Changes between Initial Version and Version 1 of Ticket #16055


Ignore:
Timestamp:
Oct 2, 2024, 9:47:10 AM (13 months ago)
Author:
Eric Pettersen
Comment:

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Unmodified
Added
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  • Ticket #16055

    • 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 moving window between screens

  • Ticket #16055 – Description

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     2078    "base" : 140703583498240,
     2079    "CFBundleShortVersionString" : "6.9",
     2080    "CFBundleIdentifier" : "com.apple.CoreFoundation",
     2081    "size" : 4829181,
     2082    "uuid" : "c5e5acb6-9e44-3aa3-bd21-0a5b4a2eee5e",
     2083    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
     2084    "name" : "CoreFoundation",
     2085    "CFBundleVersion" : "2602"
     2086  },
     2087  {
     2088    "source" : "P",
     2089    "arch" : "x86_64",
     2090    "base" : 140703582240768,
     2091    "size" : 503796,
     2092    "uuid" : "69eca28c-bfb7-35bf-ad4f-1bece712d239",
     2093    "path" : "\/usr\/lib\/libc++.1.dylib",
     2094    "name" : "libc++.1.dylib"
     2095  }
     2096],
     2097  "sharedCache" : {
     2098  "base" : 140703578660864,
     2099  "size" : 25769803776,
     2100  "uuid" : "b8509d0f-c366-3716-9a03-efa00b40318a"
     2101},
     2102  "vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=3.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                           880K       53 \nColorSync                          252K       31 \nCoreAnimation                     2944K      193 \nCoreGraphics                        32K        5 \nCoreImage                           24K        2 \nCoreServices                       820K        3 \nCoreUI image data                 5528K       48 \nFoundation                          32K        2 \nIOKit                             15.5M        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             2.4G      109 \nMALLOC guard page                   48K       12 \nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       56.2M       49 \nStack                            329.9M       49 \nVM_ALLOCATE                      341.8M      360 \nVM_ALLOCATE (reserved)           192.0M        3         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            46.0M      836 \n__DATA_CONST                      60.3M      434 \n__DATA_DIRTY                      1691K      221 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       219.5M      223 \n__OBJC_RO                         71.9M        1 \n__OBJC_RW                         2201K        2 \n__TEXT                             1.1G      833 \ndyld private memory                 40K        2 \nmapped file                      261.6M       81 \nshared memory                     3508K       28 \n===========                     =======  ======= \nTOTAL                              5.0G     3597 \nTOTAL, minus reserved VM space     4.8G     3597 \n",
     2103  "legacyInfo" : {
     2104  "threadTriggered" : {
     2105    "name" : "CrBrowserMain",
     2106    "queue" : "com.apple.main-thread"
     2107  }
     2108},
     2109  "logWritingSignature" : "39f331149a618a3d25e804068401d33d0c5777c2",
     2110  "trialInfo" : {
     2111  "rollouts" : [
     2112    {
     2113      "rolloutId" : "645197bf528fbf3c3af54105",
     2114      "factorPackIds" : {
     2115        "SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION" : "663e65b4a1526e1ca0e288a1"
     2116      },
     2117      "deploymentId" : 240000002
     2118    },
     2119    {
     2120      "rolloutId" : "644114de41e7236e6177f9bd",
     2121      "factorPackIds" : {
     2122
     2123      },
     2124      "deploymentId" : 240000013
     2125    }
     2126  ],
     2127  "experiments" : [
     2128    {
     2129      "treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
     2130      "experimentId" : "6639bc6ba73d460582162323",
     2131      "deploymentId" : 400000006
     2132    },
     2133    {
     2134      "treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
     2135      "experimentId" : "6643969b3099cf28e049862f",
     2136      "deploymentId" : 400000007
     2137    }
     2138  ]
     2139}
     2140}
     2141===== Log before crash start =====
     2142Startup Messages 
     2143--- 
     2144note | available bundle cache has not been initialized yet 
     2145 
     2146You can double click a model's Name or ID in the model panel to edit those
     2147fields 
     2148UCSF ChimeraX version: 1.8 (2024-06-10) 
     2149© 2016-2024 Regents of the University of California. All rights reserved. 
     2150How to cite UCSF ChimeraX 
     2151
     2152> open 22895 fromDatabase emdb format ccp4
     2153
     2154Summary of feedback from opening 22895 fetched from emdb 
     2155--- 
     2156notes | Fetching compressed map 22895 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22895/map/emd_22895.map.gz 
     2157Fetching map header 22895 from
     2158ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22895/header/emd-22895.xml 
     2159 
     2160Opened emdb 22895 as #1, grid size 300,300,300, pixel 2.17, shown at level
     21610.05, step 2, values float32 
     2162
     2163> close session
     2164
     2165> open 7ao8 fromDatabase pdbe_bio format mmcif
     2166
     2167Summary of feedback from opening 7ao8 fetched from pdbe_bio 
     2168--- 
     2169warning | Missing or incomplete sequence information. Inferred polymer connectivity. 
     2170 
     2171notes | Fetching compressed 7ao8 bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/7ao8-assembly-1.cif.gz 
     2172Fetching CCD IHP from
     2173https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/IHP/IHP.cif 
     2174Fetching CCD ZN from
     2175https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 
     2176Fetching CCD K from
     2177https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif 
     2178 
     21797ao8 bioassembly 1 title: 
     2180Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex [more info...] 
