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Opened 4 months ago
Last modified 4 months ago
#18437 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.5-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x000000031e9db000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d9cf000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c9c3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b9b7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a9ab000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031999f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000318993000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000317987000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031697b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031596f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000314963000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001fcc9cf80 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 149 in combine
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 522 in bind
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 376 in cn_peptide_bond
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/cmd.py", line 205 in cmd_join_peptide
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 774 in _jm_apply_cb
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 1193 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
{"app_name":"ChimeraX","timestamp":"2025-08-13 11:57:03.00 -0500","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.7.5 (23H527)","roots_installed":0,"name":"ChimeraX","incident_id":"768FAD03-8C28-4584-9D53-0453ECA121A0"}
{
"uptime" : 540000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1729093738,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 43753,
"osVersion" : {
"train" : "macOS 14.7.5",
"build" : "23H527",
"releaseType" : "User"
},
"captureTime" : "2025-08-13 11:56:47.4985 -0500",
"codeSigningMonitor" : 1,
"incident" : "768FAD03-8C28-4584-9D53-0453ECA121A0",
"pid" : 88829,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-25 16:34:15.0603 -0500",
"procStartAbsTime" : 3739027603256,
"procExitAbsTime" : 13034171129605,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"84939D93-11DF-572A-B9E1-4AFEBE55A994","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D838229F-FA46-F28D-A6DE-DAAA28E4700D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 5467,
"sleepWakeUUID" : "50C948D9-D3CF-4221-BBCA-C38458D40500",
"sip" : "enabled",
"vmRegionInfo" : "0x1000000205 is in 0x1000000000-0x7000000000; bytes after start: 517 bytes before end: 412316859898\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) fc0000000-1000000000 [ 1.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GPU Carveout (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000001000000205","rawCodes":[2,68719477253],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000001000000205"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":88829},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x1000000205 is in 0x1000000000-0x7000000000; bytes after start: 517 bytes before end: 412316859898\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) fc0000000-1000000000 [ 1.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GPU Carveout (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6156107048},{"value":99},{"value":95},{"value":0},{"value":0},{"value":11263280794378408253},{"value":11263280794315939517},{"value":14757395258967641293},{"value":4294967286},{"value":6156106978},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8711154688},{"value":0},{"value":10},{"value":8536051584,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8536051808,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4333848112,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":0},{"value":1},{"value":1},{"value":6156108880}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6792916000},"cpsr":{"value":1073745920},"fp":{"value":6156107120},"sp":{"value":6156107088},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/workingon.closed0716.cxs" format session
opened ChimeraX session
> close session
> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/aDmX.sequence" format fasta
No such database '/users/aho2840/desktop/satchell lab/mcfhomologs/mcf'
> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/aDmX.sequence" format fasta
No such database '/users/aho2840/desktop/satchell lab/mcfhomologs/mcf'
> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/workingon.07.02.25.cxs" format session
opened ChimeraX session
> hide #!1 models
> hide #!3 models
> show #9 models
> log metadata #9
The model has no metadata
> log chains #9
Chain information for cDmX.best_model.pdb #9
---
Chain | Description
A | No description available
> sequence chain #9/A
Alignment identifier is 9/A
> save /Users/aho2840/Desktop/dmxinchimera format fasta alignment 9/A
> close session
> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/workingon.07.02.25.cxs" format session
opened ChimeraX session
> close session
> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/workingon.closed0716.cxs" format session
opened ChimeraX session
> hide #!9 models
> hide #90 models
> show #109 models
> log metadata #109
The model has no metadata
> log chains #109
Chain information for C7BKP9.ranked_0.pdb #109
---
Chain | Description
A | No description available
> sequence chain #109/A
Alignment identifier is 109/A
> select
> #109/A:1731-1734,1737-1740,1848-1851,1946-1952,1955-1963,1969-1975,1979-1983,2008-2012,2055-2057,2071-2075,2078-2085,2090-2093,2106-2110,2116-2118,2159-2161,2165-2169,2195-2200,2223-2227,2272-2274,2289-2290,2294-2296,2315-2317,2529-2536,2545-2554,2557-2562,2580-2583,2599-2605,2631-2634,2762-2770,2782-2790,2798-2803,2808-2814,2852-2855,2879-2882,2918-2925,2929-2935
3318 atoms, 3331 bonds, 196 residues, 1 model selected
> select
> #109/A:93-114,123-132,143-161,166-196,200-227,237-256,258-260,264-318,324-327,330-349,358-360,362-368,376-405,428-437,444-447,451-463,472-517,527-566,568-582,590-657,667-688,700-712,714-716,726-740,750-756,760-782,794-818,828-849,852-864,876-882,887-931,1006-1009,1018-1036,1047-1063,1069-1085,1089-1107,1119-1137,1139-1152,1163-1173,1219-1225,1229-1235,1334-1337,1341-1343,1379-1385,1391-1404,1521-1526,1568-1579,1585-1592,1596-1602,1612-1626,1634-1648,1652-1665,1669-1681,1693-1705,1718-1720,1722-1724,1746-1758,1767-1781,1786-1791,1796-1804,1810-1819,1821-1842,1854-1857,1865-1877,1881-1893,1903-1913,1915-1918,1933-1935,1937-1940,1986-1999,2027-2031,2130-2154,2178-2190,2207-2218,2228-2230,2234-2239,2241-2251,2255-2270,2291-2293,2303-2305,2322-2337,2342-2344,2348-2358,2360-2362,2364-2382,2392-2394,2399-2409,2412-2415,2485-2494,2496-2503,2510-2522,2565-2571,2584-2594,2608-2616,2625-2627,2637-2646,2727-2742,2744-2748,2755-2761,2824-2826,2832-2843,2847-2849,2861-2870,2888-2895,2898-2909
22522 atoms, 22610 bonds, 1369 residues, 1 model selected
> show #!9 models
> show #1 models
> show #26 models
> hide #26 models
> show #38 models
> hide #38 models
> hide #!9 models
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> matchmaker #109 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with C7BKP9.ranked_0.pdb,
chain A (#109), sequence alignment score = 175.4
RMSD between 67 pruned atom pairs is 1.137 angstroms; (across all 172 pairs:
7.039)
> show #!87 models
> matchmaker #87 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with 6ii6, chain A (#87),
sequence alignment score = 1498.3
RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
1.561)
> hide #1 models
> hide #109 models
> hide #!87 models
> show #!9 models
> show #109 models
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with 6ii6, chain A (#9),
sequence alignment score = 1498.3
RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
1.561)
> hide #109 models
> show #109 models
> select #109/A:1746
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #109/A:1746-1750
78 atoms, 78 bonds, 5 residues, 1 model selected
> select #109/A:1746
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #109/A:1746-1758
208 atoms, 208 bonds, 13 residues, 1 model selected
> select #109/A:1746
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #109/A:1746-1800
863 atoms, 871 bonds, 55 residues, 1 model selected
> select #109/A:1746
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #109/A:1746-1825
1244 atoms, 1254 bonds, 80 residues, 1 model selected
> select #109/A:1746
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #109/A:1746-1895
2333 atoms, 2353 bonds, 150 residues, 1 model selected
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> select #109/A:2031
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:1746-2031
4485 atoms, 4530 bonds, 286 residues, 1 model selected
> color sel purple
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> select #109/A:2382
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2078-2382
4892 atoms, 4947 bonds, 305 residues, 1 model selected
> select #109/A:2382
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2378-2382
92 atoms, 91 bonds, 5 residues, 1 model selected
> select #109/A:2382
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2078-2382
4892 atoms, 4947 bonds, 305 residues, 1 model selected
> color sel medium blue
> select
> #109/A:93-114,123-132,143-161,166-196,200-227,237-256,258-260,264-318,324-327,330-349,358-360,362-368,376-405,428-437,444-447,451-463,472-517,527-566,568-582,590-657,667-688,700-712,714-716,726-740,750-756,760-782,794-818,828-849,852-864,876-882,887-931,1006-1009,1018-1036,1047-1063,1069-1085,1089-1107,1119-1137,1139-1152,1163-1173,1219-1225,1229-1235,1334-1337,1341-1343,1379-1385,1391-1404,1521-1526,1568-1579,1585-1592,1596-1602,1612-1626,1634-1648,1652-1665,1669-1681,1693-1705,1718-1720,1722-1724,1746-1758,1767-1781,1786-1791,1796-1804,1810-1819,1821-1842,1854-1857,1865-1877,1881-1893,1903-1913,1915-1918,1933-1935,1937-1940,1986-1999,2027-2031,2130-2154,2178-2190,2207-2218,2228-2230,2234-2239,2241-2251,2255-2270,2291-2293,2303-2305,2322-2337,2342-2344,2348-2358,2360-2362,2364-2382,2392-2394,2399-2409,2412-2415,2485-2494,2496-2503,2510-2522,2565-2571,2584-2594,2608-2616,2625-2627,2637-2646,2727-2742,2744-2748,2755-2761,2824-2826,2832-2843,2847-2849,2861-2870,2888-2895,2898-2909
22522 atoms, 22610 bonds, 1369 residues, 1 model selected
> select #109/A:2405-2406
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #109/A:2405-2409
92 atoms, 93 bonds, 5 residues, 1 model selected
> select #109/A:2441
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #109/A:2405-2441
545 atoms, 551 bonds, 37 residues, 1 model selected
> select #109/A:2383
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #109/A:2383-2441
890 atoms, 899 bonds, 59 residues, 1 model selected
> select #109/A:2382
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2377-2382
102 atoms, 101 bonds, 6 residues, 1 model selected
> select #109/A:2469
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #109/A:2469-2474
103 atoms, 103 bonds, 6 residues, 1 model selected
> select #109/A:2649
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #109/A:2469-2649
2900 atoms, 2935 bonds, 181 residues, 1 model selected
> select #109/A:2521
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #109/A:2521-2572
840 atoms, 851 bonds, 52 residues, 1 model selected
> select #109/A:2485-2486
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #109/A:2485-2646
2596 atoms, 2628 bonds, 162 residues, 1 model selected
> color sel forest green
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> select
> #109/A:93-114,123-132,143-161,166-196,200-227,237-256,258-260,264-318,324-327,330-349,358-360,362-368,376-405,428-437,444-447,451-463,472-517,527-566,568-582,590-657,667-688,700-712,714-716,726-740,750-756,760-782,794-818,828-849,852-864,876-882,887-931,1006-1009,1018-1036,1047-1063,1069-1085,1089-1107,1119-1137,1139-1152,1163-1173,1219-1225,1229-1235,1334-1337,1341-1343,1379-1385,1391-1404,1521-1526,1568-1579,1585-1592,1596-1602,1612-1626,1634-1648,1652-1665,1669-1681,1693-1705,1718-1720,1722-1724,1746-1758,1767-1781,1786-1791,1796-1804,1810-1819,1821-1842,1854-1857,1865-1877,1881-1893,1903-1913,1915-1918,1933-1935,1937-1940,1986-1999,2027-2031,2130-2154,2178-2190,2207-2218,2228-2230,2234-2239,2241-2251,2255-2270,2291-2293,2303-2305,2322-2337,2342-2344,2348-2358,2360-2362,2364-2382,2392-2394,2399-2409,2412-2415,2485-2494,2496-2503,2510-2522,2565-2571,2584-2594,2608-2616,2625-2627,2637-2646,2727-2742,2744-2748,2755-2761,2824-2826,2832-2843,2847-2849,2861-2870,2888-2895,2898-2909
22522 atoms, 22610 bonds, 1369 residues, 1 model selected
> select #109/A:1746
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #109/A:1746-2031
4485 atoms, 4530 bonds, 286 residues, 1 model selected
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> hide #109 models
> show #90 models
> show #84 models
> hide #90 models
> log metadata #84
The model has no metadata
> log chains #84
Chain information for AF-C4ULG3-F1-model_v4.pdb #84
---
Chain | Description | UniProt
A | toxin AFP18 | AFP18_YERRA 1-2123
> sequence chain #84/A
Alignment identifier is 84/A
> select #84/A:1430
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #84/A:1430-1437
68 atoms, 67 bonds, 8 residues, 1 model selected
> select #84/A:1430
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #84/A:1430-1713
2242 atoms, 2281 bonds, 284 residues, 1 model selected
> select #84/A:256
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #84/A:256-778
4091 atoms, 4142 bonds, 523 residues, 1 model selected
> hide #!9 models
> select #84/A:664-665
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #84/A:664-715
389 atoms, 393 bonds, 52 residues, 1 model selected
> select #84/A:727-778
389 atoms, 394 bonds, 52 residues, 1 model selected
> select #84/A:256-778
4091 atoms, 4142 bonds, 523 residues, 1 model selected
> color sel medium blue
> select add #84
16760 atoms, 17065 bonds, 2123 residues, 1 model selected
> select subtract #84
Nothing selected
> select #84/A:1151
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1151
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1404
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #84/A:1151-1404
1937 atoms, 1969 bonds, 254 residues, 1 model selected
> select
> #84/A:55-76,78-86,98-106,112-154,162-193,202-217,230-232,256-288,294-323,346-386,397-433,435-452,458-488,491-493,495-511,516-587,596-618,623-641,643-645,652-670,679-684,689-709,723-748,757-778,781-798,800-811,818-839,927-929,938-940,943-962,969-979,1027-1029,1032-1037,1040-1043,1063-1071,1077-1080,1091-1109,1116-1127,1151-1159,1161-1177,1181-1201,1206-1208,1210-1230,1236-1246,1280-1292,1296-1305,1310-1323,1330-1333,1336-1344,1391-1404,1409-1411,1430-1442,1451-1465,1470-1475,1480-1488,1494-1503,1505-1526,1538-1541,1549-1561,1565-1577,1581-1583,1585-1594,1598-1602,1614-1617,1619-1621,1667-1680,1708-1713,1718-1720,1807-1836,1859-1871,1889-1898,1909-1911,1915-1920,1924-1932,1936-1951,1972-1974,2003-2017,2023-2025,2029-2039,2041-2043,2045-2062,2080-2093
9231 atoms, 9299 bonds, 1157 residues, 1 model selected
> select #84/A:256
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #84/A:256-778
4091 atoms, 4142 bonds, 523 residues, 1 model selected
> color sel #040e52ff
> select add #84
16760 atoms, 17065 bonds, 2123 residues, 1 model selected
> select subtract #84
Nothing selected
> select
> #84/A:55-76,78-86,98-106,112-154,162-193,202-217,230-232,256-288,294-323,346-386,397-433,435-452,458-488,491-493,495-511,516-587,596-618,623-641,643-645,652-670,679-684,689-709,723-748,757-778,781-798,800-811,818-839,927-929,938-940,943-962,969-979,1027-1029,1032-1037,1040-1043,1063-1071,1077-1080,1091-1109,1116-1127,1151-1159,1161-1177,1181-1201,1206-1208,1210-1230,1236-1246,1280-1292,1296-1305,1310-1323,1330-1333,1336-1344,1391-1404,1409-1411,1430-1442,1451-1465,1470-1475,1480-1488,1494-1503,1505-1526,1538-1541,1549-1561,1565-1577,1581-1583,1585-1594,1598-1602,1614-1617,1619-1621,1667-1680,1708-1713,1718-1720,1807-1836,1859-1871,1889-1898,1909-1911,1915-1920,1924-1932,1936-1951,1972-1974,2003-2017,2023-2025,2029-2039,2041-2043,2045-2062,2080-2093
9231 atoms, 9299 bonds, 1157 residues, 1 model selected
> select #84/A:1428-1430
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #84/A:1430-1771
2729 atoms, 2779 bonds, 342 residues, 1 model selected
> select #84/A:1431
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #84/A:1431-1720
2289 atoms, 2330 bonds, 290 residues, 1 model selected
> select #84/A:1429-1430
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #84/A:1430-1763
2659 atoms, 2707 bonds, 334 residues, 1 model selected
> select #84/A:1430
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #84/A:1430-1713
2242 atoms, 2281 bonds, 284 residues, 1 model selected
> select #84/A:1714
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #84/A:1714-2123
3310 atoms, 3382 bonds, 410 residues, 1 model selected
> color sel #040e52ff
> select add #84
16760 atoms, 17065 bonds, 2123 residues, 1 model selected
> select subtract #84
Nothing selected
> select #84/A:1181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1181-1372
1455 atoms, 1478 bonds, 192 residues, 1 model selected
> color sel red
> select #84/A:1756
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1756-2062
2499 atoms, 2556 bonds, 307 residues, 1 model selected
> color sel blue
> select add #84
16760 atoms, 17065 bonds, 2123 residues, 1 model selected
> select subtract #84
Nothing selected
> select #84/A:1718
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #84/A:1718-1755
314 atoms, 318 bonds, 38 residues, 1 model selected
> color sel blue
> select #84/A:2093
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1718-2093
3065 atoms, 3131 bonds, 376 residues, 1 model selected
> color sel blue
> undo
> color sel blue
> select #84/A:1181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1181-1372
1455 atoms, 1478 bonds, 192 residues, 1 model selected
> select #84/A:1372-1373
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #84/A:1372-1379
63 atoms, 63 bonds, 8 residues, 1 model selected
> select #84/A:1181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1181-1379
1508 atoms, 1531 bonds, 199 residues, 1 model selected
> select #84/A:1181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1181-1379
1508 atoms, 1531 bonds, 199 residues, 1 model selected
> select #84/A:1151
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #84/A:1151-1404
1937 atoms, 1969 bonds, 254 residues, 1 model selected
> color sel red
> select add #84
16760 atoms, 17065 bonds, 2123 residues, 1 model selected
> select subtract #84
Nothing selected
> hide #84 models
> show #!78 models
> log metadata #78
No models had metadata
> log chains #78
Chain information for 8adb #78
---
Chain | Description | UniProt
A | Wc-VDT1 | D6YWY5_WADCW 279-493
> log metadata #78
No models had metadata
> log chains #78
Chain information for 8adb #78
---
Chain | Description | UniProt
A | Wc-VDT1 | D6YWY5_WADCW 279-493
> sequence chain #78/A
Alignment identifier is 78/A
> select #78/A:293
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #78/A:293-493
3033 atoms, 3061 bonds, 1 pseudobond, 196 residues, 2 models selected
> show #89 models
> matchmaker #89 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
AF-D6YWY5-F1-model_v4.pdb, chain A (#89), sequence alignment score = 118.2
RMSD between 35 pruned atom pairs is 1.066 angstroms; (across all 182 pairs:
16.490)
> matchmaker #78 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with 8adb, chain A (#78),
sequence alignment score = 101
RMSD between 32 pruned atom pairs is 1.292 angstroms; (across all 162 pairs:
12.300)
> select add #78
3385 atoms, 3275 bonds, 1 pseudobond, 350 residues, 2 models selected
> select subtract #78
Nothing selected
> hide #!78 models
> hide #89 models
> show #89 models
> show #1 models
> hide #1 models
> show #1 models
> show #8 models
> hide #8 models
> show #!9 models
> hide #1 models
> hide #89 models
> show #!78 models
> hide #!78 models
> show #89 models
> log metadata #89
The model has no metadata
> log chains #89
Chain information for AF-D6YWY5-F1-model_v4.pdb #89
---
Chain | Description | UniProt
A | uncharacterized protein | D6YWY5_WADCW 1-494
> sequence chain #89/A
Alignment identifier is 89/A
> select #89/A:271
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #89/A:271-275
41 atoms, 42 bonds, 5 residues, 1 model selected
> select #89/A:275
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #89/A:88-275
1508 atoms, 1543 bonds, 188 residues, 1 model selected
> select #89/A:308-310
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #89/A:308-484
1367 atoms, 1393 bonds, 177 residues, 1 model selected
> select #89/A:494
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #89/A:485-494
84 atoms, 85 bonds, 10 residues, 1 model selected
> select #89/A:308
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #89/A:308-494
1451 atoms, 1479 bonds, 187 residues, 1 model selected
> select #89/A:88
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #89/A:88-275
1508 atoms, 1543 bonds, 188 residues, 1 model selected
> color sel purple
> select add #89
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> select subtract #89
Nothing selected
> hide #89 models
> show #90 models
> log metadata #90
The model has no metadata
> log chains #90
Chain information for AF-Q9TZA7-F1-model_v4.pdb #90
---
Chain | Description | UniProt
A | BTB domain-containing protein | Q9TZA7_CAEEL 1-213
> sequence chain #89/A
Alignment identifier is 89/A
> log metadata #90
The model has no metadata
> log chains #90
Chain information for AF-Q9TZA7-F1-model_v4.pdb #90
---
Chain | Description | UniProt
A | BTB domain-containing protein | Q9TZA7_CAEEL 1-213
> sequence chain #90/A
Alignment identifier is 90/A
> matchmaker #90 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
AF-Q9TZA7-F1-model_v4.pdb, chain A (#90), sequence alignment score = 80.1
RMSD between 6 pruned atom pairs is 1.018 angstroms; (across all 131 pairs:
19.039)
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #90 models
> show #101 models
> matchmaker #101 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
WP_231937687.1.ranked_0.pdb, chain A (#101), sequence alignment score = 170.8
RMSD between 65 pruned atom pairs is 0.876 angstroms; (across all 187 pairs:
7.094)
> log metadata #101
The model has no metadata
> log chains #101
Chain information for WP_231937687.1.ranked_0.pdb #101
---
Chain | Description
A | No description available
> sequence chain #101/A
Alignment identifier is 101/A
> select #101/A:667
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #101/A:664-667
60 atoms, 61 bonds, 4 residues, 1 model selected
> select #101/A:664
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #101/A:664-666
49 atoms, 50 bonds, 3 residues, 1 model selected
> select #101/A:251
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #101/A:251
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #101/A:666
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #101/A:666-668
48 atoms, 49 bonds, 3 residues, 1 model selected
> sym #9
6ii6 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains A,C
2| author_and_software_defined_assembly| 1 copy of chains B,D
> log metadata #9
No models had metadata
> log chains #9
Chain information for 6ii6 #9
---
Chain | Description
A | Putative RTX-toxin
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:3350
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:3350-3352
25 atoms, 24 bonds, 3 residues, 1 model selected
> select clear
> select #101/A:561
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #101/A:561-563
54 atoms, 53 bonds, 3 residues, 1 model selected
> select #9/A:3482
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:3482
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #101/A:524
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #101/A:524-726
3245 atoms, 3281 bonds, 203 residues, 1 model selected
> select #101/A:727
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #101/A:727-1744
16157 atoms, 16303 bonds, 1018 residues, 1 model selected
> show sel cartoons
> select #101/A:1744
18 atoms, 18 bonds, 1 residue, 1 model selected
> select #101/A:1744
18 atoms, 18 bonds, 1 residue, 1 model selected
> select #101/A:1285
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #101/A:1285-1295
185 atoms, 187 bonds, 11 residues, 1 model selected
> select #101/A:1296
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #101/A:1296-1397
1587 atoms, 1602 bonds, 102 residues, 1 model selected
> select #101/A:1262
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #101/A:1262-1397
2133 atoms, 2154 bonds, 136 residues, 1 model selected
> select #101/A:1373
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #101/A:1373-1430
902 atoms, 908 bonds, 58 residues, 1 model selected
> select
> #101/A:9-11,15-19,45-50,207-211,249-252,334-336,340-345,348-356,635-638,658-662,667-673,676-681,685-689,723-726,761-764,767-770,779-781,803-805,892-899,905-912,917-924,1146-1148,1153-1156,1165-1168,1175-1177,1182-1185,1207-1211,1227-1231,1262-1265,1270-1279,1285-1289,1296-1299,1302-1306,1312-1315,1339-1343,1349-1352,1357-1362,1369-1372,1380-1385,1392-1397,1405-1410,1414-1416,1423-1426,1433-1435,1440-1444,1450-1454,1461-1468,1475-1479,1486-1491,1495-1500,1508-1515,1528-1532,1536-1540,1548-1554,1588-1590,1594-1599,1602-1607,1613-1615,1621-1625,1631-1633,1642-1646,1655-1657,1669-1674,1679-1685,1688-1696,1710-1712,1717-1719,1734-1738
5775 atoms, 5767 bonds, 344 residues, 1 model selected
> select #101/A:1296
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #101/A:1296-1695
6309 atoms, 6380 bonds, 400 residues, 1 model selected
> select #101/A:1296
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #101/A:1296-1744
7111 atoms, 7189 bonds, 449 residues, 1 model selected
> select #101/A:1165
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #101/A:1165-1185
315 atoms, 315 bonds, 21 residues, 1 model selected
> select #101/A:1165
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #101/A:1165-1744
9160 atoms, 9257 bonds, 580 residues, 1 model selected
> select #101/A:1146-1196
764 atoms, 765 bonds, 51 residues, 1 model selected
> select #101/A:1146-1744
9443 atoms, 9540 bonds, 599 residues, 1 model selected
> color sel light gray
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> color sel light gray
> color sel gray
> select add #101
27933 atoms, 28182 bonds, 1744 residues, 1 model selected
> select subtract #101
Nothing selected
> hide #101 models
> show #!94 models
> log metadata #94
No models had metadata
> log chains #94
Chain information for GMGC10.017_810_714.ranked_0.pdb #94
---
Chain | Description
A | No description available
> sequence chain #94/A
Alignment identifier is 94/A
> select #94/A:1531
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #94/A:1531-1698
2589 atoms, 2603 bonds, 168 residues, 1 model selected
> select #94/A:1521-1522
35 atoms, 35 bonds, 2 residues, 1 model selected
> select #94/A:1521-1737
3349 atoms, 3376 bonds, 217 residues, 1 model selected
> select #94/A:1521-1737
3349 atoms, 3376 bonds, 217 residues, 1 model selected
> select #94/A:1521-2166
9849 atoms, 9937 bonds, 646 residues, 1 model selected
> select #94/A:1489
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #94/A:1489-1494
95 atoms, 95 bonds, 6 residues, 1 model selected
> select #94/A:2167-2168
26 atoms, 25 bonds, 2 residues, 1 model selected
> select #94/A:2167-2223
852 atoms, 861 bonds, 57 residues, 1 model selected
> select #94/A:2166
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #94/A:2153-2166
229 atoms, 231 bonds, 14 residues, 1 model selected
> select #94/A:2166
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #94/A:1672-2166
7579 atoms, 7652 bonds, 495 residues, 1 model selected
> select #94/A:1421-2166
11301 atoms, 11402 bonds, 746 residues, 1 model selected
> select add #94
34588 atoms, 34892 bonds, 2223 residues, 2 models selected
> select subtract #94
1 model selected
> hide #!94 models
> show #77 models
> log metadata #77
The model has no metadata
> log chains #77
Chain information for AF-A0A097A1Q2-F1-model_v4.pdb #77
---
Chain | Description
A | putative RTX-toxin
> sequence chain #77/A
Alignment identifier is 77/A
> select
> #77/A:16-22,31-46,52-68,70-72,75-93,96-98,111-113,117-125,127-129,153-155
613 atoms, 609 bonds, 83 residues, 1 model selected
> save /Users/aho2840/Desktop/1q2 format fasta alignment 77/A
> select add #77
1274 atoms, 1295 bonds, 171 residues, 1 model selected
> select subtract #77
Nothing selected
> hide #77 models
> show #75 models
> log metadata #75
The model has no metadata
> log chains #75
Chain information for AF-A0A0K0E9U3-F1-model_v4.pdb #75
---
Chain | Description
A | ubiquitinyl hydrolase 1
> sequence chain #75/A
Alignment identifier is 75/A
> select #75/A:204-252
396 atoms, 398 bonds, 49 residues, 1 model selected
> select #75/A
2008 atoms, 2043 bonds, 252 residues, 1 model selected
> matchmaker #75 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
AF-A0A0K0E9U3-F1-model_v4.pdb, chain A (#75), sequence alignment score = 64.1
RMSD between 27 pruned atom pairs is 1.251 angstroms; (across all 166 pairs:
20.318)
> select subtract #75
Nothing selected
> select add #75
