size
    5094 400,400,400, pixel 0.86, shown at level 0.214, step 2, values float32 
    5095 
    5096 > close session
    5097 
    5098 > open /Users/haandrew/Documents/progress/2026/Cryo-
    5099 > EM/2025-09-25/ecsnd40_scribo/cryosparc_P1_J49_001_volume_map_sharp.mrc
    5100 
    5101 Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #1, grid size 128,128,128,
    5102 pixel 3.32, shown at level 1.35, step 1, values float32 
    5103 
    5104 > open /Users/haandrew/Documents/progress/2026/Cryo-
    5105 > EM/2025-09-25/ecsnd40_scribo/cryosparc_P1_J49_001_volume_map.mrc
    5106 
    5107 Opened cryosparc_P1_J49_001_volume_map.mrc as #2, grid size 128,128,128, pixel
    5108 3.32, shown at level 1.03, step 1, values float32 
    5109 
    5110 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
    5111 > 0/NU refinement /cryosparc_P1_J97_002_volume_map_sharp.mrc"
    5112 
    5113 Opened cryosparc_P1_J97_002_volume_map_sharp.mrc as #3, grid size 128,128,128,
    5114 pixel 3.32, shown at level 0.721, step 1, values float32 
    5115 
    5116 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
    5117 > 0/NU refinement /cryosparc_P1_J97_002_volume_map.mrc"
    5118 
    5119 Opened cryosparc_P1_J97_002_volume_map.mrc as #4, grid size 128,128,128, pixel
    5120 3.32, shown at level 0.721, step 1, values float32 
    5121 
    5122 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
    5123 > 0/NU refinement /cryosparc_P1_J98_001_volume_map_sharp.mrc"
    5124 
    5125 Opened cryosparc_P1_J98_001_volume_map_sharp.mrc as #5, grid size 128,128,128,
    5126 pixel 3.32, shown at level 1.11, step 1, values float32 
    5127 
    5128 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J96_ class
    5129 > 0/NU refinement /cryosparc_P1_J98_001_volume_map.mrc"
    5130 
    5131 Opened cryosparc_P1_J98_001_volume_map.mrc as #6, grid size 128,128,128, pixel
    5132 3.32, shown at level 0.905, step 1, values float32 
    5133 
    5134 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5135 > 1/NU-refinement /cryosparc_P1_J103_001_volume_map_sharp.mrc"
    5136 
    5137 Opened cryosparc_P1_J103_001_volume_map_sharp.mrc as #7, grid size
    5138 128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32 
    5139 
    5140 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5141 > 1/NU-refinement /cryosparc_P1_J103_001_volume_map.mrc"
    5142 
    5143 Opened cryosparc_P1_J103_001_volume_map.mrc as #8, grid size 128,128,128,
    5144 pixel 3.32, shown at level 1.04, step 1, values float32 
    5145 
    5146 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5147 > 1/NU-refinement /cryosparc_P1_J104_001_volume_map_sharp.mrc"
    5148 
    5149 Opened cryosparc_P1_J104_001_volume_map_sharp.mrc as #9, grid size
    5150 128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32 
    5151 
    5152 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5153 > 1/NU-refinement /cryosparc_P1_J104_001_volume_map.mrc"
    5154 
    5155 Opened cryosparc_P1_J104_001_volume_map.mrc as #10, grid size 128,128,128,
    5156 pixel 3.32, shown at level 1.04, step 1, values float32 
    5157 
    5158 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5159 > 1/NU-refinement /cryosparc_P1_J108_001_volume_map_sharp.mrc"
    5160 
    5161 Opened cryosparc_P1_J108_001_volume_map_sharp.mrc as #11, grid size
    5162 128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32 
    5163 
    5164 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/J102_ class
    5165 > 1/NU-refinement /cryosparc_P1_J108_001_volume_map.mrc"
    5166 
    5167 Opened cryosparc_P1_J108_001_volume_map.mrc as #12, grid size 128,128,128,
    5168 pixel 3.32, shown at level 0.863, step 1, values float32 
    5169 
    5170 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
    5171 > 10.1038/8BN3.cif"
    5172 
    5173 8BN3.cif title: 
    5174 Yeast 80S, ES7s delta, eIF5A, Stm1 containing [more info...] 
    5175  
    5176 Chain information for 8BN3.cif #13 
    5177 --- 
    5178 Chain | Description | UniProt 
    5179 1 | 25S ribosomal RNA |   
    5180 2 | 18S ribosomal RNA |   
    5181 3 | 5S ribosomal RNA |   
    5182 4 | 5.8S ribosomal RNA |   
    5183 B | 60S ribosomal protein L1-A | RL1A_YEAST 1-217 
    5184 C0 | Small ribosomal subunit protein eS10A | RS10A_YEAST 1-96 
    5185 C1 | Small ribosomal subunit protein uS17A | RS11A_YEAST 2-156 
    5186 C3 | 40S ribosomal protein S13 | RS13_YEAST 2-151 
    5187 C4 | 40S ribosomal protein S14-B | RS14B_YEAST 11-137 
    5188 C5 | RPS15 isoform 1 | A0A6A5Q6F2_YEASX 8-131 
    5189 C6 | 40S ribosomal protein S16-A | RS16A_YEAST 3-143 
    5190 C7 | ES17 | A0A0J9X224_LACKL 2-126 
    5191 C8 | 40S ribosomal protein S18-A | RS18A_YEAST 2-146 
    5192 C9 | 40S ribosomal protein S19-A | RS19A_YEAST 2-144 
    5193 D0 | RPS20 isoform 1 | A0A6A5PVE9_YEASX 15-121 
    5194 D1 | Small ribosomal subunit protein eS21A | RS21A_YEAST 1-87 
    5195 D2 | RPS22A isoform 1 | A0A6A5PSE9_YEASX 2-130 
    5196 D3 | 40S ribosomal protein S23-A | RS23A_YEAST 2-145 
    5197 D4 | 40S ribosomal protein S24-A | RS24A_YEAST 2-135 
    5198 D5 | 40S ribosomal protein S25 | A0A6A5PZ18_YEASX 36-105 
    5199 D6 | RPS26B isoform 1 | A0A6A5Q0E8_YEASX 2-98 
    5200 D7 | 40S ribosomal protein S27-A | RS27A_YEAST 2-82 
    5201 D8 | RPS28A isoform 1 | A0A6A5Q700_YEASX 5-67 
    5202 D9 | RPS29A isoform 1 | A0A6A5PV92_YEASX 4-56 
    5203 E0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-61 
    5204 E1 | RPS31 isoform 1 | A0A6A5PU37_YEASX 82-152 
    5205 L2 | 60S ribosomal protein L2-A | RL2A_YEAST 2-253 
    5206 L3 | 60S ribosomal protein L3 | A0A6A5Q627_YEASX 2-387 
    5207 L4 | RPL4A isoform 1 | A0A6A5Q3W0_YEASX 2-362 
    5208 L5 | RPL5 isoform 1 | A0A6A5Q0W8_YEASX -2-296 
    5209 L6 | 60S ribosomal protein L6-A |   
    5210 L7 | 60S ribosomal protein L7-A | RL7A_YEAST 23-244 
    5211 L8 | 60S ribosomal protein L8-A | RL8A_YEAST 24-256 
    5212 L9 | RPL9A isoform 1 | A0A8H4FCT7_YEASX 1-189 
    5213 M0 | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 2-219 
    5214 M1 | RPL11B isoform 1 | A0A6A5PYM2_YEASX 6-173 
    5215 M3 | 60S ribosomal protein L13-A | RL13A_YEAST 2-194 
    5216 M4 | 60S ribosomal protein L14-A | RL14A_YEAST 3-138 
    5217 M5 | Ribosomal protein L15 | A0A8H4BX09_YEASX 2-203 
    5218 M6 | 60S ribosomal protein L16-A | RL16A_YEAST 3-199 
    5219 M7 | 60S ribosomal protein L17-A | RL17A_YEAST 2-184 
    5220 M8 | 60S ribosomal protein L18-A | RL18A_YEAST 2-186 
    5221 M9 | 60S ribosomal protein L19-A | RL19A_YEAST 2-189 
    5222 N0 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 
    5223 N1 | 60S ribosomal protein L21-A | RL21A_YEAST 2-160 
    5224 N2 | 60S ribosomal protein L22-A | RL22A_YEAST 9-108 
    5225 N3 | 60S ribosomal protein L23-A | RL23A_YEAST 2-137 
    5226 N4 | RPL24A isoform 1 | A0A6A5PY83_YEASX 1-98 
    5227 N5 | 60S ribosomal protein L25 | RL25_YEAST 22-142 
    5228 N6 | Large ribosomal subunit protein uL24A | RL26A_YEAST 2-127 
    5229 N7 | 60S ribosomal protein L27-A | RL27A_YEAST 2-136 
    5230 N8 | 60S ribosomal protein L28 | RL28_YEAST 2-149 
    5231 N9 | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 2-57 
    5232 O0 | 60S ribosomal protein L30 | RL30_YEAST 9-105 
    5233 O1 | 60S ribosomal protein L31-A | RL31A_YEAST 4-112 
    5234 O2 | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 2-128 
    5235 O3 | 60S ribosomal protein L33-A | RL33A_YEAST 2-107 
    5236 O4 | Large ribosomal subunit protein eL34A | RL34A_YEAST 2-112 
    5237 O5 | 60S ribosomal protein L35-A | RL35A_YEAST 2-120 
    5238 O6 | 60S ribosomal protein L36-A | RL36A_YEAST 2-100 
    5239 O7 | Large ribosomal subunit protein eL37A | RL37A_YEAST 2-87 
    5240 O8 | RPL38 isoform 1 | A0A6A5PUL8_YEASX 2-78 
    5241 O9 | 60S ribosomal protein L39 | RL39_YEAST 2-51 
    5242 P | 60S ribosomal protein L41-A |   
    5243 Q0 | 60S ribosomal protein L40-A | RL40A_YEAST 77-128 
    5244 Q1 | Large ribosomal subunit protein eL41B | RL41B_YEAST 1-25 
    5245 Q2 | 60S ribosomal protein L42-A | RL44A_YEAST 2-106 
    5246 Q3 | 60S ribosomal protein L43-A | RL43A_YEAST 2-92 
    5247 S0 | Small ribosomal subunit protein uS2A | RSSA1_YEAST 2-252 
    5248 S1 | Small ribosomal subunit protein eS1 | A0A6A5PRY4_YEASX 20-233 
    5249 S2 | RPS2 isoform 1 | A0A6A5PWF7_YEASX 34-250 
    5250 S3 | 40S ribosomal protein S3 | A0A6A5Q3Q1_YEASX 3-225 
    5251 S4 | Small ribosomal subunit protein eS4A | RS4A_YEAST 2-261 
    5252 S5 | Rps5p | A0A1L4AA68_YEASX 20-225 
    5253 S6 | Small ribosomal subunit protein eS6A | RS6A_YEAST 1-226 
    5254 S7 | 40S ribosomal protein S7-A | RS7A_YEAST 4-187 
    5255 S8 | 40S ribosomal protein S8 | A0A0J9X221_LACKL 2-200 
    5256 S9 | Small ribosomal subunit protein uS4A | RS9A_YEAST 2-186 
    5257 SM | STM1 isoform 1 | A0A8H4FBL9_YEASX 21-138 
    5258 SR | Small ribosomal subunit protein RACK1 | GBLP_YEAST 2-319 
    5259 eI | Eukaryotic translation initiation factor 5A | A0A8H8ULI0_YEASX 10-154 
    5260  
    5261 Non-standard residues in 8BN3.cif #13 
    5262 --- 
    5263 3HE —
    5264 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione 
    5265 5CT — Hypusine (N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine) 
    5266 K — potassium ion 
    5267 MG — magnesium ion 
    5268 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) 