     2181 
     2182Chain information for 7ao8 bioassembly 1 #1 
     2183--- 
     2184Chain | Description 
     2185A | Methyl-CpG-binding domain protein 2 
     2186B C | Metastasis-associated protein MTA1 
     2187D E | Histone deacetylase 1 
     2188 
     2189Non-standard residues in 7ao8 bioassembly 1 #1 
     2190--- 
     2191IHP — (IHP) 
     2192K — (K) 
     2193ZN — (ZN) 
     2194 
     2195Opened 1 biological assemblies for 7ao8 
     2196
     2197> select
     2198
     219910905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected 
     2200
     2201> surface hidePatches (#!1 & sel)
     2202
     2203> cartoon hide (#!1 & sel)
     2204
     2205> hide (#!1 & sel) target a
     2206
     2207> show (#!1 & sel) target ab
     2208
     2209> color sel bypolymer
     2210
     2211> color sel bychain
     2212
     2213> color sel byhetero
     2214
     2215> rainbow sel
     2216
     2217> coulombic sel
     2218
     2219The following residues are missing heavy (non-hydrogen) atoms, which may
     2220result in inaccurate electrostatics: 
     2221/A MET 150 
     2222/A LYS 161 
     2223/A LYS 167 
     2224/A SER 171 
     2225/A LYS 174 
     2226/A ARG 195 
     2227/A LYS 212 
     2228/B LYS 182 
     2229/B GLU 183 
     2230/B GLU 185 
     2231/B ARG 193 
     2232/B HIS 239 
     2233/B ASP 334 
     2234/B ARG 335 
     2235/B GLN 339 
     2236/B LYS 340 
     2237/C LYS 182 
     2238/C GLU 183 
     2239/C GLU 185 
     2240/C ARG 193 
     2241/C HIS 239 
     2242/C ASP 334 
     2243/C ARG 335 
     2244/C GLN 339 
     2245/C LYS 340 
     2246/D LYS 74 
     2247/D ARG 80 
     2248/D LYS 89 
     2249/D GLU 108 
     2250/D ASN 349 
     2251/E LYS 74 
     2252/E ARG 80 
     2253/E LYS 89 
     2254/E GLU 108 
     2255/E ASN 349 
     2256
     2257Using Amber 20 recommended default charges and atom types for standard
     2258residues 
     2259Coulombic values for 7ao8 bioassembly 1_A SES surface #1.2: minimum, -8.35,
     2260mean 1.20, maximum 14.50 
     2261Coulombic values for 7ao8 bioassembly 1_B SES surface #1.3: minimum, -19.19,
     2262mean -2.62, maximum 10.83 
     2263Coulombic values for 7ao8 bioassembly 1_C SES surface #1.4: minimum, -19.54,
     2264mean -2.62, maximum 10.95 
     2265Coulombic values for 7ao8 bioassembly 1_D SES surface #1.5: minimum, -21.06,
     2266mean -1.85, maximum 13.50 
     2267Coulombic values for 7ao8 bioassembly 1_E SES surface #1.6: minimum, -21.19,
     2268mean -1.85, maximum 13.91 
     2269To also show corresponding color key, enter the above coulombic command and
     2270add key true 
     2271
     2272> mlp sel
     2273
     2274Map values for surface "7ao8 bioassembly 1_A SES surface": minimum -29.29,
     2275mean -5.537, maximum 19.02 
     2276Map values for surface "7ao8 bioassembly 1_B SES surface": minimum -33.44,
     2277mean -4.484, maximum 23.82 
     2278Map values for surface "7ao8 bioassembly 1_C SES surface": minimum -33.16,
     2279mean -4.426, maximum 23.76 
     2280Map values for surface "7ao8 bioassembly 1_D SES surface": minimum -31.16,
     2281mean -4.932, maximum 21.93 
     2282Map values for surface "7ao8 bioassembly 1_E SES surface": minimum -30.62,
     2283mean -4.957, maximum 21.47 
     2284To also show corresponding color key, enter the above mlp command and add key
     2285true 
     2286
     2287> select
     2288
     228910905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected 
     2290
     2291> hide (#!1 & sel) target a
     2292
     2293> surface hidePatches (#!1 & sel)
     2294
     2295> cartoon (#!1 & sel)
     2296
     2297> set bgColor white
     2298
     2299> set bgColor #ffffff00
     2300
     2301> select clear
     2302
     2303> select
     2304
     230510905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected 
     2306
     2307> cartoon style (#!1 & sel) modeHelix tube sides 20
     2308
     2309> cartoon style (#!1 & sel & coil) xsection oval
     2310
     2311> cartoon style (#!1 & sel) xsection barbell modeHelix default
     2312
     2313> cartoon style (#!1 & sel) modeHelix tube sides 20
     2314
     2315> select clear
     2316
     2317> select /D/E
     2318
     23195928 atoms, 6084 bonds, 738 residues, 1 model selected 
     2320
     2321> ui tool show "Color Actions"
     2322
     2323> color sel dark salmon
     2324
     2325> select /B/C
     2326
     23274412 atoms, 4496 bonds, 8 pseudobonds, 548 residues, 2 models selected 
     2328
     2329> ui tool show "Color Actions"
     2330
     2331> color sel medium aquamarine
     2332
     2333> color sel olive
     2334
     2335> color sel lime green
     2336
     2337> color sel forest green
     2338
     2339> color sel medium sea green
     2340
     2341> color sel sea green
     2342
     2343> color sel olive drab
     2344
     2345> color sel medium aquamarine
     2346
     2347> color sel light sea green
     2348
     2349> color sel sea green
     2350
     2351> select /A
     2352
     2353487 atoms, 500 bonds, 64 residues, 1 model selected 
     2354
     2355> color sel deep sky blue
     2356
     2357> select clear
     2358
     2359> select
     2360
     236110905 atoms, 11152 bonds, 8 pseudobonds, 1358 residues, 2 models selected 
     2362
     2363> lighting flat
     2364
     2365> lighting full
     2366
     2367> lighting soft
     2368
     2369> lighting simple
     2370
     2371> lighting full
     2372
     2373> graphics silhouettes false
     2374
     2375> graphics silhouettes true
     2376
     2377> graphics silhouettes false
     2378
     2379> graphics silhouettes true
     2380
     2381> graphics silhouettes false
     2382
     2383> graphics silhouettes true
     2384
     2385> select clear
     2386
     2387> save "/Users/mahesh/Desktop/7AO8 HDAC1-MTA1-MBD2.cxs"
     2388
     2389> save /Users/mahesh/Desktop/image1.png supersample 3
     2390
     2391> open 11837 fromDatabase emdb format ccp4
     2392
     2393Summary of feedback from opening 11837 fetched from emdb 
     2394--- 
     2395notes | Fetching compressed map 11837 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11837/map/emd_11837.map.gz 
     2396Fetching map header 11837 from
     2397ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11837/header/emd-11837.xml 
     2398 
     2399Opened emdb 11837 as #2, grid size 300,300,300, pixel 1.09, shown at level
     24000.01, step 2, values float32, fit PDB 7ao8 
     2401
     2402> lighting soft
     2403
     2404> lighting simple
     2405
     2406> lighting soft
     2407
     2408> lighting full
     2409
     2410> lighting soft
     2411
     2412> transparency 50
     2413
     2414> surface dust #2 size 10.9
     2415
     2416> fitmap #1 inMap #2
     2417
     2418Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 (#2) using 10905 atoms 
     2419average map value = 0.01372, steps = 40 
     2420shifted from previous position = 0.108 
     2421rotated from previous position = 0.433 degrees 
     2422atoms outside contour = 2740, contour level = 0.01 
     2423 
     2424Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 (#2) coordinates: 
     2425Matrix rotation and translation 