2008 atoms, 2043 bonds, 252 residues, 1 model selected
> select subtract #75
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #75/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #75/A:1-26
212 atoms, 215 bonds, 26 residues, 1 model selected
> select #75/A:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #75/A:1-238
1898 atoms, 1932 bonds, 238 residues, 1 model selected
> select #75/A:240
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #75/A:240
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #75/A:194
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #75/A:171-194
183 atoms, 187 bonds, 24 residues, 1 model selected
> select #75/A:170
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:1-170
1359 atoms, 1386 bonds, 170 residues, 1 model selected
> color sel purple
> select add #75
2008 atoms, 2043 bonds, 252 residues, 1 model selected
> select subtract #75
Nothing selected
> select #75/A:252
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:252
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #75
2008 atoms, 2043 bonds, 252 residues, 1 model selected
> select subtract #75
Nothing selected
> hide #75 models
> show #100 models
> matchmaker #100 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
WP_148121377.1.ranked_0.pdb, chain A (#100), sequence alignment score = 124.8
RMSD between 57 pruned atom pairs is 1.106 angstroms; (across all 188 pairs:
9.164)
> hide #!9 models
> log metadata #100
The model has no metadata
> log chains #100
Chain information for WP_148121377.1.ranked_0.pdb #100
---
Chain | Description
A | No description available
> sequence chain #100/A
Alignment identifier is 100/A
> select #100/A:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #100/A:351-421
1223 atoms, 1234 bonds, 71 residues, 1 model selected
> select #100/A:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #100/A:422-424
42 atoms, 41 bonds, 3 residues, 1 model selected
> select #100/A:421-422
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #100/A:421-437
276 atoms, 275 bonds, 17 residues, 1 model selected
> show #!9 models
> select #100/A:747
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #100/A:421-747
5307 atoms, 5372 bonds, 327 residues, 1 model selected
> select #100/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #100/A:1-294
4843 atoms, 4906 bonds, 294 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #100 & sel to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
WP_148121377.1.ranked_0.pdb, chain A (#100), sequence alignment score = 129.3
RMSD between 53 pruned atom pairs is 0.785 angstroms; (across all 180 pairs:
20.140)
> matchmaker #100 & sel to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
WP_148121377.1.ranked_0.pdb, chain A (#100), sequence alignment score = 129.3
RMSD between 53 pruned atom pairs is 0.785 angstroms; (across all 180 pairs:
20.140)
> select add #100
31107 atoms, 31455 bonds, 1953 residues, 1 model selected
> select subtract #100
Nothing selected
> select #100/A:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #100/A:421-747
5307 atoms, 5372 bonds, 327 residues, 1 model selected
> color sel purple
> select add #100
31107 atoms, 31455 bonds, 1953 residues, 1 model selected
> select subtract #100
Nothing selected
> hide #100 models
> show #93 models
> log metadata #93
The model has no metadata
> log chains #93
Chain information for C4K5K2.ranked_0.pdb #93
---
Chain | Description
A | No description available
> sequence chain #93/A
Alignment identifier is 93/A
> matchmaker #93 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with C4K5K2.ranked_0.pdb,
chain A (#93), sequence alignment score = 133.9
RMSD between 51 pruned atom pairs is 0.709 angstroms; (across all 196 pairs:
19.970)
> select #93/A:309
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #93/A:1-309
5161 atoms, 5230 bonds, 309 residues, 1 model selected
> select #93/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:1-294
4887 atoms, 4952 bonds, 294 residues, 1 model selected
> color sel purple
> select #93/A:1243
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:1243-1300
888 atoms, 896 bonds, 58 residues, 1 model selected
> select #93/A:1243-1901
10228 atoms, 10326 bonds, 659 residues, 1 model selected
> color sel #941751ff
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> select #93/A:303
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #93/A:303-1251
15310 atoms, 15476 bonds, 949 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #93 & sel to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with C4K5K2.ranked_0.pdb,
chain A (#93), sequence alignment score = 121.2
RMSD between 51 pruned atom pairs is 1.196 angstroms; (across all 187 pairs:
7.810)
> matchmaker #93 & sel to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with C4K5K2.ranked_0.pdb,
chain A (#93), sequence alignment score = 121.2
RMSD between 51 pruned atom pairs is 1.196 angstroms; (across all 187 pairs:
7.810)
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> ui mousemode right select
Drag select of 804 residues
> hide sel cartoons
Drag select of 606 residues
> hide sel cartoons
Drag select of 54 residues
> hide sel cartoons
Drag select of 108 residues
> hide sel cartoons
Drag select of 12 residues
> hide sel cartoons
> ui mousemode right "translate selected models"
> view matrix models
> #93,-0.54652,0.1758,0.81879,36.258,-0.76539,0.2919,-0.57355,17.296,-0.33984,-0.94015,-0.024975,11.622
> undo
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> select #93/A:462
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #93/A:412-462
782 atoms, 788 bonds, 51 residues, 1 model selected
> select #93/A:425
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #93/A:425-450
404 atoms, 407 bonds, 26 residues, 1 model selected
> show sel cartoons
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> select #93/A:424
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:374-424
831 atoms, 835 bonds, 51 residues, 1 model selected
> show sel cartoons
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> select #93/A:464
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #93/A:464-516
866 atoms, 871 bonds, 53 residues, 1 model selected
> select #93/A:416
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:416-748
5417 atoms, 5478 bonds, 333 residues, 1 model selected
> select #93/A:416
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:416-742
5313 atoms, 5373 bonds, 327 residues, 1 model selected
> select #93/A:1912-1960
748 atoms, 759 bonds, 49 residues, 1 model selected
> select #93/A
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> show sel cartoons
> select subtract #93
Nothing selected
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> select #93/A:263
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #93/A:263-364
1780 atoms, 1800 bonds, 102 residues, 1 model selected
> select #93/A:86-136
849 atoms, 851 bonds, 51 residues, 1 model selected
> select #93/A:35-136
1703 atoms, 1716 bonds, 102 residues, 1 model selected
> select #93/A:295
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #93/A:295-415
2101 atoms, 2122 bonds, 121 residues, 1 model selected
> color sel #040e52ff
> select #93/A:416
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:416-742
5313 atoms, 5373 bonds, 327 residues, 1 model selected
> color sel purple
> select #93/A:743
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #93/A:743-1242
7907 atoms, 7989 bonds, 500 residues, 1 model selected
> color sel #040e52ff
> select #93/A:1902
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #93/A:1902-1960
896 atoms, 908 bonds, 59 residues, 1 model selected
> color sel #040e52ff
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> hide #93 models
> show #104 models
> show #105 models
> select add #104
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #104
Nothing selected
> log metadata #105
The model has no metadata
> log chains #105
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105
---
Chain | Description
A | No description available
> sequence chain #105/A
Alignment identifier is 105/A
> log metadata #104
The model has no metadata
> log chains #104
Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104
---
Chain | Description
A | No description available
> sequence chain #104/A
Alignment identifier is 104/A
Already setting window visible!
> select
> #105/A:10-18,30-42,46-68,70-76,109-128,144-152,159-161,182-190,196-198,201-210,221-229,231-245,259-289,301-303,316-328,334-354,361-379,383-385,394-403,447-458,469-472,487-492,494-505,511-518,530-535,547-555,561-563,568-576,581-597,603-605,624-635,646-670,674-689,695-704,710-726,732-740,743-752,766-775,778-790,793-804,809-821,828-833,836-855,859-869,879-896,915-927,935-958,975-977,984-991,995-1018,1020-1022,1026-1038,1043-1082,1331-1333,1394-1396,1434-1442,1546-1548
10303 atoms, 10318 bonds, 667 residues, 1 model selected
> select #105/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #105/A:1-43
683 atoms, 687 bonds, 43 residues, 1 model selected
> select #105/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #105/A:1-200
3067 atoms, 3094 bonds, 200 residues, 1 model selected
> select #105/A:201
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:201-209
138 atoms, 139 bonds, 9 residues, 1 model selected
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> matchmaker #9 to #104
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb, chain A (#104)
with 6ii6, chain A (#9), sequence alignment score = 105.4
RMSD between 4 pruned atom pairs is 0.393 angstroms; (across all 200 pairs:
44.701)
> undo
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with 6ii6, chain A (#9),
sequence alignment score = 1498.3
RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
1.561)
> hide #!9 models
> select subtract #105
Nothing selected
> hide #105 models
> show #105 models
> matchmaker #9 to #105
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
6ii6, chain A (#9), sequence alignment score = 270
RMSD between 108 pruned atom pairs is 1.145 angstroms; (across all 292 pairs:
10.773)
> show #!9 models
> select #105/A:300
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:300-303
61 atoms, 61 bonds, 4 residues, 1 model selected
> select #105/A:299
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #105/A:291-299
141 atoms, 141 bonds, 9 residues, 1 model selected
> toolshed show
> ui tool show "Renumber Residues"
> select #105/A:260-310
775 atoms, 779 bonds, 51 residues, 1 model selected
> select #105/A:260-410
2225 atoms, 2237 bonds, 151 residues, 1 model selected
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> hide #105 models
> show #105 models
> select #105/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #105/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> ui tool show "Renumber Residues"
> renumber #105/A seqStart 1800
1601 residues renumbered
> select #105/A:2100
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #105/A:2100-2404
4566 atoms, 4593 bonds, 305 residues, 1 model selected
> select #105/A:2100
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #105/A:2100-2111
167 atoms, 167 bonds, 12 residues, 1 model selected
> select #105/A:2099
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:2077-2099
345 atoms, 346 bonds, 23 residues, 1 model selected
> select
> #105/A:1809-1817,1829-1841,1845-1867,1869-1875,1908-1927,1943-1951,1958-1960,1981-1989,1995-1997,2000-2009,2020-2028,2030-2044,2058-2088,2100-2102,2115-2127,2133-2153,2160-2178,2182-2184,2193-2202,2246-2257,2268-2271,2286-2291,2293-2304,2310-2317,2329-2334,2346-2354,2360-2362,2367-2375,2380-2396,2402-2404,2423-2434,2445-2469,2473-2488,2494-2503,2509-2525,2531-2539,2542-2551,2565-2574,2577-2589,2592-2603,2608-2620,2627-2632,2635-2654,2658-2668,2678-2695,2714-2726,2734-2757,2774-2776,2783-2790,2794-2817,2819-2821,2825-2837,2842-2881,3130-3132,3193-3195,3233-3241,3345-3347
10303 atoms, 10318 bonds, 667 residues, 1 model selected
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> select #105/A:2058-2059
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #105/A:2058-2088
474 atoms, 475 bonds, 31 residues, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:2000-2047
752 atoms, 762 bonds, 48 residues, 1 model selected
> select #105/A:2305
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #105/A:2305-2323
280 atoms, 280 bonds, 19 residues, 1 model selected
> color sel #040e52ff
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> select #104/A:210
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #104/A:210-580
5606 atoms, 5651 bonds, 371 residues, 1 model selected
> select #104/A:210
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #104/A:210-572
5487 atoms, 5531 bonds, 363 residues, 1 model selected
> select #104/A:209
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #104/A:1-209
3205 atoms, 3238 bonds, 209 residues, 1 model selected
> color sel #040e52ff
> select #104/A:573
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #104/A:573-576
54 atoms, 54 bonds, 4 residues, 1 model selected
> select #104/A:573-576
54 atoms, 54 bonds, 4 residues, 1 model selected
> select #104/A:573-918
5213 atoms, 5272 bonds, 346 residues, 1 model selected
> select #104/A:573-1221
9872 atoms, 9977 bonds, 649 residues, 1 model selected
> color sel #040e52ff
> select #104/A:1223
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #104/A:1223-1273
734 atoms, 736 bonds, 51 residues, 1 model selected
> select #104/A:1222
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #104/A:1222-1324
1472 atoms, 1477 bonds, 103 residues, 1 model selected
> select #104/A:1222-1706
7297 atoms, 7351 bonds, 485 residues, 1 model selected
> color sel black
> select #104/A:1707
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #104/A:1707-1716
150 atoms, 152 bonds, 10 residues, 1 model selected
> show #!45 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> select add #104
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #104
Nothing selected
> hide #105 models
> hide #104 models
> show #!45 models
> hide #!45 models
> show #!45 models
> select add #45
1013 atoms, 1012 bonds, 253 residues, 2 models selected
> show #!9 cartoons
> select subtract #45
Nothing selected
> select add #45
1013 atoms, 1012 bonds, 253 residues, 2 models selected
> select subtract #45
Nothing selected
> hide #!45 models
> hide #!9 models
> show #!45 models
> select add #45
1013 atoms, 1012 bonds, 253 residues, 2 models selected
> show #45.2 models
> view matrix models #45,1,0,0,40.708,0,1,0,63.372,0,0,1,-69.846
> hide #45.2 models
> hide #!45 models
> select subtract #45.2
1 model selected
> select add #45
1013 atoms, 1012 bonds, 253 residues, 2 models selected
> select subtract #45
Nothing selected
> open "/Users/aho2840/Downloads/ranked_0 (4).pdb"
Chain information for ranked_0 (4).pdb #110
---
Chain | Description
A | No description available
> open "/Users/aho2840/Downloads/ranked_0 (5).pdb"
Chain information for ranked_0 (5).pdb #111
---
Chain | Description
A | No description available
> rename #110 GMGC10.011_528_202.ranked_0.1800.3500.pdb
> rename #110 GMGC10.011_528_202.ranked_0.3247.3500.pdb
> rename #110 GMGC10.011_528_202.ranked_0.3247.4160.pdb
> rename #111 GMGC10.011_528_202.ranked_0.4000.3500.pdb
> rename #111 GMGC10.011_528_202.ranked_0.4000.5243.pdb
> matchmaker #110 to #105
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110), sequence alignment
score = 1226.3
RMSD between 129 pruned atom pairs is 0.511 angstroms; (across all 253 pairs:
31.842)
> matchmaker #111 to #110
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
GMGC10.011_528_202.ranked_0.4000.5243.pdb, chain A (#111), sequence alignment
score = 708.7
RMSD between 7 pruned atom pairs is 1.070 angstroms; (across all 161 pairs:
16.247)
> show #105 models
> select #105/A:3156
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #105/A:3156-3314
2426 atoms, 2447 bonds, 159 residues, 1 model selected
> select #105/A:3250
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #105/A:3250-3400
2361 atoms, 2384 bonds, 151 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #110 to #105 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110), sequence alignment
score = 752.3
RMSD between 8 pruned atom pairs is 1.302 angstroms; (across all 151 pairs:
18.005)
> matchmaker #110 to #105 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110), sequence alignment
score = 752.3
RMSD between 8 pruned atom pairs is 1.302 angstroms; (across all 151 pairs:
18.005)
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> select #105/A:3250
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #105/A:3250-3400
2361 atoms, 2384 bonds, 151 residues, 1 model selected
> log metadata #110
The model has no metadata
> log chains #110
Chain information for GMGC10.011_528_202.ranked_0.3247.4160.pdb #110
---
Chain | Description
A | No description available
> sequence chain #110/A
Alignment identifier is 110/A
> select #110/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #110/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show "Renumber Residues"
> renumber #110/A seqStart 3247
913 residues renumbered
> renumber #110/A seqStart 3247
0 residues renumbered
> select #110/A:3247
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #110/A:3247-3501
3918 atoms, 3955 bonds, 255 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #110 & sel to #105 & sel
No 'to' model specified
> select #105/A:3250
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #105/A:3250-3400
2361 atoms, 2384 bonds, 151 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #110 & sel to #105 & sel
No molecules/chains to match specified
> select #110/A:3501
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #110/A:3247-3501
3918 atoms, 3955 bonds, 255 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #105 to #110 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105), sequence alignment
score = 1226.3
RMSD between 129 pruned atom pairs is 0.511 angstroms; (across all 253 pairs:
31.842)
> matchmaker #105 to #110 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105), sequence alignment
score = 1226.3
RMSD between 129 pruned atom pairs is 0.511 angstroms; (across all 253 pairs:
31.842)
> select add #110
13993 atoms, 14133 bonds, 913 residues, 1 model selected
> select subtract #110
Nothing selected
> select #110/A:3247
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #110/A:3247-3499
3894 atoms, 3931 bonds, 253 residues, 1 model selected
> view matrix models
> #110,0.15907,0.871,0.46482,23.648,0.26589,-0.49121,0.82946,67.554,0.95079,-0.0083555,-0.30973,62.328
> undo
> hide sel cartoons
> select #110/A:3500
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #110/A:3500-3579
1231 atoms, 1241 bonds, 80 residues, 1 model selected
> view matrix models
> #110,0.15907,0.871,0.46482,-35.338,0.26589,-0.49121,0.82946,31.014,0.95079,-0.0083555,-0.30973,38.751
> select #105/A:3393
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #105/A:3393-3400
129 atoms, 128 bonds, 8 residues, 1 model selected
> view matrix models
> #105,0.070652,0.61953,-0.78179,58.534,-0.84869,0.44916,0.27924,77.982,0.52415,0.64377,0.55752,4.1016
> undo
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> select #110/A:3247
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #110/A:3247-3263
270 atoms, 271 bonds, 17 residues, 1 model selected
> select #110/A:3247
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #110/A:3247-3510
4063 atoms, 4102 bonds, 264 residues, 1 model selected
> select #110/A:3504-3505
38 atoms, 38 bonds, 2 residues, 1 model selected
> select #110/A:3504-3510
114 atoms, 115 bonds, 7 residues, 1 model selected
> select #110/A:3500
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #110/A:3500-3534
585 atoms, 590 bonds, 35 residues, 1 model selected
> view matrix models
> #110,0.15907,0.871,0.46482,-22.055,0.26589,-0.49121,0.82946,63.614,0.95079,-0.0083555,-0.30973,185.11
> ui mousemode right "rotate selected models"
> view matrix models
> #110,0.47262,-0.25828,0.84257,-25.085,-0.61466,-0.78176,0.10513,73.004,0.63153,-0.56758,-0.52823,188.63
> view matrix models
> #110,0.50805,-0.24833,0.82475,-25.704,-0.63892,-0.75081,0.16751,73.694,0.57763,-0.61206,-0.54012,189.36
> view matrix models
> #110,0.41155,-0.2799,0.86734,-24.051,-0.56296,-0.82648,0.00040731,71.684,0.71673,-0.48845,-0.49771,187.53
> view matrix models
> #110,0.53239,-0.24265,0.81098,-26.137,-0.65303,-0.72733,0.21107,74.134,0.53863,-0.64196,-0.54568,189.91
> view matrix models
> #110,0.58365,-0.23401,0.77755,-27.073,-0.6754,-0.67148,0.30488,74.962,0.45077,-0.7031,-0.54996,191.19
> view matrix models
> #110,0.50053,-0.26305,0.82479,-25.595,-0.61091,-0.78236,0.12122,73.03,0.6134,-0.56455,-0.55229,188.78
> view matrix models
> #110,0.54811,-0.2445,0.79987,-26.43,-0.65256,-0.72323,0.22609,74.204,0.52321,-0.64588,-0.55596,190.09
> view matrix models
> #110,0.49249,-0.26667,0.82845,-25.457,-0.60267,-0.79124,0.10358,72.815,0.62789,-0.5503,-0.5504,188.57
> view matrix models
> #110,0.56859,-0.23809,0.78741,-26.798,-0.66661,-0.69423,0.27144,74.654,0.48202,-0.67923,-0.55345,190.71
> view matrix models
> #110,-0.45753,-0.84636,0.27265,-14.236,-0.8879,0.41828,-0.19153,75.864,0.048064,-0.32971,-0.94286,195.29
> view matrix models
> #110,0.16212,-0.729,0.66504,-21.465,-0.98276,-0.17998,0.042289,78.334,0.088865,-0.66043,-0.74561,195.61
> ui mousemode right "translate selected models"
> view matrix models
> #110,0.16212,-0.729,0.66504,13.429,-0.98276,-0.17998,0.042289,14.171,0.088865,-0.66043,-0.74561,150.07
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> view matrix models
> #110,0.16212,-0.729,0.66504,56.796,-0.98276,-0.17998,0.042289,30.661,0.088865,-0.66043,-0.74561,177.29
> ui mousemode right "translate selected models"
> view matrix models
> #110,0.16212,-0.729,0.66504,62.215,-0.98276,-0.17998,0.042289,36.02,0.088865,-0.66043,-0.74561,170.42
> view matrix models
> #110,0.16212,-0.729,0.66504,47.904,-0.98276,-0.17998,0.042289,38.086,0.088865,-0.66043,-0.74561,171.89
> view matrix models
> #110,0.16212,-0.729,0.66504,48.471,-0.98276,-0.17998,0.042289,4.313,0.088865,-0.66043,-0.74561,146.61
> ui mousemode right "rotate selected models"
> view matrix models
> #110,0.13868,-0.7211,0.67881,48.894,-0.9903,-0.095156,0.10124,4.7482,-0.0084073,-0.68627,-0.7273,148.15
> view matrix models
> #110,0.14058,-0.72184,0.67763,48.86,-0.99007,-0.10231,0.096411,4.7183,-0.00026617,-0.68445,-0.72906,148.02
> view matrix models
> #110,0.15864,-0.728,0.66697,48.533,-0.9845,-0.16785,0.05096,4.3863,0.074849,-0.66471,-0.74334,146.83
> ui mousemode right "translate selected models"
> view matrix models
> #110,0.15864,-0.728,0.66697,47.311,-0.9845,-0.16785,0.05096,2.404,0.074849,-0.66471,-0.74334,145.71
> select add #110
13993 atoms, 14133 bonds, 913 residues, 1 model selected
> select subtract #110
Nothing selected
> select #110/A:3513
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #110/A:3513-3555
692 atoms, 697 bonds, 43 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #110,0.15864,-0.728,0.66697,45.54,-0.9845,-0.16785,0.05096,3.5472,0.074849,-0.66471,-0.74334,148.09
> view matrix models
> #110,0.15864,-0.728,0.66697,43.732,-0.9845,-0.16785,0.05096,4.7486,0.074849,-0.66471,-0.74334,147.21
> view matrix models
> #110,0.15864,-0.728,0.66697,43.927,-0.9845,-0.16785,0.05096,4.2323,0.074849,-0.66471,-0.74334,146.75
> view matrix models
> #110,0.15864,-0.728,0.66697,43.656,-0.9845,-0.16785,0.05096,3.9038,0.074849,-0.66471,-0.74334,146.59
> select add #110
13993 atoms, 14133 bonds, 913 residues, 1 model selected
> select subtract #110
Nothing selected
> ui mousemode right "translate selected models"
> log metadata #111
The model has no metadata
> log chains #111
Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111
---
Chain | Description
A | No description available
> sequence chain #111/A
Alignment identifier is 111/A
> ui tool show "Renumber Residues"
> renumber #111/A seqStart 4000
1244 residues renumbered
> renumber #111/A seqStart 4000
0 residues renumbered
> matchmaker #111 to #110
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.3247.4160.pdb, chain A (#110) with
GMGC10.011_528_202.ranked_0.4000.5243.pdb, chain A (#111), sequence alignment
score = 708.7
RMSD between 7 pruned atom pairs is 1.070 angstroms; (across all 161 pairs:
16.247)
> select #110/A:3297
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #110/A:3297-3303
115 atoms, 116 bonds, 7 residues, 1 model selected
> select #110/A:3297-3298
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #110/A:3298-3499
3100 atoms, 3130 bonds, 202 residues, 1 model selected
> select #110/A:3500-3501
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #110/A:3500-3562
975 atoms, 983 bonds, 63 residues, 1 model selected
> select add #110
13993 atoms, 14133 bonds, 913 residues, 1 model selected
> select subtract #110
Nothing selected
> select #111/A:4158-4159
32 atoms, 32 bonds, 2 residues, 1 model selected
> select #111/A:4000-4159
2425 atoms, 2448 bonds, 160 residues, 1 model selected
> hide sel cartoons
> select #111/A:4160
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #111/A:4160-4184
417 atoms, 419 bonds, 25 residues, 1 model selected
> select #110/A:4152
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #110/A:4152-4159
115 atoms, 116 bonds, 8 residues, 1 model selected
> select #111/A:4160-4161
28 atoms, 27 bonds, 2 residues, 1 model selected
> select #111/A:4160-4181
363 atoms, 364 bonds, 22 residues, 1 model selected
> view matrix models
> #111,-0.93959,0.29781,0.16873,42.264,-0.33284,-0.67993,-0.65339,-38.87,-0.07986,-0.67008,0.73798,108.14
> view matrix models
> #111,-0.93959,0.29781,0.16873,42.797,-0.33284,-0.67993,-0.65339,-42.124,-0.07986,-0.67008,0.73798,107.72
> ui mousemode right "rotate selected models"
> view matrix models
> #111,-0.62713,0.69959,0.34245,41.74,-0.75038,-0.42473,-0.5065,-39.054,-0.20889,-0.57461,0.79132,108.71
> ui mousemode right "translate selected models"
> view matrix models
> #111,-0.62713,0.69959,0.34245,39.779,-0.75038,-0.42473,-0.5065,-28.572,-0.20889,-0.57461,0.79132,111.29
> view matrix models
> #111,-0.62713,0.69959,0.34245,41.276,-0.75038,-0.42473,-0.5065,-30.269,-0.20889,-0.57461,0.79132,108.14
> view matrix models
> #111,-0.62713,0.69959,0.34245,40.683,-0.75038,-0.42473,-0.5065,-26.478,-0.20889,-0.57461,0.79132,111.91
> ui mousemode right "rotate selected models"
> view matrix models
> #111,-0.97688,0.12135,0.17602,41.593,-0.21316,-0.48928,-0.84568,-29.863,-0.016504,-0.86364,0.50383,110.14
> ui mousemode right "translate selected models"
> view matrix models
> #111,-0.97688,0.12135,0.17602,43.383,-0.21316,-0.48928,-0.84568,-27.172,-0.016504,-0.86364,0.50383,105.83
> ui mousemode right "rotate selected models"
> view matrix models
> #111,-0.99466,0.089736,0.051026,43.43,-0.098489,-0.67688,-0.72947,-28.271,-0.030922,-0.7306,0.6821,106.19
> ui mousemode right "translate selected models"
> view matrix models
> #111,-0.99466,0.089736,0.051026,45.183,-0.098489,-0.67688,-0.72947,-41.19,-0.030922,-0.7306,0.6821,108.26
> view matrix models
> #111,-0.99466,0.089736,0.051026,45.845,-0.098489,-0.67688,-0.72947,-42.078,-0.030922,-0.7306,0.6821,107.43
> ui mousemode right "rotate selected models"
> view matrix models
> #111,-0.9879,0.15505,0.0031988,45.944,-0.10909,-0.68007,-0.72499,-42.021,-0.11024,-0.71657,0.68875,107.94
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> view matrix models
> #111,-0.9879,0.15505,0.0031988,46.032,-0.10909,-0.68007,-0.72499,-38.774,-0.11024,-0.71657,0.68875,110.99
> view matrix models
> #111,-0.9879,0.15505,0.0031988,46.099,-0.10909,-0.68007,-0.72499,-38.417,-0.11024,-0.71657,0.68875,111.67
> view matrix models
> #111,-0.9879,0.15505,0.0031988,50.478,-0.10909,-0.68007,-0.72499,-37.638,-0.11024,-0.71657,0.68875,114.86
> view matrix models
> #111,-0.9879,0.15505,0.0031988,54.429,-0.10909,-0.68007,-0.72499,-39.744,-0.11024,-0.71657,0.68875,112.26
> view matrix models
> #111,-0.9879,0.15505,0.0031988,53.684,-0.10909,-0.68007,-0.72499,-39.925,-0.11024,-0.71657,0.68875,111.24
> view matrix models
> #111,-0.9879,0.15505,0.0031988,53.467,-0.10909,-0.68007,-0.72499,-39.84,-0.11024,-0.71657,0.68875,111.92
> select add #111
18385 atoms, 18537 bonds, 1244 residues, 1 model selected
> select subtract #111
Nothing selected
> select #110/A:4159
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #110/A:3797-4159
5587 atoms, 5653 bonds, 363 residues, 1 model selected
> color sel #040e52ff
> select #111/A:4000-4001
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #111/A
18385 atoms, 18537 bonds, 1244 residues, 1 model selected
> color sel #040e52ff
> select #110/A:3247
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #110/A
13993 atoms, 14133 bonds, 913 residues, 1 model selected
> color sel #040e52ff
> select subtract #110
Nothing selected
> show #104 models
> log metadata #104
The model has no metadata
> log chains #104
Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104
---
Chain | Description
A | No description available
> sequence chain #104/A
Alignment identifier is 104/A
> select #104/A:1-2
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #104/A
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> color sel #040e52ff
Already setting window visible!