    5269 ZN — zinc ion 
    5270  
    5271 11 atoms have alternate locations. Control/examine alternate locations with
    5272 Altloc Explorer [start tool...] or the altlocs command. 
    5273 
    5274 > hide #!12 models
    5275 
    5276 > hide #!11 models
    5277 
    5278 > hide #!10 models
    5279 
    5280 > hide #!9 models
    5281 
    5282 > hide #!8 models
    5283 
    5284 > hide #!7 models
    5285 
    5286 > hide #!6 models
    5287 
    5288 > hide #!5 models
    5289 
    5290 > hide #!4 models
    5291 
    5292 > hide #!3 models
    5293 
    5294 > hide #!1 models
    5295 
    5296 > hide #!2 models
    5297 
    5298 > show #!1 models
    5299 
    5300 > select add #1
    5301 
    5302 2 models selected 
    5303 
    5304 > view matrix models #1,1,0,0,-77.885,0,1,0,-82.845,0,0,1,264.99
    5305 
    5306 > ui mousemode right "rotate selected models"
    5307 
    5308 > view matrix models
    5309 > #1,-0.98534,-0.14956,0.082036,364.9,0.15644,-0.60059,0.7841,72.381,-0.067999,0.78544,0.61519,186.94
    5310 
    5311 > view matrix models
    5312 > #1,-0.91922,-0.35372,-0.17299,449.03,0.032347,-0.50569,0.86211,61.831,-0.39242,0.78687,0.47628,285.45
    5313 
    5314 > view matrix models
    5315 > #1,0.78258,-0.59551,0.18149,62.202,-0.61166,-0.6812,0.40229,335.2,-0.11594,-0.42583,-0.89734,780.65
    5316 
    5317 > view matrix models
    5318 > #1,0.60971,-0.76823,0.19512,134.61,-0.79261,-0.5925,0.14392,408.6,0.0050465,-0.2424,-0.97016,729.42
    5319 
    5320 > ui mousemode right "translate selected models"
    5321 
    5322 > view matrix models
    5323 > #1,0.60971,-0.76823,0.19512,179.95,-0.79261,-0.5925,0.14392,459.05,0.0050465,-0.2424,-0.97016,453.45
    5324 
    5325 Must specify one map, got 0 
    5326 
    5327 > fitmap #13 inMap #1
    5328 
    5329 Fit molecule 8BN3.cif (#13) to map cryosparc_P1_J49_001_volume_map_sharp.mrc
    5330 (#1) using 201660 atoms 
    5331 average map value = 0.8785, steps = 100 
    5332 shifted from previous position = 12.8 
    5333 rotated from previous position = 11.1 degrees 
    5334 atoms outside contour = 167040, contour level = 1.3494 
    5335  
    5336 Position of 8BN3.cif (#13) relative to
    5337 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    5338 Matrix rotation and translation 
    5339 0.65584968 -0.74067363 0.14582099 202.50006646 
    5340 -0.73031822 -0.67143512 -0.12573852 501.85180835 
    5341 0.19104054 -0.02403016 -0.98128796 361.42298213 
    5342 Axis 0.90982978 -0.40451043 0.09263410 
    5343 Axis point 0.00000000 290.40740866 178.20792008 
    5344 Rotation angle (degrees) 176.79583012 
    5345 Shift along axis 14.71639185 
    5346  
    5347 
    5348 > hide #!1 models
    5349 
    5350 > show #!1 models
    5351 
    5352 > hide #!13 models
    5353 
    5354 > show #!2 models
    5355 
    5356 > select subtract #1
    5357 
    5358 Nothing selected 
    5359 
    5360 > select add #2
    5361 
    5362 2 models selected 
    5363 
    5364 > view matrix models #2,1,0,0,-196.92,0,1,0,-275.06,0,0,1,20.825
    5365 
    5366 > ui mousemode right "rotate selected models"
    5367 
    5368 > view matrix models
    5369 > #2,0.84944,0.29244,0.43925,-319.5,0.12244,-0.91891,0.37499,37.095,0.51329,-0.26475,-0.81636,346.19
    5370 
    5371 > view matrix models
    5372 > #2,0.09898,-0.8071,0.58206,54.422,0.98403,-0.0075873,-0.17786,-234.39,0.14796,0.59037,0.79346,-96.832
    5373 
    5374 > view matrix models
    5375 > #2,0.096664,-0.80131,0.59038,51.928,0.98625,-0.0027749,-0.16525,-238.57,0.13405,0.59824,0.79003,-94.776
    5376 
    5377 > view matrix models
    5378 > #2,-0.91463,0.31644,0.25165,101.44,-0.21527,-0.90802,0.35938,112.06,0.34222,0.27453,0.89862,-92.734
    5379 
    5380 > view matrix models
    5381 > #2,-0.96898,0.12837,-0.21117,251.19,-0.065215,-0.95704,-0.28253,224.23,-0.23837,-0.25999,0.93573,143.13
    5382 
    5383 > view matrix models
    5384 > #2,0.60659,-0.75834,-0.23869,104.35,-0.76626,-0.6377,0.078712,232.85,-0.2119,0.13515,-0.9679,449.96
    5385 
    5386 > view matrix models
    5387 > #2,0.63412,-0.75563,-0.16406,82.094,-0.74362,-0.6541,0.13849,218.94,-0.21196,0.034178,-0.97668,473.78
    5388 
    5389 > ui mousemode right "translate selected models"
    5390 
    5391 > view matrix models
    5392 > #2,0.63412,-0.75563,-0.16406,53.202,-0.74362,-0.6541,0.13849,244.2,-0.21196,0.034178,-0.97668,471.88
    5393 
    5394 > view matrix models
    5395 > #2,0.63412,-0.75563,-0.16406,237.24,-0.74362,-0.6541,0.13849,468.19,-0.21196,0.034178,-0.97668,430.77
    5396 
    5397 > fitmap #2 inMap #1
    5398 
    5399 Fit map cryosparc_P1_J49_001_volume_map.mrc in map
    5400 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20953 points 
    5401 correlation = 0.9918, correlation about mean = 0.843, overlap = 4.752e+04 
    5402 steps = 124, shift = 18.5, angle = 20.8 degrees 
    5403  
    5404 Position of cryosparc_P1_J49_001_volume_map.mrc (#2) relative to
    5405 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    5406 Matrix rotation and translation 
    5407 0.99999996 -0.00024974 -0.00020887 0.12635677 
    5408 0.00024970 0.99999998 -0.00015085 0.00699286 
    5409 0.00020891 0.00015080 0.99999998 -0.10194766 
    5410 Axis 0.42036197 -0.58217057 0.69596928 
    5411 Axis point 23.16499136 542.83512047 0.00000000 
    5412 Rotation angle (degrees) 0.02055816 
    5413 Shift along axis -0.02190789 
    5414  
    5415 
    5416 > select subtract #2
    5417 
    5418 Nothing selected 
    5419 
    5420 > hide #!2 models
    5421 
    5422 > select add #3
    5423 
    5424 2 models selected 
    5425 
    5426 > show #!3 models
    5427 
    5428 > view matrix models #3,1,0,0,40.953,0,1,0,-307.01,0,0,1,-5.0511
    5429 
    5430 > volume #3 level 0.3894
    5431 
    5432 > ui mousemode right "rotate selected models"
    5433 
    5434 > view matrix models
    5435 > #3,-0.57638,0.7749,-0.25944,269.35,0.048851,0.34959,0.93563,-390.8,0.81572,0.52661,-0.23935,-9.6521
    5436 
    5437 > view matrix models
    5438 > #3,-0.58918,0.71997,-0.36676,307.49,0.027464,0.47149,0.88144,-399.6,0.80753,0.50926,-0.29757,8.7028
    5439 
    5440 > view matrix models
    5441 > #3,-0.81182,0.4742,-0.3407,399.82,-0.17891,0.35341,0.9182,-339.73,0.55582,0.80637,-0.20207,-21.592
    5442 
    5443 > hide #!3 models
    5444 
    5445 > show #!4 models
    5446 
    5447 > select subtract #3
    5448 
    5449 Nothing selected 
    5450 
    5451 > hide #!4 models
    5452 
    5453 > show #!4 models
    5454 
    5455 > hide #!4 models
    5456 
    5457 > show #!5 models
    5458 
    5459 > select add #5
    5460 
    5461 2 models selected 
    5462 
    5463 > view matrix models
    5464 > #5,0.96748,0.20643,-0.14617,-4.8407,-0.13708,0.91357,0.38289,-34.846,0.21257,-0.3504,0.91216,46.725
    5465 
    5466 > ui mousemode right "move picked models"
    5467 
    5468 > view matrix models
    5469 > #5,0.96748,0.20643,-0.14617,-9.6451,-0.13708,0.91357,0.38289,-328.73,0.21257,-0.3504,0.91216,19.868
    5470 
    5471 > view matrix models
    5472 > #5,0.96748,0.20643,-0.14617,-87.654,-0.13708,0.91357,0.38289,-432.87,0.21257,-0.3504,0.91216,-51.34
    5473 
    5474 > view matrix models
    5475 > #5,0.96748,0.20643,-0.14617,-137.77,-0.13708,0.91357,0.38289,-428.28,0.21257,-0.3504,0.91216,-64.854
    5476 
    5477 > ui mousemode right "rotate selected models"
    5478 
    5479 > view matrix models
    5480 > #5,0.91286,0.31669,-0.25766,-125.47,-0.32278,0.94627,0.019499,-319.02,0.24999,0.065367,0.96604,-170.12
    5481 
    5482 > view matrix models
    5483 > #5,0.98317,0.18107,0.024322,-172.03,-0.18141,0.98333,0.012507,-354.74,-0.021651,-0.016709,0.99963,-103.52
    5484 
    5485 > view matrix models
    5486 > #5,0.88751,-0.45408,0.07828,-32.144,0.46072,0.87174,-0.16676,-427.73,0.0074834,0.18407,0.98289,-147.58
    5487 
    5488 > view matrix models
    5489 > #5,0.90317,-0.42922,-0.0066065,-22.52,0.39554,0.83808,-0.37573,-362.74,0.16681,0.33674,0.9267,-200.51
    5490 
    5491 > view matrix models
    5492 > #5,0.89285,-0.44665,0.057694,-30.421,0.44774,0.86654,-0.22051,-412.52,0.048498,0.22272,0.97368,-162.18
    5493 
    5494 > view matrix models
    5495 > #5,0.95827,0.21943,0.18319,-208.53,-0.1872,0.96607,-0.17793,-309.49,-0.21602,0.13621,0.96684,-87.57
    5496 
    5497 > ui mousemode right "move picked models"
    5498 
    5499 > view matrix models
    5500 > #5,0.95827,0.21943,0.18319,-65.576,-0.1872,0.96607,-0.17793,56.394,-0.21602,0.13621,0.96684,-13.032
    5501 
    5502 > view matrix models
    5503 > #5,0.95827,0.21943,0.18319,-411.42,-0.1872,0.96607,-0.17793,53.196,-0.21602,0.13621,0.96684,84.331
    5504 
    5505 > ui mousemode right "rotate selected models"
    5506 
    5507 > view matrix models
    5508 > #5,0.95171,0.22036,0.21376,-416.74,-0.24459,0.96505,0.094094,7.5927,-0.18556,-0.14183,0.97234,134.31
    5509 
    5510 > view matrix models
    5511 > #5,0.86834,-0.46825,-0.16348,-176.73,0.26519,0.7169,-0.64477,109.41,0.41911,0.51653,0.74669,-80.251
    5512 
    5513 > view matrix models
    5514 > #5,0.89131,0.35369,-0.28368,-325.99,-0.39524,0.91269,-0.10389,91.972,0.22216,0.20472,0.95328,-18.51
    5515 
    5516 > view matrix models
    5517 > #5,-0.23191,-0.73124,-0.64149,209.13,0.93481,0.014811,-0.35483,53.103,0.26897,-0.68196,0.68013,213.14
    5518 
    5519 > view matrix models
    5520 > #5,-0.91802,0.35733,-0.17188,27.546,-0.16434,-0.73736,-0.6552,502.16,-0.36086,-0.57325,0.73564,310.46
    5521 
    5522 > view matrix models
    5523 > #5,-0.77973,0.58391,-0.22598,-36.716,-0.46873,-0.78367,-0.40762,522.73,-0.41511,-0.21191,0.88475,215.38
    5524 
    5525 > view matrix models
    5526 > #5,0.73487,0.66946,-0.10857,-395.82,-0.45634,0.36965,-0.80939,366.97,-0.50173,0.64434,0.57715,121.74
    5527 
    5528 > view matrix models
    5529 > #5,0.8822,0.33885,0.32696,-450.77,-0.30763,0.94045,-0.14462,76.579,-0.35649,0.027,0.93391,143.27
    5530 
    5531 > view matrix models
    5532 > #5,0.94884,0.21626,0.23005,-418.75,-0.16928,0.96347,-0.20754,56.282,-0.26653,0.15798,0.95079,93.793
    5533 
    5534 > select up
    5535 
    5536 201660 atoms, 214206 bonds, 18543 residues, 25 models selected 
    5537 
    5538 > select subtract #12
    5539 
    5540 201660 atoms, 214206 bonds, 18543 residues, 23 models selected 
    5541 
    5542 > select subtract #10
    5543 
    5544 201660 atoms, 214206 bonds, 18543 residues, 21 models selected 
    5545 
    5546 > select subtract #9
    5547 
    5548 201660 atoms, 214206 bonds, 18543 residues, 19 models selected 
    5549 
    5550 > select subtract #11
    5551 
    5552 201660 atoms, 214206 bonds, 18543 residues, 17 models selected 
    5553 
    5554 > select add #13
    5555 
    5556 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 20 models
    5557 selected 
    5558 
    5559 > select subtract #13
    5560 
    5561 16 models selected 
    5562 
    5563 > select add #13
    5564 
    5565 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 20 models
    5566 selected 
    5567 
    5568 > select subtract #8
    5569 
    5570 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 18 models
    5571 selected 
    5572 
    5573 > select subtract #7
    5574 
    5575 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 16 models
    5576 selected 
    5577 
    5578 > select subtract #6
    5579 
    5580 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 14 models
    5581 selected 
    5582 
    5583 > select subtract #5