     24260.99999838 -0.00040214 0.00175640 -0.22730647 
     24270.00041502 0.99997301 -0.00733480 1.04537688 
     2428-0.00175340 0.00733552 0.99997156 -0.81881106 
     2429Axis 0.97112974 0.23233792 0.05409358 
     2430Axis point 0.00000000 112.01316108 142.81256742 
     2431Rotation angle (degrees) 0.43277190 
     2432Shift along axis -0.02215581 
     2433 
     2434
     2435> vop gaussian #2 sdev 3.27
     2436
     2437Opened emdb 11837 gaussian as #3, grid size 300,300,300, pixel 1.09, shown at
     2438step 1, values float32 
     2439
     2440> undo
     2441
     2442> vop gaussian #3 sdev 3.27
     2443
     2444Opened emdb 11837 gaussian as #4, grid size 300,300,300, pixel 1.09, shown at
     2445step 1, values float32 
     2446
     2447> fitmap #1 inMap #4
     2448
     2449Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 gaussian (#4) using
     245010905 atoms 
     2451average map value = 0.01102, steps = 56 
     2452shifted from previous position = 0.178 
     2453rotated from previous position = 2.33 degrees 
     2454atoms outside contour = 327, contour level = 0.0057979 
     2455 
     2456Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 gaussian (#4)
     2457coordinates: 
     2458Matrix rotation and translation 
     24590.99991161 0.01092539 -0.00757739 -0.45477356 
     2460-0.01068805 0.99947198 0.03068439 -3.24350914 
     24610.00790863 -0.03060069 0.99950040 3.92324664 
     2462Axis -0.91738182 -0.23181168 -0.32353353 
     2463Axis point -0.00000000 125.37484276 108.62010700 
     2464Rotation angle (degrees) 1.91415905 
     2465Shift along axis -0.10021753 
     2466 
     2467
     2468> hide #!4 models
     2469
     2470> show #!2 models
     2471
     2472> hide #!3 target m
     2473
     2474> lighting flat
     2475
     2476> lighting full
     2477
     2478> lighting soft
     2479
     2480> select clear
     2481
     2482> graphics silhouettes false
     2483
     2484> surface dust #2 size 10.9
     2485
     2486> volume zone #2 nearAtoms #1 range 6.54
     2487
     2488> volume #!2 region all imageMode "full region"
     2489
     2490> volume unzone #!2
     2491
     2492> mousemode rightMode "crop volume"
     2493
     2494> volume #2 orthoplanes xyz positionPlanes 150,150,150 style image region all
     2495
     2496> mousemode rightMode "move planes"
     2497
     2498> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
     2499> 0,0,1 tiltedSlabOffset 163.5 tiltedSlabSpacing 1.09 tiltedSlabPlaneCount 10
     2500
     2501> mousemode rightMode "rotate slab"
     2502
     2503> volume #!2 planes z style image imageMode "full region"
     2504
     2505> mousemode rightMode "move planes"
     2506
     2507> volume #!2 step 2
     2508
     2509> volume #!2 step 1
     2510
     2511> volume #!2 showOutlineBox false
     2512
     2513> volume #!2 showOutlineBox true
     2514
     2515> transparency #1.2-6 0
     2516
     2517> volume #!2 style image
     2518
     2519> volume #!2 style mesh
     2520
     2521> volume #!2 style surface
     2522
     2523> fitmap #1 inMap #2
     2524
     2525Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 (#2) using 10905 atoms 
     2526average map value = 0, steps = 24 
     2527shifted from previous position = 0 
     2528rotated from previous position = 0 degrees 
     2529atoms outside contour = 10905, contour level = 0.01 
     2530 
     2531Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 (#2) coordinates: 
     2532Matrix rotation and translation 
     25330.99991161 0.01092539 -0.00757739 -0.45477356 
     2534-0.01068805 0.99947198 0.03068439 -3.24350914 
     25350.00790863 -0.03060069 0.99950040 3.92324664 
     2536Axis -0.91738182 -0.23181168 -0.32353353 
     2537Axis point -0.00000000 125.37484276 108.62010700 
     2538Rotation angle (degrees) 1.91415905 
     2539Shift along axis -0.10021753 
     2540 
     2541
     2542> volume zone #2 nearAtoms #1 range 6.54
     2543
     2544> fitmap #1 inMap #2
     2545
     2546Fit molecule 7ao8 bioassembly 1 (#1) to map emdb 11837 (#2) using 10905 atoms 
     2547average map value = 0.01372, steps = 84 
     2548shifted from previous position = 0.17 
     2549rotated from previous position = 2.35 degrees 
     2550atoms outside contour = 3538, contour level = 0.01 
     2551 
     2552Position of 7ao8 bioassembly 1 (#1) relative to emdb 11837 (#2) coordinates: 
     2553Matrix rotation and translation 
     25540.99999837 -0.00041146 0.00175879 -0.21424317 
     25550.00042479 0.99997111 -0.00758967 1.08464848 
     2556-0.00175562 0.00759040 0.99996965 -0.85893578 
     2557Axis 0.97283184 0.22522462 0.05359187 
     2558Axis point 0.00000000 113.65990138 142.78019786 
     2559Rotation angle (degrees) 0.44702617 
     2560Shift along axis -0.01016501 
     2561 
     2562
     2563> vop gaussian #2 sdev 3.27
     2564
     2565Opened emdb 11837 gaussian as #5, grid size 300,300,300, pixel 1.09, shown at
     2566step 1, values float32 
     2567
     2568> hide #!5 models
     2569
     2570> close session
     2571
     2572> open 21382 fromDatabase emdb format ccp4
     2573
     2574Summary of feedback from opening 21382 fetched from emdb 
     2575--- 
     2576notes | Fetching compressed map 21382 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-21382/map/emd_21382.map.gz 
     2577Fetching map header 21382 from
     2578ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-21382/header/emd-21382.xml 
     2579 
     2580Opened emdb 21382 as #1, grid size 148,148,148, pixel 2.79, shown at level
     25810.12, step 1, values float32 
     2582
     2583> transparency 50
     2584
     2585> volume hide
     2586
     2587> volume show
     2588
     2589> volume style surface
     2590
     2591> volume style mesh
     2592
     2593> cartoon
     2594
     2595> select
     2596
     25972 models selected 
     2598No visible atoms or bonds selected 
     2599
     2600> close session
     2601
     2602> open 22906 fromDatabase emdb format ccp4
     2603
     2604Summary of feedback from opening 22906 fetched from emdb 
     2605--- 
     2606notes | Fetching compressed map 22906 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22906/map/emd_22906.map.gz 
     2607Fetching map header 22906 from
     2608ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22906/header/emd-22906.xml 
     2609 
     2610Opened emdb 22906 as #1, grid size 256,256,256, pixel 2.4, shown at level
     26110.309, step 1, values float32 
     2612
     2613> open 22895 fromDatabase emdb format ccp4
     2614
     2615Opened emdb 22895 as #2, grid size 300,300,300, pixel 2.17, shown at level
     26160.05, step 2, values float32 
     2617
     2618> transparency 50
     2619
     2620> transparency 0
     2621
     2622> volume showOutlineBox true
     2623
     2624> volume region all imageMode "full region"
     2625
     2626> volume unzone
     2627
     2628> mousemode rightMode "crop volume"
     2629
     2630> volume region all imageMode "full region"
     2631
     2632> volume unzone
     2633
     2634> mousemode rightMode "crop volume"
     2635
     2636Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
     2637models, 2 maps. 