> select #105/A:3353-3400
770 atoms, 777 bonds, 48 residues, 1 model selected
> select #105/A
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> color sel #040e52ff
> select subtract #105
Nothing selected
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:2000-2304
4600 atoms, 4636 bonds, 305 residues, 1 model selected
> color sel purple
> show #!9 models
> matchmaker #9 to #105
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.1800.3500.pdb, chain A (#105) with
6ii6, chain A (#9), sequence alignment score = 270
RMSD between 108 pruned atom pairs is 1.145 angstroms; (across all 292 pairs:
10.773)
> hide #!9 models
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> show #!9 models
> select #104/A:208
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #104/A:208-209
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #104/A:210
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #104/A:210-572
5487 atoms, 5531 bonds, 363 residues, 1 model selected
> color sel black
> select #104/A:1222
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #104/A:1222-1226
66 atoms, 65 bonds, 5 residues, 1 model selected
> select #104/A:1222
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #104/A:1222-1706
7297 atoms, 7351 bonds, 485 residues, 1 model selected
> color sel black
> select add #104
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #104
Nothing selected
> select #111/A:4513
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #111/A:4467-4513
707 atoms, 714 bonds, 47 residues, 1 model selected
> select #111/A:4413
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #111/A:4413
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #111/A:4529
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #111/A:4529-4540
167 atoms, 167 bonds, 12 residues, 1 model selected
> select #111/A:4529
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #111/A:4529-4672
2029 atoms, 2039 bonds, 144 residues, 1 model selected
> select #111/A:4394-4672
4060 atoms, 4092 bonds, 279 residues, 1 model selected
> select #111/A:4358
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #111/A:4358-4393
553 atoms, 557 bonds, 36 residues, 1 model selected
> select #111/A:4358-4561
3067 atoms, 3098 bonds, 204 residues, 1 model selected
> select #111/A:4358-4672
4613 atoms, 4650 bonds, 315 residues, 1 model selected
> select #111/A:4358-4832
6891 atoms, 6945 bonds, 475 residues, 1 model selected
> view matrix models
> #111,-0.9879,0.15505,0.0031988,-8.1987,-0.10909,-0.68007,-0.72499,71.437,-0.11024,-0.71657,0.68875,123.17
> undo
> select #111/A:4832
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #111/A:4832-4877
715 atoms, 721 bonds, 46 residues, 1 model selected
> select #111/A:4949
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #111/A:4931-4949
286 atoms, 286 bonds, 19 residues, 1 model selected
> select #111/A:4952
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #111/A:4750-4952
3012 atoms, 3033 bonds, 203 residues, 1 model selected
> select #111/A:4810
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #111/A:4759-4810
756 atoms, 762 bonds, 52 residues, 1 model selected
> select #111/A:4854
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #111/A:4757-4854
1492 atoms, 1503 bonds, 98 residues, 1 model selected
> select #111/A:4761
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #111/A:4761
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #111/A:4759-4760
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #111/A:4759-4762
59 atoms, 58 bonds, 4 residues, 1 model selected
> select #111/A:4769
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #111/A:4769-4774
95 atoms, 95 bonds, 6 residues, 1 model selected
> select #111/A:4826
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #111/A:4826-4832
117 atoms, 116 bonds, 7 residues, 1 model selected
> select #111/A:4931
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #111/A:4931-4938
109 atoms, 108 bonds, 8 residues, 1 model selected
> select #111/A:4891
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #111/A:4884-4891
141 atoms, 140 bonds, 8 residues, 1 model selected
> select #111/A:4854
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #111/A:4851-4854
66 atoms, 66 bonds, 4 residues, 1 model selected
> select #111/A:4804-4854
816 atoms, 821 bonds, 51 residues, 1 model selected
> select #111/A:4358-4854
7272 atoms, 7330 bonds, 497 residues, 1 model selected
> color sel #941751ff
> select add #111
18385 atoms, 18537 bonds, 1244 residues, 1 model selected
> select subtract #111
Nothing selected
> select #111/A:5065
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #111/A:5065-5122
814 atoms, 816 bonds, 58 residues, 1 model selected
> select #111/A:5065
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #111/A:5065-5212
2149 atoms, 2163 bonds, 148 residues, 1 model selected
> view matrix models
> #111,-0.9879,0.15505,0.0031988,51.419,-0.10909,-0.68007,-0.72499,-38.212,-0.11024,-0.71657,0.68875,109.14
> undo
> select #111/A:5035
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #111/A:5035-5243
3025 atoms, 3048 bonds, 209 residues, 1 model selected
> color sel #945200ff
> select add #111
18385 atoms, 18537 bonds, 1244 residues, 1 model selected
> select subtract #111
Nothing selected
> hide #111 models
> hide #110 models
> hide #105 models
> hide #104 models
> show #97 models
> rename #97 A0A2X2DF79.ranked_0.pdb
> log metadata #97
The model has no metadata
> log chains #97
Chain information for A0A2X2DF79.ranked_0.pdb #97
---
Chain | Description
A | No description available
> sequence chain #97/A
Alignment identifier is 97/A
> matchmaker #97 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with A0A2X2DF79.ranked_0.pdb, chain A (#97),
sequence alignment score = 398.6
RMSD between 127 pruned atom pairs is 1.100 angstroms; (across all 305 pairs:
11.055)
> select #97/A:1306
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #97/A:619-1306
10786 atoms, 10903 bonds, 688 residues, 1 model selected
> select #97/A:1960
22 atoms, 22 bonds, 1 residue, 1 model selected
> select #97/A:1960
22 atoms, 22 bonds, 1 residue, 1 model selected
> select add #97
31322 atoms, 31645 bonds, 1960 residues, 1 model selected
> select subtract #97
Nothing selected
> hide #97 models
> show #92 models
> log metadata #92
The model has no metadata
> log chains #92
Chain information for B6XGD1.ranked_0.pdb #92
---
Chain | Description
A | No description available
> sequence chain #92/A
Alignment identifier is 92/A
> select #92/A:419
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #92/A:419-737
5065 atoms, 5111 bonds, 319 residues, 1 model selected
> select #92/A:419
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #92/A:419-710
4622 atoms, 4667 bonds, 292 residues, 1 model selected
> select #92/A:711
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #92/A:711-714
48 atoms, 47 bonds, 4 residues, 1 model selected
> select #92/A:419
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #92/A:419-710
4622 atoms, 4667 bonds, 292 residues, 1 model selected
> select #92/A:418
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #92/A:401-418
271 atoms, 271 bonds, 18 residues, 1 model selected
> select #92/A:419
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #92/A:419-710
4622 atoms, 4667 bonds, 292 residues, 1 model selected
> select #92/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #92/A
33408 atoms, 33762 bonds, 2103 residues, 1 model selected
> color sel #040e52ff
> select #92/A:318-368
878 atoms, 880 bonds, 51 residues, 1 model selected
> select #92/A:267-368
1722 atoms, 1730 bonds, 102 residues, 1 model selected
> select #92/A:419
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #92/A:419-710
4622 atoms, 4667 bonds, 292 residues, 1 model selected
> color sel purple
> matchmaker #92 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with B6XGD1.ranked_0.pdb, chain A (#92),
sequence alignment score = 401.5
RMSD between 133 pruned atom pairs is 1.062 angstroms; (across all 317 pairs:
13.801)
> select add #92
33408 atoms, 33762 bonds, 2103 residues, 1 model selected
> select subtract #92
Nothing selected
> select #92/A:739
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #92/A:739-789
851 atoms, 859 bonds, 51 residues, 1 model selected
> select #92/A:1370-1419
789 atoms, 797 bonds, 50 residues, 1 model selected
> select #92/A:739-1419
10732 atoms, 10845 bonds, 681 residues, 1 model selected
> select #92/A:739
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #92/A:739-1419
10732 atoms, 10845 bonds, 681 residues, 1 model selected
> color sel cornflower blue
> select add #92
33408 atoms, 33762 bonds, 2103 residues, 1 model selected
> select subtract #92
Nothing selected
> hide #92 models
> show #88 models
> log metadata #88
The model has no metadata
> log chains #88
Chain information for Mcf2.ranked_0.pdb #88
---
Chain | Description
A | No description available
> sequence chain #88/A
Alignment identifier is 88/A
> select #88/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #88/A:1-627
9728 atoms, 9811 bonds, 627 residues, 1 model selected
> select #88/A:2339-2388
718 atoms, 724 bonds, 50 residues, 1 model selected
> select #88/A
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> select subtract #88
Nothing selected
> select add #88
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> select subtract #88
Nothing selected
> ui mousemode right select
Drag select of 384 residues
> select #88/A:674
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #88/A:674
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #88/A:670
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #88/A:670-971
4617 atoms, 4665 bonds, 302 residues, 1 model selected
> select
> #88/A:5-21,24-39,46-49,59-69,80-94,112-114,117-122,133-138,153-167,202-215,249-267,271-281,294-302,319-326,328-334,340-344,447-450,460-462,520-538,541-544,571-598,608-652,654-656,662-665,676-700,716-725,730-767,776-783,791-822,827-840,844-848,858-867,911-924,927-930,949-954,965-967,972-994,996-1024,1035-1037,1067-1086,1104-1132,1139-1156,1162-1173,1177-1180,1187-1190,1211-1217,1221-1229,1231-1234,1277-1302,1375-1379,1416-1418,1424-1431,1586-1589,1596-1605,1646-1650,1739-1747,1754-1765,1929-1932,1938-1944,2016-2022,2082-2102,2225-2228,2288-2290,2307-2317,2327-2329,2352-2360
12054 atoms, 12098 bonds, 758 residues, 1 model selected
> select #88/A:670-971
4617 atoms, 4665 bonds, 302 residues, 1 model selected
> select #88/A:612-613
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #88/A:561-613
882 atoms, 889 bonds, 53 residues, 1 model selected
> select #88/A:676-677
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #88/A:676-700
372 atoms, 376 bonds, 25 residues, 1 model selected
> matchmaker #89 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
sequence alignment score = 111.4
RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
25.856)
> matchmaker #88 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with Mcf2.ranked_0.pdb, chain A (#88), sequence
alignment score = 405.2
RMSD between 128 pruned atom pairs is 0.972 angstroms; (across all 303 pairs:
12.736)
Drag select of 651 residues
> select #88/A:973
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #88/A:973-974
28 atoms, 27 bonds, 2 residues, 1 model selected
> select #88/A:967
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #88/A:965-967
45 atoms, 44 bonds, 3 residues, 1 model selected
Drag select of 651 residues
> select #88/A:973
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #88/A:973-975
44 atoms, 43 bonds, 3 residues, 1 model selected
> select
> #88/A:5-21,24-39,46-49,59-69,80-94,112-114,117-122,133-138,153-167,202-215,249-267,271-281,294-302,319-326,328-334,340-344,447-450,460-462,520-538,541-544,571-598,608-652,654-656,662-665,676-700,716-725,730-767,776-783,791-822,827-840,844-848,858-867,911-924,927-930,949-954,965-967,972-994,996-1024,1035-1037,1067-1086,1104-1132,1139-1156,1162-1173,1177-1180,1187-1190,1211-1217,1221-1229,1231-1234,1277-1302,1375-1379,1416-1418,1424-1431,1586-1589,1596-1605,1646-1650,1739-1747,1754-1765,1929-1932,1938-1944,2016-2022,2082-2102,2225-2228,2288-2290,2307-2317,2327-2329,2352-2360
12054 atoms, 12098 bonds, 758 residues, 1 model selected
> select #88/A:967
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #88/A:965-967
45 atoms, 44 bonds, 3 residues, 1 model selected
> select #88/A:676
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #88/A:676-967
4470 atoms, 4515 bonds, 292 residues, 1 model selected
> select #88/A:2339-2388
718 atoms, 724 bonds, 50 residues, 1 model selected
> select #88/A
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> show sel cartoons
> select #88/A:675-725
807 atoms, 816 bonds, 51 residues, 1 model selected
> select #88/A:675-820
2252 atoms, 2276 bonds, 146 residues, 1 model selected
> select #88/A:924
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #88/A:924-974
769 atoms, 774 bonds, 51 residues, 1 model selected
> select #88/A:676
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #88/A:676-967
4470 atoms, 4515 bonds, 292 residues, 1 model selected
> color sel purple
> select add #88
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> select subtract #88
Nothing selected
> select #88/A:281
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #88/A:133-281
2274 atoms, 2293 bonds, 149 residues, 1 model selected
> select #88/A:125-126
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #88/A:125-281
2412 atoms, 2433 bonds, 157 residues, 1 model selected
> select clear
> select #88/A:125
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:125-281
2412 atoms, 2433 bonds, 157 residues, 1 model selected
> ui mousemode right "translate selected models"
> color sel yellow
> select #88/A:996
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:996-1675
10412 atoms, 10525 bonds, 680 residues, 1 model selected
> select add #88
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> select subtract #88
Nothing selected
> select #88/A:996
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:996-1005
156 atoms, 156 bonds, 10 residues, 1 model selected
> select #88/A:1675
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #88/A:1501-1675
2672 atoms, 2699 bonds, 175 residues, 1 model selected
> select #88/A:1675
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #88/A:1663-1675
195 atoms, 198 bonds, 13 residues, 1 model selected
> select #88/A:996
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:996-1096
1624 atoms, 1644 bonds, 101 residues, 1 model selected
> select #88/A:1675
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #88/A:1416-1675
4077 atoms, 4122 bonds, 260 residues, 1 model selected
> select #88/A:1675
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #88/A:1665-1675
154 atoms, 155 bonds, 11 residues, 1 model selected
> select #88/A:1625-1675
784 atoms, 794 bonds, 51 residues, 1 model selected
> select #88/A:1312-1675
5730 atoms, 5797 bonds, 364 residues, 1 model selected
> select #88/A:996
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:996-1675
10412 atoms, 10525 bonds, 680 residues, 1 model selected
> color sel cornflower blue
> select add #88
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> select subtract #88
Nothing selected
> select #88/A:2388
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #88/A:2388
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #88/A:2342-2388
675 atoms, 680 bonds, 47 residues, 1 model selected
> select #88/A
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> color sel #040e52ff
> select #88/A:705
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #88/A:705-812
1656 atoms, 1672 bonds, 108 residues, 1 model selected
> select #88/A:676
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #88/A:676-967
4470 atoms, 4515 bonds, 292 residues, 1 model selected
> color sel purple
> select #88/A:996
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:996-1094
1586 atoms, 1605 bonds, 99 residues, 1 model selected
> select #88/A:996
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:996-1665
10270 atoms, 10381 bonds, 670 residues, 1 model selected
> select #88/A:996-1675
10412 atoms, 10525 bonds, 680 residues, 1 model selected
> color sel cornflower blue
> select #88/A:125
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #88/A:125-281
2412 atoms, 2433 bonds, 157 residues, 1 model selected
> color sel yellow
> select add #88
36672 atoms, 37035 bonds, 2388 residues, 1 model selected
> select subtract #88
Nothing selected
> hide #88 models
> show #95 models
> log metadata #95
The model has no metadata
> log chains #95
Chain information for MGYP000860465678.ranked_0.pdb #95
---
Chain | Description
A | No description available
> sequence chain #95/A
Alignment identifier is 95/A
> select #95/A:1-2
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #95/A
31954 atoms, 32283 bonds, 1998 residues, 1 model selected
> select subtract #95
Nothing selected
> matchmaker #95 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP000860465678.ranked_0.pdb, chain A
(#95), sequence alignment score = 382.4
RMSD between 134 pruned atom pairs is 1.003 angstroms; (across all 296 pairs:
7.540)
> select #95/A:730
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #95/A:730-732
41 atoms, 40 bonds, 3 residues, 1 model selected
> select #95/A:980
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #95/A:980-1031
728 atoms, 734 bonds, 52 residues, 1 model selected
> select #95/A:737
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:737-1397
10498 atoms, 10612 bonds, 661 residues, 1 model selected
> select #95/A:721
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #95/A:721-799
1295 atoms, 1309 bonds, 79 residues, 1 model selected
> select #95/A:716
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #95/A:563-716
2515 atoms, 2538 bonds, 154 residues, 1 model selected
> select #95/A:1646
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #95/A:1629-1646
253 atoms, 255 bonds, 18 residues, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1391-1397
126 atoms, 127 bonds, 7 residues, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1395-1397
50 atoms, 49 bonds, 3 residues, 1 model selected
> select #95/A:1398
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #95/A:1398-1998
9522 atoms, 9624 bonds, 601 residues, 1 model selected
> color sel #040e52ff
> select #95/A:1741
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #95/A:1741-1841
1557 atoms, 1566 bonds, 101 residues, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1391-1397
126 atoms, 127 bonds, 7 residues, 1 model selected
> select add #95
31954 atoms, 32283 bonds, 1998 residues, 1 model selected
> select subtract #95
Nothing selected
> select #95/A:1391
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #95/A:1391-1397
126 atoms, 127 bonds, 7 residues, 1 model selected
> select #95/A:1385-1386
41 atoms, 42 bonds, 2 residues, 1 model selected
> select #95/A:1378-1386
150 atoms, 152 bonds, 9 residues, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1316-1397
1344 atoms, 1363 bonds, 82 residues, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1392-1397
104 atoms, 105 bonds, 6 residues, 1 model selected
> select #95/A:1395-1396
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #95/A:1389-1396
145 atoms, 146 bonds, 8 residues, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:1292-1397
1709 atoms, 1730 bonds, 106 residues, 1 model selected
> select #95/A:1397
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #95/A:721-1397
10753 atoms, 10869 bonds, 677 residues, 1 model selected
> select add #95
31954 atoms, 32283 bonds, 1998 residues, 1 model selected
> select subtract #95
Nothing selected
> hide #95 models
> show #54 models
> matchmaker #54 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2X2DBV1-F1-model_v4.pdb, chain A
(#54), sequence alignment score = 359.9
RMSD between 135 pruned atom pairs is 0.987 angstroms; (across all 298 pairs:
8.517)
> log metadata #54
The model has no metadata
> log chains #54
Chain information for AF-A0A2X2DBV1-F1-model_v4.pdb #54
---
Chain | Description
A | toxin B
> sequence chain #54/A
Alignment identifier is 54/A
> select #54/A:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #54/A:364-568
1640 atoms, 1666 bonds, 205 residues, 1 model selected
> select #54/A:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #54/A:364-658
2355 atoms, 2401 bonds, 295 residues, 1 model selected
> select #54/A:361-362
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #54/A:357-362
55 atoms, 55 bonds, 6 residues, 1 model selected
> select #54/A:658
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #54/A:654-658
38 atoms, 38 bonds, 5 residues, 1 model selected
> select #54/A:663
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #54/A:663-1269
4877 atoms, 4991 bonds, 607 residues, 1 model selected
> select #54/A:663
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #54/A:663-668
46 atoms, 45 bonds, 6 residues, 1 model selected
> select #54/A:663
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #54/A:663-1269
4877 atoms, 4991 bonds, 607 residues, 1 model selected
> select #54/A:612
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #54/A:562-612
427 atoms, 440 bonds, 51 residues, 1 model selected
> select add #54
10263 atoms, 10482 bonds, 1269 residues, 1 model selected
> select subtract #54
Nothing selected
> hide #54 models
> show #91 models
> log metadata #91
The model has no metadata
> log chains #91
Chain information for A0A4P2SNJ1.longerNterm.ranked_0.pdb #91
---
Chain | Description
A | No description available
> sequence chain #91/A
Alignment identifier is 91/A
> select #91/A:254-255
29 atoms, 29 bonds, 2 residues, 1 model selected
> select #91/A:254-259
83 atoms, 83 bonds, 6 residues, 1 model selected
> select #91/A:304-305
37 atoms, 36 bonds, 2 residues, 1 model selected
> select #91/A:304-309
99 atoms, 98 bonds, 6 residues, 1 model selected
> matchmaker #91 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with A0A4P2SNJ1.longerNterm.ranked_0.pdb, chain
A (#91), sequence alignment score = 180.1
RMSD between 57 pruned atom pairs is 0.921 angstroms; (across all 231 pairs:
21.738)
> log metadata #43
The model has no metadata
> log chains #43
Chain information for AF-A0A1Y3API8-F1-model_v4.pdb #43
---
Chain | Description
A | rhodanese domain-containing protein
> sequence chain #43/A
Alignment identifier is 43/A
> open "/Users/aho2840/Desktop/Satchell Lab/MCFHomologs/A0A097A1Q2.1.A
> Putative RTX-toxin.pdb"
A0A097A1Q2.1.A Putative RTX-toxin.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) aMCF [more info...]