    5584 
    5585 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 12 models
    5586 selected 
    5587 
    5588 > select subtract #4
    5589 
    5590 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 10 models
    5591 selected 
    5592 
    5593 > select subtract #3
    5594 
    5595 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 8 models
    5596 selected 
    5597 
    5598 > select subtract #2
    5599 
    5600 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 6 models
    5601 selected 
    5602 
    5603 > select subtract #1
    5604 
    5605 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 4 models
    5606 selected 
    5607 
    5608 > select add #5
    5609 
    5610 201660 atoms, 214206 bonds, 6055 pseudobonds, 18543 residues, 6 models
    5611 selected 
    5612 
    5613 > select subtract #13
    5614 
    5615 2 models selected 
    5616 
    5617 > volume flip #5
    5618 
    5619 Opened cryosparc_P1_J98_001_volume_map_sharp.mrc z flip as #14, grid size
    5620 128,128,128, pixel 3.32, shown at step 1, values float32 
    5621 
    5622 > volume flip #6
    5623 
    5624 Opened cryosparc_P1_J98_001_volume_map.mrc z flip as #15, grid size
    5625 128,128,128, pixel 3.32, shown at step 1, values float32 
    5626 
    5627 > show #!6 models
    5628 
    5629 > hide #!6 models
    5630 
    5631 > show #!5 models
    5632 
    5633 > hide #!5 models
    5634 
    5635 > select subtract #5
    5636 
    5637 Nothing selected 
    5638 
    5639 > select add #14
    5640 
    5641 2 models selected 
    5642 
    5643 > select subtract #14
    5644 
    5645 Nothing selected 
    5646 
    5647 > hide #!15 models
    5648 
    5649 > select add #14
    5650 
    5651 2 models selected 
    5652 
    5653 > ui mousemode right "translate selected models"
    5654 
    5655 > view matrix models
    5656 > #14,0.94884,0.21626,0.23005,-200.24,-0.16928,0.96347,-0.20754,389.5,-0.26653,0.15798,0.95079,214.06
    5657 
    5658 > view matrix models
    5659 > #14,0.94884,0.21626,0.23005,33.871,-0.16928,0.96347,-0.20754,311.45,-0.26653,0.15798,0.95079,80.444
    5660 
    5661 > view matrix models
    5662 > #14,0.94884,0.21626,0.23005,44.353,-0.16928,0.96347,-0.20754,329.8,-0.26653,0.15798,0.95079,89.212
    5663 
    5664 > ui mousemode right "rotate selected models"
    5665 
    5666 > view matrix models
    5667 > #14,-0.71291,0.41457,-0.56559,517.35,0.053037,0.8361,0.546,151.71,0.69925,0.35925,-0.61805,174.7
    5668 
    5669 > view matrix models
    5670 > #14,-0.58449,0.65424,-0.47994,422.99,0.51395,0.75622,0.40495,101.5,0.62787,-0.0099738,-0.77825,299.56
    5671 
    5672 > view matrix models
    5673 > #14,-0.8665,0.48146,-0.13182,444.67,0.43712,0.85936,0.26538,125.48,0.24105,0.17233,-0.95509,379.75
    5674 
    5675 > ui mousemode right "translate selected models"
    5676 
    5677 > view matrix models
    5678 > #14,-0.8665,0.48146,-0.13182,311.43,0.43712,0.85936,0.26538,-133.04,0.24105,0.17233,-0.95509,298.98
    5679 
    5680 > view matrix models
    5681 > #14,-0.8665,0.48146,-0.13182,301.97,0.43712,0.85936,0.26538,-136.62,0.24105,0.17233,-0.95509,310.84
    5682 
    5683 > fitmap #14 inMap #1
    5684 
    5685 Fit map cryosparc_P1_J98_001_volume_map_sharp.mrc z flip in map
    5686 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20953 points 
    5687 correlation = 0.9505, correlation about mean = 0.4196, overlap = 3.735e+04 
    5688 steps = 120, shift = 5.47, angle = 21.3 degrees 
    5689  
    5690 Position of cryosparc_P1_J98_001_volume_map_sharp.mrc z flip (#14) relative to
    5691 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    5692 Matrix rotation and translation 
    5693 -0.98107258 -0.17597274 -0.08080949 475.02696300 
    5694 0.18036378 -0.98229514 -0.05064740 396.29523914 
    5695 -0.07046621 -0.06426388 0.99544194 29.15789413 
    5696 Axis -0.03816849 -0.02899337 0.99885061 
    5697 Axis point 220.23575583 219.94877769 0.00000000 
    5698 Rotation angle (degrees) 169.72497776 
    5699 Shift along axis -0.49661611 
    5700  
    5701 
    5702 > select subtract #14
    5703 
    5704 Nothing selected 
    5705 
    5706 > hide #!14 models
    5707 
    5708 > show #!15 models
    5709 
    5710 > select add #15
    5711 
    5712 2 models selected 
    5713 
    5714 > view matrix models #15,1,0,0,-30.286,0,1,0,3.6156,0,0,1,-7.5317
    5715 
    5716 > view matrix models #15,1,0,0,54.499,0,1,0,286.05,0,0,1,78.7
    5717 
    5718 > ui mousemode right "rotate selected models"
    5719 
    5720 > view matrix models
    5721 > #15,0.38321,0.55433,-0.73883,223.3,-0.04452,0.81004,0.58468,211.72,0.92259,-0.19116,0.3351,66.212
    5722 
    5723 > view matrix models
    5724 > #15,-0.60794,0.79331,0.032641,217.8,0.79308,0.60477,0.072661,187.69,0.037902,0.070061,-0.99682,475.37
    5725 
    5726 > view matrix models
    5727 > #15,-0.76941,-0.038666,0.63758,295.68,-0.043359,0.99903,0.0082611,293.51,-0.63728,-0.021289,-0.77034,586.7
    5728 
    5729 > view matrix models
    5730 > #15,-0.82432,0.035511,0.565,307.03,0.28199,0.89116,0.3554,175.4,-0.49089,0.45229,-0.74462,453.42
    5731 
    5732 > view matrix models
    5733 > #15,-0.73021,0.40214,0.55234,214.67,0.61034,0.74726,0.26284,156.35,-0.30705,0.52905,-0.7911,409.24
    5734 
    5735 > view matrix models
    5736 > #15,-0.99085,0.12541,0.049984,431.11,0.13499,0.92425,0.35714,198.71,-0.0014104,0.36062,-0.93271,410.24
    5737 
    5738 > view matrix models
    5739 > #15,-0.79071,0.40291,0.46091,246.24,0.50008,0.85939,0.10664,188.9,-0.35314,0.31482,-0.88101,481.78
    5740 
    5741 > ui mousemode right "translate selected models"
    5742 
    5743 > view matrix models
    5744 > #15,-0.79071,0.40291,0.46091,159.61,0.50008,0.85939,0.10664,-103.2,-0.35314,0.31482,-0.88101,387.36
    5745 
    5746 > fitmap #15 inMap #1
    5747 
    5748 Fit map cryosparc_P1_J98_001_volume_map.mrc z flip in map
    5749 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20969 points 
    5750 correlation = 0.9542, correlation about mean = 0.4157, overlap = 2.885e+04 
    5751 steps = 136, shift = 17.4, angle = 23.8 degrees 
    5752  
    5753 Position of cryosparc_P1_J98_001_volume_map.mrc z flip (#15) relative to
    5754 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    5755 Matrix rotation and translation 
    5756 -0.98115236 -0.17557997 -0.08069518 474.87459910 
    5757 0.17995399 -0.98237696 -0.05051806 396.33801347 
    5758 -0.07040312 -0.06408733 0.99545779 29.12375621 
    5759 Axis -0.03812219 -0.02891500 0.99885465 
    5760 Axis point 220.19725747 219.91262044 0.00000000 
    5761 Rotation angle (degrees) 169.74841221 
    5762 Shift along axis -0.47297300 
    5763  
    5764 
    5765 > hide #!5-6 target m
    5766 
    5767 > hide #!15 models
    5768 
    5769 > show #!7 models
    5770 
    5771 > select add #7
    5772 
    5773 4 models selected 
    5774 
    5775 > view matrix models
    5776 > #7,1,0,0,139.29,0,1,0,237.58,0,0,1,70.239,#15,-0.7502,0.63514,0.18384,309.98,0.66091,0.712,0.23716,89.6,0.01973,0.29942,-0.95392,401.76
    5777 
    5778 > ui mousemode right "rotate selected models"
    5779 
    5780 > view matrix models
    5781 > #7,0.93246,0.33104,-0.1447,117.53,-0.3533,0.91924,-0.17369,364.71,0.075513,0.21308,0.97411,17.029,#15,-0.4836,0.78461,0.38796,179.73,0.86916,0.37811,0.31874,110.8,0.1034,0.49134,-0.86481,321.33
    5782 
    5783 > view matrix models
    5784 > #7,0.90255,0.41887,-0.099714,96.482,-0.43047,0.88295,-0.18734,391.06,0.0095722,0.21201,0.97722,30.361,#15,-0.40222,0.84163,0.36039,155.49,0.9028,0.29916,0.30896,124.82,0.15222,0.44963,-0.88015,324.59
    5785 
    5786 > ui mousemode right "translate selected models"
    5787 
    5788 > view matrix models
    5789 > #7,0.90255,0.41887,-0.099714,-59.667,-0.43047,0.88295,-0.18734,129.28,0.0095722,0.21201,0.97722,-64.029,#15,-0.40222,0.84163,0.36039,-0.6584,0.9028,0.29916,0.30896,-136.96,0.15222,0.44963,-0.88015,230.2
    5790 
    5791 > view matrix models
    5792 > #7,0.90255,0.41887,-0.099714,32.414,-0.43047,0.88295,-0.18734,453.43,0.0095722,0.21201,0.97722,139.71,#15,-0.40222,0.84163,0.36039,91.423,0.9028,0.29916,0.30896,187.19,0.15222,0.44963,-0.88015,433.95
    5793 
    5794 > view matrix models
    5795 > #7,0.90255,0.41887,-0.099714,28.655,-0.43047,0.88295,-0.18734,445.31,0.0095722,0.21201,0.97722,119.74,#15,-0.40222,0.84163,0.36039,87.664,0.9028,0.29916,0.30896,179.08,0.15222,0.44963,-0.88015,413.97
    5796 
    5797 > ui mousemode right "rotate selected models"
    5798 
    5799 > view matrix models
    5800 > #7,0.99429,-0.062625,0.086398,66.861,0.081239,0.96923,-0.23237,330.61,-0.069187,0.23807,0.96878,132.74,#15,-0.7856,0.61279,0.085524,274.48,0.57505,0.67211,0.46646,124.01,0.22836,0.41563,-0.8804,406.87
    5801 
    5802 > ui mousemode right "translate selected models"
    5803 
    5804 > view matrix models
    5805 > #7,0.99429,-0.062625,0.086398,-17.957,0.081239,0.96923,-0.23237,29.936,-0.069187,0.23807,0.96878,-50.171,#15,-0.7856,0.61279,0.085524,189.66,0.57505,0.67211,0.46646,-176.66,0.22836,0.41563,-0.8804,223.97
    5806 
    5807 > fitmap #7 inMap #1
    5808 
    5809 Fit map cryosparc_P1_J103_001_volume_map_sharp.mrc in map
    5810 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20957 points 
    5811 correlation = 0.6005, correlation about mean = 0.05396, overlap = 1.802e+04 
    5812 steps = 148, shift = 14.4, angle = 17.8 degrees 
    5813  
    5814 Position of cryosparc_P1_J103_001_volume_map_sharp.mrc (#7) relative to
    5815 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    5816 Matrix rotation and translation 
    5817 0.76581617 -0.61952749 0.17236961 147.91850026 
    5818 -0.62449626 -0.78043353 -0.03046179 517.53025941 
    5819 0.15339494 -0.08431604 -0.98456122 406.01213584 
    5820 Axis -0.93961909 0.33105949 -0.08669243 
    5821 Axis point 0.00000000 287.91796449 192.22828107 
    5822 Rotation angle (degrees) 178.35782179 
    5823 Shift along axis -2.85192000 
    5824  
    5825 
    5826 > hide #!7 models
    5827 
    5828 > select subtract #7
    5829 
    5830 2 models selected 
    5831 
    5832 > volume flip #7
    5833 
    5834 Opened cryosparc_P1_J103_001_volume_map_sharp.mrc z flip as #16, grid size
    5835 128,128,128, pixel 3.32, shown at step 1, values float32 
    5836 
    5837 > volume flip #8
    5838 
    5839 Opened cryosparc_P1_J103_001_volume_map.mrc z flip as #17, grid size
    5840 128,128,128, pixel 3.32, shown at step 1, values float32 
    5841 
    5842 > select subtract #15
    5843 
    5844 Nothing selected 
    5845 
    5846 > select add #16
    5847 
    5848 2 models selected 
    5849 
    5850 > select add #17
    5851 
    5852 4 models selected 
    5853 
    5854 > view matrix models
    5855 > #16,0.97661,0.20537,-0.06361,295.5,-0.2149,0.94132,-0.26027,79.798,0.0064257,0.26785,0.96344,-42.97,#17,1,0,0,343.73,0,1,0,-13.806,0,0,1,22.177
    5856 
    5857 > select subtract #16
    5858 
    5859 2 models selected 
    5860 
    5861 > select subtract #17
    5862 
    5863 Nothing selected 
    5864 
    5865 > hide #!17 models
    5866 
    5867 > select add #16
    5868 
    5869 2 models selected 
    5870 
    5871 > view matrix models
    5872 > #16,0.97661,0.20537,-0.06361,494.67,-0.2149,0.94132,-0.26027,42.666,0.0064257,0.26785,0.96344,-125.77
    5873 
    5874 > view matrix models
    5875 > #16,0.97661,0.20537,-0.06361,539.22,-0.2149,0.94132,-0.26027,-157.44,0.0064257,0.26785,0.96344,-126.98
    5876 