     2638
     2639Hide dust shortcut requires a displayed map surface 
     2640
     2641> fitmap #1 inMap #2
     2642
     2643Fit map emdb 22906 in map emdb 22895 using 129614 points 
     2644correlation = 0.8164, correlation about mean = 0.2136, overlap = 2.192e+05 
     2645steps = 316, shift = 31.3, angle = 19.5 degrees 
     2646 
     2647Position of emdb 22906 (#1) relative to emdb 22895 (#2) coordinates: 
     2648Matrix rotation and translation 
     26490.98705471 0.14422045 0.07016744 -42.95438264 
     2650-0.11713550 0.94708340 -0.29885164 167.00769044 
     2651-0.10955494 0.28676382 0.95171646 -52.66959165 
     2652Axis 0.87930593 0.26985448 -0.39242789 
     2653Axis point 0.00000000 228.42765842 493.13138733 
     2654Rotation angle (degrees) 19.45088577 
     2655Shift along axis 27.96674605 
     2656 
     2657
     2658> vop subtract #1 #2 minrms True
     2659
     2660Opened volume difference as #3, grid size 256,256,256, pixel 2.4, shown at
     2661step 1, values float32 
     2662Minimum RMS scale factor for "emdb 22895 #2" above level 0.05 is 0.32815 
     2663 
     2664
     2665> vop gaussian #3 sdev 7.2
     2666
     2667Opened volume difference gaussian as #4, grid size 256,256,256, pixel 2.4,
     2668shown at step 1, values float32 
     2669
     2670> volume show
     2671
     2672> volume style surface
     2673
     2674> volume style mesh
     2675
     2676> volume style image
     2677
     2678> volume showOutlineBox false
     2679
     2680> volume step 1
     2681
     2682> volume step 2
     2683
     2684> volume planes z style image imageMode "full region"
     2685
     2686> mousemode rightMode "move planes"
     2687
     2688> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
     2689> 0,0,1 tiltedSlabOffset 307.2 tiltedSlabSpacing 2.4 tiltedSlabPlaneCount 10
     2690
     2691> mousemode rightMode "rotate slab"
     2692
     2693> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
     2694> 0,0,1 tiltedSlabOffset 325.5 tiltedSlabSpacing 2.17 tiltedSlabPlaneCount 10
     2695
     2696> mousemode rightMode "rotate slab"
     2697
     2698> volume #3 style image region all imageMode "tilted slab" tiltedSlabAxis
     2699> 0,0,1 tiltedSlabOffset 307.2 tiltedSlabSpacing 2.4 tiltedSlabPlaneCount 10
     2700
     2701> mousemode rightMode "rotate slab"
     2702
     2703> volume #4 style image region all imageMode "tilted slab" tiltedSlabAxis
     2704> 0,0,1 tiltedSlabOffset 307.2 tiltedSlabSpacing 2.4 tiltedSlabPlaneCount 10
     2705
     2706> mousemode rightMode "rotate slab"
     2707
     2708> volume #1 orthoplanes xyz positionPlanes 128,128,128 style image region all
     2709
     2710> mousemode rightMode "move planes"
     2711
     2712> volume #2 orthoplanes xyz positionPlanes 150,150,150 style image region all
     2713
     2714> mousemode rightMode "move planes"
     2715
     2716> volume #3 orthoplanes xyz positionPlanes 128,128,128 style image region all
     2717
     2718> mousemode rightMode "move planes"
     2719
     2720> volume #4 orthoplanes xyz positionPlanes 128,128,128 style image region all
     2721
     2722> mousemode rightMode "move planes"
     2723
     2724> volume region all imageMode "full region"
     2725
     2726> volume unzone
     2727
     2728> mousemode rightMode "crop volume"
     2729
     2730Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
     2731models, 4 maps. 
     2732
     2733Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
     2734models, 4 maps. 
     2735
     2736Hide dust shortcut requires a displayed map surface 
     2737
     2738Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
     2739got 0 atomic models, 4 maps. 
     2740
     2741> lighting full
     2742
     2743> lighting soft
     2744
     2745> lighting simple
     2746
     2747> volume #1 level -0.127,0 level 0.1448,0.8 level 3.236,1
     2748
     2749> volume #1 level -0.127,0 level 0.6492,0.7846 level 3.236,1
     2750
     2751> volume #2 level -0.09525,0 level 0.2742,0.8 level 4.668,1
     2752
     2753> volume #2 level -0.09525,0 level 0.4796,0.6769 level 4.668,1
     2754
     2755> volume #3 level -0.127,0 level -0.0887,0.7538 level 3.236,1
     2756
     2757> close session
     2758
     2759> open 22906 format ccp4 fromDatabase emdb
     2760
     2761Opened emdb 22906 as #1, grid size 256,256,256, pixel 2.4, shown at level
     27620.309, step 1, values float32 
     2763
     2764> graphics silhouettes true
     2765
     2766> lighting flat
     2767
     2768> graphics silhouettes false
     2769
     2770> lighting full
     2771
     2772> open 22895 fromDatabase emdb format ccp4
     2773
     2774Opened emdb 22895 as #2, grid size 300,300,300, pixel 2.17, shown at level
     27750.05, step 2, values float32 
     2776
     2777> lighting full
     2778
     2779> transparency 40
     2780
     2781> surface
     2782
     2783No atomic models open. 