Chain information for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
---
Chain | Description
A | No description available
> hide #112 models
> show #112 models
> log metadata #112
Metadata for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
---
Title | SWISS-MODEL SERVER (https://swissmodel.expasy.org) aMCF
Citation | Swiss-model: homology modelling of protein structures andcomplexes PMID: 29788355
Experimental method | Theoretical model (swiss-model server)
> log chains #112
Chain information for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
---
Chain | Description
A | No description available
> sequence chain #112/A
Alignment identifier is 112/A
> sym #9
6ii6 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains A,C
2| author_and_software_defined_assembly| 1 copy of chains B,D
> log metadata #9
No models had metadata
> log chains #9
Chain information for 6ii6 #9
---
Chain | Description
A | Putative RTX-toxin
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:3267
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:3267-3269
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #9/A:3349
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/A:3349-3351
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #9/A:3352
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:3350-3352
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #9/A:3269
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:3267-3269
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #9/A:3352
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:3350-3352
25 atoms, 24 bonds, 3 residues, 1 model selected
> show #109 models
> hide #112 models
> hide #109 models
> show #72 models
> log metadata #72
The model has no metadata
> log chains #72
Chain information for AF-Q327I5-F1-model_v4.pdb #72
---
Chain | Description | UniProt
A | OSPD2 | Q327I5_SHIDS 1-572
> sequence chain #72/A
Alignment identifier is 72/A
> select #72/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:1-106
847 atoms, 860 bonds, 106 residues, 1 model selected
> select #72/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:1-250
2039 atoms, 2085 bonds, 250 residues, 1 model selected
> hide #91 models
> matchmaker #72 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 126.1
RMSD between 10 pruned atom pairs is 1.365 angstroms; (across all 189 pairs:
18.434)
> ui tool show Matchmaker
> matchmaker #72 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 34.4
RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
19.731)
> matchmaker #72 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 34.4
RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
19.731)
> select add #72
4592 atoms, 4687 bonds, 572 residues, 1 model selected
> select subtract #72
Nothing selected
> hide #72 models
> show #99 models
> log metadata #99
The model has no metadata
> log chains #99
Chain information for WP_095034189.1.ranked_0.pdb #99
---
Chain | Description
A | No description available
> sequence chain #99/A
Alignment identifier is 99/A
> select #99/A:324
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #99/A:322-324
44 atoms, 45 bonds, 3 residues, 1 model selected
> select #99/A:343
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #99/A:1-343
5585 atoms, 5652 bonds, 343 residues, 1 model selected
> view matrix models
> #99,-0.24018,-0.60835,-0.75645,11.198,0.83562,0.26701,-0.48005,61.266,0.49402,-0.7474,0.44422,112.71
> undo
> select #99/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #99/A:349-499
2447 atoms, 2466 bonds, 151 residues, 1 model selected
> view matrix models
> #99,-0.24018,-0.60835,-0.75645,5.0569,0.83562,0.26701,-0.48005,32.943,0.49402,-0.7474,0.44422,41.557
> select #99/A:349-499,501-502
2477 atoms, 2495 bonds, 153 residues, 1 model selected
> select #99/A:349-502
2491 atoms, 2510 bonds, 154 residues, 1 model selected
> select add #99
8782 atoms, 8876 bonds, 543 residues, 1 model selected
> select subtract #99
Nothing selected
> hide #99 models
> show #100 models
> log metadata #100
The model has no metadata
> log chains #100
Chain information for WP_148121377.1.ranked_0.pdb #100
---
Chain | Description
A | No description available
> sequence chain #100/A
Alignment identifier is 100/A
> select #100/A:1386
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #100/A:1386
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #100/A:1386-1422
560 atoms, 564 bonds, 37 residues, 1 model selected
> select #100/A:1428
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #100/A:1386-1428
619 atoms, 623 bonds, 43 residues, 1 model selected
> view matrix models
> #100,-0.75361,-0.61809,-0.2237,28.604,-0.07069,0.41455,-0.90728,101.69,0.65351,-0.66792,-0.3561,72.831
> select #100/A:1367
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #100/A:1367-1953
9141 atoms, 9226 bonds, 587 residues, 1 model selected
> select add #100
31107 atoms, 31455 bonds, 1953 residues, 1 model selected
> select subtract #100
Nothing selected
> hide #100 models
> show #93 models
> log metadata #93
The model has no metadata
> log chains #93
Chain information for C4K5K2.ranked_0.pdb #93
---
Chain | Description
A | No description available
> sequence chain #93/A
Alignment identifier is 93/A
> select #93/A:1751
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #93/A:1751-1880
1905 atoms, 1915 bonds, 130 residues, 1 model selected
> select #93/A:1863
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #93/A:1751-1863
1613 atoms, 1623 bonds, 113 residues, 1 model selected
> select #93/A:1862
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #93/A:1860-1862
28 atoms, 27 bonds, 3 residues, 1 model selected
> select #93/A:1863
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #93/A:1751-1863
1613 atoms, 1623 bonds, 113 residues, 1 model selected
> select #93/A:1751
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #93/A:1751-1753
38 atoms, 37 bonds, 3 residues, 1 model selected
> select #93/A:1396
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #93/A:1396-1413
272 atoms, 273 bonds, 18 residues, 1 model selected
> select #93/A:1435-1437
43 atoms, 43 bonds, 3 residues, 1 model selected
> select #93/A:1396-1435
552 atoms, 555 bonds, 40 residues, 1 model selected
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> hide #93 models
> show #35 models
> log metadata #35
The model has no metadata
> log chains #35
Chain information for AF-A0A7U6JX76-F1-model_v4.pdb #35
---
Chain | Description
A | EFA1/lifa-like protein, N-terminal part
> sequence chain #35/A
Alignment identifier is 35/A
> select #35/A:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #35/A:165-229
528 atoms, 533 bonds, 65 residues, 1 model selected
> select #35/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #35/A:161-164
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #35/A:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #35/A:209-210
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #35/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #35/A:161-229
559 atoms, 564 bonds, 69 residues, 1 model selected
> select #35/A:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:152-229
634 atoms, 639 bonds, 78 residues, 1 model selected
> select #35/A:261
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:261-363
826 atoms, 847 bonds, 103 residues, 1 model selected
> select #35/A:164-166
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #35/A:166-253
704 atoms, 712 bonds, 88 residues, 1 model selected
> select #35/A:754
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #35/A:754-805
416 atoms, 426 bonds, 52 residues, 1 model selected
> select #35/A:253
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #35/A:167-253
695 atoms, 703 bonds, 87 residues, 1 model selected
> select #35/A:165-253
711 atoms, 719 bonds, 89 residues, 1 model selected
> view matrix models
> #35,0.22503,-0.93827,0.26272,7.1151,0.23315,0.31365,0.92047,40.856,-0.94605,-0.14588,0.28934,83.248
> select add #35
9990 atoms, 10180 bonds, 1238 residues, 1 model selected
> hide #35 models
> select subtract #35
Nothing selected
> show #38 models
> matchmaker #38 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A0K3YVA7-F1-model_v4.pdb, chain A
(#38), sequence alignment score = 929.6
RMSD between 298 pruned atom pairs is 0.887 angstroms; (across all 338 pairs:
1.776)
> log metadata #38
The model has no metadata
> log chains #38
Chain information for AF-A0A0K3YVA7-F1-model_v4.pdb #38
---
Chain | Description
A | EFA1/lifa-like protein
> sequence chain #38/A
Alignment identifier is 38/A
> select #38/A:151
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:151-490
2732 atoms, 2788 bonds, 340 residues, 1 model selected
> select #38/A:144-145
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #38/A:1-145
1097 atoms, 1117 bonds, 145 residues, 1 model selected
> select add #38
3870 atoms, 3947 bonds, 490 residues, 1 model selected
> select subtract #38
Nothing selected
> hide #38 models
> show #43 models
> log metadata #43
The model has no metadata
> log chains #43
Chain information for AF-A0A1Y3API8-F1-model_v4.pdb #43
---
Chain | Description
A | rhodanese domain-containing protein
> sequence chain #43/A
Alignment identifier is 43/A
> select #43/A:115-116
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #43/A:1-116
880 atoms, 889 bonds, 116 residues, 1 model selected
> select #43/A:132
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:1-132
1014 atoms, 1026 bonds, 132 residues, 1 model selected
> show #84 models
> select add #43
6371 atoms, 6504 bonds, 812 residues, 1 model selected
> select subtract #43
Nothing selected
> hide #43 models
> hide #!9 models
> hide #84 models
> show #43 models
> select #43/A:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #43/A:1-132
1014 atoms, 1026 bonds, 132 residues, 1 model selected
> color sel red
> select add #43
6371 atoms, 6504 bonds, 812 residues, 1 model selected
> select subtract #43
Nothing selected
> hide #43 models
> show #111 models
> show #104 models
> show #105 models
> show #110 models
> log metadata #111
The model has no metadata
> log chains #111
Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111
---
Chain | Description
A | No description available
> sequence chain #111/A
Alignment identifier is 111/A
> select #111/A:4583
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #111/A:4583-4816
3249 atoms, 3269 bonds, 234 residues, 1 model selected
> select #111/A:4583-4832
3480 atoms, 3501 bonds, 250 residues, 1 model selected
> select #111/A:4583-4854
3861 atoms, 3886 bonds, 272 residues, 1 model selected
> select #111/A:4573
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #111/A:4573-4816
3428 atoms, 3449 bonds, 244 residues, 1 model selected
> view matrix models
> #111,-0.9879,0.15505,0.0031988,27.034,-0.10909,-0.68007,-0.72499,-18.027,-0.11024,-0.71657,0.68875,102.91
> undo
> select #111/A:4621-4671
662 atoms, 663 bonds, 51 residues, 1 model selected
> select #111/A:4621-4671
662 atoms, 663 bonds, 51 residues, 1 model selected
> select #111/A:4583
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #111/A:4583-4816
3249 atoms, 3269 bonds, 234 residues, 1 model selected
> select #111/A:4583-4817
3256 atoms, 3276 bonds, 235 residues, 1 model selected
> select add #111
18385 atoms, 18537 bonds, 1244 residues, 1 model selected
> select subtract #111
Nothing selected
> hide #111 models
> hide #110 models
> hide #105 models
> hide #104 models
> show #96 models
> log metadata #96
The model has no metadata
> log chains #96
Chain information for MGYP003605169772.ranked_0.pdb #96
---
Chain | Description
A | No description available
> sequence chain #96/A
Alignment identifier is 96/A
> select #96/A:942
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #96/A:942-1234
4430 atoms, 4471 bonds, 293 residues, 1 model selected
> select #96/A:941
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #96/A:1-941
14637 atoms, 14805 bonds, 941 residues, 1 model selected
> color sel #040e52ff
> select #96/A:1062
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #96/A:1061-1062
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #96/A:819
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #96/A:819-936
1722 atoms, 1740 bonds, 118 residues, 1 model selected
> select #96/A:815-816
27 atoms, 27 bonds, 2 residues, 1 model selected
> select #96/A:765-816
763 atoms, 771 bonds, 52 residues, 1 model selected
> select #96/A:907-908
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #96/A:819-907
1325 atoms, 1336 bonds, 89 residues, 1 model selected
> view matrix models
> #96,0.61612,0.18057,0.76667,-0.57975,-0.38691,-0.77845,0.49428,21.519,0.68607,-0.60117,-0.40975,90.045
> select add #96
19067 atoms, 19277 bonds, 1234 residues, 1 model selected
> select subtract #96
Nothing selected
> hide #96 models
> show #112 models
> log metadata #112
Metadata for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
---
Title | SWISS-MODEL SERVER (https://swissmodel.expasy.org) aMCF
Citation | Swiss-model: homology modelling of protein structures andcomplexes PMID: 29788355
Experimental method | Theoretical model (swiss-model server)
> log chains #112
Chain information for A0A097A1Q2.1.A Putative RTX-toxin.pdb #112
---
Chain | Description
A | No description available
> sequence chain #112/A
Alignment identifier is 112/A
> show #!78 models
> log metadata #78
No models had metadata
> log chains #78
Chain information for 8adb #78
---
Chain | Description | UniProt
A | Wc-VDT1 | D6YWY5_WADCW 279-493
> sequence chain #78/A
Alignment identifier is 78/A
> hide #!78 models
> show #19 models
> log metadata #19
The model has no metadata
> log chains #19
Chain information for AF-D6YWY5-F1-model_v4.pdb #19
---
Chain | Description | UniProt
A | uncharacterized protein | D6YWY5_WADCW 1-494
> sequence chain #19/A
Alignment identifier is 19/A
> show #!9 models
> matchmaker #19 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#19),
sequence alignment score = 111.4
RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
25.856)
> hide #112 models
> select #19/A:494
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #19/A
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> color sel #040e52ff
> select #19/A:72-121
397 atoms, 400 bonds, 50 residues, 1 model selected
> select #19/A:72-120
389 atoms, 392 bonds, 49 residues, 1 model selected
> select #19/A:472
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #19/A:472
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #19/A:86-88
23 atoms, 23 bonds, 3 residues, 1 model selected
> select #19/A:88-275
1508 atoms, 1543 bonds, 188 residues, 1 model selected
> color sel purple
> select #19/A:308
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #19/A:308-494
1451 atoms, 1479 bonds, 187 residues, 1 model selected
> color sel purple
> select #19/A:25
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #19/A:25-80
415 atoms, 423 bonds, 56 residues, 1 model selected
> select #19/A:25
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #19/A:25-80
415 atoms, 423 bonds, 56 residues, 1 model selected
> color sel #929000ff
> select add #19
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> select subtract #19
Nothing selected
> hide #19 models
> show #109 models
> matchmaker #109 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with C7BKP9.ranked_0.pdb, chain A (#109),
sequence alignment score = 292.3
RMSD between 75 pruned atom pairs is 1.064 angstroms; (across all 284 pairs:
10.403)
> log metadata #109
The model has no metadata
> log chains #109
Chain information for C7BKP9.ranked_0.pdb #109
---
Chain | Description
A | No description available
> sequence chain #109/A
Alignment identifier is 109/A
> select #109/A:527
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #109/A:527-712
2996 atoms, 3017 bonds, 186 residues, 1 model selected
> select #109/A:712
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #109/A:706-712
113 atoms, 112 bonds, 7 residues, 1 model selected
> select #109/A:526
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:1-526
8497 atoms, 8568 bonds, 526 residues, 1 model selected
> color sel #040e52ff
> select #109/A:526-527
33 atoms, 33 bonds, 2 residues, 1 model selected
> select #109/A:527-712
2996 atoms, 3017 bonds, 186 residues, 1 model selected
> color sel #945200ff
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> select #109/A:713
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #109/A:713-1745
16672 atoms, 16831 bonds, 1033 residues, 1 model selected
> color sel #040e52ff
> select #109/A:1746
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #109/A:1746-2031
4485 atoms, 4530 bonds, 286 residues, 1 model selected
> select #109/A:2054-2055
26 atoms, 25 bonds, 2 residues, 1 model selected
> select #109/A:2032-2054
351 atoms, 353 bonds, 23 residues, 1 model selected
> color sel #040e52ff
> select #109/A:2055-2056
40 atoms, 40 bonds, 2 residues, 1 model selected
> select #109/A:2055-2394
5465 atoms, 5528 bonds, 340 residues, 1 model selected
> select #109/A:2055
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2382
5280 atoms, 5340 bonds, 328 residues, 1 model selected
> select #109/A:2053
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #109/A:2052-2053
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #109/A:2382
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2382
5280 atoms, 5340 bonds, 328 residues, 1 model selected
> color sel blue
> select #109/A:2383-2533
2311 atoms, 2333 bonds, 151 residues, 1 model selected
> select #109/A:2383-2675
4554 atoms, 4610 bonds, 293 residues, 1 model selected
> select #109/A:2632
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #109/A:2632-2732
1559 atoms, 1592 bonds, 101 residues, 1 model selected
> select #109/A:2055
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2274
3589 atoms, 3634 bonds, 220 residues, 1 model selected
> select #109/A:2055
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2296
3923 atoms, 3971 bonds, 242 residues, 1 model selected
> select #109/A:2055
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2288
3804 atoms, 3850 bonds, 234 residues, 1 model selected
> select #109/A:2055
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2279
3666 atoms, 3711 bonds, 225 residues, 1 model selected
> select #109/A:2055
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2274
3589 atoms, 3634 bonds, 220 residues, 1 model selected
> select #109/A:2057-2107
837 atoms, 849 bonds, 51 residues, 1 model selected
> select #109/A:2057-2112
918 atoms, 930 bonds, 56 residues, 1 model selected
> select #109/A:2055
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2059
94 atoms, 95 bonds, 5 residues, 1 model selected
> select #109/A:2382
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #109/A:2055-2382
5280 atoms, 5340 bonds, 328 residues, 1 model selected
> select #109/A:2484
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #109/A:2383-2484
1535 atoms, 1551 bonds, 102 residues, 1 model selected
> select #109/A:2383
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #109/A:2383-2484
1535 atoms, 1551 bonds, 102 residues, 1 model selected
> color sel #040e52ff
> select #109/A:2485
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #109/A:2485-2486
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #109/A:2646
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #109/A:2485-2646
2596 atoms, 2628 bonds, 162 residues, 1 model selected
> select #109/A:2647
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #109/A:2647-2957
4741 atoms, 4803 bonds, 311 residues, 1 model selected
> color sel #040e52ff
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> show #!94 models
> hide #109 models
> hide #!94 models
> show #112 models
> hide #112 models
> show #112 models
> matchmaker #112 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with A0A097A1Q2.1.A Putative RTX-toxin.pdb,
chain A (#112), sequence alignment score = 835.5
RMSD between 171 pruned atom pairs is 0.264 angstroms; (across all 171 pairs:
0.264)
> hide #112 models
> show #!94 models
> matchmaker #94 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
(#94), sequence alignment score = 196.4
RMSD between 49 pruned atom pairs is 0.960 angstroms; (across all 284 pairs:
32.428)
> log metadata #94
No models had metadata
> log chains #94
Chain information for GMGC10.017_810_714.ranked_0.pdb #94
---
Chain | Description
A | No description available
> sequence chain #94/A
Alignment identifier is 94/A
> select #94/A:1531
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #94/A:1531-1638
1604 atoms, 1616 bonds, 108 residues, 1 model selected
> select #94/A:1531-1532
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #94/A:1531-1689
2440 atoms, 2454 bonds, 159 residues, 1 model selected
> select #94/A:1531
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #94/A:1531-1683
2335 atoms, 2348 bonds, 153 residues, 1 model selected
> view matrix models
> #94,-0.35268,0.092262,0.93118,19.032,-0.8443,0.39768,-0.35918,87.956,-0.40345,-0.91288,-0.062356,83.392
> select #94/A:1737
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1531-1737
3222 atoms, 3248 bonds, 207 residues, 1 model selected
> select #94/A:1521
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #94/A:1521-1683
2462 atoms, 2476 bonds, 163 residues, 1 model selected
> select #94/A:1421
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1421-1683
3914 atoms, 3941 bonds, 263 residues, 1 model selected
> select #94/A:1421
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1421-1422
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #94/A:1421
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1421-1429
137 atoms, 136 bonds, 9 residues, 1 model selected
> select #94/A:1420
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1418-1420
59 atoms, 59 bonds, 3 residues, 1 model selected
> select #94/A:1420
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1401-1420
342 atoms, 347 bonds, 20 residues, 1 model selected
> select #94/A:1420
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1398-1420
397 atoms, 402 bonds, 23 residues, 1 model selected
> select #94/A:1397
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #94/A:1376-1397
362 atoms, 364 bonds, 22 residues, 1 model selected
> select #94/A:1421
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1421-1448
407 atoms, 408 bonds, 28 residues, 1 model selected
> select #94/A:1418-1419
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #94/A:1416-1419
68 atoms, 67 bonds, 4 residues, 1 model selected
> select #94/A:1683
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #94/A:1660-1683
376 atoms, 375 bonds, 24 residues, 1 model selected
> select #94/A:1684
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #94/A:1684-1700
285 atoms, 286 bonds, 17 residues, 1 model selected
> select #94/A:1737
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1421-1737
4801 atoms, 4841 bonds, 317 residues, 1 model selected
> color (#!94 & sel) #73fdffff
> color (#!94 & sel) #76d6ffff
> color (#!94 & sel) #55bef0ff
> color (#!94 & sel) #b3d7ffff
> select #94/A:1781
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #94/A:1780-1781
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #94/A:405-406
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #94/A:1-406
6407 atoms, 6461 bonds, 406 residues, 1 model selected
> select #94/A:513-562
813 atoms, 817 bonds, 50 residues, 1 model selected
> select #94/A:513-559
763 atoms, 767 bonds, 47 residues, 1 model selected
> select #94/A:354-405
812 atoms, 821 bonds, 52 residues, 1 model selected
> select #94/A:1-405
6395 atoms, 6449 bonds, 405 residues, 1 model selected
> select #94/A:550
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #94/A:550-859
4899 atoms, 4943 bonds, 310 residues, 1 model selected
> select #94/A:417-418
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #94/A:314-418
1648 atoms, 1672 bonds, 105 residues, 1 model selected
> select #94/A:859
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:550-859
4899 atoms, 4943 bonds, 310 residues, 1 model selected
> color (#!94 & sel) purple
> select #94/A:549
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #94/A:406-549
2330 atoms, 2350 bonds, 144 residues, 1 model selected
> select #94/A:1420
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:860-1420
8811 atoms, 8882 bonds, 561 residues, 1 model selected
> select #94/A:1421-1471
734 atoms, 740 bonds, 51 residues, 1 model selected
> select #94/A:1421-1737
4801 atoms, 4841 bonds, 317 residues, 1 model selected
> select #94/A:1998
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #94/A:1738-1998
4007 atoms, 4048 bonds, 261 residues, 1 model selected
> select #94/A:1999
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #94/A:1999-2147
2176 atoms, 2188 bonds, 149 residues, 1 model selected
> select #94/A:2148
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:2148-2223
1169 atoms, 1184 bonds, 76 residues, 1 model selected
> select add #94
34588 atoms, 34892 bonds, 2223 residues, 2 models selected
> select subtract #94
1 model selected
> hide #!94 models
> show #72 models
> matchmaker #72 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 126.1
RMSD between 10 pruned atom pairs is 1.365 angstroms; (across all 189 pairs:
18.434)
> show #72 models
> log metadata #72
The model has no metadata
> log chains #72
Chain information for AF-Q327I5-F1-model_v4.pdb #72
---
Chain | Description | UniProt
A | OSPD2 | Q327I5_SHIDS 1-572
> log metadata #72
The model has no metadata
> log chains #72
Chain information for AF-Q327I5-F1-model_v4.pdb #72
---
Chain | Description | UniProt
A | OSPD2 | Q327I5_SHIDS 1-572
> sequence chain #72/A
Alignment identifier is 72/A
> select #72/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:1-250
2039 atoms, 2085 bonds, 250 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #72 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 34.4
RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
19.731)
> matchmaker #72 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 34.4
RMSD between 23 pruned atom pairs is 1.153 angstroms; (across all 229 pairs:
19.731)
> select #72/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #72/A:258-261
32 atoms, 31 bonds, 4 residues, 1 model selected
> select add #72
4592 atoms, 4687 bonds, 572 residues, 1 model selected
> select subtract #72
Nothing selected
> hide #72 models
> show #46 models
> sym #46
3gqj mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chain A
2| software_defined_assembly| 2 copies of chain A
> log metadata #46
The model has no metadata
> log chains #46
Chain information for 3gqj #46
---
Chain | Description | UniProt
A | Cell Inhibiting Factor (Cif) | Q7N439_PHOLL 48-308
> sequence chain #46/A
Alignment identifier is 46/A
> hide #46 models
> show #103 models
> matchmaker #103 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q7N439-F1-model_v4.pdb, chain A (#103),
sequence alignment score = 91.8
RMSD between 9 pruned atom pairs is 1.075 angstroms; (across all 201 pairs:
21.871)
> hide #103 models
> show #103 models
> hide #!9 models
> show #46 models
> matchmaker #46 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with 3gqj, chain A (#46), sequence alignment
score = 81.1
RMSD between 13 pruned atom pairs is 1.488 angstroms; (across all 192 pairs:
19.974)
> hide #46 models
> show #!9 models
> hide #!9 models
> show #!9 models
> log metadata #103
The model has no metadata
> log chains #103
Chain information for AF-Q7N439-F1-model_v4.pdb #103
---
Chain | Description | UniProt
A | protein-glutamine deamidase cif | CIF_PHOLL 1-313
> sequence chain #103/A
Alignment identifier is 103/A
> select #103/A:58-59
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #103/A:58-313
2045 atoms, 2078 bonds, 256 residues, 1 model selected
> select #103/A:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #103/A:1-57
436 atoms, 439 bonds, 57 residues, 1 model selected
> select add #103
2481 atoms, 2518 bonds, 313 residues, 1 model selected
> select subtract #103
Nothing selected
> hide #103 models
> show #101 models
> matchmaker #101 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_231937687.1.ranked_0.pdb, chain A
(#101), sequence alignment score = 205.8
RMSD between 73 pruned atom pairs is 0.941 angstroms; (across all 296 pairs:
20.392)
> log metadata #101
The model has no metadata
> log chains #101
Chain information for WP_231937687.1.ranked_0.pdb #101
---
Chain | Description
A | No description available
> sequence chain #101/A
Alignment identifier is 101/A
> select #101/A:524
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #101/A:524-726