    5877 > view matrix models
    5878 > #16,0.97661,0.20537,-0.06361,136.85,-0.2149,0.94132,-0.26027,-224.63,0.0064257,0.26785,0.96344,-222.21
    5879 
    5880 > view matrix models
    5881 > #16,0.97661,0.20537,-0.06361,-269,-0.2149,0.94132,-0.26027,-278.64,0.0064257,0.26785,0.96344,-341.12
    5882 
    5883 > view matrix models
    5884 > #16,0.97661,0.20537,-0.06361,26.1,-0.2149,0.94132,-0.26027,-225.38,0.0064257,0.26785,0.96344,-277.91
    5885 
    5886 > view matrix models
    5887 > #16,0.97661,0.20537,-0.06361,-159.13,-0.2149,0.94132,-0.26027,-168.48,0.0064257,0.26785,0.96344,-246.2
    5888 
    5889 > ui mousemode right "rotate selected models"
    5890 
    5891 > view matrix models
    5892 > #16,-0.98171,0.0053892,0.19029,237.31,0.096549,0.87559,0.47331,-373.57,-0.16406,0.48302,-0.8601,127.03
    5893 
    5894 > view matrix models
    5895 > #16,-0.84457,0.49586,0.20204,107.34,0.53544,0.77975,0.3245,-414.86,0.0033646,0.38224,-0.92406,125.72
    5896 
    5897 > ui mousemode right "translate selected models"
    5898 
    5899 > view matrix models
    5900 > #16,-0.84457,0.49586,0.20204,299.51,0.53544,0.77975,0.3245,-395.68,0.0033646,0.38224,-0.92406,143.4
    5901 
    5902 > view matrix models
    5903 > #16,-0.84457,0.49586,0.20204,214.76,0.53544,0.77975,0.3245,-156.89,0.0033646,0.38224,-0.92406,305.37
    5904 
    5905 > fitmap #16 inMap #1
    5906 
    5907 Fit map cryosparc_P1_J103_001_volume_map_sharp.mrc z flip in map
    5908 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20957 points 
    5909 correlation = 0.9755, correlation about mean = 0.5526, overlap = 5.308e+04 
    5910 steps = 92, shift = 5.53, angle = 9.25 degrees 
    5911  
    5912 Position of cryosparc_P1_J103_001_volume_map_sharp.mrc z flip (#16) relative
    5913 to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    5914 Matrix rotation and translation 
    5915 -0.96683848 -0.25490298 -0.01574208 475.52480895 
    5916 0.25537198 -0.96564058 -0.04820192 375.16923347 
    5917 -0.00291438 -0.05062355 0.99871355 13.27964100 
    5918 Axis -0.00474420 -0.02513058 0.99967292 
    5919 Axis point 213.44254341 218.61395610 0.00000000 
    5920 Rotation angle (degrees) 165.21332178 
    5921 Shift along axis 1.59109330 
    5922  
    5923 
    5924 > hide #!16 models
    5925 
    5926 > select subtract #16
    5927 
    5928 Nothing selected 
    5929 
    5930 > show #!17 models
    5931 
    5932 > select add #17
    5933 
    5934 2 models selected 
    5935 
    5936 > view matrix models #17,1,0,0,458.15,0,1,0,-248.2,0,0,1,128.02
    5937 
    5938 > view matrix models #17,1,0,0,330.11,0,1,0,-505.1,0,0,1,-181.44
    5939 
    5940 > view matrix models #17,1,0,0,-110.63,0,1,0,-103.45,0,0,1,-51.961
    5941 
    5942 > view matrix models #17,1,0,0,-220.22,0,1,0,-330.26,0,0,1,-96.103
    5943 
    5944 > ui mousemode right "rotate selected models"
    5945 
    5946 > view matrix models
    5947 > #17,-0.99562,0.075776,-0.05482,191.89,0.046339,0.90881,0.41463,-408.19,0.08124,0.41027,-0.90834,203.05
    5948 
    5949 > view matrix models
    5950 > #17,-0.72947,0.68402,-0.00018359,2.5397,0.66833,0.71279,0.21277,-456.18,0.14567,0.15508,-0.9771,255.37
    5951 
    5952 > ui mousemode right "translate selected models"
    5953 
    5954 > view matrix models
    5955 > #17,-0.72947,0.68402,-0.00018359,283.49,0.66833,0.71279,0.21277,-354.27,0.14567,0.15508,-0.9771,306.93
    5956 
    5957 > view matrix models
    5958 > #17,-0.72947,0.68402,-0.00018359,147.46,0.66833,0.71279,0.21277,-183.03,0.14567,0.15508,-0.9771,346.62
    5959 
    5960 > fitmap #17 inMap #1
    5961 
    5962 Fit map cryosparc_P1_J103_001_volume_map.mrc z flip in map
    5963 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20954 points 
    5964 correlation = 0.9824, correlation about mean = 0.608, overlap = 3.677e+04 
    5965 steps = 152, shift = 63.8, angle = 14.7 degrees 
    5966  
    5967 Position of cryosparc_P1_J103_001_volume_map.mrc z flip (#17) relative to
    5968 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    5969 Matrix rotation and translation 
    5970 -0.96677903 -0.25511364 -0.01597928 475.61770509 
    5971 0.25559328 -0.96559949 -0.04785078 375.06880806 
    5972 -0.00322220 -0.05034533 0.99872667 13.27362394 
    5973 Axis -0.00488292 -0.02497117 0.99967625 
    5974 Axis point 213.47529806 218.59546722 0.00000000 
    5975 Rotation angle (degrees) 165.20056891 
    5976 Shift along axis 1.58101585 
    5977  
    5978 
    5979 > hide #!17 models
    5980 
    5981 > select subtract #17
    5982 
    5983 Nothing selected 
    5984 
    5985 > show #!9 models
    5986 
    5987 > select add #9
    5988 
    5989 2 models selected 
    5990 
    5991 > view matrix models #9,1,0,0,66.813,0,1,0,132.93,0,0,1,25.089
    5992 
    5993 > view matrix models #9,1,0,0,-5.4711,0,1,0,-10.379,0,0,1,-14.373
    5994 
    5995 > view matrix models #9,1,0,0,213.16,0,1,0,-70.987,0,0,1,35.886
    5996 
    5997 > hide #!9 models
    5998 
    5999 > select subtract #9
    6000 
    6001 Nothing selected 
    6002 
    6003 > volume flip #9
    6004 
    6005 Opened cryosparc_P1_J104_001_volume_map_sharp.mrc z flip as #18, grid size
    6006 128,128,128, pixel 3.32, shown at step 1, values float32 
    6007 
    6008 > volume flip #10
    6009 
    6010 Opened cryosparc_P1_J104_001_volume_map.mrc z flip as #19, grid size
    6011 128,128,128, pixel 3.32, shown at step 1, values float32 
    6012 
    6013 > hide #!18 models
    6014 
    6015 > hide #!19 models
    6016 
    6017 > show #!11 models
    6018 
    6019 > show #!12 models
    6020 
    6021 > hide #!11 models
    6022 
    6023 > select add #12
    6024 
    6025 2 models selected 
    6026 
    6027 > view matrix models #12,1,0,0,268.63,0,1,0,-66.479,0,0,1,23.067
    6028 
    6029 > volume #12 level 0.5398
    6030 
    6031 > view matrix models #12,1,0,0,81.495,0,1,0,87.616,0,0,1,-20.101
    6032 
    6033 > view matrix models #12,1,0,0,194.71,0,1,0,264.02,0,0,1,105.21
    6034 
    6035 > ui mousemode right "rotate selected models"
    6036 
    6037 > view matrix models
    6038 > #12,-0.10029,-0.84368,-0.5274,717.92,0.76343,0.27468,-0.58458,398.49,0.63806,-0.46126,0.61654,162.58
    6039 
    6040 > view matrix models
    6041 > #12,0.81932,0.56752,0.081469,83.468,0.53406,-0.70377,-0.46849,645.77,-0.20854,0.42735,-0.8797,435.7
    6042 
    6043 > ui mousemode right "translate selected models"
    6044 
    6045 > view matrix models
    6046 > #12,0.81932,0.56752,0.081469,-105.79,0.53406,-0.70377,-0.46849,334.74,-0.20854,0.42735,-0.8797,319.82
    6047 
    6048 > fitmap #12 inMap #1
    6049 
    6050 Fit map cryosparc_P1_J108_001_volume_map.mrc in map
    6051 cryosparc_P1_J49_001_volume_map_sharp.mrc using 50668 points 
    6052 correlation = 0.581, correlation about mean = 0.06365, overlap = 1.908e+04 
    6053 steps = 88, shift = 12.6, angle = 9.87 degrees 
    6054  
    6055 Position of cryosparc_P1_J108_001_volume_map.mrc (#12) relative to
    6056 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    6057 Matrix rotation and translation 
    6058 0.06114525 0.83113550 0.55269794 -90.61961165 
    6059 -0.92970330 -0.15406746 0.33453694 367.12907629 
    6060 0.36319830 -0.53430045 0.76328894 98.33563139 
    6061 Axis -0.44044208 0.09606357 -0.89262678 
    6062 Axis point 105.13661117 234.46921583 0.00000000 
    6063 Rotation angle (degrees) 99.48658293 
    6064 Shift along axis -12.59659896 
    6065  
    6066 
    6067 > hide #!12 models
    6068 
    6069 > show #!12 models
    6070 
    6071 > select subtract #12
    6072 
    6073 Nothing selected 
    6074 
    6075 > hide #!12 models
    6076 
    6077 > volume flip #11
    6078 
    6079 Opened cryosparc_P1_J108_001_volume_map_sharp.mrc z flip as #20, grid size
    6080 128,128,128, pixel 3.32, shown at step 1, values float32 
    6081 
    6082 > volume flip #12
    6083 
    6084 Opened cryosparc_P1_J108_001_volume_map.mrc z flip as #21, grid size
    6085 128,128,128, pixel 3.32, shown at step 1, values float32 
    6086 
    6087 > hide #!20 models
    6088 
    6089 > hide #!21 models
    6090 
    6091 > color #21 #ff8ad8ff models
    6092 
    6093 > color #20 #8efa00ff models
    6094 
    6095 > show #!20 models
    6096 
    6097 > show #!21 models
    6098 
    6099 > select add #20
    6100 
    6101 2 models selected 
    6102 
    6103 > select add #21
    6104 
    6105 4 models selected 
    6106 
    6107 > view matrix models
    6108 > #20,1,0,0,53.202,0,1,0,-7.5989,0,0,1,190.93,#21,0.82238,0.52086,0.22892,-84.958,0.55466,-0.64438,-0.52644,319.91,-0.12669,0.5599,-0.81882,459.54
    6109 
    6110 > view matrix models
    6111 > #20,1,0,0,67.39,0,1,0,-20.44,0,0,1,252.74,#21,0.82238,0.52086,0.22892,-70.77,0.55466,-0.64438,-0.52644,307.07,-0.12669,0.5599,-0.81882,521.35
    6112 
    6113 > hide #!21 models
    6114 
    6115 > select subtract #21
    6116 
    6117 2 models selected 
    6118 
    6119 > select subtract #20
    6120 
    6121 Nothing selected 
    6122 
    6123 > color #20 #009051ff models
    6124 
    6125 > ui mousemode right "rotate selected models"
    6126 
    6127 > select add #20
    6128 
    6129 2 models selected 
    6130 
    6131 > view matrix models
    6132 > #20,0.27636,0.8512,-0.44618,112.44,-0.80283,0.45968,0.37969,170.16,0.52829,0.25328,0.8104,137.01
    6133 
    6134 > view matrix models
    6135 > #20,-0.65371,-0.13935,0.7438,253.23,0.71992,-0.41741,0.55452,37.04,0.2332,0.89797,0.37319,144.31
    6136 
    6137 > view matrix models
    6138 > #20,0.46888,-0.87548,0.11701,336.56,0.75284,0.46541,0.46543,-145.06,-0.46193,-0.13015,0.87731,395.51
    6139 
    6140 > view matrix models
    6141 > #20,-0.21802,-0.91836,0.33028,430.92,0.9553,-0.27006,-0.12031,104.18,0.19968,0.28929,0.93618,164.59
    6142 
    6143 > ui mousemode right "translate selected models"
    6144 
    6145 > view matrix models
    6146 > #20,-0.21802,-0.91836,0.33028,360.58,0.9553,-0.27006,-0.12031,68.863,0.19968,0.28929,0.93618,-101.25
    6147 
    6148 > fitmap #20 inMap #1
    6149 
    6150 Fit map cryosparc_P1_J108_001_volume_map_sharp.mrc z flip in map
    6151 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20960 points 
    6152 correlation = 0.9607, correlation about mean = 0.5065, overlap = 3.58e+04 
    6153 steps = 164, shift = 19, angle = 31.6 degrees 
    6154  
    6155 Position of cryosparc_P1_J108_001_volume_map_sharp.mrc z flip (#20) relative
    6156 to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    6157 Matrix rotation and translation 
    6158 -0.69739435 -0.66663667 0.26312861 446.13461962 
    6159 -0.64054491 0.41508898 -0.64606760 393.09938307 
    6160 0.32147057 -0.61910959 -0.71649144 437.78580544 
    6161 Axis 0.38864826 -0.84110432 0.37615961 
    6162 Axis point 309.40142148 0.00000000 311.36461851 
    6163 Rotation angle (degrees) 178.01248299 
    6164 Shift along axis 7.42918773 
    6165  
    6166 
    6167 > hide #!20 models
    6168 
    6169 > select subtract #20
    6170 
    6171 Nothing selected 
    6172 
    6173 > show #!21 models
    6174 
    6175 > select add #21
    6176 
    6177 2 models selected 
    6178 
    6179 > ui mousemode right "rotate selected models"
    6180 
    6181 > view matrix models
    6182 > #21,-0.21616,-0.86898,0.44513,410.44,0.96297,-0.26498,-0.049669,34.863,0.16111,0.41792,0.89409,126.05
    6183 
    6184 > view matrix models
    6185 > #21,-0.11346,-0.8849,0.45175,392.11,0.98636,-0.15491,-0.05571,6.1447,0.11928,0.43927,0.8904,130.3