     2784
     2785> lighting full
     2786
     2787> lighting simple
     2788
     2789> lighting soft
     2790
     2791> lighting simple
     2792
     2793> view
     2794
     2795> ui tool show "Side View"
     2796
     2797> volume #1 level 0.309
     2798
     2799> volume #1 level 0.3328
     2800
     2801> color magenta
     2802
     2803> undo
     2804
     2805> volume #1 color #4f8f00
     2806
     2807> volume #2 color #ff85ff
     2808
     2809> volume #1 style mesh
     2810
     2811> volume #2 style mesh
     2812
     2813> volume #1 step 4
     2814
     2815> volume #1 step 1
     2816
     2817> volume #2 step 1
     2818
     2819> volume #1 style image
     2820
     2821> volume #1 style mesh
     2822
     2823> volume #1 style image maximumIntensityProjection true
     2824
     2825> volume #1 style mesh maximumIntensityProjection false
     2826
     2827> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
     2828> faces"
     2829
     2830> volume #2 style mesh
     2831
     2832> save /Users/mahesh/Desktop/22906_22895.cxs
     2833
     2834> save /Users/mahesh/Desktop/image2.png supersample 3
     2835
     2836> save "/Users/mahesh/Desktop/NURD grant/22906_22895.cxs"
     2837
     2838> close session
     2839
     2840> open 4pzs fromDatabase pdbe_bio format mmcif
     2841
     2842Summary of feedback from opening 4pzs fetched from pdbe_bio 
     2843--- 
     2844warning | Missing or incomplete sequence information. Inferred polymer connectivity. 
     2845 
     2846notes | Fetching compressed 4pzs bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/4pzs-assembly-1.cif.gz 
     2847Fetching CCD ACO from
     2848https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/ACO/ACO.cif 
     2849Fetching CCD DMS from
     2850https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif 
     2851 
     28524pzs bioassembly 1 title: 
     2853Crystal structure of p300 histone acetyltransferase domain in complex with
     2854Acetyl-Coenzyme A [more info...] 
     2855 
     2856Chain information for 4pzs bioassembly 1 #1 
     2857--- 
     2858Chain | Description 
     2859A | Histone acetyltransferase p300 
     2860 
     2861Non-standard residues in 4pzs bioassembly 1 #1 
     2862--- 
     2863ACO — (ACO) 
     2864DMS — (DMS) 
     2865 
     286611 atoms have alternate locations. Control/examine alternate locations with
     2867Altloc Explorer [start tool...] or the altlocs command. 
     2868Opened 1 biological assemblies for 4pzs 
     2869
     2870> ui tool show "Show Sequence Viewer"
     2871
     2872> close session
     2873
     2874> open 4bhw fromDatabase pdbe_bio format mmcif
     2875
     2876Summary of feedback from opening 4bhw fetched from pdbe_bio 
     2877--- 
     2878warning | Missing or incomplete sequence information. Inferred polymer connectivity. 
     2879 
     2880notes | Fetching compressed 4bhw bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/4bhw-assembly-1.cif.gz 
     2881Fetching CCD 01K from
     2882https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/01K/01K.cif 
     2883 
     28844bhw bioassembly 1 title: 
     2885Structural basis for autoinhibition of the acetyltransferase activity of p300
     2886[more info...] 
     2887 
     2888Chain information for 4bhw bioassembly 1 #1 
     2889--- 
     2890Chain | Description 
     2891A B | HISTONE ACETYLTRANSFERASE P300 
     2892 
     2893Non-standard residues in 4bhw bioassembly 1 #1 
     2894--- 
     289501K — (01K) 
     2896ZN — (ZN) 
     2897 
     2898Opened 1 biological assemblies for 4bhw 
     2899
     2900> save "/Users/mahesh/Desktop/NURD grant/p300 4bhw.cxs"
     2901
     2902> close session
     2903
     2904> open 4pzs format mmcif fromDatabase pdbe_bio
     2905
     2906Summary of feedback from opening 4pzs fetched from pdbe_bio 
     2907--- 
     2908warning | Missing or incomplete sequence information. Inferred polymer connectivity. 
     2909 
     2910 
     29114pzs bioassembly 1 title: 
     2912Crystal structure of p300 histone acetyltransferase domain in complex with
     2913Acetyl-Coenzyme A [more info...] 
     2914 
     2915Chain information for 4pzs bioassembly 1 #1 
     2916--- 
     2917Chain | Description 
     2918A | Histone acetyltransferase p300 
     2919 
     2920Non-standard residues in 4pzs bioassembly 1 #1 
     2921--- 
     2922ACO — (ACO) 
     2923DMS — (DMS) 
     2924 
     292511 atoms have alternate locations. Control/examine alternate locations with
     2926Altloc Explorer [start tool...] or the altlocs command. 
     2927Opened 1 biological assemblies for 4pzs 
     2928
     2929> save "/Users/mahesh/Desktop/NURD grant/p300 4pzs.cxs"
     2930
     2931> close session
     2932
     2933> open 5u7g fromDatabase pdbe_bio format mmcif
     2934
     2935Summary of feedback from opening 5u7g fetched from pdbe_bio 
     2936--- 
     2937warnings | Missing or incomplete sequence information. Inferred polymer connectivity. 
     2938Missing or incomplete sequence information. Inferred polymer connectivity. 
     2939 
     2940notes | Fetching compressed 5u7g bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/5u7g-assembly-1.cif.gz 
     2941Fetching compressed 5u7g bioassembly 2 from
     2942https://www.ebi.ac.uk/pdbe/static/entry/download/5u7g-assembly-2.cif.gz 
     2943 
     29445u7g bioassembly 1 title: 
     2945Crystal Structure of the Catalytic Core of CBP [more info...] 
     2946 
     2947Chain information for 5u7g bioassembly 1 #1.1 
     2948--- 
     2949Chain | Description 
     2950A | CREB-binding protein 
     2951 
     2952Non-standard residues in 5u7g bioassembly 1 #1.1 
     2953--- 
     2954ZN — (ZN) 
     2955 
     29565u7g bioassembly 1 mmCIF Assemblies 
     2957--- 
     29581| author_and_software_defined_assembly 
     29592| author_and_software_defined_assembly 
     2960 
     29615u7g bioassembly 2 title: 
     2962Crystal Structure of the Catalytic Core of CBP [more info...] 