3245 atoms, 3281 bonds, 203 residues, 1 model selected
> select #101/A:1146
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #101/A:1146-1148
50 atoms, 49 bonds, 3 residues, 1 model selected
> select #101/A:1146
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #101/A:1146-1744
9443 atoms, 9540 bonds, 599 residues, 1 model selected
> select add #101
27933 atoms, 28182 bonds, 1744 residues, 1 model selected
> select subtract #101
Nothing selected
> hide #101 models
> show #52 models
> log metadata #52
The model has no metadata
> log chains #52
Chain information for MGYP000706081912.pdb #52
---
Chain | Description
A | No description available
> sequence chain #52/A
Alignment identifier is 52/A
> select #52/A:360
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #52/A:1-360
2963 atoms, 3015 bonds, 360 residues, 1 model selected
> matchmaker #52 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP000706081912.pdb, chain A (#52),
sequence alignment score = 226.2
RMSD between 57 pruned atom pairs is 0.989 angstroms; (across all 293 pairs:
30.191)
> select #52/A:361-362
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #52/A:361-482
1002 atoms, 1024 bonds, 122 residues, 1 model selected
> select add #52
3965 atoms, 4040 bonds, 482 residues, 1 model selected
> select subtract #52
Nothing selected
> hide #52 models
> show #75 models
> matchmaker #75 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A0K0E9U3-F1-model_v4.pdb, chain A
(#75), sequence alignment score = 79
RMSD between 27 pruned atom pairs is 1.278 angstroms; (across all 165 pairs:
19.308)
> log metadata #75
The model has no metadata
> log chains #75
Chain information for AF-A0A0K0E9U3-F1-model_v4.pdb #75
---
Chain | Description
A | ubiquitinyl hydrolase 1
> sequence chain #75/A
Alignment identifier is 75/A
> select #75/A:171-172
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #75/A:171-252
649 atoms, 656 bonds, 82 residues, 1 model selected
> color sel #040e52ff
> select add #75
2008 atoms, 2043 bonds, 252 residues, 1 model selected
> select subtract #75
Nothing selected
> select #75/A:163
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #75/A:1-163
1308 atoms, 1335 bonds, 163 residues, 1 model selected
> select add #75
2008 atoms, 2043 bonds, 252 residues, 1 model selected
> select subtract #75
Nothing selected
> hide #75 models
> show #71 models
> log metadata #71
The model has no metadata
> log chains #71
Chain information for AF-Q327D9-F1-model_v4.pdb #71
---
Chain | Description | UniProt
A | OSPD3 | Q327D9_SHIDS 1-549
> sequence chain #71/A
Alignment identifier is 71/A
> select #71/A:214-216
27 atoms, 26 bonds, 3 residues, 1 model selected
> select #71/A:1-216
1755 atoms, 1796 bonds, 216 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #71 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
sequence alignment score = 95.1
RMSD between 27 pruned atom pairs is 1.084 angstroms; (across all 175 pairs:
18.329)
> matchmaker #71 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
sequence alignment score = 95.1
RMSD between 27 pruned atom pairs is 1.084 angstroms; (across all 175 pairs:
18.329)
> select add #71
4321 atoms, 4400 bonds, 549 residues, 1 model selected
> select subtract #71
Nothing selected
> hide #71 models
> show #!94 models
> log metadata #94
No models had metadata
> log chains #94
Chain information for GMGC10.017_810_714.ranked_0.pdb #94
---
Chain | Description
A | No description available
> matchmaker #94 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
(#94), sequence alignment score = 196.4
RMSD between 49 pruned atom pairs is 0.960 angstroms; (across all 284 pairs:
32.428)
> sequence chain #94/A
Alignment identifier is 94/A
> select #94/A:404-405
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #94/A:1-405
6395 atoms, 6449 bonds, 405 residues, 1 model selected
> hide #!9 models
> select #94/A:550
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #94/A:406-550
2349 atoms, 2369 bonds, 145 residues, 1 model selected
> select #94/A:520
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #94/A:520
16 atoms, 15 bonds, 1 residue, 1 model selected
> select
> #94/A:13-33,38-45,49-62,66-82,92-144,154-164,166-168,172-182,188-200,209-222,242-270,281-290,299-308,353-365,380-382,388-393,415-420,423-433,486-506,516-518,537-539,545-547,550-565,576-585,595-602,605-624,628-630,633-660,679-699,702-721,726-742,809-824,831-833,852-859,866-873,885-890,902-907,911-914,919-927,934-947,963-977,988-1000,1002-1008,1018-1034,1041-1056,1058-1060,1068-1081,1089-1102,1113-1129,1133-1160,1169-1197,1202-1215,1220-1247,1275-1297,1306-1314,1317-1319,1330-1336,1343-1354,1361-1369,1400-1405,1410-1412,1417-1419,1510-1515,1655-1657,1739-1742,1838-1840,1853-1860,1863-1865,1868-1879,1917-1919,2122-2124,2150-2152,2155-2161,2173-2184
13898 atoms, 13930 bonds, 857 residues, 1 model selected
> select #94/A:549
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #94/A:434-549
1872 atoms, 1888 bonds, 116 residues, 1 model selected
> select #94/A:406-549
2330 atoms, 2350 bonds, 144 residues, 1 model selected
> select #94/A:859
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:550-859
4899 atoms, 4943 bonds, 310 residues, 1 model selected
> select #94/A:1420
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:860-1420
8811 atoms, 8882 bonds, 561 residues, 1 model selected
> select #94/A:1737
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:1421-1737
4801 atoms, 4841 bonds, 317 residues, 1 model selected
> select #94/A:1998
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #94/A:1738-1998
4007 atoms, 4048 bonds, 261 residues, 1 model selected
> select #94/A:1999-2000
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #94/A:1999-2223
3345 atoms, 3373 bonds, 225 residues, 1 model selected
> select #94/A:1999
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #94/A:1999-2147
2176 atoms, 2188 bonds, 149 residues, 1 model selected
> select #94/A:2148
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #94/A:2148-2223
1169 atoms, 1184 bonds, 76 residues, 1 model selected
> select add #94
34588 atoms, 34892 bonds, 2223 residues, 2 models selected
> select subtract #94
1 model selected
> hide #!94 models
> show #8 models
> log metadata #8
The model has no metadata
> log chains #8
Chain information for AF-Q60XN1-F1-model_v4.pdb #8
---
Chain | Description | UniProt
A | ataxin-3 homolog | ATX3_CAEBR 1-319
> sequence chain #8/A
Alignment identifier is 8/A
> show #!9 models
> matchmaker #8 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q60XN1-F1-model_v4.pdb, chain A (#8),
sequence alignment score = 85.4
RMSD between 5 pruned atom pairs is 1.161 angstroms; (across all 217 pairs:
34.528)
> hide #8 models
> show #8 models
> matchmaker #1 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with 6ii0.cropped.06.25.23.pdb, chain B (#1),
sequence alignment score = 1498.3
RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
1.561)
> matchmaker #8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
AF-Q60XN1-F1-model_v4.pdb, chain A (#8), sequence alignment score = 63.8
RMSD between 13 pruned atom pairs is 0.566 angstroms; (across all 192 pairs:
39.787)
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #8/A:179
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1-179
1446 atoms, 1477 bonds, 179 residues, 1 model selected
> select #8/A:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:188-190
27 atoms, 27 bonds, 3 residues, 1 model selected
> select #8/A:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:188-208
179 atoms, 182 bonds, 21 residues, 1 model selected
> select #8/A:205-206
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:205-207
26 atoms, 25 bonds, 3 residues, 1 model selected
> select #8/A:207
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:196-207
102 atoms, 103 bonds, 12 residues, 1 model selected
> select #8/A:243
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:243-254
92 atoms, 91 bonds, 12 residues, 1 model selected
> select #8/A:231
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:223-231
61 atoms, 60 bonds, 9 residues, 1 model selected
> select #8/A:221
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:221
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:221
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:221-232
89 atoms, 88 bonds, 12 residues, 1 model selected
> select #8/A:293
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/A:293-316
207 atoms, 207 bonds, 24 residues, 1 model selected
> select #8/A:89-92,110-114,119-125,128-132,140-142,160-165
268 atoms, 271 bonds, 30 residues, 1 model selected
> select #8/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1-179
1446 atoms, 1477 bonds, 179 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #8 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q60XN1-F1-model_v4.pdb, chain A (#8),
sequence alignment score = 61.9
RMSD between 6 pruned atom pairs is 0.950 angstroms; (across all 153 pairs:
26.130)
> matchmaker #8 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q60XN1-F1-model_v4.pdb, chain A (#8),
sequence alignment score = 61.9
RMSD between 6 pruned atom pairs is 0.950 angstroms; (across all 153 pairs:
26.130)
> select add #8
2517 atoms, 2565 bonds, 319 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #!9 models
> show #1 models
> hide #8 models
> show #!9 models
> hide #!9 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #1 models
> show #1 models
> hide #8 models
> show #8 models
> hide #1 models
> show #1 models
> select add #8
2517 atoms, 2565 bonds, 319 residues, 1 model selected
> view matrix models
> #8,-0.25102,-0.52287,-0.81461,-3.9588,-0.96789,0.12376,0.21882,73.446,-0.0136,0.84338,-0.53714,71.947
> view matrix models
> #8,-0.25102,-0.52287,-0.81461,4.6156,-0.96789,0.12376,0.21882,49.504,-0.0136,0.84338,-0.53714,62.421
> view matrix models
> #8,-0.25102,-0.52287,-0.81461,40.206,-0.96789,0.12376,0.21882,92.988,-0.0136,0.84338,-0.53714,75.666
> view matrix models
> #8,-0.25102,-0.52287,-0.81461,41.642,-0.96789,0.12376,0.21882,94.077,-0.0136,0.84338,-0.53714,76.323
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.99821,0.034809,-0.048623,66.586,0.035089,0.31745,0.94762,117.22,0.048421,-0.94763,0.31566,99.863
> view matrix models
> #8,0.99339,-0.09014,0.07114,68.419,-0.046511,0.25058,0.96698,116.31,-0.10499,-0.96389,0.24473,96.45
> view matrix models
> #8,0.99542,0.010348,0.09507,67.658,-0.095363,0.18192,0.97868,116.04,-0.007168,-0.98326,0.18207,98.234
> view matrix models
> #8,-0.64407,-0.65726,-0.39139,37.553,-0.71229,0.70186,-0.0064905,92.403,0.27897,0.2746,-0.9202,85.272
> view matrix models
> #8,-0.60155,-0.29358,-0.74293,32.782,-0.42497,0.90511,-0.013568,96.286,0.67642,0.30756,-0.66923,94.621
> view matrix models
> #8,0.48565,-0.73646,0.47092,66.693,-0.62741,0.081455,0.77442,104.88,-0.60869,-0.67156,-0.4225,79.259
> view matrix models
> #8,-0.60353,-0.59059,-0.53568,36.847,-0.68804,0.72526,-0.024424,92.563,0.40293,0.35383,-0.84407,87.522
> view matrix models
> #8,0.74809,-0.45538,0.48269,69.45,-0.54575,-0.0083843,0.83791,107.79,-0.37752,-0.89026,-0.25479,87.084
> view matrix models
> #8,0.97723,0.10994,0.18147,66.885,-0.19053,0.078401,0.97855,115.08,0.093351,-0.99084,0.097562,99.825
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.97723,0.10994,0.18147,12.749,-0.19053,0.078401,0.97855,82.546,0.093351,-0.99084,0.097562,72.849
> view matrix models
> #8,0.97723,0.10994,0.18147,12.847,-0.19053,0.078401,0.97855,83.249,0.093351,-0.99084,0.097562,72.686
> view matrix models
> #8,0.97723,0.10994,0.18147,2.0631,-0.19053,0.078401,0.97855,88.77,0.093351,-0.99084,0.097562,86.819
> select subtract #8
Nothing selected
> hide #8 models
> show #8 models
> hide #8 models
> show #69 models
> matchmaker #69to #9
Missing or invalid "matchAtoms" argument: only initial part "#69" of atom
specifier valid
> matchmaker #69 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q9F3T4-F1-model_v4.pdb, chain A (#69),
sequence alignment score = 99.5
RMSD between 15 pruned atom pairs is 1.383 angstroms; (across all 244 pairs:
24.018)
> log metadata #69
The model has no metadata
> log chains #69
Chain information for AF-Q9F3T4-F1-model_v4.pdb #69
---
Chain | Description | UniProt
A | probable cysteine protease avirulence protein AVRPPIC2 | AVRP2_PSESJ 1-269
> sequence chain #69/A
Alignment identifier is 69/A
> hide #69 models
> show #24 models
> log metadata #24
The model has no metadata
> log chains #24
Chain information for AF-C4K468-F1-model_v4.pdb #24
---
Chain | Description | UniProt
A | putative autotransporter adhesin | C4K468_HAMD5 1-818
> sequence chain #24/A
Alignment identifier is 24/A
> matchmaker #24 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
sequence alignment score = 183.8
RMSD between 56 pruned atom pairs is 1.189 angstroms; (across all 304 pairs:
14.130)
> ui mousemode right select
Drag select of 486 residues
> select add #24
8372 atoms, 6889 bonds, 1034 residues, 2 models selected
> select subtract #24
1624 atoms, 216 residues, 1 model selected
> select add #1
2049 atoms, 1716 bonds, 587 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> show #!9 models
> hide #!9 models
> select #24/A:688
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:688-800
910 atoms, 922 bonds, 113 residues, 1 model selected
> select #24/A:687
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #24/A:359-687
2737 atoms, 2792 bonds, 329 residues, 1 model selected
> select clear
> ui mousemode right "translate selected models"
> select #24/A:359
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #24/A:359-687
2737 atoms, 2792 bonds, 329 residues, 1 model selected
> color sel purple
> select add #24
6748 atoms, 6889 bonds, 818 residues, 1 model selected
> select subtract #24
Nothing selected
> select #24/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:1-246
2026 atoms, 2073 bonds, 246 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #24 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
sequence alignment score = 189.7
RMSD between 56 pruned atom pairs is 1.042 angstroms; (across all 223 pairs:
20.806)
> select add #24
6748 atoms, 6889 bonds, 818 residues, 1 model selected
> show #!9 models
> select subtract #24
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #!9 models
> select #24/A:242-297
455 atoms, 464 bonds, 56 residues, 1 model selected
> select #24/A:242-297
455 atoms, 464 bonds, 56 residues, 1 model selected
> select #24/A:17
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #24/A:17-19
19 atoms, 18 bonds, 3 residues, 1 model selected
> sym #9
6ii6 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains A,C
2| author_and_software_defined_assembly| 1 copy of chains B,D
> log metadata #9
No models had metadata
> log chains #9
Chain information for 6ii6 #9
---
Chain | Description
A | Putative RTX-toxin
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:3482
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:3482
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> select subtract #9
Nothing selected
> matchmaker #24 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
sequence alignment score = 183.8
RMSD between 56 pruned atom pairs is 1.189 angstroms; (across all 304 pairs:
14.130)
> select #24/A:515
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #24/A:515-517
26 atoms, 25 bonds, 3 residues, 1 model selected
> select #24/A:502
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #24/A:502-504
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #24/A:500
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #24/A:500-502
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #24/A:497
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #24/A:497-499
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #24/A:499
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:499-501
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #9/A:3482
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:3482
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
> hide #24 models
> show #21 models
> log metadata #21
The model has no metadata
> log chains #21
Chain information for AF-A0A4V0NNU7-F1-model_v4.pdb #21
---
Chain | Description
A | peptidase_C58 domain-containing protein
> sequence chain #21/A
Alignment identifier is 21/A
> matchmaker #21 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4V0NNU7-F1-model_v4.pdb, chain A
(#21), sequence alignment score = 208.3
RMSD between 54 pruned atom pairs is 0.914 angstroms; (across all 285 pairs:
23.672)
> hide #21 models
> show #20 models
> matchmaker #20 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4V0NNP3-F1-model_v4.pdb, chain A
(#20), sequence alignment score = 167.5
RMSD between 54 pruned atom pairs is 0.979 angstroms; (across all 290 pairs:
24.128)
> show #98 models
> hide #20 models
> matchmaker #98 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
sequence alignment score = 189.7
RMSD between 60 pruned atom pairs is 1.387 angstroms; (across all 312 pairs:
13.944)
> log metadata #98
The model has no metadata
> log chains #98
Chain information for WP_095034161.1.ranked_0.pdb #98
---
Chain | Description
A | No description available
> sequence chain #98/A
Alignment identifier is 98/A
> select #98/A:555
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #98/A:555-557
46 atoms, 45 bonds, 3 residues, 1 model selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> select #98/A:417
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #98/A:417-774
5818 atoms, 5888 bonds, 358 residues, 1 model selected
> show #!9 models
> color sel purple
> select #98/A:416
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #98/A:1-416
6947 atoms, 7030 bonds, 416 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #98 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
sequence alignment score = 157.2
RMSD between 52 pruned atom pairs is 0.820 angstroms; (across all 263 pairs:
23.967)
> matchmaker #98 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
sequence alignment score = 157.2
RMSD between 52 pruned atom pairs is 0.820 angstroms; (across all 263 pairs:
23.967)
> select add #98
12765 atoms, 12919 bonds, 774 residues, 1 model selected
> select subtract #98
Nothing selected
> hide #98 models
> show #18 models
> log metadata #18
The model has no metadata
> log chains #18
Chain information for AF-A0A4P2SM79-F1-model_v4.pdb #18
---
Chain | Description
A | peptidase_C58 domain-containing protein
> sequence chain #18/A
Alignment identifier is 18/A
> matchmaker #18 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
(#18), sequence alignment score = 204.4
RMSD between 54 pruned atom pairs is 1.295 angstroms; (across all 314 pairs:
14.398)
> select #18/A:415-416
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #18/A:1-416
3498 atoms, 3581 bonds, 416 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #18 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
(#18), sequence alignment score = 175
RMSD between 51 pruned atom pairs is 0.849 angstroms; (across all 283 pairs:
24.132)
> matchmaker #18 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
(#18), sequence alignment score = 175
RMSD between 51 pruned atom pairs is 0.849 angstroms; (across all 283 pairs:
24.132)
> select add #18
6435 atoms, 6589 bonds, 774 residues, 1 model selected
> select subtract #18
Nothing selected
> hide #18 models
> show #100 models
> log metadata #100
The model has no metadata
> log chains #100
Chain information for WP_148121377.1.ranked_0.pdb #100
---
Chain | Description
A | No description available
> sequence chain #100/A
Alignment identifier is 100/A
> matchmaker #100 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_148121377.1.ranked_0.pdb, chain A
(#100), sequence alignment score = 196.6
RMSD between 63 pruned atom pairs is 1.204 angstroms; (across all 298 pairs:
14.062)
> select #100/A:1367-1422
865 atoms, 872 bonds, 56 residues, 1 model selected
> select #100/A:1367-1953
9141 atoms, 9226 bonds, 587 residues, 1 model selected
> select add #100
31107 atoms, 31455 bonds, 1953 residues, 1 model selected
> select subtract #100
Nothing selected
> hide #100 models
> show #93 models
> matchmaker #93 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
sequence alignment score = 190.5
RMSD between 59 pruned atom pairs is 1.280 angstroms; (across all 299 pairs:
13.592)
> log metadata #93
The model has no metadata
> log chains #93
Chain information for C4K5K2.ranked_0.pdb #93
---
Chain | Description
A | No description available
> sequence chain #93/A
Alignment identifier is 93/A
> select #93/A:294
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #93/A:1-294
4887 atoms, 4952 bonds, 294 residues, 1 model selected
> select #93/A:742
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #93/A:416-742
5313 atoms, 5373 bonds, 327 residues, 1 model selected
> select #93/A:1243
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:1243-1917
10482 atoms, 10583 bonds, 675 residues, 1 model selected
> select #93/A:1243
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:1243-1910
10354 atoms, 10453 bonds, 668 residues, 1 model selected
> select #93/A:1243
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #93/A:1243-1901
10228 atoms, 10326 bonds, 659 residues, 1 model selected
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> hide #93 models
> show #23 models
> log metadata #23
The model has no metadata
> log chains #23
Chain information for AF-C4K3P9-F1-model_v4.pdb #23
---
Chain | Description | UniProt
A | putative RTX-family protein-1 | C4K3P9_HAMD5 1-1196
> sequence chain #23/A
Alignment identifier is 23/A
> matchmaker #23 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
sequence alignment score = 183.4
RMSD between 61 pruned atom pairs is 1.222 angstroms; (across all 303 pairs:
14.576)
> hide #23 models
> show #100 models
> hide #100 models
> show #93 models
> hide #93 models
> show #23 models
> hide #!9 models
> ui mousemode right select
Drag select of 362 residues
> select #23/A:478-479
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #23/A:478-812
2760 atoms, 2827 bonds, 335 residues, 1 model selected
> select #23/A:478
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:478-485
63 atoms, 63 bonds, 8 residues, 1 model selected
> show #!9 models
> select #23/A:767
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:431-767
2777 atoms, 2843 bonds, 337 residues, 1 model selected
> color sel purple
> select #23/A:307-308
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #23/A:1-308
2566 atoms, 2635 bonds, 308 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #23 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
sequence alignment score = 163.6
RMSD between 53 pruned atom pairs is 0.972 angstroms; (across all 257 pairs:
25.421)
> hide #!9 models
> select add #23
9794 atoms, 10025 bonds, 1196 residues, 1 model selected
> select subtract #23
Nothing selected
> log metadata #24
The model has no metadata
> log chains #24
Chain information for AF-C4K468-F1-model_v4.pdb #24
---
Chain | Description | UniProt
A | putative autotransporter adhesin | C4K468_HAMD5 1-818
> sequence chain #24/A
Alignment identifier is 24/A
> log metadata #98
The model has no metadata
> log chains #98
Chain information for WP_095034161.1.ranked_0.pdb #98
---
Chain | Description
A | No description available
> sequence chain #98/A
Alignment identifier is 98/A
> show #!9 models
> hide #23 models
> show #106 models
> show #107 models
> hide #107 models
> hide #106 models
> show #106 models
> hide #106 models
> show #107 models
> hide #107 models
> show #108 models
> hide #108 models
> show #106 models
> hide #106 models
> show #108 models
> hide #108 models
> show #106 models
> show #107 models
> show #108 models
> hide #106 models
> hide #107 models
> hide #108 models
> show #106 models
> show #107 models
> hide #107 models
> hide #106 models
> show #106 models
> hide #106 models
> show #107 models
> hide #107 models
> show #108 models
> hide #108 models
> show #91 models
> log metadata #91
The model has no metadata
> log chains #91
Chain information for A0A4P2SNJ1.longerNterm.ranked_0.pdb #91
---
Chain | Description
A | No description available
> sequence chain #91/A
Alignment identifier is 91/A
> hide #91 models
> show #91 models
> hide #91 models
> show #17 models
> log metadata #17
The model has no metadata
> log chains #17
Chain information for AF-A0A2D3T3R8-F1-model_v4.pdb #17
---
Chain | Description
A | uncharacterized protein
> sequence chain #17/A
Alignment identifier is 17/A
> matchmaker #17 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2D3T3R8-F1-model_v4.pdb, chain A
(#17), sequence alignment score = 161.4
RMSD between 53 pruned atom pairs is 0.936 angstroms; (across all 297 pairs:
21.092)
> hide #17 models
> show #25 models
> log metadata #25
The model has no metadata
> log chains #25
Chain information for AF-C4K5L0-F1-model_v4.pdb #25
---
Chain | Description | UniProt
A | putative RTX-family protein-15 | C4K5L0_HAMD5 1-555
> matchmaker #25 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K5L0-F1-model_v4.pdb, chain A (#25),
sequence alignment score = 202.4
RMSD between 71 pruned atom pairs is 0.846 angstroms; (across all 300 pairs:
16.095)
> log metadata #25
The model has no metadata
> log chains #25
Chain information for AF-C4K5L0-F1-model_v4.pdb #25
---
Chain | Description | UniProt
A | putative RTX-family protein-15 | C4K5L0_HAMD5 1-555
> sequence chain #25/A
Alignment identifier is 25/A
> hide #25 models
> show #99 models
> log metadata #99
The model has no metadata
> log chains #99
Chain information for WP_095034189.1.ranked_0.pdb #99
---
Chain | Description
A | No description available
> sequence chain #99/A
Alignment identifier is 99/A
> matchmaker #99 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_095034189.1.ranked_0.pdb, chain A (#99),
sequence alignment score = 201
RMSD between 46 pruned atom pairs is 0.814 angstroms; (across all 293 pairs:
22.670)
> select #99/A:348-349
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #99/A:349-502
2491 atoms, 2510 bonds, 154 residues, 1 model selected
> color sel #73fa79ff
> color sel #7bf78bff
> color sel #b3f7acff
> color sel #b4f78fff
> color sel #d1f7b1ff
> color sel #c6f78dff
> color sel #abf789ff
> color sel #bff7b8ff
> color sel #b1f798ff
> color sel #aef77eff
> color sel #5bf7abff
> color sel #c9f7cfff
> color sel #dcf4f7ff
> color sel #cbf7e2ff
> color sel #a1f7cbff
> color sel #93f7a8ff
> color sel #92f7a7ff
> color sel #b2f7c9ff
> color sel #aaf7a6ff
> color sel #dcf79fff
> color sel #d0f7b0ff
> color sel #b8db9cff
> color sel #c2e6a4ff
> select add #99
8782 atoms, 8876 bonds, 543 residues, 1 model selected
> select subtract #99
Nothing selected
> select #99/A:349
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #99/A:349-502
2491 atoms, 2510 bonds, 154 residues, 1 model selected
> color sel #c1e6a4ff
> color sel #c0e4a3ff
> color sel #bee1a1ff
> color sel #bbde9eff
> color sel #badd9eff
> select add #99
8782 atoms, 8876 bonds, 543 residues, 1 model selected
> select subtract #99
Nothing selected
> hide #99 models
> show #!78 models
> hide #!78 models
> show #89 models
> matchmaker #89 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
sequence alignment score = 111.4
RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
25.856)
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> log metadata #89
The model has no metadata
> log chains #89
Chain information for AF-D6YWY5-F1-model_v4.pdb #89
---
Chain | Description | UniProt
A | uncharacterized protein | D6YWY5_WADCW 1-494
> sequence chain #89/A
Alignment identifier is 89/A
> select #89/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #89/A:111-116
38 atoms, 37 bonds, 6 residues, 1 model selected
> select add #89
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> select subtract #89
Nothing selected
> ui mousemode right select
Drag select of 201 residues
> select #89/A:282
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #89/A:282-494
1660 atoms, 1691 bonds, 213 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #89 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
sequence alignment score = 119.4
RMSD between 32 pruned atom pairs is 1.387 angstroms; (across all 165 pairs:
11.925)
> matchmaker #89 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
sequence alignment score = 119.4
RMSD between 32 pruned atom pairs is 1.387 angstroms; (across all 165 pairs:
11.925)
> select add #89
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> select subtract #89
Nothing selected