    6186 
    6187 > ui mousemode right "translate selected models"
    6188 
    6189 > view matrix models
    6190 > #21,-0.11346,-0.8849,0.45175,337,0.98636,-0.15491,-0.05571,11.919,0.11928,0.43927,0.8904,-124.26
    6191 
    6192 > fitmap #21 inMap #1
    6193 
    6194 Fit map cryosparc_P1_J108_001_volume_map.mrc z flip in map
    6195 cryosparc_P1_J49_001_volume_map_sharp.mrc using 50668 points 
    6196 correlation = 0.9363, correlation about mean = 0.5935, overlap = 4.442e+04 
    6197 steps = 152, shift = 35.3, angle = 21.8 degrees 
    6198  
    6199 Position of cryosparc_P1_J108_001_volume_map.mrc z flip (#21) relative to
    6200 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    6201 Matrix rotation and translation 
    6202 -0.69726654 -0.66670565 0.26329245 446.12009666 
    6203 -0.64067666 0.41490792 -0.64605324 393.19130505 
    6204 0.32148523 -0.61915665 -0.71644417 437.79327448 
    6205 Axis 0.38873206 -0.84105079 0.37619271 
    6206 Axis point 309.45157406 0.00000000 311.39100265 
    6207 Rotation angle (degrees) 178.01744087 
    6208 Shift along axis 7.42196968 
    6209  
    6210 
    6211 > hide #!21 models
    6212 
    6213 > select subtract #21
    6214 
    6215 Nothing selected 
    6216 
    6217 > show #!19 models
    6218 
    6219 > select add #19
    6220 
    6221 2 models selected 
    6222 
    6223 > view matrix models #19,1,0,0,-42.02,0,1,0,18.881,0,0,1,314.82
    6224 
    6225 > ui mousemode right "rotate selected models"
    6226 
    6227 > view matrix models
    6228 > #19,0.92212,-0.028777,0.38583,-100.57,-0.24883,0.71952,0.64836,-7.1838,-0.29627,-0.69388,0.65632,591.17
    6229 
    6230 > view matrix models
    6231 > #19,0.99752,0.017141,0.068256,-59.305,-0.025979,0.99107,0.13078,-1.2232,-0.065404,-0.13223,0.98906,357.94
    6232 
    6233 > view matrix models
    6234 > #19,0.9668,-0.13527,-0.21679,38.066,0.016927,0.88043,-0.47387,139.06,0.25497,0.45447,0.85349,198.86
    6235 
    6236 > view matrix models
    6237 > #19,-0.49114,0.42795,0.75871,27.093,0.85871,0.38412,0.33922,-108.28,-0.14627,0.81812,-0.55614,505.13
    6238 
    6239 > view matrix models
    6240 > #19,-0.47256,-0.0534,0.87968,96.019,0.65138,0.65118,0.38945,-129.43,-0.59362,0.75704,-0.27294,552.87
    6241 
    6242 > view matrix models
    6243 > #19,-0.57038,0.12072,0.81246,95.281,0.42332,0.89086,0.16482,-82.984,-0.70389,0.43794,-0.55923,701.35
    6244 
    6245 > view matrix models
    6246 > #19,-0.65223,0.20302,0.73033,113.03,0.25959,0.96503,-0.036441,-21.272,-0.71219,0.16582,-0.68212,784.4
    6247 
    6248 > view matrix models
    6249 > #19,-0.58584,0.1396,0.79831,97.665,0.39097,0.91153,0.12751,-72.533,-0.70988,0.38682,-0.58859,719.2
    6250 
    6251 > view matrix models
    6252 > #19,-0.50292,0.01387,0.86422,91.957,0.57494,0.75195,0.32251,-119.79,-0.64538,0.65908,-0.38615,607.55
    6253 
    6254 > view matrix models
    6255 > #19,-0.46848,-0.063909,0.88116,96.988,0.66228,0.63471,0.39815,-130.2,-0.58473,0.7701,-0.25503,544.57
    6256 
    6257 > view matrix models
    6258 > #19,-0.57142,0.43933,0.69316,55.504,0.79737,0.497,0.34233,-118.99,-0.1941,0.74832,-0.63431,545.88
    6259 
    6260 > view matrix models
    6261 > #19,-0.61617,0.64013,0.45888,73.124,0.74524,0.66237,0.0767,-86,-0.25485,0.38923,-0.88518,684.62
    6262 
    6263 > ui mousemode right "translate selected models"
    6264 
    6265 > view matrix models
    6266 > #19,-0.61617,0.64013,0.45888,101.76,0.74524,0.66237,0.0767,-131.88,-0.25485,0.38923,-0.88518,367.72
    6267 
    6268 > fitmap #19 inMap #1
    6269 
    6270 Fit map cryosparc_P1_J104_001_volume_map.mrc z flip in map
    6271 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20967 points 
    6272 correlation = 0.9772, correlation about mean = 0.6042, overlap = 3.685e+04 
    6273 steps = 116, shift = 25.4, angle = 15.8 degrees 
    6274  
    6275 Position of cryosparc_P1_J104_001_volume_map.mrc z flip (#19) relative to
    6276 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    6277 Matrix rotation and translation 
    6278 -0.98947893 -0.14464668 0.00295998 453.74695953 
    6279 0.14458261 -0.98936543 -0.01587127 396.30669175 
    6280 0.00522423 -0.01527633 0.99986965 2.25096215 
    6281 Axis 0.00205693 -0.00782830 0.99996724 
    6282 Axis point 212.46654917 214.65452905 0.00000000 
    6283 Rotation angle (degrees) 171.68476065 
    6284 Shift along axis 0.08180356 
    6285  
    6286 
    6287 > select subtract #19
    6288 
    6289 Nothing selected 
    6290 
    6291 > hide #!19 models
    6292 
    6293 > show #!18 models
    6294 
    6295 > select add #18
    6296 
    6297 2 models selected 
    6298 
    6299 > view matrix models #18,1,0,0,17.023,0,1,0,-45.334,0,0,1,132.41
    6300 
    6301 > view matrix models #18,1,0,0,61.372,0,1,0,-65.864,0,0,1,274.99
    6302 
    6303 > ui mousemode right "move picked models"
    6304 
    6305 > view matrix models #18,1,0,0,70.962,0,1,0,-60.184,0,0,1,300.78
    6306 
    6307 > ui mousemode right "move picked models"
    6308 
    6309 > view matrix models #18,1,0,0,68.685,0,1,0,-62.07,0,0,1,294.92
    6310 
    6311 > ui mousemode right "rotate selected models"
    6312 
    6313 > view matrix models
    6314 > #18,-0.74784,0.64006,-0.17624,344.71,0.61749,0.76812,0.16939,-181.02,0.24379,0.017855,-0.96966,655.34
    6315 
    6316 > view matrix models
    6317 > #18,-0.21411,0.5917,0.77721,40.569,0.73477,0.62183,-0.27099,-83.023,-0.64364,0.51305,-0.5679,657.09
    6318 
    6319 > view matrix models
    6320 > #18,-0.72069,0.48857,0.49183,228.93,0.63686,0.74687,0.19129,-185.39,-0.27387,0.45109,-0.84942,650.97
    6321 
    6322 > ui mousemode right "translate selected models"
    6323 
    6324 > view matrix models
    6325 > #18,-0.72069,0.48857,0.49183,291.93,0.63686,0.74687,0.19129,-210.76,-0.27387,0.45109,-0.84942,358.77
    6326 
    6327 > view matrix models
    6328 > #18,-0.72069,0.48857,0.49183,179.04,0.63686,0.74687,0.19129,-177.75,-0.27387,0.45109,-0.84942,251.83
    6329 
    6330 > view matrix models
    6331 > #18,-0.72069,0.48857,0.49183,128.54,0.63686,0.74687,0.19129,-142.08,-0.27387,0.45109,-0.84942,334.07
    6332 
    6333 > fitmap #18 inMap #1
    6334 
    6335 Fit map cryosparc_P1_J104_001_volume_map_sharp.mrc z flip in map
    6336 cryosparc_P1_J49_001_volume_map_sharp.mrc using 20955 points 
    6337 correlation = 0.9714, correlation about mean = 0.5654, overlap = 5.321e+04 
    6338 steps = 128, shift = 4.2, angle = 19.3 degrees 
    6339  
    6340 Position of cryosparc_P1_J104_001_volume_map_sharp.mrc z flip (#18) relative
    6341 to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    6342 Matrix rotation and translation 
    6343 -0.98953295 -0.14427756 0.00292143 453.69602792 
    6344 0.14421537 -0.98942289 -0.01562912 396.34010493 
    6345 0.00514547 -0.01504421 0.99987359 2.19822617 
    6346 Axis 0.00202739 -0.00770889 0.99996823 
    6347 Axis point 212.47705459 214.62658713 0.00000000 
    6348 Rotation angle (degrees) 171.70608844 
    6349 Shift along axis 0.06263310 
    6350  
    6351 
    6352 > select subtract #18
    6353 
    6354 Nothing selected 
    6355 
    6356 > hide #!18 models
    6357 
    6358 > show #!17 models
    6359 
    6360 > hide #!17 models
    6361 
    6362 > volume #1 level 0.7168
    6363 
    6364 > surface dust #1 size 33.2
    6365 
    6366 > hide #!1 models
    6367 
    6368 > show #!14 models
    6369 
    6370 > show #!15 models
    6371 
    6372 > hide #!14 models
    6373 
    6374 > hide #!15 models
    6375 
    6376 > show #!15 models
    6377 
    6378 > show #!14 models
    6379 
    6380 > fitmap #15 inMap #14
    6381 
    6382 Fit map cryosparc_P1_J98_001_volume_map.mrc z flip in map
    6383 cryosparc_P1_J98_001_volume_map_sharp.mrc z flip using 20969 points 
    6384 correlation = 0.9933, correlation about mean = 0.872, overlap = 3.502e+04 
    6385 steps = 124, shift = 27.2, angle = 14.9 degrees 
    6386  
    6387 Position of cryosparc_P1_J98_001_volume_map.mrc z flip (#15) relative to
    6388 cryosparc_P1_J98_001_volume_map_sharp.mrc z flip (#14) coordinates: 
    6389 Matrix rotation and translation 
    6390 1.00000001 -0.00004692 -0.00002196 -0.00759824 
    6391 0.00004692 0.99999999 0.00012920 -0.05710014 
    6392 0.00002196 -0.00012920 1.00000000 0.00947988 
    6393 Axis -0.92817399 -0.15775244 0.33705670 
    6394 Axis point 0.00000000 23.11236043 418.44568493 
    6395 Rotation angle (degrees) 0.00797543 
    6396 Shift along axis 0.01925543 
    6397  
    6398 
    6399 > volume #14 level 0.5902
    6400 
    6401 > volume #15 level 0.2948
    6402 
    6403 > surface dust #14 size 33.2
    6404 
    6405 > surface dust #15 size 33.2
    6406 
    6407 > hide #!14 models
    6408 
    6409 > hide #!15 models
    6410 
    6411 > show #!15 models
    6412 
    6413 > hide #!15 models
    6414 
    6415 > show #!2 models
    6416 
    6417 > show #!1 models
    6418 
    6419 > hide #!2 models
    6420 
    6421 > volume #1 level 0.3519
    6422 
    6423 > ui mousemode right "mark point"
    6424 
    6425 > marker #22 position 156.8,222.4,140.8 color #d783ff radius 5
    6426 
    6427 > marker #22 position 154.5,221.6,141 color #d783ff radius 5
    6428 
    6429 > hide #!1 models
    6430 
    6431 > ui mousemode right "delete markers"
    6432 
    6433 > hide #22 target m
    6434 
    6435 > show #!1 models
    6436 
    6437 > select add #22
    6438 
    6439 3 atoms, 3 residues, 1 model selected 
    6440 
    6441 > select subtract #22
    6442 
    6443 Nothing selected 
    6444 
    6445 > show #22 models
    6446 
    6447 > hide #!1 models
    6448 
    6449 > hide #22 target m
    6450 
    6451 > close #22
    6452 
    6453 > show #!1 models
    6454 
    6455 > ui mousemode right "mark plane"
    6456 
    6457 > ui mousemode right "mark point"
    6458 
    6459 > marker #22 position 174.3,163.2,167.1 color #d783ff radius 5
    6460 
    6461 > ui mousemode right "move markers"
    6462 
    6463 > hide #!1 models
    6464 
    6465 > marker change #22:1 position 154.8,168.4,139.2
    6466 
    6467 > ui mousemode right "delete markers"
    6468 
    6469 > marker delete #22:2
    6470 
    6471 > ui mousemode right "move markers"
    6472 
    6473 > close #22
    6474 
    6475 > show #!1 models
    6476 
    6477 > ui mousemode right "move markers"
    6478 
    6479 > ui mousemode right "mark point"
    6480 
    6481 > marker #22 position 176.4,193.4,182.5 color #d783ff radius 5
    6482 
    6483 > marker #22 position 176.4,193.4,182.6 color #d783ff radius 5
    6484 
    6485 > hide #!1 models
    6486 
    6487 > ui mousemode right "delete markers"
    6488 
    6489 > marker delete #22:2
    6490 
    6491 > marker delete #22:1
    6492 
    6493 > show #!1 models
    6494 
    6495 > ui mousemode right "mark point"
    6496 
    6497 > marker #22 position 166,182.7,180.8 color #d783ff radius 5
    6498 
    6499 > marker #22 position 166,182.8,181.9 color #d783ff radius 5
    6500 
    6501 > marker #22 position 171.9,186.3,185.4 color #d783ff radius 5
    6502 
    6503 > marker #22 position 172.2,186.4,185.5 color #d783ff radius 5
    6504 
    6505 > hide #!1 models
    6506 
    6507 > ui mousemode right "delete markers"
    6508 
    6509 > marker delete #22:4
    6510 
    6511 > marker delete #22:3
    6512 
    6513 > ui mousemode right "move markers"
    6514 
    6515 > select add #22
    6516 
    6517 2 atoms, 2 residues, 1 model selected 
    6518 