     2963 
     2964Chain information for 5u7g bioassembly 2 #1.2 
     2965--- 
     2966Chain | Description 
     2967B | CREB-binding protein 
     2968 
     2969Non-standard residues in 5u7g bioassembly 2 #1.2 
     2970--- 
     2971ZN — (ZN) 
     2972 
     29735u7g bioassembly 2 mmCIF Assemblies 
     2974--- 
     29751| author_and_software_defined_assembly 
     29762| author_and_software_defined_assembly 
     2977 
     2978Opened 2 biological assemblies for 5u7g 
     2979
     2980> select #1.1/A
     2981
     29824426 atoms, 4554 bonds, 3 pseudobonds, 547 residues, 2 models selected 
     2983
     2984> hide (#!1.1 & sel) target a
     2985
     2986> cartoon hide (#!1.1 & sel)
     2987
     2988> hide (#!1.1 & sel) target a
     2989
     2990> select #1.1/A
     2991
     29924426 atoms, 4554 bonds, 3 pseudobonds, 547 residues, 2 models selected 
     2993
     2994> hide (#!1.1 & sel) target a
     2995
     2996> ui tool show "Show Sequence Viewer"
     2997
     2998> sequence chain #1.1/A #1.2/B
     2999
     3000Alignment identifier is 1 
     3001
     3002
     3003===== Log before crash end =====
     3004
     3005Log:
     3006Startup Messages 
     3007--- 
     3008note | available bundle cache has not been initialized yet 
     3009 
     3010UCSF ChimeraX version: 1.8 (2024-06-10) 
     3011© 2016-2024 Regents of the University of California. All rights reserved. 
     3012How to cite UCSF ChimeraX 
     3013
     3014
     3015
     3016
     3017OpenGL version: 4.1 ATI-5.5.17
     3018OpenGL renderer: AMD Radeon Pro 570X OpenGL Engine
     3019OpenGL vendor: ATI Technologies Inc.
     3020
     3021Python: 3.11.4
     3022Locale: UTF-8
     3023Qt version: PyQt6 6.6.1, Qt 6.6.1
     3024Qt runtime version: 6.6.3
     3025Qt platform: cocoa
     3026Hardware:
     3027
     3028    Hardware Overview:
     3029
     3030      Model Name: iMac
     3031      Model Identifier: iMac19,1
     3032      Processor Name: 6-Core Intel Core i5
     3033      Processor Speed: 3 GHz
     3034      Number of Processors: 1
     3035      Total Number of Cores: 6
     3036      L2 Cache (per Core): 256 KB
     3037      L3 Cache: 9 MB
     3038      Memory: 96 GB
     3039      System Firmware Version: 2022.100.22.0.0
     3040      OS Loader Version: 580.140.1~8
     3041      SMC Version (system): 2.46f12
     3042
     3043Software:
     3044
     3045    System Software Overview:
     3046
     3047      System Version: macOS 14.6.1 (23G93)
     3048      Kernel Version: Darwin 23.6.0
     3049      Time since boot: 44 days, 13 hours, 56 minutes
     3050
     3051Graphics/Displays:
     3052
     3053    Radeon Pro 570X:
     3054
     3055      Chipset Model: Radeon Pro 570X
     3056      Type: GPU
     3057      Bus: PCIe
     3058      PCIe Lane Width: x16
     3059      VRAM (Total): 4 GB
     3060      Vendor: AMD (0x1002)
     3061      Device ID: 0x67df
     3062      Revision ID: 0x00c5
     3063      ROM Revision: 113-D0008A-042
     3064      VBIOS Version: 113-D0008A14GL-003
     3065      EFI Driver Version: 01.B1.042
     3066      Metal Support: Metal 2
     3067      Displays:
     3068        iMac:
     3069          Display Type: Built-In Retina LCD
     3070          Resolution: Retina 5K (5120 x 2880)
     3071          Framebuffer Depth: 30-Bit Color (ARGB2101010)
     3072          Main Display: Yes
     3073          Mirror: Off
     3074          Online: Yes
     3075          Automatically Adjust Brightness: Yes
     3076          Connection Type: Internal
     3077        LG FULL HD:
     3078          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
     3079          UI Looks like: 1920 x 1080 @ 60.00Hz
     3080          Framebuffer Depth: 30-Bit Color (ARGB2101010)
     3081          Display Serial Number: 005NTBKDQ053
     3082          Mirror: Off
     3083          Online: Yes
     3084          Rotation: Supported
     3085          Connection Type: DVI or HDMI
     3086          Adapter Firmware Version: 0.00
     3087
     3088
     3089Installed Packages:
     3090    alabaster: 0.7.16
     3091    appdirs: 1.4.4
     3092    appnope: 0.1.4
     3093    asttokens: 2.4.1
     3094    Babel: 2.15.0
     3095    beautifulsoup4: 4.12.3
     3096    blockdiag: 3.0.0
     3097    blosc2: 2.0.0
     3098    build: 1.2.1
     3099    certifi: 2023.11.17
     3100    cftime: 1.6.4
     3101    charset-normalizer: 3.3.2
     3102    ChimeraX-AddCharge: 1.5.17
     3103    ChimeraX-AddH: 2.2.6
     3104    ChimeraX-AlignmentAlgorithms: 2.0.2
     3105    ChimeraX-AlignmentHdrs: 3.5
     3106    ChimeraX-AlignmentMatrices: 2.1
     3107    ChimeraX-Alignments: 2.12.7
     3108    ChimeraX-AlphaFold: 1.0