> select #89/A:171
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #89/A:116-171
460 atoms, 468 bonds, 56 residues, 1 model selected
> select add #89
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> select subtract #89
Nothing selected
> hide #89 models
> show #89 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
Drag select of 178 residues
> matchmaker #89 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-D6YWY5-F1-model_v4.pdb, chain A (#89),
sequence alignment score = 111.4
RMSD between 37 pruned atom pairs is 1.149 angstroms; (across all 266 pairs:
25.856)
> show #!9 models
> select add #89
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> select subtract #89
Nothing selected
> hide #89 models
> show #89 models
> hide #!9 models
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
Drag select of 189 residues
> select #89/A:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #89/A:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #89/A:88
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #89/A:88-275
1508 atoms, 1543 bonds, 188 residues, 1 model selected
> select #89/A:276-277
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #89/A:276-494
1708 atoms, 1740 bonds, 219 residues, 1 model selected
> color sel #040e52ff
> select #89/A:25-27
29 atoms, 31 bonds, 3 residues, 1 model selected
> select #89/A:25-90
492 atoms, 502 bonds, 66 residues, 1 model selected
> select #89/A:25
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #89/A:25-80
415 atoms, 423 bonds, 56 residues, 1 model selected
> color sel #445215ff
> color sel #4b5b17ff
> color sel #4c5c18ff
> color sel #4d5e18ff
> color sel #596c1cff
> color sel #6d8422ff
> color sel #7d9827ff
> color sel #8aa82bff
> color sel #8caa2cff
> color sel #8cab2cff
> color sel #8ba92cff
> color sel #85a22aff
> color sel #809c28ff
> color sel #7e9928ff
> color sel #7e9a28ff
> color sel #849a10ff
> color sel #7e9a05ff
> color sel #7f9a05ff
> color sel #7f9b06ff
> color sel #819d06ff
> color sel #829f06ff
> color sel #84a006ff
> color sel #85a206ff
> color sel #86a306ff
> color sel #89a706ff
> color sel #8baa06ff
> color sel #8ead06ff
> color sel #90af06ff
> color sel #91b006ff
> color sel #92b206ff
> color sel #93b206ff
> color sel #90b203ff
> color sel #91b203ff
> color sel #92b204ff
> color sel #92b203ff
> color sel #93b203ff
> color sel #94b203ff
> color sel #95b203ff
> color sel #96b203ff
> color sel #98b204ff
> color sel #9ab204ff
> color sel #9bb204ff
> color sel #a3b202ff
> color sel #a7b200ff
> color sel #a6b201ff
> color sel #a2b209ff
> color sel #a1b20bff
> color sel #a1b20dff
> color sel #a0b20eff
> color sel #a0b20fff
> color sel #a0b210ff
> color sel #a6b21aff
> color sel #a7b21cff
> color sel #a7b21dff
> color sel #a8b21eff
> color sel #a8b21dff
> color sel #a9b21dff
> color sel #aab21dff
> color sel #abb21dff
> color sel #adb21eff
> color sel #adb21dff
> color sel #afb21eff
> color sel #b2b21fff
> color sel #b2b11fff
> color sel #b2b01fff
> color sel #b2ab20ff
> color sel #b2a820ff
> color sel #b2a71fff
> color sel #b2a81eff
> color sel #b2a81dff
> color sel #b0a61dff
> color sel #afa51cff
> color sel #ada31cff
> color sel #aca21cff
> color sel #aba11cff
> color sel #aaa11cff
> color sel #a99f1bff
> color sel #a89e1bff
> color sel #a79e1bff
> color sel #a69d1bff
> color sel #a59c1bff
> color sel #a49b1bff
> select add #92
33823 atoms, 34185 bonds, 2159 residues, 2 models selected
> select subtract #92
415 atoms, 423 bonds, 56 residues, 1 model selected
> select add #89
3887 atoms, 3974 bonds, 494 residues, 1 model selected
> select subtract #89
Nothing selected
> hide #89 models
> show #110 models
> show #111 models
> select clear
> ui mousemode right "translate selected models"
> show #104 models
> show #105 models
> hide #104 models
> hide #105 models
> hide #110 models
> hide #111 models
> show #67 models
> log metadata #67
The model has no metadata
> log chains #67
Chain information for 1ukf #67
---
Chain | Description | UniProt
A | Avirulence protein AVRPPH3 | AVRP3_PSESH 81-267
> sequence chain #67/A
Alignment identifier is 67/A
> sequence chain #67/A
Alignment identifier is 67/A
> show #112 models
> hide #112 models
> show #112 models
> hide #112 models
> show #102 models
> log metadata #102
The model has no metadata
> log chains #102
Chain information for AF-Q52430-F1-model_v4.pdb #102
---
Chain | Description | UniProt
A | cysteine protease avirulence protein avrpphb | AVRP3_PSESH 1-267
> sequence chain #102/A
Alignment identifier is 102/A
> matchmaker #102 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q52430-F1-model_v4.pdb, chain A (#102),
sequence alignment score = 75
RMSD between 16 pruned atom pairs is 0.930 angstroms; (across all 200 pairs:
25.752)
> hide #67 models
> show #!9 models
> select #102/A:80-81
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #102/A:1-81
598 atoms, 611 bonds, 81 residues, 1 model selected
> select #102/A:136-137
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #102/A:136-138
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #102/A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #102/A:81-82
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #102/A:79-80
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #102/A:79-80
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #102/A:81-82
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #102/A:81-82
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #102/A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #102/A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #040e52ff
> select #102/A:82-85,98-107,114-121,126-148,153-164,181-193,237-239,241-254
666 atoms, 671 bonds, 87 residues, 1 model selected
> select add #102
2017 atoms, 2057 bonds, 267 residues, 1 model selected
> select subtract #102
Nothing selected
> hide #102 models
> show #86 models
> matchmaker #86 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q9AMW4-F1-model_v4.pdb, chain A (#86),
sequence alignment score = 87.8
RMSD between 30 pruned atom pairs is 0.803 angstroms; (across all 234 pairs:
23.197)
> log metadata #86
The model has no metadata
> log chains #86
Chain information for AF-Q9AMW4-F1-model_v4.pdb #86
---
Chain | Description | UniProt
A | putative cysteine protease yopt-like BLR2058 | Y2058_BRADU 1-298
> sequence chain #86/A
Alignment identifier is 86/A
> hide #86 models
> show #85 models
> log metadata #85
The model has no metadata
> log chains #85
Chain information for AF-Q89T99-F1-model_v4.pdb #85
---
Chain | Description | UniProt
A | putative cysteine protease yopt-like BLR2140 | Y2140_BRADU 1-271
> sequence chain #85/A
Alignment identifier is 85/A
> matchmaker #85 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q89T99-F1-model_v4.pdb, chain A (#85),
sequence alignment score = 83.5
RMSD between 30 pruned atom pairs is 0.963 angstroms; (across all 195 pairs:
24.092)
> hide #85 models
> show #73 models
> log metadata #73
The model has no metadata
> log chains #73
Chain information for AF-P55730-F1-model_v4.pdb #73
---
Chain | Description | UniProt
A | putative cysteine protease yopt-like Y4ZC | Y4ZC_SINFN 1-261
> sequence chain #73/A
Alignment identifier is 73/A
> matchmaker #73 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-P55730-F1-model_v4.pdb, chain A (#73),
sequence alignment score = 72.4
RMSD between 25 pruned atom pairs is 0.955 angstroms; (across all 190 pairs:
24.079)
> hide #73 models
> show #43 models
> log metadata #43
The model has no metadata
> log chains #43
Chain information for AF-A0A1Y3API8-F1-model_v4.pdb #43
---
Chain | Description
A | rhodanese domain-containing protein
> sequence chain #43/A
Alignment identifier is 43/A
> matchmaker #43 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A1Y3API8-F1-model_v4.pdb, chain A
(#43), sequence alignment score = 317.2
RMSD between 75 pruned atom pairs is 0.980 angstroms; (across all 295 pairs:
14.271)
> hide #43 models
> show #84 models
> matchmaker #84 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4ULG3-F1-model_v4.pdb, chain A (#84),
sequence alignment score = 321.7
RMSD between 101 pruned atom pairs is 1.004 angstroms; (across all 280 pairs:
9.316)
> show #43 models
> hide #43 models
> hide #84 models
> show #109 models
> hide #109 models
> show #110 models
> hide #110 models
> show #111 models
> show #109 models
> hide #111 models
> log metadata #109
The model has no metadata
> log chains #109
Chain information for C7BKP9.ranked_0.pdb #109
---
Chain | Description
A | No description available
> sequence chain #109/A
Alignment identifier is 109/A
> select #109/A:527-528
29 atoms, 29 bonds, 2 residues, 1 model selected
> select #109/A:527-756
3689 atoms, 3719 bonds, 230 residues, 1 model selected
> select #109/A:527
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #109/A:527-712
2996 atoms, 3017 bonds, 186 residues, 1 model selected
> select #109/A:527-528
29 atoms, 29 bonds, 2 residues, 1 model selected
> select #109/A:527-713
3010 atoms, 3031 bonds, 187 residues, 1 model selected
> color sel #945200ff
> color sel #8b551cff
> color sel #8d571cff
> color sel #9e6120ff
> color sel #a66621ff
> color sel #ac6a22ff
> color sel #b06c23ff
> color sel #bd7326ff
> color sel #bd7426ff
> color sel #c17627ff
> color sel #c1802aff
> color sel #c17e29ff
> color sel #c17b20ff
> color sel #c1791aff
> color sel #c17715ff
> color sel #c17511ff
> color sel #c17510ff
> color sel #c1760eff
> color sel #c1760dff
> color sel #c1770dff
> color sel #c1770cff
> color sel #c1780cff
> color sel #c1790aff
> color sel #c17b08ff
> color sel #c17c07ff
> color sel #c17d06ff
> color sel #c17e06ff
> color sel #c27e06ff
> color sel #c88206ff
> color sel #ca8306ff
> color sel #ca8406ff
> color sel #cb8406ff
> color sel #cd8506ff
> color sel #d08706ff
> color sel #cf8706ff
> color sel #c98306ff
> color sel #c37f06ff
> color sel #c27e06ff
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> select #109/A:527
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #109/A:527-713
3010 atoms, 3031 bonds, 187 residues, 1 model selected
> color sel #945200ff
> color sel #8b551cff
> color sel #8f581dff
> color sel #9c601fff
> color sel #9e6120ff
> color sel #a06220ff
> color sel #a46521ff
> color sel #a56521ff
> color sel #a86722ff
> color sel #a96822ff
> color sel #aa6822ff
> color sel #ab6922ff
> color sel #b06c23ff
> color sel #b26d24ff
> color sel #b46e24ff
> select add #109
47153 atoms, 47629 bonds, 2957 residues, 1 model selected
> select subtract #109
Nothing selected
> show #111 models
> hide #111 models
> hide #109 models
> show #109 models
> hide #109 models
> show #74 models
> matchmaker #74 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001564015939.pdb, chain A (#74),
sequence alignment score = 205.5
RMSD between 86 pruned atom pairs is 1.408 angstroms; (across all 190 pairs:
16.441)
> hide #74 models
> show #81 models
> matchmaker #81 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A1JU65-F1-model_v4.pdb, chain A (#81),
sequence alignment score = 167
RMSD between 24 pruned atom pairs is 1.316 angstroms; (across all 252 pairs:
17.802)
> hide #81 models
> show #83 models
> matchmaker #83 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q93RN4-F1-model_v4.pdb, chain A (#83),
sequence alignment score = 154.3
RMSD between 61 pruned atom pairs is 1.078 angstroms; (across all 253 pairs:
13.858)
> hide #83 models
> show #46 models
> sym #46
3gqj mmCIF Assemblies
---
1| author_defined_assembly| 1 copy of chain A
2| software_defined_assembly| 2 copies of chain A
> log metadata #46
The model has no metadata
> log chains #46
Chain information for 3gqj #46
---
Chain | Description | UniProt
A | Cell Inhibiting Factor (Cif) | Q7N439_PHOLL 48-308
> sequence chain #46/A
Alignment identifier is 46/A
> log metadata #36
The model has no metadata
> log chains #36
Chain information for pdb3efy.ent #36
---
Chain | Description | UniProt
A B | cif (cell cycle inhibiting factor) | Q7WRZ5_ECOLX 100-282
> sequence chain #36/A#36/B
Alignment identifier is 1
> log metadata #6
The model has no metadata
> log chains #6
Chain information for 2ffg.pdb #6
---
Chain | Description | UniProt
A B | YKUJ | O34588_BACSU 1-79
> hide #46 models
> log metadata #47
No models had metadata
> log chains #47
Chain information for 8p52 #47
---
Chain | Description | UniProt
A | Toxin protein | Q8KT65_PHOLU 1-2929
> show #82 models
> log metadata #82
The model has no metadata
> log chains #82
Chain information for AF-O68703-F1-model_v4.pdb #82
---
Chain | Description | UniProt
A | cysteine protease yopt | YOPT_YERPE 1-322
> sequence chain #82/A
Alignment identifier is 82/A
> matchmaker #82 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-O68703-F1-model_v4.pdb, chain A (#82),
sequence alignment score = 155.7
RMSD between 60 pruned atom pairs is 1.095 angstroms; (across all 245 pairs:
14.853)
> show #38 models
> log metadata #38
The model has no metadata
> log chains #38
Chain information for AF-A0A0K3YVA7-F1-model_v4.pdb #38
---
Chain | Description
A | EFA1/lifa-like protein
> sequence chain #38/A
Alignment identifier is 38/A
> select #38/A:145
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:1-145
1097 atoms, 1117 bonds, 145 residues, 1 model selected
> select #38/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:1-150
1138 atoms, 1158 bonds, 150 residues, 1 model selected
> color sel #040e52ff
> select #38/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:1-145
1097 atoms, 1117 bonds, 145 residues, 1 model selected
> color sel #030d52ff
> color sel #040e52ff
> color sel #050f52ff
> color sel #0a1452ff
> color sel #0d1652ff
> color sel #0f1852ff
> color sel #121a52ff
> color sel #151d52ff
> color sel #181f52ff
> color sel #1a2152ff
> color sel #1b2152ff
> color sel #1c2152ff
> color sel #1d2252ff
> color sel #1e2252ff
> color sel #1e2152ff
> color sel #212252ff
> color sel #2b2852ff
> color sel #2e2a52ff
> color sel #302c52ff
> color sel #312d52ff
> color sel #322e52ff
> color sel #322f52ff
> color sel #323052ff
> color sel #413e6bff
> color sel #494578ff
> color sel #4a4679ff
> color sel #4b477bff
> color sel #4d497eff
> color sel #4e4980ff
> color sel #4d4a80ff
> color sel #4d4880ff
> color sel #4d4680ff
> color sel #4c4280ff
> color sel #4c3f80ff
> color sel #4c3e80ff
> color sel #4c3d80ff
> color sel #4c3c80ff
> color sel #4d3c80ff
> color sel #4d3980ff
> color sel #4d3680ff
> color sel #4d3580ff
> color sel #4c3480ff
> color sel #4f3980ff
> color sel #513b80ff
> color sel #513c80ff
> color sel #533e80ff
> color sel #564280ff
> color sel #594480ff
> color sel #5a4680ff
> color sel #5b4680ff
> color sel #5b4780ff
> color sel #5b4680ff
> color sel #593c80ff
> color sel #542b80ff
> color sel #501b80ff
> color sel #4f1980ff
> color sel #4f1880ff
> color sel #4d1680ff
> color sel #441080ff
> color sel #3d0c80ff
> color sel #3b0a80ff
> color sel #3a0a80ff
> color sel #390a80ff
> color sel #380980ff
> color sel #360880ff
> color sel #350880ff
> color sel #350780ff
> color sel #340780ff
> color sel #300580ff
> color sel #2e0480ff
> color sel #2d0480ff
> color sel #2d047fff
> color sel #2d047dff
> color sel #2c047dff
> color sel #2c047bff
> color sel #2b047aff
> color sel #2b0479ff
> color sel #2a0477ff
> color sel #2a0476ff
> color sel #2a0475ff
> color sel #290474ff
> color sel #2b0674ff
> color sel #2c0774ff
> color sel #2f0b74ff
> color sel #341074ff
> color sel #381574ff
> color sel #3c1b74ff
> color sel #3e1d74ff
> color sel #3f1e74ff
> color sel #3f1f74ff
> color sel #3f1e74ff
> color sel #3e1e72ff
> color sel #3d1e71ff
> color sel #3c1d6fff
> color sel #3b1d6dff
> color sel #3b1c6cff
> color sel #391c6aff
> color sel #381b68ff
> color sel #371b66ff
> color sel #371b65ff
> select add #38
3870 atoms, 3947 bonds, 490 residues, 1 model selected
> select subtract #38
Nothing selected
> hide #38 models
> show #41 models
> log metadata #41
The model has no metadata
> log chains #41
Chain information for AF-A0A3W5Y7A7-F1-model_v4.pdb #41
---
Chain | Description
A | uncharacterized protein
> sequence chain #41/A
Alignment identifier is 41/A
> matchmaker #41 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A3W5Y7A7-F1-model_v4.pdb, chain A
(#41), sequence alignment score = 930.7
RMSD between 280 pruned atom pairs is 0.685 angstroms; (across all 298 pairs:
1.326)
> hide #41 models
> show #39 models
> log metadata #39
The model has no metadata
> log chains #39
Chain information for AF-A0A2X3JAL5-F1-model_v4.pdb #39
---
Chain | Description
A | EFA1/lifa-like protein
> sequence chain #39/A
Alignment identifier is 39/A
> hide #39 models
> hide #82 models
> show #39 models
> matchmaker #39 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2X3JAL5-F1-model_v4.pdb, chain A
(#39), sequence alignment score = 1054.4
RMSD between 315 pruned atom pairs is 0.673 angstroms; (across all 343 pairs:
1.660)
> hide #39 models
> show #35 models
> matchmaker #35 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7U6JX76-F1-model_v4.pdb, chain A
(#35), sequence alignment score = 1035.8
RMSD between 314 pruned atom pairs is 0.728 angstroms; (across all 343 pairs:
2.052)
> log metadata #35
The model has no metadata
> log chains #35
Chain information for AF-A0A7U6JX76-F1-model_v4.pdb #35
---
Chain | Description
A | EFA1/lifa-like protein, N-terminal part
> sequence chain #35/A
Alignment identifier is 35/A
> hide #35 models
> show #40 models
> log metadata #40
The model has no metadata
> log chains #40
Chain information for AF-A0A376U9H5-F1-model_v4.pdb #40
---
Chain | Description
A | EFA1/lifa-like protein
> sequence chain #40/A
Alignment identifier is 40/A
> matchmaker #40 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A376U9H5-F1-model_v4.pdb, chain A
(#40), sequence alignment score = 1050.8
RMSD between 316 pruned atom pairs is 0.697 angstroms; (across all 343 pairs:
2.132)
> hide #40 models
> show #65 models
> log metadata #65
The model has no metadata
> log chains #65
Chain information for AF-A0A2T4FGD4-F1-model_v4.pdb #65
---
Chain | Description
A | uncharacterized protein
> sequence chain #65/A
Alignment identifier is 65/A
> matchmaker #65 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2T4FGD4-F1-model_v4.pdb, chain A
(#65), sequence alignment score = 328.4
RMSD between 116 pruned atom pairs is 0.971 angstroms; (across all 291 pairs:
8.697)
> hide #65 models
> show #61 models
> matchmaker #61 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003613210660.pdb, chain A (#61),
sequence alignment score = 251.9
RMSD between 96 pruned atom pairs is 1.039 angstroms; (across all 196 pairs:
6.185)
> hide #61 models
> show #63 models
> matchmaker #63 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7Z6MWD8-F1-model_v4.pdb, chain A
(#63), sequence alignment score = 318.1
RMSD between 109 pruned atom pairs is 1.021 angstroms; (across all 290 pairs:
8.681)
> log metadata #63
The model has no metadata
> log chains #63
Chain information for AF-A0A7Z6MWD8-F1-model_v4.pdb #63
---
Chain | Description
A | uncharacterized protein
> sequence chain #63/A
Alignment identifier is 63/A
> show #60 models
> hide #63 models
> matchmaker #60 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003607098654.pdb, chain A (#60),
sequence alignment score = 252.9
RMSD between 84 pruned atom pairs is 0.881 angstroms; (across all 209 pairs:
4.498)
> hide #60 models
> show #64 models
> log metadata #64
The model has no metadata
> log chains #64
Chain information for AF-A0A656YJH9-F1-model_v4 (1).pdb #64
---
Chain | Description
A | uncharacterized protein
> sequence chain #64/A
Alignment identifier is 64/A
> matchmaker #64 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A656YJH9-F1-model_v4 (1).pdb, chain A
(#64), sequence alignment score = 367.2
RMSD between 108 pruned atom pairs is 1.011 angstroms; (across all 303 pairs:
7.242)
> hide #64 models
> show #62 models
> log metadata #62
The model has no metadata
> log chains #62
Chain information for AF-A0A7X1AT80-F1-model_v4.pdb #62
---
Chain | Description
A | uncharacterized protein
> sequence chain #62/A
Alignment identifier is 62/A
> matchmaker #62 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7X1AT80-F1-model_v4.pdb, chain A
(#62), sequence alignment score = 362.8
RMSD between 133 pruned atom pairs is 1.005 angstroms; (across all 278 pairs:
7.096)
> hide #62 models
> show #55 models
> log metadata #55
The model has no metadata
> log chains #55
Chain information for MGYP003605169772.pdb #55
---
Chain | Description
A | No description available
> sequence chain #55/A
Alignment identifier is 55/A
> show #96 models
> hide #55 models
> matchmaker #96 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003605169772.ranked_0.pdb, chain A
(#96), sequence alignment score = 378.7
RMSD between 133 pruned atom pairs is 1.066 angstroms; (across all 289 pairs:
8.432)
> log metadata #96
The model has no metadata
> log chains #96
Chain information for MGYP003605169772.ranked_0.pdb #96
---
Chain | Description
A | No description available
> sequence chain #96/A
Alignment identifier is 96/A
> select #96/A:818-819
41 atoms, 40 bonds, 2 residues, 1 model selected
> select #96/A:819-907
1325 atoms, 1336 bonds, 89 residues, 1 model selected
> color sel #ff7e79ff
> color sel #ef8d85ff
> color sel #ef8d86ff
> color sel #ef908cff
> color sel #ef9495ff
> color sel #ef969dff
> color sel #ef98aaff
> color sel #ef9ab4ff
> color sel #ef9bb9ff
> color sel #ef9bbbff
> color sel #ef9cbdff
> color sel #ef9cbfff
> color sel #ef9cc1ff
> color sel #ef9cc2ff
> color sel #ef9bc1ff
> color sel #ef97bfff
> color sel #ef93bcff
> color sel #ef8bb5ff
> color sel #ef86b0ff
> color sel #ef85afff
> color sel #ef82acff
> color sel #ef7ca6ff
> color sel #ef79a3ff
> color sel #ef80a8ff
> color sel #ef7fa8ff
> color sel #ef80a3ff
> color sel #ef7f9fff
> color sel #ef809eff
> color sel #ef809dff
> color sel #ef819aff
> color sel #ef8095ff
> color sel #ef7f94ff
> color sel #ef7e93ff
> color sel #ef7c91ff
> color sel #ef798eff
> color sel #ef768bff
> color sel #ef7489ff
> color sel #ef7287ff
> color sel #ef6c80ff
> color sel #ef6b80ff
> color sel #ef6b7fff
> color sel #ef6c7dff
> color sel #ef717fff
> color sel #ef717eff
> color sel #ef717dff
> color sel #ef717cff
> color sel #ef7079ff
> color sel #ef7078ff
> color sel #ef7077ff
> color sel #ef6f76ff
> color sel #ef6e76ff
> color sel #ef6975ff
> color sel #ef6976ff
> color sel #ef6a72ff
> color sel #ef6b73ff
> color sel #ef6b75ff
> color sel #ef6b79ff
> color sel #ef6c7eff
> color sel #ef6d82ff
> color sel #ef6d85ff
> color sel #ef6e86ff
> color sel #ef6e89ff
> color sel #ee6e89ff
> color sel #ec6d88ff
> color sel #ea6c86ff
> color sel #e76b85ff
> color sel #e56a83ff
> select add #96
19067 atoms, 19277 bonds, 1234 residues, 1 model selected
> select subtract #96
Nothing selected
> hide #96 models
> show #66 models
> log metadata #66
The model has no metadata
> log chains #66
Chain information for AF-A0A7Y1H706-F1-model_v4.pdb #66
---
Chain | Description
A | uncharacterized protein
> sequence chain #66/A
Alignment identifier is 66/A
> matchmaker #66 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7Y1H706-F1-model_v4.pdb, chain A
(#66), sequence alignment score = 356.6
RMSD between 101 pruned atom pairs is 1.011 angstroms; (across all 289 pairs:
8.691)
> hide #66 models
> show #70 models
> log metadata #70
The model has no metadata
> log chains #70
Chain information for MGYP000967698752.pdb #70
---
Chain | Description
A | No description available
> sequence chain #70/A
Alignment identifier is 70/A
> matchmaker #70 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP000967698752.pdb, chain A (#70),
sequence alignment score = 390.3
RMSD between 87 pruned atom pairs is 0.959 angstroms; (across all 261 pairs:
10.937)
> hide #70 models
> show #59 models
> matchmaker #59 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003580314631.pdb, chain A (#59),
sequence alignment score = 308.2
RMSD between 92 pruned atom pairs is 1.075 angstroms; (across all 214 pairs:
5.876)
> hide #59 models
> show #51 models
> log metadata #51
The model has no metadata
> log chains #51
Chain information for MGYP003392964057.pdb #51
---
Chain | Description
A | No description available
> matchmaker #51 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003392964057.pdb, chain A (#51),
sequence alignment score = 173.6
RMSD between 63 pruned atom pairs is 1.174 angstroms; (across all 170 pairs:
10.258)
> hide #51 models
> show #49 models
> matchmaker #49 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003443402579.pdb, chain A (#49),
sequence alignment score = 259.8
RMSD between 93 pruned atom pairs is 1.207 angstroms; (across all 252 pairs:
11.060)
> show #48 models
> hide #49 models
> matchmaker #48 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003405926657.pdb, chain A (#48),
sequence alignment score = 252.6
RMSD between 94 pruned atom pairs is 0.977 angstroms; (across all 232 pairs:
7.888)
> show #68 models
> log metadata #68
The model has no metadata
> log chains #68
Chain information for AF-A0A2R7TF17-F1-model_v4.pdb #68
---
Chain | Description
A | uncharacterized protein
> sequence chain #68/A
Alignment identifier is 68/A
> matchmaker #68 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2R7TF17-F1-model_v4.pdb, chain A
(#68), sequence alignment score = 322.1
RMSD between 115 pruned atom pairs is 1.131 angstroms; (across all 311 pairs:
11.935)
> hide #68 models
> show #58 models
> log metadata #58
The model has no metadata
> log chains #58
Chain information for MGYP003469346235.pdb #58
---
Chain | Description
A | No description available
> matchmaker #58 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003469346235.pdb, chain A (#58),
sequence alignment score = 260
RMSD between 112 pruned atom pairs is 0.911 angstroms; (across all 214 pairs:
4.268)
> hide #48 models
> hide #58 models
> show #57 models
> matchmaker #57 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001106352814.pdb, chain A (#57),
sequence alignment score = 257.4
RMSD between 108 pruned atom pairs is 0.961 angstroms; (across all 204 pairs:
6.932)
> hide #57 models
> show #56 models
> matchmaker #56 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001094995491.pdb, chain A (#56),
sequence alignment score = 219.4
RMSD between 81 pruned atom pairs is 0.883 angstroms; (across all 176 pairs:
6.421)
> show #76 models
> hide #56 models
> matchmaker #76 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001011426704.pdb, chain A (#76),
sequence alignment score = 250.7
RMSD between 136 pruned atom pairs is 1.144 angstroms; (across all 235 pairs:
4.027)
> log metadata #76
The model has no metadata
> log chains #76
Chain information for MGYP001011426704.pdb #76
---
Chain | Description
A | No description available
> sequence chain #76/A
Alignment identifier is 76/A
> select #76/A:279
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #76/A
2143 atoms, 2185 bonds, 279 residues, 1 model selected
> color sel purple
> select subtract #76
Nothing selected
> hide #76 models
> show #44 models
> matchmaker #44 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A3A3FFL6-F1-model_v4.pdb, chain A
(#44), sequence alignment score = 336.7
RMSD between 120 pruned atom pairs is 1.136 angstroms; (across all 290 pairs:
7.449)
> log metadata #44
The model has no metadata
> log chains #44
Chain information for AF-A0A3A3FFL6-F1-model_v4.pdb #44
---
Chain | Description
A | peptidase_C58 domain-containing protein
> sequence chain #44/A
Alignment identifier is 44/A
> hide #44 models
> show #92 models
> log metadata #92
The model has no metadata
> log chains #92
Chain information for B6XGD1.ranked_0.pdb #92
---
Chain | Description
A | No description available
> sequence chain #92/A
Alignment identifier is 92/A
> hide #92 models
> show #97 models
> log metadata #97
The model has no metadata
> log chains #97
Chain information for A0A2X2DF79.ranked_0.pdb #97
---
Chain | Description
A | No description available
> sequence chain #97/A
Alignment identifier is 97/A
> hide #97 models
> show #88 models
> log metadata #88
The model has no metadata
> log chains #88
Chain information for Mcf2.ranked_0.pdb #88
---
Chain | Description
A | No description available
> sequence chain #88/A
Alignment identifier is 88/A
> hide #88 models
> show #!47 models
> log metadata #47
No models had metadata
> log chains #47
Chain information for 8p52 #47
---
Chain | Description | UniProt
A | Toxin protein | Q8KT65_PHOLU 1-2929
> matchmaker #47 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with 8p52, chain A (#47), sequence alignment
score = 363.5