    6519 > marker change #22:1 position 153.9,198.1,208.6
    6520 
    6521 > ui mousemode right "delete markers"
    6522 
    6523 > ~select
    6524 
    6525 Nothing selected 
    6526 
    6527 > ui mousemode right "move markers"
    6528 
    6529 > ui mousemode right "resize markers"
    6530 
    6531 > marker change #22:2 radius 5
    6532 
    6533 > ui mousemode right "delete markers"
    6534 
    6535 > marker delete #22:1
    6536 
    6537 > ui mousemode right "move markers"
    6538 
    6539 > ui mousemode right "resize markers"
    6540 
    6541 > marker change #22:2 radius 21.07
    6542 
    6543 > ui mousemode right "move markers"
    6544 
    6545 > marker change #22:2 position 135.7,190,200.8
    6546 
    6547 > show #!1 models
    6548 
    6549 > marker change #22:2 position 197.4,124.4,201.9
    6550 
    6551 > marker change #22:2 position 193.5,130.4,178.4
    6552 
    6553 > marker change #22:2 position 189.4,129.1,178.4
    6554 
    6555 > hide #!1 models
    6556 
    6557 > show #!1 models
    6558 
    6559 > hide #22 models
    6560 
    6561 > show #22 models
    6562 
    6563 > select add #22
    6564 
    6565 1 atom, 1 residue, 1 model selected 
    6566 
    6567 > transparency #22 20
    6568 
    6569 > transparency #22 80
    6570 
    6571 > transparency sel 80
    6572 
    6573 > marker change #22 color #d49df9
    6574 
    6575 > marker change #22 color #d39cf7
    6576 
    6577 > marker change #22 color #cd97f1
    6578 
    6579 > marker change #22 color #c18fe3
    6580 
    6581 > marker change #22 color #ac7fca
    6582 
    6583 > marker change #22 color #a57ac2
    6584 
    6585 > marker change #22 color #a177bd
    6586 
    6587 > marker change #22 color #9e74b9
    6588 
    6589 > marker change #22 color #9d74b8
    6590 
    6591 > marker change #22 color #9b73b6
    6592 
    6593 > marker change #22 color #9871b3
    6594 
    6595 > marker change #22 color #956eaf
    6596 
    6597 > marker change #22 color #936dad
    6598 
    6599 > marker change #22 color #926cab
    6600 
    6601 > marker change #22 color #916baa
    6602 
    6603 > marker change #22 color #8f6aa8
    6604 
    6605 > marker change #22 color #8e69a7
    6606 
    6607 > marker change #22 color #8d68a6
    6608 
    6609 > marker change #22 color #8c68a5
    6610 
    6611 > marker change #22 color #8a66a2
    6612 
    6613 > marker change #22 color #8965a0
    6614 
    6615 > marker change #22 color #86639d
    6616 
    6617 > marker change #22 color #805e96
    6618 
    6619 > marker change #22 color #7e5d93
    6620 
    6621 > marker change #22 color #7d5c93
    6622 
    6623 > marker change #22 color #7c5b91
    6624 
    6625 > marker change #22 color #7a5a90
    6626 
    6627 > marker change #22 color #78598d
    6628 
    6629 > marker change #22 color #76578a
    6630 
    6631 > marker change #22 color #735588
    6632 
    6633 > marker change #22 color #715485
    6634 
    6635 > marker change #22 color #6e5181
    6636 
    6637 > marker change #22 color #6c507f
    6638 
    6639 > marker change #22 color #6b4f7d
    6640 
    6641 > marker change #22 color #684d7a
    6642 
    6643 > marker change #22 color #664c78
    6644 
    6645 > marker change #22 color #654b77
    6646 
    6647 > marker change #22 color #634974
    6648 
    6649 > marker change #22 color #624873
    6650 
    6651 > marker change #22 color #614872
    6652 
    6653 > marker change #22 color #604771
    6654 
    6655 > marker change #22 color #5f4670
    6656 
    6657 > marker change #22 color #5e466f
    6658 
    6659 > marker change #22 color #5d456e
    6660 
    6661 > marker change #22 color #5c446c
    6662 
    6663 > marker change #22 color #5a436a
    6664 
    6665 > marker change #22 color #594168
    6666 
    6667 > marker change #22 color #584167
    6668 
    6669 > marker change #22 color #553f64
    6670 
    6671 > marker change #22 color #523d60
    6672 
    6673 > marker change #22 color #503b5e
    6674 
    6675 > marker change #22 color #4f3a5d
    6676 
    6677 > marker change #22 color #4c385a
    6678 
    6679 > marker change #22 color #4a3656
    6680 
    6681 > marker change #22 color #473554
    6682 
    6683 > marker change #22 color #453351
    6684 
    6685 > marker change #22 color #402f4b
    6686 
    6687 > marker change #22 color #3d2d47
    6688 
    6689 > marker change #22 color #392a43
    6690 
    6691 > marker change #22 color #372941
    6692 
    6693 > marker change #22 color #34273d
    6694 
    6695 > marker change #22 color #31243a
    6696 
    6697 > marker change #22 color #2e2236
    6698 
    6699 > marker change #22 color #2b2033
    6700 
    6701 > marker change #22 color #271d2e
    6702 
    6703 > marker change #22 color #251b2c
    6704 
    6705 > marker change #22 color #241b2a
    6706 
    6707 > marker change #22 color #241a2a
    6708 
    6709 > marker change #22 color #231a29
    6710 
    6711 > marker change #22 color #221928
    6712 
    6713 > marker change #22 color #231a29
    6714 
    6715 > marker change #22 color #241b2b
    6716 
    6717 > marker change #22 color #302439
    6718 
    6719 > marker change #22 color #402f4b
    6720 
    6721 > marker change #22 color #503b5e
    6722 
    6723 > marker change #22 color #624873
    6724 
    6725 > marker change #22 color #a77bc4
    6726 
    6727 > marker change #22 color #b989da
    6728 
    6729 > marker change #22 color #c592e7
    6730 
    6731 > marker change #22 color #cd97f0
    6732 
    6733 > marker change #22 color #cf99f3
    6734 
    6735 > marker change #22 color #d29bf7
    6736 
    6737 > marker change #22 color #d49cf8
    6738 
    6739 > marker change #22 color #d49cf9
    6740 
    6741 > marker change #22 color #d69efb
    6742 
    6743 > marker change #22:2 position 182.9,125.9,177.7
    6744 
    6745 > marker change #22:2 position 187.8,127.5,181.3
    6746 
    6747 > marker change #22:2 position 189.3,128.5,182.8
    6748 
    6749 > transparency #22 80
    6750 
    6751 > transparency 80
    6752 
    6753 > transparency 0
    6754 
    6755 > transparency sel 60
    6756 
    6757 > color #22 #d69efb80
    6758 
    6759 > marker change #22:2 position 191.1,132.5,186.9
    6760 
    6761 > color zone #1 near #22 distance 3
    6762 
    6763 > hide #22 models
    6764 
    6765 > show #22 models
    6766 
    6767 > ui mousemode right "translate selected models"
    6768 
    6769 > view matrix models #22,1,0,0,-1.1495,0,1,0,6.218,0,0,1,-5.4765
    6770 
    6771 > color zone #1 near #22 distance 10
    6772 
    6773 > hide #22 models
    6774 
    6775 > show #22 models
    6776 
    6777 > view matrix models #22,1,0,0,-2.0282,0,1,0,9.2927,0,0,1,-7.23
    6778 
    6779 > view matrix models #22,1,0,0,-2.0371,0,1,0,8.9451,0,0,1,-6.0522
    6780 
    6781 > view matrix models #22,1,0,0,-4.2482,0,1,0,9.8188,0,0,1,-5.3853
    6782 
    6783 > color zone #1 near #22 distance 10
    6784 
    6785 > hide #22 models
    6786 
    6787 > show #22 models
    6788 
    6789 > measure center #22
    6790 
    6791 Center of mass of 1 atoms = (186.81, 142.31, 181.50) 
    6792 
    6793 > color zone #1 center 186.81, 142.31, 181.50 dis 20
    6794 
    6795 Expected a keyword 
    6796 
    6797 > color zone #1 near #22 distance 20
    6798 
    6799 > hide #22 models
    6800 
    6801 > show #22 models
    6802 
    6803 > save "/Users/haandrew/Documents/progress/2026/Cryo-EM/working session 2026
    6804 > .tif" width 864 height 587 supersample 3
    6805 
    6806 > save "/Users/haandrew/Documents/progress/2026/Cryo-EM/working session
    6807 > 2026.cxs"
    6808 
    6809 > hide #22 models
    6810 
    6811 > select subtract #22
    6812 
    6813 Nothing selected 
    6814 
    6815 > close session
    6816 
    6817 > open "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /100625_allmaps
    6818 > overlay .cxs"
    6819 
    6820 Opened ec8 ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1, grid size
    6821 128,128,128, pixel 3.35, shown at level 1.07, step 1, values float32 
    6822 Opened cryosparc_P1_J21_class_04_00082_volume.mrc as #2, grid size
    6823 128,128,128, pixel 3.32, shown at level 0.34, step 1, values float32 
    6824 Opened cryosparc_P1_J21_class_03_00082_volume.mrc as #3, grid size
    6825 128,128,128, pixel 3.32, shown at level 0.108, step 1, values float32 
    6826 Opened cryosparc_P1_J21_class_02_00082_volume.mrc as #4, grid size
    6827 128,128,128, pixel 3.32, shown at level 0.0537, step 1, values float32 
    6828 Opened cryosparc_P1_J21_class_01_00082_volume.mrc as #5, grid size
    6829 128,128,128, pixel 3.32, shown at level 0.303, step 1, values float32 
    6830 Opened cryosparc_P1_J21_class_00_00082_volume.mrc as #6, grid size
    6831 128,128,128, pixel 3.32, shown at level 0.249, step 1, values float32 
    6832 Opened cryosparc_P1_J21_class_00_00082_volume.mrc z flip as #7, grid size
    6833 128,128,128, pixel 3.32, shown at level 0.311, step 1, values float32 
    6834 Opened cryosparc_P1_J21_class_01_00082_volume.mrc z flip as #8, grid size
    6835 128,128,128, pixel 3.32, shown at level 0.498, step 1, values float32 
    6836 opened ChimeraX session 
    6837 
    6838 > close session
    6839 
    6840 > open "/Users/haandrew/Documents/progress/2025/Cryo-
    6841 > EM/20250506_scRibso_SND1/maps/best session.cxs"
    6842 
    6843 Opened cryosparc_P1_J22_class_00_00062_volume_sharp.mrc as #1.1, grid size
    6844 128,128,128, pixel 3.35, shown at level 0.391, step 1, values float32 
    6845 Opened cryosparc_P1_J22_class_04_00062_volume_sharp.mrc as #1.2, grid size
    6846 128,128,128, pixel 3.35, shown at level 0.715, step 1, values float32 
    6847 Opened cryosparc_P1_J22_class_03_00062_volume_sharp.mrc as #1.3, grid size
    6848 128,128,128, pixel 3.35, shown at level 0.425, step 1, values float32 
    6849 Opened cryosparc_P1_J22_class_02_00062_volume_sharp.mrc as #1.4, grid size
    6850 128,128,128, pixel 3.35, shown at level 0.731, step 1, values float32 
    6851 Opened cryosparc_P1_J22_class_01_00062_volume_sharp.mrc as #1.5, grid size
    6852 128,128,128, pixel 3.35, shown at level 0.169, step 1, values float32 
    6853 Opened apo ribso _ cryosparc_P26_J24_001_volume_map.mrc as #1.6, grid size
    6854 128,128,128, pixel 3.35, shown at level 1.13, step 1, values float32 
    6855 Opened cryosparc_P1_J22_class_00_00062_volume_sharp.mrc z flip as #2, grid
    6856 size 128,128,128, pixel 3.35, shown at level 0.471, step 1, values float32 
    6857 Opened cryosparc_P1_J22_class_03_00062_volume_sharp.mrc z flip as #3, grid
    6858 size 128,128,128, pixel 3.35, shown at level 0.443, step 1, values float32 
    6859 Opened cryosparc_P1_J22_class_03_00062_volume_sharp.mrc z flip z flip as #4,
    6860 grid size 128,128,128, pixel 3.35, shown at level 0.265, step 1, values
    6861 float32 
    6862 Opened cryosparc_P1_J22_class_02_00062_volume_sharp.mrc z flip as #6, grid
    6863 size 128,128,128, pixel 3.35, shown at level 0.564, step 1, values float32 
    6864 Opened cryosparc_P1_J22_class_01_00062_volume_sharp.mrc z flip z flip as #7,
    6865 grid size 128,128,128, pixel 3.35, shown at level 0.28, step 1, values float32 
    6866 Opened apo ribso _ cryosparc_P26_J24_001_volume_map.mrc as #8, grid size
    6867 128,128,128, pixel 3.35, shown at level 0.693, step 1, values float32 
    6868 Opened apo ribso _ cryosparc_P26_J24_001_volume_map.mrc z flip as #9, grid