     3109    ChimeraX-AltlocExplorer: 1.1.1
     3110    ChimeraX-AmberInfo: 1.0
     3111    ChimeraX-Arrays: 1.1
     3112    ChimeraX-Atomic: 1.57.1
     3113    ChimeraX-AtomicLibrary: 14.0.6
     3114    ChimeraX-AtomSearch: 2.0.1
     3115    ChimeraX-AxesPlanes: 2.4
     3116    ChimeraX-BasicActions: 1.1.2
     3117    ChimeraX-BILD: 1.0
     3118    ChimeraX-BlastProtein: 2.4.6
     3119    ChimeraX-BondRot: 2.0.4
     3120    ChimeraX-BugReporter: 1.0.1
     3121    ChimeraX-BuildStructure: 2.12.1
     3122    ChimeraX-Bumps: 1.0
     3123    ChimeraX-BundleBuilder: 1.2.7
     3124    ChimeraX-ButtonPanel: 1.0.1
     3125    ChimeraX-CageBuilder: 1.0.1
     3126    ChimeraX-CellPack: 1.0
     3127    ChimeraX-Centroids: 1.4
     3128    ChimeraX-ChangeChains: 1.1
     3129    ChimeraX-CheckWaters: 1.4
     3130    ChimeraX-ChemGroup: 2.0.1
     3131    ChimeraX-Clashes: 2.2.4
     3132    ChimeraX-ColorActions: 1.0.5
     3133    ChimeraX-ColorGlobe: 1.0
     3134    ChimeraX-ColorKey: 1.5.6
     3135    ChimeraX-CommandLine: 1.2.5
     3136    ChimeraX-ConnectStructure: 2.0.1
     3137    ChimeraX-Contacts: 1.0.1
     3138    ChimeraX-Core: 1.8
     3139    ChimeraX-CoreFormats: 1.2
     3140    ChimeraX-coulombic: 1.4.3
     3141    ChimeraX-Crosslinks: 1.0
     3142    ChimeraX-Crystal: 1.0
     3143    ChimeraX-CrystalContacts: 1.0.1
     3144    ChimeraX-DataFormats: 1.2.3
     3145    ChimeraX-Dicom: 1.2.4
     3146    ChimeraX-DiffPlot: 1.0
     3147    ChimeraX-DistMonitor: 1.4.2
     3148    ChimeraX-DockPrep: 1.1.3
     3149    ChimeraX-Dssp: 2.0
     3150    ChimeraX-EMDB-SFF: 1.0
     3151    ChimeraX-ESMFold: 1.0
     3152    ChimeraX-FileHistory: 1.0.1
     3153    ChimeraX-FunctionKey: 1.0.1
     3154    ChimeraX-Geometry: 1.3
     3155    ChimeraX-gltf: 1.0
     3156    ChimeraX-Graphics: 1.1.1
     3157    ChimeraX-Hbonds: 2.4
     3158    ChimeraX-Help: 1.2.2
     3159    ChimeraX-HKCage: 1.3
     3160    ChimeraX-IHM: 1.1
     3161    ChimeraX-ImageFormats: 1.2
     3162    ChimeraX-IMOD: 1.0
     3163    ChimeraX-IO: 1.0.1
     3164    ChimeraX-ItemsInspection: 1.0.1
     3165    ChimeraX-IUPAC: 1.0
     3166    ChimeraX-Label: 1.1.10
     3167    ChimeraX-ListInfo: 1.2.2
     3168    ChimeraX-Log: 1.1.6
     3169    ChimeraX-LookingGlass: 1.1
     3170    ChimeraX-Maestro: 1.9.1
     3171    ChimeraX-Map: 1.2
     3172    ChimeraX-MapData: 2.0
     3173    ChimeraX-MapEraser: 1.0.1
     3174    ChimeraX-MapFilter: 2.0.1
     3175    ChimeraX-MapFit: 2.0
     3176    ChimeraX-MapSeries: 2.1.1
     3177    ChimeraX-Markers: 1.0.1
     3178    ChimeraX-Mask: 1.0.2
     3179    ChimeraX-MatchMaker: 2.1.3
     3180    ChimeraX-MCopy: 1.0
     3181    ChimeraX-MDcrds: 2.7.1
     3182    ChimeraX-MedicalToolbar: 1.0.3
     3183    ChimeraX-Meeting: 1.0.1
     3184    ChimeraX-MLP: 1.1.1
     3185    ChimeraX-mmCIF: 2.14.1
     3186    ChimeraX-MMTF: 2.2
     3187    ChimeraX-Modeller: 1.5.17
     3188    ChimeraX-ModelPanel: 1.5
     3189    ChimeraX-ModelSeries: 1.0.1
     3190    ChimeraX-Mol2: 2.0.3
     3191    ChimeraX-Mole: 1.0
     3192    ChimeraX-Morph: 1.0.2
     3193    ChimeraX-MouseModes: 1.2
     3194    ChimeraX-Movie: 1.0
     3195    ChimeraX-Neuron: 1.0
     3196    ChimeraX-Nifti: 1.2
     3197    ChimeraX-NMRSTAR: 1.0.2
     3198    ChimeraX-NRRD: 1.2
     3199    ChimeraX-Nucleotides: 2.0.3
     3200    ChimeraX-OpenCommand: 1.13.5
     3201    ChimeraX-PDB: 2.7.5
     3202    ChimeraX-PDBBio: 1.0.1
     3203    ChimeraX-PDBLibrary: 1.0.4
     3204    ChimeraX-PDBMatrices: 1.0
     3205    ChimeraX-PickBlobs: 1.0.1
     3206    ChimeraX-Positions: 1.0
     3207    ChimeraX-PresetMgr: 1.1.1
     3208    ChimeraX-PubChem: 2.2
     3209    ChimeraX-ReadPbonds: 1.0.1
     3210    ChimeraX-Registration: 1.1.2
     3211    ChimeraX-RemoteControl: 1.0
     3212    ChimeraX-RenderByAttr: 1.4.1
     3213    ChimeraX-RenumberResidues: 1.1
     3214    ChimeraX-ResidueFit: 1.0.1
     3215    ChimeraX-RestServer: 1.2
     3216    ChimeraX-RNALayout: 1.0
     3217    ChimeraX-RotamerLibMgr: 4.0
     3218    ChimeraX-RotamerLibsDunbrack: 2.0
     3219    ChimeraX-RotamerLibsDynameomics: 2.0
     3220    ChimeraX-RotamerLibsRichardson: 2.0
     3221    ChimeraX-SaveCommand: 1.5.1
     3222    ChimeraX-SchemeMgr: 1.0
     3223    ChimeraX-SDF: 2.0.2
     3224    ChimeraX-Segger: 1.0
     3225    ChimeraX-Segment: 1.0.1
     3226    ChimeraX-Segmentations: 3.0.15
     3227    ChimeraX-SelInspector: 1.0
     3228    ChimeraX-SeqView: 2.11.2
     3229    ChimeraX-Shape: 1.0.1
     3230    ChimeraX-Shell: 1.0.1
     3231    ChimeraX-Shortcuts: 1.1.1
     3232    ChimeraX-ShowSequences: 1.0.3
     3233    ChimeraX-SideView: 1.0.1