RMSD between 115 pruned atom pairs is 1.082 angstroms; (across all 307 pairs:
15.407)
> log metadata #47
No models had metadata
> log chains #47
Chain information for 8p52 #47
---
Chain | Description | UniProt
A | Toxin protein | Q8KT65_PHOLU 1-2929
> sequence chain #47/A
Alignment identifier is 47/A
> select #47/A:968
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:968-970
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #47/A:996
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #47/A:968-996
223 atoms, 227 bonds, 29 residues, 1 model selected
> view matrix models
> #47,-0.74537,0.41033,-0.52541,120.04,-0.45766,0.25812,0.85084,-18.258,0.48474,0.87464,-0.0046032,-50.831
> view matrix models
> #47,-0.74537,0.41033,-0.52541,98.946,-0.45766,0.25812,0.85084,0.71671,0.48474,0.87464,-0.0046032,-115.16
> select #47/A:1576-1577
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #47/A:1576-1666
748 atoms, 760 bonds, 91 residues, 1 model selected
> select #47/A:1576
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:1575-1576
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #47/A:1576-1603
225 atoms, 224 bonds, 28 residues, 1 model selected
> select #47/A:1599-1600
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #47/A:1576-1600
200 atoms, 199 bonds, 25 residues, 1 model selected
> color sel #040e52ff
> select #47/A:1909
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #47/A:1810-1909
683 atoms, 692 bonds, 100 residues, 1 model selected
> select #47/A:1809
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #47/A:1809-1909
687 atoms, 696 bonds, 101 residues, 1 model selected
> select #47/A:1810
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #47/A:1810-1907
671 atoms, 680 bonds, 98 residues, 1 model selected
> select #47/A:1810
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #47/A:1810-1908
675 atoms, 684 bonds, 99 residues, 1 model selected
> view matrix models
> #47,-0.74537,0.41033,-0.52541,105.06,-0.45766,0.25812,0.85084,-12.022,0.48474,0.87464,-0.0046032,-149.14
> color sel #040e52ff
> select add #47
22783 atoms, 23225 bonds, 1 pseudobond, 2914 residues, 2 models selected
> select subtract #47
Nothing selected
> select #47/A:2188-2189
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #47/A:2188-2217
242 atoms, 248 bonds, 30 residues, 1 model selected
> select #47/A:2188-2189
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #47/A:2188-2213
209 atoms, 214 bonds, 26 residues, 1 model selected
> select #47/A:2188-2189
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #47/A:2188-2212
200 atoms, 205 bonds, 25 residues, 1 model selected
> color sel #040e52ff
> select add #47
22783 atoms, 23225 bonds, 1 pseudobond, 2914 residues, 2 models selected
> select subtract #47
Nothing selected
> matchmaker #47 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with 8p52, chain A (#47), sequence alignment
score = 363.5
RMSD between 115 pruned atom pairs is 1.082 angstroms; (across all 307 pairs:
15.407)
> hide #!47 models
> show #54 models
> log metadata #54
The model has no metadata
> log chains #54
Chain information for AF-A0A2X2DBV1-F1-model_v4.pdb #54
---
Chain | Description
A | toxin B
> sequence chain #54/A
Alignment identifier is 54/A
> matchmaker #54 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2X2DBV1-F1-model_v4.pdb, chain A
(#54), sequence alignment score = 359.9
RMSD between 135 pruned atom pairs is 0.987 angstroms; (across all 298 pairs:
8.517)
> hide #54 models
> show #50 models
> show #95 models
> hide #50 models
> log metadata #95
The model has no metadata
> log chains #95
Chain information for MGYP000860465678.ranked_0.pdb #95
---
Chain | Description
A | No description available
> sequence chain #95/A
Alignment identifier is 95/A
> hide #95 models
> show #53 models
> log metadata #53
The model has no metadata
> log chains #53
Chain information for AF-B6XGD5-F1-model_v4.pdb #53
---
Chain | Description | UniProt
A | cysteine protease domain, yopt-type | B6XGD5_9GAMM 1-966
> sequence chain #53/A
Alignment identifier is 53/A
> matchmaker #53 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-B6XGD5-F1-model_v4.pdb, chain A (#53),
sequence alignment score = 383.9
RMSD between 114 pruned atom pairs is 0.934 angstroms; (across all 277 pairs:
10.206)
> save "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"
> hide #53 models
> show #103 models
> matchmaker #103 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q7N439-F1-model_v4.pdb, chain A (#103),
sequence alignment score = 91.8
RMSD between 9 pruned atom pairs is 1.075 angstroms; (across all 201 pairs:
21.871)
> hide #103 models
> select add #53
7840 atoms, 7983 bonds, 966 residues, 1 model selected
> select subtract #53
Nothing selected
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> color sel gray
> color sel light gray
> color sel dark gray
> select subtract #9
Nothing selected
> color #9 #040e5200
> color #9 #040e52cc
> color #9 #c0c0c0ff
> show #10 models
> hide #10 models
> show #32 models
> hide #32 models
> show #53 models
> hide #53 models
> show #103 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> hide #103 models
> show #103 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #6 models
> hide #6 models
> show #!9 models
> undo
> hide #!7 models
> show #!9 models
> hide #103 models
> show #103 models
> hide #103 models
> show #103 models
> hide #103 models
> show #103 models
> hide #103 models
> show #103 models
> hide #103 models
> show #103 models
> matchmaker #103 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
AF-Q7N439-F1-model_v4.pdb, chain A (#103), sequence alignment score = 58.6
RMSD between 24 pruned atom pairs is 1.518 angstroms; (across all 208 pairs:
15.755)
> matchmaker #1 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with 6ii0.cropped.06.25.23.pdb, chain B (#1),
sequence alignment score = 1498.3
RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
1.561)
> matchmaker #103 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
AF-Q7N439-F1-model_v4.pdb, chain A (#103), sequence alignment score = 58.6
RMSD between 24 pruned atom pairs is 1.518 angstroms; (across all 208 pairs:
15.755)
> hide #!9 models
> show #!9 models
> hide #103 models
> show #103 models
> hide #103 models
> show #103 models
> hide #103 models
> hide #!9 models
> show #1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #1 models
> show #103 models
> hide #103 models
> show #103 models
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> color sel #c0c0c0ff
> color sel #c0c0c0fb
> color sel #c0c0c0f8
> color sel #c0c0c0f6
> color sel #c0c0c0f4
> color sel #c0c0c0f3
> color sel #c0c0c0eb
> color sel #c0c0c0ea
> color sel #c0c0c0e3
> color sel #c0c0c0df
> color sel #c0c0c0dc
> color sel #c0c0c0db
> color sel #c0c0c0d7
> color sel #c0c0c0d4
> color sel #c0c0c0d1
> color sel #c0c0c0d0
> color sel #c0c0c0ce
> color sel #c0c0c0c6
> color sel #c0c0c0be
> color sel #c0c0c0cc
> color sel #c0c0c0db
> color sel #c0c0c0da
> color sel #c0c0c0d7
> color sel #c0c0c0d4
> color sel #c0c0c0d2
> color sel #c0c0c0d1
> color sel #c0c0c0cf
> color sel #c0c0c0cd
> color sel #c0c0c0cc
> select subtract #9
Nothing selected
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> color sel #c0c0c0cb
> color sel #c0c0c0b5
> color sel #c0c0c0a8
> color sel #c0c0c0a7
> color sel #c0c0c0a6
> color sel #c0c0c0a3
> color sel #c0c0c0a4
> color sel #c0c0c0a5
> color sel #c0c0c0a6
> select subtract #9
Nothing selected
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> color sel #c0c0c0a5
> color sel #c0c0c090
> color sel #c0c0c08e
> color sel #c0c0c089
> color sel #c0c0c087
> color sel #c0c0c086
> color sel #c0c0c084
> color sel #c0c0c083
> color sel #c0c0c082
> color sel #c0c0c081
> color sel #c0c0c080
> select subtract #9
Nothing selected
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> color sel #c0c0c07f
> color sel #c0c0c06d
> color sel #c0c0c066
> color sel #c0c0c064
> color sel #c0c0c062
> color sel #c0c0c05f
> color sel #c0c0c05e
> color sel #c0c0c05b
> color sel #c0c0c05a
> color sel #c0c0c056
> color sel #c0c0c052
> color sel #c0c0c04a
> color sel #c0c0c03b
> color sel #c0c0c03e
> color sel #c0c0c043
> color sel #c0c0c048
> color sel #c0c0c04b
> color sel #c0c0c04e
> color sel #c0c0c050
> color sel #c0c0c051
> color sel #c0c0c052
> color sel #c0c0c053
> color sel #c0c0c052
> color sel #c0c0c050
> color sel #c0c0c04f
> color sel #c0c0c04e
> color sel #c0c0c04c
> color sel #c0c0c04d
> select subtract #9
Nothing selected
> select add #103
2481 atoms, 2518 bonds, 313 residues, 1 model selected
> hide #!9 models
> select subtract #103
Nothing selected
> select add #103
2481 atoms, 2518 bonds, 313 residues, 1 model selected
> select subtract #103
Nothing selected
> hide #103 models
> show #!9 models
> color #9 #c0c0c04c
> color #9 #c0c0c04a
> color #9 #c0c0c044
> color #9 #c0c0c03d
> color #9 #c0c0c03a
> color #9 #c0c0c032
> color #9 #c0c0c02e
> color #9 #c0c0c02c
> color #9 #c0c0c02a
> color #9 #c0c0c026
> color #9 #c0c0c023
> color #9 #c0c0c022
> color #9 #c0c0c021
> color #9 #c0c0c022
> color #9 #c0c0c024
> color #9 #c0c0c026
> show #103 models
> hide #103 models
> hide #!9 models
> show #!9 models
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select subtract #9
1 model selected
> show #103 models
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #103 models
> select add #9
3249 atoms, 2729 bonds, 917 residues, 1 model selected
> color (#!9 & sel) #c0c0c027
> color (#!9 & sel) #c0c0c029
> color (#!9 & sel) #c0c0c02e
> color (#!9 & sel) #c0c0c034
> color (#!9 & sel) #c0c0c038
> color (#!9 & sel) #c0c0c03c
> color (#!9 & sel) #c0c0c04c
> color (#!9 & sel) #c0c0c055
> color (#!9 & sel) #c0c0c058
> color (#!9 & sel) #c0c0c05a
> color (#!9 & sel) #c0c0c063
> color (#!9 & sel) #c0c0c067
> color (#!9 & sel) #c0c0c074
> color (#!9 & sel) #c0c0c07d
> color (#!9 & sel) #c0c0c07f
> color (#!9 & sel) #c0c0c080
> color (#!9 & sel) #c0c0c081
> color (#!9 & sel) #c0c0c084
> color (#!9 & sel) #c0c0c086
> color (#!9 & sel) #c0c0c085
> color (#!9 & sel) #c0c0c080
> select subtract #9
1 model selected
> show #103 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #103 models
> show #89 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #89 models
> show #77 models
> hide #77 models
> show #75 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #75 models
> show #38 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #38 models
> show #43 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #43 models
> show #17 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #17 models
> show #68 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #68 models
> show #65 models
> save /Users/aho2840/Desktop/image2.png supersample 3
> matchmaker #65 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2T4FGD4-F1-model_v4.pdb, chain A
(#65), sequence alignment score = 328.4
RMSD between 116 pruned atom pairs is 0.971 angstroms; (across all 291 pairs:
8.697)
> turn x 180
> turn y 180
> save /Users/aho2840/Desktop/image2.png supersample 3
> turn y 180
> hide #65 models
> show #54 models
> matchmaker #54 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2X2DBV1-F1-model_v4.pdb, chain A
(#54), sequence alignment score = 359.9
RMSD between 135 pruned atom pairs is 0.987 angstroms; (across all 298 pairs:
8.517)
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #54 models
> show #97 models
> matchmaker #97 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with A0A2X2DF79.ranked_0.pdb, chain A (#97),
sequence alignment score = 398.6
RMSD between 127 pruned atom pairs is 1.100 angstroms; (across all 305 pairs:
11.055)
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #97 models
> show #39 models
> matchmaker #39 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A2X3JAL5-F1-model_v4.pdb, chain A
(#39), sequence alignment score = 1054.4
RMSD between 315 pruned atom pairs is 0.673 angstroms; (across all 343 pairs:
1.660)
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #39 models
> show #40 models
> matchmaker #40 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A376U9H5-F1-model_v4.pdb, chain A
(#40), sequence alignment score = 1050.8
RMSD between 316 pruned atom pairs is 0.697 angstroms; (across all 343 pairs:
2.132)
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #40 models
> show #44 models
> matchmaker #404to #9
Missing or invalid "matchAtoms" argument: only initial part "#404" of atom
specifier valid
> matchmaker #44to #9
Missing or invalid "matchAtoms" argument: only initial part "#44" of atom
specifier valid
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #44 models
> show #41 models
> matchmaker #41 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A3W5Y7A7-F1-model_v4.pdb, chain A
(#41), sequence alignment score = 930.7
RMSD between 280 pruned atom pairs is 0.685 angstroms; (across all 298 pairs:
1.326)
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #41 models
> show #18 models
> matchmaker #18 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
(#18), sequence alignment score = 204.4
RMSD between 54 pruned atom pairs is 1.295 angstroms; (across all 314 pairs:
14.398)
> save /Users/aho2840/Desktop/image1.png supersample 3
> log metadata #18
The model has no metadata
> log chains #18
Chain information for AF-A0A4P2SM79-F1-model_v4.pdb #18
---
Chain | Description
A | peptidase_C58 domain-containing protein
> sequence chain #18/A
Alignment identifier is 18/A
> ui mousemode right select
Drag select of 589 residues
> select #18/A:407-463
443 atoms, 449 bonds, 57 residues, 1 model selected
> select #18/A:1-463
3869 atoms, 3958 bonds, 463 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #18 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4P2SM79-F1-model_v4.pdb, chain A
(#18), sequence alignment score = 175
RMSD between 51 pruned atom pairs is 0.849 angstroms; (across all 283 pairs:
24.132)
> select add #18
6435 atoms, 6589 bonds, 774 residues, 1 model selected
> select subtract #18
Nothing selected
> select clear
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #18 models
> show #91 models
> matchmaker #91 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with A0A4P2SNJ1.longerNterm.ranked_0.pdb, chain
A (#91), sequence alignment score = 180.1
RMSD between 57 pruned atom pairs is 0.921 angstroms; (across all 231 pairs:
21.738)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #91 models
> show #20 models
> matchmaker #20 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4V0NNP3-F1-model_v4.pdb, chain A
(#20), sequence alignment score = 167.5
RMSD between 54 pruned atom pairs is 0.979 angstroms; (across all 290 pairs:
24.128)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #20 models
> show #21 models
> matchmaker #21 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A4V0NNU7-F1-model_v4.pdb, chain A
(#21), sequence alignment score = 208.3
RMSD between 54 pruned atom pairs is 0.914 angstroms; (across all 285 pairs:
23.672)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #21 models
> show #64 models
> matchmaker #64 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A656YJH9-F1-model_v4 (1).pdb, chain A
(#64), sequence alignment score = 367.2
RMSD between 108 pruned atom pairs is 1.011 angstroms; (across all 303 pairs:
7.242)
> save /Users/aho2840/Desktop/image1.png supersample 3
> matchmaker #35 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7U6JX76-F1-model_v4.pdb, chain A
(#35), sequence alignment score = 1035.8
RMSD between 314 pruned atom pairs is 0.728 angstroms; (across all 343 pairs:
2.052)
> hide #64 models
> show #35 models
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #35 models
> show #62 models
> matchmaker #62 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7X1AT80-F1-model_v4.pdb, chain A
(#62), sequence alignment score = 362.8
RMSD between 133 pruned atom pairs is 1.005 angstroms; (across all 278 pairs:
7.096)
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #62 models
> show #66 models
> turn y 180
> matchmaker #66 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7Y1H706-F1-model_v4.pdb, chain A
(#66), sequence alignment score = 356.6
RMSD between 101 pruned atom pairs is 1.011 angstroms; (across all 289 pairs:
8.691)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #66 models
> show #63 models
> matchmaker #63 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A0A7Z6MWD8-F1-model_v4.pdb, chain A
(#63), sequence alignment score = 318.1
RMSD between 109 pruned atom pairs is 1.021 angstroms; (across all 290 pairs:
8.681)
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> hide #63 models
> show #81 models
> matchmaker #81 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-A1JU65-F1-model_v4.pdb, chain A (#81),
sequence alignment score = 167
RMSD between 24 pruned atom pairs is 1.316 angstroms; (across all 252 pairs:
17.802)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #81 models
> show #84 models
> matchmaker #84 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4ULG3-F1-model_v4.pdb, chain A (#84),
sequence alignment score = 321.7
RMSD between 101 pruned atom pairs is 1.004 angstroms; (across all 280 pairs:
9.316)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #84 models
> show #102 models
> matchmaker #102 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q52430-F1-model_v4.pdb, chain A (#102),
sequence alignment score = 75
RMSD between 16 pruned atom pairs is 0.930 angstroms; (across all 200 pairs:
25.752)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #102 models
> show #92 models
> matchmaker #92 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with B6XGD1.ranked_0.pdb, chain A (#92),
sequence alignment score = 401.5
RMSD between 133 pruned atom pairs is 1.062 angstroms; (across all 317 pairs:
13.801)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #92 models
> show #53 models
> matchmaker #53 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-B6XGD5-F1-model_v4.pdb, chain A (#53),
sequence alignment score = 383.9
RMSD between 114 pruned atom pairs is 0.934 angstroms; (across all 277 pairs:
10.206)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #53 models
> show #23 models
> matchmaker #23 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
sequence alignment score = 183.4
RMSD between 61 pruned atom pairs is 1.222 angstroms; (across all 303 pairs:
14.576)
> save /Users/aho2840/Desktop/image1.png supersample 3
> ui mousemode right select
Drag select of 351 residues
> ui tool show Matchmaker
> matchmaker #23 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
sequence alignment score = 165.1
RMSD between 53 pruned atom pairs is 0.972 angstroms; (across all 279 pairs:
25.183)
> matchmaker #23 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K3P9-F1-model_v4.pdb, chain A (#23),
sequence alignment score = 165.1
RMSD between 53 pruned atom pairs is 0.972 angstroms; (across all 279 pairs:
25.183)
> select add #23
9794 atoms, 10025 bonds, 1196 residues, 1 model selected
> select subtract #23
Nothing selected
> select clear
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #23 models
> show #24 models
> matchmaker #24 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
sequence alignment score = 183.8
RMSD between 56 pruned atom pairs is 1.189 angstroms; (across all 304 pairs:
14.130)
> save /Users/aho2840/Desktop/image1.png supersample 3
> ui mousemode right select
Drag select of 271 residues
> ui tool show Matchmaker
> matchmaker #24 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
sequence alignment score = 171.6
RMSD between 45 pruned atom pairs is 1.057 angstroms; (across all 234 pairs:
21.465)
> matchmaker #24 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K468-F1-model_v4.pdb, chain A (#24),
sequence alignment score = 171.6
RMSD between 45 pruned atom pairs is 1.057 angstroms; (across all 234 pairs:
21.465)
> select add #24
6748 atoms, 6889 bonds, 818 residues, 1 model selected
> select subtract #24
Nothing selected
> select clear
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #24 models
> show #93 models
> matchmaker #93 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
sequence alignment score = 190.5
RMSD between 59 pruned atom pairs is 1.280 angstroms; (across all 299 pairs:
13.592)
> save /Users/aho2840/Desktop/image1.png supersample 3
> ui mousemode right select
Drag select of 333 residues
> ui tool show Matchmaker
> matchmaker #93 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
sequence alignment score = 186.6
RMSD between 49 pruned atom pairs is 0.723 angstroms; (across all 252 pairs:
25.651)
> matchmaker #93 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with C4K5K2.ranked_0.pdb, chain A (#93),
sequence alignment score = 186.6
RMSD between 49 pruned atom pairs is 0.723 angstroms; (across all 252 pairs:
25.651)
> select add #93
31332 atoms, 31675 bonds, 1960 residues, 1 model selected
> select subtract #93
Nothing selected
> select clear
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #93 models
> show #25 models
> matchmaker #25 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-C4K5L0-F1-model_v4.pdb, chain A (#25),
sequence alignment score = 202.4
RMSD between 71 pruned atom pairs is 0.846 angstroms; (across all 300 pairs:
16.095)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #25 models
> show #!94 models
> matchmaker #94 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
(#94), sequence alignment score = 196.4
RMSD between 49 pruned atom pairs is 0.960 angstroms; (across all 284 pairs:
32.428)
> save /Users/aho2840/Desktop/image1.png supersample 3
> ui mousemode right select
Drag select of 609 residues
> ui tool show Matchmaker
> matchmaker #!94 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with GMGC10.017_810_714.ranked_0.pdb, chain A
(#94), sequence alignment score = 167.3
RMSD between 47 pruned atom pairs is 1.286 angstroms; (across all 245 pairs:
11.473)
> select add #94
34588 atoms, 34892 bonds, 2223 residues, 2 models selected
> select subtract #94
1 model selected
> select clear
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> hide #!94 models
> show #!47 models
> matchmaker #47 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with 8p52, chain A (#47), sequence alignment
score = 363.5
RMSD between 115 pruned atom pairs is 1.082 angstroms; (across all 307 pairs:
15.407)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #!47 models
> show #88 models
> matchmaker #88 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with Mcf2.ranked_0.pdb, chain A (#88), sequence
alignment score = 405.2
RMSD between 128 pruned atom pairs is 0.972 angstroms; (across all 303 pairs:
12.736)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #88 models
> show #52 models
> matchmaker #52 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP000706081912.pdb, chain A (#52),
sequence alignment score = 226.2
RMSD between 57 pruned atom pairs is 0.989 angstroms; (across all 293 pairs:
30.191)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #52 models
> show #95 models
> matchmaker #95 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP000860465678.ranked_0.pdb, chain A
(#95), sequence alignment score = 382.4
RMSD between 134 pruned atom pairs is 1.003 angstroms; (across all 296 pairs:
7.540)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #95 models
> show #70 models
> matchmaker #70 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP000967698752.pdb, chain A (#70),
sequence alignment score = 390.3
RMSD between 87 pruned atom pairs is 0.959 angstroms; (across all 261 pairs:
10.937)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #70 models
> show #76 models
> matchmaker #76 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001011426704.pdb, chain A (#76),
sequence alignment score = 250.7
RMSD between 136 pruned atom pairs is 1.144 angstroms; (across all 235 pairs:
4.027)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #76 models
> show #56 models
> matchmaker #56 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001094995491.pdb, chain A (#56),
sequence alignment score = 219.4
RMSD between 81 pruned atom pairs is 0.883 angstroms; (across all 176 pairs:
6.421)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #56 models
> show #57 models
> matchmaker #57 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001106352814.pdb, chain A (#57),
sequence alignment score = 257.4
RMSD between 108 pruned atom pairs is 0.961 angstroms; (across all 204 pairs:
6.932)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #57 models
> show #74 models
> matchmaker #74 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP001564015939.pdb, chain A (#74),
sequence alignment score = 205.5
RMSD between 86 pruned atom pairs is 1.408 angstroms; (across all 190 pairs:
16.441)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #74 models
> show #51 models
> matchmaker #51 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003392964057.pdb, chain A (#51),
sequence alignment score = 173.6
RMSD between 63 pruned atom pairs is 1.174 angstroms; (across all 170 pairs:
10.258)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #51 models
> show #48 models
> matchmaker #48 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003405926657.pdb, chain A (#48),
sequence alignment score = 252.6
RMSD between 94 pruned atom pairs is 0.977 angstroms; (across all 232 pairs:
7.888)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #48 models
> show #49 models
> matchmaker #49 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003443402579.pdb, chain A (#49),
sequence alignment score = 259.8
RMSD between 93 pruned atom pairs is 1.207 angstroms; (across all 252 pairs:
11.060)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #49 models
> show #58 models
> matchmaker #58 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003469346235.pdb, chain A (#58),
sequence alignment score = 260
RMSD between 112 pruned atom pairs is 0.911 angstroms; (across all 214 pairs:
4.268)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #58 models
> show #59 models
> matchmaker #59 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003580314631.pdb, chain A (#59),
sequence alignment score = 308.2
RMSD between 92 pruned atom pairs is 1.075 angstroms; (across all 214 pairs:
5.876)
> hide #59 models
> show #58 models
> hide #58 models
> show #59 models
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #59 models
> show #96 models
> matchmaker #96 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003605169772.ranked_0.pdb, chain A
(#96), sequence alignment score = 378.7
RMSD between 133 pruned atom pairs is 1.066 angstroms; (across all 289 pairs:
8.432)
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #96 models
> show #60 models
> matchmaker #60 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003607098654.pdb, chain A (#60),
sequence alignment score = 252.9
RMSD between 84 pruned atom pairs is 0.881 angstroms; (across all 209 pairs:
4.498)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #60 models
> show #61 models
> save /Users/aho2840/Desktop/image1.png supersample 3
> matchmaker #61 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with MGYP003613210660.pdb, chain A (#61),
sequence alignment score = 251.9
RMSD between 96 pruned atom pairs is 1.039 angstroms; (across all 196 pairs:
6.185)
> save /Users/aho2840/Desktop/image2.png supersample 3
> hide #61 models
> show #73 models
> matchmaker #73 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-P55730-F1-model_v4.pdb, chain A (#73),
sequence alignment score = 72.4
RMSD between 25 pruned atom pairs is 0.955 angstroms; (across all 190 pairs:
24.079)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #73 models
> show #109 models
> matchmaker #109 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with C7BKP9.ranked_0.pdb, chain A (#109),
sequence alignment score = 292.3
RMSD between 75 pruned atom pairs is 1.064 angstroms; (across all 284 pairs:
10.403)
> turn y 180
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #109 models
> show #71 models
> matchmaker #71 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
sequence alignment score = 132.8
RMSD between 7 pruned atom pairs is 0.829 angstroms; (across all 185 pairs:
28.982)
> ui mousemode right select
Drag select of 210 residues
> ui tool show Matchmaker
> matchmaker #71 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327D9-F1-model_v4.pdb, chain A (#71),
sequence alignment score = 89.5
RMSD between 26 pruned atom pairs is 1.053 angstroms; (across all 175 pairs:
17.568)
> select add #71
4321 atoms, 4400 bonds, 549 residues, 1 model selected