    6869 size 128,128,128, pixel 3.35, shown at level 2.85, step 1, values float32 
    6870 Opened focmap trna.mrc as #13, grid size 128,128,128, pixel 3.35, shown at
    6871 level 0.063, step 1, values float32 
    6872 Opened cryosparc_P1_J22_class_00_00062_volume_sharp.mrc as #14, grid size
    6873 128,128,128, pixel 3.35, shown at level 1.35, step 1, values float32 
    6874 
    6875 > set bgColor #ffffff00
    6876 
    6877 opened ChimeraX session 
    6878 Showing cryosparc_P1_J22_class_00_00062_volume_sharp z flip.seg - 18 regions,
    6879 18 surfaces 
    6880 
    6881 > volume #14 level 0.405
    6882 
    6883 > ui tool show "Side View"
    6884 
    6885 > lighting full
    6886 
    6887 > lighting shadows false
    6888 
    6889 > lighting flat
    6890 
    6891 > graphics silhouettes false
    6892 
    6893 > lighting shadows true intensity 0.5
    6894 
    6895 > lighting flat
    6896 
    6897 > lighting full
    6898 
    6899 > lighting soft
    6900 
    6901 > lighting simple
    6902 
    6903 > lighting soft
    6904 
    6905 > set bgColor black
    6906 
    6907 > set bgColor transparent
    6908 
    6909 > hide #!5 models
    6910 
    6911 > show #!5 models
    6912 
    6913 > hide #!14 models
    6914 
    6915 > hide #!13 models
    6916 
    6917 > close session
    6918 
    6919 > open "/Users/haandrew/Documents/progress/2026/Cryo-EM/working session
    6920 > 2026.cxs" format session
    6921 
    6922 Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #1, grid size 128,128,128,
    6923 pixel 3.32, shown at level 0.352, step 1, values float32 
    6924 Opened cryosparc_P1_J49_001_volume_map.mrc as #2, grid size 128,128,128, pixel
    6925 3.32, shown at level 1.03, step 1, values float32 
    6926 Opened cryosparc_P1_J97_002_volume_map_sharp.mrc as #3, grid size 128,128,128,
    6927 pixel 3.32, shown at level 0.389, step 1, values float32 
    6928 Opened cryosparc_P1_J97_002_volume_map.mrc as #4, grid size 128,128,128, pixel
    6929 3.32, shown at level 0.721, step 1, values float32 
    6930 Opened cryosparc_P1_J98_001_volume_map_sharp.mrc as #5, grid size 128,128,128,
    6931 pixel 3.32, shown at level 1.11, step 1, values float32 
    6932 Opened cryosparc_P1_J98_001_volume_map.mrc as #6, grid size 128,128,128, pixel
    6933 3.32, shown at level 0.905, step 1, values float32 
    6934 Opened cryosparc_P1_J103_001_volume_map_sharp.mrc as #7, grid size
    6935 128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32 
    6936 Opened cryosparc_P1_J103_001_volume_map.mrc as #8, grid size 128,128,128,
    6937 pixel 3.32, shown at level 1.04, step 1, values float32 
    6938 Opened cryosparc_P1_J104_001_volume_map_sharp.mrc as #9, grid size
    6939 128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32 
    6940 Opened cryosparc_P1_J104_001_volume_map.mrc as #10, grid size 128,128,128,
    6941 pixel 3.32, shown at level 1.04, step 1, values float32 
    6942 Opened cryosparc_P1_J108_001_volume_map_sharp.mrc as #11, grid size
    6943 128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32 
    6944 Opened cryosparc_P1_J108_001_volume_map.mrc as #12, grid size 128,128,128,
    6945 pixel 3.32, shown at level 0.54, step 1, values float32 
    6946 Opened cryosparc_P1_J98_001_volume_map_sharp.mrc z flip as #14, grid size
    6947 128,128,128, pixel 3.32, shown at level 0.59, step 1, values float32 
    6948 Opened cryosparc_P1_J98_001_volume_map.mrc z flip as #15, grid size
    6949 128,128,128, pixel 3.32, shown at level 0.295, step 1, values float32 
    6950 Opened cryosparc_P1_J103_001_volume_map_sharp.mrc z flip as #16, grid size
    6951 128,128,128, pixel 3.32, shown at level 1.41, step 1, values float32 
    6952 Opened cryosparc_P1_J103_001_volume_map.mrc z flip as #17, grid size
    6953 128,128,128, pixel 3.32, shown at level 1.04, step 1, values float32 
    6954 Opened cryosparc_P1_J104_001_volume_map_sharp.mrc z flip as #18, grid size
    6955 128,128,128, pixel 3.32, shown at level 1.4, step 1, values float32 
    6956 Opened cryosparc_P1_J104_001_volume_map.mrc z flip as #19, grid size
    6957 128,128,128, pixel 3.32, shown at level 1.04, step 1, values float32 
    6958 Opened cryosparc_P1_J108_001_volume_map_sharp.mrc z flip as #20, grid size
    6959 128,128,128, pixel 3.32, shown at level 1.01, step 1, values float32 
    6960 Opened cryosparc_P1_J108_001_volume_map.mrc z flip as #21, grid size
    6961 128,128,128, pixel 3.32, shown at level 0.54, step 1, values float32 
    6962 opened ChimeraX session 
    6963 
    6964 > select zone #1 near #22 dis 20
    6965 
    6966 Missing or invalid "range" argument: Expected a number 
    6967 
    6968 > select zone #1 near #22 dis 20
    6969 
    6970 Missing or invalid "range" argument: Expected a number 
    6971 
    6972 > select zone #1 near #22 dis 10
    6973 
    6974 Missing or invalid "range" argument: Expected a number 
    6975 
    6976 > view matrix models #22,1,0,0,-2.2078,0,1,0,10.085,0,0,1,-6.0799
    6977 
    6978 > select zone #1 in #22
    6979 
    6980 Missing or invalid "range" argument: Expected a number 
    6981 
    6982 > select zone #1 on #22
    6983 
    6984 Missing or invalid "range" argument: Expected a number 
    6985 
    6986 > view matrix models #22,1,0,0,-3.4988,0,1,0,9.7971,0,0,1,-3.1823
    6987 
    6988 > open /Users/haandrew/Documents/progress/2026/Cryo-EM/scRibosome-
    6989 > twoSND1_merge_for_P2J138.pdb
    6990 
    6991 Chain information for scRibosome-twoSND1_merge_for_P2J138.pdb #23 
    6992 --- 
    6993 Chain | Description 
    6994 1 | No description available 
    6995 2 | No description available 
    6996 C1 | No description available 
    6997 C2 | No description available 
    6998 C3 | No description available 
    6999 C4 | No description available 
    7000 LA | No description available 
    7001 LB | No description available 
    7002 LC | No description available 
    7003 LD | No description available 
    7004 LE | No description available 
    7005 LF | No description available 
    7006 LG | No description available 
    7007 LH | No description available 
    7008 LI | No description available 
    7009 LJ | No description available 
    7010 LL | No description available 
    7011 LM | No description available 
    7012 LN | No description available 
    7013 LO | No description available 
    7014 LP | No description available 
    7015 LQ | No description available 
    7016 LR | No description available 
    7017 LS | No description available 
    7018 LT | No description available 
    7019 LU | No description available 
    7020 LV | No description available 
    7021 LW | No description available 
    7022 LX | No description available 
    7023 LY | No description available 
    7024 LZ | No description available 
    7025 La | No description available 
    7026 Lb | No description available 
    7027 Lc | No description available 
    7028 Ld | No description available 
    7029 Le | No description available 
    7030 Lf | No description available 
    7031 Lg | No description available 
    7032 Lh | No description available 
    7033 Li | No description available 
    7034 Lj | No description available 
    7035 Lk | No description available 
    7036 Ll | No description available 
    7037 Lm | No description available 
    7038 Ln | No description available 
    7039 Lo | No description available 
    7040 Lp | No description available 
    7041 SA | No description available 
    7042 SB | No description available 
    7043 SC | No description available 
    7044 SD | No description available 
    7045 SE | No description available 
    7046 SF | No description available 
    7047 SG | No description available 
    7048 SH | No description available 
    7049 SI | No description available 
    7050 SJ | No description available 
    7051 SK | No description available 
    7052 SL | No description available 
    7053 SM | No description available 
    7054 SN | No description available 
    7055 SO | No description available 
    7056 SP | No description available 
    7057 SQ | No description available 
    7058 SR | No description available 
    7059 SS | No description available 
    7060 ST | No description available 
    7061 SU | No description available 
    7062 SV | No description available 
    7063 SW | No description available 
    7064 SX | No description available 
    7065 SY | No description available 
    7066 SZ | No description available 
    7067 Sa | No description available 
    7068 Sb | No description available 
    7069 Sc | No description available 
    7070 Sd | No description available 
    7071 Se | No description available 
    7072 Sf | No description available 
    7073 Sg | No description available 
    7074 s | No description available 
    7075  
    7076 
    7077 > open /Users/haandrew/Documents/progress/2026/Cryo-EM/scRibosome-
    7078 > twoSND1_merge_for_P2J138.pdb
    7079 
    7080 Chain information for scRibosome-twoSND1_merge_for_P2J138.pdb #24 
    7081 --- 
    7082 Chain | Description 
    7083 1 | No description available 
    7084 2 | No description available 
    7085 C1 | No description available 
    7086 C2 | No description available 
    7087 C3 | No description available 
    7088 C4 | No description available 
    7089 LA | No description available 
    7090 LB | No description available 
    7091 LC | No description available 
    7092 LD | No description available 
    7093 LE | No description available 
    7094 LF | No description available 
    7095 LG | No description available 
    7096 LH | No description available 
    7097 LI | No description available 
    7098 LJ | No description available 
    7099 LL | No description available 
    7100 LM | No description available 
    7101 LN | No description available 
    7102 LO | No description available 
    7103 LP | No description available 
    7104 LQ | No description available 
    7105 LR | No description available 
    7106 LS | No description available 
    7107 LT | No description available 
    7108 LU | No description available 
    7109 LV | No description available 
    7110 LW | No description available 
    7111 LX | No description available 
    7112 LY | No description available 
    7113 LZ | No description available 
    7114 La | No description available 
    7115 Lb | No description available 
    7116 Lc | No description available 
    7117 Ld | No description available 
    7118 Le | No description available 
    7119 Lf | No description available 
    7120 Lg | No description available 
    7121 Lh | No description available 
    7122 Li | No description available 
    7123 Lj | No description available 
    7124 Lk | No description available 
    7125 Ll | No description available 
    7126 Lm | No description available 
    7127 Ln | No description available 
    7128 Lo | No description available 
    7129 Lp | No description available 
    7130 SA | No description available 
    7131 SB | No description available 
    7132 SC | No description available 
    7133 SD | No description available 
    7134 SE | No description available 
    7135 SF | No description available 
    7136 SG | No description available 
    7137 SH | No description available 
    7138 SI | No description available 
    7139 SJ | No description available 
    7140 SK | No description available 
    7141 SL | No description available 
    7142 SM | No description available 
    7143 SN | No description available 
    7144 SO | No description available 