     3234    ChimeraX-Smiles: 2.1.2
     3235    ChimeraX-SmoothLines: 1.0
     3236    ChimeraX-SpaceNavigator: 1.0
     3237    ChimeraX-StdCommands: 1.16.5
     3238    ChimeraX-STL: 1.0.1
     3239    ChimeraX-Storm: 1.0
     3240    ChimeraX-StructMeasure: 1.2.1
     3241    ChimeraX-Struts: 1.0.1
     3242    ChimeraX-Surface: 1.0.1
     3243    ChimeraX-SwapAA: 2.0.1
     3244    ChimeraX-SwapRes: 2.5
     3245    ChimeraX-TapeMeasure: 1.0
     3246    ChimeraX-TaskManager: 1.0
     3247    ChimeraX-Test: 1.0
     3248    ChimeraX-Toolbar: 1.1.2
     3249    ChimeraX-ToolshedUtils: 1.2.4
     3250    ChimeraX-Topography: 1.0
     3251    ChimeraX-ToQuest: 1.0
     3252    ChimeraX-Tug: 1.0.1
     3253    ChimeraX-UI: 1.39.1
     3254    ChimeraX-uniprot: 2.3
     3255    ChimeraX-UnitCell: 1.0.1
     3256    ChimeraX-ViewDockX: 1.4.3
     3257    ChimeraX-VIPERdb: 1.0
     3258    ChimeraX-Vive: 1.1
     3259    ChimeraX-VolumeMenu: 1.0.1
     3260    ChimeraX-vrml: 1.0
     3261    ChimeraX-VTK: 1.0
     3262    ChimeraX-WavefrontOBJ: 1.0
     3263    ChimeraX-WebCam: 1.0.2
     3264    ChimeraX-WebServices: 1.1.4
     3265    ChimeraX-Zone: 1.0.1
     3266    colorama: 0.4.6
     3267    comm: 0.2.2
     3268    contourpy: 1.2.1
     3269    cxservices: 1.2.2
     3270    cycler: 0.12.1
     3271    Cython: 3.0.10
     3272    debugpy: 1.8.1
     3273    decorator: 5.1.1
     3274    docutils: 0.20.1
     3275    executing: 2.0.1
     3276    filelock: 3.13.4
     3277    fonttools: 4.53.0
     3278    funcparserlib: 2.0.0a0
     3279    glfw: 2.7.0
     3280    grako: 3.16.5
     3281    h5py: 3.11.0
     3282    html2text: 2024.2.26
     3283    idna: 3.7
     3284    ihm: 1.0
     3285    imagecodecs: 2024.1.1
     3286    imagesize: 1.4.1
     3287    ipykernel: 6.29.2
     3288    ipython: 8.21.0
     3289    ipywidgets: 8.1.3
     3290    jedi: 0.19.1
     3291    jinja2: 3.1.4
     3292    jupyter-client: 8.6.0
     3293    jupyter-core: 5.7.2
     3294    jupyterlab-widgets: 3.0.11
     3295    kiwisolver: 1.4.5
     3296    line-profiler: 4.1.2
     3297    lxml: 5.2.1
     3298    lz4: 4.3.3
     3299    MarkupSafe: 2.1.5
     3300    matplotlib: 3.8.4
     3301    matplotlib-inline: 0.1.7
     3302    msgpack: 1.0.8
     3303    nest-asyncio: 1.6.0
     3304    netCDF4: 1.6.5
     3305    networkx: 3.3
     3306    nibabel: 5.2.0
     3307    nptyping: 2.5.0
     3308    numexpr: 2.10.0
     3309    numpy: 1.26.4
     3310    openvr: 1.26.701
     3311    packaging: 23.2
     3312    ParmEd: 4.2.2
     3313    parso: 0.8.4
     3314    pep517: 0.13.1
     3315    pexpect: 4.9.0
     3316    pillow: 10.3.0
     3317    pip: 24.0
     3318    pkginfo: 1.10.0
     3319    platformdirs: 4.2.2
     3320    prompt-toolkit: 3.0.47
     3321    psutil: 5.9.8
     3322    ptyprocess: 0.7.0
     3323    pure-eval: 0.2.2
     3324    py-cpuinfo: 9.0.0
     3325    pycollada: 0.8
     3326    pydicom: 2.4.4
     3327    pygments: 2.17.2
     3328    pynmrstar: 3.3.4
     3329    pynrrd: 1.0.0
     3330    PyOpenGL: 3.1.7
     3331    PyOpenGL-accelerate: 3.1.7
     3332    pyopenxr: 1.0.3401
     3333    pyparsing: 3.1.2
     3334    pyproject-hooks: 1.1.0
     3335    PyQt6-commercial: 6.6.1
     3336    PyQt6-Qt6: 6.6.3
     3337    PyQt6-sip: 13.6.0
     3338    PyQt6-WebEngine-commercial: 6.6.0
     3339    PyQt6-WebEngine-Qt6: 6.6.3
     3340    python-dateutil: 2.9.0.post0
     3341    pytz: 2024.1
     3342    pyzmq: 26.0.3
     3343    qtconsole: 5.5.1
     3344    QtPy: 2.4.1
     3345    RandomWords: 0.4.0
     3346    requests: 2.31.0
     3347    scipy: 1.13.0
     3348    setuptools: 69.5.1
     3349    setuptools-scm: 8.0.4
     3350    sfftk-rw: 0.8.1
     3351    six: 1.16.0
     3352    snowballstemmer: 2.2.0
     3353    sortedcontainers: 2.4.0
     3354    soupsieve: 2.5
     3355    sphinx: 7.2.6
     3356    sphinx-autodoc-typehints: 2.0.1
     3357    sphinxcontrib-applehelp: 1.0.8
     3358    sphinxcontrib-blockdiag: 3.0.0
     3359    sphinxcontrib-devhelp: 1.0.6
     3360    sphinxcontrib-htmlhelp: 2.0.5
     3361    sphinxcontrib-jsmath: 1.0.1
     3362    sphinxcontrib-qthelp: 1.0.7
     3363    sphinxcontrib-serializinghtml: 1.1.10
     3364    stack-data: 0.6.3
     3365    superqt: 0.6.3
     3366    tables: 3.8.0
     3367    tcia-utils: 1.5.1
     3368    tifffile: 2024.1.30
     3369    tinyarray: 1.2.4
     3370    tornado: 6.4.1
     3371    traitlets: 5.14.2
     3372    typing-extensions: 4.12.2
     3373    tzdata: 2024.1
     3374    urllib3: 2.2.1
     3375    wcwidth: 0.2.13
     3376    webcolors: 1.13
     3377    wheel: 0.43.0
     3378    wheel-filename: 1.4.1
     3379    widgetsnbextension: 4.0.11
     3380}}}