> select subtract #71
Nothing selected
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #71 models
> show #72 models
> matchmaker #72 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 126.1
RMSD between 10 pruned atom pairs is 1.365 angstroms; (across all 189 pairs:
18.434)
> ui mousemode right select
Drag select of 377 residues
> ui tool show Matchmaker
> matchmaker #72 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 49.7
RMSD between 5 pruned atom pairs is 1.045 angstroms; (across all 46 pairs:
16.497)
Drag select of 193 residues
> ui tool show Matchmaker
> matchmaker #72 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 44.7
RMSD between 15 pruned atom pairs is 1.296 angstroms; (across all 168 pairs:
18.337)
> matchmaker #72 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 44.7
RMSD between 15 pruned atom pairs is 1.296 angstroms; (across all 168 pairs:
18.337)
> select add #72
4592 atoms, 4687 bonds, 572 residues, 1 model selected
> select subtract #72
Nothing selected
> select clear
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #72 models
> show #8 models
> hide #8 models
> show #85 models
> matchmaker #85 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q89T99-F1-model_v4.pdb, chain A (#85),
sequence alignment score = 83.5
RMSD between 30 pruned atom pairs is 0.963 angstroms; (across all 195 pairs:
24.092)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #85 models
> show #83 models
> matchmaker #83 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q93RN4-F1-model_v4.pdb, chain A (#83),
sequence alignment score = 154.3
RMSD between 61 pruned atom pairs is 1.078 angstroms; (across all 253 pairs:
13.858)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #83 models
> show #86 models
> matchmaker #86 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q9AMW4-F1-model_v4.pdb, chain A (#86),
sequence alignment score = 87.8
RMSD between 30 pruned atom pairs is 0.803 angstroms; (across all 234 pairs:
23.197)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #86 models
> show #69 models
> matchmaker #69 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-Q9F3T4-F1-model_v4.pdb, chain A (#69),
sequence alignment score = 99.5
RMSD between 15 pruned atom pairs is 1.383 angstroms; (across all 244 pairs:
24.018)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #69 models
> show #98 models
> matchmaker #98 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
sequence alignment score = 189.7
RMSD between 60 pruned atom pairs is 1.387 angstroms; (across all 312 pairs:
13.944)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #98 models
> show #99 models
> matchmaker #99 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_095034189.1.ranked_0.pdb, chain A (#99),
sequence alignment score = 201
RMSD between 46 pruned atom pairs is 0.814 angstroms; (across all 293 pairs:
22.670)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #99 models
> show #100 models
> matchmaker #100 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_148121377.1.ranked_0.pdb, chain A
(#100), sequence alignment score = 196.6
RMSD between 63 pruned atom pairs is 1.204 angstroms; (across all 298 pairs:
14.062)
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> save /Users/aho2840/Desktop/image1.png supersample 3
> turn y 180
> ui mousemode right select
Drag select of 355 residues
> ui tool show Matchmaker
> matchmaker #100 & sel to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_148121377.1.ranked_0.pdb, chain A
(#100), sequence alignment score = 177.3
RMSD between 56 pruned atom pairs is 0.910 angstroms; (across all 272 pairs:
24.833)
> select add #100
31107 atoms, 31455 bonds, 1953 residues, 1 model selected
> select subtract #100
Nothing selected
> select clear
> ui mousemode right "translate selected models"
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #100 models
> show #101 models
> matchmaker #101 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with WP_231937687.1.ranked_0.pdb, chain A
(#101), sequence alignment score = 205.8
RMSD between 73 pruned atom pairs is 0.941 angstroms; (across all 296 pairs:
20.392)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #101 models
> show #82 models
> matchmaker #82 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6ii6, chain A (#9) with AF-O68703-F1-model_v4.pdb, chain A (#82),
sequence alignment score = 155.7
RMSD between 60 pruned atom pairs is 1.095 angstroms; (across all 245 pairs:
14.853)
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #82 models
> show #60 models
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #60 models
> show #61 models
> save /Users/aho2840/Desktop/image1.png supersample 3
> hide #61 models
> show #104 models
> hide #!9 models
> hide #104 models
> show #105 models
> show #104 models
> hide #105 models
> log metadata #104
The model has no metadata
> log chains #104
Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104
---
Chain | Description
A | No description available
> sequence chain #104/A
Alignment identifier is 104/A
> ui mousemode right select
Drag select of 1999 residues
> select add #104
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #104
Nothing selected
> hide #104 models
> show #105 models
Drag select of 1401 residues
> log metadata #105
The model has no metadata
> log chains #105
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105
---
Chain | Description
A | No description available
> sequence chain #105/A
Alignment identifier is 105/A
> select add #105
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #105
Nothing selected
> hide #105 models
> show #110 models
> log metadata #110
The model has no metadata
> log chains #110
Chain information for GMGC10.011_528_202.ranked_0.3247.4160.pdb #110
---
Chain | Description
A | No description available
> sequence chain #110/A
Alignment identifier is 110/A
Drag select of 658 residues
> select add #110
13993 atoms, 14133 bonds, 913 residues, 1 model selected
> select subtract #110
Nothing selected
Drag select of 660 residues
> select add #110
13993 atoms, 14133 bonds, 913 residues, 1 model selected
> select subtract #110
Nothing selected
> hide #110 models
> show #111 models
> log metadata #111
The model has no metadata
> log chains #111
Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111
---
Chain | Description
A | No description available
> sequence chain #111/A
Alignment identifier is 111/A
Drag select of 1084 residues
> select add #111
18385 atoms, 18537 bonds, 1244 residues, 1 model selected
> select subtract #111
Nothing selected
> hide #111 models
> show #105 models
> log metadata #105
The model has no metadata
> log chains #105
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105
---
Chain | Description
A | No description available
> sequence chain #105/A
Alignment identifier is 105/A
Drag select of 1401 residues
> select #105/A:1999
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #105/A:1800-1999
3067 atoms, 3094 bonds, 200 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select
> #105/A:2000-2009,2020-2028,2030-2044,2058-2088,2100-2102,2115-2127,2133-2153,2160-2178,2182-2184,2193-2202,2246-2257,2268-2271,2286-2291,2293-2304,2310-2317,2329-2334,2346-2354,2360-2362,2367-2375,2380-2396,2402-2404,2423-2434,2445-2469,2473-2488,2494-2503,2509-2525,2531-2539,2542-2551,2565-2574,2577-2589,2592-2603,2608-2620,2627-2632,2635-2654,2658-2668,2678-2695,2714-2726,2734-2757,2774-2776,2783-2790,2794-2817,2819-2821,2825-2837,2842-2881,3130-3132,3193-3195,3233-3241,3345-3347
8794 atoms, 8805 bonds, 571 residues, 1 model selected
> select #105/A:2159-2215
853 atoms, 856 bonds, 57 residues, 1 model selected
> select #105/A:2159-2215
853 atoms, 856 bonds, 57 residues, 1 model selected
> select
> #105/A:2000-2009,2020-2028,2030-2044,2058-2088,2100-2102,2115-2127,2133-2153,2160-2178,2182-2184,2193-2202,2246-2257,2268-2271,2286-2291,2293-2304,2310-2317,2329-2334,2346-2354,2360-2362,2367-2375,2380-2396,2402-2404,2423-2434,2445-2469,2473-2488,2494-2503,2509-2525,2531-2539,2542-2551,2565-2574,2577-2589,2592-2603,2608-2620,2627-2632,2635-2654,2658-2668,2678-2695,2714-2726,2734-2757,2774-2776,2783-2790,2794-2817,2819-2821,2825-2837,2842-2881,3130-3132,3193-3195,3233-3241,3345-3347
8794 atoms, 8805 bonds, 571 residues, 1 model selected
> select add #105
21077 atoms, 21241 bonds, 1401 residues, 1 model selected
> select subtract #105
Nothing selected
> hide #105 models
> show #110 models
> log metadata #110
The model has no metadata
> log chains #110
Chain information for GMGC10.011_528_202.ranked_0.3247.4160.pdb #110
---
Chain | Description
A | No description available
> sequence chain #110/A
Alignment identifier is 110/A
Drag select of 660 residues
> select #110/A:3499
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #110/A:3247-3499
3894 atoms, 3931 bonds, 253 residues, 1 model selected
> select #110/A:3596-3597
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #110/A:3596-3767
2572 atoms, 2590 bonds, 172 residues, 1 model selected
> select #110/A:3498-3499
33 atoms, 32 bonds, 2 residues, 1 model selected
> select #110/A:3247-3499
3894 atoms, 3931 bonds, 253 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #110 models
> show #111 models
> log metadata #111
The model has no metadata
> log chains #111
Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111
---
Chain | Description
A | No description available
> sequence chain #111/A
Alignment identifier is 111/A
Drag select of 1084 residues
> select #111/A:4159
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #111/A:4000-4159
2425 atoms, 2448 bonds, 160 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #111 models
> select #111/A:4583
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #111/A:4583-4640
794 atoms, 797 bonds, 58 residues, 1 model selected
> select add #111
15960 atoms, 16088 bonds, 1084 residues, 1 model selected
> select subtract #111
Nothing selected
> show #111 models
> show #110 models
> select clear
> ui mousemode right "translate selected models"
> hide #111 models
> show #105 models
> hide #105 models
> show #105 models
> show #104 models
> hide #110 models
> hide #105 models
> hide #104 models
> show #104 models
> show #105 models
> toolshed show
QGestureManager::deliverEvent: could not find the target for gesture
> combine #104,#105 name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine #104, #105 name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine #104, #105 close false name GMGC10.011_528_202.1.3500
Expected a keyword
> select
> #111/A:4160-4171,4176-4187,4194-4196,4200-4202,4205-4213,4218-4226,4231-4239,4247-4254,4263-4273,4277-4290,4295-4303,4309-4318,4322-4337,4411-4413,4820-4822,4839-4841,4855-4865,4884-4891,5150-5156,5170-5176
2584 atoms, 2582 bonds, 167 residues, 1 model selected
> combine #104, #105, close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine #104, #105, close false name GMGC10.011_528_202.1.3500
Expected a keyword
> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> select add #111
15960 atoms, 16088 bonds, 1084 residues, 1 model selected
> select subtract #111
Nothing selected
> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine # 104, # 105 close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> ui tool show "Build Structure"
No atoms selected
> toolshed show
> combine # 104, # 105, close false name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine # 104, # 105, close false, name "GMGC10.011_528_202.1.3500"
Expected a keyword
> ui tool show "Build Structure"
No atoms selected
> select add #104
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select add #105
51441 atoms, 51879 bonds, 3400 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
Multiple N- and C-terminii in atoms
> combine # 104, # 105 close false retainIds false name
> "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine # 104, # 105 close false retainIds false name "Combine"
Expected a keyword
> combine # 104, # 105 close false retainIds false name model-name "Combine"
Expected a keyword
> combine #104, #105 name "GMGC10.011_528_202.1.3500" close false
Expected a keyword
> combine #104, #105 name "GMGC10.011_528_202.1.3500" close false
Expected a keyword
> select subtract #104
21077 atoms, 21241 bonds, 1401 residues, 1 model selected
> select subtract #105
Nothing selected
> combine #104, #105 name "GMGC10.011_528_202.1.3500" close false
Expected a keyword
> combine #104, #105 name "Combine" close false
Expected a keyword
> combine #104, #105 name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine modelId close false
Invalid "modelId" argument: Expected an integer
> combine #104, #105 name "GMGC10.011_528_202.1.3500"
Expected a keyword
> combine #104, #105
Expected a keyword
> combine modelId #104, #105
Invalid "modelId" argument: Expected an integer
> combine #104, #105 name "GMGC10.011_528_202.1.3500"
Expected a keyword
> close false
Expected a models specifier or a keyword
> combine #104, #105 name "GMGC10.011_528_202.1.3500"
Expected a keyword
> close false
Expected a models specifier or a keyword
> combine #104, #105
Expected a keyword
> help combine
> hide #104 models
> hide #105 models
> combine #104, #105 name "GMGC10.011_528_202.1.3500"
Expected a keyword
> close false
Expected a models specifier or a keyword
> combine #104, #105
Expected a keyword
> log metadata #104
The model has no metadata
> log chains #104
Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104
---
Chain | Description
A | No description available
> sequence chain #104/A
Alignment identifier is 104/A
> log metadata #105
The model has no metadata
> log chains #105
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105
---
Chain | Description
A | No description available
> sequence chain #105/A
Alignment identifier is 105/A
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
No chain-terminal carbons in atoms
> show #104 models
> show #105 models
> select add #105
21077 atoms, 21241 bonds, 1401 residues, 1 model selected
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
No chain-initial nitrogens in atoms
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
No chain-terminal carbons in atoms
> select add #104
30378 atoms, 30652 bonds, 2000 residues, 2 models selected
> select subtract #104
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #104
30378 atoms, 30652 bonds, 2000 residues, 2 models selected
> select add #105
51441 atoms, 51879 bonds, 3400 residues, 2 models selected
> select subtract #105
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #104
Nothing selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
No chain-terminal carbons in atoms
> select add #105
21077 atoms, 21241 bonds, 1401 residues, 1 model selected
> select subtract #105
Nothing selected
> select #104/A:1999
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #105/A:2000
14 atoms, 14 bonds, 1 residue, 1 model selected
> view matrix models
> #105,0.070652,0.61953,-0.78179,102.78,-0.84869,0.44916,0.27924,15.837,0.52415,0.64377,0.55752,337.8
> undo
> select add #105
21077 atoms, 21241 bonds, 1401 residues, 1 model selected
> select subtract #105
Nothing selected
> open /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1.2000.pdb
Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113
---
Chain | Description
A | No description available
> open
> /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114
---
Chain | Description
A | No description available
> hide #105 models
> hide #104 models
> select clear
> select #105/A:2000-2009
158 atoms, 160 bonds, 10 residues, 1 model selected
> log metadata #113
The model has no metadata
> log chains #113
Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113
---
Chain | Description
A | No description available
> sequence chain #113/A
Alignment identifier is 113/A
> log metadata #114
The model has no metadata
> log chains #114
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114
---
Chain | Description
A | No description available
> sequence chain #114/A
Alignment identifier is 114/A
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #114/A:1-220
3369 atoms, 3404 bonds, 220 residues, 1 model selected
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> matchmaker #114 & sel to #113
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GMGC10.011_528_202.ranked_0.1.2000.pdb, chain A (#113) with
GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb, chain A (#114), sequence
alignment score = 104.4
RMSD between 7 pruned atom pairs is 1.517 angstroms; (across all 188 pairs:
20.322)
> undo
> select add #105
21077 atoms, 21241 bonds, 1401 residues, 1 model selected
> select subtract #105
Nothing selected
> ui tool show "Build Structure"
> log metadata #113
The model has no metadata
> log chains #113
Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113
---
Chain | Description
A | No description available
> sequence chain #113/A
Alignment identifier is 113/A
> log metadata #114
The model has no metadata
> log chains #114
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114
---
Chain | Description
A | No description available
> sequence chain #114/A
Alignment identifier is 114/A
> select sequence #113:1
Nothing selected
> select #113/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #113/A:1
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel purple
> view matrix models #113,1,0,0,42.424,0,1,0,100.81,0,0,1,51.661
> select
> #113/A:10-18,30-42,46-68,70-76,109-128,144-152,159-161,182-190,196-198,201-210,221-229,231-245,259-289,301-303,316-328,334-354,361-379,383-385,394-403,447-458,469-472,487-492,494-505,511-518,530-535,547-555,561-563,568-576,581-597,603-605,624-635,646-670,674-689,695-704,710-726,732-740,743-752,766-775,778-790,793-804,809-821,828-833,836-855,859-869,879-896,915-927,935-958,975-977,984-991,995-1018,1020-1022,1026-1038,1043-1082,1331-1333,1394-1396,1434-1442,1546-1548
10303 atoms, 10318 bonds, 667 residues, 1 model selected
> select sequence #113:1601
Nothing selected
> color #113-114 blue
> select sequence #113:1601
Nothing selected
> select sequence #113:1601
Nothing selected
> select sequence #113:1601
Nothing selected
> color #113-114 red
> select sequence #113:1601
Nothing selected
> color #113-114 blue
> select #113/A:1601
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #113/A:1601
18 atoms, 17 bonds, 1 residue, 1 model selected
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #113
Nothing selected
> select sequence #113:1600
Nothing selected
> select sequence #113:1
Nothing selected
> select sequence #113:1
Nothing selected
> ui tool show "Build Structure"
> select sequence #113:1
Nothing selected
> select sequence #114:1
Nothing selected
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> color sel light sea green
> select subtract #114
Nothing selected
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #114
Nothing selected
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #113
Nothing selected
> select clear
> select sequence #113:1601
Nothing selected
> help help:user/findseq.html
> select sequence #113:1601.a
Nothing selected
Already setting window visible!
> select sequence #113:500
Nothing selected
> select sequence #113/A:1
Nothing selected
> select #113/A:1551-1601
811 atoms, 818 bonds, 51 residues, 1 model selected
> select #113/A:1551-1601
811 atoms, 818 bonds, 51 residues, 1 model selected
> select #113/A:1551-1601
811 atoms, 818 bonds, 51 residues, 1 model selected
> select #113/A:1328
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #113/A:1328
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #113
Nothing selected
> select backbone
430695 atoms, 430577 bonds, 4 pseudobonds, 89407 residues, 119 models selected
> select add #114
448950 atoms, 449107 bonds, 4 pseudobonds, 89407 residues, 121 models selected
> select subtract #114
418586 atoms, 418469 bonds, 4 pseudobonds, 87408 residues, 120 models selected
> view matrix models
> 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> ui mousemode right select
> select clear
> select sequence #113/A:1601
Nothing selected
> select sequence #113:1601
Nothing selected
> select sequence #113/M:1601
Nothing selected
> select sequence #113:1601
Nothing selected
> select sequence "#113: 1601"
Nothing selected
> select sequence "#113: 1"
Nothing selected
> select sequence #113:1
Nothing selected
> select sequence #114:1
Nothing selected
Drag select of 6 residues
> select clear
> ui mousemode right select
> ui mousemode right "translate selected models"
> select #113/A:1328-1389
953 atoms, 961 bonds, 62 residues, 1 model selected
> select #113/A:1328-1453
1904 atoms, 1921 bonds, 126 residues, 1 model selected
> view matrix models #113,1,0,0,22.022,0,1,0,112.04,0,0,1,61.437
> view matrix models #113,1,0,0,24.063,0,1,0,110.97,0,0,1,61.129
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #113
Nothing selected
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel red
> view matrix models
> #114,0.46432,0.27628,0.84147,47.474,0.84179,0.15767,-0.51627,1.4006,-0.27531,0.94806,-0.15936,-37.274
> view matrix models
> #114,0.46432,0.27628,0.84147,58.356,0.84179,0.15767,-0.51627,23.459,-0.27531,0.94806,-0.15936,-40.269
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> view matrix models
> #114,0.46432,0.27628,0.84147,93.568,0.84179,0.15767,-0.51627,-5.0543,-0.27531,0.94806,-0.15936,-49.126
> view matrix models
> #114,0.46432,0.27628,0.84147,104.47,0.84179,0.15767,-0.51627,20.736,-0.27531,0.94806,-0.15936,-52.157
> select subtract #114
Nothing selected
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> view matrix models #113,1,0,0,12.507,0,1,0,55.885,0,0,1,64.573
> select #113/A:1601
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #113/A:1601
18 atoms, 17 bonds, 1 residue, 1 model selected
> color sel lime
> view matrix models #113,1,0,0,8.1859,0,1,0,37.47,0,0,1,57.072
> ui mousemode right "rotate selected models"
> view matrix models
> #113,0.98482,-0.048637,-0.16663,8.0868,0.16349,-0.062719,0.98455,42.791,-0.058336,-0.99685,-0.053815,58.863
> view matrix models
> #113,0.99064,0.053136,-0.1257,7.8474,0.12547,-0.71686,0.68584,44.296,-0.053665,-0.69519,-0.71682,57.407
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #113
Nothing selected
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> select subtract #113
Nothing selected
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> view matrix models
> #114,0.31496,0.52687,0.78944,100.53,0.43207,-0.82017,0.37501,21.258,0.84506,0.22298,-0.48596,-30.471
> view matrix models
> #114,0.33794,0.48758,0.80502,101,-0.0026174,-0.85485,0.51886,18.665,0.94116,-0.17745,-0.28761,-26.645
> ui mousemode right "translate selected models"
> view matrix models
> #114,0.33794,0.48758,0.80502,108.85,-0.0026174,-0.85485,0.51886,35.154,0.94116,-0.17745,-0.28761,-18.01
> ui mousemode right "rotate selected models"
> view matrix models
> #114,0.28427,0.57713,0.76558,107.87,0.017549,-0.80152,0.59771,32.511,0.95858,-0.15648,-0.23797,-19.425
> view matrix models
> #114,0.13603,0.53223,0.8356,107.2,0.20108,-0.84072,0.50275,35.359,0.97009,0.099631,-0.22138,-24.759
> select subtract #114
Nothing selected
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #114
Nothing selected
> select add #113
24144 atoms, 24336 bonds, 1601 residues, 1 model selected
> view matrix models
> #113,0.38071,0.92446,0.020559,0.79506,-0.39119,0.14087,0.90947,38.033,0.83787,-0.35429,0.41527,63.822
> view matrix models
> #113,0.091164,0.83199,0.54725,-0.59859,-0.99583,0.077897,0.047464,33.082,-0.0031402,-0.5493,0.83562,58.619
> ui mousemode right "translate selected models"
> view matrix models
> #113,0.091164,0.83199,0.54725,28.726,-0.99583,0.077897,0.047464,35.39,-0.0031402,-0.5493,0.83562,56.768
> view matrix models
> #113,0.091164,0.83199,0.54725,33.333,-0.99583,0.077897,0.047464,30.744,-0.0031402,-0.5493,0.83562,53.596
> select subtract #113
Nothing selected
> ui mousemode right select
Drag select of 2 residues
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
> select add #114
54505 atoms, 54972 bonds, 3600 residues, 1 model selected
> select subtract #114
Nothing selected
> select add #114
54505 atoms, 54972 bonds, 3600 residues, 1 model selected
> select subtract #114
Nothing selected
> select #114/A:1602
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #114/A:1602-1610
152 atoms, 152 bonds, 9 residues, 1 model selected
> log metadata #104
The model has no metadata
> log chains #104
Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104
---
Chain | Description
A | No description available
> sequence chain #104/A
Alignment identifier is 104/A
> select add #114
54505 atoms, 54972 bonds, 3600 residues, 1 model selected
> select subtract #114
Nothing selected
> log metadata #114
The model has no metadata
> log chains #114
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114
---
Chain | Description
A | No description available
> sequence chain #114/A
Alignment identifier is 114/A
Drag select of 259 residues
> undo
Undo failed, probably because structures have been modified.
> select add #114
54505 atoms, 54972 bonds, 3600 residues, 1 model selected
> select subtract #114
Nothing selected
> close #114
> open /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1.2000.pdb
Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113
---
Chain | Description
A | No description available
> open
> /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114
---
Chain | Description
A | No description available
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
Drag select of 187 residues
> ui mousemode right "translate selected models"
> select add #113
26356 atoms, 24336 bonds, 1742 residues, 2 models selected
> select subtract #113
2212 atoms, 141 residues, 1 model selected
> view matrix models #114,1,0,0,-78.219,0,1,0,37.594,0,0,1,-98.102
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #114
Nothing selected
> log metadata #113
The model has no metadata
> log chains #113
Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113
---
Chain | Description
A | No description available
> sequence chain #113/A
Alignment identifier is 113/A
> select #113/A:1601
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #113/A:1601
18 atoms, 17 bonds, 1 residue, 1 model selected
> color sel lime
> log metadata #113
The model has no metadata
> log chains #113
Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113
---
Chain | Description
A | No description available
> log metadata #114
The model has no metadata
> log chains #114
Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114
---
Chain | Description
A | No description available
> sequence chain #114/A
Alignment identifier is 114/A
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #114/A:113-170
872 atoms, 877 bonds, 58 residues, 1 model selected
> select #114/A:113-170
872 atoms, 877 bonds, 58 residues, 1 model selected
> select #114/A:115-116
28 atoms, 28 bonds, 2 residues, 1 model selected
> select #114/A:115-357
3627 atoms, 3657 bonds, 243 residues, 1 model selected
> select #114/A:340-396
827 atoms, 830 bonds, 57 residues, 1 model selected
> select #114/A:340-584
3675 atoms, 3701 bonds, 245 residues, 1 model selected
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #114/A:3
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #114/A:3-302
4580 atoms, 4624 bonds, 300 residues, 1 model selected
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #114/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> view matrix models #114,1,0,0,-56.047,0,1,0,65.157,0,0,1,-25.546
> view matrix models #114,1,0,0,-34.375,0,1,0,59.469,0,0,1,-7.3837
> color sel red
> ui mousemode right "rotate selected models"
> view matrix models
> #114,-0.27005,0.020461,-0.96263,-15.976,-0.72402,0.65474,0.21703,61.228,0.63472,0.75557,-0.162,2.1519
> ui mousemode right "translate selected models"
> view matrix models
> #114,-0.27005,0.020461,-0.96263,-1.4491,-0.72402,0.65474,0.21703,36.958,0.63472,0.75557,-0.162,-2.3183
> ui mousemode right select
> select add #114
30364 atoms, 30638 bonds, 1999 residues, 1 model selected
> select subtract #114
Nothing selected
Drag select of 2 residues
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Compositor returned null texture
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z160000B1LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.5 (23H527)
Kernel Version: Darwin 23.6.0
Time since boot: 28 days, 14 hours, 57 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403210048
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
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