    7145 SP | No description available 
    7146 SQ | No description available 
    7147 SR | No description available 
    7148 SS | No description available 
    7149 ST | No description available 
    7150 SU | No description available 
    7151 SV | No description available 
    7152 SW | No description available 
    7153 SX | No description available 
    7154 SY | No description available 
    7155 SZ | No description available 
    7156 Sa | No description available 
    7157 Sb | No description available 
    7158 Sc | No description available 
    7159 Sd | No description available 
    7160 Se | No description available 
    7161 Sf | No description available 
    7162 Sg | No description available 
    7163 s | No description available 
    7164  
    7165 
    7166 > hide #22 models
    7167 
    7168 > select subtract #22
    7169 
    7170 Nothing selected 
    7171 
    7172 > hide #!23 models
    7173 
    7174 > select add #24
    7175 
    7176 205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected 
    7177 
    7178 > view matrix models #24,1,0,0,-47.345,0,1,0,-16.265,0,0,1,-284.06
    7179 
    7180 > ui mousemode right "rotate selected models"
    7181 
    7182 > view matrix models
    7183 > #24,0.38469,0.75102,0.53665,-181.53,-0.8147,0.54956,-0.18508,287.88,-0.43392,-0.36601,0.82326,-80.021
    7184 
    7185 > view matrix models
    7186 > #24,-0.97505,0.015931,-0.22143,418.67,-0.17847,-0.64944,0.73917,195.67,-0.13203,0.76025,0.63608,-331.01
    7187 
    7188 > view matrix models
    7189 > #24,0.016709,0.84126,0.54037,-121.86,-0.69581,-0.37833,0.6105,279.15,0.71803,-0.3862,0.57903,-269.89
    7190 
    7191 > view matrix models
    7192 > #24,-0.86869,0.49473,-0.024937,257.7,-0.092377,-0.11234,0.98937,15.836,0.48666,0.86176,0.14329,-378.34
    7193 
    7194 > view matrix models
    7195 > #24,-0.77243,-0.10111,-0.627,485.54,-0.54131,-0.41155,0.73322,226.61,-0.33218,0.90576,0.26316,-237.86
    7196 
    7197 > view matrix models
    7198 > #24,-0.99256,0.10607,-0.05974,369.75,-0.09536,-0.37242,0.92315,82.915,0.075669,0.92198,0.37976,-353.16
    7199 
    7200 > view matrix models
    7201 > #24,-0.95953,-0.27399,-0.065004,440.24,-0.13242,0.23529,0.96286,-39.852,-0.24852,0.93251,-0.26205,-148.94
    7202 
    7203 > select subtract #24
    7204 
    7205 Nothing selected 
    7206 
    7207 > select add #1
    7208 
    7209 2 models selected 
    7210 
    7211 > view matrix models
    7212 > #1,-0.90535,0.14613,-0.39873,421.82,0.18893,0.97949,-0.069999,-37.647,0.38032,-0.13871,-0.91439,341.68
    7213 
    7214 > view matrix models
    7215 > #1,-0.82515,0.39791,0.40098,192.71,0.4908,0.85643,0.16011,-120.59,-0.27971,0.32892,-0.90199,378.49
    7216 
    7217 > view matrix models
    7218 > #1,-0.258,0.8852,-0.3871,127.01,0.88631,0.057368,-0.45953,89.012,-0.38457,-0.46165,-0.79936,547.73
    7219 
    7220 > view matrix models
    7221 > #1,-0.96477,0.093937,-0.24576,414.95,0.26309,0.3365,-0.90419,248.88,-0.0022395,-0.93699,-0.34936,478.92
    7222 
    7223 > view matrix models
    7224 > #1,-0.20474,-0.92379,-0.32355,486.81,0.2983,0.25594,-0.91952,261.63,0.93226,-0.28477,0.22317,30.87
    7225 
    7226 > view matrix models
    7227 > #1,0.75697,-0.63034,0.17224,124.37,0.38566,0.21818,-0.89647,246.73,0.52751,0.74503,0.40825,-139.38
    7228 
    7229 > view matrix models
    7230 > #1,0.99549,-0.034587,0.08832,-35.315,0.094074,0.47895,-0.87279,247.89,-0.012114,0.87716,0.48005,-68.479
    7231 
    7232 > view matrix models
    7233 > #1,0.94272,0.2833,0.17612,-109.1,0.021763,0.4746,-0.87993,265.39,-0.33287,0.83336,0.44125,15.79
    7234 
    7235 > volume flip #1
    7236 
    7237 Opened cryosparc_P1_J49_001_volume_map_sharp.mrc z flip as #25, grid size
    7238 128,128,128, pixel 3.32, shown at step 1, values float32 
    7239 
    7240 > select subtract #1
    7241 
    7242 Nothing selected 
    7243 
    7244 > select add #25
    7245 
    7246 2 models selected 
    7247 
    7248 > view matrix models
    7249 > #25,0.26615,0.91771,-0.2949,-0.94922,-0.63647,-0.062458,-0.76877,496.14,-0.72393,0.3923,0.56747,166.14
    7250 
    7251 > surface dust #25 size 33.2
    7252 
    7253 > view matrix models
    7254 > #25,-0.30131,0.88316,0.35949,-20.836,-0.70113,0.050305,-0.71125,472.94,-0.64624,-0.46636,0.60406,323.75
    7255 
    7256 > view matrix models
    7257 > #25,0.27328,0.95867,0.079168,-94.72,-0.23202,0.14556,-0.96176,410.32,-0.93353,0.24446,0.26221,309.67
    7258 
    7259 > view matrix models
    7260 > #25,0.94663,0.25102,-0.20221,-23.017,-0.11327,-0.32826,-0.93777,480.53,-0.30178,0.91062,-0.28231,157.59
    7261 
    7262 > view matrix models
    7263 > #25,-0.25382,0.43303,0.86491,-48.29,0.96697,0.092183,0.23762,-97.85,0.023167,0.89665,-0.44213,128.11
    7264 
    7265 > view matrix models
    7266 > #25,-0.14914,0.98041,-0.12863,35.703,0.78448,0.19651,0.5882,-160.04,0.60196,-0.013183,-0.79842,279.26
    7267 
    7268 > view matrix models
    7269 > #25,0.23096,0.44593,-0.86476,233.81,0.75856,0.47406,0.44705,-181.91,0.6093,-0.75922,-0.22878,308.62
    7270 
    7271 > view matrix models
    7272 > #25,0.95591,-0.0778,-0.28316,62.851,0.28693,0.042326,0.95701,-105.4,-0.062471,-0.99607,0.062783,434.58
    7273 
    7274 > view matrix models
    7275 > #25,0.93594,-0.33771,-0.09979,81.175,0.12321,0.048597,0.99119,-80.033,-0.32989,-0.93999,0.087096,473.35
    7276 
    7277 > hide #!25 models
    7278 
    7279 > select subtract #25
    7280 
    7281 Nothing selected 
    7282 
    7283 > show #!1 models
    7284 
    7285 > select add #1
    7286 
    7287 2 models selected 
    7288 
    7289 > view matrix models
    7290 > #1,0.99881,0.0028587,0.048629,-36.066,0.038894,0.55424,-0.83145,235.28,-0.029329,0.83235,0.55347,-69.955
    7291 
    7292 > view matrix models
    7293 > #1,0.96872,0.22419,0.10643,-88.169,-0.035649,0.55012,-0.83432,252.36,-0.24559,0.80443,0.5409,-16.179
    7294 
    7295 > ui mousemode right "translate selected models"
    7296 
    7297 > view matrix models
    7298 > #1,0.96872,0.22419,0.10643,-143.94,-0.035649,0.55012,-0.83432,262.05,-0.24559,0.80443,0.5409,-266.7
    7299 
    7300 > view matrix models
    7301 > #1,0.96872,0.22419,0.10643,-504.82,-0.035649,0.55012,-0.83432,221.36,-0.24559,0.80443,0.5409,-165.02
    7302 
    7303 > ui mousemode right "rotate selected models"
    7304 
    7305 > view matrix models
    7306 > #1,0.81324,0.082368,-0.57607,-306.54,0.25323,-0.94138,0.22288,266.99,-0.52395,-0.32714,-0.78642,397.03
    7307 
    7308 > view matrix models
    7309 > #1,-0.93493,-0.19574,-0.29595,63.437,0.34872,-0.35285,-0.86827,338.96,0.065525,-0.91498,0.39815,162.68
    7310 
    7311 > select add #24
    7312 
    7313 205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 4 models selected 
    7314 
    7315 > select subtract #1
    7316 
    7317 205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected 
    7318 
    7319 > view matrix models
    7320 > #24,-0.62219,0.43549,0.65056,72.683,0.65482,-0.16594,0.73735,-79.179,0.42906,0.88477,-0.18192,-301.2
    7321 
    7322 > view matrix models
    7323 > #24,0.57832,-0.4931,0.64992,3.0833,-0.49957,-0.84387,-0.19572,503.03,0.64496,-0.21149,-0.73437,-8.892
    7324 
    7325 > view matrix models
    7326 > #24,-0.52237,-0.56532,0.63839,255.21,-0.7069,0.70578,0.046568,183.97,-0.47689,-0.42695,-0.7683,281.34
    7327 
    7328 > view matrix models
    7329 > #24,-0.96939,0.23301,0.077349,309.99,0.20616,0.94364,-0.25894,6.3294,-0.13333,-0.23506,-0.96279,210.9
    7330 
    7331 > view matrix models
    7332 > #24,0.012267,0.99837,0.055722,-48.998,0.66549,-0.049744,0.74475,-106.41,0.7463,0.027947,-0.66502,-93.502
    7333 
    7334 > view matrix models
    7335 > #24,0.59817,0.64144,0.48035,-193.08,0.014275,-0.60785,0.79392,134.44,0.80124,-0.46805,-0.37276,-67.922
    7336 
    7337 > select subtract #24
    7338 
    7339 Nothing selected 
    7340 
    7341 > select add #1
    7342 
    7343 2 models selected 
    7344 
    7345 > view matrix models
    7346 > #1,0.64008,-0.70548,0.3043,-278.08,0.47923,0.057027,-0.87583,226.18,0.60053,0.70643,0.37459,-288.66
    7347 
    7348 > view matrix models
    7349 > #1,0.75954,0.54606,0.35345,-578.28,0.35792,0.10286,-0.92807,252.28,-0.54313,0.83141,-0.11732,22.446
    7350 
    7351 > view matrix models
    7352 > #1,-0.40351,0.91492,-0.010188,-340.31,0.30106,0.12225,-0.94574,263.61,-0.86403,-0.38468,-0.32477,388.83
    7353 
    7354 > view matrix models
    7355 > #1,-0.11579,0.78119,-0.61346,-252.44,0.83268,-0.26037,-0.48873,142.44,-0.54152,-0.5674,-0.62033,418.66
    7356 
    7357 > view matrix models
    7358 > #1,-0.97955,0.17307,-0.10263,-43.818,-0.11148,-0.89144,-0.43921,464.44,-0.16751,-0.41878,0.8925,8.1223
    7359 
    7360 > view matrix models
    7361 > #1,-0.85026,0.462,-0.25222,-102.48,-0.34373,-0.85024,-0.39868,496.36,-0.39864,-0.25228,0.88173,23.435
    7362 
    7363 > view matrix models
    7364 > #1,-0.44465,0.62583,-0.64081,-145.09,0.060262,-0.6929,-0.71851,441.81,-0.89368,-0.3581,0.27038,271.17
    7365 
    7366 > ui mousemode right "translate selected models"
    7367 
    7368 > view matrix models
    7369 > #1,-0.44465,0.62583,-0.64081,61.453,0.060262,-0.6929,-0.71851,463,-0.89368,-0.3581,0.27038,-26.983
    7370 
    7371 > view matrix models
    7372 > #1,-0.44465,0.62583,-0.64081,293.85,0.060262,-0.6929,-0.71851,446.65,-0.89368,-0.3581,0.27038,103.73
    7373 
    7374 > view matrix models
    7375 > #1,-0.44465,0.62583,-0.64081,263.76,0.060262,-0.6929,-0.71851,452.88,-0.89368,-0.3581,0.27038,121.44
    7376 
    7377 Must specify one map, got 0 
    7378 Must specify one map, got 0 
    7379 
    7380 > fitmap #1 inmodel #24
    7381 
    7382 Expected a keyword 
    7383 
    7384 > fitmap #24 inMap #1
    7385 
    7386 Fit molecule scRibosome-twoSND1_merge_for_P2J138.pdb (#24) to map
    7387 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) using 205688 atoms 
    7388 average map value = 0.88, steps = 92 
    7389 shifted from previous position = 16.7 
    7390 rotated from previous position = 14.4 degrees 
    7391 atoms outside contour = 30417, contour level = 0.35186 
    7392  
    7393 Position of scRibosome-twoSND1_merge_for_P2J138.pdb (#24) relative to
    7394 cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates: 
    7395 Matrix rotation and translation 
    7396 -0.99066496 0.13426151 -0.02359580 401.31992681 
    7397 0.13331980 0.99035331 0.03776419 -35.55227660 
    7398 0.02843846 0.03426587 -0.99900805 408.66727182 
    7399 Axis -0.06706868 -0.99758500 -0.01805412 
    7400 Axis point 199.18350637 0.00000000 207.27925730 
    7401 Rotation angle (degrees) 178.50555012 
    7402 Shift along axis 1.17229208 
    7403  
    7404 
    7405 > select subtract #1
    7406 
    7407 Nothing selected 
    7408 
    7409 > hide #!1 models
    7410 
    7411 > show #!1 models
    7412 
    7413 > volume #1 level 0.9412
    7414 
    7415 > select add #1
    7416 
    7417 2 models selected 
    7418 
    7419 > view matrix models
    7420 > #1,-0.44465,0.62583,-0.64081,422.57,0.060262,-0.6929,-0.71851,239.24,-0.89368,-0.3581,0.27038,91.634
    7421 
    7422 > view matrix models
    7423 > #1,-0.44465,0.62583,-0.64081,396.54,0.060262,-0.6929,-0.71851,411.62,-0.89368,-0.3581,0.27038,216.17
    7424 
    7425 > view matrix models
    7426 > #1,-0.44465,0.62583,-0.64081,264.96,0.060262,-0.6929,-0.71851,447.21,-0.89368,-0.3581,0.27038,113.7
     651[deleted to fit within ticket limits]
     652
    7427653
    7428654> fitmap #24 inMap #1